diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 458b8daaef..6d5a774b70 100644
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -80,15 +80,6 @@ REQUIRED OPTIONS
                               "-sim_year list" to list valid simulation years
                               (default 2000)
 OPTIONS
-     -bgc "value"             Build CLM with BGC package [ sp | bgc ]
-                              (default is sp).
-                                CLM Biogeochemistry mode
-                                sp    = Satellite Phenology (SP)
-                                    This toggles off the namelist variable: use_cn
-                                bgc   = Carbon Nitrogen with methane, nitrification, vertical soil C,
-                                        CENTURY decomposition
-                                    This toggles on the namelist variables:
-                                          use_cn, use_lch4, use_nitrif_denitrif, use_vertsoilc, use_century_decomp
      -[no-]chk_res            Also check [do NOT check] to make sure the resolution and
                               land-mask is valid.
      -clm_demand "list"       List of variables to require on clm namelist besides the usuals.
@@ -105,8 +96,6 @@ OPTIONS
      -co2_ppmv "value"        Set CO2 concentration to use when co2_type is constant (ppmv).
      -csmdata "dir"           Root directory of CESM input data.
                               Can also be set by using the CSMDATA environment variable.
-     -glc_nec <name>          Glacier number of elevation classes [0 | 3 | 5 | 10 | 36]
-                              (default is 0) (standard option with land-ice model is 10)
      -help [or -h]            Print usage to STDOUT.
      -ignore_ic_date          Ignore the date on the initial condition files
                               when determining what input initial condition file to use.
@@ -150,7 +139,7 @@ OPTIONS
 
 Note: The precedence for setting the values of namelist variables is (highest to lowest):
       0. namelist values set by specific command-line options, like, -d, -sim_year
-             (i.e.  compset choice and CLM_BLDNML_OPTS, CLM_ACCELERATED_SPINUP, LND_TUNING_MODE env_run variables)
+             (i.e.  compset choice and CLM_BLDNML_OPTS, LND_TUNING_MODE env_run variables)
      (NOTE: If you try to contradict these settings by methods below, an error will be triggered)
       1. values set on the command-line using the -namelist option,
              (i.e. CLM_NAMELIST_OPTS env_run variable)
@@ -180,7 +169,6 @@ sub process_commandline {
                co2_ppmv              => undef,
                clm_demand            => "null",
                help                  => 0,
-               glc_nec               => "default",
                l_ncpl                => undef,
                lnd_frac              => undef,
                dir                   => "$cwd",
@@ -210,7 +198,6 @@ sub process_commandline {
              "ignore_warnings!"          => \$opts{'ignore_warnings'},
              "chk_res!"                  => \$opts{'chk_res'},
              "note!"                     => \$opts{'note'},
-             "glc_nec=i"                 => \$opts{'glc_nec'},
              "d:s"                       => \$opts{'dir'},
              "h|help"                    => \$opts{'help'},
              "ignore_ic_date"            => \$opts{'ignore_ic_date'},
@@ -531,9 +518,7 @@ sub process_namelist_commandline_options {
   setup_cmdl_chk_res($opts, $defaults);
   setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults);
   setup_cmdl_mask($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_cmdl_bgc($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv);
   setup_cmdl_maxpft($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv);
-  setup_cmdl_glc_nec($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_rcp($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_simulation_year($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_run_type($opts, $nl_flags, $definition, $defaults, $nl);
@@ -604,91 +589,6 @@ sub setup_cmdl_mask {
   $log->verbose_message("CLM land mask is $nl_flags->{'mask'}");
 }
 
-#-------------------------------------------------------------------------------
-sub setup_cmdl_bgc {
-  # BGC - alias for group of biogeochemistry related use_XXX namelists
-
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $cfg, $physv) = @_;
-
-  my $val;
-  my $var = "bgc";
-
-  $val = $opts->{$var};
-  $nl_flags->{'bgc_mode'} = $val;
-
-  my $var = "bgc_mode";
-  if ( $nl_flags->{$var} eq "default" ) {
-     $nl_flags->{$var} = $defaults->get_value($var);
-  }
-  my $group = $definition->get_group_name($var);
-  $nl->set_variable_value($group, $var, quote_string( $nl_flags->{$var} ) );
-  if (  ! $definition->is_valid_value( $var, quote_string( $nl_flags->{$var}) ) ) {
-    my @valid_values   = $definition->get_valid_values( $var );
-    $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values");
-  }
-  $log->verbose_message("Using $nl_flags->{$var} for bgc.");
-
-  # now set the actual name list variables based on the bgc alias
-  if ($nl_flags->{$var} eq "bgc" ) {
-    $nl_flags->{'use_cn'} = ".true.";
-  } else {
-    $nl_flags->{'use_cn'} = ".false.";
-  }
-  if ( defined($nl->get_value("use_cn")) && ($nl_flags->{'use_cn'} ne $nl->get_value("use_cn")) ) {
-    $log->fatal_error("The namelist variable use_cn is inconsistent with the -bgc option");
-  }
-
-  {
-	# If the variable has already been set use it, if not set to the value defined by the bgc_mode
-	my @list  = (  "use_lch4", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp" );
-	my $ndiff = 0;
-        my %settings = ( 'bgc_mode'=>$nl_flags->{'bgc_mode'} );
-	foreach my $var ( @list ) {
-            my $default_setting = $defaults->get_value($var, \%settings );
-	    if ( ! defined($nl->get_value($var))  ) {
-		$nl_flags->{$var} = $default_setting;
-	    } else {
-		if ( $nl->get_value($var) ne $default_setting ) {
-		    $ndiff += 1;
-		}
-		$nl_flags->{$var} = $nl->get_value($var);
-	    }
-	    $val = $nl_flags->{$var};
-	    my $group = $definition->get_group_name($var);
-	    $nl->set_variable_value($group, $var, $val);
-	    if (  ! $definition->is_valid_value( $var, $val ) ) {
-		my @valid_values   = $definition->get_valid_values( $var );
-		$log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-	    }
-	}
-	# If all the variables are different report it as an error
-	if ( $ndiff == ($#list + 1) ) {
-	    $log->fatal_error("You are contradicting the -bgc setting with the namelist variables: @list" );
-	}
-  }
-
-  # Now set use_cn
-  foreach $var ( "use_cn" ) {
-     $val = $nl_flags->{$var};
-     $group = $definition->get_group_name($var);
-     $nl->set_variable_value($group, $var, $val);
-     if (  ! $definition->is_valid_value( $var, $val ) ) {
-       my @valid_values   = $definition->get_valid_values( $var );
-       $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-     }
-  }
-  my $var = "use_fun";
-  if ( ! defined($nl->get_value($var)) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'},
-                 'use_nitrif_denitrif'=>$nl_flags->{'use_nitrif_denitrif'} );
-  }
-  if ( (! &value_is_true($nl_flags->{'use_nitrif_denitrif'}) ) && &value_is_true($nl->get_value('use_fun')) ) {
-     $log->fatal_error("When FUN is on, use_nitrif_denitrif MUST also be on!");
-  }
-} # end bgc
-
-
 #-------------------------------------------------------------------------------
 
 sub setup_cmdl_maxpft {
@@ -704,14 +604,6 @@ sub setup_cmdl_maxpft {
   }
   $nl_flags->{'maxpft'} = $val;
 
-  if ( ($nl_flags->{'bgc_mode'} ne "sp") && ($nl_flags->{'maxpft'} != $maxpatchpft) ) {
-    $log->fatal_error("** For CN or BGC mode you MUST set max patch PFT's to $maxpatchpft\n" .
-                "**\n" .
-                "** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence:\n" .
-                "** * by the command-line options -bgc and -maxpft\n" .
-                "** * by a default configuration file, specified by -defaults\n" .
-                "**");
-  }
   if ( $nl_flags->{'maxpft'} > $maxpatchpft ) {
     $log->fatal_error("** Max patch PFT's can NOT exceed $maxpatchpft\n" .
                 "**\n" .
@@ -724,41 +616,6 @@ sub setup_cmdl_maxpft {
     $log->warning("running with maxpft NOT equal to $maxpatchpft is " .
             "NOT validated / scientifically supported." );
   }
-  $log->verbose_message("Using $nl_flags->{'maxpft'} for maxpft.");
-
-  $var = "maxpatch_pft";
-  $val = $nl_flags->{'maxpft'};
-  my $group = $definition->get_group_name($var);
-  $nl->set_variable_value($group, $var, $val);
-  if (  ! $definition->is_valid_value( $var, $val ) ) {
-    my @valid_values   = $definition->get_valid_values( $var );
-    $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_cmdl_glc_nec {
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
-
-  my $val;
-  my $var = "glc_nec";
-
-  if ( $opts->{$var} ne "default" ) {
-    $val = $opts->{$var};
-  } else {
-    $val = $defaults->get_value($var);
-  }
-
-  $nl_flags->{'glc_nec'} = $val;
-  $opts->{'glc_nec'} = $val;
-  my $group = $definition->get_group_name($var);
-  $nl->set_variable_value($group, $var, $val);
-  if (  ! $definition->is_valid_value( $var, $val ) ) {
-    my @valid_values   = $definition->get_valid_values( $var );
-    $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-  }
-  $log->verbose_message("Glacier number of elevation classes is $val");
 }
 
 #-------------------------------------------------------------------------------
@@ -839,15 +696,13 @@ sub setup_cmdl_run_type {
   my $var = "clm_start_type";
   if (defined $opts->{$var}) {
     if ($opts->{$var} eq "default" ) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
-                  'use_cndv'=>$nl_flags->{'use_cndv'} );
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
     } else {
       my $group = $definition->get_group_name($var);
       $nl->set_variable_value($group, $var, quote_string( $opts->{$var} ) );
     }
   } else {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
-                  'use_cndv'=>$nl_flags->{'use_cndv'} );
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
   }
   $nl_flags->{'clm_start_type'} = $nl->get_value($var);
 }
@@ -944,9 +799,6 @@ sub process_namelist_commandline_use_case {
     $settings{'sim_year'}       = $nl_flags->{'sim_year'};
     $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'};
     $settings{'phys'}           = $nl_flags->{'phys'};
-    $settings{'use_cn'}      = $nl_flags->{'use_cn'};
-    $settings{'use_cndv'}    = $nl_flags->{'use_cndv'};
-    $settings{'cnfireson'}   = $nl_flags->{'cnfireson'};
     # Loop over the variables specified in the use case.
     # Add each one to the namelist.
     my @vars = $uc_defaults->get_variable_names();
@@ -1004,72 +856,11 @@ sub process_namelist_inline_logic {
   setup_logic_delta_time($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_decomp_performance($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl,  $envxml_ref, $physv);
-  setup_logic_dynamic_plant_nitrogen_alloc($opts, $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_hydrstress($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_dynamic_roots($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_params_file($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_create_crop_landunit($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_soilstate($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
 
-  #########################################
-  # namelist group: atm2lnd_inparm
-  #########################################
-  setup_logic_atm_forcing($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #########################################
-  # namelist group: lnd2atm_inparm
-  #########################################
-  setup_logic_lnd2atm($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  ###############################
-  # namelist group: clmu_inparm #
-  ###############################
-  setup_logic_urban($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  ##################################
-  # namelist group: bgc_shared
-  ##################################
-  setup_logic_bgc_shared($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #############################################
-  # namelist group: soilwater_movement_inparm #
-  #############################################
-  setup_logic_soilwater_movement($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #############################################
-  # namelist group: rooting_profile_inparm    #
-  #############################################
-  setup_logic_rooting_profile($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  ####################################
-  # namelist group: cnvegcarbonstate #
-  ####################################
-  setup_logic_cnvegcarbonstate($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #############################################
-  # namelist group: soil_resis_inparm #
-  #############################################
-  setup_logic_soil_resis($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #############################################
-  # namelist group: canopyhydrology_inparm #
-  #############################################
-  setup_logic_canopyhydrology($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #####################################
-  # namelist group: clm_canopy_inparm #
-  #####################################
-  setup_logic_canopy($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-
-  #######################################################################
-  # namelist groups: clm_hydrology1_inparm and clm_soilhydrology_inparm #
-  #######################################################################
-  setup_logic_hydrology_switches($nl, $physv);
-
 }
 
 #-------------------------------------------------------------------------------
@@ -1196,58 +987,7 @@ sub setup_logic_glacier {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv) = @_;
 
-  my $var = "maxpatch_glcmec";
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'val'=>$nl_flags->{'glc_nec'} );
-
-  my $val = $nl->get_value($var);
-  if ( $val != $nl_flags->{'glc_nec'} ) {
-    $log->fatal_error("$var set to $val does NOT agree with -glc_nec argument of $nl_flags->{'glc_nec'} (set with GLC_NEC env variable)");
-  }
-
-  if ( $nl_flags->{'glc_nec'} < 1 ) {
-     $log->fatal_error("For clm4_5 and later, GLC_NEC must be at least 1.");
-  }
-
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glc_snow_persistence_max_days');
-
-  # Dependence of albice on glc_nec has gone away starting in CLM4_5. Thus, we
-  # can remove glc_nec from the following call once we ditch CLM4_0.
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'albice', 'glc_nec'=>$nl_flags->{'glc_nec'});
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior');
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_melt_behavior');
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_ice_runoff_behavior');
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_params_file {
-  # get param data. For 4_0, pft-physiology, for 4_5 old
-  # pft-physiology was used but now now includes CN and BGC century
-  # parameters.
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'paramfile', 
-              'phys'=>$nl_flags->{'phys'},
-              'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_create_crop_landunit {
-  # Create crop land unit
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  my $var = 'create_crop_landunit';
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
-}
-#-------------------------------------------------------------------------------
-
-sub setup_logic_urban {
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
 
 #-------------------------------------------------------------------------------
@@ -1262,17 +1002,6 @@ sub error_if_set {
    }
 }
 
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_soilstate {
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
- add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'organic_frac_squared' );
- add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_layerstruct' );
- add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_bedrock' );
-}
-
 #-------------------------------------------------------------------------------
 
 sub setup_logic_demand {
@@ -1287,14 +1016,7 @@ sub setup_logic_demand {
   $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'};
   $settings{'mask'}           = $nl_flags->{'mask'};
   $settings{'rcp'}            = $nl_flags->{'rcp'};
-  $settings{'glc_nec'}        = $nl_flags->{'glc_nec'};
   # necessary for demand to be set correctly
-  $settings{'use_cn'}              = $nl_flags->{'use_cn'};
-  $settings{'use_cndv'}            = $nl_flags->{'use_cndv'};
-  $settings{'use_lch4'}            = $nl_flags->{'use_lch4'};
-  $settings{'use_nitrif_denitrif'} = $nl_flags->{'use_nitrif_denitrif'};
-  $settings{'use_vertsoilc'}       = $nl_flags->{'use_vertsoilc'};
-  $settings{'use_century_decomp'}  = $nl_flags->{'use_century_decomp'};
 
   my $demand = $nl->get_value('clm_demand');
   if (defined($demand)) {
@@ -1346,13 +1068,9 @@ sub setup_logic_surface_dataset {
   }
   $flanduse_timeseries = $nl_flags->{'flanduse_timeseries'};
 
-  if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) {
-      $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." );
-  }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat',
               'hgrid'=>$nl_flags->{'res'},
-              'sim_year'=>$nl_flags->{'sim_year'},
-              'glc_nec'=>$nl_flags->{'glc_nec'});
+              'sim_year'=>$nl_flags->{'sim_year'});
   
   # MML: try and add my own namelist variable for mml_surdat forcing file
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'mml_surdat');
@@ -1413,9 +1131,7 @@ sub setup_logic_initial_conditions {
     } else {
        delete( $settings{'sim_year'} );
     }
-    foreach my $item ( "mask", "maxpft", "glc_nec", "use_cn", "use_cndv", 
-                       "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", 
-                     ) {
+    foreach my $item ( "mask", "maxpft" ) {
        $settings{$item}    = $nl_flags->{$item};
     }
     if ($opts->{'ignore_ic_year'}) {
@@ -1447,7 +1163,7 @@ sub setup_logic_initial_conditions {
              }
           } 
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar,
-                     'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(),
+                     'phys'=>$physv->as_string(),
                      'sim_year'=>$settings{'sim_year'}, 'nofail'=>1 );
           $settings{$useinitvar} = $nl->get_value($useinitvar);
           if ( $try > 1 ) {
@@ -1457,9 +1173,8 @@ sub setup_logic_initial_conditions {
           if ( &value_is_true($nl->get_value($useinitvar) ) ) {
 
              add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes",
-                        'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, 
-                        'glc_nec'=>$nl_flags->{'glc_nec'},
-                        'use_cn'=>$nl_flags->{'use_cn'}, 'nofail'=>1 );
+                        'sim_year'=>$settings{'sim_year'},
+                        'nofail'=>1 );
              my $attributes_string = remove_leading_and_trailing_quotes($nl->get_value("init_interp_attributes"));
              foreach my $pair ( split( /\s/, $attributes_string) ) {
                 if ( $pair =~ /^([a-z_]+)=([a-z._0-9]+)$/ ) {
@@ -1491,222 +1206,6 @@ sub setup_logic_initial_conditions {
 
 #-------------------------------------------------------------------------------
 
-sub setup_logic_bgc_shared {
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  if ( $nl_flags->{'bgc_mode'} ne "sp" ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'constrain_stress_deciduous_onset', 'phys'=>$physv->as_string() );
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_hydrology_switches {
-  #
-  # Check on Switches for hydrology
-  #
-  my ($nl, $physv) = @_;
-
-  my $subgrid    = $nl->get_value('subgridflag' );
-  my $origflag   = $nl->get_value('origflag'    );
-  my $h2osfcflag = $nl->get_value('h2osfcflag'  );
-  if ( $origflag == 1 && $subgrid == 1 ) {
-    $log->fatal_error("if origflag is ON, subgridflag can NOT also be on!");
-  }
-  if ( $h2osfcflag == 1 && $subgrid != 1 ) {
-    $log->fatal_error("if h2osfcflag is ON, subgridflag can NOT be off!");
-  }
-  # These should NOT be set for CLM5.0 and beyond
-  if ( $physv->as_long() > $physv->as_long("clm4_5") ) {
-     foreach my $var ( "origflag", "h2osfcflag", "oldfflag" ) {
-        my $val = $nl->get_value($var);
-        if ( defined($val) ) {
-           $log->fatal_error( "ERROR:: $var=$val is deprecated and can only be used with CLM4.5" );
-        }
-     }
-  }
-  # Test bad configurations
-  my $lower   = $nl->get_value( 'lower_boundary_condition'  );
-  my $use_bed = $nl->get_value( 'use_bedrock'               );
-  my $soilmtd = $nl->get_value( 'soilwater_movement_method' );
-  if ( defined($soilmtd) && defined($lower) && $soilmtd == 0 && $lower != 4 ) {
-      $log->fatal_error( "If soil water movement method is zeng-decker -- lower_boundary_condition can only be aquifer" );
-  }
-  if ( defined($soilmtd) && defined($lower) && $soilmtd == 1 && $lower == 4 ) {
-      $log->fatal_error( "If soil water movement method is adaptive -- lower_boundary_condition can NOT be aquifer" );
-  }
-  if ( defined($use_bed) && defined($lower) && (&value_is_true($use_bed)) && $lower != 2 ) {
-     $log->fatal_error( "If use_bedrock is on -- lower_boundary_condition can only be flux" );
-  }
-  if ( defined($h2osfcflag) && defined($lower) && $h2osfcflag == 0 && $lower != 4 ) {
-     $log->fatal_error( "If h2osfcflag is 0 lower_boundary_condition can only be aquifer" );
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_dynamic_plant_nitrogen_alloc {
-  #
-  # dynamic plant nitrogen allocation model, bgc=bgc
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  if ( &value_is_true($nl_flags->{'use_cn'}) ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_flexibleCN',
-                'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'} );
-    $nl_flags->{'use_flexibleCN'} = $nl->get_value('use_flexibleCN');
-
-    if ( &value_is_true($nl_flags->{'use_flexibleCN'}) ) {
-      # TODO(bja, 2015-04) make this depend on > clm 5.0 and bgc mode at some point.
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'MM_Nuptake_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'downreg_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'plant_ndemand_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'substrate_term_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'nscalar_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'temp_scalar_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'CNratio_floating',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reduce_dayl_factor',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'vcmax_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'CN_residual_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'CN_partition_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'CN_evergreen_phenology_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'} );
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'carbon_resp_opt',
-                  'use_flexibleCN'=>$nl_flags->{'use_flexibleCN'}, 'use_fun'=>$nl->get_value('use_fun') );
-      if ( $nl->get_value('carbon_resp_opt') == 1 && &value_is_true($nl->get_value('use_fun')) ) {
-        $log->fatal_error("carbon_resp_opt should NOT be set to 1 when FUN is also on");
-      }
-    }
-  } elsif ( ! &value_is_true($nl_flags->{'use_cn'}) ) {
-     if ( &value_is_true($nl->get_value('use_flexibleCN')) ) {
-        $log->fatal_error("use_flexibleCN can ONLY be set if CN is on");
-     }
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_hydrstress {
-  #
-  # Plant hydraulic stress model
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  # TODO(kwo, 2015-09) make this depend on > clm 5.0 at some point.
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hydrstress' );
-  $nl_flags->{'use_hydrstress'} = $nl->get_value('use_hydrstress');
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_dynamic_roots {
-  #
-  # dynamic root model
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_dynroot', 'phys'=>$physv->as_string(), 'bgc_mode'=>$nl_flags->{'bgc_mode'});
-  my $use_dynroot = $nl->get_value('use_dynroot');
-  if ( &value_is_true($use_dynroot) && ($nl_flags->{'bgc_mode'} eq "sp") ) {
-    $log->fatal_error("Cannot turn dynroot mode on mode bgc=sp\n" .
-                "Set the bgc mode to 'cn' or 'bgc'.");
-  }
-  if ( &value_is_true( $use_dynroot ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) {
-     $log->fatal_error("Cannot turn use_dynroot on when use_hydrstress is on" );
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_canopy {
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-  #
-  # Canopy state
-  #
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults,
-              $nl, 'leaf_mr_vcm', 'phys'=>$nl_flags->{'phys'} )
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_soilwater_movement {
-  # soilwater_movement require clm4_5/clm5_0
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilwater_movement_method' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upper_boundary_condition' );
-
-  my $soilmtd = $nl->get_value("soilwater_movement_method");
-  my $use_bed = $nl->get_value('use_bedrock'              );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 
-  'lower_boundary_condition', 
-  'soilwater_movement_method'=>$soilmtd, 'use_bedrock'=>$use_bed
- );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtmin' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'verySmall' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerUpper' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'xTolerLower' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'expensive' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'inexpensive' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'flux_calculation' );
-}
-#-------------------------------------------------------------------------------
-
-sub setup_logic_cnvegcarbonstate {
-  #  MUST be AFTER: setup_logic_dynamic_plant_nitrogen_alloc as depends on mm_nuptake_opt which is set there
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  if ( &value_is_true($nl->get_value('use_cn')) ) {
-    my $mmnuptake = $nl->get_value('mm_nuptake_opt');
-    if ( ! defined($mmnuptake) ) { $mmnuptake = ".false."; }
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'initial_vegC', 
-                'use_cn' => $nl->get_value('use_cn'), 'mm_nuptake_opt' => $mmnuptake );
-  }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_rooting_profile {
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_water' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'rooting_profile_method_carbon' );
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_soil_resis {
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_resis_method' );
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_canopyhydrology {
-  #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
-}
-
-#-------------------------------------------------------------------------------
-
 sub setup_logic_snowpack {
   #
   # Snowpack related options
@@ -1715,87 +1214,11 @@ sub setup_logic_snowpack {
 
   if ($physv->as_long() >= $physv->as_long("clm4_5")) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'nlevsno');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'h2osno_max');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'int_snow_max');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'n_melt_glcmec');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fresh_snw_rds_max');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');
-
-    if (remove_leading_and_trailing_quotes($nl->get_value('snow_overburden_compaction_method')) eq 'Vionnet2012') {
-       # overburden_compress_tfactor isn't used if we're using the Vionnet2012
-       # snow overburden compaction method, so make sure the user hasn't tried
-       # to set it
-       if (defined($nl->get_value('overburden_compress_tfactor'))) {
-          $log->fatal_error('overburden_compress_tfactor is set, but does not apply when using snow_overburden_compaction_method=Vionnet2012');
-       }
-    } else {
-       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'overburden_compress_tfactor');
-    }
   }
 }
 
 #-------------------------------------------------------------------------------
 
-sub setup_logic_atm_forcing {
-   #
-   # Options related to atmospheric forcings
-   #
-   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-   if ($physv->as_long() >= $physv->as_long("clm4_5")) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glcmec_downscale_longwave');
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'repartition_rain_snow');
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lapse_rate');
-
-      my $var;
-
-      foreach $var ("lapse_rate_longwave",
-                    "longwave_downscaling_limit") {
-         if ( &value_is_true($nl->get_value("glcmec_downscale_longwave")) ) {
-            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
-         } else {
-            if (defined($nl->get_value($var))) {
-               $log->fatal_error("$var can only be set if glcmec_downscale_longwave is true");
-            }
-         }
-      }
-
-      foreach $var ("precip_repartition_glc_all_snow_t",
-                    "precip_repartition_glc_all_rain_t",
-                    "precip_repartition_nonglc_all_snow_t",
-                    "precip_repartition_nonglc_all_rain_t") {
-         if ( &value_is_true($nl->get_value("repartition_rain_snow")) ){
-            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
-         } else {
-            if (defined($nl->get_value($var))) {
-               $log->fatal_error("$var can only be set if repartition_rain_snow is true");
-            }
-         }
-      }
-   }
-}
-
-#-------------------------------------------------------------------------------
-
-sub setup_logic_lnd2atm {
-   #
-   # Options related to fields sent to atmosphere
-   #
-   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-
-   if ($physv->as_long() >= $physv->as_long("clm4_5")) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'melt_non_icesheet_ice_runoff');
-   }
-}
-
-#-------------------------------------------------------------------------------
-
 sub write_output_files {
   my ($opts, $nl_flags, $defaults, $nl, $physv) = @_;
 
@@ -1813,21 +1236,10 @@ sub write_output_files {
 
   # CLM component
   my @groups = qw(clm_inparm 
-                 lai_streams atm2lnd_inparm lnd2atm_inparm 
-                 cnvegcarbonstate
                  finidat_consistency_checks 
                  clm_initinterp_inparm 
-                 soilwater_movement_inparm rooting_profile_inparm
-                 soil_resis_inparm bgc_shared 
-                 clmu_inparm clm_soilstate_inparm 
-                 clm_soilhydrology_inparm
                  clm_glacier_behavior);
 
- if ( $physv->as_long() >= $physv->as_long("clm4_5") ) {
-   push @groups, "cn_general";
-   push @groups, "clm_canopy_inparm";
- }
-
   my $outfile;
   $outfile = "$opts->{'dir'}/lnd_in";
   $nl->write($outfile, 'groups'=>\@groups, 'note'=>"$note" );
diff --git a/bld/configure b/bld/configure
index 9823585f85..b9b58f1bae 100755
--- a/bld/configure
+++ b/bld/configure
@@ -47,7 +47,7 @@ OPTIONS
      or double leading dashes.  A consequence of this is that single letter options may
      NOT be bundled.
 
-     -bgc <name>            Build CLM with BGC package [ none | cn | cndv ] 
+     -bgc <name>            Build CLM with BGC package [ none | cn ] 
                             (default is none).
      -cache <file>          Name of output cache file (default: config_cache.xml).
      -cachedir <file>       Name of directory where output cache file is written 
@@ -58,7 +58,7 @@ OPTIONS
      -cppdefs <string>      A string of user specified CPP defines.  Appended to
                             Makefile defaults.  e.g. -cppdefs '-DVAR1 -DVAR2'
      -crop <name>           Toggle for prognostic crop model. [on | off] (default is off) 
-                            (can ONLY be turned on when BGC type is CN or CNDV)
+                            (can ONLY be turned on when BGC type is CN)
      -comp_intf <name>      Component interface to use (ESMF or MCT) (default MCT)
      -defaults <file>       Specify full path to a configuration file which will be used 
                             to supply defaults instead of the defaults in bld/config_files.
@@ -66,22 +66,12 @@ OPTIONS
                             Parameters relating to the build which are system dependent will
                             be ignored.
      -help [or -h]          Print usage to STDOUT.
-     -nofire                Turn off wildfires for BGC setting of CN 
-                            (default includes fire for CN)
      -noio                  Turn history output completely off (typically for testing).
      -phys <name>           Value of clm4_5, or clm5_0 (default is clm4_5)   
      -silent [or -s]        Turns on silent mode - only fatal messages issued.
      -sitespf_pt <name>     Setup for the given site specific single-point resolution.
      -snicar_frc <name>     Turn on SNICAR radiative forcing calculation. [on | off] 
                             (default is off)
-     -spinup <name>         CLM 4.0 Only. For CLM 4.5, spinup is controlled from build-namelist.
-                            Turn on given spinup mode for BGC setting of CN		  (level)
-                              AD            Turn on Accelerated Decomposition from	      (2)
-                                            bare-soil
-                              exit          Jump directly from AD spinup to normal mode	      (1)
-                              normal        Normal decomposition ("final spinup mode")	      (0)
-                                            (default)
-                            The recommended sequence is 2-1-0
      -usr_src <dir1>[,<dir2>[,<dir3>[...]]]
                             Directories containing user source code.
      -verbose [or -v]       Turn on verbose echoing of settings made by configure.
@@ -121,14 +111,11 @@ my $commandline = "$cfgdir/configure @ARGV";
 my %opts = (
 	    cache       => "config_cache.xml",
             phys        => "clm4_5",
-            nofire      => undef,
             noio        => undef,
             cimeroot    => undef,
             clm_root    => undef,
-            spinup      => "normal",
 	    );
 GetOptions(
-    "spinup=s"                  => \$opts{'spinup'}, 
     "bgc=s"                     => \$opts{'bgc'}, 
     "cache=s"                   => \$opts{'cache'},
     "cachedir=s"                => \$opts{'cachedir'},
@@ -140,7 +127,6 @@ GetOptions(
     "defaults=s"                => \$opts{'defaults'},
     "clm4me=s"                  => \$opts{'clm4me'},
     "h|help"                    => \$opts{'help'},
-    "nofire"                    => \$opts{'nofire'},
     "noio"                      => \$opts{'noio'},
     "phys=s"                    => \$opts{'phys'},
     "snicar_frc=s"              => \$opts{'snicar_frc'}, 
diff --git a/bld/namelist_files/namelist_defaults.xsl b/bld/namelist_files/namelist_defaults.xsl
index 96cb2b6edf..3085d98ff7 100644
--- a/bld/namelist_files/namelist_defaults.xsl
+++ b/bld/namelist_files/namelist_defaults.xsl
@@ -20,17 +20,15 @@
     </ul>
     <h3>Miscellaneous items include:</h3>
     <ol>
-       <li>Biogeochemistry (BGC) type (none, CN, CNDV)</li>
+       <li>Biogeochemistry (BGC) type (none, CN)</li>
        <li>Initial condition date (ymd - year month day)</li>
        <li>Initial condition time of day (tod) (sec)</li>
        <li>Maximum number of Plant Function Types (maxpft)</li>
-       <li>Number of glacier multiple elevation classes (glc_nec)</li>
        <li>Site specific point name (sitespf_pt)</li>
        <li>Crop model (crop)</li>
        <li>Data model forcing source (forcing)</li>
        <li>Representative concentration pathway for future scenarios (rcp)</li>
        <li>New good wood harvest (newwoodharv)</li>
-       <li>CN Spin-up mode (spinup)</li>
        <li>Type of file (type)</li>
        <li>Grid mapping to (to_hgrid)</li>
        <li>Land-mask mapping to (to_lmask)</li>
@@ -121,9 +119,6 @@
         <xsl:if test="string-length(@maxpft)>0">
         maxpft=<xsl:value-of select="@maxpft"/>
         </xsl:if>
-        <xsl:if test="string-length(@glc_nec)>0">
-        glc_nec=<xsl:value-of select="@glc_nec"/>
-        </xsl:if>
         <xsl:if test="string-length(@sitespf_pt)>0">
         sitespf_pt=<xsl:value-of select="@sitespf_pt"/>
         </xsl:if>
@@ -133,12 +128,6 @@
         <xsl:if test="string-length(@crop)>0">
         crop=<xsl:value-of select="@crop"/>
         </xsl:if>
-        <xsl:if test="string-length(@irrig)>0">
-        irrig=<xsl:value-of select="@irrig"/>
-        </xsl:if>
-        <xsl:if test="string-length(@spinup)>0">
-        spinup=<xsl:value-of select="@spinup"/>
-        </xsl:if>
         <xsl:if test="string-length(@source)>0">
         forcing=<xsl:value-of select="@source"/>
         </xsl:if>
diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
index 6d7e927c5a..ad7a327384 100644
--- a/bld/namelist_files/namelist_defaults_clm4_5.xml
+++ b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -30,162 +30,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- CO2 type -->
 <co2_type>constant</co2_type>
 
-<!-- Default Biogeochemistry mode -->
-<bgc_mode >sp</bgc_mode>
-
-<!-- Albedo for glaciers -->
-<albice phys="clm5_0">0.50,0.30</albice>
-<albice phys="clm4_5">0.60,0.40</albice>
-
-<!-- Default urban air conditioning/heating and wasteheat -->
-<urban_hac phys="clm5_0" >ON_WASTEHEAT</urban_hac>
-<urban_hac phys="clm4_5" >ON</urban_hac>
-
-<building_temp_method phys="clm5_0">1</building_temp_method>
-<building_temp_method phys="clm4_5">0</building_temp_method>
-
-<!-- Default urban traffic flux -->
-<urban_traffic>.false.</urban_traffic>
-
-<!-- Soil state settings -->
-<organic_frac_squared phys="clm4_5" >.true.</organic_frac_squared>
-<organic_frac_squared phys="clm5_0" >.false.</organic_frac_squared>
-
-<soil_layerstruct phys="clm5_0">20SL_8.5m</soil_layerstruct>
-<soil_layerstruct phys="clm4_5">10SL_3.5m</soil_layerstruct>
-
-<use_bedrock phys="clm5_0" use_fates =".true.">.false.</use_bedrock>
-<use_bedrock phys="clm5_0" vichydro ="1"      >.false.</use_bedrock>
-<use_bedrock phys="clm5_0">.true.</use_bedrock>
-<use_bedrock phys="clm4_5">.false.</use_bedrock>
-
-
-<!-- Rooting profile namelist defaults -->
-<rooting_profile_method_water  phys="clm5_0">1</rooting_profile_method_water>
-<rooting_profile_method_water  phys="clm4_5">0</rooting_profile_method_water>
-
-<rooting_profile_method_carbon phys="clm5_0">1</rooting_profile_method_carbon>
-<rooting_profile_method_carbon phys="clm4_5">1</rooting_profile_method_carbon>
-
-<!-- Soil evaporative resistance namelist defaults -->
-<soil_resis_method phys="clm5_0">1</soil_resis_method>
-<soil_resis_method phys="clm4_5">0</soil_resis_method>
-
-<!-- atm2lnd defaults -->
-<repartition_rain_snow phys="clm5_0">.true.</repartition_rain_snow>
-<repartition_rain_snow phys="clm4_5">.false.</repartition_rain_snow>
-
-<glcmec_downscale_longwave>.true.</glcmec_downscale_longwave>
-
-<!-- Pritchard et al. (GRL, 35, 2008) use 0.006 -->
-<lapse_rate>0.006</lapse_rate>
-
-<!-- Based on Van Tricht et al. (2016, TC) Figure 6, doi:10.5194/tc-10-2379-2016 -->
-<lapse_rate_longwave>0.032</lapse_rate_longwave>
-
-<longwave_downscaling_limit>0.5</longwave_downscaling_limit>
-
-<precip_repartition_nonglc_all_snow_t>0.</precip_repartition_nonglc_all_snow_t>
-<precip_repartition_nonglc_all_rain_t>2.</precip_repartition_nonglc_all_rain_t>
-<!-- For CLM45, we used the same rain-snow partitioning for glaciers as for other landunits -->
-<precip_repartition_glc_all_snow_t phys="clm4_5">0.</precip_repartition_glc_all_snow_t>
-<precip_repartition_glc_all_rain_t phys="clm4_5">2.</precip_repartition_glc_all_rain_t>
-<!-- For CLM5, we assume rain at somewhat cooler temperatures. The main
-     motivation is to increase glacier melt, which otherwise is too low in
-     CESM2. The physical justification is that the 0 - 2 C ramp used elsewhere
-     makes sense for typical atmospheric profiles; but over glaciers, inversions
-     are more common, so it is more reasonable to expect rain despite
-     below-freezing near-surface temperatures. -->
-<precip_repartition_glc_all_snow_t phys="clm5_0">-2.</precip_repartition_glc_all_snow_t>
-<precip_repartition_glc_all_rain_t phys="clm5_0">0.</precip_repartition_glc_all_rain_t>
-
-<!-- lnd2atm defaults -->
-<melt_non_icesheet_ice_runoff phys="clm4_5">.false.</melt_non_icesheet_ice_runoff>
-<melt_non_icesheet_ice_runoff phys="clm5_0">.true.</melt_non_icesheet_ice_runoff>
-
-<!-- Canopy hydrology namelist defaults -->
-<use_clm5_fpi phys="clm5_0">.true.</use_clm5_fpi>
-<interception_fraction phys="clm5_0">1.0</interception_fraction>
-<maximum_leaf_wetted_fraction phys="clm5_0">0.05</maximum_leaf_wetted_fraction>
-
-<use_clm5_fpi phys="clm4_5">.false.</use_clm5_fpi>
-<interception_fraction phys="clm4_5">0.25</interception_fraction>
-<maximum_leaf_wetted_fraction phys="clm4_5">1.0</maximum_leaf_wetted_fraction>
-
-<!-- Soilwater movement namelist defaults -->
-<soilwater_movement_method phys="clm4_5">0</soilwater_movement_method>
-<soilwater_movement_method phys="clm5_0">1</soilwater_movement_method>
-
-<upper_boundary_condition phys="clm4_5" >1</upper_boundary_condition>
-<upper_boundary_condition phys="clm5_0" >1</upper_boundary_condition>
-
-<lower_boundary_condition soilwater_movement_method="0"                       >4</lower_boundary_condition>
-<lower_boundary_condition soilwater_movement_method="1" use_bedrock=".true."  >2</lower_boundary_condition>
-<lower_boundary_condition soilwater_movement_method="1" use_bedrock=".false." >2</lower_boundary_condition>
-<lower_boundary_condition soilwater_movement_method="1" use_bedrock=".false." vichydro="1" >3</lower_boundary_condition>
-
-<dtmin>60.</dtmin>      
-<verySmall>1.e-8</verySmall>
-<xTolerUpper>1.e-1</xTolerUpper> 
-<xTolerLower>1.e-2</xTolerLower> 
-<expensive>42</expensive>
-<inexpensive>1</inexpensive>
-<flux_calculation>1</flux_calculation>
-
-<!-- Irrigation namelist defaults -->
-<irrig_min_lai>0.0</irrig_min_lai>
-<irrig_start_time>21600</irrig_start_time>
-<irrig_length>14400</irrig_length>
-<irrig_target_smp>-3400.</irrig_target_smp>  <!-- -3400 is a standard value for field capacity -->
-<irrig_depth>0.6</irrig_depth>
-<irrig_threshold_fraction phys="clm5_0">1.0</irrig_threshold_fraction>
-<irrig_threshold_fraction phys="clm4_5">0.5</irrig_threshold_fraction>
-<irrig_river_volume_threshold>0.1</irrig_river_volume_threshold>
-
-<!--  River storage derived lake evaporation and irrigation limitation  -->
-<limit_irrigation_if_rof_enabled phys="clm5_0">.false.</limit_irrigation_if_rof_enabled>
-<limit_irrigation_if_rof_enabled              >.false.</limit_irrigation_if_rof_enabled>
-
-<!-- Snow veg treatment -->
-<snowveg_flag phys="clm4_5" >OFF</snowveg_flag>
-<snowveg_flag phys="clm5_0" >ON_RAD</snowveg_flag>
-
 <!-- Snow pack settings-->
 <nlevsno phys="clm5_0" >12</nlevsno>
 <nlevsno phys="clm4_5" >5</nlevsno>
-<h2osno_max phys="clm5_0" >10000.0</h2osno_max>
-<h2osno_max phys="clm4_5" >1000.0</h2osno_max>
-
-<int_snow_max phys="clm5_0">2000.</int_snow_max>
-<!-- For clm4_5, make this effectively unlimited -->
-<int_snow_max phys="clm4_5">1.e30</int_snow_max>
-
-<n_melt_glcmec phys="clm5_0">10.0d00</n_melt_glcmec>
-<n_melt_glcmec phys="clm4_5">10.0</n_melt_glcmec>
-
-<wind_dependent_snow_density phys="clm5_0" >.true.</wind_dependent_snow_density>
-<wind_dependent_snow_density phys="clm4_5" >.false.</wind_dependent_snow_density>
-
-<snow_overburden_compaction_method phys="clm5_0">'Vionnet2012'</snow_overburden_compaction_method>
-<snow_overburden_compaction_method phys="clm4_5">'Anderson1976'</snow_overburden_compaction_method>
-
-<lotmp_snowdensity_method phys="clm5_0">'Slater2017'</lotmp_snowdensity_method>
-<lotmp_snowdensity_method phys="clm4_5">'TruncatedAnderson1976'</lotmp_snowdensity_method>
-
-<upplim_destruct_metamorph   phys="clm4_5">100.d00</upplim_destruct_metamorph>
-<upplim_destruct_metamorph   phys="clm5_0">175.d00</upplim_destruct_metamorph>
-
-<fresh_snw_rds_max phys="clm4_5">54.526d00</fresh_snw_rds_max>
-<fresh_snw_rds_max phys="clm5_0">204.526d00</fresh_snw_rds_max>
-
-<overburden_compress_tfactor>0.08d00</overburden_compress_tfactor>
-
-<reset_snow>.false.</reset_snow>
-<reset_snow_glc>.false.</reset_snow_glc>
-<!-- Set default reset_snow_glc_ela value to very large so that, by
-     default, all glacier columns will be reset if reset_snow_glc is set
-     to .true. -->
-<reset_snow_glc_ela>1.e9</reset_snow_glc_ela>
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
@@ -194,116 +41,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
      Antarctica: multiple -->
 <glacier_region_behavior>'single_at_atm_topo','virtual','virtual','multiple'</glacier_region_behavior>
 
-<!-- Default glacier melt behavior is:
-     Mountain glaciers: remains_in_place
-     Greenland - inside CISM grid but outside Greenland itself: replaced_by_ice
-     Greenland itself: replaced_by_ice
-     Antarctica: replaced_by_ice -->
-<glacier_region_melt_behavior>'remains_in_place','replaced_by_ice','replaced_by_ice','replaced_by_ice'</glacier_region_melt_behavior>
-
-<!-- Default glacier ice runoff behavior is:
-     Mountain glaciers: melted
-     Greenland - inside CISM grid but outside Greenland itself: melted
-     Greenland itself: remains_ice
-     Antarctica: remains_ice -->
-<glacier_region_ice_runoff_behavior>'melted','melted','remains_ice','remains_ice'</glacier_region_ice_runoff_behavior>
-
-<!-- This parameter is tied (in a scientific sense) to h2osno_max: For large
-     values of h2osno_max, glc_snow_persistence_max_days should be 0; for small
-     values of h2osno_max, glc_snow_persistence_max_days should be non-zero. For
-     simplicity, we tie the defaults for both of these options to the overall
-     CLM phys version, rather than having some intermediate option that controls
-     the defaults for both h2osno_max and glc_snow_persistence_max_days. -->
-<glc_snow_persistence_max_days phys="clm5_0" >0</glc_snow_persistence_max_days>
-<glc_snow_persistence_max_days phys="clm4_5" >7300</glc_snow_persistence_max_days>
-
 <!-- ================================================================== -->
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c171117.nc</paramfile>
-<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c170913.nc</paramfile>
 
-<!-- ================================================================== -->
-<!-- FATES default parameter file                                       -->
-<!-- ================================================================== -->
-
-<fates_paramfile>lnd/clm2/paramdata/fates_params_2troppftclones.c171018.nc</fates_paramfile>
-
-<!-- ========================================================================================  -->
-<!-- clm 5.0 BGC nitrogen model                                                                -->
-<!-- ========================================================================================  -->
-<use_flexibleCN phys="clm5_0" use_cn=".true.">.true.</use_flexibleCN>
-<use_flexibleCN phys="clm5_0"                >.false.</use_flexibleCN>
-<use_flexibleCN phys="clm4_5"                >.false.</use_flexibleCN>
-
-<!-- LUNA model: Leaf Utilization of Nitrogen for Assimilation -->
-<use_luna phys="clm5_0"  >.true.</use_luna>
-<use_luna phys="clm5_0" use_fates=".true." >.false.</use_luna>
-<use_luna phys="clm4_5"  >.false.</use_luna>
-
-<!-- Flexible CN options -->
-<MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
-<downreg_opt                use_flexibleCN=".true." >.false.</downreg_opt>
-<plant_ndemand_opt          use_flexibleCN=".true." >3</plant_ndemand_opt>
-<substrate_term_opt         use_flexibleCN=".true." >.true.</substrate_term_opt>
-<nscalar_opt                use_flexibleCN=".true." >.true.</nscalar_opt>
-<temp_scalar_opt            use_flexibleCN=".true." >.true.</temp_scalar_opt>
-<CNratio_floating           use_flexibleCN=".true." >.true.</CNratio_floating>
-<reduce_dayl_factor         use_flexibleCN=".true." >.false.</reduce_dayl_factor>
-<vcmax_opt                  use_flexibleCN=".true." >3</vcmax_opt>
-<CN_residual_opt            use_flexibleCN=".true." >1</CN_residual_opt>
-<CN_partition_opt           use_flexibleCN=".true." >1</CN_partition_opt>
-<CN_evergreen_phenology_opt use_flexibleCN=".true." >1</CN_evergreen_phenology_opt>
-<carbon_resp_opt            use_flexibleCN=".true." use_fun=".false.">1</carbon_resp_opt>
-<carbon_resp_opt            use_flexibleCN=".true." use_fun=".true." >0</carbon_resp_opt>
-
-
-<!-- LUNA options -->
-<!-- lnc_opt determines how nitrogen is made available for luna -->
-<!-- lnc_opt true means use leaf-N from BGC model -->
-<!-- lnc_opt false means base on LAI and CN ratio from parameter file -->
-<lnc_opt use_cn=".true."   >.true.</lnc_opt>
-<lnc_opt use_cn=".false."  >.false.</lnc_opt>
-
-<use_fertilizer>.false.</use_fertilizer>
-<use_fertilizer use_crop=".true." phys="clm4_5">.true.</use_fertilizer>
-<use_fertilizer use_crop=".true." phys="clm5_0">.true.</use_fertilizer>
-
-<jmaxb1 use_luna=".true." phys="clm5_0">0.093563</jmaxb1>
-
-<use_grainproduct>.false.</use_grainproduct>
-<use_grainproduct use_crop=".true." phys="clm4_5">.false.</use_grainproduct> <!-- 1-year grain product pool default to off for clm45 if crop is turned on -->
-<use_grainproduct use_crop=".true." phys="clm5_0">.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
-
-<initial_seed_at_planting use_crop=".true." phys="clm5_0">3.d00</initial_seed_at_planting>
-<initial_seed_at_planting use_crop=".true." phys="clm4_5">1.d00</initial_seed_at_planting>
-
-
-<!-- turnover time modifications    -->
-<decomp_depth_efolding phys="clm4_5">0.5</decomp_depth_efolding>
-<decomp_depth_efolding phys="clm5_0">10.0</decomp_depth_efolding>
-
-<!-- use additional stress deciduous onset trigger    -->
-<constrain_stress_deciduous_onset phys="clm4_5">.false.</constrain_stress_deciduous_onset>
-<constrain_stress_deciduous_onset phys="clm5_0">.true.</constrain_stress_deciduous_onset>
-
-<!-- dynamic roots -->
-<use_dynroot phys="clm4_5">.false.</use_dynroot>
-<use_dynroot phys="clm5_0" bgc_mode="sp">.false.</use_dynroot>
-<use_dynroot phys="clm5_0" bgc_mode="cn">.false.</use_dynroot>
-<use_dynroot phys="clm5_0" bgc_mode="fates">.false.</use_dynroot>
-<use_dynroot phys="clm5_0" bgc_mode="bgc">.false.</use_dynroot>
-
-<!-- Guardrail for ensuring leaf-Nitrogen doesn't go too small or negative on updates -->
-<use_nguardrail phys="clm4_5"                 >.false.</use_nguardrail>
-<use_nguardrail phys="clm5_0" use_cn=".false.">.false.</use_nguardrail>
-<use_nguardrail phys="clm5_0" use_cn=".true." >.true.</use_nguardrail>
-
-<!-- Plant hydraulic stress -->
-<use_hydrstress phys="clm4_5"                 >.false.</use_hydrstress>
-<use_hydrstress phys="clm5_0" use_fates=".true." >.false.</use_hydrstress>
-<use_hydrstress phys="clm5_0" use_fates=".false.">.true.</use_hydrstress>
 <!--
 
      Initial condition files to use and or interpolate from
@@ -317,9 +59,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <init_interp_sim_years>1850,2000</init_interp_sim_years>
 
 <!-- Interpolate from an initial condition file at startup? -->
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1850">.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2000">.true.</use_init_interp>
-<use_init_interp                                                        >.false.</use_init_interp>
+<use_init_interp sim_year="1850">.true.</use_init_interp>
+<use_init_interp sim_year="2000">.true.</use_init_interp>
+<use_init_interp                >.false.</use_init_interp>
 
 <!--
   Set attributes to find specific matching finidat files below
@@ -327,40 +69,41 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
   set up. If more finidat files are added you may need to add more of these.
   Or one specific file will be chosen over another.
 -->
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_GSWP3v1"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.false. glc_nec=10
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm4_5_GSWP3v1"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v6 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_CRUv7"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.false. irrigate=.false. glc_nec=10
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm4_5_CRUv7"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v6 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm4_5_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm4_5_cam6.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10
-</init_interp_attributes>
-
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_GSWP3v1"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10
+<!--
+  Which is correct? The next or the previous one?
+-->
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm5_0_GSWP3v1"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v6 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm5_0_CRUv7"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v6 
 </init_interp_attributes>
-
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_CRUv7"
->hgrid=0.9x1.25 maxpft=17 mask=gx1v6 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10
+<!--
+  Which is correct? The next or the previous one?
+-->
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm5_0_CRUv7"
+>hgrid=0.9x1.25 maxpft=17 mask=gx1v6 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10
+<init_interp_attributes sim_year="1850" lnd_tuning_mode="clm5_0_cam6.0"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false."
->hgrid=1.9x2.5 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
+<init_interp_attributes sim_year="2000" 
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v6 
 </init_interp_attributes>
 
 <!-- MML 2 degree resolution -->
@@ -375,62 +118,62 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
                            (if it will work on an exact match, leave use_init_interp off)
 -->
 
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".false."
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm4_5_GSWP3v1"
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcGs.0901-01-01.0.9x1.25_gx1v6_simyr1850_c180204.nc
 </finidat>
 
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".false."
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm4_5_CRUv7"
 >lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v6_simyr1850_c180204.nc
 </finidat>
 
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm4_5_cam6.0"
 >lnd/clm2/initdata_map/clmi.B1850.0161-01-01.0.9x1.25_gx1v7_simyr1850_c180130.nc
 </finidat>
 
 
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".false." use_vertsoilc=".false." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm5_0_GSWP3v1"
 >lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0181-01-01.0.9x1.25_gx1v6_simyr1850_c171214.nc
 </finidat>
 
 
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false." use_init_interp=".true."
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" use_init_interp=".true."
          lnd_tuning_mode="clm5_0_GSWP3v1"
 >lnd/clm2/initdata_map/clmi.I1850Clm50BgcCrop.1366-01-01.0.9x1.25_gx1v6_simyr1850_c171213.nc
 </finidat>
 
 
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm5_0_CRUv7"
 >lnd/clm2/initdata_map/clmi.I1850Clm50BgcCropCru.1526-01-01.0.9x1.25_gx1v6_simyr1850_c180109.nc
 </finidat>
 
 
-<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
+<finidat hgrid="0.9x1.25"  maxpft="79"  mask="gx1v7"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm5_0_cam6.0"
 >lnd/clm2/initdata_map/clmi.B1850.0161-01-01.0.9x1.25_gx1v7_simyr1850_c180130.nc
 </finidat>
 
-<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6" use_cn=".false." use_cndv=".false." use_fates=".false."
-         ic_ymd="18500101" use_nitrif_denitrif=".false." use_vertsoilc=".false." sim_year="1850"
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
+<finidat hgrid="0.9x1.25"  maxpft="17"  mask="gx1v6"
+         ic_ymd="18500101" sim_year="1850"
+         ic_tod="0" 
          lnd_tuning_mode="clm5_0_CRUv7"
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v6_simyr1850_c180110.nc
 </finidat>
@@ -442,147 +185,115 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Present day crop spinup at 2-degree with irrigation on -->
-<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
-         ic_ymd="20110101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="2000"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."  use_init_interp=".true."
+<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v6"
+         ic_ymd="20110101" sim_year="2000"
+         ic_tod="0" use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.IGM2000GSWP3CLM50BGCCROPIRR.2011-01-01.1.9x2.5_gx1v6_gl5_simyr2000_c170419.nc
 </finidat>
 
-<!-- FATES on for 2000 (MUST be an exact match - can't interpolate files for FATES -->
-<finidat hgrid="4x5"  maxpft="17"  mask="gx3v7" use_cn=".false." use_fates=".true."
-         ic_ymd="20000101"  use_nitrif_denitrif=".false." use_vertsoilc=".true." sim_year="2000"
-         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true."
->lnd/clm2/initdata_map/clmi.I2000Clm45Fates.0121-01-01.4x5_mgx3v7_simyr2000_c180122.nc
-</finidat>
-
-<finidat hgrid="1x1_brazil"  maxpft="17"  mask="navy" use_cn=".false." use_fates=".true."
-         ic_ymd="20000101"  use_nitrif_denitrif=".false." use_vertsoilc=".true." sim_year="2000"
-         ic_tod="0" glc_nec="0" use_crop=".false." irrigate=".true."
->lnd/clm2/initdata_map/clmi.I2000Clm45Fates.0101-01-01.1x1_brazil_simyr2000_c180120.nc
-</finidat>
-
-
 <!-- for present day simulations - year 2000 -->
-<fsurdat hgrid="360x720cru"   sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="360x720cru"   sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="48x96"     sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="48x96"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_48x96_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
 
-<fsurdat hgrid="0.47x0.63"  sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="0.47x0.63"  sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_0.47x0.63_16pfts_Irrig_CMIP6_simyr2000_c170919.nc</fsurdat>
-<fsurdat hgrid="0.9x1.25"  sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="0.9x1.25"  sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_0.9x1.25_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="1.9x2.5"   sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_1.9x2.5_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="4x5"       sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="4x5"       sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_4x5_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="10x15"     sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="10x15"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_10x15_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
 
-<fsurdat hgrid="ne120np4"    sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="ne120np4"    sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne120np4_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="ne30np4"     sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="ne30np4"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne30np4_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="ne16np4"     sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="ne16np4"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne16np4_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
 
-<fsurdat hgrid="5x5_amazon"    sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="5x5_amazon"    sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_brazil"    sim_year="2000" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="1x1_brazil"    sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_1x1_brazil_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
 
 <!-- Needed for SCAM (Single Column Atmosphere Model) -->
-<fsurdat hgrid="64x128"      sim_year="2000" use_crop=".false." irrigate=".true."
+<fsurdat hgrid="64x128"      sim_year="2000" 
 >lnd/clm2/surfdata_map/surfdata_64x128_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
 
 <!-- Crop surface datasets -->
-<fsurdat hgrid="0.47x0.63"  sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="0.47x0.63"  sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_0.47x0.63_78pfts_CMIP6_simyr2000_c170919.nc</fsurdat>
-<fsurdat hgrid="0.9x1.25"  sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="0.9x1.25"  sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="1.9x2.5"   sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_1.9x2.5_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="0.125x0.125"  sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="0.125x0.125"  sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_0.125x0.125_mp24_simyr2000_c150114.nc</fsurdat>
-<fsurdat hgrid="10x15"     sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="10x15"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="4x5"       sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="4x5"       sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_4x5_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="1x1_numaIA"       sim_year="2000" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_1x1_numaIA_78pfts_CMIP6_simyr2000_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_smallvilleIA" sim_year="2000" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_1x1_smallvilleIA_78pfts_CMIP6_simyr2000_c171214.nc</fsurdat>
 
-<fsurdat hgrid="ne120np4"    sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="ne120np4"    sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="ne30np4"     sim_year="2000" use_crop=".true.">
+<fsurdat hgrid="ne30np4"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne30np4_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
-<fsurdat hgrid="ne16np4"     sim_year="2000" use_crop=".true." >
+<fsurdat hgrid="ne16np4"     sim_year="2000" >
 lnd/clm2/surfdata_map/surfdata_ne16np4_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
 
-<!-- 100% Urban single-point datasets (only for sim-year=2000) -->
-<fsurdat hgrid="1x1_camdenNJ"        sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/surfdata_1x1_camdenNJ_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/surfdata_1x1_vancouverCAN_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/surfdata_1x1_mexicocityMEX_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/surfdata_1x1_urbanc_alpha_16pfts_Irrig_CMIP6_simyr2000_c171214.nc</fsurdat>
-
 <!-- for pre-industrial simulations - year 1850 without crop -->
-<fsurdat hgrid="360x720cru"   sim_year="1850" use_crop=".false." irrigate=".true." >
+<fsurdat hgrid="360x720cru"   sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="48x96"        sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="48x96"        sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_48x96_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
 
-<fsurdat hgrid="0.47x0.63"  sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="0.47x0.63"  sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_0.47x0.63_16pfts_Irrig_CMIP6_simyr1850_c170919.nc</fsurdat>
-<fsurdat hgrid="0.9x1.25"     sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="0.9x1.25"     sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_0.9x1.25_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="1.9x2.5"      sim_year="1850" use_crop=".false." >
+<fsurdat hgrid="1.9x2.5"      sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_1.9x2.5_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="10x15"        sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="10x15"        sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_10x15_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="4x5"          sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="4x5"          sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_4x5_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
 
-<fsurdat hgrid="1x1_brazil"    sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="1x1_brazil"    sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_1x1_brazil_16pfts_Irrig_CMIP6_simyr1850_c171214.nc</fsurdat>
 
 
-<fsurdat hgrid="ne120np4"     sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="ne120np4"     sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_ne120np4_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="ne30np4"      sim_year="1850" use_crop=".false." irrigate=".true.">
+<fsurdat hgrid="ne30np4"      sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_ne30np4_16pfts_Irrig_CMIP6_simyr1850_c170824.nc</fsurdat>
 
 <!-- pre-industrial with crop -->
-<fsurdat hgrid="360x720cru"   sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="360x720cru"   sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_360x720cru_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="48x96"        sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="48x96"        sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_48x96_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
 
-<fsurdat hgrid="0.47x0.63"  sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="0.47x0.63"  sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_0.47x0.63_78pfts_CMIP6_simyr1850_c170919.nc</fsurdat>
-<fsurdat hgrid="0.9x1.25"  sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="0.9x1.25"  sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="1.9x2.5"   sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="1.9x2.5"   sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_1.9x2.5_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="10x15"     sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="10x15"     sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="4x5"       sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="4x5"       sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_4x5_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_1x1_smallvilleIA_78pfts_CMIP6_simyr1850_c171214.nc</fsurdat>
-<fsurdat hgrid="1x1_numaIA"       sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/surfdata_1x1_numaIA_78pfts_CMIP6_simyr1850_c170917.nc</fsurdat>
 
-<fsurdat hgrid="1x1_brazil"    sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="1x1_brazil"    sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_1x1_brazil_78pfts_CMIP6_simyr1850_c171214.nc</fsurdat>
 
-<fsurdat hgrid="ne30np4"      sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="ne30np4"      sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_ne30np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
-<fsurdat hgrid="ne120np4"     sim_year="1850" use_crop=".true." >
+<fsurdat hgrid="ne120np4"     sim_year="1850" >
 lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurdat>
 
 <!-- Dynamic PFT surface datasets (relative to {csmdata}) -->
@@ -591,1498 +302,195 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
      dataset (arbitrarily, RCP8.5) for the historical period, because all of the
      RCP datasets contain the 1850-2000 period as well as the future period. -->
 
-<flanduse_timeseries hgrid="0.47x0.63"      sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.47x0.63_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c171025.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="48x96"         sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="ne120np4"      sim_year_range="1850-2000"  irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne30np4"       sim_year_range="1850-2000"  irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.47x0.63"      sim_year_range="1850-2000" 
+>lnd/clm2/surfdata_map/landuse.timeseries_0.47x0.63_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c171025.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000" 
+>lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000" 
+>lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000" 
+>lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="48x96"         sim_year_range="1850-2000" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="ne120np4"      sim_year_range="1850-2000"  
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne30np4"       sim_year_range="1850-2000"  
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <!-- Dynamic PFT surface datasets for crop -->
 
 <flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="48x96"         sim_year_range="1850-2000"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1x1_numaIA"    sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne120np4"      sim_year_range="1850-2000" 
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4"       sim_year_range="1850-2000" 
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<!-- Note that this transient file only goes up to year 1855.
-     This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
-<flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
- use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_c160127.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <!-- Dynamic PFT surface datasets for future scenarios(relative to {csmdata}) -->
 
 <!-- Other future scenario Dynamic PFT datasets with crop off -->
-<flanduse_timeseries hgrid="360x720cru"    rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="0.9x1.25"      rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1.9x2.5"       rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="48x96"         rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne30np4"       rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne120np4"      rcp="8.5" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="1x1_brazil"    rcp="8.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="360x720cru"    rcp="6"   sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="0.9x1.25"      rcp="6"   sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1.9x2.5"       rcp="6"   sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         rcp="6"   sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="48x96"         rcp="6"   sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne30np4"       rcp="6"   sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="360x720cru"    rcp="4.5" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="0.9x1.25"      rcp="4.5" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1.9x2.5"       rcp="4.5" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         rcp="4.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="48x96"         rcp="4.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne120np4"      rcp="4.5" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne30np4"       rcp="4.5" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<flanduse_timeseries hgrid="360x720cru"    rcp="2.6" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="0.9x1.25"      rcp="2.6" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="1.9x2.5"       rcp="2.6" sim_year_range="1850-2100"  irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         rcp="2.6" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="48x96"         rcp="2.6" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="ne30np4"       rcp="2.6" sim_year_range="1850-2100" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="360x720cru"    rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.9x1.25"      rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="10x15"         rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="48x96"         rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne30np4"       rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne120np4"      rcp="8.5" sim_year_range="1850-2100"  
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="1x1_brazil"    rcp="8.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="360x720cru"    rcp="6"   sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.9x1.25"      rcp="6"   sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       rcp="6"   sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="10x15"         rcp="6"   sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="48x96"         rcp="6"   sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne30np4"       rcp="6"   sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="360x720cru"    rcp="4.5" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.9x1.25"      rcp="4.5" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       rcp="4.5" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="10x15"         rcp="4.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="48x96"         rcp="4.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne120np4"      rcp="4.5" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne30np4"       rcp="4.5" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+
+<flanduse_timeseries hgrid="360x720cru"    rcp="2.6" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="0.9x1.25"      rcp="2.6" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="1.9x2.5"       rcp="2.6" sim_year_range="1850-2100"
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="10x15"         rcp="2.6" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="48x96"         rcp="2.6" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+<flanduse_timeseries hgrid="ne30np4"       rcp="2.6" sim_year_range="1850-2100" 
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <!-- Other future scenario Dynamic PFT datasets with crop on -->
 <flanduse_timeseries hgrid="360x720cru"    rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="4x5"           rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="48x96"         rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4"       rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne120np4"      rcp="8.5" sim_year_range="1850-2100" 
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    rcp="8.5" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    rcp="6"   sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      rcp="6"   sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       rcp="6"   sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         rcp="6"   sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="4x5"           rcp="6"   sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="48x96"         rcp="6"   sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4"       rcp="6"   sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    rcp="4.5" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      rcp="4.5" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       rcp="4.5" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         rcp="4.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="4x5"           rcp="4.5" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="48x96"         rcp="4.5" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne120np4"      rcp="4.5" sim_year_range="1850-2100" 
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne120np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4"       rcp="4.5" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="360x720cru"    rcp="2.6" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      rcp="2.6" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       rcp="2.6" sim_year_range="1850-2100" 
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="10x15"         rcp="2.6" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="4x5"           rcp="2.6" sim_year_range="1850-2100"
- use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="48x96"         rcp="2.6" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4"       rcp="2.6" sim_year_range="1850-2100"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
-
-<!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
-<use_fun phys="clm5_0" use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
-<use_fun                                                           >.false.</use_fun>
-
-<!-- Scalar of leaf respiration to vcmax (used for SP mode and with luna)-->
-<leaf_mr_vcm phys="clm5_0" >0.015d00</leaf_mr_vcm>
-<leaf_mr_vcm phys="clm4_5" >0.015d00</leaf_mr_vcm>
-
-<!-- Initial Carbon stocks for BGC -->
-<initial_Cstocks phys="clm4_5" use_cn=".true."  use_fates=".false." use_century_decomp=".true." >20.0d00, 20.0d00, 20.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_0" use_cn=".true."  use_fates=".false." use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm4_5" use_cn=".false." use_fates=".true."  use_century_decomp=".true." >20.0d00, 20.0d00, 20.0d00</initial_Cstocks>
-<initial_Cstocks phys="clm5_0" use_cn=".false." use_fates=".true."  use_century_decomp=".true." >200.0d00, 200.0d00, 200.0d00</initial_Cstocks>
-
-<initial_Cstocks_depth phys="clm5_0" use_cn=".true."   use_fates=".false." use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm4_5" use_cn=".true."   use_fates=".false." use_century_decomp=".true." >0.3</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm5_0" use_cn=".false."  use_fates=".true."  use_century_decomp=".true." >1.50d00</initial_Cstocks_depth>
-<initial_Cstocks_depth phys="clm4_5" use_cn=".false."  use_fates=".true."  use_century_decomp=".true." >0.3</initial_Cstocks_depth>
-
-<initial_vegC phys="clm5_0" use_cn=".true."  mm_nuptake_opt=".true." >100.d00</initial_vegC>
-<initial_vegC phys="clm4_5" use_cn=".true."  mm_nuptake_opt=".true." >20.d00</initial_vegC>
-<initial_vegC phys="clm5_0" use_cn=".true."  mm_nuptake_opt=".false.">1.d00</initial_vegC>
-<initial_vegC phys="clm4_5" use_cn=".true."  mm_nuptake_opt=".false.">1.d00</initial_vegC>
-
-<!-- SNICAR (SNow, ICe, and Aerosol Radiative model) datasets -->
-<!--  ***********  Resolution independent:   ***********  -->
-<fsnowoptics >lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc</fsnowoptics>
-<fsnowaging  >lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc</fsnowaging>
-
-<!-- LAI streams namelist defaults -->
-<use_lai_streams        >.false.</use_lai_streams>
-<stream_year_first_lai  >2001</stream_year_first_lai>
-<stream_year_last_lai   >2013</stream_year_last_lai>
-<model_year_align_lai   >2001</model_year_align_lai>
-
-<stream_fldfilename_lai hgrid="360x720cru"       >lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc</stream_fldfilename_lai>
+ >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <lai_mapalgo>bilinear</lai_mapalgo>
 
 <lai_mapalgo  hgrid="1x1_brazil"          >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_mexicocityMEX"   >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_vancouverCAN"    >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_urbanc_alpha"    >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_camdenNJ"        >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="1x1_brazil"          >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_mexicocityMEX"   >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_vancouverCAN"    >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_urbanc_alpha"    >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_camdenNJ"        >nn</lai_mapalgo>
-<lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 
-<!-- Create crop on a separate land-unit -->
-<create_crop_landunit     use_fates=".false.">.true.</create_crop_landunit>
-<create_crop_landunit     use_fates=".true." >.false.</create_crop_landunit>
-
-
 <!-- =========================================  -->
 <!-- Performance issues                         -->
 <!-- =========================================  -->
 
 <nsegspc                   >35</nsegspc>
 
-<!-- =========================================  -->
-<!-- Mapping Data                               -->
-<!-- =========================================  -->
-
-
-<!-- mapping files for 0.1x0.1 START added on Wed Jul 25 17:01:27 2012--> 
-
-<map frm_hgrid="0.1x0.1"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.1x0.1_nomask_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.5x0.5_AVHRR_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.5x0.5_MODIS_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.25x0.25_MODIS_to_0.1x0.1_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.5x0.5_nomask_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_10x10min_nomask_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_3x3min_MODIS_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_3x3min_MODIS-wCsp_to_0.1x0.1_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_5x5min_IGBP-GSDP_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_5x5min_ISRIC-WISE_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ORNL-Soil" to_hgrid="0.1x0.1" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.1x0.1/map_5x5min_ORNL-Soil_to_0.1x0.1_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_5x5min_nomask_to_0.1x0.1_nomask_aave_da_c120406.nc</map>
-<map frm_hgrid="ne120np4"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_ne120np4_nomask_to_0.1x0.1_nomask_aave_da_c120711.nc</map>
-<map frm_hgrid="4x5"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_4x5_nomask_to_0.1x0.1_nomask_aave_da_c120706.nc</map>
-<map frm_hgrid="1.9x2.5"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_1.9x2.5_nomask_to_0.1x0.1_nomask_aave_da_c120709.nc</map>
-<map frm_hgrid="ne240np4"    frm_lmask="nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_ne240np4_nomask_to_0.1x0.1_nomask_aave_da_c120711.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_0.9x1.25_GRDC_to_0.1x0.1_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_360x720_cruncep_to_0.1x0.1_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="0.1x0.1"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.1x0.1/map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.1x0.1_nomask_aave_da_c130405.nc</map>
-
-<!-- mapping files for 0.1x0.1 END --> 
-
-<!-- mapping files for 1x1_asphaltjungleNJ START added on Thu Jul 19 13:06:18 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_0.5x0.5_AVHRR_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_0.5x0.5_MODIS_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_0.25x0.25_MODIS_to_1x1_asphaltjungleNJ_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_0.5x0.5_nomask_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_10x10min_nomask_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_MODIS_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_MODIS-wCsp_to_1x1_asphaltjungleNJ_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_USGS_to_1x1_asphaltjungleNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_LandScan2004_to_1x1_asphaltjungleNJ_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_5x5min_IGBP-GSDP_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_5x5min_ISRIC-WISE_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_asphaltjungleNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_5x5min_ORNL-Soil_to_1x1_asphaltjungleNJ_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_5x5min_nomask_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_asphaltjungleNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_GLOBE-Gardner_to_1x1_asphaltjungleNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_asphaltjungleNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_asphaltjungleNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_0.9x1.25_GRDC_to_1x1_asphaltjungleNJ_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_360x720_cruncep_to_1x1_asphaltjungleNJ_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_asphaltjungleNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_asphaltjungleNJ_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_asphaltjungleNJ END --> 
-
-<!-- mapping files for 1x1_brazil START added on Thu Jul 19 13:06:18 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_0.5x0.5_AVHRR_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_0.5x0.5_MODIS_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
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-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_0.5x0.5_nomask_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_10x10min_nomask_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
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-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_MODIS-wCsp_to_1x1_brazil_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_USGS_to_1x1_brazil_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_LandScan2004_to_1x1_brazil_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_5x5min_IGBP-GSDP_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_5x5min_ISRIC-WISE_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_brazil" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_brazil/map_5x5min_ORNL-Soil_to_1x1_brazil_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_5x5min_nomask_to_1x1_brazil_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_brazil" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_GLOBE-Gardner_to_1x1_brazil_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_brazil" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_brazil_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_0.9x1.25_GRDC_to_1x1_brazil_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_360x720_cruncep_to_1x1_brazil_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_brazil"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_brazil/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_brazil_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_brazil END --> 
-
-<!-- mapping files for 1x1_camdenNJ START added on Thu Jul 19 13:06:18 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_0.5x0.5_AVHRR_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_0.5x0.5_MODIS_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_0.25x0.25_MODIS_to_1x1_camdenNJ_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_0.5x0.5_nomask_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_10x10min_nomask_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_MODIS_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_MODIS-wCsp_to_1x1_camdenNJ_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_USGS_to_1x1_camdenNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_LandScan2004_to_1x1_camdenNJ_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_5x5min_IGBP-GSDP_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_5x5min_ISRIC-WISE_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_camdenNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_5x5min_ORNL-Soil_to_1x1_camdenNJ_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_5x5min_nomask_to_1x1_camdenNJ_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_camdenNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_GLOBE-Gardner_to_1x1_camdenNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_camdenNJ" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_camdenNJ_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_0.9x1.25_GRDC_to_1x1_camdenNJ_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_360x720_cruncep_to_1x1_camdenNJ_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_camdenNJ"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_camdenNJ_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_camdenNJ END --> 
-
-<!-- mapping files for 1x1_mexicocityMEX START added on Thu Jul 19 13:06:18 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_AVHRR_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.25x0.25_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.5x0.5_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_10x10min_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODIS-wCsp_to_1x1_mexicocityMEX_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_USGS_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_LandScan2004_to_1x1_mexicocityMEX_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_IGBP-GSDP_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_ISRIC-WISE_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_mexicocityMEX" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_ORNL-Soil_to_1x1_mexicocityMEX_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_5x5min_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_mexicocityMEX" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_GLOBE-Gardner_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_mexicocityMEX" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_mexicocityMEX_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_0.9x1.25_GRDC_to_1x1_mexicocityMEX_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_360x720_cruncep_to_1x1_mexicocityMEX_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_mexicocityMEX"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_mexicocityMEX_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_mexicocityMEX END --> 
-
-<!-- mapping files for 1x1_numaIA START added on Thu Jul 19 13:06:18 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_AVHRR_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_MODIS_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.25x0.25_MODIS_to_1x1_numaIA_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.5x0.5_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_10x10min_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODIS_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODIS-wCsp_to_1x1_numaIA_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_USGS_to_1x1_numaIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_LandScan2004_to_1x1_numaIA_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_IGBP-GSDP_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_ISRIC-WISE_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_numaIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_ORNL-Soil_to_1x1_numaIA_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_5x5min_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_numaIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_GLOBE-Gardner_to_1x1_numaIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_numaIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_numaIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_0.9x1.25_GRDC_to_1x1_numaIA_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_360x720_cruncep_to_1x1_numaIA_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_numaIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_numaIA/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_numaIA_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_numaIA END --> 
-
-<!-- mapping files for 1x1_smallvilleIA START added on Thu Jul 19 13:06:19 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_AVHRR_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.25x0.25_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.5x0.5_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_10x10min_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODIS-wCsp_to_1x1_smallvilleIA_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_USGS_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_LandScan2004_to_1x1_smallvilleIA_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_IGBP-GSDP_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_ISRIC-WISE_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_smallvilleIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_ORNL-Soil_to_1x1_smallvilleIA_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_5x5min_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_smallvilleIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_GLOBE-Gardner_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_smallvilleIA" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_smallvilleIA_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_0.9x1.25_GRDC_to_1x1_smallvilleIA_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_360x720_cruncep_to_1x1_smallvilleIA_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_smallvilleIA"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_smallvilleIA_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_smallvilleIA END --> 
-
-<!-- mapping files for 1x1_urbanc_alpha START added on Thu Jul 19 13:06:19 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_AVHRR_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.25x0.25_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.5x0.5_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_10x10min_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODIS-wCsp_to_1x1_urbanc_alpha_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_USGS_to_1x1_urbanc_alpha_nomask_aave_da_c120928.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_LandScan2004_to_1x1_urbanc_alpha_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_IGBP-GSDP_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_ISRIC-WISE_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_urbanc_alpha" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_ORNL-Soil_to_1x1_urbanc_alpha_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_5x5min_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_urbanc_alpha" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_GLOBE-Gardner_to_1x1_urbanc_alpha_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_urbanc_alpha" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_urbanc_alpha_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_0.9x1.25_GRDC_to_1x1_urbanc_alpha_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_360x720_cruncep_to_1x1_urbanc_alpha_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_urbanc_alpha"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_urbanc_alpha_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_urbanc_alpha END --> 
-
-<!-- mapping files for 1x1_vancouverCAN START added on Thu Jul 19 13:06:19 2012--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_AVHRR_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.25x0.25_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="nomask"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.5x0.5_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_10x10min_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODIS-wCsp_to_1x1_vancouverCAN_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"   to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_USGS_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004" to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_LandScan2004_to_1x1_vancouverCAN_nomask_aave_da_c121114.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_IGBP-GSDP_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_ISRIC-WISE_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1x1_vancouverCAN" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_ORNL-Soil_to_1x1_vancouverCAN_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_5x5min_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1x1_vancouverCAN" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_GLOBE-Gardner_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1x1_vancouverCAN" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_GLOBE-Gardner-mergeGIS_to_1x1_vancouverCAN_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_0.9x1.25_GRDC_to_1x1_vancouverCAN_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_360x720_cruncep_to_1x1_vancouverCAN_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1x1_vancouverCAN"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1x1_vancouverCAN_nomask_aave_da_c130403.nc</map>
-
-<!-- mapping files for 1x1_vancouverCAN END --> 
-
-<!-- mapping files for 0.47x0.63 start --> 
-
-<map frm_hgrid="0.25x0.25"    frm_lmask="MODIS"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_0.25x0.25_MODIS_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_0.5x0.5_AVHRR_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_0.5x0.5_MODIS_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_0.9x1.25_GRDC_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="IGBPmergeICESatGIS"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_10x10min_IGBPmergeICESatGIS_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_10x10min_nomask_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_360x720cru_cruncep_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="GLOBE-Gardner-mergeGIS"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="GLOBE-Gardner"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_GLOBE-Gardner_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_LandScan2004_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_MODIS-wCsp_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_USGS_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_5x5min_IGBP-GSDP_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_5x5min_ISRIC-WISE_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_5x5min_nomask_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil"  to_hgrid="0.47x0.63"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.47x0.63/map_5x5min_ORNL-Soil_to_0.47x0.63_nomask_aave_da_c170914.nc</map>
-
-<!-- mapping files for 0.47x0.63 END --> 
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="0.9x1.25" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_landuse_to_0.9x1.25_aave_da_110307.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="0.9x1.25"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_0.25x0.25_MODIS_to_0.9x1.25_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="0.9x1.25" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_lanwat_to_0.9x1.25_aave_da_110307.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_10minx10min_topo_to_0.9x1.25_aave_da_110630.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_5minx5min_soitex_to_0.9x1.25_aave_da_110722.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_5minx5min_irrig_to_0.9x1.25_aave_da_110529.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_5x5min_ISRIC-WISE_to_0.9x1.25_nomask_aave_da_c120525.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_5x5min_ORNL-Soil_to_0.9x1.25_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="0.9x1.25"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODIS_to_0.9x1.25_nomask_aave_da_c120523.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="0.9x1.25"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODIS-wCsp_to_0.9x1.25_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="0.9x1.25"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_USGS_to_0.9x1.25_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_LandScan2004_to_0.9x1.25_nomask_aave_da_c120522.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_GLOBE-Gardner_to_0.9x1.25_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="0.9x1.25" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.9x1.25_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="0.9x1.25"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_0.9x1.25_GRDC_to_0.9x1.25_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="0.9x1.25"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_360x720_cruncep_to_0.9x1.25_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="0.9x1.25"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.9x1.25/map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.9x1.25_nomask_aave_da_c130405.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="1.9x2.5" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_landuse_to_1.9x2.5_aave_da_110307.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="1.9x2.5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_0.25x0.25_MODIS_to_1.9x2.5_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="1.9x2.5" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_lanwat_to_1.9x2.5_aave_da_110307.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_10minx10min_topo_to_1.9x2.5_aave_da_110307.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_5minx5min_soitex_to_1.9x2.5_aave_da_110307.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_nomask_to_1.9x2.5_nomask_aave_da_c120606.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_ISRIC-WISE_to_1.9x2.5_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_ORNL-Soil_to_1.9x2.5_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="1.9x2.5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODIS_to_1.9x2.5_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="1.9x2.5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODIS-wCsp_to_1.9x2.5_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="1.9x2.5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_USGS_to_1.9x2.5_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_LandScan2004_to_1.9x2.5_nomask_aave_da_c120522.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_GLOBE-Gardner_to_1.9x2.5_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="1.9x2.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_GLOBE-Gardner-mergeGIS_to_1.9x2.5_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="1.9x2.5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_0.9x1.25_GRDC_to_1.9x2.5_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="1.9x2.5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_360x720_cruncep_to_1.9x2.5_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="1.9x2.5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/1.9x2.5/map_1km-merge-10min_HYDRO1K-merge-nomask_to_1.9x2.5_nomask_aave_da_c130405.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_0.5x0.5_landuse_to_10x15_aave_da_110307.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_0.25x0.25_MODIS_to_10x15_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_0.5x0.5_lanwat_to_10x15_aave_da_110307.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="10x15"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_10minx10min_topo_to_10x15_aave_da_110307.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="10x15"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_5minx5min_soitex_to_10x15_aave_da_110307.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="10x15"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_5x5min_nomask_to_10x15_nomask_aave_da_c120327.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="10x15" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_5x5min_ISRIC-WISE_to_10x15_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="10x15" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_5x5min_ORNL-Soil_to_10x15_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="10x15"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODIS_to_10x15_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="10x15"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODIS-wCsp_to_10x15_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="10x15"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_USGS_to_10x15_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="10x15" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_LandScan2004_to_10x15_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="10x15" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_GLOBE-Gardner_to_10x15_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="10x15" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/10x15/map_3x3min_GLOBE-Gardner-mergeGIS_to_10x15_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_0.9x1.25_GRDC_to_10x15_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_360x720_cruncep_to_10x15_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="10x15"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/10x15/map_1km-merge-10min_HYDRO1K-merge-nomask_to_10x15_nomask_aave_da_c130411.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"      to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_0.5x0.5_MODIS_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_0.25x0.25_MODIS_to_360x720cru_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"      to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_0.5x0.5_AVHRR_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask"     to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_10x10min_nomask_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP"  to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_5x5min_IGBP-GSDP_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask"     to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_5x5min_nomask_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_5x5min_ISRIC-WISE_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="360x720cru" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_5x5min_ORNL-Soil_to_360x720cru_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"      to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODIS_to_360x720_nomask_aave_da_c120830.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp" to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODIS-wCsp_to_360x720cru_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"       to_hgrid="360x720cru"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_USGS_to_360x720_nomask_aave_da_c121128.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="360x720cru" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_LandScan2004_to_360x720_nomask_aave_da_c121017.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="360x720cru" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_GLOBE-Gardner_to_360x720_nomask_aave_da_c121128.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="360x720cru" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/360x720/map_3x3min_GLOBE-Gardner-mergeGIS_to_360x720_nomask_aave_da_c121128.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_0.9x1.25_GRDC_to_360x720_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_360x720_cruncep_to_360x720_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="360x720cru"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/360x720/map_1km-merge-10min_HYDRO1K-merge-nomask_to_360x720_nomask_aave_da_c130403.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_0.5x0.5_MODIS_to_512x1024_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_0.25x0.25_MODIS_to_512x1024_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_0.5x0.5_AVHRR_to_512x1024_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="512x1024"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_10x10min_nomask_to_512x1024_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="512x1024"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_5x5min_IGBP-GSDP_to_512x1024_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="512x1024"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_5x5min_nomask_to_512x1024_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="512x1024" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_5x5min_ISRIC-WISE_to_512x1024_nomask_aave_da_c120906.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="512x1024" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_5x5min_ORNL-Soil_to_512x1024_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="512x1024"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODIS_to_512x1024_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp" to_hgrid="512x1024"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODIS-wCsp_to_512x1024_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="512x1024"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_USGS_to_512x1024_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="512x1024" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_LandScan2004_to_512x1024_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="512x1024" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_GLOBE-Gardner_to_512x1024_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="512x1024" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/512x1024/map_3x3min_GLOBE-Gardner-mergeGIS_to_512x1024_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_0.9x1.25_GRDC_to_512x1024_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_360x720_cruncep_to_512x1024_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="512x1024"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/512x1024/map_1km-merge-10min_HYDRO1K-merge-nomask_to_512x1024_nomask_aave_da_c130403.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_0.5x0.5_MODIS_to_128x256_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_0.25x0.25_MODIS_to_128x256_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_0.5x0.5_AVHRR_to_128x256_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="128x256"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_10x10min_nomask_to_128x256_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="128x256"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_5x5min_IGBP-GSDP_to_128x256_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="128x256"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_5x5min_nomask_to_128x256_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="128x256" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_5x5min_ISRIC-WISE_to_128x256_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="128x256" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_5x5min_ORNL-Soil_to_128x256_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="128x256"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODIS_to_128x256_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="128x256"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODIS-wCsp_to_128x256_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="128x256"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_USGS_to_128x256_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="128x256" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_LandScan2004_to_128x256_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="128x256" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_GLOBE-Gardner_to_128x256_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="128x256" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/128x256/map_3x3min_GLOBE-Gardner-mergeGIS_to_128x256_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_0.9x1.25_GRDC_to_128x256_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_360x720_cruncep_to_128x256_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="128x256"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/128x256/map_1km-merge-10min_HYDRO1K-merge-nomask_to_128x256_nomask_aave_da_c130403.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_0.5x0.5_MODIS_to_64x128_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_0.25x0.25_MODIS_to_64x128_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_0.5x0.5_AVHRR_to_64x128_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="64x128"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_10x10min_nomask_to_64x128_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="64x128"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_5x5min_IGBP-GSDP_to_64x128_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="64x128"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_5x5min_nomask_to_64x128_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="64x128" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_5x5min_ISRIC-WISE_to_64x128_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="64x128" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_5x5min_ORNL-Soil_to_64x128_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="64x128"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODIS_to_64x128_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="64x128"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODIS-wCsp_to_64x128_nomask_aave_da_c160428.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="64x128"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_USGS_to_64x128_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="64x128" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_LandScan2004_to_64x128_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="64x128" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_GLOBE-Gardner_to_64x128_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="64x128" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/64x128/map_3x3min_GLOBE-Gardner-mergeGIS_to_64x128_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_0.9x1.25_GRDC_to_64x128_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_360x720_cruncep_to_64x128_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="64x128"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/64x128/map_1km-merge-10min_HYDRO1K-merge-nomask_to_64x128_nomask_aave_da_c130403.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_0.5x0.5_MODIS_to_48x96_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_0.25x0.25_MODIS_to_48x96_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_0.5x0.5_AVHRR_to_48x96_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="48x96"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_10x10min_nomask_to_48x96_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="48x96"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_5x5min_IGBP-GSDP_to_48x96_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="48x96"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_5x5min_nomask_to_48x96_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="48x96" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_5x5min_ISRIC-WISE_to_48x96_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="48x96" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_5x5min_ORNL-Soil_to_48x96_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="48x96"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODIS_to_48x96_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="48x96"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODIS-wCsp_to_48x96_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="48x96"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_USGS_to_48x96_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="48x96" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_LandScan2004_to_48x96_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="48x96" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_GLOBE-Gardner_to_48x96_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="48x96" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/48x96/map_3x3min_GLOBE-Gardner-mergeGIS_to_48x96_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_0.9x1.25_GRDC_to_48x96_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_360x720_cruncep_to_48x96_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="48x96"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/48x96/map_1km-merge-10min_HYDRO1K-merge-nomask_to_48x96_nomask_aave_da_c130405.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_MODIS_to_32x64_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_0.25x0.25_MODIS_to_32x64_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_AVHRR_to_32x64_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="32x64"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_10x10min_nomask_to_32x64_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="32x64"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_5x5min_IGBP-GSDP_to_32x64_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="32x64"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_5x5min_nomask_to_32x64_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="32x64" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_5x5min_ISRIC-WISE_to_32x64_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="32x64" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_5x5min_ORNL-Soil_to_32x64_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="32x64"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_MODIS_to_32x64_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="32x64"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_MODIS-wCsp_to_32x64_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="32x64"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_USGS_to_32x64_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="32x64" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_LandScan2004_to_32x64_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="32x64" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner_to_32x64_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="32x64" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner-mergeGIS_to_32x64_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_0.9x1.25_GRDC_to_32x64_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_360x720_cruncep_to_32x64_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="32x64"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/32x64/map_1km-merge-10min_HYDRO1K-merge-nomask_to_32x64_nomask_aave_da_c130405.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_MODIS_to_8x16_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_0.25x0.25_MODIS_to_8x16_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_AVHRR_to_8x16_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="8x16"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_10x10min_nomask_to_8x16_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="8x16"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_5x5min_IGBP-GSDP_to_8x16_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="8x16"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_5x5min_nomask_to_8x16_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="8x16" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_5x5min_ISRIC-WISE_to_8x16_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="8x16" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_5x5min_ORNL-Soil_to_8x16_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="8x16"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_MODIS_to_8x16_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="8x16"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_MODIS-wCsp_to_8x16_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="8x16"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_USGS_to_8x16_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="8x16" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_LandScan2004_to_8x16_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="8x16" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner_to_8x16_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="8x16" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner-mergeGIS_to_8x16_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_0.9x1.25_GRDC_to_8x16_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_360x720_cruncep_to_8x16_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="8x16"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/8x16/map_1km-merge-10min_HYDRO1K-merge-nomask_to_8x16_nomask_aave_da_c130411.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="4x5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_MODIS_to_4x5_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="4x5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/4x5/map_0.25x0.25_MODIS_to_4x5_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="4x5"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_AVHRR_to_4x5_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="4x5"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_10x10min_nomask_to_4x5_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="4x5"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_5x5min_IGBP-GSDP_to_4x5_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="4x5"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_5x5min_nomask_to_4x5_nomask_aave_da_c110822.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="4x5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_5x5min_ISRIC-WISE_to_4x5_nomask_aave_da_c120906.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="4x5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_5x5min_ORNL-Soil_to_4x5_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="4x5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODIS_to_4x5_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="4x5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODIS-wCsp_to_4x5_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="4x5"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_3x3min_USGS_to_4x5_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="4x5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/4x5/map_3x3min_LandScan2004_to_4x5_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="4x5" to_lmask="nomask"
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->lnd/clm2/mappingdata/maps/ne4np4/map_5x5min_ISRIC-WISE_to_ne4np4_nomask_aave_da_c120906.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne4np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_5x5min_ORNL-Soil_to_ne4np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne4np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_MODIS_to_ne4np4_nomask_aave_da_c120906.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne4np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_MODIS-wCsp_to_ne4np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne4np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_USGS_to_ne4np4_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne4np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_LandScan2004_to_ne4np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne4np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_GLOBE-Gardner_to_ne4np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne4np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne4np4_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne4np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_3x3min_LandScan2004_to_ne4np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne4np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne4np4/map_0.9x1.25_GRDC_to_ne4np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne4np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne4np4/map_360x720_cruncep_to_ne4np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne4np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne4np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne4np4_nomask_aave_da_c130411.nc</map>
-<map frm_hgrid="ne4np4"    frm_lmask="nomask" to_hgrid="0.5x0.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne4np4/map_ne4np4_nomask_to_0.5x0.5_nomask_aave_da_c110923.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_0.5x0.5_MODIS_to_ne16np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_0.25x0.25_MODIS_to_ne16np4_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_0.5x0.5_AVHRR_to_ne16np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="ne16np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_10x10min_nomask_to_ne16np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="ne16np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_5x5min_IGBP-GSDP_to_ne16np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="ne16np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_5x5min_nomask_to_ne16np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="ne16np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_5x5min_ISRIC-WISE_to_ne16np4_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne16np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_5x5min_ORNL-Soil_to_ne16np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne16np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_MODIS_to_ne16np4_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne16np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_MODIS-wCsp_to_ne16np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne16np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_USGS_to_ne16np4_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne16np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_LandScan2004_to_ne16np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne16np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_GLOBE-Gardner_to_ne16np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne16np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne16np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_0.9x1.25_GRDC_to_ne16np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_360x720_cruncep_to_ne16np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne16np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne16np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne16np4_nomask_aave_da_c130408.nc</map>
-<map frm_hgrid="ne16np4"    frm_lmask="nomask" to_hgrid="0.5x0.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne16np4/map_ne16np4_nomask_to_0.5x0.5_nomask_aave_da_c110922.nc</map>
-
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="ne30np4" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_0.5x0.5_landuse_to_ne30np4_aave_da_110320.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="ne30np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_0.25x0.25_MODIS_to_ne30np4_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="ne30np4" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_0.5x0.5_lanwat_to_ne30np4_aave_da_110320.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_10minx10min_topo_to_ne30np4_aave_da_110320.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_5minx5min_soitex_to_ne30np4_aave_da_110320.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_5minx5min_irrig_to_ne30np4_aave_da_110720.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_5x5min_ISRIC-WISE_to_ne30np4_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_5x5min_ORNL-Soil_to_ne30np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne30np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_MODIS_to_ne30np4_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne30np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_MODIS-wCsp_to_ne30np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne30np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_USGS_to_ne30np4_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_LandScan2004_to_ne30np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_GLOBE-Gardner_to_ne30np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne30np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne30np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne30np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_0.9x1.25_GRDC_to_ne30np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne30np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_360x720_cruncep_to_ne30np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne30np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne30np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne30np4_nomask_aave_da_c130405.nc</map>
-
-<map frm_hgrid="ne30np4"  frm_lmask="nomask" to_hgrid="0.5x0.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne30np4/map_ne30np4_to_0.5x0.5rtm_aave_da_110320.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_0.5x0.5_MODIS_to_ne60np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_0.25x0.25_MODIS_to_ne60np4_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_0.5x0.5_AVHRR_to_ne60np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="ne60np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_10x10min_nomask_to_ne60np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="ne60np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_5x5min_IGBP-GSDP_to_ne60np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="ne60np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_5x5min_nomask_to_ne60np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="ne60np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_5x5min_ISRIC-WISE_to_ne60np4_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne60np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_5x5min_ORNL-Soil_to_ne60np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne60np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_MODIS_to_ne60np4_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne60np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_MODIS-wCsp_to_ne60np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne60np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_USGS_to_ne60np4_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne60np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_LandScan2004_to_ne60np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne60np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_GLOBE-Gardner_to_ne60np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne60np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne60np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_0.9x1.25_GRDC_to_ne60np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_360x720_cruncep_to_ne60np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne60np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne60np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne60np4_nomask_aave_da_c130405.nc</map>
-<map frm_hgrid="ne60np4"    frm_lmask="nomask" to_hgrid="0.5x0.5" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne60np4/map_ne60np4_nomask_to_0.5x0.5_nomask_aave_da_c110922.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="ne120np4" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_0.5x0.5_landuse_to_ne120np4_aave_da_110320.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="ne120np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_0.25x0.25_MODIS_to_ne120np4_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="ne120np4" to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_0.5x0.5_lanwat_to_ne120np4_aave_da_110320.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_10minx10min_topo_to_ne120np4_aave_da_110320.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP"  to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_5minx5min_soitex_to_ne120np4_aave_da_110320.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_5x5min_ISRIC-WISE_to_ne120np4_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_5x5min_ORNL-Soil_to_ne120np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_5minx5min_irrig_to_ne120np4_aave_da_110817.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_MODIS_to_ne120np4_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_MODIS-wCsp_to_ne120np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_USGS_to_ne120np4_nomask_aave_da_c120913.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_LandScan2004_to_ne120np4_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_GLOBE-Gardner_to_ne120np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne120np4_nomask_aave_da_c120924.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne120np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne120np4/map_3x3min_USGS_to_ne120np4_nomask_aave_da_c120913.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne120np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_0.9x1.25_GRDC_to_ne120np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne120np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_360x720_cruncep_to_ne120np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne120np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne120np4_nomask_aave_da_c130405.nc</map>
-
-<!-- mapping files for ne120np4 START added on Wed Sep 19 09:10:57 2012-->
-<!-- Created by lnd/clm/bld/namelist_files/createMapEntry.pl--> 
-
-<map frm_hgrid="0.1x0.1"    frm_lmask="nomask"  to_hgrid="ne120np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne120np4/map_0.1x0.1_nomask_to_ne120np4_nomask_aave_da_c120706.nc</map>
-
-<!-- mapping files for ne120np4 END --> 
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_MODIS_to_5x5_amazon_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_0.25x0.25_MODIS_to_5x5_amazon_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_0.5x0.5_AVHRR_to_5x5_amazon_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="5x5_amazon"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_10x10min_nomask_to_5x5_amazon_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="5x5_amazon"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_IGBP-GSDP_to_5x5_amazon_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="5x5_amazon"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_nomask_to_5x5_amazon_nomask_aave_da_c110920.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="5x5_amazon" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_ISRIC-WISE_to_5x5_amazon_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="5x5_amazon" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_5x5min_ORNL-Soil_to_5x5_amazon_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="5x5_amazon"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_MODIS_to_5x5_amazon_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="5x5_amazon"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_MODIS-wCsp_to_5x5_amazon_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="5x5_amazon"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_USGS_to_5x5_amazon_nomask_aave_da_c120927.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="5x5_amazon" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_LandScan2004_to_5x5_amazon_nomask_aave_da_c120518.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="5x5_amazon" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_GLOBE-Gardner_to_5x5_amazon_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="5x5_amazon" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/5x5_amazon/map_3x3min_GLOBE-Gardner-mergeGIS_to_5x5_amazon_nomask_aave_da_c120923.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_0.9x1.25_GRDC_to_5x5_amazon_nomask_aave_da_c130309.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_360x720_cruncep_to_5x5_amazon_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="5x5_amazon"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/5x5_amazon/map_1km-merge-10min_HYDRO1K-merge-nomask_to_5x5_amazon_nomask_aave_da_c130403.nc</map>
-
-<map frm_hgrid="0.5x0.5"  frm_lmask="MODIS"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_0.5x0.5_MODIS_to_ne240np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_0.25x0.25_MODIS_to_ne240np4_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.5x0.5"  frm_lmask="AVHRR"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_0.5x0.5_AVHRR_to_ne240np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="10x10min" frm_lmask="nomask" to_hgrid="ne240np4"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_10x10min_nomask_to_ne240np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="IGBP-GSDP" to_hgrid="ne240np4"  to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_IGBP-GSDP_to_ne240np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="nomask" to_hgrid="ne240np4"     to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_nomask_to_ne240np4_nomask_aave_da_c110922.nc</map>
-<map frm_hgrid="5x5min"   frm_lmask="ISRIC-WISE" to_hgrid="ne240np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_ISRIC-WISE_to_ne240np4_nomask_aave_da_c111115.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="ne240np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_5x5min_ORNL-Soil_to_ne240np4_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS"  to_hgrid="ne240np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_MODIS_to_ne240np4_nomask_aave_da_c111111.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="MODIS-wCsp"  to_hgrid="ne240np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_MODIS-wCsp_to_ne240np4_nomask_aave_da_c160425.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="USGS"   to_hgrid="ne240np4"    to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_USGS_to_ne240np4_nomask_aave_da_c120926.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="LandScan2004" to_hgrid="ne240np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_LandScan2004_to_ne240np4_nomask_aave_da_c120521.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner" to_hgrid="ne240np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_GLOBE-Gardner_to_ne240np4_nomask_aave_da_c120925.nc</map>
-<map frm_hgrid="3x3min"   frm_lmask="GLOBE-Gardner-mergeGIS" to_hgrid="ne240np4" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_3x3min_GLOBE-Gardner-mergeGIS_to_ne240np4_nomask_aave_da_c120925.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_0.9x1.25_GRDC_to_ne240np4_nomask_aave_da_c130308.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_360x720_cruncep_to_ne240np4_nomask_aave_da_c130326.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="ne240np4"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/ne240np4/map_1km-merge-10min_HYDRO1K-merge-nomask_to_ne240np4_nomask_aave_da_c130405.nc</map>
-<map frm_hgrid="ne240np4"    frm_lmask="nomask" to_hgrid="0.5x0.5"   to_lmask="nomask"
->lnd/clm2/mappingdata/maps/ne240np4/map_ne240np4_nomask_to_0.5x0.5_nomask_aave_da_c110922.nc</map>
-
-<!-- mapping files for 0.125x0.125 START added on Fri Aug  1 15:44:32 2014-->
-<!-- Created by lnd/clm/bld/namelist_files/createMapEntry.pl--> 
-
-<map frm_hgrid="0.5x0.5"    frm_lmask="AVHRR"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_0.5x0.5_AVHRR_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="0.5x0.5"    frm_lmask="MODIS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_0.5x0.5_MODIS_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="0.25x0.25"  frm_lmask="MODIS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_0.25x0.25_MODIS_to_0.125x0.125_nomask_aave_da_c170321.nc</map>
-<map frm_hgrid="0.9x1.25"    frm_lmask="GRDC"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_0.9x1.25_GRDC_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="IGBPmergeICESatGIS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_10x10min_IGBPmergeICESatGIS_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="10x10min"    frm_lmask="nomask"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_10x10min_nomask_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="1km-merge-10min"    frm_lmask="HYDRO1K-merge-nomask"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="360x720cru"    frm_lmask="cruncep"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_360x720cru_cruncep_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="GLOBE-Gardner-mergeGIS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_GLOBE-Gardner-mergeGIS_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="GLOBE-Gardner"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_GLOBE-Gardner_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="LandScan2004"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_LandScan2004_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_MODIS_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="MODIS-wCsp"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_MODIS-wCsp_to_0.125x0.125_nomask_aave_da_c160427.nc</map>
-<map frm_hgrid="3x3min"    frm_lmask="USGS"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_3x3min_USGS_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="IGBP-GSDP"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_5x5min_IGBP-GSDP_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ISRIC-WISE"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_5x5min_ISRIC-WISE_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="ORNL-Soil" to_hgrid="0.125x0.125" to_lmask="nomask"
->lnd/clm2/mappingdata/maps/0.125x0.125/map_5x5min_ORNL-Soil_to_0.125x0.125_nomask_aave_da_c170706.nc</map>
-<map frm_hgrid="5x5min"    frm_lmask="nomask"  to_hgrid="0.125x0.125"   to_lmask="nomask" 
->lnd/clm2/mappingdata/maps/0.125x0.125/map_5x5min_nomask_to_0.125x0.125_nomask_aave_da_c140702.nc</map>
-
-<!-- mapping files for 0.125x0.125 END -->
-
 <!-- =========================================  -->
 <!-- Defaults for modelio namelist              -->
 <!-- =========================================  -->
@@ -2090,36 +498,4 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <diri>.</diri>
 <diro>.</diro>
 
-<!-- =========================================  -->
-<!-- Defaults for different BGC modes           -->
-<!-- =========================================  -->
-
-<use_vertsoilc       bgc_mode="sp"  >.false.</use_vertsoilc>
-<use_century_decomp  bgc_mode="sp"  >.false.</use_century_decomp>
-<use_lch4            bgc_mode="sp"  >.false.</use_lch4>
-<use_nitrif_denitrif bgc_mode="sp"  >.false.</use_nitrif_denitrif>
-
-<use_vertsoilc       bgc_mode="cn"  >.false.</use_vertsoilc>
-<use_century_decomp  bgc_mode="cn"  >.false.</use_century_decomp>
-<use_lch4            bgc_mode="cn"  >.false.</use_lch4>
-<use_nitrif_denitrif bgc_mode="cn"  >.false.</use_nitrif_denitrif>
-
-<use_vertsoilc       bgc_mode="bgc" >.true.</use_vertsoilc>
-<use_century_decomp  bgc_mode="bgc" >.true.</use_century_decomp>
-<use_lch4            bgc_mode="bgc" >.true.</use_lch4>
-<use_nitrif_denitrif bgc_mode="bgc" >.true.</use_nitrif_denitrif>
-
-<use_vertsoilc       bgc_mode="fates"  >.true.</use_vertsoilc>
-<use_century_decomp  bgc_mode="fates"  >.true.</use_century_decomp>
-<use_lch4            bgc_mode="fates"  >.false.</use_lch4>
-<use_nitrif_denitrif bgc_mode="fates"  >.false.</use_nitrif_denitrif>
-
-<!-- ===== FATES DEFAULTS =========== -->
-<use_fates_spitfire            use_fates=".true.">.false.</use_fates_spitfire>
-<use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
-<use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
-<use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
-<use_fates_logging             use_fates=".true.">.false.</use_fates_logging>
-<use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
-
 </namelist_defaults>
diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml
index 9d8e3da454..a3e7e368ef 100644
--- a/bld/namelist_files/namelist_defaults_overall.xml
+++ b/bld/namelist_files/namelist_defaults_overall.xml
@@ -15,11 +15,6 @@ determine default values for namelists.
 <!-- Default CLM start-type -->
 <clm_start_type phys="clm4_5"                   >startup</clm_start_type>
 <clm_start_type phys="clm5_0"                   >startup</clm_start_type>
-<clm_start_type phys="clm5_0" use_cndv=".true." >arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5" use_cndv=".true." >arb_ic</clm_start_type>
-<clm_start_type phys="clm5_0" use_fates=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5" use_fates=".true.">arb_ic</clm_start_type>
-<clm_start_type bgc_spinup="on"                 >cold</clm_start_type> <!-- CLM 4.5 -->
 
 <!-- Default location of {csmdata} -->
 <csmdata>/fs/cgd/csm/inputdata</csmdata>
@@ -28,13 +23,6 @@ determine default values for namelists.
 <res sitespf_pt="none"               >1.9x2.5</res>
 <res sitespf_pt="1x1_brazil"         >1x1_brazil</res>
 <res sitespf_pt="5x5_amazon"         >5x5_amazon</res>
-<res sitespf_pt="1x1_camdenNJ"       >1x1_camdenNJ</res>
-<res sitespf_pt="1x1_vancouverCAN"   >1x1_vancouverCAN</res>
-<res sitespf_pt="1x1_mexicocityMEX"  >1x1_mexicocityMEX</res>
-<res sitespf_pt="1x1_asphaltjungleNJ">1x1_asphaltjungleNJ</res>
-<res sitespf_pt="1x1_urbanc_alpha"   >1x1_urbanc_alpha</res>
-<res sitespf_pt="1x1_numaIA"         >1x1_numaIA</res>
-<res sitespf_pt="1x1_smallvilleIA"   >1x1_smallvilleIA</res>
 
 <!-- Default simulation year -->
 <sim_year>2000</sim_year>
@@ -53,9 +41,6 @@ determine default values for namelists.
 <!-- Default representative concentration pathway for future scenarios -->
 <rcp>-999.9</rcp>
 
-<!-- Default irrigation -->
-<irrig>.false.</irrig>
-
 <!-- Default land/ocean mask type -->
 <mask hgrid="0.23x0.31"           >gx1v6</mask>
 <mask hgrid="0.47x0.63"           >gx1v6</mask>
@@ -79,24 +64,7 @@ determine default values for namelists.
 <mask hgrid="ne30"                >gx1v6</mask>
 
 <mask hgrid="5x5_amazon"          >navy</mask>
-<mask hgrid="1x1_camdenNJ"        >navy</mask>
-<mask hgrid="1x1_vancouverCAN"    >navy</mask>
-<mask hgrid="1x1_mexicocityMEX"   >navy</mask>
-<mask hgrid="1x1_asphaltjungleNJ" >navy</mask>
 <mask hgrid="1x1_brazil"          >navy</mask>
-<mask hgrid="1x1_urbanc_alpha"    >test</mask>
-<mask hgrid="1x1_numaIA"          >navy</mask>
-<mask hgrid="1x1_smallvilleIA"    >test</mask>
 <mask                             >gx1v6</mask>
 
-<!-- Default glacier model options -->
-
-<glc_dyntopo         >.false.</glc_dyntopo>
-<glc_nec glc_nec="0" >0</glc_nec>
-<glc_nec glc_nec="1" >1</glc_nec>
-<glc_nec glc_nec="3" >3</glc_nec>
-<glc_nec glc_nec="5" >5</glc_nec>
-<glc_nec glc_nec="10">10</glc_nec>
-<glc_nec glc_nec="36">36</glc_nec>
-
 </namelist_defaults>
diff --git a/bld/namelist_files/namelist_definition.xsl b/bld/namelist_files/namelist_definition.xsl
index 545d810e52..a83d4d7dc1 100644
--- a/bld/namelist_files/namelist_definition.xsl
+++ b/bld/namelist_files/namelist_definition.xsl
@@ -54,84 +54,6 @@
       <xsl:apply-templates select="entry[@category='clm_physics']"/>
     </table>
 
-    <table border="1" cellpadding="10">
-    <caption>CLM Namelist Lake Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='clm_lake']"/>
-    </table>
-
-    <table border="1" cellpadding="10">
-    <caption>CLM Biogeochemistry (BGC) Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='bgc']"/>
-    </table>
-
-    <table border="1" cellpadding="10">
-    <caption>CLM Biogeochemistry Namelist Nitrogen Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='clm_nitrogen']"/>
-    </table>
-
-    <table border="1" cellpadding="10">
-    <caption>CLM Namelist Methane Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='clm_methane']"/>
-    </table>
-
-    <table border="1" cellpadding="10">
-    <caption>CLM Namelist Vertical CN Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='clm_vertcn']"/>
-    </table>
-
-    <table border="1" cellpadding="10">
-    <caption>CLM Namelist Carbon Isotope Model Options</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='clm_isotope']"/>
-    </table>
-
     <table border="1" cellpadding="10">
     <caption>CLM Namelist Datasets</caption>
       <tr>
@@ -314,21 +236,6 @@
 
 <hr/>
 
-<h2>Namelist items for Driver MEGAN Physics</h2>
-    <table border="1" cellpadding="10">
-    <caption>Driver Physics</caption>
-      <tr>
-      <th rowspan="2">Name</th>
-      <th rowspan="2">Type</th>
-      <th>Description</th>
-      </tr>
-      <tr>
-      <th colspan="1">Valid values</th>
-      </tr>
-      <xsl:apply-templates select="entry[@category='drv_physics']"/>
-    </table>
-
-
 <h2>Namelist items for Driver Dry Deposition</h2>
     <table border="1" cellpadding="10">
     <caption>Driver Dry-Deposition Namelist Options</caption>
diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
index 0ded48143e..6ebee1a964 100644
--- a/bld/namelist_files/namelist_definition_clm4_5.xml
+++ b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -77,253 +77,6 @@ Type of CO2 feedback.
     diagnostic = use the diagnostic value sent from the atmosphere
 </entry>
 
-
-<entry id="suplnitro" type="char*15" category="clm_physics"
-       group="clm_inparm" valid_values="NONE,ALL" >
-Supplemental Nitrogen mode and for what type of vegetation it's turned on for. 
-In this mode Nitrogen is unlimited rather than prognosed and in general vegetation is 
-over-productive.
-    NONE           = No vegetation types get supplemental Nitrogen
-    ALL            = Supplemental Nitrogen is active for all vegetation types
-</entry>
-
-<entry id="create_crop_landunit" type="logical" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-If TRUE, separate the vegetated landunit into a crop landunit and a natural vegetation landunit
-</entry>
-
-<entry id="all_active" type="logical" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-If TRUE, make ALL pfts, columns and landunits active, even those with 0 weight.
-This means that computations will be run even over these 0-weight points.
-
-THIS IS ONLY FOR TESTING PURPOSES - IT HAS NOT BEEN CHECKED FOR SCIENTIFIC VALIDITY.
-</entry>
-
-<entry id="organic_frac_squared" type="logical" category="clm_physics"
-       group="clm_soilstate_inparm" valid_values="" >
-If TRUE, square the organic fraction when it's used (as was done in CLM4.5)
-Otherwise use the fraction straight up              (the default for CLM5.0)
-</entry>
-
-<entry id="soil_layerstruct" type="char*16" category="clm_physics"
-       group="clm_inparm" valid_values="10SL_3.5m,23SL_3.5m,49SL_10m,20SL_8.5m" >
-10SL_3.5m    = standard CLM4 and CLM4.5 version
-23SL_3.5m    = more vertical layers for permafrost simulations 
-49SL_10m     = 49 layer soil column, 10m of soil, 5 bedrock layers
-20SL_8.5m    = 20 layer soil column, 8m of soil, 5 bedrock layers
-</entry>
-
-<entry id="use_bedrock" type="logical" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-If TRUE, use variable soil depth.
-
-If present on surface dataset, use depth to bedrock information to
-specify spatially variable soil thickness. If not present, use bottom
-of soil column (nlevsoi).
-</entry>
-
-<entry id="rooting_profile_method_water" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="0,1,2" >
-Index of rooting profile for water
-
-Changes rooting profile from Zeng 2001 double exponential (0) to
-Jackson 1996 single exponential (1) to Koven uniform exponential (2).
-</entry>
-
-<entry id="rooting_profile_method_carbon" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="0,1,2" >
-Index of rooting profile for carbon
-
-Changes rooting profile from Zeng 2001 double exponential (0) to
-Jackson 1996 single exponential (1) to Koven uniform exponential (2).
-</entry>
-
-<entry id="rooting_profile_method_soilcarbon" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="0,1,2" >
-Index of rooting profile for soil carbon
-
-Changes rooting profile from Zeng 2001 double exponential (0) to
-Jackson 1996 single exponential (1) to Koven uniform exponential (2).
-</entry>
-
-<entry id="rooting_profile_varindex_water" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="1,2" >
-Variant index of rooting profile for water
-(Currently only used for Jackson 1996 method)
-</entry>
-
-<entry id="rooting_profile_varindex_carbon" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="1,2" >
-Variant index of rooting profile for carbon and soil carbon
-(Currently only used for Jackson 1996 method)
-</entry>
-
-<entry id="rooting_profile_method_carbon" type="integer" category="clm_physics"
-       group="rooting_profile_inparm" valid_values="0,1,2" >
-Index of rooting profile for carbon
-
-Changes rooting profile from Zeng 2001 double exponential (0) to
-Jackson 1996 single exponential (1) to Koven uniform exponential (2).
-</entry>
-
-<entry id="soil_resis_method" type="integer" category="clm_physics"
-       group="soil_resis_inparm" valid_values="0,1" >
-Index of evaporative resistance method.
-
-Changes soil evaporative resistance method from Sakaguchi and Zeng
-2009 Beta function (0) to Swenson and Lawrence 2014 dry surface layer
-formulation (1).
-</entry>
-
-<entry id="freelivfix_slope_wET" type="real" category="clm_physics"
-       group="mineral_nitrogen_dynamics" >
-Slope of free living Nitrogen fixation with annual ET
-</entry>
-
-<entry id="freelivfix_intercept" type="real" category="clm_physics"
-       group="mineral_nitrogen_dynamics" >
-Intercept of free living Nitrogen fixation with zero annual ET
-</entry>
-
-<entry id="interception_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Fraction of intercepted precipitation
-</entry>
-
-<entry id="use_clm5_fpi" type="logical" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-If TRUE use clm5 equation for fraction of intercepted precipitation
-</entry>
-
-<entry id="maximum_leaf_wetted_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Maximum fraction of leaf that may be wet prior to drip occuring
-</entry>
-
-<entry id="soilwater_movement_method" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="0,1" >
-Index of solution method of Richards equation.
-
-Change method for richards equation solution and boundary
-conditions.
-
-CLM 4.5 - soilwater_movement_method = 0 (Zeng and Decker, 2009, method). 
-CLM 5.0 - soilwater_movement_method = 1 (adaptive time stepping moisture form from Martyn Clark).
-
-1 (adaptive time stepping moisture form
-</entry>
-
-<entry id="upper_boundary_condition" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="1" >
-Index of upper boundary condition for Richards equation.
-</entry>
-
-<entry id="lower_boundary_condition" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="1,2,3,4" >
-Index of lower boundary condition for Richards equation.
-
-lower_boundary_condition = 1 : flux lower boundary condition                                     (use with soilwater_movement_method=adaptive time stepping)
-lower_boundary_condition = 2 : zero-flux lower boundary condition                                (use with soilwater_movement_method=adaptive time stepping)
-lower_boundary_condition = 3 : water table head-based lower boundary condition w/ aquifer layer. (use with soilwater_movement_method=adaptive time stepping)
-lower_boundary_condition = 4 : 11-layer solution w/ aquifer layer                                (only used with soilwater_movement_method=Zeng&Decker 2009)
-
-TODO(bja, 2015-09) these should be strings so they have meaningful names instead of ints. 
-</entry>
-
-<entry id="dtmin" type="real" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-minimum time step length (seconds) for adaptive time stepping in richards equation
-</entry>
-<entry id="verySmall" type="real" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-a very small number: used to check for sub step completion for adaptive time stepping in richards equation
-</entry>
-<entry id="xTolerUpper" type="real" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-tolerance to halve length of substep for adaptive time stepping in richards equation
-</entry>
-<entry id="xTolerLower" type="real" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-tolerance to double length of substep for adaptive time stepping in richards equation
-</entry>
-<entry id="expensive" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-
-</entry>
-<entry id="inexpensive" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-
-</entry>
-<entry id="flux_calculation" type="integer" category="clm_physics"
-       group="soilwater_movement_inparm" valid_values="" >
-
-</entry>
-
-<entry id="irrig_min_lai" type="real" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Minimum leaf area index for irrigation to occur
-</entry>
-
-<entry id="irrig_start_time" type="integer" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Time of day to check whether we need irrigation, seconds (0 = midnight).
-We start applying the irrigation in the time step FOLLOWING this time.
-</entry>
-
-<entry id="irrig_length" type="integer" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Desired amount of time to irrigate per day (sec).
-Actual time may differ if this is not a multiple of dtime.
-</entry>
-
-<entry id="irrig_target_smp" type="real" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Target soil matric potential for irrigation (mm).
-When we irrigate, we aim to bring the total soil moisture in the top (irrig_depth) m of soil up to this level.
-</entry>
-
-<entry id="irrig_depth" type="real" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Soil depth to which we measure for irrigation (m)
-</entry>
-
-<entry id="irrig_threshold_fraction" type="real" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Determines soil moisture threshold at which we irrigate.
-If h2osoi_liq_wilting_point is the soil moisture level at wilting point and
-h2osoi_liq_target is the soil moisture level at the target irrigation level
-(given by irrig_target_smp), then the threshold at which we irrigate is
-    h2osoi_liq_wilting_point +
-         irrig_threshold_fraction*(h2osoi_liq_target - h2osoi_liq_wilting_point)
-A value of 1 means that we irrigate whenever soil moisture falls below the target.
-A value of 0 means that we only irrigate when soil moisture falls below the wilting point.
-</entry>
-
-<entry id="irrig_river_volume_threshold" type="real" category="clm_physics"
-       group="irrigation_inparm" valid_values="">
-Threshold for river water volume below which irrigation is shut off (as a fraction of available river water), if limit_irrigation_if_rof_enabled is .true.
-A threshold of 0 means allow all river water to be used;
-a threshold of 0.1 means allow 90% of the river volume to be used; etc.
-</entry>
-
-<entry id="limit_irrigation_if_rof_enabled" type="logical" category="clm_physics"
-       group="irrigation_inparm" valid_values="" >
-If TRUE, limit irrigation when river storage drops below a threshold.
-Only applies if using an active runoff (ROF) model; otherwise, river storage-based limitation
-is turned off regardless of the setting of this namelist variable.
-</entry>
-
-<entry id="irrigate" type="logical" category="clm_physics"
-       group="clm_inparm"  >
-If TRUE, irrigation will be active.
-</entry> 
-
-<entry id="maxpatch_glcmec" type="integer"  category="clm_physics"
-       group="clm_inparm" valid_values="1,3,5,10,36" >
-Number of  multiple elevation classes over glacier points.
-</entry>
-
 <entry id="glacier_region_behavior" type="char*32(10)" category="clm_physics"
        group="clm_glacier_behavior"
        valid_values="multiple,virtual,single_at_atm_topo" >
@@ -342,68 +95,6 @@ Allowed values are:
 Behavior of 'virtual' is required in the region where we have an ice sheet model
 </entry>
 
-<entry id="glacier_region_melt_behavior" type="char*32(10)" category="clm_physics"
-       group="clm_glacier_behavior"
-       valid_values="replaced_by_ice,remains_in_place" >
-Treatment of ice melt for each glacier region (GLACIER_REGION in surface dataset).
-First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
-second to GLACIER_REGION with ID 1, etc.
-Allowed values are:
-'replaced_by_ice': any melted ice runs off and is immediately replaced by solid ice;
-   this results in positive liquid runoff and negative ice runoff
-'remains_in_place': any melted ice remains in place as liquid until it refreezes;
-   thus, ice melt does not result in any runoff
-IMPORTANT NOTE: Regions with the 'remains_in_place' behavior also do not
-compute SMB (because negative SMB would be pretty much meaningless in
-those regions). Thus, you cannot use this behavior where GLC is
-operating.
-Regions with the 'replaced_by_ice' behavior also compute SMB for the
-vegetated column.
-</entry>
-
-<entry id="glacier_region_ice_runoff_behavior" type="char*32(10)" category="clm_physics"
-       group="clm_glacier_behavior"
-       valid_values="remains_ice,melted" >
-Treatment of ice runoff for each glacier region (GLACIER_REGION in surface dataset).
-First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
-second to GLACIER_REGION with ID 1, etc.
-Allowed values are:
-'remains_ice': ice runoff is sent to the river model as ice; this is a crude parameterization
-   of iceberg calving, and so is appropriate in regions where there is substantial iceberg calving
-   in reality
-'melted': ice runoff generated by the CLM physics (primarily due to snow capping) is melted
-   (generating a negative sensible heat flux) and runs off as liquid; this is appropriate in
-   regions that have little iceberg calving in reality. This can be important to avoid unrealistic
-   cooling of the ocean and consequent runaway sea ice growth.
-Only applies when melt_non_icesheet_ice_runoff is .true.
-</entry>
-
-<entry id="glc_snow_persistence_max_days" type="integer" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-Number of days before one considers the perennially snow-covered point 'land ice'
-(and thus capable of generating a positive surface mass balance for the glacier model).
-This is meant to compensate for the fact that, with small values of h2osno_max,
-the onset of a snow-capped state (and thus conversion to land ice) can occur in an
-unrealistically short amount of time.
-Thus, in general, large values of h2osno_max should have glc_snow_persistence_max_days = 0;
-small values of h2osno_max should have glc_snow_persistence_max_days > 0.
-</entry>
-
-<entry id="albice" type="real(2)" category="clm_physics"
-       group="clm_inparm" >
-Visible and Near-infrared albedo's for glacier ice
-</entry>
-
-<entry id="leaf_mr_vcm" type="real" category="clm_physics"
-       group="clm_canopy_inparm" >
-Scalar of leaf respiration to vcmax
-</entry>
-
-<entry id="Jmaxb1" type="real" category="clm_physics"
-       group="luna" >
-baseline proportion of nitrogen allocated for electron transport (J)
-</entry>
-
 <entry id="dtime" type="real"  category="clm_physics" 
        group="clm_inparm" valid_values="">
 Time step (seconds)
@@ -415,42 +106,6 @@ Override the start type from the driver: it can only be
 set to 3 meaning branch.
 </entry>
 
-<entry id="use_fates" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the FATES model
-(use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!)
-</entry>
-
-<entry id="use_luna" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen
-LUNA operates on C3 and non-crop vegetation (see vcmax_opt for how other veg is handled)
-LUNA: Leaf Utilization of Nitrogen for Assimilation
-</entry>
-
-<entry id="use_hydrstress" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the plant hydraulic stress model
-</entry>
-
-<entry id="lnc_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".false.">
-How LUNA and Photosynthesis (if needed) will get Leaf nitrogen content
-   lnc_opt = true  get from leaf N from CN model
-   lnc_opt = false get based on LAI and fixed CN ratio from parameter file
-</entry>
-
-<entry id="paramfile" type="char*256" category="datasets"
-       input_pathname="abs" group="clm_inparm" valid_values="" >
-Full pathname datafile with plant function type (PFT) constants combined with
-constants for biogeochem modules
-</entry>
-
-<entry id="fates_paramfile" type="char*256" category="datasets"
-       input_pathname="abs" group="clm_inparm" valid_values="" >
-Full pathname datafile with fates parameters
-</entry>
-
 <entry id="fsurdat" type="char*256"     category="datasets"
        input_pathname="abs" group="clm_inparm" valid_values="" >
 Full pathname of surface data file.
@@ -590,553 +245,24 @@ Perturbation limit when doing error growth test
 If FALSE, don't write any restart files.
 </entry>
 
-<entry id="urban_hac" type="char*16" category="clm_physics"
-       group="clmu_inparm" valid_values="OFF,ON,ON_WASTEHEAT" >
-Turn urban air conditioning/heating ON or OFF and add wasteheat:
-    OFF          = Air conditioning/heating is OFF in buildings, internal temperature allowed to float freely
-    ON           = Air conditioning/heating is ON in buildings, internal temperature constrained
-    ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon
-</entry>
-
-<entry id="urban_traffic" type="logical" category="clm_physics"
-       group="clmu_inparm" valid_values="" >
-If TRUE, urban traffic flux will be activated (Currently NOT implemented).
-</entry>
-
-<entry id="building_temp_method" type="integer" category="clm_physics"
-       group="clmu_inparm" valid_values="0,1" >
-0 = simpler method (clm4_5)
-1 = prognostic calculation of interior building temp (clm5_0)
-</entry>
-
 <entry id="wrtdia" type="logical" category="history"
        group="clm_inparm" valid_values="" >
 If TRUE, write diagnostic of global radiative temperature written to CLM log file.
 </entry>
 
-<entry id="subgridflag" type="integer" category="clm_physics"
-       group="clm_inparm" valid_values="0,1" >
-Subgrid fluxes for snow
-</entry>
-
-<entry id="snowveg_flag" type="char*10" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="OFF,ON,ON_RAD" >
-Turn vegetation snow canopy ON, OFF, or ON with albedo influence (ON_RAD)
-</entry>
-
 <!-- ========================================================================================  -->
 <!-- Former CPP tokens -->
 <!-- ========================================================================================  -->
-<entry id="use_lch4" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-Turn on methane model. Standard part of CLM45BGC model.
-</entry>
-
-<entry id="use_cn" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-CLM Biogeochemistry mode : Carbon Nitrogen model (CN) 
-(or CLM45BGC if phys=clm4_5, vsoilc_centbgc='on', and clm4me='on')
-</entry>
-
-<entry id="use_fun" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-Turn the Fixation and Uptate of Nitrogen model version 2 (FUN2.0)
-Requires the CN model to work (either CN or CNDV).
-</entry>
-
-<entry id="use_nitrif_denitrif" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-Nitrification/denitrification splits the prognostic mineral N pool into two 
-   mineral N pools: NO3 and NH4, and includes the transformations between them.
-Requires the CN model to work (either CN or CNDV).
-</entry>
-
-<entry id="use_vertsoilc" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-Turn on vertical soil carbon.
-Requires the CN or FATES model to work (either CN or CNDV).
-</entry>
-
-<entry id="use_century_decomp" type="logical" category="bgc"
-       group="clm_inparm" valid_values="" value=".false.">
-Use parameters for decomposition from the CENTURY Carbon model
-Requires the CN or FATES model to work (either CN or CNDV).
-</entry>
-
-<entry id="use_crop" type="logical" category="physics"
-       group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the prognostic crop model
-</entry>
-
-<entry id="initial_seed_at_planting" type="real" category="physics"
-       group="cnphenology" valid_values="" value="1.0d00">
-Initial seed Carbon to use at planting
-(only used when CN is on as well as crop)
-</entry>
 
 <entry id="use_noio" type="logical" category="default_settings"
        group="clm_inparm" valid_values="" value=".false." >
 Toggle to turn all history output completely OFF (possibly used for testing)
 </entry>
 
-<entry id="maxpatch_pft" type="integer" category="physics"
-       group="clm_inparm" valid_values="" value="17">
-Max number of plant functional types in naturally vegetated landunit.
-</entry>
-
-<entry id="use_dynroot" type="logical" category="physics"
-       group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the dynamic root model
-</entry>
-
-<!--                                                   -->
-<!-- mkmapdata  namelist                               -->
-<!--                                                   -->
-<entry id="scripgriddata" type="char*256" category="mkmapdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-SCRIP format grid data file
-</entry>
-
-<entry id="scripgriddata_lrgfile_needed" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="none,64bit_offset,netcdf4" >
-Flag to pass to the ESMF mapping utility, telling it what kind of large
-file support is needed for an output file generated with this grid as
-either the source or destination ('none', '64bit_offset' or 'netcdf4'). 
-</entry>
-
-<entry id="scripgriddata_type" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="SCRIP,UGRID" >
-Flag to pass to the ESMF mapping utility, telling it what kind of grid
-file this is (SCRIP or UGRID).
-</entry>
-
-<entry id="scripgriddata_meshname" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="" >
-For UGRID files, flag to pass to the ESMF mapping utility, telling it the
-name of the dummy variable that has all of the topology information stored
-in its attributes. (Only used if scripgriddata_src_type = UGRID.)
-</entry>
-
-<!--                                                   -->
-<!-- mksurfdata namelist                               -->
-<!--                                                   -->
-<entry id="mksrf_filename" type="char*256" category="mksurfdata"
-       group="default_settings" 
-       valid_values="mksrf_fsoitex,mksrf_forganic,mksrf_flakwat,mksrf_fwetlnd,mksrf_fmax,mksrf_fmax,mksrf_fglacier,mksrf_fglacierregion,mksrf_fvocef,mksrf_furbtopo,firrig,mksrf_furban,mksrf_fvegtyp,mksrf_fhrvtyp,mksrf_fsoicol,mksrf_flai,mksrf_fgdp,mksrf_fpeat,mksrf_fsoildepth,mksrf_fabm,mksrf_ftopostats,mksrf_fvic,mksrf_fch4" >
-Filename for mksurfdata_map to remap raw data into the output surface dataset
-</entry>
-
-<entry id="mksrf_fvegtyp" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Plant Function Type dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fhrvtyp" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Harvest dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fglacier" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Dataset for percent glacier land-unit for mksurfdata
-</entry>
-
-<entry id="mksrf_fglacierregion" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Dataset for glacier region ID for mksurfdata
-</entry>
-
-<entry id="mksrf_furbtopo" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Dataset for topography used to define urban threshold
-</entry>
-
-<entry id="mksrf_flai" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Leaf Area Index dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fsoitex" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Soil texture dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fsoicol" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Soil color dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fmax" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Soil max fraction dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_ffrac" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-High resolution land mask/fraction dataset for mksurfdata
-(used for glacier_mec land-units)
-</entry>
-
-<entry id="mksrf_gridtype" type="char*256" category="mksurfdata"
-       group="clmexp" value="global" valid_values="global,regional" >
-Type of grid to create for mksurfdata
-</entry>
-
-<entry id="mksrf_fgrid" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Grid file at the output resolution for mksurfdata
-</entry>
-
-<entry id="mksrf_fdynuse" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Text file with filepaths (or list of XML elements) for vegetation fractions
-and harvesting for each year to run over for mksurfdata to be able to model
-transient land-use change
-</entry>
-
-<entry id="mksrf_ftopo" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-High resolution topography dataset for mksurfdata
-(used for glacier_mec land-units)
-</entry>
-
-<entry id="mksrf_firrig" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Irrigation dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_forganic" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Organic soil dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_flakwat" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Lake water dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fwetlnd" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Wetland dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_furban" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Urban dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fvocef" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Biogenic Volatile Organic Compounds (VOC) emissions dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fgdp" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-GDP dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fpeat" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Peat dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fsoildepth" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Soil depth dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fabm" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Agricultural burning dominant month dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_ftopostats" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Topography statistics dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fvic" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-VIC parameters dataset for mksurfdata
-</entry>
-
-<entry id="mksrf_fch4" type="char*256" category="mksurfdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Inversion-derived CH4 parameters dataset for mksurfdata
-</entry>
-
-<entry id="outnc_double" type="logical" category="mksurfdata"
-       group="clmexp" value=".true.">
-If TRUE, output variables in double precision for mksurfdata
-</entry>
-
-<entry id="all_urban" type="logical" category="mksurfdata"
-       group="clmexp" value=".false.">
-If TRUE, ignore other files, and set the output percentage to 100% urban and
-zero for other land-use types.
-</entry>
-
-<entry id="no_inlandwet" type="logical" category="mksurfdata"
-       group="clmexp" value=".true.">
-If TRUE, set wetland to 0% over land (renormalizing other landcover types as needed);
-wetland will only be used for ocean points.
-</entry>
-
-<entry id="numpft" type="integer" category="mksurfdata"
-       group="clmexp" value="16" valid_values="16,20" >
-Number of Plant Functional Types (excluding bare-soil)
-</entry>
-
-<entry id="pft_idx" type="integer" category="mksurfdata"
-       group="clmexp"
-       valid_values="0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20" >
-Plant Function Type index to override global file with for mksurfdata
-</entry>
-
-<entry id="pft_frc" type="real" category="mksurfdata"
-       group="clmexp" valid_values="">
-Plant Function Type fraction to override global file with for mksurfdata
-</entry>
-
-<entry id="soil_color" type="integer" category="mksurfdata"
-       group="clmexp"
-       valid_values="0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20" >
-Soil color index to override global file with for mksurfdata
-</entry>
-
-<entry id="soil_fmax" type="real" category="mksurfdata"
-       group="clmexp" >
-Soil maximum fraction to override global file with for mksurfdata
-</entry>
-
-<entry id="soil_sand" type="real" category="mksurfdata"
-       group="clmexp" >
-Soil percent sand to override global file with for mksurfdata
-</entry>
-
-<entry id="soil_clay" type="real" category="mksurfdata"
-       group="clmexp" >
-Soil percent clay to override global file with for mksurfdata
-</entry>
-
-
-<!--                                                   -->
-<!-- mkgriddata namelist                               -->
-<!--                                                   -->
-<entry id="mksrf_fnavyoro" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Orography file with surface heights and land area fraction
-</entry>
-
-<entry id="mksrf_fclmgrid" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-CLM grid file
-</entry>
-
-<entry id="mksrf_fccsmdom" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-CESM domain file
-</entry>
-
-<entry id="mksrf_fcamfile" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-CAM file
-</entry>
-
-<entry id="mksrf_frawtopo" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Raw topography file
-</entry>
-
-<entry id="mksrf_fcamtopo" type="char*256" category="mkgriddata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-CAM topography file
-</entry>
-
-<entry id="mksrf_lsmlon" type="integer" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Number of longitudes to use for a regional grid (for single-point set to 1)
-</entry>
-
-<entry id="mksrf_lsmlat" type="integer" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Number of latitudes to use for a regional grid (for single-point set to 1)
-</entry>
-
-<entry id="mksrf_edgen" type="real" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Northern edge of the regional grid
-</entry>
-
-<entry id="mksrf_edges" type="real" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Southern edge of the regional grid
-</entry>
-
-<entry id="mksrf_edgee" type="real" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Eastern edge of the regional grid
-</entry>
-
-<entry id="mksrf_edgew" type="real" category="mkgriddata"
-       group="clmexp" valid_values="" >
-Western edge of the regional grid
-</entry>
-
-
-<!--             -->
-<!-- mkghg       -->
-<!--             -->
-<entry id="mkghg_bndtvghg" type="char*256" category="tools"
-       input_pathname="abs" group="clmexp" valid_values="" >
-Historical greenhouse gas concentrations from CAM, only used
-by getco2_historical.ncl
-</entry>
-
-<!--                                                   -->
-<!-- files needed for tools/ncl_scripts                -->
-<!--                                                   -->
-<entry id="faerdep" type="char*256"  category="tools" 
-       input_pathname="abs" group="clmexp" valid_values="" >
-Aerosol deposition file name (only used for aerdepregrid.ncl)
-</entry>
-
-<entry id="f_fracdata" type="char*256" category="tools"
-       input_pathname="abs" group="domain_nl" valid_values="" >
-Full pathname of CLM fraction dataset (only used for mkdatadomain).
-</entry>
-
-<entry id="f_griddata" type="char*256" category="tools"
-       input_pathname="abs" group="domain_nl" valid_values="" >
-Full pathname of CLM grid dataset (only used for mkdatadomain).
-</entry>
-
-<entry id="f_domain" type="char*256" category="tools"
-       input_pathname="abs" group="domain_nl" valid_values="" >
-Full pathname of output domain dataset (only used for mkdatadomain).
-</entry>
-
-<entry id="dtype" type="char*5" category="tools"
-       group="domain_nl" valid_values="datm,docn" >
-Type of domain file to create (ocean or atmosphere) (only used for mkdatadomain)
-</entry>
-
-<!-- ========================================================================================  -->
-<!-- Namelist items controlling atmospheric forcings                                           -->
-<!-- ========================================================================================  -->
-
-<entry id="repartition_rain_snow" type="logical" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-If TRUE, repartition rain/snow from atmosphere based on temperature.
-</entry>
-
-<entry id="glcmec_downscale_longwave" type="logical" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-If TRUE, downscale longwave radiation over glc_mec landunits.
-This downscaling is conservative.
-<default>Default: .true.</default>
-</entry>
-
-<entry id="lapse_rate" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Surface temperature lapse rate (K m-1)
-A positive value means a decrease in temperature with increasing height
-</entry>
-
-<entry id="lapse_rate_longwave" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Longwave radiation lapse rate (W m-2 m-1)
-A positive value means a decrease in LW radiation with increasing height
-Only relevant if glcmec_downscale_longwave is .true.
-</entry>
-
-<entry id="longwave_downscaling_limit" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Relative limit for how much longwave downscaling can be done (unitless)
-The pre-normalized, downscaled longwave is restricted to be in the range
-[lwrad*(1-longwave_downscaling_limit), lwrad*(1+longwave_downscaling_limit)]
-This parameter must be in the range [0,1]
-Only relevant if glcmec_downscale_longwave is .true.
-</entry>
-
-<entry id="precip_repartition_glc_all_snow_t" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Temperature below which all precipitation falls as snow, for glacier columns (deg C)
-Only relevant if repartition_rain_snow is .true.
-</entry>
-
-<entry id="precip_repartition_glc_all_rain_t" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Temperature above which all precipitation falls as rain, for glacier columns (deg C)
-Only relevant if repartition_rain_snow is .true.
-</entry>
-
-<entry id="precip_repartition_nonglc_all_snow_t" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Temperature below which all precipitation falls as snow, for non-glacier columns (deg C)
-Only relevant if repartition_rain_snow is .true.
-</entry>
-
-<entry id="precip_repartition_nonglc_all_rain_t" type="real" category="clm_physics"
-       group="atm2lnd_inparm" valid_values="" >
-Temperature above which all precipitation falls as rain, for non-glacier columns (deg C)
-Only relevant if repartition_rain_snow is .true.
-</entry>
-
 <!-- ========================================================================================  -->
 <!-- Namelist items controlling fields sent to atmosphere                                      -->
 <!-- ========================================================================================  -->
 
-<entry id="melt_non_icesheet_ice_runoff" type="logical" category="clm_physics"
-       group="lnd2atm_inparm" valid_values="" >
-If TRUE, ice runoff generated from non-glacier columns and glacier columns outside icesheet regions
-is converted to liquid, with an appropriate sensible heat flux.
-That is, the atmosphere (rather than the ocean) melts the ice.
-(Exception: ice runoff generated to ensure conservation with dynamic landunits remains as ice.)
-</entry>
-
-<!-- ========================================================================================  -->
-<!-- lai_streams streams Namelist (when phys = CLM4_5)                              -->
-<!-- ========================================================================================  -->
-
-<!-- LAI -->
-<entry id="use_lai_streams" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on use of LAI streams in place of the LAI on the surface dataset when using Satellite Phenology mode.
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="stream_year_first_lai" type="integer" category="datasets"
-       group="lai_streams" valid_values="" >
-First year to loop over for LAI data
-</entry>
-
-<entry id="stream_year_last_lai" type="integer" category="datasets"
-       group="lai_streams" valid_values="" >
-Last year to loop over for LAI data
-</entry>
-
-<entry id="model_year_align_lai" type="integer" category="datasets"
-       group="lai_streams" valid_values="" >
-Simulation year that aligns with stream_year_first_lai value
-</entry>
-
-<entry id="stream_fldfilename_lai" type="char*256(30)" category="datasets"
-       input_pathname="abs" group="lai_streams" valid_values="" >
-Filename of input stream data for LAI
-</entry>
-
-<entry id="lai_mapalgo" type="char*256" category="datasets"
-       group="lai_streams" valid_values="bilinear,nn,nnoni,nnonj,spval,copy" >
-Mapping method from LAI input file to the model resolution
-    bilinear = bilinear interpolation
-    nn       = nearest neighbor
-    nnoni    = nearest neighbor on the "i" (longitude) axis
-    nnonj    = nearest neighbor on the "j" (latitude) axis
-    spval    = set to special value
-    copy     = copy using the same indices
-</entry>
-
 <entry id="diri" type="char*256" category="datm"
        group="modelio" valid_values="">
 datm input directory
@@ -1176,19 +302,6 @@ Horizontal grid resolutions for mksurfdata input files
 <!-- Generic issues (resolution, mask etc.)                                                    -->
 <!-- ========================================================================================  -->
 
-<entry id="finundation_res" type="char*10" category="default_settings"
-       group="default_settings" valid_values="none,1.9x2.5" >
-Resolution of finundated inversion streams dataset (stream_fldfilename_ch4finundated)
-to use for methane model
-(only applies when CN and methane model are turned on)
-</entry>
-       
-<entry id="light_res" type="char*10" category="default_settings"
-       group="default_settings" valid_values="none,360x720,94x192">
-Resolution of Lightning dataset to use for CN fire model
-(only applies when CN and the CN fire model are turned on)
-</entry>
-
 <entry id="chk_res" type="integer"  category="default_settings"
        group="default_settings" valid_values="0,1" >
 Check that the resolution and land-mask is valid before continuing.
@@ -1213,7 +326,7 @@ CLM run type.
 <entry id="res" type="char*30" category="default_settings"
        group="default_settings"  
        valid_values=
-"512x1024,360x720cru,128x256,64x128,48x96,32x64,8x16,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,5x5_amazon,1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4,ne60np4,ne120np4,ne240np4,1km-merge-10min">
+"512x1024,360x720cru,128x256,64x128,48x96,32x64,8x16,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,5x5_amazon,1x1_brazil,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4,ne60np4,ne120np4,ne240np4,1km-merge-10min">
 Horizontal resolutions
 Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for CLM tools
 </entry> 
@@ -1240,11 +353,6 @@ the configuration of model version and atmospheric forcing. To run well constant
 to run with a different type of atmospheric forcing.
 </entry> 
 
-<entry id="megan" type="integer" category="default_settings"
-       group="default_settings"  valid_values="0,1">
-If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds)
-</entry> 
-
 <entry id="sim_year" type="integer" category="default_settings"
        group="default_settings" valid_values=
 "1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1980,1985,1995,2000,2005,2015,2025,2035,2045,2055,2065,2075,2085,2095,2105">
@@ -1289,217 +397,6 @@ How close in years to use when looking for an initial condition file (finidat) i
 Simulation years you can look for in initial condition files (finidat) if interpolation is turned on (use_init_interp is .true.)
 </entry>
 
-<entry id="clm_accelerated_spinup" type="char*3" category="default_settings"
-       group="default_settings" valid_values="on,off" >
-Command line argument for setting up your simulation in a mode for faster
-throughput. By default turns off some options, and sets up for a lower level
-of output. When bgc_mode is some level of prognostic BGC (so NOT Satellite Phenology)
-it also sets up for accelerated decomposition.
-NOTE: THIS CORRESPONDS DIRECTLY TO THE env_run.xml VARIABLE OF THE SAME NAME.
-      Set the env_run variable, rather than setting this directly.
-</entry>
-
-<entry id="bgc_mode" type="char*5" category="default_settings"
-       group="default_settings" valid_values="sp,cn,bgc,fates" >
-Command line arguement for biogeochemistry mode for CLM4.5
-   sp  = Satellitte Phenology
-   cn  = Carbon Nitrogen model
-   bgc = CLM4.5 BGC model with: 
-        CENTURY model pools 
-        Nitrification/De-nitrification
-        Methane model
-        Vertically resolved Carbon
-   fates = FATES/ED ecosystem demography model with below ground BGC:
-</entry>
-
-<!-- ========================================================================================  -->
-<!-- namelist elements associated with the vertical CN model                                   -->
-<!-- ========================================================================================  -->
-
-<entry id="spinup_state" type="integer" category="clm_vertcn"
-       group="clm_inparm" valid_values="0,1,2" >
-Flag for setting the state of the Accelerated decomposition spinup state for the BGC model.  
-   0 = normal model behavior; 
-   1 = AD spinup (standard)
-   2 = AD spinup (accelerated spinup from Ricciuto, doesn't work for CNDV and not implemented for CN soil decomposition)
-Entering and exiting spinup mode occurs automatically by comparing the namelist and restart file values for this variable.
-NOTE: THIS CAN ONLY BE SET TO NON-ZERO WHEN BGC_MODE IS NOT SATELITE PHENOLOGY!
-</entry>
-
-<!-- turnover time modifications    -->
-<entry id="decomp_depth_efolding" type="real" category="clm_vertcn"
-       group="bgc_shared" valid_values="" >
-E-folding depth over which decomposition is slowed with depth in all soils.
-</entry>
-
-<entry id="froz_q10" type="real" category="clm_vertcn"
-       group="clm_inparm" valid_values="" >
-separate q10 for frozen soil respiration rates.  default to same as above zero rates
-</entry>
-
-<!-- rooting parameters    -->
-
-<!-- General CN flags -->
-<entry id="reseed_dead_plants" type="logical" category="clm_physics"
-       group="cn_general" valid_values="" >
-Flag to reseed any dead plants on startup from reading the initial conditions file
-</entry>
-
-<entry id="use_c14_bombspike" type="logical" category="clm_isotope"
-       group="clm_inparm" valid_values="" >
-Flag to use the atmospheric time series of C14 concentrations from bomb fallout and Seuss effect, rather than natural abundance C14 (nominally set as 10^-12 mol C14 / mol C)
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="atm_c14_filename" type="char*256" category="clm_isotope"
-       input_pathname="abs" group="clm_inparm" valid_values="" >
-Filename with time series of atmospheric Delta C14 data.  variables in file are "time" and "Delta14co2_in_air". time variable is in format: years since 1850-01-01 0:0:0.0  units are permil.
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="use_c13_timeseries" type="logical" category="clm_isotope"
-       group="clm_inparm" valid_values="" >
-Flag to use the atmospheric time series of C13 concentrations from natural abundance and the Seuss Effect, rather than static values.
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="atm_c13_filename" type="char*256" category="clm_isotope"
-       input_pathname="abs" group="clm_inparm" valid_values="" >
-Filename with time series of atmospheric Delta C13 data, which use CMIP6 format.  variables in file are "time" and "delta13co2_in_air".  time variable is in format: years since 1850-01-01 0:0:0.0. units are permil.
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-
-<!-- permfrost-specific flags    -->
-
-<!-- stress deciduous onset trigger    -->
-<entry id="constrain_stress_deciduous_onset" type="logical" category="clm_physics"
-       group="bgc_shared" valid_values="" >
-If TRUE use additional stress deciduous onset trigger
-</entry>
-
-<entry id="use_nguardrail" type="logical" category="clm_physics"
-       group="clm_inparm" value=".false.">
-Apply the guardrail for leaf-Nitrogen that ensures it doesn't go negative or too small
-</entry>
-
-
-<!-- ========================================================================================  -->
-<!-- namelist elements associated with the clm 5.0 BGC flexible CN Model                       -->
-<!-- ========================================================================================  -->
-<entry id="use_flexibleCN" type="logical" category="clm_nitrogen"
-       group="clm_inparm" value=".false.">
-Allow the CN ratio to flexibly change with the simulation, rather than being fixed
-</entry>
-
-<entry id="MM_Nuptake_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".false.">
-   Michaelis Menten nitrogen uptake kinetics
-</entry>
-
-<entry id="initial_vegC" type="real" category="clm_nitrogen"
-       group="cnvegcarbonstate" >
-How much Carbon to initialize vegetation pools (leafc/frootc and storage) to when -- Michaelis Menten nitrogen uptake kinetics is on
-</entry>
-
-<entry id="downreg_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".false.">
-   GPP downregulation for use_flexibleCN option
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="plant_ndemand_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,1,2,3">
-   Plant nitrogen demand for use_flexibleCN option
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="substrate_term_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".true.">
-   Michaelis Menten substrate limitation for use_flexibleCN option
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="nscalar_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".true.">
-   Michaelis Menten nitrogen limitation for use_flexibleCN option
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="temp_scalar_opt" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".true.">
-   Michaelis Menten temperature limitation for use_flexibleCN option
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="CNratio_floating" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".false.">
-   Flexible CN ratio used for Phenology
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="reduce_dayl_factor" type="logical" category="clm_nitrogen"
-       group="clm_nitrogen" value=".false.">
-   Reduce day length factor
-(NOT implemented)
-</entry>
-
-<entry id="vcmax_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,3,4">
-Vcmax calculation for Photosynthesis
-    vcmax_opt = 4 As for vcmax_opt=0, but using leafN, and exponential if tree  (EXPERIMENTAL NOT TESTED!)
-    vcmax_opt = 3 Based on leafN and VCAD (used with Luna for crop and C4 vegetation)
-    vcmax_opt = 0 Based on canopy top and foilage Nitrogen limitation factor from params file (clm4.5)
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="CN_residual_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,1">
-Residual option for flexible-CN
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="CN_partition_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,1">
-Partition option for flexible-CN
-   CN_partition_opt = 1
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="CN_evergreen_phenology_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,1">
-Evergreen phenology option for CNPhenology
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<entry id="carbon_resp_opt" type="integer" category="clm_nitrogen"
-       group="clm_nitrogen" valid_values="0,1">
-Carbon respiration option to burn off carbon when CN ratio is too high (do NOT use when FUN is on)
-(EXPERIMENTAL and NOT tested)
-</entry>
-
-<!-- ========================================================================================  -->
-<!-- namelist elements associated with the Hydrology1Mod                                       -->
-<!-- ========================================================================================  -->
-
-<entry id="oldfflag" type="integer" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="0,1" >
-Use old snow cover fraction from Niu et al. 2007
-(deprecated -- will be removed)
-</entry>
-
-<entry id="h2osfcflag" type="integer" category="clm_physics"
-       group="clm_soilhydrology_inparm" valid_values="0,1" >
-If surface water is active or not
-(deprecated -- will be removed)
-</entry>
-
-<entry id="origflag" type="integer" category="clm_physics"
-       group="clm_soilhydrology_inparm" valid_values="0,1" >
-Use original CLM4 soil hydraulic properties
-(deprecated -- will be removed)
-</entry>
-
 <!-- ========================================================================================  -->
 <!-- Namelist options related to finidat consistency checks                                    -->
 <!-- ========================================================================================  -->
@@ -1516,16 +413,6 @@ If TRUE (which is the default), check consistency between pct_pft on the finidat
 and pct_pft read from the surface dataset. This check is only done for a NON-transient run.
 </entry>
 
-<!-- ========================================================================================  -->
-<!-- Namelist options related to dynpft consistency checks                                     -->
-<!-- ========================================================================================  -->
-
-<entry id="check_dynpft_consistency" type="logical" category="datasets"
-       group="dynpft_consistency_checks" valid_values="" >
-If TRUE (which is the default), check consistency between pct_nat_pft on the flanduse_timeseries file
-and pct_nat_pft read from the surface dataset.
-</entry>
-
 <!-- ========================================================================================  -->
 <!-- Namelist options related to the snow pack                                                 -->
 <!-- ========================================================================================  -->
@@ -1536,125 +423,6 @@ Number of snow layers.
 Values less than 5 are mainly useful for testing, and should not be used for science.
 </entry>
 
-<entry id="h2osno_max" type="real" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-Maximum snow depth in mm H2O equivalent. Additional mass gains will be capped when this depth 
-is exceeded.
-Changes in this value should possibly be accompanied by changes in:
-- nlevsno: larger values of h2osno_max should be accompanied by increases in nlevsno
-- glc_snow_persistence_max_days: large values of h2osno_max should generally have
-  glc_snow_persistence_max_days = 0; small values of h2osno_max should generally have
-  glc_snow_persistence_max_days > 0.
-</entry>
-
-<entry id="int_snow_max" type="real" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-Limit applied to integrated snowfall when determining changes in snow-covered fraction during melt
-(mm H2O)
-</entry>
-
-<entry id="n_melt_glcmec" type="real" category="clm_physics"
-       group="clm_inparm" valid_values="" >
-SCA shape parameter for glc_mec (glacier multiple elevation class) columns
-For most columns, n_melt is based on the standard deviation of 1km topography in the grid cell;
-but glc_mec columns already account for subgrid topographic variability through their use of
-multiple elevation classes; thus, to avoid double-accounting for topographic variability
-in these columns, we use a fixed value of n_melt.
-</entry>
-
-<entry id="wind_dependent_snow_density" type="logical" category="clm_physics"
-       group="clm_snowhydrology_inparm" valid_values="" >
-If TRUE, the density of new snow depends on wind speed, and there is also
-wind-dependent snow compaction.
-</entry>
-
-<entry id="snow_overburden_compaction_method" type="char*64" category="clm_physics"
-       group="clm_snowhydrology_inparm"
-       valid_values="Vionnet2012,Anderson1976">
-Method used to compute snow overburden compaction
-Anderson1976 -- older method, default in CLM45
-Vionnet2012 --- newer method, default in CLM50
-</entry>
-
-<entry id="lotmp_snowdensity_method" type="char*25" category="clm_physics"
-       group="clm_snowhydrology_inparm"    valid_values="Slater2017,TruncatedAnderson1976" >
-Snow density method to use for low temperatures (below -15C)
-TruncatedAnderson1976 -- Truncate the Anderson-1976 equation at the value for -15C
-Slater2017 ------------- Use equation from Slater that increases snow density for very cold temperatures  (Arctic, Antarctic)
-</entry>
-
-<entry id="upplim_destruct_metamorph" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Upper Limit on Destructive Metamorphism Compaction [kg/m3]
-</entry>
-
-<entry id="overburden_compress_Tfactor" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Snow compaction overburden exponential factor (1/K)
-Not used for snow_overburden_compaction_method=Vionnet2012
-</entry>
-
-<entry id="min_wind_snowcompact" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Minimum wind speed tht results in compaction (m/s)
-</entry>
-
-<entry id="fresh_snw_rds_max" type="real" category="clm_physics"
-       group="aerosol"   >
-maximum warm (at freezing) fresh snow effective radius [microns]
-</entry>
-
-<entry id="reset_snow" type="logical" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-If set to .true., then reset the snow pack over non-glacier columns to a small value.
-This is useful when transitioning from a spinup under one set of atmospheric forcings
-to a run under a different set of atmospheric forcings: By resetting too-large snow packs,
-we make it more likely that points will remain only seasonally snow-covered under the new
-atmospheric forcings. (This is particularly true in a coupled run, where starting with a
-too-large snow pack can cool the atmosphere, thus maintaining the too-large snow pack.)
-
-WARNING: Setting this to .true. will break water conservation for approximately the first
-day of the new run. This is by design: The excess snow is completely removed from the system.
-</entry>
-
-<entry id="reset_snow_glc" type="logical" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-If set to .true., then reset the snow pack over glacier columns to a small value.
-This is useful when transitioning from a spinup under one set of atmospheric forcings
-to a run under a different set of atmospheric forcings: By resetting too-large snow packs,
-we make it more likely that points will remain only seasonally snow-covered under the new
-atmospheric forcings. (This is particularly true in a coupled run, where starting with a
-too-large snow pack can cool the atmosphere, thus maintaining the too-large snow pack.)
-
-See also reset_snow_glc_ela, which controls the elevation below which
-glacier columns are reset.
-
-WARNING: Setting this to .true. will break water conservation for approximately the first
-day of the new run. This is by design: The excess snow is completely removed from the system.
-
-WARNING: This variable is intended for short test runs, and generally
-should not be used for scientific production runs. By resetting snow
-below a given elevation, you risk forcing the system to evolve
-differently in areas below and above reset_snow_glc_ela.
-</entry>
-
-<entry id="reset_snow_glc_ela" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Only relevant if reset_snow_glc is .true.
-
-When resetting snow pack over glacier columns, one can choose to do this over all glacier
-columns, or only those below a certain elevation. A typical use case is to reset only those 
-columns that have a seasonal snow pack in the real world, i.e. SMB less than 0, also known as 
-the equilibrium line altitude (ELA). This parameter sets a single global ELA value. By
-setting this parameter to a large value (i.e. 10000 m), all glacier columns will be reset.
-
-WARNING: This variable is intended for short test runs, and generally
-should not be used for scientific production runs. By resetting snow
-below a given elevation, you risk forcing the system to evolve
-differently in areas below and above reset_snow_glc_ela.
-</entry>
-
-
 <!-- ========================================================================================  -->
 <!-- Namelist options related to initInterp                                                    -->
 <!-- ========================================================================================  -->
diff --git a/bld/namelist_files/namelist_definition_drv.xml b/bld/namelist_files/namelist_definition_drv.xml
index 493f2f2a01..4c3c4004c4 100644
--- a/bld/namelist_files/namelist_definition_drv.xml
+++ b/bld/namelist_files/namelist_definition_drv.xml
@@ -11,7 +11,6 @@
 
   <entry id="start_type" type="char*64" category="expdef"   group="seq_infodata_inparm" valid_values="startup,branch,continue"> </entry>
   <entry id="start_ymd"  type="integer" category="time"     group="seq_timemgr_inparm"> </entry>
-  <entry id="glc_nec"    type="integer" category="seq_flds" group="seq_cplflds_inparm"> </entry>
 
 </namelist_definition>
 
diff --git a/cime_config/buildnml b/cime_config/buildnml
index 77477cbdd0..173189afb3 100755
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -44,7 +44,6 @@ def buildnml(case, caseroot, compname):
     clm_bldnml_opts = case.get_value("CLM_BLDNML_OPTS")
     clm_nml_use_case = case.get_value("CLM_NML_USE_CASE")
     clm_force_coldstart = case.get_value("CLM_FORCE_COLDSTART")
-    clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP")
     comp_glc = case.get_value("COMP_GLC")
     comp_atm = case.get_value("COMP_ATM")
     lnd_grid = case.get_value("LND_GRID")
@@ -58,13 +57,8 @@ def buildnml(case, caseroot, compname):
     run_refcase = case.get_value("RUN_REFCASE")
     run_refdate = case.get_value("RUN_REFDATE")
     run_reftod = case.get_value("RUN_REFTOD")
-    glc_nec = case.get_value("GLC_NEC")
     mask = case.get_value("MASK_GRID")
 
-
-    if ( clm_accelerated_spinup != "off" ):
-        expect(False, "CLM_ACCELERATED_SPINUP is not OFF -- SLIM can not use this!" )
-
     # -----------------------------------------------------
     # Clear out old data
     # -----------------------------------------------------
@@ -202,11 +196,11 @@ def buildnml(case, caseroot, compname):
 
         command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm  start_ymd=%s/ \" "
                    "%s %s -res %s -clm_start_type %s -envxml_dir %s -l_ncpl %s "
-                   "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s "
+                   "-lnd_frac %s -co2_ppmv %s -co2_type %s -config %s "
                    "%s %s"
                    %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, 
                      usecase, lnd_grid, start_type, caseroot, lnd_ncpl,
-                     lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file, 
+                     lndfrac_file, ccsm_co2_ppmv, clm_co2_type, config_cache_file, 
                      clm_bldnml_opts, gridmask))
 
         rc, out, err = run_cmd(command, from_dir=clmconf)
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index ab8a8c9e51..b858907da8 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -14,10 +14,9 @@
 
   <!-- Descriptions of all the different valid configurations for different model versions -->
   <description modifier_mode="1">
-    <desc lnd="CLM45[%SP][%BGC]" >clm4.5:</desc>
-    <desc lnd="CLM50[%SP][%BGC]" >clm5.0:</desc>
-    <desc option="SP"            >Satellite phenology:</desc>
-    <desc option="BGC"           >BGC (vert. resol. CN and methane):</desc>
+    <desc lnd="CLM45[%SP]">clm4.5:</desc>
+    <desc lnd="CLM50[%SP]">clm5.0:</desc>
+    <desc option="SP"     >Satellite phenology:</desc>
   </description>
 
   <entry id="COMP_LND">
@@ -70,10 +69,7 @@
     <default_value></default_value>
     <values>
       <value compset="_CLM45%[^_]*SP"		 >-bgc sp</value>
-      <value compset="_CLM45%[^_]*BGC"		 >-bgc bgc</value>
-
       <value compset="_CLM50%[^_]*SP"		 >-bgc sp</value>
-      <value compset="_CLM50%[^_]*BGC"		 >-bgc bgc</value>
     </values>
     <group>run_component_clm</group>
     <file>env_run.xml</file>
@@ -86,8 +82,6 @@
     <default_value>constant</default_value>
     <values>
       <value compset="_CAM"     >diagnostic</value>
-      <value compset="_BGC%BDRD"   >diagnostic</value>
-      <value compset="_BGC%BPRP"   >prognostic</value>
       <value compset="HIST.*_DATM" >diagnostic</value>
     </values>
     <group>run_component_clm</group>
@@ -116,16 +110,6 @@
       This is an advanced flag and should only be used by expert users.</desc>
   </entry>
 
-  <entry id="CLM_ACCELERATED_SPINUP">
-    <type>char</type>
-    <valid_values>off</valid_values>
-    <default_value>off</default_value>
-    <group>run_component_clm</group>
-    <file>env_run.xml</file>
-    <desc>Turn on any settings for accellerating the model spinup. This is unused for SLIM!
-    </desc>
-  </entry>
-
   <entry id="CLM_FORCE_COLDSTART">
     <type>char</type>
     <valid_values>on,off</valid_values>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 47d76184a1..a5373349cc 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -12,7 +12,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_slim"/>
     </machines>
     <options>
-      <option name="wallclock">01:20:00</option>
+      <option name="wallclock">02:00:00</option>
       <option name="comment">Longer smoke test with SOM for CAM5</option>
     </options>
   </test>
diff --git a/cime_config/testdefs/testmods_dirs/clm/2000_CMIP6_AMIP_1deg_ensemble/shell_commands b/cime_config/testdefs/testmods_dirs/clm/2000_CMIP6_AMIP_1deg_ensemble/shell_commands
new file mode 100755
index 0000000000..5d3544865c
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/2000_CMIP6_AMIP_1deg_ensemble/shell_commands
@@ -0,0 +1,2 @@
+#!/bin/bash
+./xmlchange CLM_FORCE_COLDSTART="on"
diff --git a/cime_config/testdefs/testmods_dirs/clm/default/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/default/user_nl_clm
index 82ac77de65..2efcc6c9bf 100644
--- a/cime_config/testdefs/testmods_dirs/clm/default/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/default/user_nl_clm
@@ -16,4 +16,4 @@
          'MML_diag1_1d', 'MML_diag2_1d', 'MML_diag3_1d', 'MML_diag1_2d', 'MML_diag2_2d', 'MML_diag3_2d', 'MML_q_excess',
 'MML_lh_excess',
          'MML_q_demand', 'MML_lh_demand', 'mml_err_h2o', 'mml_err_h2osno', 'mml_err_seb', 'mml_err_soi', 'mml_err_sol', 'WIND',
-         'THBOT', 'RAIN', 'SNOW', 'RH'
+         'RH'
diff --git a/cime_config/user_nl_clm b/cime_config/user_nl_clm
index b225eb1d00..9755f60435 100644
--- a/cime_config/user_nl_clm
+++ b/cime_config/user_nl_clm
@@ -11,6 +11,5 @@
 !                        (includes $inst_string for multi-ensemble cases)
 !                        or with CLM_FORCE_COLDSTART to do a cold start
 !                        or set it with an explicit filename here.
-! Set maxpatch_glcmec    with GLC_NEC                            option
 !----------------------------------------------------------------------------------
 
diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90
deleted file mode 100644
index f2811d290a..0000000000
--- a/src/biogeochem/CNBalanceCheckMod.F90
+++ /dev/null
@@ -1,358 +0,0 @@
-module CNBalanceCheckMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module for carbon/nitrogen mass balance checking.
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use shr_infnan_mod                  , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                     , only : errMsg => shr_log_errMsg
-  use decompMod                       , only : bounds_type
-  use abortutils                      , only : endrun
-  use clm_varctl                      , only : iulog, use_nitrif_denitrif
-  use clm_time_manager                , only : get_step_size
-  use CNVegNitrogenFluxType           , only : cnveg_nitrogenflux_type
-  use CNVegNitrogenStateType          , only : cnveg_nitrogenstate_type
-  use CNVegCarbonFluxType             , only : cnveg_carbonflux_type
-  use CNVegCarbonStateType            , only : cnveg_carbonstate_type
-  use SoilBiogeochemNitrogenfluxType  , only : soilbiogeochem_nitrogenflux_type
-  use SoilBiogeochemCarbonfluxType    , only : soilbiogeochem_carbonflux_type
-  use ColumnType                      , only : col                
-  use GridcellType                    , only : grc
-  use CNSharedParamsMod               , only : use_fun
-
-  !
-  implicit none
-  private
-  ! 
-  ! !PUBLIC TYPES:
-  type, public :: cn_balance_type
-     private
-     real(r8), pointer :: begcb_col(:)        ! (gC/m2) carbon mass, beginning of time step 
-     real(r8), pointer :: endcb_col(:)        ! (gC/m2) carbon mass, end of time step
-     real(r8), pointer :: begnb_col(:)        ! (gN/m2) nitrogen mass, beginning of time step 
-     real(r8), pointer :: endnb_col(:)        ! (gN/m2) nitrogen mass, end of time step 
-   contains
-     procedure , public  :: Init
-     procedure , public  :: BeginCNBalance
-     procedure , public  :: CBalanceCheck
-     procedure , public  :: NBalanceCheck
-     procedure , private :: InitAllocate 
-  end type cn_balance_type
-  !
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds)
-    class(cn_balance_type)         :: this
-    type(bounds_type) , intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    class(cn_balance_type)         :: this
-    type(bounds_type) , intent(in) :: bounds  
-
-    integer :: begc, endc
-
-    begc = bounds%begc; endc= bounds%endc
-
-    allocate(this%begcb_col(begc:endc)) ; this%begcb_col(:) = nan
-    allocate(this%endcb_col(begc:endc)) ; this%endcb_col(:) = nan
-    allocate(this%begnb_col(begc:endc)) ; this%begnb_col(:) = nan
-    allocate(this%endnb_col(begc:endc)) ; this%endnb_col(:) = nan
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine BeginCNBalance(this, bounds, num_soilc, filter_soilc, &
-       cnveg_carbonstate_inst, cnveg_nitrogenstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Calculate beginning column-level carbon/nitrogen balance, for mass conservation check
-    !
-    ! Should be called after the CN state summaries have been computed for this time step
-    ! (which should be after the dynamic landunit area updates and the associated filter
-    ! updates - i.e., using the new version of the filters)
-    !
-    ! !ARGUMENTS:
-    class(cn_balance_type)         , intent(inout) :: this
-    type(bounds_type)              , intent(in)    :: bounds          
-    integer                        , intent(in)    :: num_soilc       ! number of soil columns filter
-    integer                        , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(cnveg_carbonstate_type)   , intent(in)    :: cnveg_carbonstate_inst
-    type(cnveg_nitrogenstate_type) , intent(in)    :: cnveg_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc,c
-    !-----------------------------------------------------------------------
-
-    associate(                                            & 
-         col_begcb    => this%begcb_col                  , & ! Output: [real(r8) (:)]  (gC/m2) carbon mass, beginning of time step
-         col_begnb    => this%begnb_col                  , & ! Output: [real(r8) (:)]  (gN/m2) nitrogen mass, beginning of time step 
-         totcolc      => cnveg_carbonstate_inst%totc_col , & ! Input:  [real(r8) (:)]  (gC/m2) total column carbon, incl veg and cpool
-         totcoln      => cnveg_nitrogenstate_inst%totn_col & ! Input:  [real(r8) (:)]  (gN/m2) total column nitrogen, incl veg 
-         )
-    
-    do fc = 1,num_soilc
-       c = filter_soilc(fc)
-       col_begcb(c) = totcolc(c)
-       col_begnb(c) = totcoln(c)
-    end do
-
-    end associate
-
-  end subroutine BeginCNBalance
- 
-  !-----------------------------------------------------------------------
-  subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
-       soilbiogeochem_carbonflux_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Perform carbon mass conservation check for column and patch
-    !
-    ! !ARGUMENTS:
-    class(cn_balance_type)               , intent(inout) :: this
-    type(bounds_type)                    , intent(in)    :: bounds          
-    integer                              , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                              , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(soilbiogeochem_carbonflux_type) , intent(in)    :: soilbiogeochem_carbonflux_inst
-    type(cnveg_carbonflux_type)          , intent(in)    :: cnveg_carbonflux_inst
-    type(cnveg_carbonstate_type)         , intent(inout) :: cnveg_carbonstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,err_index    ! indices
-    integer  :: fc             ! lake filter indices
-    logical  :: err_found      ! error flag
-    real(r8) :: dt             ! radiation time step (seconds)
-    real(r8) :: col_cinputs
-    real(r8) :: col_coutputs
-    real(r8) :: col_errcb(bounds%begc:bounds%endc) 
-    !-----------------------------------------------------------------------
-
-    associate(                                                                            & 
-         col_begcb               =>    this%begcb_col                                   , & ! Input:  [real(r8) (:) ]  (gC/m2) carbon mass, beginning of time step 
-         col_endcb               =>    this%endcb_col                                   , & ! Output: [real(r8) (:) ]  (gC/m2) carbon mass, end of time step 
-         wood_harvestc           =>    cnveg_carbonflux_inst%wood_harvestc_col          , & ! Input:  [real(r8) (:) ]  (gC/m2/s) wood harvest (to product pools)
-         grainc_to_cropprodc     =>    cnveg_carbonflux_inst%grainc_to_cropprodc_col    , & ! Input:  [real(r8) (:) ]  (gC/m2/s) grain C to 1-year crop product pool
-         gpp                     =>    cnveg_carbonflux_inst%gpp_col                    , & ! Input:  [real(r8) (:) ]  (gC/m2/s) gross primary production
-         er                      =>    cnveg_carbonflux_inst%er_col                     , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total ecosystem respiration, autotrophic + heterotrophic
-         col_fire_closs          =>    cnveg_carbonflux_inst%fire_closs_col             , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total column-level fire C loss
-         col_hrv_xsmrpool_to_atm =>    cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_col    , & ! Input:  [real(r8) (:) ]  (gC/m2/s) excess MR pool harvest mortality 
-
-         som_c_leached           =>    soilbiogeochem_carbonflux_inst%som_c_leached_col , & ! Input:  [real(r8) (:) ]  (gC/m2/s) total SOM C loss from vertical transport 
-
-         totcolc                 =>    cnveg_carbonstate_inst%totc_col                    & ! Input:  [real(r8) (:) ]  (gC/m2) total column carbon, incl veg and cpool
-         )
-
-      ! set time steps
-      dt = real( get_step_size(), r8 )
-
-      err_found = .false.
-      do fc = 1,num_soilc
-         c = filter_soilc(fc)
-
-         ! calculate the total column-level carbon storage, for mass conservation check
-         col_endcb(c) = totcolc(c)
-
-         ! calculate total column-level inputs
-         col_cinputs = gpp(c)
-
-         ! calculate total column-level outputs
-         ! er = ar + hr, col_fire_closs includes patch-level fire losses
-         col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c)
-
-         ! Fluxes to product pools are included in column-level outputs: the product
-         ! pools are not included in totcolc, so are outside the system with respect to
-         ! these balance checks. (However, the dwt flux to product pools is NOT included,
-         ! since col_begcb is initialized after the dynamic area adjustments - i.e.,
-         ! after the dwt term has already been taken out.)
-         col_coutputs = col_coutputs + &
-              wood_harvestc(c) + &
-              grainc_to_cropprodc(c)
-
-         ! subtract leaching flux
-         col_coutputs = col_coutputs - som_c_leached(c)
-
-         ! calculate the total column-level carbon balance error for this time step
-         col_errcb(c) = (col_cinputs - col_coutputs)*dt - &
-              (col_endcb(c) - col_begcb(c))
-
-         ! check for significant errors
-         if (abs(col_errcb(c)) > 1e-7_r8) then
-            err_found = .true.
-            err_index = c
-         end if
-          if (abs(col_errcb(c)) > 1e-8_r8) then
-            write(iulog,*) 'cbalance warning',c,col_errcb(c),col_endcb(c)
-         end if
-
-
-
-      end do ! end of columns loop
-
-      if (err_found) then
-         c = err_index
-         write(iulog,*)'column cbalance error    = ', col_errcb(c), c
-         write(iulog,*)'Latdeg,Londeg=',grc%latdeg(col%gridcell(c)),grc%londeg(col%gridcell(c))
-         write(iulog,*)'begcb                    = ',col_begcb(c)
-         write(iulog,*)'endcb                    = ',col_endcb(c)
-         write(iulog,*)'delta store              = ',col_endcb(c)-col_begcb(c)
-         write(iulog,*)'--- Inputs ---'
-         write(iulog,*)'gpp                      = ',gpp(c)*dt
-         write(iulog,*)'--- Outputs ---'
-         write(iulog,*)'er                       = ',er(c)*dt
-         write(iulog,*)'col_fire_closs           = ',col_fire_closs(c)*dt
-         write(iulog,*)'col_hrv_xsmrpool_to_atm  = ',col_hrv_xsmrpool_to_atm(c)*dt
-         write(iulog,*)'wood_harvestc            = ',wood_harvestc(c)*dt
-         write(iulog,*)'grainc_to_cropprodc      = ',grainc_to_cropprodc(c)*dt
-         write(iulog,*)'-1*som_c_leached         = ',som_c_leached(c)*dt
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-      end if
-
-    end associate
-
-  end subroutine CBalanceCheck
-
-  !-----------------------------------------------------------------------
-  subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, &
-       soilbiogeochem_nitrogenflux_inst, cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Perform nitrogen mass conservation check
-    !
-    ! !USES:
-    use clm_varctl, only : use_crop
-    !
-    ! !ARGUMENTS:
-    class(cn_balance_type)                  , intent(inout) :: this
-    type(bounds_type)                       , intent(in)    :: bounds          
-    integer                                 , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc                                      (:) ! filter for soil columns
-    type(soilbiogeochem_nitrogenflux_type)  , intent(in)    :: soilbiogeochem_nitrogenflux_inst
-    type(cnveg_nitrogenflux_type)           , intent(in)    :: cnveg_nitrogenflux_inst
-    type(cnveg_nitrogenstate_type)          , intent(inout) :: cnveg_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,err_index,j  ! indices
-    integer :: fc             ! lake filter indices
-    logical :: err_found      ! error flag
-    real(r8):: dt             ! radiation time step (seconds)
-    real(r8):: col_ninputs(bounds%begc:bounds%endc) 
-    real(r8):: col_noutputs(bounds%begc:bounds%endc) 
-    real(r8):: col_errnb(bounds%begc:bounds%endc) 
-    !-----------------------------------------------------------------------
-
-    associate(                                                                             & 
-         col_begnb           => this%begnb_col                                           , & ! Input:  [real(r8) (:) ]  (gN/m2) nitrogen mass, beginning of time step   
-         col_endnb           => this%endnb_col                                           , & ! Output: [real(r8) (:) ]  (gN/m2) nitrogen mass, end of time step         
-         ndep_to_sminn       => soilbiogeochem_nitrogenflux_inst%ndep_to_sminn_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s) atmospheric N deposition to soil mineral N        
-         nfix_to_sminn       => soilbiogeochem_nitrogenflux_inst%nfix_to_sminn_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s) symbiotic/asymbiotic N fixation to soil mineral N 
-         ffix_to_sminn       => soilbiogeochem_nitrogenflux_inst%ffix_to_sminn_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s) free living N fixation to soil mineral N         
-         fert_to_sminn       => soilbiogeochem_nitrogenflux_inst%fert_to_sminn_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s)                                         
-         soyfixn_to_sminn    => soilbiogeochem_nitrogenflux_inst%soyfixn_to_sminn_col    , & ! Input:  [real(r8) (:) ]  (gN/m2/s)                                         
-         supplement_to_sminn => soilbiogeochem_nitrogenflux_inst%supplement_to_sminn_col , & ! Input:  [real(r8) (:) ]  (gN/m2/s) supplemental N supply                           
-         denit               => soilbiogeochem_nitrogenflux_inst%denit_col               , & ! Input:  [real(r8) (:) ]  (gN/m2/s) total rate of denitrification           
-         sminn_leached       => soilbiogeochem_nitrogenflux_inst%sminn_leached_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s) soil mineral N pool loss to leaching   
-         smin_no3_leached    => soilbiogeochem_nitrogenflux_inst%smin_no3_leached_col    , & ! Input:  [real(r8) (:) ]  (gN/m2/s) soil mineral NO3 pool loss to leaching 
-         smin_no3_runoff     => soilbiogeochem_nitrogenflux_inst%smin_no3_runoff_col     , & ! Input:  [real(r8) (:) ]  (gN/m2/s) soil mineral NO3 pool loss to runoff   
-         f_n2o_nit           => soilbiogeochem_nitrogenflux_inst%f_n2o_nit_col           , & ! Input:  [real(r8) (:) ]  (gN/m2/s) flux of N2o from nitrification 
-         som_n_leached       => soilbiogeochem_nitrogenflux_inst%som_n_leached_col       , & ! Input:  [real(r8) (:) ]  (gN/m2/s) total SOM N loss from vertical transport
-
-         col_fire_nloss      => cnveg_nitrogenflux_inst%fire_nloss_col                   , & ! Input:  [real(r8) (:) ]  (gN/m2/s) total column-level fire N loss 
-         wood_harvestn       => cnveg_nitrogenflux_inst%wood_harvestn_col                , & ! Input:  [real(r8) (:) ]  (gN/m2/s) wood harvest (to product pools)
-         grainn_to_cropprodn => cnveg_nitrogenflux_inst%grainn_to_cropprodn_col          , & ! Input:  [real(r8) (:) ]  (gN/m2/s) grain N to 1-year crop product pool
-
-         totcoln             => cnveg_nitrogenstate_inst%totn_col                          & ! Input:  [real(r8) (:) ]  (gN/m2) total column nitrogen, incl veg 
-         )
-
-      ! set time steps
-      dt = real( get_step_size(), r8 )
-
-      err_found = .false.
-      do fc = 1,num_soilc
-         c=filter_soilc(fc)
-
-         ! calculate the total column-level nitrogen storage, for mass conservation check
-         col_endnb(c) = totcoln(c)
-
-         ! calculate total column-level inputs
-         col_ninputs(c) = ndep_to_sminn(c) + nfix_to_sminn(c) + supplement_to_sminn(c)
-         
-         if(use_fun)then
-            col_ninputs(c) = col_ninputs(c) + ffix_to_sminn(c) ! for FUN, free living fixation is a seprate flux. RF. 
-         endif
-     
-         if (use_crop) then
-            col_ninputs(c) = col_ninputs(c) + fert_to_sminn(c) + soyfixn_to_sminn(c)
-         end if
-
-         ! calculate total column-level outputs
-         col_noutputs(c) = denit(c) + col_fire_nloss(c)
-
-         ! Fluxes to product pools are included in column-level outputs: the product
-         ! pools are not included in totcoln, so are outside the system with respect to
-         ! these balance checks. (However, the dwt flux to product pools is NOT included,
-         ! since col_begnb is initialized after the dynamic area adjustments - i.e.,
-         ! after the dwt term has already been taken out.)
-         col_noutputs(c) = col_noutputs(c) + &
-              wood_harvestn(c) + &
-              grainn_to_cropprodn(c)
-
-         if (.not. use_nitrif_denitrif) then
-            col_noutputs(c) = col_noutputs(c) + sminn_leached(c)
-         else
-            col_noutputs(c) = col_noutputs(c) + f_n2o_nit(c)
-
-            col_noutputs(c) = col_noutputs(c) + smin_no3_leached(c) + smin_no3_runoff(c)
-         end if
-
-         col_noutputs(c) = col_noutputs(c) - som_n_leached(c)
-
-         ! calculate the total column-level nitrogen balance error for this time step
-         col_errnb(c) = (col_ninputs(c) - col_noutputs(c))*dt - &
-              (col_endnb(c) - col_begnb(c))
-
-         if (abs(col_errnb(c)) > 1e-3_r8) then
-            err_found = .true.
-            err_index = c
-         end if
-         
-         if (abs(col_errnb(c)) > 1e-7_r8) then
-            write(iulog,*) 'nbalance warning',c,col_errnb(c),col_endnb(c)
-            write(iulog,*)'inputs,ffix,nfix,ndep = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt
-            write(iulog,*)'outputs,lch,roff,dnit = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt
-         end if
-
-      end do ! end of columns loop
-
-      if (err_found) then
-         c = err_index
-         write(iulog,*)'column nbalance error    = ',col_errnb(c), c
-         write(iulog,*)'Latdeg,Londeg            = ',grc%latdeg(col%gridcell(c)),grc%londeg(col%gridcell(c))
-         write(iulog,*)'begnb                    = ',col_begnb(c)
-         write(iulog,*)'endnb                    = ',col_endnb(c)
-         write(iulog,*)'delta store              = ',col_endnb(c)-col_begnb(c)
-         write(iulog,*)'input mass               = ',col_ninputs(c)*dt
-         write(iulog,*)'output mass              = ',col_noutputs(c)*dt
-         write(iulog,*)'net flux                 = ',(col_ninputs(c)-col_noutputs(c))*dt
-         write(iulog,*)'inputs,ffix,nfix,ndep    = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt
-         write(iulog,*)'outputs,ffix,nfix,ndep   = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt
-        
-         
-         
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-      end if
-
-    end associate
-
-  end subroutine NBalanceCheck
-
-end module CNBalanceCheckMod
diff --git a/src/biogeochem/CNDVType.F90 b/src/biogeochem/CNDVType.F90
deleted file mode 100644
index daacd84574..0000000000
--- a/src/biogeochem/CNDVType.F90
+++ /dev/null
@@ -1,519 +0,0 @@
-module CNDVType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module containing routines to drive the annual dynamic vegetation
-  ! that works with CN, reset related variables,
-  ! and initialize/reset time invariant variables
-  !
-  ! !USES:
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use shr_log_mod  , only : errMsg => shr_log_errMsg
-  use abortutils   , only : endrun
-  use decompMod    , only : bounds_type
-  use clm_varctl   , only : use_cndv, iulog
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC DATA TYPES:
-  !
-  ! DGVM-specific ecophysiological constants structure (patch-level)
-  type, public :: dgv_ecophyscon_type
-     real(r8), pointer :: crownarea_max(:)   ! patch tree maximum crown area [m2]
-     real(r8), pointer :: tcmin(:)           ! patch minimum coldest monthly mean temperature [units?]
-     real(r8), pointer :: tcmax(:)           ! patch maximum coldest monthly mean temperature [units?]
-     real(r8), pointer :: gddmin(:)          ! patch minimum growing degree days (at or above 5 C)
-     real(r8), pointer :: twmax(:)           ! patch upper limit of temperature of the warmest month [units?]
-     real(r8), pointer :: reinickerp(:)      ! patch parameter in allometric equation
-     real(r8), pointer :: allom1(:)          ! patch parameter in allometric
-     real(r8), pointer :: allom2(:)          ! patch parameter in allometric
-     real(r8), pointer :: allom3(:)          ! patch parameter in allometric
-  end type dgv_ecophyscon_type
-  type(dgv_ecophyscon_type), public :: dgv_ecophyscon
-  !
-  ! DGVM state variables structure
-  type, public :: dgvs_type
-     real(r8), pointer, public :: agdd_patch        (:) ! patch accumulated growing degree days above 5
-     real(r8), pointer, public :: agddtw_patch      (:) ! patch accumulated growing degree days above twmax
-     real(r8), pointer, public :: agdd20_patch      (:) ! patch 20-yr running mean of agdd
-     real(r8), pointer, public :: tmomin20_patch    (:) ! patch 20-yr running mean of tmomin
-     logical , pointer, public :: present_patch     (:) ! patch whether PATCH present in patch
-     logical , pointer, public :: pftmayexist_patch (:) ! patch if .false. then exclude seasonal decid patches from tropics
-     real(r8), pointer, public :: nind_patch        (:) ! patch number of individuals (#/m**2)
-     real(r8), pointer, public :: lm_ind_patch      (:) ! patch individual leaf mass
-     real(r8), pointer, public :: lai_ind_patch     (:) ! patch LAI per individual
-     real(r8), pointer, public :: fpcinc_patch      (:) ! patch foliar projective cover increment (fraction) 
-     real(r8), pointer, public :: fpcgrid_patch     (:) ! patch foliar projective cover on gridcell (fraction)
-     real(r8), pointer, public :: fpcgridold_patch  (:) ! patch last yr's fpcgrid
-     real(r8), pointer, public :: crownarea_patch   (:) ! patch area that each individual tree takes up (m^2)
-     real(r8), pointer, public :: greffic_patch     (:)
-     real(r8), pointer, public :: heatstress_patch  (:)
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: Restart
-     procedure , public  :: InitAccBuffer
-     procedure , public  :: InitAccVars
-     procedure , public  :: UpdateAccVars
-     procedure , private :: InitAllocate 
-     procedure , private :: InitCold     
-     procedure , private :: InitHistory
-  end type dgvs_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    ! Note - need allocation so that associate statements can be used
-    ! at run time for NAG (allocation of variables is needed) - history
-    ! should only be initialized if use_cndv is true
-
-    call this%InitAllocate (bounds)
-
-    if (use_cndv) then
-       call this%InitCold (bounds)
-       call this%InitHistory (bounds)
-    end if
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar     , only : numpft
-    use pftconMod      , only : allom1s, allom2s, allom1, allom2, allom3, reinickerp
-    use pftconMod      , only : ntree, nbrdlf_dcd_brl_shrub
-    use pftconMod      , only : pftcon
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begp, endp
-    integer  :: m
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-  
-    allocate(this%agdd_patch        (begp:endp)) ;     this%agdd_patch        (:) = nan
-    allocate(this%agddtw_patch      (begp:endp)) ;     this%agddtw_patch      (:) = nan
-    allocate(this%agdd20_patch      (begp:endp)) ;     this%agdd20_patch      (:) = nan
-    allocate(this%tmomin20_patch    (begp:endp)) ;     this%tmomin20_patch    (:) = nan
-    allocate(this%present_patch     (begp:endp)) ;     this%present_patch     (:) = .false.
-    allocate(this%pftmayexist_patch (begp:endp)) ;     this%pftmayexist_patch (:) = .true.
-    allocate(this%nind_patch        (begp:endp)) ;     this%nind_patch        (:) = nan
-    allocate(this%lm_ind_patch      (begp:endp)) ;     this%lm_ind_patch      (:) = nan
-    allocate(this%lai_ind_patch     (begp:endp)) ;     this%lai_ind_patch     (:) = nan
-    allocate(this%fpcinc_patch      (begp:endp)) ;     this%fpcinc_patch      (:) = nan
-    allocate(this%fpcgrid_patch     (begp:endp)) ;     this%fpcgrid_patch     (:) = nan
-    allocate(this%fpcgridold_patch  (begp:endp)) ;     this%fpcgridold_patch  (:) = nan
-    allocate(this%crownarea_patch   (begp:endp)) ;     this%crownarea_patch   (:) = nan
-    allocate(this%greffic_patch     (begp:endp)) ;     this%greffic_patch     (:) = nan
-    allocate(this%heatstress_patch  (begp:endp)) ;     this%heatstress_patch  (:) = nan
-
-    allocate(dgv_ecophyscon%crownarea_max (0:numpft)) 
-    allocate(dgv_ecophyscon%tcmin         (0:numpft))         
-    allocate(dgv_ecophyscon%tcmax         (0:numpft))         
-    allocate(dgv_ecophyscon%gddmin        (0:numpft))        
-    allocate(dgv_ecophyscon%twmax         (0:numpft))         
-    allocate(dgv_ecophyscon%reinickerp    (0:numpft))    
-    allocate(dgv_ecophyscon%allom1        (0:numpft))        
-    allocate(dgv_ecophyscon%allom2        (0:numpft))        
-    allocate(dgv_ecophyscon%allom3        (0:numpft))        
-
-    do m = 0,numpft
-       dgv_ecophyscon%crownarea_max(m) = pftcon%pftpar20(m)
-       dgv_ecophyscon%tcmin(m)         = pftcon%pftpar28(m)
-       dgv_ecophyscon%tcmax(m)         = pftcon%pftpar29(m)
-       dgv_ecophyscon%gddmin(m)        = pftcon%pftpar30(m)
-       dgv_ecophyscon%twmax(m)         = pftcon%pftpar31(m)
-       dgv_ecophyscon%reinickerp(m)    = reinickerp
-       dgv_ecophyscon%allom1(m)        = allom1
-       dgv_ecophyscon%allom2(m)        = allom2
-       dgv_ecophyscon%allom3(m)        = allom3
-       ! modification for shrubs by X.D.Z
-       if (m > ntree .and. m <= nbrdlf_dcd_brl_shrub ) then 
-          dgv_ecophyscon%allom1(m) = allom1s
-          dgv_ecophyscon%allom2(m) = allom2s
-       end if
-    end do
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !USES:
-    use shr_kind_mod  , only : r8 => shr_kind_r8
-    use shr_const_mod , only : SHR_CONST_TKFRZ
-    use decompMod     , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this 
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: p           ! patch index
-    !-----------------------------------------------------------------------
-
-    do p = bounds%begp,bounds%endp
-       this%present_patch(p)   = .false.
-       this%crownarea_patch(p) = 0._r8
-       this%nind_patch(p)      = 0._r8
-       this%agdd20_patch(p)    = 0._r8
-       this%tmomin20_patch(p)  = SHR_CONST_TKFRZ - 5._r8 !initialize this way for Phenology code
-    end do
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize history variables
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-    
-    call hist_addfld1d (fname='AGDD', units='K',  &
-         avgflag='A', long_name='growing degree-days base 5C', &
-         ptr_patch=this%agdd_patch, default='inactive')
-
-  end subroutine InitHistory
-
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !DESCRIPTION:
-    ! Read/Write module information to/from restart file.
-    !
-    ! !USES:
-    use clm_varcon , only : spval  
-    use spmdMod    , only : masterproc
-    use decompMod  , only : get_proc_global
-    use restUtilMod
-    use ncdio_pio
-    use pio
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: j,c,p		! indices
-    logical           :: readvar	! determine if variable is on initial file
-    logical           :: do_io		! whether to do i/o for the given variable
-    integer           :: nump_global	! total number of patches, globally
-    integer           :: dimlen         ! dimension length
-    integer           :: ier            ! error status
-    integer           :: itemp		! temporary 
-    integer , pointer :: iptemp(:)	! pointer to memory to be allocated
-    integer           :: err_code       ! error code
-    !-----------------------------------------------------------------------
-
-    ! Get expected total number of points, for later error checks
-    call get_proc_global(np=nump_global)
-
-    call restartvar(ncid=ncid, flag=flag, varname='CROWNAREA', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%crownarea_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='nind', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%nind_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='fpcgrid', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fpcgrid_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='fpcgridold', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fpcgridold_patch)
-
-    ! tmomin20
-    do_io = .true.
-    if (flag == 'read') then
-       ! On a read, confirm that this variable has the expected size; if not, don't
-       ! read it (instead leave it at its arbitrary initial value). This is needed to
-       ! support older initial conditions for which this variable had a different size.
-       call ncd_inqvdlen(ncid, 'TMOMIN20', 1, dimlen, err_code)
-       if (dimlen /= nump_global) then
-          do_io = .false.
-       end if
-    end if
-    if (do_io) then
-       call restartvar(ncid=ncid, flag=flag, varname='TMOMIN20', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='',units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%tmomin20_patch)
-    end if
-
-    ! agdd20
-    do_io = .true.
-    if (flag == 'read') then
-       ! On a read, confirm that this variable has the expected size; if not, don't
-       ! read it (instead leave it at its arbitrary initial value). This is needed to
-       ! support older initial conditions for which this variable had a different size.
-       call ncd_inqvdlen(ncid, 'AGDD20', 1, dimlen, err_code)
-       if (dimlen /= nump_global) then
-          do_io = .false.
-       end if
-    end if
-    if (do_io) then
-       call restartvar(ncid=ncid, flag=flag, varname='AGDD20', xtype=ncd_double,  &
-            dim1name='pft',&
-            long_name='',units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%agdd20_patch)
-    end if
-
-    ! present  
-    if (flag == 'read' .or. flag == 'write') then
-       allocate (iptemp(bounds%begp:bounds%endp), stat=ier)
-    end if
-    if (flag == 'write') then
-       do p = bounds%begp,bounds%endp
-          iptemp(p) = 0
-          if (this%present_patch(p)) iptemp(p) = 1
-       end do
-    end if
-    call restartvar(ncid=ncid, flag=flag, varname='present', xtype=ncd_int,  &
-         dim1name='pft',&
-         long_name='',units='', &
-         interpinic_flag='interp', readvar=readvar, data=iptemp)
-    if (flag=='read' .and. readvar) then
-       do p = bounds%begp,bounds%endp
-          this%present_patch(p) = .false.
-          if (iptemp(p) == 1) this%present_patch(p) = .true.
-       end do
-    end if
-    if (flag == 'read' .or. flag == 'write') then
-       deallocate (iptemp)
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='heatstress', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%heatstress_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='greffic', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%greffic_patch)
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    ! Each interval and accumulation type is unique to each field processed.
-    ! Routine [initAccBuffer] defines the fields to be processed
-    ! and the type of accumulation. 
-    ! Routine [updateCNDVAccVars] does the actual accumulation for a given field.
-    ! Fields are accumulated by calls to subroutine [update_accum_field]. 
-    ! To accumulate a field, it must first be defined in subroutine [initAccVars] 
-    ! and then accumulated by calls to [updateCNDVAccVars].
-    !
-    ! This should only be called if use_cndv is true.
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    !
-    ! !LOCAL VARIABLES:
-    integer, parameter :: not_used = huge(1)
-
-    !---------------------------------------------------------------------
-
-    ! The following are accumulated fields.
-    ! These types of fields are accumulated until a trigger value resets
-    ! the accumulation to zero (see subroutine update_accum_field).
-    ! Hence, [accper] is not valid.
-
-    call init_accum_field (name='AGDDTW', units='K', &
-         desc='growing degree-days base twmax', accum_type='runaccum', accum_period=not_used, &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    call init_accum_field (name='AGDD', units='K', &
-         desc='growing degree-days base 5C', accum_type='runaccum', accum_period=not_used,  &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! This should only be called if use_cndv is true.
-    !
-    ! !USES 
-    use accumulMod       , only : extract_accum_field
-    use clm_time_manager , only : get_nstep
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: nstep
-    integer :: ier            ! error status
-    real(r8), pointer :: rbufslp(:)  ! temporary
-
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Allocate needed dynamic memory for single level patch field
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)' in '
-       call endrun(msg=" allocation error for rbufslp"//&
-            errMsg(sourcefile, __LINE__))
-    endif
-
-    nstep = get_nstep()
-
-    call extract_accum_field ('AGDDTW', rbufslp, nstep) 
-    this%agddtw_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('AGDD', rbufslp, nstep) 
-    this%agdd_patch(begp:endp) = rbufslp(begp:endp)
-
-    deallocate(rbufslp)
-
-  end subroutine InitAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine UpdateAccVars(this, bounds, t_a10_patch, t_ref2m_patch)
-    !
-    ! !DESCRIPTION:
-    ! Update accumulated variables. Should be called every time step.
-    !
-    ! This should only be called if use_cndv is true.
-    !
-    ! !USES:
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    use clm_time_manager , only : get_step_size, get_nstep, get_curr_date
-    use pftconMod        , only : ndllf_dcd_brl_tree
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
-    !
-    ! !ARGUMENTS:
-    class(dgvs_type)  , intent(inout) :: this
-    type(bounds_type) , intent(in)    :: bounds
-    ! COMPILER_BUG(wjs, 2014-11-30, pgi 14.7) These arrays get resized to 0 when running
-    ! with threading with pgi 14.7 on yellowstone. My standard workarounds weren't
-    ! working; the only thing that I can find that works is to change them to pointers
-!    real(r8)          , intent(in)    :: t_a10_patch( bounds%begp:)      ! 10-day running mean of the 2 m temperature (K)
-!    real(r8)          , intent(in)    :: t_ref2m_patch( bounds%begp:)    ! 2 m height surface air temperature (K)
-    real(r8), pointer , intent(in)    :: t_a10_patch(:)      ! 10-day running mean of the 2 m temperature (K)
-    real(r8), pointer , intent(in)    :: t_ref2m_patch(:)    ! 2 m height surface air temperature (K)
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: p          ! index
-    integer           :: ier        ! error status
-    integer           :: dtime      ! timestep size [seconds]
-    integer           :: nstep      ! timestep number
-    integer           :: year       ! year (0, ...) for nstep
-    integer           :: month      ! month (1, ..., 12) for nstep
-    integer           :: day        ! day of month (1, ..., 31) for nstep
-    integer           :: secs       ! seconds into current date for nstep
-    integer           :: begp, endp
-    real(r8), pointer :: rbufslp(:) ! temporary single level - patch level
-    !-----------------------------------------------------------------------
-    
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(t_a10_patch)   == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(t_ref2m_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-
-    dtime = get_step_size()
-    nstep = get_nstep()
-    call get_curr_date (year, month, day, secs)
-
-    ! Allocate needed dynamic memory for single level patch field
-
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'update_accum_hist allocation error for rbuf1dp'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Accumulate growing degree days based on 10-day running mean temperature.
-    ! The trigger to reset the accumulated values to zero is -99999.
-    
-    ! Accumulate and extract AGDDTW (gdd base twmax, which is 23 deg C
-    ! for boreal woody patches)
-    
-    do p = begp,endp
-       rbufslp(p) = max(0._r8, &
-            (t_a10_patch(p) - SHR_CONST_TKFRZ - dgv_ecophyscon%twmax(ndllf_dcd_brl_tree)) &
-            * dtime/SHR_CONST_CDAY)
-       if (month==1 .and. day==1 .and. secs==int(dtime)) rbufslp(p) = accumResetVal
-    end do
-    call update_accum_field  ('AGDDTW', rbufslp, nstep)
-    call extract_accum_field ('AGDDTW', this%agddtw_patch, nstep)
-
-    ! Accumulate and extract AGDD
-
-    do p = begp,endp
-       rbufslp(p) = max(0.0_r8, &
-            (t_ref2m_patch(p) - (SHR_CONST_TKFRZ + 5.0_r8)) * dtime/SHR_CONST_CDAY)
-       !
-       ! Fix (for bug 1858) from Sam Levis to reset the annual AGDD variable
-       ! 
-       if (month==1 .and. day==1 .and. secs==int(dtime)) rbufslp(p) = accumResetVal
-    end do
-    call update_accum_field  ('AGDD', rbufslp, nstep)
-    call extract_accum_field ('AGDD', this%agdd_patch, nstep)
-
-    deallocate(rbufslp)
-
-  end subroutine UpdateAccVars
-
-end module CNDVType
diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
deleted file mode 100644
index ea3abb5c6c..0000000000
--- a/src/biogeochem/CNDriverMod.F90
+++ /dev/null
@@ -1,37 +0,0 @@
-module CNDriverMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Ecosystem dynamics: phenology, vegetation
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use decompMod                       , only : bounds_type
-  use perf_mod                        , only : t_startf, t_stopf
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: CNDriverInit         ! Ecosystem dynamics: initialization
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine CNDriverInit(bounds, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Initialzation of the CN Ecosystem dynamics.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                      , intent(in)    :: bounds      
-    character(len=*)                       , intent(in)    :: NLFilename     ! Namelist filename
-    !-----------------------------------------------------------------------
-    
-  end subroutine CNDriverInit
-
-end  module CNDriverMod
diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90
deleted file mode 100644
index a2f8c4fd89..0000000000
--- a/src/biogeochem/CNGapMortalityMod.F90
+++ /dev/null
@@ -1,493 +0,0 @@
-module CNGapMortalityMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding routines used in gap mortality for coupled carbon
-  ! nitrogen code.
-  !
-  ! !USES:
-  use shr_kind_mod            , only : r8 => shr_kind_r8
-  use decompMod               , only : bounds_type
-  use abortutils              , only : endrun
-  use shr_log_mod             , only : errMsg => shr_log_errMsg
-  use pftconMod               , only : pftcon
-  use CNDVType                , only : dgvs_type
-  use CNVegCarbonStateType    , only : cnveg_carbonstate_type
-  use CNVegCarbonFluxType     , only : cnveg_carbonflux_type
-  use CNVegNitrogenStateType  , only : cnveg_nitrogenstate_type
-  use CNVegNitrogenFluxType   , only : cnveg_nitrogenflux_type
-  use CanopyStateType         , only : canopystate_type            
-  use ColumnType              , only : col                
-  use PatchType               , only : patch                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams
-  public :: CNGapMortality
-
-  type, private :: params_type
-     real(r8):: am     ! mortality rate based on annual rate, fractional mortality (1/yr)
-     real(r8):: k_mort ! coeff. of growth efficiency in mortality equation
-  end type params_type
-  !
-  type(params_type), private :: params_inst
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: CNGap_PatchToColumn
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    ! Read in parameters
-    !
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t,ncd_io
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNGapMortParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    tString='r_mort'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%am=tempr
-
-    tString='k_mort'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_mort=tempr   
-    
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, &
-       cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, &  
-       leaf_prof_patch, froot_prof_patch, croot_prof_patch, stem_prof_patch)  
-    !
-    ! !DESCRIPTION:
-    ! Gap-phase mortality routine for coupled carbon-nitrogen code (CN)
-    !
-    ! !USES:
-    use clm_time_manager , only: get_days_per_year
-    use clm_varpar       , only: nlevdecomp_full
-    use clm_varcon       , only: secspday
-    use clm_varctl       , only: use_cndv, spinup_state
-    use pftconMod        , only: npcropmin
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)               , intent(in)    :: bounds
-    integer                         , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                         , intent(in)    :: filter_soilc(:) ! column filter for soil points
-    integer                         , intent(in)    :: num_soilp       ! number of soil patches in filter
-    integer                         , intent(in)    :: filter_soilp(:) ! patch filter for soil points
-    type(dgvs_type)                 , intent(inout) :: dgvs_inst
-    type(cnveg_carbonstate_type)    , intent(in)    :: cnveg_carbonstate_inst
-    type(cnveg_nitrogenstate_type)  , intent(in)    :: cnveg_nitrogenstate_inst
-    type(cnveg_carbonflux_type)     , intent(inout) :: cnveg_carbonflux_inst
-    type(cnveg_nitrogenflux_type)   , intent(inout) :: cnveg_nitrogenflux_inst
-    type(canopystate_type)          , intent(in)    :: canopystate_inst            
-    real(r8)                        , intent(in)    :: leaf_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: froot_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: croot_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: stem_prof_patch(bounds%begp:,1:)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p             ! patch index
-    integer :: fp            ! patch filter index
-    real(r8):: am            ! rate for fractional mortality (1/yr)
-    real(r8):: m             ! rate for fractional mortality (1/s)
-    real(r8):: mort_max      ! asymptotic max mortality rate (/yr)
-    real(r8):: k_mort = 0.3  ! coeff of growth efficiency in mortality equation
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(leaf_prof_patch)   == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(froot_prof_patch)  == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(croot_prof_patch)  == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(stem_prof_patch)   == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-
-    associate(                                         & 
-         ivt        =>    patch%itype                  , & ! Input:  [integer  (:) ]  patch vegetation type                                
-
-         woody      =>    pftcon%woody               , & ! Input:  binary flag for woody lifeform                    
-         
-         greffic    =>    dgvs_inst%greffic_patch    , & ! Input:  [real(r8) (:) ]                                                    
-         heatstress =>    dgvs_inst%heatstress_patch , & ! Input:  [real(r8) (:) ]    
-         
-         leafcn  	=>    pftcon%leafcn               , & ! Input:  [real(r8) (:)]  leaf C:N (gC/gN)                        
-         frootcn    =>    pftcon%frootcn              , & ! Input:  [real(r8) (:)]  fine root C:N (gC/gN)                  
-         livewdcn   =>    pftcon%livewdcn             , & ! Input:  [real(r8) (:)]  live wood (phloem and ray parenchyma) C:N (gC/gN) 
-         laisun     =>    canopystate_inst%laisun_patch  , & ! Input:  [real(r8) (:)   ]  sunlit projected leaf area index      
-         laisha     =>    canopystate_inst%laisha_patch  , & ! Input:  [real(r8) (:)   ]  shaded projected leaf area index   
-                                                         
-         nind       =>    dgvs_inst%nind_patch         & ! Output: [real(r8) (:) ]  number of individuals (#/m2) added by F. Li and S. Levis
-         )
-
-      ! set the mortality rate based on annual rate
-      am = params_inst%am
-      ! set coeff of growth efficiency in mortality equation 
-      k_mort = params_inst%k_mort
-
-      ! patch loop
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-
-         if (use_cndv) then
-            ! Stress mortality from lpj's subr Mortality.
-
-            if (woody(ivt(p)) == 1._r8) then
-
-               if (ivt(p) == 8) then
-                  mort_max = 0.03_r8 ! BDT boreal
-               else
-                  mort_max = 0.01_r8 ! original value for all patches
-               end if
-
-               ! heatstress and greffic calculated in Establishment once/yr
-
-               ! Mortality rate inversely related to growth efficiency
-               ! (Prentice et al 1993)
-               am = mort_max / (1._r8 + k_mort * greffic(p))
-
-               ! Mortality rate inversely related to growth efficiency
-               ! (Prentice et al 1993)
-               am = mort_max / (1._r8 + k_mort * greffic(p))
-
-               am = min(1._r8, am + heatstress(p))
-            else ! lpj didn't set this for grasses; cn does
-               ! set the mortality rate based on annual rate
-               am = params_inst%am
-            end if
-
-         end if
-
-         m  = am/(get_days_per_year() * secspday)
-
-         !------------------------------------------------------
-         ! patch-level gap mortality carbon fluxes
-         !------------------------------------------------------
-
-         ! displayed pools
-         cnveg_carbonflux_inst%m_leafc_to_litter_patch(p)               = cnveg_carbonstate_inst%leafc_patch(p)               * m
-         cnveg_carbonflux_inst%m_frootc_to_litter_patch(p)              = cnveg_carbonstate_inst%frootc_patch(p)              * m
-         cnveg_carbonflux_inst%m_livestemc_to_litter_patch(p)           = cnveg_carbonstate_inst%livestemc_patch(p)           * m
-         cnveg_carbonflux_inst%m_livecrootc_to_litter_patch(p)          = cnveg_carbonstate_inst%livecrootc_patch(p)          * m
-         if (spinup_state == 2 .and. .not. use_cndv) then   !accelerate mortality of dead woody pools 
-           cnveg_carbonflux_inst%m_deadstemc_to_litter_patch(p)         = cnveg_carbonstate_inst%deadstemc_patch(p)  * m * 10._r8
-           cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch(p)        = cnveg_carbonstate_inst%deadcrootc_patch(p) * m * 10._r8        
-         else
-           cnveg_carbonflux_inst%m_deadstemc_to_litter_patch(p)         = cnveg_carbonstate_inst%deadstemc_patch(p)           * m
-           cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch(p)        = cnveg_carbonstate_inst%deadcrootc_patch(p)          * m
-         end if
-
-         ! storage pools
-         cnveg_carbonflux_inst%m_leafc_storage_to_litter_patch(p)       = cnveg_carbonstate_inst%leafc_storage_patch(p)       * m
-         cnveg_carbonflux_inst%m_frootc_storage_to_litter_patch(p)      = cnveg_carbonstate_inst%frootc_storage_patch(p)      * m
-         cnveg_carbonflux_inst%m_livestemc_storage_to_litter_patch(p)   = cnveg_carbonstate_inst%livestemc_storage_patch(p)   * m
-         cnveg_carbonflux_inst%m_deadstemc_storage_to_litter_patch(p)   = cnveg_carbonstate_inst%deadstemc_storage_patch(p)   * m
-         cnveg_carbonflux_inst%m_livecrootc_storage_to_litter_patch(p)  = cnveg_carbonstate_inst%livecrootc_storage_patch(p)  * m
-         cnveg_carbonflux_inst%m_deadcrootc_storage_to_litter_patch(p)  = cnveg_carbonstate_inst%deadcrootc_storage_patch(p)  * m
-         cnveg_carbonflux_inst%m_gresp_storage_to_litter_patch(p)       = cnveg_carbonstate_inst%gresp_storage_patch(p)       * m
-         
-         ! transfer pools
-         cnveg_carbonflux_inst%m_leafc_xfer_to_litter_patch(p)          = cnveg_carbonstate_inst%leafc_xfer_patch(p)          * m
-         cnveg_carbonflux_inst%m_frootc_xfer_to_litter_patch(p)         = cnveg_carbonstate_inst%frootc_xfer_patch(p)         * m
-         cnveg_carbonflux_inst%m_livestemc_xfer_to_litter_patch(p)      = cnveg_carbonstate_inst%livestemc_xfer_patch(p)      * m
-         cnveg_carbonflux_inst%m_deadstemc_xfer_to_litter_patch(p)      = cnveg_carbonstate_inst%deadstemc_xfer_patch(p)      * m
-         cnveg_carbonflux_inst%m_livecrootc_xfer_to_litter_patch(p)     = cnveg_carbonstate_inst%livecrootc_xfer_patch(p)     * m
-         cnveg_carbonflux_inst%m_deadcrootc_xfer_to_litter_patch(p)     = cnveg_carbonstate_inst%deadcrootc_xfer_patch(p)     * m
-         cnveg_carbonflux_inst%m_gresp_xfer_to_litter_patch(p)          = cnveg_carbonstate_inst%gresp_xfer_patch(p)          * m
-
-         !------------------------------------------------------
-         ! patch-level gap mortality nitrogen fluxes
-         !------------------------------------------------------
-
-         ! displayed pools
-         cnveg_nitrogenflux_inst%m_leafn_to_litter_patch(p)            = cnveg_nitrogenstate_inst%leafn_patch(p)               * m
-         cnveg_nitrogenflux_inst%m_frootn_to_litter_patch(p)           = cnveg_nitrogenstate_inst%frootn_patch(p)              * m
-         cnveg_nitrogenflux_inst%m_livestemn_to_litter_patch(p)        = cnveg_nitrogenstate_inst%livestemn_patch(p)           * m
-         cnveg_nitrogenflux_inst%m_livecrootn_to_litter_patch(p)       = cnveg_nitrogenstate_inst%livecrootn_patch(p)          * m
-
-         if (spinup_state == 2 .and. .not. use_cndv) then   !accelerate mortality of dead woody pools 
-           cnveg_nitrogenflux_inst%m_deadstemn_to_litter_patch(p)      = cnveg_nitrogenstate_inst%deadstemn_patch(p)  * m * 10._r8
-           cnveg_nitrogenflux_inst%m_deadcrootn_to_litter_patch(p)     = cnveg_nitrogenstate_inst%deadcrootn_patch(p) * m * 10._r8
-         else
-           cnveg_nitrogenflux_inst%m_deadstemn_to_litter_patch(p)      = cnveg_nitrogenstate_inst%deadstemn_patch(p)           * m 
-           cnveg_nitrogenflux_inst%m_deadcrootn_to_litter_patch(p)     = cnveg_nitrogenstate_inst%deadcrootn_patch(p)          * m 
-         end if
-
-         if (ivt(p) < npcropmin) then
-            cnveg_nitrogenflux_inst%m_retransn_to_litter_patch(p) = cnveg_nitrogenstate_inst%retransn_patch(p) * m
-         end if
-            
-         ! storage pools
-         cnveg_nitrogenflux_inst%m_leafn_storage_to_litter_patch(p)       = cnveg_nitrogenstate_inst%leafn_storage_patch(p)      * m
-         cnveg_nitrogenflux_inst%m_frootn_storage_to_litter_patch(p)      = cnveg_nitrogenstate_inst%frootn_storage_patch(p)     * m
-         cnveg_nitrogenflux_inst%m_livestemn_storage_to_litter_patch(p)   = cnveg_nitrogenstate_inst%livestemn_storage_patch(p)  * m
-         cnveg_nitrogenflux_inst%m_deadstemn_storage_to_litter_patch(p)   = cnveg_nitrogenstate_inst%deadstemn_storage_patch(p)  * m
-         cnveg_nitrogenflux_inst%m_livecrootn_storage_to_litter_patch(p)  = cnveg_nitrogenstate_inst%livecrootn_storage_patch(p) * m
-         cnveg_nitrogenflux_inst%m_deadcrootn_storage_to_litter_patch(p)  = cnveg_nitrogenstate_inst%deadcrootn_storage_patch(p) * m
-
-         ! transfer pools
-         cnveg_nitrogenflux_inst%m_leafn_xfer_to_litter_patch(p)          = cnveg_nitrogenstate_inst%leafn_xfer_patch(p)         * m
-         cnveg_nitrogenflux_inst%m_frootn_xfer_to_litter_patch(p)         = cnveg_nitrogenstate_inst%frootn_xfer_patch(p)        * m
-         cnveg_nitrogenflux_inst%m_livestemn_xfer_to_litter_patch(p)      = cnveg_nitrogenstate_inst%livestemn_xfer_patch(p)     * m
-         cnveg_nitrogenflux_inst%m_deadstemn_xfer_to_litter_patch(p)      = cnveg_nitrogenstate_inst%deadstemn_xfer_patch(p)     * m
-         cnveg_nitrogenflux_inst%m_livecrootn_xfer_to_litter_patch(p)     = cnveg_nitrogenstate_inst%livecrootn_xfer_patch(p)    * m
-         cnveg_nitrogenflux_inst%m_deadcrootn_xfer_to_litter_patch(p)     = cnveg_nitrogenstate_inst%deadcrootn_xfer_patch(p)    * m
-
-         ! added by F. Li and S. Levis
-         if (use_cndv) then
-            if (woody(ivt(p)) == 1._r8)then
-               if (cnveg_carbonstate_inst%livestemc_patch(p) + cnveg_carbonstate_inst%deadstemc_patch(p)> 0._r8)then
-                  nind(p)=nind(p)*(1._r8-m)
-               else
-                  nind(p) = 0._r8 
-               end if
-            end if
-         end if
-
-      end do ! end of patch loop
-
-      ! gather all patch-level litterfall fluxes to the column
-      ! for litter C and N inputs
-
-      call CNGap_PatchToColumn(bounds, num_soilc, filter_soilc, &
-           cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, &
-           leaf_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), &
-           froot_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), & 
-           croot_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), &
-           stem_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full))
-
-    end associate
-
-  end subroutine CNGapMortality
-
-  !-----------------------------------------------------------------------
-  subroutine CNGap_PatchToColumn (bounds, num_soilc, filter_soilc, &
-       cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, &
-       leaf_prof_patch, froot_prof_patch, croot_prof_patch, stem_prof_patch)
-    !
-    ! !DESCRIPTION:
-    ! gathers all patch-level gap mortality fluxes to the column level and
-    ! assigns them to the three litter pools
-    !
-    ! !USES:
-    use clm_varpar , only : maxpatch_pft, nlevdecomp, nlevdecomp_full
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)               , intent(in)    :: bounds
-    integer                         , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                         , intent(in)    :: filter_soilc(:) ! soil column filter
-    type(cnveg_carbonflux_type)     , intent(inout) :: cnveg_carbonflux_inst
-    type(cnveg_nitrogenflux_type)   , intent(inout) :: cnveg_nitrogenflux_inst
-    real(r8)                        , intent(in)    :: leaf_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: froot_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: croot_prof_patch(bounds%begp:,1:)
-    real(r8)                        , intent(in)    :: stem_prof_patch(bounds%begp:,1:)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc,c,pi,p,j               ! indices
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(leaf_prof_patch)   == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(froot_prof_patch)  == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(croot_prof_patch)  == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(stem_prof_patch)   == (/bounds%endp,nlevdecomp_full/)), errMsg(sourcefile, __LINE__))
-
-    associate(                                                                                                 & 
-         leaf_prof                           => leaf_prof_patch                                              , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of leaves                         
-         froot_prof                          => froot_prof_patch                                             , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of fine roots                     
-         croot_prof                          => croot_prof_patch                                             , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of coarse roots                   
-         stem_prof                           => stem_prof_patch                                              , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of stems                          
-
-         ivt                                 => patch%itype                                                    , & ! Input:  [integer  (:)   ]  patch vegetation type                                
-         wtcol                               => patch%wtcol                                                    , & ! Input:  [real(r8) (:)   ]  patch weight relative to column (0-1)               
-         
-         lf_flab                             => pftcon%lf_flab                                               , & ! Input:  [real(r8) (:)   ]  leaf litter labile fraction                       
-         lf_fcel                             => pftcon%lf_fcel                                               , & ! Input:  [real(r8) (:)   ]  leaf litter cellulose fraction                    
-         lf_flig                             => pftcon%lf_flig                                               , & ! Input:  [real(r8) (:)   ]  leaf litter lignin fraction                       
-         fr_flab                             => pftcon%fr_flab                                               , & ! Input:  [real(r8) (:)   ]  fine root litter labile fraction                  
-         fr_fcel                             => pftcon%fr_fcel                                               , & ! Input:  [real(r8) (:)   ]  fine root litter cellulose fraction               
-         fr_flig                             => pftcon%fr_flig                                               , & ! Input:  [real(r8) (:)   ]  fine root litter lignin fraction                  
-         
-         m_leafc_to_litter                   => cnveg_carbonflux_inst%m_leafc_to_litter_patch                , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootc_to_litter                  => cnveg_carbonflux_inst%m_frootc_to_litter_patch               , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemc_to_litter               => cnveg_carbonflux_inst%m_livestemc_to_litter_patch            , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemc_to_litter               => cnveg_carbonflux_inst%m_deadstemc_to_litter_patch            , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootc_to_litter              => cnveg_carbonflux_inst%m_livecrootc_to_litter_patch           , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootc_to_litter              => cnveg_carbonflux_inst%m_deadcrootc_to_litter_patch           , & ! Input:  [real(r8) (:)   ]                                                    
-         m_leafc_storage_to_litter           => cnveg_carbonflux_inst%m_leafc_storage_to_litter_patch        , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootc_storage_to_litter          => cnveg_carbonflux_inst%m_frootc_storage_to_litter_patch       , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemc_storage_to_litter       => cnveg_carbonflux_inst%m_livestemc_storage_to_litter_patch    , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemc_storage_to_litter       => cnveg_carbonflux_inst%m_deadstemc_storage_to_litter_patch    , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootc_storage_to_litter      => cnveg_carbonflux_inst%m_livecrootc_storage_to_litter_patch   , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootc_storage_to_litter      => cnveg_carbonflux_inst%m_deadcrootc_storage_to_litter_patch   , & ! Input:  [real(r8) (:)   ]                                                    
-         m_gresp_storage_to_litter           => cnveg_carbonflux_inst%m_gresp_storage_to_litter_patch        , & ! Input:  [real(r8) (:)   ]                                                    
-         m_leafc_xfer_to_litter              => cnveg_carbonflux_inst%m_leafc_xfer_to_litter_patch           , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootc_xfer_to_litter             => cnveg_carbonflux_inst%m_frootc_xfer_to_litter_patch          , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemc_xfer_to_litter          => cnveg_carbonflux_inst%m_livestemc_xfer_to_litter_patch       , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemc_xfer_to_litter          => cnveg_carbonflux_inst%m_deadstemc_xfer_to_litter_patch       , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootc_xfer_to_litter         => cnveg_carbonflux_inst%m_livecrootc_xfer_to_litter_patch      , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootc_xfer_to_litter         => cnveg_carbonflux_inst%m_deadcrootc_xfer_to_litter_patch      , & ! Input:  [real(r8) (:)   ]                                                    
-         m_gresp_xfer_to_litter              => cnveg_carbonflux_inst%m_gresp_xfer_to_litter_patch           , & ! Input:  [real(r8) (:)   ]                                                    
-         gap_mortality_c_to_litr_met_c       => cnveg_carbonflux_inst%gap_mortality_c_to_litr_met_c_col      , & ! Output: [real(r8) (:,:) ]  C fluxes associated with gap mortality to litter metabolic pool (gC/m3/s)
-         gap_mortality_c_to_litr_cel_c       => cnveg_carbonflux_inst%gap_mortality_c_to_litr_cel_c_col      , & ! Output: [real(r8) (:,:) ]  C fluxes associated with gap mortality to litter cellulose pool (gC/m3/s)
-         gap_mortality_c_to_litr_lig_c       => cnveg_carbonflux_inst%gap_mortality_c_to_litr_lig_c_col      , & ! Output: [real(r8) (:,:) ]  C fluxes associated with gap mortality to litter lignin pool (gC/m3/s)
-         gap_mortality_c_to_cwdc             => cnveg_carbonflux_inst%gap_mortality_c_to_cwdc_col            , & ! Output: [real(r8) (:,:) ]  C fluxes associated with gap mortality to CWD pool (gC/m3/s)
-         
-         m_leafn_to_litter                   => cnveg_nitrogenflux_inst%m_leafn_to_litter_patch              , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootn_to_litter                  => cnveg_nitrogenflux_inst%m_frootn_to_litter_patch             , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemn_to_litter               => cnveg_nitrogenflux_inst%m_livestemn_to_litter_patch          , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemn_to_litter               => cnveg_nitrogenflux_inst%m_deadstemn_to_litter_patch          , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootn_to_litter              => cnveg_nitrogenflux_inst%m_livecrootn_to_litter_patch         , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootn_to_litter              => cnveg_nitrogenflux_inst%m_deadcrootn_to_litter_patch         , & ! Input:  [real(r8) (:)   ]                                                    
-         m_retransn_to_litter                => cnveg_nitrogenflux_inst%m_retransn_to_litter_patch           , & ! Input:  [real(r8) (:)   ]                                                    
-         m_leafn_storage_to_litter           => cnveg_nitrogenflux_inst%m_leafn_storage_to_litter_patch      , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootn_storage_to_litter          => cnveg_nitrogenflux_inst%m_frootn_storage_to_litter_patch     , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemn_storage_to_litter       => cnveg_nitrogenflux_inst%m_livestemn_storage_to_litter_patch  , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemn_storage_to_litter       => cnveg_nitrogenflux_inst%m_deadstemn_storage_to_litter_patch  , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootn_storage_to_litter      => cnveg_nitrogenflux_inst%m_livecrootn_storage_to_litter_patch , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootn_storage_to_litter      => cnveg_nitrogenflux_inst%m_deadcrootn_storage_to_litter_patch , & ! Input:  [real(r8) (:)   ]                                                    
-         m_leafn_xfer_to_litter              => cnveg_nitrogenflux_inst%m_leafn_xfer_to_litter_patch         , & ! Input:  [real(r8) (:)   ]                                                    
-         m_frootn_xfer_to_litter             => cnveg_nitrogenflux_inst%m_frootn_xfer_to_litter_patch        , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livestemn_xfer_to_litter          => cnveg_nitrogenflux_inst%m_livestemn_xfer_to_litter_patch     , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadstemn_xfer_to_litter          => cnveg_nitrogenflux_inst%m_deadstemn_xfer_to_litter_patch     , & ! Input:  [real(r8) (:)   ]                                                    
-         m_livecrootn_xfer_to_litter         => cnveg_nitrogenflux_inst%m_livecrootn_xfer_to_litter_patch    , & ! Input:  [real(r8) (:)   ]                                                    
-         m_deadcrootn_xfer_to_litter         => cnveg_nitrogenflux_inst%m_deadcrootn_xfer_to_litter_patch    , & ! Input:  [real(r8) (:)   ]                                                    
-         gap_mortality_n_to_litr_met_n       => cnveg_nitrogenflux_inst%gap_mortality_n_to_litr_met_n_col    , & ! Output: [real(r8) (:,:) ]  N fluxes associated with gap mortality to litter metabolic pool (gN/m3/s)
-         gap_mortality_n_to_litr_cel_n       => cnveg_nitrogenflux_inst%gap_mortality_n_to_litr_cel_n_col    , & ! Output: [real(r8) (:,:) ]  N fluxes associated with gap mortality to litter cellulose pool (gN/m3/s)
-         gap_mortality_n_to_litr_lig_n       => cnveg_nitrogenflux_inst%gap_mortality_n_to_litr_lig_n_col    , & ! Output: [real(r8) (:,:) ]  N fluxes associated with gap mortality to litter lignin pool (gN/m3/s)
-         gap_mortality_n_to_cwdn             => cnveg_nitrogenflux_inst%gap_mortality_n_to_cwdn_col            & ! Output: [real(r8) (:,:) ]  N fluxes associated with gap mortality to CWD pool (gN/m3/s)
-         )
-
-      do j = 1,nlevdecomp
-         do pi = 1,maxpatch_pft
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-
-               if (pi <=  col%npatches(c)) then
-                  p = col%patchi(c) + pi - 1
-
-                  if (patch%active(p)) then
-
-                     ! leaf gap mortality carbon fluxes
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          m_leafc_to_litter(p) * lf_flab(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_c_to_litr_cel_c(c,j) = gap_mortality_c_to_litr_cel_c(c,j) + &
-                          m_leafc_to_litter(p) * lf_fcel(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_c_to_litr_lig_c(c,j) = gap_mortality_c_to_litr_lig_c(c,j) + &
-                          m_leafc_to_litter(p) * lf_flig(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-
-                     ! fine root gap mortality carbon fluxes
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          m_frootc_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_c_to_litr_cel_c(c,j) = gap_mortality_c_to_litr_cel_c(c,j) + &
-                          m_frootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_c_to_litr_lig_c(c,j) = gap_mortality_c_to_litr_lig_c(c,j) + &
-                          m_frootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j)
-
-                     ! wood gap mortality carbon fluxes
-                     gap_mortality_c_to_cwdc(c,j)  = gap_mortality_c_to_cwdc(c,j)  + &
-                          (m_livestemc_to_litter(p) + m_deadstemc_to_litter(p))  * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + &
-                          (m_livecrootc_to_litter(p) + m_deadcrootc_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-                     ! storage gap mortality carbon fluxes
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          (m_leafc_storage_to_litter(p) + m_gresp_storage_to_litter(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j)  + &
-                          (m_livestemc_storage_to_litter(p) + m_deadstemc_storage_to_litter(p)) * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          (m_livecrootc_storage_to_litter(p) + m_deadcrootc_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-                     ! transfer gap mortality carbon fluxes
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          (m_leafc_xfer_to_litter(p) + m_gresp_xfer_to_litter(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j)  = gap_mortality_c_to_litr_met_c(c,j)  + &
-                          (m_livestemc_xfer_to_litter(p) + m_deadstemc_xfer_to_litter(p))  * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_c_to_litr_met_c(c,j) = gap_mortality_c_to_litr_met_c(c,j) + &
-                          (m_livecrootc_xfer_to_litter(p) + m_deadcrootc_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-                     ! leaf gap mortality nitrogen fluxes
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_leafn_to_litter(p) * lf_flab(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_n_to_litr_cel_n(c,j) = gap_mortality_n_to_litr_cel_n(c,j) + &
-                          m_leafn_to_litter(p) * lf_fcel(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_n_to_litr_lig_n(c,j) = gap_mortality_n_to_litr_lig_n(c,j) + &
-                          m_leafn_to_litter(p) * lf_flig(ivt(p)) * wtcol(p) * leaf_prof(p,j)
-
-                     ! fine root litter nitrogen fluxes
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_frootn_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_n_to_litr_cel_n(c,j) = gap_mortality_n_to_litr_cel_n(c,j) + &
-                          m_frootn_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_n_to_litr_lig_n(c,j) = gap_mortality_n_to_litr_lig_n(c,j) + &
-                          m_frootn_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j)
-
-                     ! wood gap mortality nitrogen fluxes
-                     gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j)  + &
-                          (m_livestemn_to_litter(p) + m_deadstemn_to_litter(p))  * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j) + &
-                          (m_livecrootn_to_litter(p) + m_deadcrootn_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-                     ! retranslocated N pool gap mortality fluxes
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j)
-
-                     ! storage gap mortality nitrogen fluxes
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_leafn_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_frootn_storage_to_litter(p) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j)  = gap_mortality_n_to_litr_met_n(c,j) + &
-                          (m_livestemn_storage_to_litter(p) + m_deadstemn_storage_to_litter(p))  * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          (m_livecrootn_storage_to_litter(p) + m_deadcrootn_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-                     ! transfer gap mortality nitrogen fluxes
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_leafn_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          m_frootn_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          (m_livestemn_xfer_to_litter(p) + m_deadstemn_xfer_to_litter(p))  * wtcol(p) * stem_prof(p,j)
-                     gap_mortality_n_to_litr_met_n(c,j) = gap_mortality_n_to_litr_met_n(c,j) + &
-                          (m_livecrootn_xfer_to_litter(p) + m_deadcrootn_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j)
-
-
-                  end if
-               end if
-
-            end do
-         end do
-      end do
-
-    end associate
-
-  end subroutine CNGap_PatchToColumn
-
-end module CNGapMortalityMod
diff --git a/src/biogeochem/CNMRespMod.F90 b/src/biogeochem/CNMRespMod.F90
deleted file mode 100644
index 74ff1a9d3a..0000000000
--- a/src/biogeochem/CNMRespMod.F90
+++ /dev/null
@@ -1,237 +0,0 @@
-module CNMRespMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding maintenance respiration routines for coupled carbon
-  ! nitrogen code.
-  !
-  ! !USES:
-  use shr_kind_mod           , only : r8 => shr_kind_r8
-  use shr_const_mod          , only : SHR_CONST_TKFRZ
-  use clm_varpar             , only : nlevgrnd
-  use clm_varcon             , only : spval
-  use decompMod              , only : bounds_type
-  use abortutils             , only : endrun
-  use shr_log_mod            , only : errMsg => shr_log_errMsg
-  use pftconMod              , only : npcropmin, pftcon
-  use SoilStateType          , only : soilstate_type
-  use CanopyStateType        , only : canopystate_type
-  use TemperatureType        , only : temperature_type
-  use PhotosynthesisMod      , only : photosyns_type
-  use CNVegcarbonfluxType    , only : cnveg_carbonflux_type
-  use CNVegnitrogenstateType , only : cnveg_nitrogenstate_type
-  use CNSharedParamsMod      , only : CNParamsShareInst
-  use PatchType              , only : patch                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams           ! Read in parameters from file
-  public :: CNMResp              ! Apply maintenance respiration
-
-  type, private :: params_type
-     real(r8) :: br      = spval ! base rate for maintenance respiration (gC/gN/s)
-     real(r8) :: br_root = spval ! base rate for maintenance respiration for roots (gC/gN/s)
-  end type params_type
-
-  type(params_type), private :: params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    ! Read parameters (call AFTER CNMRespReadNML!)
-    !
-    ! !USES:
-    use ncdio_pio , only : file_desc_t,ncd_io
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNMRespParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    tString='br_mr'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%br=tempr
-
-    if ( params_inst%br_root == spval ) then
-       params_inst%br_root = params_inst%br
-    end if
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  ! FIX(SPM,032414) this shouldn't even be called with fates on.
-  !
-  subroutine CNMResp(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       canopystate_inst, soilstate_inst, temperature_inst, photosyns_inst, &
-       cnveg_carbonflux_inst, cnveg_nitrogenstate_inst)
-    !
-    ! !DESCRIPTION:
-    !
-    ! !ARGUMENTS:
-    use clm_varcon  , only : tfrz
-    
-    type(bounds_type)              , intent(in)    :: bounds          
-    integer                        , intent(in)    :: num_soilc       ! number of soil points in column filter
-    integer                        , intent(in)    :: filter_soilc(:) ! column filter for soil points
-    integer                        , intent(in)    :: num_soilp       ! number of soil points in patch filter
-    integer                        , intent(in)    :: filter_soilp(:) ! patch filter for soil points
-    type(canopystate_type)         , intent(in)    :: canopystate_inst
-    type(soilstate_type)           , intent(in)    :: soilstate_inst
-    type(temperature_type)         , intent(in)    :: temperature_inst
-    type(photosyns_type)           , intent(in)    :: photosyns_inst
-    type(cnveg_carbonflux_type)    , intent(inout) :: cnveg_carbonflux_inst
-    type(cnveg_nitrogenstate_type) , intent(in)    :: cnveg_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,p,j   ! indices
-    integer :: fp      ! soil filter patch index
-    integer :: fc      ! soil filter column index
-    real(r8):: br      ! base rate (gC/gN/s)
-    real(r8):: br_root ! root base rate (gC/gN/s)
-    real(r8):: q10     ! temperature dependence
-
-    real(r8):: tc      ! temperature correction, 2m air temp (unitless)
-    real(r8):: tcsoi(bounds%begc:bounds%endc,nlevgrnd) ! temperature correction by soil layer (unitless)
-    !-----------------------------------------------------------------------
-
-    associate(                                                            &    
-         ivt            =>    patch%itype                                 , & ! Input:  [integer  (:)   ]  patch vegetation type                                
-
-         woody          =>    pftcon%woody                              , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
-
-         frac_veg_nosno =>    canopystate_inst%frac_veg_nosno_patch     , & ! Input:  [integer  (:)   ]  fraction of vegetation not covered by snow (0 OR 1) [-]
-         laisun         =>    canopystate_inst%laisun_patch             , & ! Input:  [real(r8) (:)   ]  sunlit projected leaf area index                  
-         laisha         =>    canopystate_inst%laisha_patch             , & ! Input:  [real(r8) (:)   ]  shaded projected leaf area index                  
-
-         crootfr        =>    soilstate_inst%crootfr_patch              , & ! Input:  [real(r8) (:,:) ]  fraction of roots for carbon in each soil layer  (nlevgrnd)
-
-         t_soisno       =>    temperature_inst%t_soisno_col             , & ! Input:  [real(r8) (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
-         t_ref2m        =>    temperature_inst%t_ref2m_patch            , & ! Input:  [real(r8) (:)   ]  2 m height surface air temperature (Kelvin)       
-
-         t10            => temperature_inst%t_a10_patch                 , & ! Input:  [real(r8) (:)   ]  10-day running mean of the 2 m temperature (K)
- 
-         lmrsun         =>    photosyns_inst%lmrsun_patch               , & ! Input:  [real(r8) (:)   ]  sunlit leaf maintenance respiration rate (umol CO2/m**2/s)
-         lmrsha         =>    photosyns_inst%lmrsha_patch               , & ! Input:  [real(r8) (:)   ]  shaded leaf maintenance respiration rate (umol CO2/m**2/s)
-         rootstem_acc   =>    photosyns_inst%rootstem_acc               , & ! Input:  [logical        ]  root and stem acclimation switch
-
-         frootn         =>    cnveg_nitrogenstate_inst%frootn_patch     , & ! Input:  [real(r8) (:)   ]  (gN/m2) fine root N                               
-         livestemn      =>    cnveg_nitrogenstate_inst%livestemn_patch  , & ! Input:  [real(r8) (:)   ]  (gN/m2) live stem N                               
-         livecrootn     =>    cnveg_nitrogenstate_inst%livecrootn_patch , & ! Input:  [real(r8) (:)   ]  (gN/m2) live coarse root N                        
-         grainn         =>    cnveg_nitrogenstate_inst%grainn_patch     , & ! Input:  [real(r8) (:)   ]  (kgN/m2) grain N
-
-         leaf_mr        =>    cnveg_carbonflux_inst%leaf_mr_patch       , & ! Output: [real(r8) (:)   ]                                                    
-         froot_mr       =>    cnveg_carbonflux_inst%froot_mr_patch      , & ! Output: [real(r8) (:)   ]                                                    
-         livestem_mr    =>    cnveg_carbonflux_inst%livestem_mr_patch   , & ! Output: [real(r8) (:)   ]                                                    
-         livecroot_mr   =>    cnveg_carbonflux_inst%livecroot_mr_patch  , & ! Output: [real(r8) (:)   ]                                                    
-         grain_mr       =>    cnveg_carbonflux_inst%grain_mr_patch        & ! Output: [real(r8) (:)   ]                                                    
-
-         )
-
-      ! base rate for maintenance respiration is from:
-      ! M. Ryan, 1991. Effects of climate change on plant respiration.
-      ! Ecological Applications, 1(2), 157-167.
-      ! Original expression is br = 0.0106 molC/(molN h)
-      ! Conversion by molecular weights of C and N gives 2.525e-6 gC/(gN s)
-      ! set constants
-      br      = params_inst%br
-      br_root = params_inst%br_root
-     
-      ! Peter Thornton: 3/13/09 
-      ! Q10 was originally set to 2.0, an arbitrary choice, but reduced to 1.5 as part of the tuning
-      ! to improve seasonal cycle of atmospheric CO2 concentration in global
-      ! simulatoins
-      Q10 = CNParamsShareInst%Q10
-
-      ! column loop to calculate temperature factors in each soil layer
-      do j=1,nlevgrnd
-         do fc = 1, num_soilc
-            c = filter_soilc(fc)
-
-            ! calculate temperature corrections for each soil layer, for use in
-            ! estimating fine root maintenance respiration with depth
-            tcsoi(c,j) = Q10**((t_soisno(c,j)-SHR_CONST_TKFRZ - 20.0_r8)/10.0_r8)
-         end do
-      end do
-
-      ! patch loop for leaves and live wood
-      do fp = 1, num_soilp
-         p = filter_soilp(fp)
-
-         ! calculate maintenance respiration fluxes in
-         ! gC/m2/s for each of the live plant tissues.
-         ! Leaf and live wood MR
-
-         tc = Q10**((t_ref2m(p)-SHR_CONST_TKFRZ - 20.0_r8)/10.0_r8)
-         
-         !RF: acclimation of root and stem respiration fluxes
-         ! n.b. we do not yet know if this is defensible scientifically (awaiting data analysis)
-         ! turning this on will increase R and decrease productivity in boreal forests, A LOT. :)
-
-         if(rootstem_acc)then 
-           br      = br      * 10._r8**(-0.00794_r8*((t10(p)-tfrz)-25._r8))
-           br_root = br_root * 10._r8**(-0.00794_r8*((t10(p)-tfrz)-25._r8))
-         end if
-
-         if (frac_veg_nosno(p) == 1) then
-
-            leaf_mr(p) = lmrsun(p) * laisun(p) * 12.011e-6_r8 + &
-                         lmrsha(p) * laisha(p) * 12.011e-6_r8
-
-         else !nosno
-
-            leaf_mr(p) = 0._r8
-
-         end if
-
-         if (woody(ivt(p)) == 1) then
-            livestem_mr(p) = livestemn(p)*br*tc
-            livecroot_mr(p) = livecrootn(p)*br_root*tc
-         else if (ivt(p) >= npcropmin) then
-            livestem_mr(p) = livestemn(p)*br*tc
-            grain_mr(p) = grainn(p)*br*tc
-         end if
-      end do
-
-      ! soil and patch loop for fine root
-
-      do j = 1,nlevgrnd
-         do fp = 1,num_soilp
-            p = filter_soilp(fp)
-            c = patch%column(p)
-
-            ! Fine root MR
-            ! crootfr(j) sums to 1.0 over all soil layers, and
-            ! describes the fraction of root mass for carbon that is in each
-            ! layer.  This is used with the layer temperature correction
-            ! to estimate the total fine root maintenance respiration as a
-            ! function of temperature and N content.
-            if(rootstem_acc)then
-               br_root = br_root * 10._r8**(-0.00794_r8*((t10(p)-tfrz)-25._r8))
-            end if
-            froot_mr(p) = froot_mr(p) + frootn(p)*br_root*tcsoi(c,j)*crootfr(p,j)
-            
-         end do
-      end do
-
-    end associate
-
-  end subroutine CNMResp
-
-end module CNMRespMod
diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90
deleted file mode 100644
index 0d367efea9..0000000000
--- a/src/biogeochem/CNNDynamicsMod.F90
+++ /dev/null
@@ -1,375 +0,0 @@
-module CNNDynamicsMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module for mineral nitrogen dynamics (deposition, fixation, leaching)
-  ! for coupled carbon-nitrogen code.
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use decompMod                       , only : bounds_type
-  use clm_varcon                      , only : dzsoi_decomp, zisoi
-  use clm_varctl                      , only : use_nitrif_denitrif, use_vertsoilc, nfix_timeconst
-  use subgridAveMod                   , only : p2c
-  use atm2lndType                     , only : atm2lnd_type
-  use CNVegStateType                  , only : cnveg_state_type
-  use CNVegCarbonFluxType             , only : cnveg_carbonflux_type
-  use CNVegNitrogenStateType	      , only : cnveg_nitrogenstate_type
-  use CNVegNitrogenFluxType	      , only : cnveg_nitrogenflux_type
-  use SoilBiogeochemStateType         , only : soilbiogeochem_state_type
-  use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemNitrogenFluxType  , only : soilbiogeochem_nitrogenflux_type
-  use WaterStateType                  , only : waterstate_type
-  use WaterFluxType                   , only : waterflux_type
-  use CropType                        , only : crop_type
-  use ColumnType                      , only : col                
-  use PatchType                       , only : patch                
-  use perf_mod                        , only : t_startf, t_stopf
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: CNNDeposition               ! Update N deposition rate from atm forcing
-  public :: CNNFixation                 ! Update N Fixation rate
-  public :: CNNFert                     ! Update N fertilizer for crops
-  public :: CNSoyfix                    ! N Fixation for soybeans
-  public :: CNFreeLivingFixation        ! N free living fixation
-
-  !
-  ! !PRIVATE DATA MEMBERS:
-  type, private :: params_type
-     real(r8) :: freelivfix_intercept   ! intercept of line of free living fixation with annual ET
-     real(r8) :: freelivfix_slope_wET   ! slope of line of free living fixation with annual ET
-  end type params_type
-  type(params_type) :: params_inst
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine CNNDeposition( bounds, &
-       atm2lnd_inst, soilbiogeochem_nitrogenflux_inst )
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, update the nitrogen deposition rate
-    ! from atmospheric forcing. For now it is assumed that all the atmospheric
-    ! N deposition goes to the soil mineral N pool.
-    ! This could be updated later to divide the inputs between mineral N absorbed
-    ! directly into the canopy and mineral N entering the soil pool.
-    !
-    ! !USES:
-    use CNSharedParamsMod    , only: use_fun
-    ! !ARGUMENTS:
-    type(bounds_type)        , intent(in)    :: bounds  
-    type(atm2lnd_type)       , intent(in)    :: atm2lnd_inst
-    type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g,c                    ! indices
-    !-----------------------------------------------------------------------
-    
-    associate(                                                                & 
-         forc_ndep     =>  atm2lnd_inst%forc_ndep_grc ,                       & ! Input:  [real(r8) (:)]  nitrogen deposition rate (gN/m2/s)
-         ndep_to_sminn =>  soilbiogeochem_nitrogenflux_inst%ndep_to_sminn_col & ! Output: [real(r8) (:)]  atmospheric N deposition to soil mineral N (gN/m2/s)
-         )
-      
-      ! Loop through columns
-      do c = bounds%begc, bounds%endc
-         g = col%gridcell(c)
-         ndep_to_sminn(c) = forc_ndep(g)
-
-      end do
-
-    end associate
-
-  end subroutine CNNDeposition
-
-  !-----------------------------------------------------------------------
-  subroutine CNFreeLivingFixation(num_soilc, filter_soilc, &
-       waterflux_inst, soilbiogeochem_nitrogenflux_inst)
-
-
-    use clm_time_manager , only : get_days_per_year, get_step_size
-    use shr_sys_mod      , only : shr_sys_flush
-    use clm_varcon       , only : secspday, spval
- 
-    integer                                , intent(in)    :: num_soilc       ! number of soil columns in filter                                                                                                                     
-    integer                                , intent(in)    :: filter_soilc(:) ! filter for soil columns                                                                                                                                  
-   
-    type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst 
-    type(waterflux_type)                   , intent(inout) :: waterflux_inst 
-    !
-    ! !LOCAL VARIABLES:                                                                                                                                                                                                           
-    integer  :: c,fc            !indices     
-    real(r8) :: dayspyr         !days per year 
-    real(r8) :: secs_per_year   !seconds per year   
-
-       associate(                                                                        &
-                  AnnET            => waterflux_inst%AnnET,                              & ! Input:  [real(:)  ] : Annual average ET flux mmH20/s
-                  freelivfix_slope => params_inst%freelivfix_slope_wET,                  & ! Input:  [real     ] : slope of fixation with ET
-                  freelivfix_inter => params_inst%freelivfix_intercept,                  & ! Input:  [real     ] : intercept of fixation with ET
-                  ffix_to_sminn    => soilbiogeochem_nitrogenflux_inst%ffix_to_sminn_col & ! Output: [real(:)  ] : free living N fixation to soil mineral N (gN/m2/s)
-                ) 
-       
-       dayspyr = get_days_per_year()
-       secs_per_year = dayspyr*24_r8*3600_r8
-
-       do fc = 1,num_soilc
-           c = filter_soilc(fc)
-          ffix_to_sminn(c) = (freelivfix_slope*(max(0._r8,AnnET(c))*secs_per_year) + freelivfix_inter )/secs_per_year !(units g N m-2 s-1)  
-
-       end do
-
-  end associate
-  end subroutine CNFreeLivingFixation
-
-  !-----------------------------------------------------------------------
-  subroutine CNNFixation(num_soilc, filter_soilc, &
-       cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, update the nitrogen fixation rate
-    ! as a function of annual total NPP. This rate gets updated once per year.
-    ! All N fixation goes to the soil mineral N pool.
-    !
-    ! !USES:
-    use clm_time_manager , only : get_days_per_year, get_step_size
-    use shr_sys_mod      , only : shr_sys_flush
-    use clm_varcon       , only : secspday, spval
-    use CNSharedParamsMod    , only: use_fun
-    !
-    ! !ARGUMENTS:
-    integer                                , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(cnveg_carbonflux_type)            , intent(inout) :: cnveg_carbonflux_inst
-    type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst 
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,fc                  ! indices
-    real(r8) :: t                     ! temporary
-    real(r8) :: dayspyr               ! days per year
-    !-----------------------------------------------------------------------
-
-    associate(                                                                & 
-         cannsum_npp    => cnveg_carbonflux_inst%annsum_npp_col ,             & ! Input:  [real(r8) (:)]  nitrogen deposition rate (gN/m2/s)                
-         col_lag_npp    => cnveg_carbonflux_inst%lag_npp_col    ,             & ! Input: [real(r8) (:)]  (gC/m2/s) lagged net primary production           
-
-         nfix_to_sminn  => soilbiogeochem_nitrogenflux_inst%nfix_to_sminn_col & ! Output: [real(r8) (:)]  symbiotic/asymbiotic N fixation to soil mineral N (gN/m2/s)
-         )
-
-      dayspyr = get_days_per_year()
-
-      if ( nfix_timeconst > 0._r8 .and. nfix_timeconst < 500._r8 ) then
-         ! use exponential relaxation with time constant nfix_timeconst for NPP - NFIX relation
-         ! Loop through columns
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)         
-
-            if (col_lag_npp(c) /= spval) then
-               ! need to put npp in units of gC/m^2/year here first
-               t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * col_lag_npp(c)*(secspday * dayspyr))))/(secspday * dayspyr)  
-               nfix_to_sminn(c) = max(0._r8,t)
-            else
-               nfix_to_sminn(c) = 0._r8
-            endif
-         end do
-      else
-         ! use annual-mean values for NPP-NFIX relation
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-
-            t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * cannsum_npp(c))))/(secspday * dayspyr)
-            nfix_to_sminn(c) = max(0._r8,t)
-         end do
-      endif
-      if(use_fun)then
-        nfix_to_sminn(c) = 0.0_r8
-      end if
-
-    end associate
-
-  end subroutine CNNFixation
- 
-  !-----------------------------------------------------------------------
-  subroutine CNNFert(bounds, num_soilc, filter_soilc, &
-       cnveg_nitrogenflux_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, update the nitrogen fertilizer for crops
-    ! All fertilizer goes into the soil mineral N pool.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                      , intent(in)    :: bounds  
-    integer                                , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(cnveg_nitrogenflux_type)          , intent(in)    :: cnveg_nitrogenflux_inst
-    type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst 
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,fc                 ! indices
-    !-----------------------------------------------------------------------
-
-    associate(                                                                  &   
-         fert          =>    cnveg_nitrogenflux_inst%fert_patch ,               & ! Input:  [real(r8) (:)]  nitrogen fertilizer rate (gN/m2/s)                
-         fert_to_sminn =>    soilbiogeochem_nitrogenflux_inst%fert_to_sminn_col & ! Output: [real(r8) (:)]                                                    
-         )
-      
-      call p2c(bounds, num_soilc, filter_soilc, &
-           fert(bounds%begp:bounds%endp), &
-           fert_to_sminn(bounds%begc:bounds%endc))
-
-    end associate
-
-  end subroutine CNNFert
-
-  !-----------------------------------------------------------------------
-  subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       waterstate_inst, crop_inst, cnveg_state_inst, cnveg_nitrogenflux_inst , &
-       soilbiogeochem_state_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! This routine handles the fixation of nitrogen for soybeans based on
-    ! the EPICPHASE model M. Cabelguenne et al., Agricultural systems 60: 175-196, 1999
-    ! N-fixation is based on soil moisture, plant growth phase, and availibility of
-    ! nitrogen in the soil root zone.
-    !
-    ! !USES:
-    use pftconMod, only : ntmp_soybean, nirrig_tmp_soybean
-    use pftconMod, only : ntrp_soybean, nirrig_trp_soybean
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                       , intent(in)    :: bounds  
-    integer                                 , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    integer                                 , intent(in)    :: num_soilp       ! number of soil patches in filter
-    integer                                 , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    type(waterstate_type)                   , intent(in)    :: waterstate_inst
-    type(crop_type)                         , intent(in)    :: crop_inst
-    type(cnveg_state_type)                  , intent(in)    :: cnveg_state_inst
-    type(cnveg_nitrogenflux_type)           , intent(inout) :: cnveg_nitrogenflux_inst
-    type(soilbiogeochem_state_type)         , intent(in)    :: soilbiogeochem_state_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(in)    :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst 
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fp,p,c
-    real(r8):: fxw,fxn,fxg,fxr             ! soil water factor, nitrogen factor, growth stage factor
-    real(r8):: soy_ndemand                 ! difference between nitrogen supply and demand
-    real(r8):: GDDfrac
-    real(r8):: sminnthreshold1, sminnthreshold2
-    real(r8):: GDDfracthreshold1, GDDfracthreshold2
-    real(r8):: GDDfracthreshold3, GDDfracthreshold4
-    !-----------------------------------------------------------------------
-
-    associate(                                                                      & 
-         wf               =>  waterstate_inst%wf_col                      ,         & ! Input:  [real(r8) (:) ]  soil water as frac. of whc for top 0.5 m          
-
-         hui              =>  crop_inst%gddplant_patch                    ,         & ! Input:  [real(r8) (:) ]  gdd since planting (gddplant)                    
-         croplive         =>  crop_inst%croplive_patch                    ,         & ! Input:  [logical  (:) ]  true if planted and not harvested                  
-
-         gddmaturity      =>  cnveg_state_inst%gddmaturity_patch          ,         & ! Input:  [real(r8) (:) ]  gdd needed to harvest                             
-
-         plant_ndemand    =>  cnveg_nitrogenflux_inst%plant_ndemand_patch ,         & ! Input:  [real(r8) (:) ]  N flux required to support initial GPP (gN/m2/s)  
-         soyfixn          =>  cnveg_nitrogenflux_inst%soyfixn_patch       ,         & ! Output: [real(r8) (:) ]  nitrogen fixed to each soybean crop               
-
-         fpg              =>  soilbiogeochem_state_inst%fpg_col           ,         & ! Input:  [real(r8) (:) ]  fraction of potential gpp (no units)              
-
-         sminn            =>  soilbiogeochem_nitrogenstate_inst%sminn_col ,         & ! Input:  [real(r8) (:) ]  (kgN/m2) soil mineral N                           
-         soyfixn_to_sminn =>  soilbiogeochem_nitrogenflux_inst%soyfixn_to_sminn_col & ! Output: [real(r8) (:) ]                                                    
-         )
-
-      sminnthreshold1 = 30._r8
-      sminnthreshold2 = 10._r8
-      GDDfracthreshold1 = 0.15_r8
-      GDDfracthreshold2 = 0.30_r8
-      GDDfracthreshold3 = 0.55_r8
-      GDDfracthreshold4 = 0.75_r8
-
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-         c = patch%column(p)
-
-         ! if soybean currently growing then calculate fixation
-
-         if (croplive(p) .and. &
-              (patch%itype(p) == ntmp_soybean .or. &
-               patch%itype(p) == nirrig_tmp_soybean .or. &
-               patch%itype(p) == ntrp_soybean .or. &
-               patch%itype(p) == nirrig_trp_soybean) ) then
-
-            ! difference between supply and demand
-
-            if (fpg(c) < 1._r8) then
-               soy_ndemand = 0._r8
-               soy_ndemand = plant_ndemand(p) - plant_ndemand(p)*fpg(c)
-
-               ! fixation depends on nitrogen, soil water, and growth stage
-
-               ! soil water factor
-
-               fxw = 0._r8
-               fxw = wf(c)/0.85_r8
-
-               ! soil nitrogen factor (Beth says: CHECK UNITS)
-
-               if (sminn(c) > sminnthreshold1) then
-                  fxn = 0._r8
-               else if (sminn(c) > sminnthreshold2 .and. sminn(c) <= sminnthreshold1) then
-                  fxn = 1.5_r8 - .005_r8 * (sminn(c) * 10._r8)
-               else if (sminn(c) <= sminnthreshold2) then
-                  fxn = 1._r8
-               end if
-
-               ! growth stage factor
-               ! slevis: to replace GDDfrac, assume...
-               ! Beth's crit_offset_gdd_def is similar to my gddmaturity
-               ! Beth's ac_gdd (base 5C) similar to my hui=gddplant (base 10
-               ! for soy) 
-               ! Ranges below are not firm. Are they lit. based or tuning based?
-
-               GDDfrac = hui(p) / gddmaturity(p)
-
-               if (GDDfrac <= GDDfracthreshold1) then
-                  fxg = 0._r8
-               else if (GDDfrac > GDDfracthreshold1 .and. GDDfrac <= GDDfracthreshold2) then
-                  fxg = 6.67_r8 * GDDfrac - 1._r8
-               else if (GDDfrac > GDDfracthreshold2 .and. GDDfrac <= GDDfracthreshold3) then
-                  fxg = 1._r8
-               else if (GDDfrac > GDDfracthreshold3 .and. GDDfrac <= GDDfracthreshold4) then
-                  fxg = 3.75_r8 - 5._r8 * GDDfrac
-               else  ! GDDfrac > GDDfracthreshold4
-                  fxg = 0._r8
-               end if
-
-               ! calculate the nitrogen fixed by the soybean
-
-               fxr = min(1._r8, fxw, fxn) * fxg 
-               fxr = max(0._r8, fxr)
-               soyfixn(p) =  fxr * soy_ndemand
-               soyfixn(p) = min(soyfixn(p), soy_ndemand)
-
-            else ! if nitrogen demand met, no fixation
-
-               soyfixn(p) = 0._r8
-
-            end if
-
-         else ! if not live soybean, no fixation
-
-            soyfixn(p) = 0._r8
-
-         end if
-      end do
-
-      call p2c(bounds, num_soilc, filter_soilc, &
-           soyfixn(bounds%begp:bounds%endp), &
-           soyfixn_to_sminn(bounds%begc:bounds%endc))
-
-    end associate
-
-  end subroutine CNSoyfix
-
-end module CNNDynamicsMod
diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
deleted file mode 100644
index b54cff51be..0000000000
--- a/src/biogeochem/CNPhenologyMod.F90
+++ /dev/null
@@ -1,247 +0,0 @@
-module CNPhenologyMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !MODULE: CNPhenologyMod
-  !
-  ! !DESCRIPTION:
-  ! Module holding routines used in phenology model for coupled carbon
-  ! nitrogen code.
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use shr_log_mod                     , only : errMsg => shr_log_errMsg
-  use shr_sys_mod                     , only : shr_sys_flush
-  use decompMod                       , only : bounds_type
-  use clm_varpar                      , only : numpft, nlevdecomp_full
-  use clm_varctl                      , only : iulog, use_cndv
-  use clm_varcon                      , only : tfrz
-  use abortutils                      , only : endrun
-  use CanopyStateType                 , only : canopystate_type
-  use CNDVType                        , only : dgvs_type
-  use CNVegstateType                  , only : cnveg_state_type
-  use CNVegCarbonStateType            , only : cnveg_carbonstate_type
-  use CNVegCarbonFluxType             , only : cnveg_carbonflux_type
-  use CNVegnitrogenstateType          , only : cnveg_nitrogenstate_type
-  use CNVegnitrogenfluxType           , only : cnveg_nitrogenflux_type
-  use CropType                        , only : crop_type
-  use pftconMod                       , only : pftcon
-  use SoilStateType                   , only : soilstate_type
-  use TemperatureType                 , only : temperature_type
-  use WaterstateType                  , only : waterstate_type
-  use ColumnType                      , only : col                
-  use GridcellType                    , only : grc                
-  use PatchType                       , only : patch   
-  use atm2lndType                     , only : atm2lnd_type             
-  use atm2lndType                     , only : atm2lnd_type
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams           ! Read parameters
-  public :: CNPhenologyInit      ! Initialization
-  !
-  ! !PRIVATE DATA MEMBERS:
-  type, private :: params_type
-     real(r8) :: crit_dayl       ! critical day length for senescence
-     real(r8) :: ndays_on     	 ! number of days to complete leaf onset
-     real(r8) :: ndays_off	 ! number of days to complete leaf offset
-     real(r8) :: fstor2tran      ! fraction of storage to move to transfer for each onset
-     real(r8) :: crit_onset_fdd  ! critical number of freezing days to set gdd counter
-     real(r8) :: crit_onset_swi  ! critical number of days > soilpsi_on for onset
-     real(r8) :: soilpsi_on      ! critical soil water potential for leaf onset
-     real(r8) :: crit_offset_fdd ! critical number of freezing days to initiate offset
-     real(r8) :: crit_offset_swi ! critical number of water stress days to initiate offset
-     real(r8) :: soilpsi_off     ! critical soil water potential for leaf offset
-     real(r8) :: lwtop   	 ! live wood turnover proportion (annual fraction)
-  end type params_type
-
-  type(params_type) :: params_inst
-
-  real(r8) :: dt                            ! radiation time step delta t (seconds)
-  real(r8) :: fracday                       ! dtime as a fraction of day
-  real(r8) :: crit_dayl                     ! critical daylength for offset (seconds)
-  real(r8) :: ndays_on                      ! number of days to complete onset
-  real(r8) :: ndays_off                     ! number of days to complete offset
-  real(r8) :: fstor2tran                    ! fraction of storage to move to transfer on each onset
-  real(r8) :: crit_onset_fdd                ! critical number of freezing days
-  real(r8) :: crit_onset_swi                ! water stress days for offset trigger
-  real(r8) :: soilpsi_on                    ! water potential for onset trigger (MPa)
-  real(r8) :: crit_offset_fdd               ! critical number of freezing degree days to trigger offset
-  real(r8) :: crit_offset_swi               ! water stress days for offset trigger
-  real(r8) :: soilpsi_off                   ! water potential for offset trigger (MPa)
-  real(r8) :: lwtop                         ! live wood turnover proportion (annual fraction)
-
-  ! CropPhenology variables and constants
-  real(r8) :: p1d, p1v                      ! photoperiod factor constants for crop vernalization
-  real(r8) :: hti                           ! cold hardening index threshold for vernalization
-  real(r8) :: tbase                         ! base temperature for vernalization
-
-  integer, parameter :: NOT_Planted   = 999 ! If not planted   yet in year
-  integer, parameter :: NOT_Harvested = 999 ! If not harvested yet in year
-  integer, parameter :: inNH       = 1      ! Northern Hemisphere
-  integer, parameter :: inSH       = 2      ! Southern Hemisphere
-  integer, pointer   :: inhemi(:)           ! Hemisphere that patch is in 
-
-  integer, allocatable :: minplantjday(:,:) ! minimum planting julian day
-  integer, allocatable :: maxplantjday(:,:) ! maximum planting julian day
-  integer              :: jdayyrstart(inSH) ! julian day of start of year
-
-  real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    !
-    ! !USES:
-    use ncdio_pio    , only: file_desc_t,ncd_io
-
-    ! !ARGUMENTS:
-    implicit none
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNPhenolParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in parameter
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    !
-    ! read in parameters
-    !   
-    tString='crit_dayl'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%crit_dayl=tempr
-
-    tString='ndays_on'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%ndays_on=tempr
-
-    tString='ndays_off'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%ndays_off=tempr
-
-    tString='fstor2tran'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%fstor2tran=tempr
-
-    tString='crit_onset_fdd'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%crit_onset_fdd=tempr
-
-    tString='crit_onset_swi'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%crit_onset_swi=tempr
-
-    tString='soilpsi_on'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%soilpsi_on=tempr
-
-    tString='crit_offset_fdd'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%crit_offset_fdd=tempr
-
-    tString='crit_offset_swi'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%crit_offset_swi=tempr
-
-    tString='soilpsi_off'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%soilpsi_off=tempr
-
-    tString='lwtop_ann'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%lwtop=tempr   
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine CNPhenologyInit(bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialization of CNPhenology. Must be called after time-manager is
-    ! initialized, and after pftcon file is read in.
-    !
-    ! !USES:
-    use clm_time_manager, only: get_step_size
-    use clm_varctl      , only: use_crop
-    use clm_varcon      , only: secspday
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds  
-    !------------------------------------------------------------------------
-
-    !
-    ! Get time-step and what fraction of a day it is
-    !
-    dt      = real( get_step_size(), r8 )
-    fracday = dt/secspday
-
-    ! set constants for CNSeasonDecidPhenology 
-    ! (critical daylength from Biome-BGC, v4.1.2)
-    crit_dayl=params_inst%crit_dayl
-
-    ! Set constants for CNSeasonDecidPhenology and CNStressDecidPhenology
-    ndays_on=params_inst%ndays_on
-    ndays_off=params_inst%ndays_off
-
-    ! set transfer parameters
-    fstor2tran=params_inst%fstor2tran
-
-    ! -----------------------------------------
-    ! Constants for CNStressDecidPhenology
-    ! -----------------------------------------
-
-    ! onset parameters
-    crit_onset_fdd=params_inst%crit_onset_fdd
-    ! critical onset gdd now being calculated as a function of annual
-    ! average 2m temp.
-    ! crit_onset_gdd = 150.0 ! c3 grass value
-    ! crit_onset_gdd = 1000.0   ! c4 grass value
-    crit_onset_swi=params_inst%crit_onset_swi
-    soilpsi_on=params_inst%soilpsi_on
-
-    ! offset parameters
-    crit_offset_fdd=params_inst%crit_offset_fdd
-    crit_offset_swi=params_inst%crit_offset_swi
-    soilpsi_off=params_inst%soilpsi_off    
-
-    ! -----------------------------------------
-    ! Constants for CNLivewoodTurnover
-    ! -----------------------------------------
-
-    ! set the global parameter for livewood turnover rate
-    ! define as an annual fraction (0.7), and convert to fraction per second
-    lwtop=params_inst%lwtop/31536000.0_r8 !annual fraction converted to per second
-
-    ! -----------------------------------------
-    ! Call any subroutine specific initialization routines
-    ! -----------------------------------------
-
-    !if ( use_crop ) call CropPhenologyInit(bounds)
-
-  end subroutine CNPhenologyInit
-
-end module CNPhenologyMod
diff --git a/src/biogeochem/CNPrecisionControlMod.F90 b/src/biogeochem/CNPrecisionControlMod.F90
deleted file mode 100644
index 8c5660d198..0000000000
--- a/src/biogeochem/CNPrecisionControlMod.F90
+++ /dev/null
@@ -1,498 +0,0 @@
-module CNPrecisionControlMod
-
-#include "shr_assert.h"
-
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION:
-  ! controls on very low values in critical state variables 
-  ! 
-  ! !USES:
-  use shr_kind_mod           , only : r8 => shr_kind_r8
-  use CNVegCarbonStateType   , only : cnveg_carbonstate_type
-  use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type
-  use PatchType              , only : patch
-  use abortutils             , only : endrun
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public:: CNPrecisionControl
-
-  ! !PUBLIC DATA:
-  real(r8), public :: ccrit    =  1.e-8_r8              ! critical carbon state value for truncation (gC/m2)
-  real(r8), public :: cnegcrit = -6.e+1_r8              ! critical negative carbon state value for abort (gC/m2)
-  real(r8), public :: ncrit    =  1.e-8_r8              ! critical nitrogen state value for truncation (gN/m2)
-  real(r8), public :: nnegcrit = -6.e+0_r8              ! critical negative nitrogen state value for abort (gN/m2)
-  real(r8), public, parameter :: n_min = 0.000000001_r8 ! Minimum Nitrogen value to use when calculating CN ratio (gN/m2)
-
-  ! !PRIVATE DATA:
-  logical, private :: prec_control_for_froot = .true.   ! If true do precision control for frootc/frootn
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !----------------------------------------------------------------------- 
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, &
-       cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, &
-       cnveg_nitrogenstate_inst)
-    !
-    ! !DESCRIPTION: 
-    ! Force leaf and deadstem c and n to 0 if they get too small.
-    !
-    ! !USES:
-    use clm_varctl , only : iulog
-    use clm_varpar , only : use_crop
-    use pftconMod  , only : nc3crop
-    use decompMod  , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)              , intent(in)    :: bounds          ! bounds
-    integer                        , intent(in)    :: num_soilp       ! number of soil patchs in filter
-    integer                        , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    type(cnveg_carbonstate_type)   , intent(inout) :: cnveg_carbonstate_inst
-    type(cnveg_carbonstate_type)   , intent(inout) :: c13_cnveg_carbonstate_inst
-    type(cnveg_carbonstate_type)   , intent(inout) :: c14_cnveg_carbonstate_inst
-    type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,j,k                             ! indices
-    integer :: fp                                ! filter indices
-    real(r8):: pc(bounds%begp:bounds%endp)       ! truncation terms for patch-level corrections Carbon
-    real(r8):: pn(bounds%begp:bounds%endp)       ! truncation terms for patch-level corrections nitrogen
-    real(r8):: pc13(bounds%begp:bounds%endp)     ! truncation terms for patch-level corrections
-    real(r8):: pc14(bounds%begp:bounds%endp)     ! truncation terms for patch-level corrections
-    !-----------------------------------------------------------------------
-
-    ! cnveg_carbonstate_inst%cpool_patch                     Output:  [real(r8) (:)     ]  (gC/m2) temporary photosynthate C pool            
-    ! cnveg_carbonstate_inst%deadcrootc_patch                Output:  [real(r8) (:)     ]  (gC/m2) dead coarse root C                        
-    ! cnveg_carbonstate_inst%deadcrootc_storage_patch        Output:  [real(r8) (:)     ]  (gC/m2) dead coarse root C storage                
-    ! cnveg_carbonstate_inst%deadcrootc_xfer_patch           Output:  [real(r8) (:)     ]  (gC/m2) dead coarse root C transfer               
-    ! cnveg_carbonstate_inst%deadstemc_patch                 Output:  [real(r8) (:)     ]  (gC/m2) dead stem C                               
-    ! cnveg_carbonstate_inst%deadstemc_storage_patch         Output:  [real(r8) (:)     ]  (gC/m2) dead stem C storage                       
-    ! cnveg_carbonstate_inst%deadstemc_xfer_patch            Output:  [real(r8) (:)     ]  (gC/m2) dead stem C transfer                      
-    ! cnveg_carbonstate_inst%frootc_patch                    Output:  [real(r8) (:)     ]  (gC/m2) fine root C                               
-    ! cnveg_carbonstate_inst%frootc_storage_patch            Output:  [real(r8) (:)     ]  (gC/m2) fine root C storage                       
-    ! cnveg_carbonstate_inst%frootc_xfer_patch               Output:  [real(r8) (:)     ]  (gC/m2) fine root C transfer                      
-    ! cnveg_carbonstate_inst%gresp_storage_patch             Output:  [real(r8) (:)     ]  (gC/m2) growth respiration storage                
-    ! cnveg_carbonstate_inst%gresp_xfer_patch                Output:  [real(r8) (:)     ]  (gC/m2) growth respiration transfer               
-    ! cnveg_carbonstate_inst%leafc_patch                     Output:  [real(r8) (:)     ]  (gC/m2) leaf C                                    
-    ! cnveg_carbonstate_inst%leafc_storage_patch             Output:  [real(r8) (:)     ]  (gC/m2) leaf C storage                            
-    ! cnveg_carbonstate_inst%leafc_xfer_patch                Output:  [real(r8) (:)     ]  (gC/m2) leaf C transfer                           
-    ! cnveg_carbonstate_inst%livecrootc_patch                Output:  [real(r8) (:)     ]  (gC/m2) live coarse root C                        
-    ! cnveg_carbonstate_inst%livecrootc_storage_patch        Output:  [real(r8) (:)     ]  (gC/m2) live coarse root C storage                
-    ! cnveg_carbonstate_inst%livecrootc_xfer_patch           Output:  [real(r8) (:)     ]  (gC/m2) live coarse root C transfer               
-    ! cnveg_carbonstate_inst%livestemc_patch                 Output:  [real(r8) (:)     ]  (gC/m2) live stem C                               
-    ! cnveg_carbonstate_inst%livestemc_storage_patch         Output:  [real(r8) (:)     ]  (gC/m2) live stem C storage                       
-    ! cnveg_carbonstate_inst%livestemc_xfer_patch            Output:  [real(r8) (:)     ]  (gC/m2) live stem C transfer                      
-    ! cnveg_carbonstate_inst%ctrunc_patch                    Output:  [real(r8) (:)     ]  (gC/m2) patch-level sink for C truncation           
-    ! cnveg_carbonstate_inst%xsmrpool_patch                  Output:  [real(r8) (:)     ]  (gC/m2) execss maint resp C pool                  
-    ! cnveg_carbonstate_inst%grainc_patch                    Output:  [real(r8) (:)     ]  (gC/m2) grain C                                   
-    ! cnveg_carbonstate_inst%grainc_storage_patch            Output:  [real(r8) (:)     ]  (gC/m2) grain C storage                           
-    ! cnveg_carbonstate_inst%grainc_xfer_patch               Output:  [real(r8) (:)     ]  (gC/m2) grain C transfer                          
-    
-    ! cnveg_nitrogenstate_inst%deadcrootn_patch              Output:  [real(r8) (:)     ]  (gN/m2) dead coarse root N                        
-    ! cnveg_nitrogenstate_inst%deadcrootn_storage_patch      Output:  [real(r8) (:)     ]  (gN/m2) dead coarse root N storage                
-    ! cnveg_nitrogenstate_inst%deadcrootn_xfer_patch         Output:  [real(r8) (:)     ]  (gN/m2) dead coarse root N transfer               
-    ! cnveg_nitrogenstate_inst%deadstemn_patch               Output:  [real(r8) (:)     ]  (gN/m2) dead stem N                               
-    ! cnveg_nitrogenstate_inst%deadstemn_storage_patch       Output:  [real(r8) (:)     ]  (gN/m2) dead stem N storage                       
-    ! cnveg_nitrogenstate_inst%deadstemn_xfer_patch          Output:  [real(r8) (:)     ]  (gN/m2) dead stem N transfer                      
-    ! cnveg_nitrogenstate_inst%frootn_patch                  Output:  [real(r8) (:)     ]  (gN/m2) fine root N                               
-    ! cnveg_nitrogenstate_inst%frootn_storage_patch          Output:  [real(r8) (:)     ]  (gN/m2) fine root N storage                       
-    ! cnveg_nitrogenstate_inst%frootn_xfer_patch             Output:  [real(r8) (:)     ]  (gN/m2) fine root N transfer                      
-    ! cnveg_nitrogenstate_inst%leafn_patch                   Output:  [real(r8) (:)     ]  (gN/m2) leaf N                                    
-    ! cnveg_nitrogenstate_inst%leafn_storage_patch           Output:  [real(r8) (:)     ]  (gN/m2) leaf N storage                            
-    ! cnveg_nitrogenstate_inst%leafn_xfer_patch              Output:  [real(r8) (:)     ]  (gN/m2) leaf N transfer                           
-    ! cnveg_nitrogenstate_inst%livecrootn_patch              Output:  [real(r8) (:)     ]  (gN/m2) live coarse root N                        
-    ! cnveg_nitrogenstate_inst%livecrootn_storage_patch      Output:  [real(r8) (:)     ]  (gN/m2) live coarse root N storage                
-    ! cnveg_nitrogenstate_inst%livecrootn_xfer_patch         Output:  [real(r8) (:)     ]  (gN/m2) live coarse root N transfer               
-    ! cnveg_nitrogenstate_inst%grainn_patch                  Output:  [real(r8) (:)     ]  (gC/m2) grain N                                   
-    ! cnveg_nitrogenstate_inst%grainn_storage_patch          Output:  [real(r8) (:)     ]  (gC/m2) grain N storage                           
-    ! cnveg_nitrogenstate_inst%grainn_xfer_patch             Output:  [real(r8) (:)     ]  (gC/m2) grain N transfer                          
-    ! cnveg_nitrogenstate_inst%livestemn_patch               Output:  [real(r8) (:)     ]  (gN/m2) live stem N                               
-    ! cnveg_nitrogenstate_inst%livestemn_storage_patch       Output:  [real(r8) (:)     ]  (gN/m2) live stem N storage                       
-    ! cnveg_nitrogenstate_inst%livestemn_xfer_patch          Output:  [real(r8) (:)     ]  (gN/m2) live stem N transfer                      
-    ! cnveg_nitrogenstate_inst%npool_patch                   Output:  [real(r8) (:)     ]  (gN/m2) temporary plant N pool                    
-    ! cnveg_nitrogenstate_inst%ntrunc_patch                  Output:  [real(r8) (:)     ]  (gN/m2) patch-level sink for N truncation           
-    ! cnveg_nitrogenstate_inst%retransn_patch                Output:  [real(r8) (:)     ]  (gN/m2) plant pool of retranslocated N            
-
-    
-    associate(                                           &
-         cs     => cnveg_carbonstate_inst              , &
-         ns     => cnveg_nitrogenstate_inst            , &
-         c13cs  => c13_cnveg_carbonstate_inst          , &
-         c14cs  => c14_cnveg_carbonstate_inst            &
-         )
-
-      ! patch loop
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-
-         ! initialize the patch-level C and N truncation terms
-         pc(p) = 0._r8
-         pn(p) = 0._r8
-      end do
-
-      ! do tests on state variables for precision control
-      ! for linked C-N state variables, perform precision test on
-      ! the C component, but truncate C, C13, and N components
-
-      ! leaf C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_patch(bounds%begp:bounds%endp), &
-                                ns%leafn_patch(bounds%begp:bounds%endp), &
-                                pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%leafc_patch, c14=c14cs%leafc_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! leaf storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_storage_patch(bounds%begp:bounds%endp), &
-                                ns%leafn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%leafc_storage_patch, c14=c14cs%leafc_storage_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! leaf transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_xfer_patch(bounds%begp:bounds%endp), &
-                                ns%leafn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%leafc_xfer_patch, c14=c14cs%leafc_xfer_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! froot C and N
-      ! EBK KO DML: For some reason frootc/frootn can go negative and allowing
-      ! it to be negative is important for C4 crops (otherwise they die) Jun/3/2016
-      if ( prec_control_for_froot ) then
-         call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_patch(bounds%begp:bounds%endp),  &
-                                   ns%frootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                   c13=c13cs%frootc_patch, c14=c14cs%frootc_patch,  &
-                                   pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), allowneg=.true. )
-      end if
-
-      ! froot storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_storage_patch(bounds%begp:bounds%endp), &
-                      ns%frootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%frootc_storage_patch, c14=c14cs%frootc_storage_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! froot transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_xfer_patch(bounds%begp:bounds%endp), &
-                                ns%frootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%frootc_xfer_patch, c14=c14cs%frootc_xfer_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      if ( use_crop )then
-         ! grain C and N
-         call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%grainc_patch(bounds%begp:bounds%endp), &
-                                   ns%grainn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                   c13=c13cs%grainc_patch, c14=c14cs%grainc_patch, &
-                                   pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), croponly=.true. )
-
-         ! grain storage C and N
-         call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%grainc_storage_patch(bounds%begp:bounds%endp), &
-                                   ns%grainn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                                   __LINE__, c13=c13cs%grainc_storage_patch, c14=c14cs%grainc_storage_patch, &
-                                   pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), croponly=.true. )
-
-         ! grain transfer C and N
-         call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%grainc_xfer_patch(bounds%begp:bounds%endp), &
-                                   ns%grainn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                   c13=c13cs%grainc_xfer_patch, c14=c14cs%grainc_xfer_patch, &
-                                   pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), croponly=.true. )
-
-         ! grain transfer C and N
-         call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%cropseedc_deficit_patch(bounds%begp:bounds%endp), &
-                                   ns%cropseedn_deficit_patch(bounds%begp:bounds%endp), pc(bounds%begp:), &
-                                   pn(bounds%begp:), __LINE__, &
-                                   c13=c13cs%cropseedc_deficit_patch, c14=c14cs%cropseedc_deficit_patch, &
-                                   pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), allowneg=.true., croponly=.true. )
-
-      end if
-
-      ! livestem C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_patch(bounds%begp:bounds%endp), &
-                                ns%livestemn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%livestemc_patch, c14=c14cs%livestemc_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! livestem storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_storage_patch(bounds%begp:bounds%endp), &
-                      ns%livestemn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%livestemc_storage_patch, c14=c14cs%livestemc_storage_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! livestem transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_xfer_patch(bounds%begp:bounds%endp), &
-                      ns%livestemn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%livestemc_xfer_patch, c14=c14cs%livestemc_xfer_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! deadstem C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_patch(bounds%begp:bounds%endp), &
-                                ns%deadstemn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%deadstemc_patch, c14=c14cs%deadstemc_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-      ! deadstem storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_storage_patch(bounds%begp:bounds%endp), &
-                      ns%deadstemn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%deadstemc_storage_patch, c14=c14cs%deadstemc_storage_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! deadstem transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_xfer_patch(bounds%begp:bounds%endp), &
-                      ns%deadstemn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%deadstemc_xfer_patch, c14=c14cs%deadstemc_xfer_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! livecroot C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_patch(bounds%begp:bounds%endp), &
-                                ns%livecrootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%livecrootc_patch, c14=c14cs%livecrootc_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! livecroot storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_storage_patch(bounds%begp:bounds%endp), &
-                      ns%livecrootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%livecrootc_storage_patch, c14=c14cs%livecrootc_storage_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! livecroot transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_xfer_patch(bounds%begp:bounds%endp), &
-                      ns%livecrootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%livecrootc_xfer_patch, c14=c14cs%livecrootc_xfer_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! deadcroot C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_patch(bounds%begp:bounds%endp), &
-                                ns%deadcrootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, &
-                                c13=c13cs%deadcrootc_patch, c14=c14cs%deadcrootc_patch, &
-                                pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! deadcroot storage C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_storage_patch(bounds%begp:bounds%endp), &
-                      ns%deadcrootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%deadcrootc_storage_patch, c14=c14cs%deadcrootc_storage_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! deadcroot transfer C and N
-      call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_xfer_patch(bounds%begp:bounds%endp), &
-                      ns%deadcrootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), &
-                      __LINE__, c13=c13cs%deadcrootc_xfer_patch, c14=c14cs%deadcrootc_xfer_patch, &
-                      pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! gresp_storage (C only)
-      call TruncateCStates( bounds, filter_soilp, num_soilp, cs%gresp_storage_patch(bounds%begp:bounds%endp), &
-                            pc(bounds%begp:), __LINE__, &
-                            c13=c13cs%gresp_storage_patch, c14=c14cs%gresp_storage_patch, &
-                            pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! gresp_xfer(c only)
-      call TruncateCStates( bounds, filter_soilp, num_soilp, cs%gresp_xfer_patch(bounds%begp:bounds%endp), &
-                            pc(bounds%begp:), __LINE__, &
-                            c13=c13cs%gresp_xfer_patch, c14=c14cs%gresp_xfer_patch, &
-                            pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      ! cpool (C only)
-      call TruncateCStates( bounds, filter_soilp, num_soilp, cs%cpool_patch(bounds%begp:bounds%endp), &
-                            pc(bounds%begp:), __LINE__, &
-                            c13=c13cs%cpool_patch, c14=c14cs%cpool_patch, &
-                            pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:) )
-
-      if ( use_crop )then
-         ! xsmrpool (C only)
-         ! xsmr is a pool to balance the budget and as such can be freely negative
-         call TruncateCStates( bounds, filter_soilp, num_soilp, cs%xsmrpool_patch(bounds%begp:bounds%endp), &
-                               pc(bounds%begp:), __LINE__, &
-                               c13=c13cs%xsmrpool_patch, c14=c14cs%xsmrpool_patch, &
-                               pc13=pc13(bounds%begp:), pc14=pc14(bounds%begp:), allowneg=.true., croponly=.true. )
-
-      end if
-
-      ! retransn (N only)
-      call TruncateNStates( bounds, filter_soilp, num_soilp, ns%retransn_patch(bounds%begp:bounds%endp), pn(bounds%begp:), &
-                            __LINE__ )
-
-      ! npool (N only)
-      call TruncateNStates( bounds, filter_soilp, num_soilp, ns%npool_patch(bounds%begp:bounds%endp), pn(bounds%begp:), &
-                            __LINE__ )
-
-      ! patch loop
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-
-         cs%ctrunc_patch(p) = cs%ctrunc_patch(p) + pc(p)
-
-         ns%ntrunc_patch(p) = ns%ntrunc_patch(p) + pn(p)
-
-       end do
-
-    end associate
-
- end subroutine CNPrecisionControl
-
- subroutine TruncateCandNStates( bounds, filter_soilp, num_soilp, carbon_patch, nitrogen_patch, pc, pn, lineno, c13, c14, &
-                                 pc13, pc14, croponly, allowneg )
-    !
-    ! !DESCRIPTION:
-    ! Truncate paired Carbon and Nitrogen states. If a paired carbon and nitrogen state iare too small truncate 
-    ! the pair of them to zero.
-    !
-    ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use clm_varctl , only : use_nguardrail
-    use clm_varctl , only : iulog
-    use pftconMod  , only : nc3crop
-    use decompMod  , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)              , intent(in)    :: bounds          ! bounds
-    integer                        , intent(in)    :: num_soilp       ! number of soil patchs in filter
-    integer                        , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    real(r8), intent(inout) :: carbon_patch(bounds%begp:)
-    real(r8), intent(inout) :: nitrogen_patch(bounds%begp:)
-    real(r8), intent(inout) :: pc(bounds%begp:)
-    real(r8), intent(inout) :: pn(bounds%begp:)
-    integer,  intent(in)    :: lineno
-    real(r8), intent(inout), optional, pointer :: c13(:)
-    real(r8), intent(inout), optional, pointer :: c14(:)
-    real(r8), intent(inout), optional :: pc13(bounds%begp:)
-    real(r8), intent(inout), optional :: pc14(bounds%begp:)
-    logical , intent(in)   , optional :: croponly
-    logical , intent(in)   , optional :: allowneg
-
-    logical :: lcroponly, lallowneg
-    integer :: fp, p
-
-    SHR_ASSERT_ALL((ubound(carbon_patch)   == (/bounds%endp/)), 'ubnd(carb)'//errMsg(sourcefile, lineno))
-    SHR_ASSERT_ALL((ubound(nitrogen_patch) == (/bounds%endp/)), 'ubnd(nitro)'//errMsg(sourcefile, lineno))
-    SHR_ASSERT_ALL((ubound(pc)             == (/bounds%endp/)), 'ubnd(pc)'//errMsg(sourcefile, lineno))
-    SHR_ASSERT_ALL((ubound(pn)             == (/bounds%endp/)), 'ubnd(pn)'//errMsg(sourcefile, lineno))
-    ! patch loop
-    lcroponly = .false.
-    if ( present(croponly) )then
-      if ( croponly ) lcroponly = .true.
-    end if
-    lallowneg = .false.
-    if ( present(allowneg) )then
-      if (  allowneg ) lallowneg = .true.
-    end if
-    do fp = 1,num_soilp
-       p = filter_soilp(fp)
-
-       if ( .not. lcroponly .or. (patch%itype(p) >= nc3crop) ) then
-          if ( .not. lallowneg .and. ((carbon_patch(p) < cnegcrit) .or. (nitrogen_patch(p) < nnegcrit)) ) then
-             write(iulog,*) 'ERROR: Carbon or Nitrogen patch negative = ', carbon_patch(p), nitrogen_patch(p)
-             write(iulog,*) 'ERROR: limits = ', cnegcrit, nnegcrit
-             call endrun(msg='ERROR: carbon or nitrogen state critically negative '//errMsg(sourcefile, lineno))
-          else if ( abs(carbon_patch(p)) < ccrit .or. (use_nguardrail .and. abs(nitrogen_patch(p)) < ncrit) ) then
-             pc(p) = pc(p) + carbon_patch(p)
-             carbon_patch(p) = 0._r8
-      
-             pn(p) = pn(p) + nitrogen_patch(p)
-             nitrogen_patch(p) = 0._r8
-   
-          end if
-       end if
-    end do
- end subroutine TruncateCandNStates
-
- subroutine TruncateCStates( bounds, filter_soilp, num_soilp, carbon_patch, pc, lineno, c13, c14, pc13, pc14, croponly, allowneg )
-    !
-    ! !DESCRIPTION:
-    ! Truncate Carbon states. If a carbon state is too small truncate it to
-    ! zero.
-    !
-    ! !USES:
-    use abortutils , only : endrun
-    use clm_varctl , only : iulog
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use pftconMod  , only : nc3crop
-    use decompMod  , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in)    :: bounds          ! bounds
-    integer          , intent(in)    :: num_soilp       ! number of soil patchs in filter
-    integer          , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    real(r8)         , intent(inout) :: carbon_patch(bounds%begp:)
-    real(r8)         , intent(inout) :: pc(bounds%begp:)
-    integer          , intent(in)    :: lineno
-    real(r8)         , intent(inout), optional, pointer :: c13(:)
-    real(r8)         , intent(inout), optional, pointer :: c14(:)
-    real(r8)         , intent(inout), optional :: pc13(bounds%begp:)
-    real(r8)         , intent(inout), optional :: pc14(bounds%begp:)
-    logical          , intent(in)   , optional :: croponly
-    logical          , intent(in)   , optional :: allowneg
-
-    logical :: lcroponly, lallowneg
-    integer :: fp, p
-
-    SHR_ASSERT_ALL((ubound(carbon_patch)   == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(pc)             == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    if ( -ccrit < cnegcrit )then
-        call endrun(msg='ERROR: cnegcrit should be less than -ccrit: '//errMsg(sourcefile, lineno))
-    end if
-    lcroponly = .false.
-    if ( present(croponly) )then
-      if ( croponly ) lcroponly = .true.
-    end if
-    lallowneg = .false.
-    if ( present(allowneg) )then
-      if (  allowneg ) lallowneg = .true.
-    end if
-    do fp = 1,num_soilp
-       p = filter_soilp(fp)
-
-       if ( .not. lcroponly .or. (patch%itype(p) >= nc3crop) ) then
-          if ( .not. lallowneg .and. (carbon_patch(p) < cnegcrit) ) then
-             write(iulog,*) 'ERROR: Carbon patch negative = ', carbon_patch(p)
-             write(iulog,*) 'ERROR: limit = ', cnegcrit
-             call endrun(msg='ERROR: carbon state critically negative '//errMsg(sourcefile, lineno))
-          else if ( abs(carbon_patch(p)) < ccrit) then
-             pc(p) = pc(p) + carbon_patch(p)
-             carbon_patch(p) = 0._r8
-   
-          end if
-       end if
-    end do
- end subroutine TruncateCStates
-
- subroutine TruncateNStates( bounds, filter_soilp, num_soilp, nitrogen_patch, pn, lineno )
-    !
-    ! !DESCRIPTION:
-    ! Truncate Nitrogen states. If a nitrogen state is too small truncate it to
-    ! zero.
-    !
-    ! !USES:
-    use abortutils , only : endrun
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use clm_varctl , only : iulog
-    use decompMod  , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)              , intent(in)    :: bounds          ! bounds
-    integer                        , intent(in)    :: num_soilp       ! number of soil patchs in filter
-    integer                        , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    real(r8), intent(inout) :: nitrogen_patch(bounds%begp:)
-    real(r8), intent(inout) :: pn(bounds%begp:)
-    integer,  intent(in)    :: lineno
-
-    integer :: fp, p
-
-    SHR_ASSERT_ALL((ubound(nitrogen_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(pn)             == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    do fp = 1,num_soilp
-       p = filter_soilp(fp)
-       if ( nitrogen_patch(p) < nnegcrit ) then
-          !write(iulog,*) 'WARNING: Nitrogen patch negative = ', nitrogen_patch
-          !call endrun(msg='ERROR: nitrogen state critically negative'//errMsg(sourcefile, lineno))
-       else if ( abs(nitrogen_patch(p)) < ncrit) then
-          pn(p) = pn(p) + nitrogen_patch(p)
-          nitrogen_patch(p) = 0._r8
-
-       end if
-    end do
- end subroutine TruncateNStates
-
-end module CNPrecisionControlMod
diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90
deleted file mode 100644
index d71d7b1568..0000000000
--- a/src/biogeochem/CNProductsMod.F90
+++ /dev/null
@@ -1,741 +0,0 @@
-module CNProductsMod
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculate loss fluxes from wood products pools, and update product pool state variables
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use shr_kind_mod            , only : r8 => shr_kind_r8
-  use shr_infnan_mod          , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod             , only : errMsg => shr_log_errMsg
-  use decompMod               , only : bounds_type
-  use abortutils              , only : endrun
-  use clm_time_manager        , only : get_step_size
-  use SpeciesBaseType         , only : species_base_type
-  use PatchType               , only : patch
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: cn_products_type
-     private
-     ! ------------------------------------------------------------------------
-     ! Public instance variables
-     ! ------------------------------------------------------------------------
-
-     real(r8), pointer, public :: product_loss_grc(:)   ! (g[C or N]/m2/s) total decomposition loss from ALL product pools
-
-     ! ------------------------------------------------------------------------
-     ! Private instance variables
-     ! ------------------------------------------------------------------------
-
-     class(species_base_type), allocatable :: species    ! C, N, C13, C14, etc.
-
-     ! States
-     real(r8), pointer :: cropprod1_grc(:)    ! (g[C or N]/m2) grain product pool, 1-year lifespan
-     real(r8), pointer :: prod10_grc(:)       ! (g[C or N]/m2) wood product pool, 10-year lifespan
-     real(r8), pointer :: prod100_grc(:)      ! (g[C or N]/m2) wood product pool, 100-year lifespan
-     real(r8), pointer :: tot_woodprod_grc(:) ! (g[C or N]/m2) total wood product pool
-
-     ! Fluxes: gains
-     real(r8), pointer :: dwt_prod10_gain_grc(:)  ! (g[C or N]/m2/s) dynamic landcover addition to 10-year wood product pool
-     real(r8), pointer :: dwt_prod100_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to 100-year wood product pool
-     real(r8), pointer :: dwt_woodprod_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to wood product pools
-     real(r8), pointer :: dwt_cropprod1_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to 1-year crop product pool
-     real(r8), pointer :: hrv_deadstem_to_prod10_patch(:)  ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool
-     real(r8), pointer :: hrv_deadstem_to_prod10_grc(:)  ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool
-     real(r8), pointer :: hrv_deadstem_to_prod100_patch(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool
-     real(r8), pointer :: hrv_deadstem_to_prod100_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool
-     real(r8), pointer :: grain_to_cropprod1_patch(:) ! (g[C or N]/m2/s) grain to 1-year crop product pool
-     real(r8), pointer :: grain_to_cropprod1_grc(:) ! (g[C or N]/m2/s) grain to 1-year crop product pool
-
-     ! Fluxes: losses
-     real(r8), pointer :: cropprod1_loss_grc(:)    ! (g[C or N]/m2/s) decomposition loss from 1-yr grain product pool
-     real(r8), pointer :: prod10_loss_grc(:)       ! (g[C or N]/m2/s) decomposition loss from 10-yr wood product pool
-     real(r8), pointer :: prod100_loss_grc(:)      ! (g[C or N]/m2/s) decomposition loss from 100-yr wood product pool
-     real(r8), pointer :: tot_woodprod_loss_grc(:) ! (g[C or N]/m2/s) decompomposition loss from all wood product pools
-
-   contains
-
-     ! Infrastructure routines
-     procedure, public  :: Init
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-     procedure, public  :: Restart
-
-     ! Science routines
-     procedure, public  :: UpdateProducts
-     procedure, private :: PartitionWoodFluxes
-     procedure, private :: PartitionGrainFluxes
-     procedure, private :: ComputeSummaryVars
-
-  end type cn_products_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, species)
-    ! !ARGUMENTS:
-    class(cn_products_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-
-    ! species tells whether this object is being used for C, N, C13, C14, etc. This is
-    ! just used for naming history and restart fields
-    class(species_base_type), intent(in) :: species
-
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'Init'
-    !-----------------------------------------------------------------------
-
-    allocate(this%species, source = species)
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    ! !ARGUMENTS:
-    class(cn_products_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp,endp
-    integer :: begg,endg
-
-    character(len=*), parameter :: subname = 'InitAllocate'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-    begg = bounds%begg
-    endg = bounds%endg
-
-    allocate(this%cropprod1_grc(begg:endg)) ; this%cropprod1_grc(:) = nan
-    allocate(this%prod10_grc(begg:endg)) ; this%prod10_grc(:) = nan
-    allocate(this%prod100_grc(begg:endg)) ; this%prod100_grc(:) = nan
-    allocate(this%tot_woodprod_grc(begg:endg)) ; this%tot_woodprod_grc(:) = nan
-
-    allocate(this%dwt_prod10_gain_grc(begg:endg)) ; this%dwt_prod10_gain_grc(:) = nan
-    allocate(this%dwt_prod100_gain_grc(begg:endg)) ; this%dwt_prod100_gain_grc(:) = nan
-    allocate(this%dwt_woodprod_gain_grc(begg:endg)) ; this%dwt_woodprod_gain_grc(:) = nan
-
-    allocate(this%dwt_cropprod1_gain_grc(begg:endg)) ; this%dwt_cropprod1_gain_grc(:) = nan
-
-    allocate(this%hrv_deadstem_to_prod10_patch(begp:endp)) ; this%hrv_deadstem_to_prod10_patch(:) = nan
-    allocate(this%hrv_deadstem_to_prod10_grc(begg:endg)) ; this%hrv_deadstem_to_prod10_grc(:) = nan
-
-    allocate(this%hrv_deadstem_to_prod100_patch(begp:endp)) ; this%hrv_deadstem_to_prod100_patch(:) = nan
-    allocate(this%hrv_deadstem_to_prod100_grc(begg:endg)) ; this%hrv_deadstem_to_prod100_grc(:) = nan
-
-    allocate(this%grain_to_cropprod1_patch(begp:endp)) ; this%grain_to_cropprod1_patch(:) = nan
-    allocate(this%grain_to_cropprod1_grc(begg:endg)) ; this%grain_to_cropprod1_grc(:) = nan
-
-    allocate(this%cropprod1_loss_grc(begg:endg)) ; this%cropprod1_loss_grc(:) = nan
-    allocate(this%prod10_loss_grc(begg:endg)) ; this%prod10_loss_grc(:) = nan
-    allocate(this%prod100_loss_grc(begg:endg)) ; this%prod100_loss_grc(:) = nan
-    allocate(this%tot_woodprod_loss_grc(begg:endg)) ; this%tot_woodprod_loss_grc(:) = nan
-    allocate(this%product_loss_grc(begg:endg)) ; this%product_loss_grc(:) = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    ! !USES:
-    use histFileMod, only : hist_addfld1d
-    use clm_varcon , only : spval
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begg,endg
-
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-
-    begg = bounds%begg
-    endg = bounds%endg
-
-    this%cropprod1_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('CROPPROD1'), &
-         units = 'g' // this%species%get_species() // '/m^2', &
-         avgflag = 'A', &
-         long_name = '1-yr grain product ' // this%species%get_species(), &
-         ptr_gcell = this%cropprod1_grc, default='inactive')
-
-    this%prod10_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('PROD10'), &
-         units = 'g' // this%species%get_species() // '/m^2', &
-         avgflag = 'A', &
-         long_name = '10-yr wood product ' // this%species%get_species(), &
-         ptr_gcell = this%prod10_grc, default='inactive')
-
-    this%prod100_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('PROD100'), &
-         units = 'g' // this%species%get_species() // '/m^2', &
-         avgflag = 'A', &
-         long_name = '100-yr wood product ' // this%species%get_species(), &
-         ptr_gcell = this%prod100_grc, default='inactive')
-
-    this%tot_woodprod_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('TOT_WOODPROD'), &
-         units = 'g' // this%species%get_species() // '/m^2', &
-         avgflag = 'A', &
-         long_name = 'total wood product ' // this%species%get_species(), &
-         ptr_gcell = this%tot_woodprod_grc, default='inactive')
-
-    this%dwt_prod10_gain_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('DWT_PROD10', suffix='_GAIN'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'landcover change-driven addition to 10-yr wood product pool', &
-         ptr_gcell = this%dwt_prod10_gain_grc, default='inactive')
-
-    this%dwt_prod100_gain_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('DWT_PROD100', suffix='_GAIN'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'landcover change-driven addition to 100-yr wood product pool', &
-         ptr_gcell = this%dwt_prod100_gain_grc, default='inactive')
-
-    this%dwt_woodprod_gain_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('DWT_WOODPROD', suffix='_GAIN'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'landcover change-driven addition to wood product pools', &
-         ptr_gcell = this%dwt_woodprod_gain_grc, default='inactive')
-
-    this%dwt_cropprod1_gain_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('DWT_CROPPROD1', suffix='_GAIN'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'landcover change-driven addition to 1-year crop product pool', &
-         ptr_gcell = this%dwt_cropprod1_gain_grc, default='inactive')
-
-    this%cropprod1_loss_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('CROPPROD1', suffix='_LOSS'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'loss from 1-yr grain product pool', &
-         ptr_gcell = this%cropprod1_loss_grc, default='inactive')
-
-    this%prod10_loss_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('PROD10', suffix='_LOSS'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'loss from 10-yr wood product pool', &
-         ptr_gcell = this%prod10_loss_grc, default='inactive')
-
-    this%prod100_loss_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('PROD100', suffix='_LOSS'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'loss from 100-yr wood product pool', &
-         ptr_gcell = this%prod100_loss_grc, default='inactive')
-
-    this%tot_woodprod_loss_grc(begg:endg) = spval
-    call hist_addfld1d( &
-         fname = this%species%hist_fname('TOT_WOODPROD', suffix='_LOSS'), &
-         units = 'g' // this%species%get_species() // '/m^2/s', &
-         avgflag = 'A', &
-         long_name = 'total loss from wood product pools', &
-         ptr_gcell = this%tot_woodprod_loss_grc, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    ! !ARGUMENTS:
-    class(cn_products_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g, p
-
-    character(len=*), parameter :: subname = 'InitCold'
-    !-----------------------------------------------------------------------
-
-    do g = bounds%begg, bounds%endg
-       this%cropprod1_grc(g) = 0._r8
-       this%prod10_grc(g) = 0._r8
-       this%prod100_grc(g) = 0._r8
-       this%tot_woodprod_grc(g) = 0._r8
-    end do
-
-    ! Need to set these patch-level fluxes to 0 everywhere for the sake of special
-    ! landunits (because they don't get set over special landunits in the run loop)
-    do p = bounds%begp, bounds%endp
-       this%hrv_deadstem_to_prod10_patch(p) = 0._r8
-       this%hrv_deadstem_to_prod100_patch(p) = 0._r8
-       this%grain_to_cropprod1_patch(p) = 0._r8
-    end do
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, &
-       template_for_missing_fields, template_multiplier)
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t, ncd_double
-    use restUtilMod, only : restartvar, set_missing_from_template, set_grc_field_from_col_field
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    type(file_desc_t), intent(inout) :: ncid
-    character(len=*), intent(in) :: flag  ! 'read' or 'write'
-
-    ! If template_for_missing_fields and template_multiplier are provided, then: When
-    ! reading the restart file, for any field not present on the restart file, the field
-    ! in this object is set equal to the corresponding field in
-    ! template_for_missing_fields times template_multiplier.
-    !
-    ! The Restart routine must have been called on template_for_missing_fields before
-    ! calling it on this object.
-    ! 
-    ! (Must provide both template_for_missing_fields and template_multiplier or neither)
-    class(cn_products_type), optional, intent(in) :: template_for_missing_fields
-    real(r8), optional, intent(in) :: template_multiplier
-
-    !
-    ! !LOCAL VARIABLES:
-    logical :: template_provided
-    logical :: readvar
-
-    character(len=*), parameter :: subname = 'Restart'
-    !-----------------------------------------------------------------------
-
-    if (present(template_for_missing_fields) .and. present(template_multiplier)) then
-       template_provided = .true.
-    else if (present(template_for_missing_fields)) then
-       call endrun(&
-            msg='template_for_missing_fields provided; must also provide template_multiplier' // &
-            errMsg(sourcefile, __LINE__))
-    else if (present(template_multiplier)) then
-       call endrun(&
-            msg='template_multiplier provided; must also provide template_for_missing_fields' // &
-            errMsg(sourcefile, __LINE__))
-    else
-       template_provided = .false.
-    end if
-
-    ! NOTE(wjs, 2016-03-29) Adding '_g' suffixes to the end of the restart field names to
-    ! distinguish these gridcell-level restart fields from the obsolete column-level
-    ! restart fields that are present on old restart files.
-
-    call restartvar(ncid=ncid, flag=flag, &
-         varname=this%species%rest_fname('cropprod1', suffix='_g'), &
-         xtype=ncd_double, dim1name='gridcell', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%cropprod1_grc)
-    if (flag == 'read' .and. .not. readvar) then
-       ! BACKWARDS_COMPATIBILITY(wjs, 2016-03-31) If the gridcell-level field isn't
-       ! present, try to find a column-level field (which may be present on an older
-       ! restart file).
-       call set_grc_field_from_col_field( &
-            bounds = bounds, &
-            ncid = ncid, &
-            varname = this%species%rest_fname('cropprod1'), &
-            data_grc = this%cropprod1_grc, &
-            readvar = readvar)
-
-       ! If we still haven't found an appropriate field on the restart file, then set
-       ! this field from the template, if provided
-       if (.not. readvar .and. template_provided) then
-          call set_missing_from_template(this%cropprod1_grc, &
-               template_for_missing_fields%cropprod1_grc, &
-               multiplier = template_multiplier)
-       end if
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, &
-         varname=this%species%rest_fname('prod10', suffix='_g'), &
-         xtype=ncd_double, dim1name='gridcell', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%prod10_grc)
-    if (flag == 'read' .and. .not. readvar) then
-       ! BACKWARDS_COMPATIBILITY(wjs, 2016-03-31) If the gridcell-level field isn't
-       ! present, try to find a column-level field (which may be present on an older
-       ! restart file).
-       call set_grc_field_from_col_field( &
-            bounds = bounds, &
-            ncid = ncid, &
-            varname = this%species%rest_fname('prod10'), &
-            data_grc = this%prod10_grc, &
-            readvar = readvar)
-
-       ! If we still haven't found an appropriate field on the restart file, then set
-       ! this field from the template, if provided
-       if (.not. readvar .and. template_provided) then
-          call set_missing_from_template(this%prod10_grc, &
-               template_for_missing_fields%prod10_grc, &
-               multiplier = template_multiplier)
-       end if
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, &
-         varname=this%species%rest_fname('prod100', suffix='_g'), &
-         xtype=ncd_double, dim1name='gridcell', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%prod100_grc)
-    if (flag == 'read' .and. .not. readvar) then
-       ! BACKWARDS_COMPATIBILITY(wjs, 2016-03-31) If the gridcell-level field isn't
-       ! present, try to find a column-level field (which may be present on an older
-       ! restart file).
-       call set_grc_field_from_col_field( &
-            bounds = bounds, &
-            ncid = ncid, &
-            varname = this%species%rest_fname('prod100'), &
-            data_grc = this%prod100_grc, &
-            readvar = readvar)
-
-       ! If we still haven't found an appropriate field on the restart file, then set
-       ! this field from the template, if provided
-       if (.not. readvar .and. template_provided) then
-          call set_missing_from_template(this%prod100_grc, &
-               template_for_missing_fields%prod100_grc, &
-               multiplier = template_multiplier)
-       end if
-    end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine UpdateProducts(this, bounds, &
-       num_soilp, filter_soilp, &
-       dwt_wood_product_gain_patch, &
-       wood_harvest_patch, &
-       dwt_crop_product_gain_patch, &
-       grain_to_cropprod_patch)
-    !
-    ! !DESCRIPTION:
-    ! Update all loss fluxes from wood and grain product pools, and update product pool
-    ! state variables for both loss and gain terms
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type) , intent(inout) :: this
-    type(bounds_type)       , intent(in)    :: bounds
-    integer                 , intent(in)    :: num_soilp       ! number of soil patches in filter
-    integer                 , intent(in)    :: filter_soilp(:) ! filter for soil patches
-
-    ! dynamic landcover addition to wood product pools (g/m2/s) [patch]; although this is
-    ! a patch-level flux, it is expressed per unit GRIDCELL area
-    real(r8), intent(in) :: dwt_wood_product_gain_patch( bounds%begp: )
-
-    ! wood harvest addition to wood product pools (g/m2/s) [patch]
-    real(r8), intent(in) :: wood_harvest_patch( bounds%begp: )
-
-    ! dynamic landcover addition to crop product pools (g/m2/s) [patch]; although this is
-    ! a patch-level flux, it is expressed per unit GRIDCELL area
-    real(r8), intent(in) :: dwt_crop_product_gain_patch( bounds%begp: )
-
-    ! grain to crop product pool (g/m2/s) [patch]
-    real(r8), intent(in) :: grain_to_cropprod_patch( bounds%begp: )
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g        ! indices
-    real(r8) :: dt       ! time step (seconds)
-    real(r8) :: kprod1   ! decay constant for 1-year product pool
-    real(r8) :: kprod10  ! decay constant for 10-year product pool
-    real(r8) :: kprod100 ! decay constant for 100-year product pool
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(dwt_wood_product_gain_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(wood_harvest_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(dwt_crop_product_gain_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(grain_to_cropprod_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-
-    call this%PartitionWoodFluxes(bounds, &
-         num_soilp, filter_soilp, &
-         dwt_wood_product_gain_patch(bounds%begp:bounds%endp), &
-         wood_harvest_patch(bounds%begp:bounds%endp))
-
-    call this%PartitionGrainFluxes(bounds, &
-         num_soilp, filter_soilp, &
-         dwt_crop_product_gain_patch(bounds%begp:bounds%endp), &
-         grain_to_cropprod_patch(bounds%begp:bounds%endp))
-
-    ! calculate losses from product pools
-    ! the following (1/s) rate constants result in ~90% loss of initial state over 1, 10 and 100 years,
-    ! respectively, using a discrete-time fractional decay algorithm.
-    kprod1  = 7.2e-8
-    kprod10 = 7.2e-9
-    kprod100 = 7.2e-10
-
-    do g = bounds%begg, bounds%endg
-       ! calculate fluxes out of product pools (1/sec)
-       this%cropprod1_loss_grc(g) = this%cropprod1_grc(g) * kprod1
-       this%prod10_loss_grc(g)    = this%prod10_grc(g)    * kprod10
-       this%prod100_loss_grc(g)   = this%prod100_grc(g)   * kprod100
-    end do
-
-    ! set time steps
-    dt = real( get_step_size(), r8 )
-
-    ! update product state variables
-    do g = bounds%begg, bounds%endg
-
-       ! fluxes into wood & grain product pools, from landcover change
-       this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%dwt_cropprod1_gain_grc(g)*dt
-       this%prod10_grc(g)    = this%prod10_grc(g)    + this%dwt_prod10_gain_grc(g)*dt
-       this%prod100_grc(g)   = this%prod100_grc(g)   + this%dwt_prod100_gain_grc(g)*dt
-
-       ! fluxes into wood & grain product pools, from harvest
-       this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%grain_to_cropprod1_grc(g)*dt
-       this%prod10_grc(g)    = this%prod10_grc(g)    + this%hrv_deadstem_to_prod10_grc(g)*dt
-       this%prod100_grc(g)   = this%prod100_grc(g)   + this%hrv_deadstem_to_prod100_grc(g)*dt
-
-       ! fluxes out of wood & grain product pools, from decomposition
-       this%cropprod1_grc(g) = this%cropprod1_grc(g) - this%cropprod1_loss_grc(g)*dt
-       this%prod10_grc(g)    = this%prod10_grc(g)    - this%prod10_loss_grc(g)*dt
-       this%prod100_grc(g)   = this%prod100_grc(g)   - this%prod100_loss_grc(g)*dt
-
-    end do
-
-    call this%ComputeSummaryVars(bounds)
-
-  end subroutine UpdateProducts
-
-  !-----------------------------------------------------------------------
-  subroutine PartitionWoodFluxes(this, bounds, &
-       num_soilp, filter_soilp, &
-       dwt_wood_product_gain_patch, &
-       wood_harvest_patch)
-    !
-    ! !DESCRIPTION:
-    ! Partition input wood fluxes into 10 and 100 year product pools
-    !
-    ! !USES:
-    use pftconMod    , only : pftcon
-    use subgridAveMod, only : p2g
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type) , intent(inout) :: this
-    type(bounds_type)       , intent(in)    :: bounds
-    integer                 , intent(in)    :: num_soilp       ! number of soil patches in filter
-    integer                 , intent(in)    :: filter_soilp(:) ! filter for soil patches
-
-    ! dynamic landcover addition to wood product pools (g/m2/s) [patch]; although this is
-    ! a patch-level flux, it is expressed per unit GRIDCELL area
-    real(r8), intent(in) :: dwt_wood_product_gain_patch( bounds%begp: )
-
-    ! wood harvest addition to wood product pools (g/m2/s) [patch]
-    real(r8), intent(in) :: wood_harvest_patch( bounds%begp: )
-
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fp
-    integer :: p
-    integer :: g
-    real(r8) :: pprod10       ! PFT proportion of deadstem to 10-year product pool
-    real(r8) :: pprod100      ! PFT proportion of deadstem to 100-year product pool
-    real(r8) :: pprod_tot     ! PFT proportion of deadstem to any product pool
-    real(r8) :: pprod10_frac  ! PFT fraction of deadstem to product pool that goes to 10-year product pool
-    real(r8) :: pprod100_frac ! PFT fraction of deadstem to product pool that goes to 100-year product pool
-
-    character(len=*), parameter :: subname = 'PartitionWoodFluxes'
-    !-----------------------------------------------------------------------
-
-    ! Partition patch-level harvest fluxes to 10 and 100-year product pools
-    do fp = 1, num_soilp
-       p = filter_soilp(fp)
-       this%hrv_deadstem_to_prod10_patch(p)  = &
-            wood_harvest_patch(p) * pftcon%pprodharv10(patch%itype(p))
-       this%hrv_deadstem_to_prod100_patch(p) = &
-            wood_harvest_patch(p) * (1.0_r8 - pftcon%pprodharv10(patch%itype(p)))
-    end do
-
-    ! Average harvest fluxes from patch to gridcell
-    call p2g(bounds, &
-         this%hrv_deadstem_to_prod10_patch(bounds%begp:bounds%endp), &
-         this%hrv_deadstem_to_prod10_grc(bounds%begg:bounds%endg), &
-         p2c_scale_type = 'unity', &
-         c2l_scale_type = 'unity', &
-         l2g_scale_type = 'unity')
-
-    call p2g(bounds, &
-         this%hrv_deadstem_to_prod100_patch(bounds%begp:bounds%endp), &
-         this%hrv_deadstem_to_prod100_grc(bounds%begg:bounds%endg), &
-         p2c_scale_type = 'unity', &
-         c2l_scale_type = 'unity', &
-         l2g_scale_type = 'unity')
-
-    ! Zero the dwt gains
-    do g = bounds%begg, bounds%endg
-       this%dwt_prod10_gain_grc(g) = 0._r8
-       this%dwt_prod100_gain_grc(g) = 0._r8
-    end do
-
-    ! Partition dynamic land cover fluxes to 10 and 100-year product pools.
-    do p = bounds%begp, bounds%endp
-       g = patch%gridcell(p)
-
-       ! Note that pprod10 + pprod100 do NOT sum to 1: some fraction of the dwt changes
-       ! was lost to other fluxes. dwt_wood_product_gain_patch gives the amount that goes
-       ! to all product pools, so we need to determine the fraction of that flux that
-       ! goes to each pool.
-       pprod10 = pftcon%pprod10(patch%itype(p))
-       pprod100 = pftcon%pprod100(patch%itype(p))
-       pprod_tot = pprod10 + pprod100
-       if (pprod_tot > 0) then
-          pprod10_frac = pprod10 / pprod_tot
-          pprod100_frac = pprod100 / pprod_tot
-       else
-          ! Avoid divide by 0
-          pprod10_frac = 0._r8
-          pprod100_frac = 0._r8
-       end if
-
-       ! Note that the patch-level fluxes are expressed per unit gridcell area. So, to go
-       ! from patch-level fluxes to gridcell-level fluxes, we simply add up the various
-       ! patch contributions, without having to multiply by any area weightings.
-       this%dwt_prod10_gain_grc(g) = this%dwt_prod10_gain_grc(g) + &
-            dwt_wood_product_gain_patch(p) * pprod10_frac
-       this%dwt_prod100_gain_grc(g) = this%dwt_prod100_gain_grc(g) + &
-            dwt_wood_product_gain_patch(p) * pprod100_frac
-    end do
-
-  end subroutine PartitionWoodFluxes
-
-  !-----------------------------------------------------------------------
-  subroutine PartitionGrainFluxes(this, bounds, &
-       num_soilp, filter_soilp, &
-       dwt_crop_product_gain_patch, &
-       grain_to_cropprod_patch)
-    !
-    ! !DESCRIPTION:
-    ! Partition input grain fluxes into crop product pools
-    !
-    ! For now this doesn't do much, since there is just a single (1-year) crop product
-    ! pool. But this provides the capability to add different crop product pools in the
-    ! future, without requiring any changes to code outside of this class. It also gives
-    ! symmetry with the wood fluxes.
-    !
-    ! !USES:
-    use subgridAveMod, only : p2g
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type) , intent(inout) :: this
-    type(bounds_type)       , intent(in)    :: bounds
-    integer                 , intent(in)    :: num_soilp       ! number of soil patches in filter
-    integer                 , intent(in)    :: filter_soilp(:) ! filter for soil patches
-
-    ! dynamic landcover addition to crop product pool (g/m2/s) [patch]; although this is
-    ! a patch-level flux, it is expressed per unit GRIDCELL area
-    real(r8), intent(in) :: dwt_crop_product_gain_patch( bounds%begp: )
-
-    ! grain to crop product pool(s) (g/m2/s) [patch]
-    real(r8)                , intent(in)    :: grain_to_cropprod_patch( bounds%begp: )
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fp
-    integer :: p
-    integer :: g
-
-    character(len=*), parameter :: subname = 'PartitionGrainFluxes'
-    !-----------------------------------------------------------------------
-
-    ! Determine gains from crop harvest
-
-    do fp = 1, num_soilp
-       p = filter_soilp(fp)
-
-       ! For now all crop product is put in the 1-year crop product pool
-       this%grain_to_cropprod1_patch(p) = grain_to_cropprod_patch(p)
-    end do
-
-    call p2g(bounds, &
-         this%grain_to_cropprod1_patch(bounds%begp:bounds%endp), &
-         this%grain_to_cropprod1_grc(bounds%begg:bounds%endg), &
-         p2c_scale_type = 'unity', &
-         c2l_scale_type = 'unity', &
-         l2g_scale_type = 'unity')
-
-    ! Determine gains from dynamic landcover
-
-    do g = bounds%begg, bounds%endg
-       this%dwt_cropprod1_gain_grc(g) = 0._r8
-    end do
-
-    do p = bounds%begp, bounds%endp
-       g = patch%gridcell(p)
-
-       ! Note that the patch-level fluxes are expressed per unit gridcell area. So, to go
-       ! from patch-level fluxes to gridcell-level fluxes, we simply add up the various
-       ! patch contributions, without having to multiply by any area weightings.
-       this%dwt_cropprod1_gain_grc(g) = this%dwt_cropprod1_gain_grc(g) + &
-            dwt_crop_product_gain_patch(p)
-    end do
-
-  end subroutine PartitionGrainFluxes
-
-
-  !-----------------------------------------------------------------------
-  subroutine ComputeSummaryVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Compute summary variables in this object: sums across multiple product pools
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_products_type) , intent(inout) :: this
-    type(bounds_type)       , intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g        ! indices
-
-    character(len=*), parameter :: subname = 'ComputeSummaryVars'
-    !-----------------------------------------------------------------------
-
-    do g = bounds%begg, bounds%endg
-
-       ! total wood products
-       this%tot_woodprod_grc(g) = &
-            this%prod10_grc(g) + &
-            this%prod100_grc(g)
-
-       ! total loss from wood products
-       this%tot_woodprod_loss_grc(g) = &
-            this%prod10_loss_grc(g) + &
-            this%prod100_loss_grc(g)
-
-       ! total loss from ALL products
-       this%product_loss_grc(g) = &
-            this%cropprod1_loss_grc(g) + &
-            this%prod10_loss_grc(g) + &
-            this%prod100_loss_grc(g)
-
-       this%dwt_woodprod_gain_grc(g) = &
-            this%dwt_prod100_gain_grc(g) + &
-            this%dwt_prod10_gain_grc(g)
-    end do
-
-  end subroutine ComputeSummaryVars
-
-
-end module CNProductsMod
diff --git a/src/biogeochem/CNSharedParamsMod.F90 b/src/biogeochem/CNSharedParamsMod.F90
deleted file mode 100644
index 42156b1158..0000000000
--- a/src/biogeochem/CNSharedParamsMod.F90
+++ /dev/null
@@ -1,192 +0,0 @@
-module CNSharedParamsMod
-
-  !-----------------------------------------------------------------------
-  !
-  ! !USES:
-  use shr_kind_mod , only: r8 => shr_kind_r8
-  implicit none
-
-  ! CNParamsShareInst.  PGI wants the type decl. public but the instance
-  ! is indeed protected.  A generic private statement at the start of the module
-  ! overrides the protected functionality with PGI
-
-  type, public  :: CNParamsShareType
-      real(r8) :: Q10                   ! temperature dependence
-      real(r8) :: minpsi                ! minimum soil water potential for heterotrophic resp	  
-      real(r8) :: cwd_fcel              ! cellulose fraction of coarse woody debris
-      real(r8) :: cwd_flig              ! lignin fraction of coarse woody debris
-      real(r8) :: froz_q10              ! separate q10 for frozen soil respiration rates
-      real(r8) :: decomp_depth_efolding ! e-folding depth for reduction in decomposition (m) 
-      real(r8) :: mino2lim              ! minimum anaerobic decomposition rate as a fraction of potential aerobic rate
-      real(r8) :: organic_max           ! organic matter content (kg/m3) where soil is assumed to act like peat
-      logical  :: constrain_stress_deciduous_onset ! if true use additional constraint on stress deciduous onset trigger
-  end type CNParamsShareType
-
-  type(CNParamsShareType), protected :: CNParamsShareInst
-
-  logical, public :: anoxia_wtsat = .false.
-  logical, public :: use_fun      = .false.             ! Use the FUN2.0 model
-  integer, public :: nlev_soildecomp_standard = 5
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-  
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine CNParamsReadShared(ncid, namelist_file)
-
-    use ncdio_pio   , only : file_desc_t
-
-    type(file_desc_t), intent(inout) :: ncid   ! pio netCDF file id
-    character(len=*),  intent(in) :: namelist_file
-
-    call CNParamsReadShared_netcdf(ncid)
-    call CNParamsReadShared_namelist(namelist_file)
-
-  end subroutine CNParamsReadShared
-  
-  !-----------------------------------------------------------------------
-  subroutine CNParamsReadShared_netcdf(ncid)
-    !
-    use ncdio_pio   , only : file_desc_t, ncd_io
-    use abortutils  , only : endrun
-    use shr_log_mod , only : errMsg => shr_log_errMsg
-    !
-    implicit none
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    character(len=32)  :: subname = 'CNParamsReadShared'
-    character(len=100) :: errCode = '-Error reading in CN and BGC shared params file. Var:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in parameter
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-    !
-    ! netcdf read here
-    !
-    tString='q10_mr'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%Q10=tempr
-
-    tString='minpsi_hr'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%minpsi=tempr 
-
-    tString='cwd_fcel'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%cwd_fcel=tempr
-
-    tString='cwd_flig'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%cwd_flig=tempr 
-
-    tString='froz_q10'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%froz_q10=tempr   
-
-    tString='mino2lim'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%mino2lim=tempr 
-    !CNParamsShareInst%mino2lim=0.2_r8 
-
-    tString='organic_max'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    CNParamsShareInst%organic_max=tempr
-
-  end subroutine CNParamsReadShared_netcdf
-  
-  !-----------------------------------------------------------------------
-  subroutine CNParamsReadShared_namelist(namelist_file)
-    !
-    ! !DESCRIPTION:
-    ! Read and initialize CN Shared parameteres from the namelist.
-    !
-    ! !USES:
-    use fileutils   , only : relavu, getavu
-    use spmdMod     , only : masterproc, mpicom, MPI_REAL8, MPI_LOGICAL
-    use shr_nl_mod  , only : shr_nl_find_group_name
-    use shr_log_mod , only : errMsg => shr_log_errMsg
-    use clm_varctl  , only : iulog
-    use abortutils  , only : endrun
-    use shr_mpi_mod , only : shr_mpi_bcast
-    
-    !
-    implicit none
-    !
-
-    character(len=*), intent(in) :: namelist_file
-    
-    integer :: i,j,n                ! loop indices
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-
-    real(r8) :: decomp_depth_efolding = 0.0_r8
-    logical  :: constrain_stress_deciduous_onset = .false.
-
-    character(len=32) :: subroutine_name = 'CNParamsReadNamelist'
-    character(len=10) :: namelist_group = 'bgc_shared'
-
-    !-----------------------------------------------------------------------
-
-    ! ----------------------------------------------------------------------
-    ! Namelist Variables
-    ! ----------------------------------------------------------------------
-
-    namelist /bgc_shared/ &
-         decomp_depth_efolding,       &
-         constrain_stress_deciduous_onset
-
-
-    ! Read namelist from standard input.
-    if (masterproc) then
-
-       write(iulog,*) 'Attempting to read CN/BGC shared namelist parameters .....'
-       unitn = getavu()
-       write(iulog,*) 'Read in ' // namelist_group // ' namelist from: ', trim(namelist_file)
-       open( unitn, file=trim(namelist_file), status='old' )
-       call shr_nl_find_group_name(unitn, namelist_group, status=ierr)
-       if (ierr == 0) then
-          read(unitn, bgc_shared, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg='error in reading in ' // namelist_group // ' namelist' // &
-                  errMsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg='error in finding ' // namelist_group // ' namelist' // &
-                  errMsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-
-    end if ! masterproc
-
-    ! Broadcast the parameters from master
-    call shr_mpi_bcast ( decomp_depth_efolding, mpicom )
-    call shr_mpi_bcast ( constrain_stress_deciduous_onset, mpicom )
-
-    ! Save the parameter to the instance
-    CNParamsShareInst%decomp_depth_efolding = decomp_depth_efolding
-    CNParamsShareInst%constrain_stress_deciduous_onset = constrain_stress_deciduous_onset
-
-    ! Output read parameters to the lnd.log
-    if (masterproc) then
-       write(iulog,*) 'CN/BGC shared namelist parameters:'
-       write(iulog,*)' '
-       write(iulog,*)'  decomp_depth_efolding = ', decomp_depth_efolding
-       write(iulog,*)'  constrain_stress_deciduous_onset = ',constrain_stress_deciduous_onset
-
-       write(iulog,*)
-
-    end if
-
-  end subroutine CNParamsReadShared_namelist
-
-end module CNSharedParamsMod
diff --git a/src/biogeochem/CNSpeciesMod.F90 b/src/biogeochem/CNSpeciesMod.F90
deleted file mode 100644
index fc89f3ac02..0000000000
--- a/src/biogeochem/CNSpeciesMod.F90
+++ /dev/null
@@ -1,68 +0,0 @@
-module CNSpeciesMod
-
-  !-----------------------------------------------------------------------
-  ! Module holding information about different species available in the CN code (C, C13,
-  ! C14, N).
-  !
-  !
-  ! NOTE(wjs, 2016-06-05) Eventually I could imagine having a cn_species base class, with
-  ! derived classes for each species type - so a cn_species_c class, a cn_species_c13
-  ! class, a cn_species_c14 class and a cn_species_n class. These would contain methods
-  ! to handle calculations specific to each species type. For example, there could be a
-  ! carbon_multiplier method that returns the species-specific multiplier that you would
-  ! apply to a variable in units of gC/m2 to give you g[this species]/m2 (this would
-  ! depend on pft type).
-  !
-  ! Basically, anywhere where there is code that has a conditional based on the constants
-  ! defined here, we could replace that with polymorphism using a cn_species class.
-  !
-  ! Eventually I think it would make sense to make this contain an instance of
-  ! species_base_type (i.e., the class used to determine history & restart field names),
-  ! with forwarding methods. So then (e.g.) a cn_products_type object would just contain a
-  ! cn_species object (which in turn would contain a species_metadata [or whatever we call
-  ! it] object).
-
-  implicit none
-  private
-
-  integer, parameter, public :: CN_SPECIES_C12 = 1
-  integer, parameter, public :: CN_SPECIES_C13 = 2
-  integer, parameter, public :: CN_SPECIES_C14 = 3
-  integer, parameter, public :: CN_SPECIES_N   = 4
-
-  public :: species_from_string  ! convert a string representation to one of the constants defined here
-
-contains
-
-  !-----------------------------------------------------------------------
-  function species_from_string(species_string) result(species)
-    !
-    ! !DESCRIPTION:
-    ! Convert a string representation to one of the constants defined here
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    integer :: species  ! function result
-    character(len=*), intent(in) :: species_string  ! string representation of species (should be lowercase)
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'species_from_string'
-    !-----------------------------------------------------------------------
-
-    select case (species_string)
-    case ('c12')
-       species = CN_SPECIES_C12
-    case ('c13')
-       species = CN_SPECIES_C13
-    case ('c14')
-       species = CN_SPECIES_C14
-    case ('n')
-       species = CN_SPECIES_N
-    end select
-
-  end function species_from_string
-
-
-end module CNSpeciesMod
diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90
deleted file mode 100644
index 3fa76b3af2..0000000000
--- a/src/biogeochem/CNVegCarbonFluxType.F90
+++ /dev/null
@@ -1,3891 +0,0 @@
-module CNVegCarbonFluxType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  !
-  ! !USES:
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use decompMod                          , only : bounds_type
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : nlevdecomp_full, nlevgrnd, nlevdecomp
-  use clm_varcon                         , only : spval, dzsoi_decomp
-  use clm_varctl                         , only : use_cndv, use_nitrif_denitrif, use_crop
-  use clm_varctl                         , only : use_grainproduct
-  use clm_varctl                         , only : iulog
-  use landunit_varcon                    , only : istsoil, istcrop, istdlak 
-  use pftconMod                          , only : npcropmin
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  use PatchType                          , only : patch                
-  use abortutils                         , only : endrun
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  type, public :: cnveg_carbonflux_type
-
-     ! gap mortality fluxes
-     real(r8), pointer :: m_leafc_to_litter_patch                   (:)     ! leaf C mortality (gC/m2/s)
-     real(r8), pointer :: m_leafc_storage_to_litter_patch           (:)     ! leaf C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_leafc_xfer_to_litter_patch              (:)     ! leaf C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_frootc_to_litter_patch                  (:)     ! fine root C mortality (gC/m2/s)
-     real(r8), pointer :: m_frootc_storage_to_litter_patch          (:)     ! fine root C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_frootc_xfer_to_litter_patch             (:)     ! fine root C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_livestemc_to_litter_patch               (:)     ! live stem C mortality (gC/m2/s)
-     real(r8), pointer :: m_livestemc_storage_to_litter_patch       (:)     ! live stem C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_livestemc_xfer_to_litter_patch          (:)     ! live stem C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_deadstemc_to_litter_patch               (:)     ! dead stem C mortality (gC/m2/s)
-     real(r8), pointer :: m_deadstemc_storage_to_litter_patch       (:)     ! dead stem C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_deadstemc_xfer_to_litter_patch          (:)     ! dead stem C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_livecrootc_to_litter_patch              (:)     ! live coarse root C mortality (gC/m2/s)
-     real(r8), pointer :: m_livecrootc_storage_to_litter_patch      (:)     ! live coarse root C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_livecrootc_xfer_to_litter_patch         (:)     ! live coarse root C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_deadcrootc_to_litter_patch              (:)     ! dead coarse root C mortality (gC/m2/s)
-     real(r8), pointer :: m_deadcrootc_storage_to_litter_patch      (:)     ! dead coarse root C storage mortality (gC/m2/s)
-     real(r8), pointer :: m_deadcrootc_xfer_to_litter_patch         (:)     ! dead coarse root C transfer mortality (gC/m2/s)
-     real(r8), pointer :: m_gresp_storage_to_litter_patch           (:)     ! growth respiration storage mortality (gC/m2/s)
-     real(r8), pointer :: m_gresp_xfer_to_litter_patch              (:)     ! growth respiration transfer mortality (gC/m2/s)
-
-     ! harvest mortality fluxes
-     real(r8), pointer :: hrv_leafc_to_litter_patch                 (:)     ! leaf C harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_leafc_storage_to_litter_patch         (:)     ! leaf C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_leafc_xfer_to_litter_patch            (:)     ! leaf C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_frootc_to_litter_patch                (:)     ! fine root C harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_frootc_storage_to_litter_patch        (:)     ! fine root C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_frootc_xfer_to_litter_patch           (:)     ! fine root C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livestemc_to_litter_patch             (:)     ! live stem C harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livestemc_storage_to_litter_patch     (:)     ! live stem C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livestemc_xfer_to_litter_patch        (:)     ! live stem C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_deadstemc_storage_to_litter_patch     (:)     ! dead stem C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_deadstemc_xfer_to_litter_patch        (:)     ! dead stem C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livecrootc_to_litter_patch            (:)     ! live coarse root C harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livecrootc_storage_to_litter_patch    (:)     ! live coarse root C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_livecrootc_xfer_to_litter_patch       (:)     ! live coarse root C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_deadcrootc_to_litter_patch            (:)     ! dead coarse root C harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_deadcrootc_storage_to_litter_patch    (:)     ! dead coarse root C storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_deadcrootc_xfer_to_litter_patch       (:)     ! dead coarse root C transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_gresp_storage_to_litter_patch         (:)     ! growth respiration storage harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_gresp_xfer_to_litter_patch            (:)     ! growth respiration transfer harvest mortality (gC/m2/s)
-     real(r8), pointer :: hrv_xsmrpool_to_atm_patch                 (:)     ! excess MR pool harvest mortality (gC/m2/s)
-
-     ! fire fluxes 
-     real(r8), pointer :: m_leafc_to_fire_patch                     (:)     ! (gC/m2/s) fire C emissions from leafc 
-     real(r8), pointer :: m_leafc_storage_to_fire_patch             (:)     ! (gC/m2/s) fire C emissions from leafc_storage             
-     real(r8), pointer :: m_leafc_xfer_to_fire_patch                (:)     ! (gC/m2/s) fire C emissions from leafc_xfer
-     real(r8), pointer :: m_livestemc_to_fire_patch                 (:)     ! (gC/m2/s) fire C emissions from livestemc
-     real(r8), pointer :: m_livestemc_storage_to_fire_patch         (:)     ! (gC/m2/s) fire C emissions from livestemc_storage       
-     real(r8), pointer :: m_livestemc_xfer_to_fire_patch            (:)     ! (gC/m2/s) fire C emissions from livestemc_xfer
-     real(r8), pointer :: m_deadstemc_to_fire_patch                 (:)     ! (gC/m2/s) fire C emissions from deadstemc_xfer
-     real(r8), pointer :: m_deadstemc_storage_to_fire_patch         (:)     ! (gC/m2/s) fire C emissions from deadstemc_storage         
-     real(r8), pointer :: m_deadstemc_xfer_to_fire_patch            (:)     ! (gC/m2/s) fire C emissions from deadstemc_xfer
-     real(r8), pointer :: m_frootc_to_fire_patch                    (:)     ! (gC/m2/s) fire C emissions from frootc
-     real(r8), pointer :: m_frootc_storage_to_fire_patch            (:)     ! (gC/m2/s) fire C emissions from frootc_storage
-     real(r8), pointer :: m_frootc_xfer_to_fire_patch               (:)     ! (gC/m2/s) fire C emissions from frootc_xfer
-     real(r8), pointer :: m_livecrootc_to_fire_patch                (:)     ! (gC/m2/s) fire C emissions from livecrootc
-     real(r8), pointer :: m_livecrootc_storage_to_fire_patch        (:)     ! (gC/m2/s) fire C emissions from livecrootc_storage     
-     real(r8), pointer :: m_livecrootc_xfer_to_fire_patch           (:)     ! (gC/m2/s) fire C emissions from livecrootc_xfer
-     real(r8), pointer :: m_deadcrootc_to_fire_patch                (:)     ! (gC/m2/s) fire C emissions from deadcrootc
-     real(r8), pointer :: m_deadcrootc_storage_to_fire_patch        (:)     ! (gC/m2/s) fire C emissions from deadcrootc_storage 
-     real(r8), pointer :: m_deadcrootc_xfer_to_fire_patch           (:)     ! (gC/m2/s) fire C emissions from deadcrootc_xfer
-     real(r8), pointer :: m_gresp_storage_to_fire_patch             (:)     ! (gC/m2/s) fire C emissions from gresp_storage 
-     real(r8), pointer :: m_gresp_xfer_to_fire_patch                (:)     ! (gC/m2/s) fire C emissions from gresp_xfer
-     real(r8), pointer :: m_leafc_to_litter_fire_patch              (:)     ! (gC/m2/s) from leafc to litter c due to fire
-     real(r8), pointer :: m_leafc_storage_to_litter_fire_patch      (:)     ! (gC/m2/s) from leafc_storage to litter C  due to fire               
-     real(r8), pointer :: m_leafc_xfer_to_litter_fire_patch         (:)     ! (gC/m2/s) from leafc_xfer to litter C  due to fire               
-     real(r8), pointer :: m_livestemc_to_litter_fire_patch          (:)     ! (gC/m2/s) from livestemc to litter C  due to fire               
-     real(r8), pointer :: m_livestemc_storage_to_litter_fire_patch  (:)     ! (gC/m2/s) from livestemc_storage to litter C due to fire      
-     real(r8), pointer :: m_livestemc_xfer_to_litter_fire_patch     (:)     ! (gC/m2/s) from livestemc_xfer to litter C due to fire      
-     real(r8), pointer :: m_livestemc_to_deadstemc_fire_patch       (:)     ! (gC/m2/s) from livestemc to deadstemc due to fire       
-     real(r8), pointer :: m_deadstemc_to_litter_fire_patch          (:)     ! (gC/m2/s) from deadstemc to litter C due to fire      
-     real(r8), pointer :: m_deadstemc_storage_to_litter_fire_patch  (:)     ! (gC/m2/s) from deadstemc_storage to litter C due to fire               
-     real(r8), pointer :: m_deadstemc_xfer_to_litter_fire_patch     (:)     ! (gC/m2/s) from deadstemc_xfer to litter C due to fire               
-     real(r8), pointer :: m_frootc_to_litter_fire_patch             (:)     ! (gC/m2/s) from frootc to litter C due to fire               
-     real(r8), pointer :: m_frootc_storage_to_litter_fire_patch     (:)     ! (gC/m2/s) from frootc_storage to litter C due to fire               
-     real(r8), pointer :: m_frootc_xfer_to_litter_fire_patch        (:)     ! (gC/m2/s) from frootc_xfer to litter C due to fire               
-     real(r8), pointer :: m_livecrootc_to_litter_fire_patch         (:)     ! (gC/m2/s) from livecrootc to litter C due to fire                     
-     real(r8), pointer :: m_livecrootc_storage_to_litter_fire_patch (:)     ! (gC/m2/s) from livecrootc_storage to litter C due to fire                     
-     real(r8), pointer :: m_livecrootc_xfer_to_litter_fire_patch    (:)     ! (gC/m2/s) from livecrootc_xfer to litter C due to fire                     
-     real(r8), pointer :: m_livecrootc_to_deadcrootc_fire_patch     (:)     ! (gC/m2/s) from livecrootc to deadstemc due to fire        
-     real(r8), pointer :: m_deadcrootc_to_litter_fire_patch         (:)     ! (gC/m2/s) from deadcrootc to litter C due to fire                       
-     real(r8), pointer :: m_deadcrootc_storage_to_litter_fire_patch (:)     ! (gC/m2/s) from deadcrootc_storage to litter C due to fire                       
-     real(r8), pointer :: m_deadcrootc_xfer_to_litter_fire_patch    (:)     ! (gC/m2/s) from deadcrootc_xfer to litter C due to fire                       
-     real(r8), pointer :: m_gresp_storage_to_litter_fire_patch      (:)     ! (gC/m2/s) from gresp_storage to litter C due to fire                       
-     real(r8), pointer :: m_gresp_xfer_to_litter_fire_patch         (:)     ! (gC/m2/s) from gresp_xfer to litter C due to fire                       
-
-     ! phenology fluxes from transfer pools                     
-     real(r8), pointer :: grainc_xfer_to_grainc_patch               (:)     ! grain C growth from storage for prognostic crop(gC/m2/s)
-     real(r8), pointer :: leafc_xfer_to_leafc_patch                 (:)     ! leaf C growth from storage (gC/m2/s)
-     real(r8), pointer :: frootc_xfer_to_frootc_patch               (:)     ! fine root C growth from storage (gC/m2/s)
-     real(r8), pointer :: livestemc_xfer_to_livestemc_patch         (:)     ! live stem C growth from storage (gC/m2/s)
-     real(r8), pointer :: deadstemc_xfer_to_deadstemc_patch         (:)     ! dead stem C growth from storage (gC/m2/s)
-     real(r8), pointer :: livecrootc_xfer_to_livecrootc_patch       (:)     ! live coarse root C growth from storage (gC/m2/s)
-     real(r8), pointer :: deadcrootc_xfer_to_deadcrootc_patch       (:)     ! dead coarse root C growth from storage (gC/m2/s)
-
-     ! leaf and fine root litterfall fluxes                          
-     real(r8), pointer :: leafc_to_litter_patch                     (:)     ! leaf C litterfall (gC/m2/s)
-     real(r8), pointer :: leafc_to_litter_fun_patch                 (:)     ! leaf C litterfall used by FUN (gC/m2/s)
-     real(r8), pointer :: frootc_to_litter_patch                    (:)     ! fine root C litterfall (gC/m2/s)
-     real(r8), pointer :: livestemc_to_litter_patch                 (:)     ! live stem C litterfall (gC/m2/s)
-     real(r8), pointer :: grainc_to_food_patch                      (:)     ! grain C to food for prognostic crop(gC/m2/s)
-     real(r8), pointer :: grainc_to_seed_patch                      (:)     ! grain C to seed for prognostic crop(gC/m2/s)
-
-     ! maintenance respiration fluxes     
-     real(r8), pointer :: cpool_to_resp_patch                       (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_leafc_resp_patch                 (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_leafc_storage_resp_patch         (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_frootc_resp_patch                (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_frootc_storage_resp_patch        (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_livecrootc_resp_patch            (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_livecrootc_storage_resp_patch    (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_livestemc_resp_patch             (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: cpool_to_livestemc_storage_resp_patch     (:)     ! CNflex excess C maintenance respiration (gC/m2/s)
-     real(r8), pointer :: leaf_mr_patch                             (:)     ! leaf maintenance respiration (gC/m2/s)
-     real(r8), pointer :: froot_mr_patch                            (:)     ! fine root maintenance respiration (gC/m2/s)
-     real(r8), pointer :: livestem_mr_patch                         (:)     ! live stem maintenance respiration (gC/m2/s)
-     real(r8), pointer :: livecroot_mr_patch                        (:)     ! live coarse root maintenance respiration (gC/m2/s)
-     real(r8), pointer :: grain_mr_patch                            (:)     ! crop grain or organs maint. respiration (gC/m2/s)
-     real(r8), pointer :: leaf_curmr_patch                          (:)     ! leaf maintenance respiration from current GPP (gC/m2/s)
-     real(r8), pointer :: froot_curmr_patch                         (:)     ! fine root maintenance respiration from current GPP (gC/m2/s)
-     real(r8), pointer :: livestem_curmr_patch                      (:)     ! live stem maintenance respiration from current GPP (gC/m2/s)
-     real(r8), pointer :: livecroot_curmr_patch                     (:)     ! live coarse root maintenance respiration from current GPP (gC/m2/s)
-     real(r8), pointer :: grain_curmr_patch                         (:)     ! crop grain or organs maint. respiration from current GPP (gC/m2/s)
-     real(r8), pointer :: leaf_xsmr_patch                           (:)     ! leaf maintenance respiration from storage (gC/m2/s)
-     real(r8), pointer :: froot_xsmr_patch                          (:)     ! fine root maintenance respiration from storage (gC/m2/s)
-     real(r8), pointer :: livestem_xsmr_patch                       (:)     ! live stem maintenance respiration from storage (gC/m2/s)
-     real(r8), pointer :: livecroot_xsmr_patch                      (:)     ! live coarse root maintenance respiration from storage (gC/m2/s)
-     real(r8), pointer :: grain_xsmr_patch                          (:)     ! crop grain or organs maint. respiration from storage (gC/m2/s)
-
-     ! photosynthesis fluxes                                   
-     real(r8), pointer :: psnsun_to_cpool_patch                     (:)     ! C fixation from sunlit canopy (gC/m2/s)
-     real(r8), pointer :: psnshade_to_cpool_patch                   (:)     ! C fixation from shaded canopy (gC/m2/s)
-
-     ! allocation fluxes, from current GPP                     
-     real(r8), pointer :: cpool_to_xsmrpool_patch                   (:)     ! allocation to maintenance respiration storage pool (gC/m2/s)
-     real(r8), pointer :: cpool_to_grainc_patch                     (:)     ! allocation to grain C for prognostic crop(gC/m2/s)
-     real(r8), pointer :: cpool_to_grainc_storage_patch             (:)     ! allocation to grain C storage for prognostic crop(gC/m2/s)
-     real(r8), pointer :: cpool_to_leafc_patch                      (:)     ! allocation to leaf C (gC/m2/s)
-     real(r8), pointer :: cpool_to_leafc_storage_patch              (:)     ! allocation to leaf C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_frootc_patch                     (:)     ! allocation to fine root C (gC/m2/s)
-     real(r8), pointer :: cpool_to_frootc_storage_patch             (:)     ! allocation to fine root C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_livestemc_patch                  (:)     ! allocation to live stem C (gC/m2/s)
-     real(r8), pointer :: cpool_to_livestemc_storage_patch          (:)     ! allocation to live stem C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_deadstemc_patch                  (:)     ! allocation to dead stem C (gC/m2/s)
-     real(r8), pointer :: cpool_to_deadstemc_storage_patch          (:)     ! allocation to dead stem C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_livecrootc_patch                 (:)     ! allocation to live coarse root C (gC/m2/s)
-     real(r8), pointer :: cpool_to_livecrootc_storage_patch         (:)     ! allocation to live coarse root C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_deadcrootc_patch                 (:)     ! allocation to dead coarse root C (gC/m2/s)
-     real(r8), pointer :: cpool_to_deadcrootc_storage_patch         (:)     ! allocation to dead coarse root C storage (gC/m2/s)
-     real(r8), pointer :: cpool_to_gresp_storage_patch              (:)     ! allocation to growth respiration storage (gC/m2/s)
-
-     ! growth respiration fluxes                               
-     real(r8), pointer :: xsmrpool_to_atm_patch                     (:)     ! excess MR pool harvest mortality (gC/m2/s)
-     real(r8), pointer :: cpool_leaf_gr_patch                       (:)     ! leaf growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_leaf_storage_gr_patch               (:)     ! leaf growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_leaf_gr_patch                    (:)     ! leaf growth respiration from storage (gC/m2/s)
-     real(r8), pointer :: cpool_froot_gr_patch                      (:)     ! fine root growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_froot_storage_gr_patch              (:)     ! fine root  growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_froot_gr_patch                   (:)     ! fine root  growth respiration from storage (gC/m2/s)
-     real(r8), pointer :: cpool_livestem_gr_patch                   (:)     ! live stem growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_livestem_storage_gr_patch           (:)     ! live stem growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_livestem_gr_patch                (:)     ! live stem growth respiration from storage (gC/m2/s)
-     real(r8), pointer :: cpool_deadstem_gr_patch                   (:)     ! dead stem growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_deadstem_storage_gr_patch           (:)     ! dead stem growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_deadstem_gr_patch                (:)     ! dead stem growth respiration from storage (gC/m2/s)
-     real(r8), pointer :: cpool_livecroot_gr_patch                  (:)     ! live coarse root growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_livecroot_storage_gr_patch          (:)     ! live coarse root growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_livecroot_gr_patch               (:)     ! live coarse root growth respiration from storage (gC/m2/s)
-     real(r8), pointer :: cpool_deadcroot_gr_patch                  (:)     ! dead coarse root growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_deadcroot_storage_gr_patch          (:)     ! dead coarse root growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_deadcroot_gr_patch               (:)     ! dead coarse root growth respiration from storage (gC/m2/s)
-
-     ! growth respiration for prognostic crop model
-     real(r8), pointer :: cpool_grain_gr_patch                      (:)     ! grain growth respiration (gC/m2/s)
-     real(r8), pointer :: cpool_grain_storage_gr_patch              (:)     ! grain growth respiration to storage (gC/m2/s)
-     real(r8), pointer :: transfer_grain_gr_patch                   (:)     ! grain growth respiration from storage (gC/m2/s)
-
-     ! annual turnover of storage to transfer pools            
-     real(r8), pointer :: grainc_storage_to_xfer_patch              (:)     ! grain C shift storage to transfer for prognostic crop model (gC/m2/s)
-     real(r8), pointer :: leafc_storage_to_xfer_patch               (:)     ! leaf C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: frootc_storage_to_xfer_patch              (:)     ! fine root C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: livestemc_storage_to_xfer_patch           (:)     ! live stem C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: deadstemc_storage_to_xfer_patch           (:)     ! dead stem C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: livecrootc_storage_to_xfer_patch          (:)     ! live coarse root C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: deadcrootc_storage_to_xfer_patch          (:)     ! dead coarse root C shift storage to transfer (gC/m2/s)
-     real(r8), pointer :: gresp_storage_to_xfer_patch               (:)     ! growth respiration shift storage to transfer (gC/m2/s)
-
-     ! turnover of livewood to deadwood
-     real(r8), pointer :: livestemc_to_deadstemc_patch              (:)     ! live stem C turnover (gC/m2/s)
-     real(r8), pointer :: livecrootc_to_deadcrootc_patch            (:)     ! live coarse root C turnover (gC/m2/s)
-
-     ! phenology: litterfall and crop fluxes
-     real(r8), pointer :: phenology_c_to_litr_met_c_col             (:,:)   ! C fluxes associated with phenology (litterfall and crop) to litter metabolic pool (gC/m3/s)
-     real(r8), pointer :: phenology_c_to_litr_cel_c_col             (:,:)   ! C fluxes associated with phenology (litterfall and crop) to litter cellulose pool (gC/m3/s)
-     real(r8), pointer :: phenology_c_to_litr_lig_c_col             (:,:)   ! C fluxes associated with phenology (litterfall and crop) to litter lignin pool (gC/m3/s)
-
-     ! gap mortality
-     real(r8), pointer :: gap_mortality_c_to_litr_met_c_col         (:,:)   ! C fluxes associated with gap mortality to litter metabolic pool (gC/m3/s)
-     real(r8), pointer :: gap_mortality_c_to_litr_cel_c_col         (:,:)   ! C fluxes associated with gap mortality to litter cellulose pool (gC/m3/s)
-     real(r8), pointer :: gap_mortality_c_to_litr_lig_c_col         (:,:)   ! C fluxes associated with gap mortality to litter lignin pool (gC/m3/s)
-     real(r8), pointer :: gap_mortality_c_to_cwdc_col               (:,:)   ! C fluxes associated with gap mortality to CWD pool (gC/m3/s)
-
-     ! fire
-     real(r8), pointer :: fire_mortality_c_to_cwdc_col              (:,:)   ! C fluxes associated with fire mortality to CWD pool (gC/m3/s)
-
-     ! harvest
-     real(r8), pointer :: harvest_c_to_litr_met_c_col               (:,:)   ! C fluxes associated with harvest to litter metabolic pool (gC/m3/s)
-     real(r8), pointer :: harvest_c_to_litr_cel_c_col               (:,:)   ! C fluxes associated with harvest to litter cellulose pool (gC/m3/s)
-     real(r8), pointer :: harvest_c_to_litr_lig_c_col               (:,:)   ! C fluxes associated with harvest to litter lignin pool (gC/m3/s)
-     real(r8), pointer :: harvest_c_to_cwdc_col                     (:,:)   ! C fluxes associated with harvest to CWD pool (gC/m3/s)
-     real(r8), pointer :: grainc_to_cropprodc_patch                 (:)     ! grain C to crop product pool (gC/m2/s)
-     real(r8), pointer :: grainc_to_cropprodc_col                   (:)     ! grain C to crop product pool (gC/m2/s)
-
-     ! fire fluxes
-     real(r8), pointer :: m_decomp_cpools_to_fire_vr_col            (:,:,:) ! vertically-resolved decomposing C fire loss (gC/m3/s)
-     real(r8), pointer :: m_decomp_cpools_to_fire_col               (:,:)   ! vertically-integrated (diagnostic) decomposing C fire loss (gC/m2/s)
-     real(r8), pointer :: m_c_to_litr_met_fire_col                  (:,:)   ! C from leaf, froot, xfer and storage C to litter labile C by fire (gC/m3/s) 
-     real(r8), pointer :: m_c_to_litr_cel_fire_col                  (:,:)   ! C from leaf, froot, xfer and storage C to litter cellulose C by fire (gC/m3/s) 
-     real(r8), pointer :: m_c_to_litr_lig_fire_col                  (:,:)   ! C from leaf, froot, xfer and storage C to litter lignin C by fire (gC/m3/s) 
-
-     ! dynamic landcover fluxes
-     real(r8), pointer :: dwt_seedc_to_leaf_patch                   (:)     ! (gC/m2/s) seed source to patch-level; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_seedc_to_leaf_grc                     (:)     ! (gC/m2/s) dwt_seedc_to_leaf_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_seedc_to_deadstem_patch               (:)     ! (gC/m2/s) seed source to patch-level; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_seedc_to_deadstem_grc                 (:)     ! (gC/m2/s) dwt_seedc_to_leaf_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_conv_cflux_patch                      (:)     ! (gC/m2/s) conversion C flux (immediate loss to atm); although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_conv_cflux_grc                        (:)     ! (gC/m2/s) dwt_conv_cflux_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_conv_cflux_dribbled_grc               (:)     ! (gC/m2/s) dwt_conv_cflux_grc dribbled evenly throughout the year
-     real(r8), pointer :: dwt_wood_productc_gain_patch              (:)     ! (gC/m2/s) addition to wood product pools from landcover change; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_crop_productc_gain_patch              (:)     ! (gC/m2/s) addition to crop product pools from landcover change; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_slash_cflux_col                       (:)     ! (gC/m2/s) conversion slash flux due to landcover change
-     real(r8), pointer :: dwt_frootc_to_litr_met_c_col              (:,:)   ! (gC/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_frootc_to_litr_cel_c_col              (:,:)   ! (gC/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_frootc_to_litr_lig_c_col              (:,:)   ! (gC/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_livecrootc_to_cwdc_col                (:,:)   ! (gC/m3/s) live coarse root to CWD due to landcover change
-     real(r8), pointer :: dwt_deadcrootc_to_cwdc_col                (:,:)   ! (gC/m3/s) dead coarse root to CWD due to landcover change
-
-     ! crop fluxes
-     real(r8), pointer :: crop_seedc_to_leaf_patch                  (:)     ! (gC/m2/s) seed source to leaf, for crops
-
-     ! summary (diagnostic) flux variables, not involved in mass balance
-     real(r8), pointer :: gpp_before_downreg_patch                  (:)     ! (gC/m2/s) gross primary production before down regulation
-     real(r8), pointer :: current_gr_patch                          (:)     ! (gC/m2/s) growth resp for new growth displayed in this timestep
-     real(r8), pointer :: transfer_gr_patch                         (:)     ! (gC/m2/s) growth resp for transfer growth displayed in this timestep
-     real(r8), pointer :: storage_gr_patch                          (:)     ! (gC/m2/s) growth resp for growth sent to storage for later display
-     real(r8), pointer :: plant_calloc_patch                        (:)     ! (gC/m2/s) total allocated C flux 
-     real(r8), pointer :: excess_cflux_patch                        (:)     ! (gC/m2/s) C flux not allocated due to downregulation 
-     real(r8), pointer :: prev_leafc_to_litter_patch                (:)     ! (gC/m2/s) previous timestep leaf C litterfall flux 
-     real(r8), pointer :: prev_frootc_to_litter_patch               (:)     ! (gC/m2/s) previous timestep froot C litterfall flux 
-     real(r8), pointer :: availc_patch                              (:)     ! (gC/m2/s) C flux available for allocation 
-     real(r8), pointer :: xsmrpool_recover_patch                    (:)     ! (gC/m2/s) C flux assigned to recovery of negative cpool
-     real(r8), pointer :: xsmrpool_c13ratio_patch                   (:)     ! C13/C(12+13) ratio for xsmrpool (proportion)
-
-     real(r8), pointer :: cwdc_hr_col                               (:)     ! (gC/m2/s) col-level coarse woody debris C heterotrophic respiration
-     real(r8), pointer :: cwdc_loss_col                             (:)     ! (gC/m2/s) col-level coarse woody debris C loss
-     real(r8), pointer :: litterc_loss_col                          (:)     ! (gC/m2/s) col-level litter C loss
-     real(r8), pointer :: frootc_alloc_patch                        (:)     ! (gC/m2/s) patch-level fine root C alloc
-     real(r8), pointer :: frootc_loss_patch                         (:)     ! (gC/m2/s) patch-level fine root C loss
-     real(r8), pointer :: leafc_alloc_patch                         (:)     ! (gC/m2/s) patch-level leaf C alloc
-     real(r8), pointer :: leafc_loss_patch                          (:)     ! (gC/m2/s) patch-level leaf C loss
-     real(r8), pointer :: woodc_alloc_patch                         (:)     ! (gC/m2/s) patch-level wood C alloc
-     real(r8), pointer :: woodc_loss_patch                          (:)     ! (gC/m2/s) patch-level wood C loss
-
-     real(r8), pointer :: gpp_patch                                 (:)     ! (gC/m2/s) patch gross primary production 
-     real(r8), pointer :: gpp_col                                   (:)     ! (gC/m2/s) column GPP flux before downregulation  (p2c)         
-     real(r8), pointer :: rr_patch                                  (:)     ! (gC/m2/s) root respiration (fine root MR + total root GR)
-     real(r8), pointer :: rr_col                                    (:)     ! (gC/m2/s) root respiration (fine root MR + total root GR) (p2c)
-     real(r8), pointer :: mr_patch                                  (:)     ! (gC/m2/s) maintenance respiration
-     real(r8), pointer :: gr_patch                                  (:)     ! (gC/m2/s) total growth respiration
-     real(r8), pointer :: ar_patch                                  (:)     ! (gC/m2/s) patch autotrophic respiration (MR + GR)
-     real(r8), pointer :: ar_col                                    (:)     ! (gC/m2/s) column autotrophic respiration (MR + GR) (p2c)      
-     real(r8), pointer :: npp_patch                                 (:)     ! (gC/m2/s) patch net primary production
-     real(r8), pointer :: npp_col                                   (:)     ! (gC/m2/s) column net primary production (p2c)                  
-     real(r8), pointer :: agnpp_patch                               (:)     ! (gC/m2/s) aboveground NPP
-     real(r8), pointer :: bgnpp_patch                               (:)     ! (gC/m2/s) belowground NPP
-     real(r8), pointer :: litfall_patch                             (:)     ! (gC/m2/s) patch litterfall (leaves and fine roots)
-     real(r8), pointer :: wood_harvestc_patch                       (:)     ! (gC/m2/s) patch-level wood harvest (to product pools)
-     real(r8), pointer :: wood_harvestc_col                         (:)     ! (gC/m2/s) column-level wood harvest (to product pools) (p2c)
-     real(r8), pointer :: slash_harvestc_patch                      (:)     ! (gC/m2/s) patch-level slash from harvest (to litter)
-     real(r8), pointer :: cinputs_patch                             (:)     ! (gC/m2/s) patch-level carbon inputs (for balance checking)
-     real(r8), pointer :: coutputs_patch                            (:)     ! (gC/m2/s) patch-level carbon outputs (for balance checking)
-     real(r8), pointer :: sr_col                                    (:)     ! (gC/m2/s) total soil respiration (HR + root resp)
-     real(r8), pointer :: er_col                                    (:)     ! (gC/m2/s) total ecosystem respiration, autotrophic + heterotrophic
-     real(r8), pointer :: litfire_col                               (:)     ! (gC/m2/s) litter fire losses
-     real(r8), pointer :: somfire_col                               (:)     ! (gC/m2/s) soil organic matter fire losses
-     real(r8), pointer :: totfire_col                               (:)     ! (gC/m2/s) total ecosystem fire losses
-     real(r8), pointer :: hrv_xsmrpool_to_atm_col                   (:)     ! (gC/m2/s) excess MR pool harvest mortality (p2c)
-
-     ! fire code
-     real(r8), pointer :: fire_closs_patch                          (:)     ! (gC/m2/s) total fire C loss 
-     real(r8), pointer :: fire_closs_p2c_col                        (:)     ! (gC/m2/s) patch2col averaged column-level fire C loss (p2c)
-     real(r8), pointer :: fire_closs_col                            (:)     ! (gC/m2/s) total patch-level fire C loss 
-
-     ! temporary and annual sums
-     real(r8), pointer :: tempsum_litfall_patch                     (:)     ! (gC/m2/yr) temporary annual sum of litfall (CNDV only for now)
-     real(r8), pointer :: annsum_litfall_patch                      (:)     ! (gC/m2/yr) annual sum of litfall (CNDV only for now)
-     real(r8), pointer :: tempsum_npp_patch                         (:)     ! (gC/m2/yr) temporary annual sum of NPP 
-     real(r8), pointer :: annsum_npp_patch                          (:)     ! (gC/m2/yr) annual sum of NPP 
-     real(r8), pointer :: annsum_npp_col                            (:)     ! (gC/m2/yr) annual sum of NPP, averaged from patch-level
-     real(r8), pointer :: lag_npp_col                               (:)     ! (gC/m2/yr) lagged net primary production
-
-     ! Summary C fluxes. 
-     real(r8), pointer :: nep_col        (:) ! (gC/m2/s) net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink
-     real(r8), pointer :: nbp_grc        (:) ! (gC/m2/s) net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux, positive for sink (same as net carbon exchange between land and atmosphere)
-     real(r8), pointer :: nee_grc        (:) ! (gC/m2/s) net ecosystem exchange of carbon, includes fire and hrv_xsmrpool, excludes landuse and harvest flux, positive for source 
-
-     ! Dynamic landcover fluxnes
-     real(r8), pointer :: landuseflux_grc(:) ! (gC/m2/s) dwt_conv_cflux+product_closs
-     real(r8), pointer :: npp_Nactive_patch                         (:)     ! C used by mycorrhizal uptake    (gC/m2/s)
-     real(r8), pointer :: npp_burnedoff_patch                       (:)     ! C that cannot be used for N uptake   (gC/m2/s)
-     real(r8), pointer :: npp_Nnonmyc_patch                         (:)     ! C used by non-myc uptake        (gC/m2/s)
-     real(r8), pointer :: npp_Nam_patch                             (:)     ! C used by AM plant              (gC/m2/s)
-     real(r8), pointer :: npp_Necm_patch                            (:)     ! C used by ECM plant             (gC/m2/s)
-     real(r8), pointer :: npp_Nactive_no3_patch                     (:)     ! C used by mycorrhizal uptake    (gC/m2/s)
-     real(r8), pointer :: npp_Nactive_nh4_patch                     (:)     ! C used by mycorrhizal uptake    (gC/m2/s)
-     real(r8), pointer :: npp_Nnonmyc_no3_patch                     (:)     ! C used by non-myc               (gC/m2/s)
-     real(r8), pointer :: npp_Nnonmyc_nh4_patch                     (:)     ! C used by non-myc               (gC/m2/s)
-     real(r8), pointer :: npp_Nam_no3_patch                         (:)     ! C used by AM plant              (gC/m2/s)
-     real(r8), pointer :: npp_Nam_nh4_patch                         (:)     ! C used by AM plant              (gC/m2/s)
-     real(r8), pointer :: npp_Necm_no3_patch                        (:)     ! C used by ECM plant             (gC/m2/s)
-     real(r8), pointer :: npp_Necm_nh4_patch                        (:)     ! C used by ECM plant             (gC/m2/s)
-     real(r8), pointer :: npp_Nfix_patch                            (:)     ! C used by Symbiotic BNF         (gC/m2/s)
-     real(r8), pointer :: npp_Nretrans_patch                        (:)     ! C used by retranslocation       (gC/m2/s)
-     real(r8), pointer :: npp_Nuptake_patch                         (:)     ! Total C used by N uptake in FUN (gC/m2/s)
-     real(r8), pointer :: npp_growth_patch                         (:)     ! Total C u for growth in FUN      (gC/m2/s)   
-     real(r8), pointer :: leafc_change_patch                        (:)     ! Total used C from leaves        (gC/m2/s)
-     real(r8), pointer :: soilc_change_patch                        (:)     ! Total used C from soil          (gC/m2/s)
- 
-   contains
-
-     procedure , public  :: Init   
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory
-     procedure , private :: InitCold
-     procedure , public  :: Restart
-     procedure , private :: RestartBulkOnly    ! Handle restart fields only present for bulk C
-     procedure , private :: RestartAllIsotopes ! Handle restart fields present for both bulk C and isotopes
-     procedure , public  :: SetValues
-
-  end type cnveg_carbonflux_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-   
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, carbon_type)
-
-    class(cnveg_carbonflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    character(len=3) , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-
-    call this%InitAllocate ( bounds, carbon_type)
-    call this%InitHistory ( bounds, carbon_type )
-    call this%InitCold (bounds )
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds, carbon_type)
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonflux_type) :: this 
-    type(bounds_type), intent(in) :: bounds 
-    character(len=*) , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    character(len=:), allocatable :: carbon_type_suffix
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%m_leafc_to_litter_patch                   (begp:endp)) ; this%m_leafc_to_litter_patch                   (:) = nan
-    allocate(this%m_frootc_to_litter_patch                  (begp:endp)) ; this%m_frootc_to_litter_patch                  (:) = nan
-    allocate(this%m_leafc_storage_to_litter_patch           (begp:endp)) ; this%m_leafc_storage_to_litter_patch           (:) = nan
-    allocate(this%m_frootc_storage_to_litter_patch          (begp:endp)) ; this%m_frootc_storage_to_litter_patch          (:) = nan
-    allocate(this%m_livestemc_storage_to_litter_patch       (begp:endp)) ; this%m_livestemc_storage_to_litter_patch       (:) = nan
-    allocate(this%m_deadstemc_storage_to_litter_patch       (begp:endp)) ; this%m_deadstemc_storage_to_litter_patch       (:) = nan
-    allocate(this%m_livecrootc_storage_to_litter_patch      (begp:endp)) ; this%m_livecrootc_storage_to_litter_patch      (:) = nan
-    allocate(this%m_deadcrootc_storage_to_litter_patch      (begp:endp)) ; this%m_deadcrootc_storage_to_litter_patch      (:) = nan
-    allocate(this%m_leafc_xfer_to_litter_patch              (begp:endp)) ; this%m_leafc_xfer_to_litter_patch              (:) = nan
-    allocate(this%m_frootc_xfer_to_litter_patch             (begp:endp)) ; this%m_frootc_xfer_to_litter_patch             (:) = nan
-    allocate(this%m_livestemc_xfer_to_litter_patch          (begp:endp)) ; this%m_livestemc_xfer_to_litter_patch          (:) = nan
-    allocate(this%m_deadstemc_xfer_to_litter_patch          (begp:endp)) ; this%m_deadstemc_xfer_to_litter_patch          (:) = nan
-    allocate(this%m_livecrootc_xfer_to_litter_patch         (begp:endp)) ; this%m_livecrootc_xfer_to_litter_patch         (:) = nan
-    allocate(this%m_deadcrootc_xfer_to_litter_patch         (begp:endp)) ; this%m_deadcrootc_xfer_to_litter_patch         (:) = nan
-    allocate(this%m_livestemc_to_litter_patch               (begp:endp)) ; this%m_livestemc_to_litter_patch               (:) = nan
-    allocate(this%m_deadstemc_to_litter_patch               (begp:endp)) ; this%m_deadstemc_to_litter_patch               (:) = nan
-    allocate(this%m_livecrootc_to_litter_patch              (begp:endp)) ; this%m_livecrootc_to_litter_patch              (:) = nan
-    allocate(this%m_deadcrootc_to_litter_patch              (begp:endp)) ; this%m_deadcrootc_to_litter_patch              (:) = nan
-    allocate(this%m_gresp_storage_to_litter_patch           (begp:endp)) ; this%m_gresp_storage_to_litter_patch           (:) = nan
-    allocate(this%m_gresp_xfer_to_litter_patch              (begp:endp)) ; this%m_gresp_xfer_to_litter_patch              (:) = nan
-    allocate(this%hrv_leafc_to_litter_patch                 (begp:endp)) ; this%hrv_leafc_to_litter_patch                 (:) = nan
-    allocate(this%hrv_leafc_storage_to_litter_patch         (begp:endp)) ; this%hrv_leafc_storage_to_litter_patch         (:) = nan
-    allocate(this%hrv_leafc_xfer_to_litter_patch            (begp:endp)) ; this%hrv_leafc_xfer_to_litter_patch            (:) = nan
-    allocate(this%hrv_frootc_to_litter_patch                (begp:endp)) ; this%hrv_frootc_to_litter_patch                (:) = nan
-    allocate(this%hrv_frootc_storage_to_litter_patch        (begp:endp)) ; this%hrv_frootc_storage_to_litter_patch        (:) = nan
-    allocate(this%hrv_frootc_xfer_to_litter_patch           (begp:endp)) ; this%hrv_frootc_xfer_to_litter_patch           (:) = nan
-    allocate(this%hrv_livestemc_to_litter_patch             (begp:endp)) ; this%hrv_livestemc_to_litter_patch             (:) = nan
-    allocate(this%hrv_livestemc_storage_to_litter_patch     (begp:endp)) ; this%hrv_livestemc_storage_to_litter_patch     (:) = nan
-    allocate(this%hrv_livestemc_xfer_to_litter_patch        (begp:endp)) ; this%hrv_livestemc_xfer_to_litter_patch        (:) = nan
-    allocate(this%hrv_deadstemc_storage_to_litter_patch     (begp:endp)) ; this%hrv_deadstemc_storage_to_litter_patch     (:) = nan
-    allocate(this%hrv_deadstemc_xfer_to_litter_patch        (begp:endp)) ; this%hrv_deadstemc_xfer_to_litter_patch        (:) = nan
-    allocate(this%hrv_livecrootc_to_litter_patch            (begp:endp)) ; this%hrv_livecrootc_to_litter_patch            (:) = nan
-    allocate(this%hrv_livecrootc_storage_to_litter_patch    (begp:endp)) ; this%hrv_livecrootc_storage_to_litter_patch    (:) = nan
-    allocate(this%hrv_livecrootc_xfer_to_litter_patch       (begp:endp)) ; this%hrv_livecrootc_xfer_to_litter_patch       (:) = nan
-    allocate(this%hrv_deadcrootc_to_litter_patch            (begp:endp)) ; this%hrv_deadcrootc_to_litter_patch            (:) = nan
-    allocate(this%hrv_deadcrootc_storage_to_litter_patch    (begp:endp)) ; this%hrv_deadcrootc_storage_to_litter_patch    (:) = nan
-    allocate(this%hrv_deadcrootc_xfer_to_litter_patch       (begp:endp)) ; this%hrv_deadcrootc_xfer_to_litter_patch       (:) = nan
-    allocate(this%hrv_gresp_storage_to_litter_patch         (begp:endp)) ; this%hrv_gresp_storage_to_litter_patch         (:) = nan
-    allocate(this%hrv_gresp_xfer_to_litter_patch            (begp:endp)) ; this%hrv_gresp_xfer_to_litter_patch            (:) = nan
-    allocate(this%hrv_xsmrpool_to_atm_patch                 (begp:endp)) ; this%hrv_xsmrpool_to_atm_patch                 (:) = nan
-    allocate(this%m_leafc_to_fire_patch                     (begp:endp)) ; this%m_leafc_to_fire_patch                     (:) = nan
-    allocate(this%m_leafc_storage_to_fire_patch             (begp:endp)) ; this%m_leafc_storage_to_fire_patch             (:) = nan
-    allocate(this%m_leafc_xfer_to_fire_patch                (begp:endp)) ; this%m_leafc_xfer_to_fire_patch                (:) = nan
-    allocate(this%m_livestemc_to_fire_patch                 (begp:endp)) ; this%m_livestemc_to_fire_patch                 (:) = nan
-    allocate(this%m_livestemc_storage_to_fire_patch         (begp:endp)) ; this%m_livestemc_storage_to_fire_patch         (:) = nan
-    allocate(this%m_livestemc_xfer_to_fire_patch            (begp:endp)) ; this%m_livestemc_xfer_to_fire_patch            (:) = nan
-    allocate(this%m_deadstemc_to_fire_patch                 (begp:endp)) ; this%m_deadstemc_to_fire_patch                 (:) = nan
-    allocate(this%m_deadstemc_storage_to_fire_patch         (begp:endp)) ; this%m_deadstemc_storage_to_fire_patch         (:) = nan
-    allocate(this%m_deadstemc_xfer_to_fire_patch            (begp:endp)) ; this%m_deadstemc_xfer_to_fire_patch            (:) = nan
-    allocate(this%m_frootc_to_fire_patch                    (begp:endp)) ; this%m_frootc_to_fire_patch                    (:) = nan
-    allocate(this%m_frootc_storage_to_fire_patch            (begp:endp)) ; this%m_frootc_storage_to_fire_patch            (:) = nan
-    allocate(this%m_frootc_xfer_to_fire_patch               (begp:endp)) ; this%m_frootc_xfer_to_fire_patch               (:) = nan
-    allocate(this%m_livecrootc_to_fire_patch                (begp:endp)) ; this%m_livecrootc_to_fire_patch                (:) = nan
-    allocate(this%m_livecrootc_storage_to_fire_patch        (begp:endp)) ; this%m_livecrootc_storage_to_fire_patch        (:) = nan
-    allocate(this%m_livecrootc_xfer_to_fire_patch           (begp:endp)) ; this%m_livecrootc_xfer_to_fire_patch           (:) = nan
-    allocate(this%m_deadcrootc_to_fire_patch                (begp:endp)) ; this%m_deadcrootc_to_fire_patch                (:) = nan
-    allocate(this%m_deadcrootc_storage_to_fire_patch        (begp:endp)) ; this%m_deadcrootc_storage_to_fire_patch        (:) = nan
-    allocate(this%m_deadcrootc_xfer_to_fire_patch           (begp:endp)) ; this%m_deadcrootc_xfer_to_fire_patch           (:) = nan
-    allocate(this%m_gresp_storage_to_fire_patch             (begp:endp)) ; this%m_gresp_storage_to_fire_patch             (:) = nan
-    allocate(this%m_gresp_xfer_to_fire_patch                (begp:endp)) ; this%m_gresp_xfer_to_fire_patch                (:) = nan
-    allocate(this%m_leafc_to_litter_fire_patch              (begp:endp)) ; this%m_leafc_to_litter_fire_patch              (:) = nan
-    allocate(this%m_leafc_storage_to_litter_fire_patch      (begp:endp)) ; this%m_leafc_storage_to_litter_fire_patch      (:) = nan
-    allocate(this%m_leafc_xfer_to_litter_fire_patch         (begp:endp)) ; this%m_leafc_xfer_to_litter_fire_patch         (:) = nan
-    allocate(this%m_livestemc_to_litter_fire_patch          (begp:endp)) ; this%m_livestemc_to_litter_fire_patch          (:) = nan
-    allocate(this%m_livestemc_storage_to_litter_fire_patch  (begp:endp)) ; this%m_livestemc_storage_to_litter_fire_patch  (:) = nan
-    allocate(this%m_livestemc_xfer_to_litter_fire_patch     (begp:endp)) ; this%m_livestemc_xfer_to_litter_fire_patch     (:) = nan
-    allocate(this%m_livestemc_to_deadstemc_fire_patch       (begp:endp)) ; this%m_livestemc_to_deadstemc_fire_patch       (:) = nan
-    allocate(this%m_deadstemc_to_litter_fire_patch          (begp:endp)) ; this%m_deadstemc_to_litter_fire_patch          (:) = nan
-    allocate(this%m_deadstemc_storage_to_litter_fire_patch  (begp:endp)) ; this%m_deadstemc_storage_to_litter_fire_patch  (:) = nan
-    allocate(this%m_deadstemc_xfer_to_litter_fire_patch     (begp:endp)) ; this%m_deadstemc_xfer_to_litter_fire_patch     (:) = nan
-    allocate(this%m_frootc_to_litter_fire_patch             (begp:endp)) ; this%m_frootc_to_litter_fire_patch             (:) = nan
-    allocate(this%m_frootc_storage_to_litter_fire_patch     (begp:endp)) ; this%m_frootc_storage_to_litter_fire_patch     (:) = nan
-    allocate(this%m_frootc_xfer_to_litter_fire_patch        (begp:endp)) ; this%m_frootc_xfer_to_litter_fire_patch        (:) = nan
-    allocate(this%m_livecrootc_to_litter_fire_patch         (begp:endp)) ; this%m_livecrootc_to_litter_fire_patch         (:) = nan
-    allocate(this%m_livecrootc_storage_to_litter_fire_patch (begp:endp)) ; this%m_livecrootc_storage_to_litter_fire_patch (:) = nan
-    allocate(this%m_livecrootc_xfer_to_litter_fire_patch    (begp:endp)) ; this%m_livecrootc_xfer_to_litter_fire_patch    (:) = nan
-    allocate(this%m_livecrootc_to_deadcrootc_fire_patch     (begp:endp)) ; this%m_livecrootc_to_deadcrootc_fire_patch     (:) = nan
-    allocate(this%m_deadcrootc_to_litter_fire_patch         (begp:endp)) ; this%m_deadcrootc_to_litter_fire_patch         (:) = nan
-    allocate(this%m_deadcrootc_storage_to_litter_fire_patch (begp:endp)) ; this%m_deadcrootc_storage_to_litter_fire_patch (:) = nan
-    allocate(this%m_deadcrootc_xfer_to_litter_fire_patch    (begp:endp)) ; this%m_deadcrootc_xfer_to_litter_fire_patch    (:) = nan
-    allocate(this%m_gresp_storage_to_litter_fire_patch      (begp:endp)) ; this%m_gresp_storage_to_litter_fire_patch      (:) = nan
-    allocate(this%m_gresp_xfer_to_litter_fire_patch         (begp:endp)) ; this%m_gresp_xfer_to_litter_fire_patch         (:) = nan
-    allocate(this%leafc_xfer_to_leafc_patch                 (begp:endp)) ; this%leafc_xfer_to_leafc_patch                 (:) = nan
-    allocate(this%frootc_xfer_to_frootc_patch               (begp:endp)) ; this%frootc_xfer_to_frootc_patch               (:) = nan
-    allocate(this%livestemc_xfer_to_livestemc_patch         (begp:endp)) ; this%livestemc_xfer_to_livestemc_patch         (:) = nan
-    allocate(this%deadstemc_xfer_to_deadstemc_patch         (begp:endp)) ; this%deadstemc_xfer_to_deadstemc_patch         (:) = nan
-    allocate(this%livecrootc_xfer_to_livecrootc_patch       (begp:endp)) ; this%livecrootc_xfer_to_livecrootc_patch       (:) = nan
-    allocate(this%deadcrootc_xfer_to_deadcrootc_patch       (begp:endp)) ; this%deadcrootc_xfer_to_deadcrootc_patch       (:) = nan
-    allocate(this%leafc_to_litter_patch                     (begp:endp)) ; this%leafc_to_litter_patch                     (:) = nan
-    allocate(this%leafc_to_litter_fun_patch                 (begp:endp)) ; this%leafc_to_litter_fun_patch                 (:) = nan
-    allocate(this%frootc_to_litter_patch                    (begp:endp)) ; this%frootc_to_litter_patch                    (:) = nan
-    allocate(this%cpool_to_resp_patch                       (begp:endp)) ; this%cpool_to_resp_patch                       (:) = nan
-    allocate(this%cpool_to_leafc_resp_patch                 (begp:endp)) ; this%cpool_to_leafc_resp_patch                 (:) = nan
-    allocate(this%cpool_to_leafc_storage_resp_patch         (begp:endp)) ; this%cpool_to_leafc_storage_resp_patch         (:) = nan
-    allocate(this%cpool_to_frootc_resp_patch                (begp:endp)) ; this%cpool_to_frootc_resp_patch                (:) = nan
-    allocate(this%cpool_to_frootc_storage_resp_patch        (begp:endp)) ; this%cpool_to_frootc_storage_resp_patch        (:) = nan
-    allocate(this%cpool_to_livecrootc_resp_patch            (begp:endp)) ; this%cpool_to_livecrootc_resp_patch            (:) = nan
-    allocate(this%cpool_to_livecrootc_storage_resp_patch    (begp:endp)) ; this%cpool_to_livecrootc_storage_resp_patch    (:) = nan
-    allocate(this%cpool_to_livestemc_resp_patch             (begp:endp)) ; this%cpool_to_livestemc_resp_patch             (:) = nan
-    allocate(this%cpool_to_livestemc_storage_resp_patch     (begp:endp)) ; this%cpool_to_livestemc_storage_resp_patch     (:) = nan
-    allocate(this%leaf_mr_patch                             (begp:endp)) ; this%leaf_mr_patch                             (:) = nan
-    allocate(this%froot_mr_patch                            (begp:endp)) ; this%froot_mr_patch                            (:) = nan
-    allocate(this%livestem_mr_patch                         (begp:endp)) ; this%livestem_mr_patch                         (:) = nan
-    allocate(this%livecroot_mr_patch                        (begp:endp)) ; this%livecroot_mr_patch                        (:) = nan
-    allocate(this%grain_mr_patch                            (begp:endp)) ; this%grain_mr_patch                            (:) = nan
-    allocate(this%leaf_curmr_patch                          (begp:endp)) ; this%leaf_curmr_patch                          (:) = nan
-    allocate(this%froot_curmr_patch                         (begp:endp)) ; this%froot_curmr_patch                         (:) = nan
-    allocate(this%livestem_curmr_patch                      (begp:endp)) ; this%livestem_curmr_patch                      (:) = nan
-    allocate(this%livecroot_curmr_patch                     (begp:endp)) ; this%livecroot_curmr_patch                     (:) = nan
-    allocate(this%grain_curmr_patch                         (begp:endp)) ; this%grain_curmr_patch                         (:) = nan
-    allocate(this%leaf_xsmr_patch                           (begp:endp)) ; this%leaf_xsmr_patch                           (:) = nan
-    allocate(this%froot_xsmr_patch                          (begp:endp)) ; this%froot_xsmr_patch                          (:) = nan
-    allocate(this%livestem_xsmr_patch                       (begp:endp)) ; this%livestem_xsmr_patch                       (:) = nan
-    allocate(this%livecroot_xsmr_patch                      (begp:endp)) ; this%livecroot_xsmr_patch                      (:) = nan
-    allocate(this%grain_xsmr_patch                          (begp:endp)) ; this%grain_xsmr_patch                          (:) = nan
-    allocate(this%psnsun_to_cpool_patch                     (begp:endp)) ; this%psnsun_to_cpool_patch                     (:) = nan
-    allocate(this%psnshade_to_cpool_patch                   (begp:endp)) ; this%psnshade_to_cpool_patch                   (:) = nan
-    allocate(this%cpool_to_xsmrpool_patch                   (begp:endp)) ; this%cpool_to_xsmrpool_patch                   (:) = nan
-    allocate(this%cpool_to_leafc_patch                      (begp:endp)) ; this%cpool_to_leafc_patch                      (:) = nan
-    allocate(this%cpool_to_leafc_storage_patch              (begp:endp)) ; this%cpool_to_leafc_storage_patch              (:) = nan
-    allocate(this%cpool_to_frootc_patch                     (begp:endp)) ; this%cpool_to_frootc_patch                     (:) = nan
-    allocate(this%cpool_to_frootc_storage_patch             (begp:endp)) ; this%cpool_to_frootc_storage_patch             (:) = nan
-    allocate(this%cpool_to_livestemc_patch                  (begp:endp)) ; this%cpool_to_livestemc_patch                  (:) = nan
-    allocate(this%cpool_to_livestemc_storage_patch          (begp:endp)) ; this%cpool_to_livestemc_storage_patch          (:) = nan
-    allocate(this%cpool_to_deadstemc_patch                  (begp:endp)) ; this%cpool_to_deadstemc_patch                  (:) = nan
-    allocate(this%cpool_to_deadstemc_storage_patch          (begp:endp)) ; this%cpool_to_deadstemc_storage_patch          (:) = nan
-    allocate(this%cpool_to_livecrootc_patch                 (begp:endp)) ; this%cpool_to_livecrootc_patch                 (:) = nan
-    allocate(this%cpool_to_livecrootc_storage_patch         (begp:endp)) ; this%cpool_to_livecrootc_storage_patch         (:) = nan
-    allocate(this%cpool_to_deadcrootc_patch                 (begp:endp)) ; this%cpool_to_deadcrootc_patch                 (:) = nan
-    allocate(this%cpool_to_deadcrootc_storage_patch         (begp:endp)) ; this%cpool_to_deadcrootc_storage_patch         (:) = nan
-    allocate(this%cpool_to_gresp_storage_patch              (begp:endp)) ; this%cpool_to_gresp_storage_patch              (:) = nan
-    allocate(this%cpool_leaf_gr_patch                       (begp:endp)) ; this%cpool_leaf_gr_patch                       (:) = nan
-    allocate(this%cpool_leaf_storage_gr_patch               (begp:endp)) ; this%cpool_leaf_storage_gr_patch               (:) = nan
-    allocate(this%transfer_leaf_gr_patch                    (begp:endp)) ; this%transfer_leaf_gr_patch                    (:) = nan
-    allocate(this%cpool_froot_gr_patch                      (begp:endp)) ; this%cpool_froot_gr_patch                      (:) = nan
-    allocate(this%cpool_froot_storage_gr_patch              (begp:endp)) ; this%cpool_froot_storage_gr_patch              (:) = nan
-    allocate(this%transfer_froot_gr_patch                   (begp:endp)) ; this%transfer_froot_gr_patch                   (:) = nan
-    allocate(this%cpool_livestem_gr_patch                   (begp:endp)) ; this%cpool_livestem_gr_patch                   (:) = nan
-    allocate(this%cpool_livestem_storage_gr_patch           (begp:endp)) ; this%cpool_livestem_storage_gr_patch           (:) = nan
-    allocate(this%transfer_livestem_gr_patch                (begp:endp)) ; this%transfer_livestem_gr_patch                (:) = nan
-    allocate(this%cpool_deadstem_gr_patch                   (begp:endp)) ; this%cpool_deadstem_gr_patch                   (:) = nan
-    allocate(this%cpool_deadstem_storage_gr_patch           (begp:endp)) ; this%cpool_deadstem_storage_gr_patch           (:) = nan
-    allocate(this%transfer_deadstem_gr_patch                (begp:endp)) ; this%transfer_deadstem_gr_patch                (:) = nan
-    allocate(this%cpool_livecroot_gr_patch                  (begp:endp)) ; this%cpool_livecroot_gr_patch                  (:) = nan
-    allocate(this%cpool_livecroot_storage_gr_patch          (begp:endp)) ; this%cpool_livecroot_storage_gr_patch          (:) = nan
-    allocate(this%transfer_livecroot_gr_patch               (begp:endp)) ; this%transfer_livecroot_gr_patch               (:) = nan
-    allocate(this%cpool_deadcroot_gr_patch                  (begp:endp)) ; this%cpool_deadcroot_gr_patch                  (:) = nan
-    allocate(this%cpool_deadcroot_storage_gr_patch          (begp:endp)) ; this%cpool_deadcroot_storage_gr_patch          (:) = nan
-    allocate(this%transfer_deadcroot_gr_patch               (begp:endp)) ; this%transfer_deadcroot_gr_patch               (:) = nan
-    allocate(this%leafc_storage_to_xfer_patch               (begp:endp)) ; this%leafc_storage_to_xfer_patch               (:) = nan
-    allocate(this%frootc_storage_to_xfer_patch              (begp:endp)) ; this%frootc_storage_to_xfer_patch              (:) = nan
-    allocate(this%livestemc_storage_to_xfer_patch           (begp:endp)) ; this%livestemc_storage_to_xfer_patch           (:) = nan
-    allocate(this%deadstemc_storage_to_xfer_patch           (begp:endp)) ; this%deadstemc_storage_to_xfer_patch           (:) = nan
-    allocate(this%livecrootc_storage_to_xfer_patch          (begp:endp)) ; this%livecrootc_storage_to_xfer_patch          (:) = nan
-    allocate(this%deadcrootc_storage_to_xfer_patch          (begp:endp)) ; this%deadcrootc_storage_to_xfer_patch          (:) = nan
-    allocate(this%gresp_storage_to_xfer_patch               (begp:endp)) ; this%gresp_storage_to_xfer_patch               (:) = nan
-    allocate(this%livestemc_to_deadstemc_patch              (begp:endp)) ; this%livestemc_to_deadstemc_patch              (:) = nan
-    allocate(this%livecrootc_to_deadcrootc_patch            (begp:endp)) ; this%livecrootc_to_deadcrootc_patch            (:) = nan
-    allocate(this%current_gr_patch                          (begp:endp)) ; this%current_gr_patch                          (:) = nan
-    allocate(this%transfer_gr_patch                         (begp:endp)) ; this%transfer_gr_patch                         (:) = nan
-    allocate(this%storage_gr_patch                          (begp:endp)) ; this%storage_gr_patch                          (:) = nan
-    allocate(this%plant_calloc_patch                        (begp:endp)) ; this%plant_calloc_patch                        (:) = nan
-    allocate(this%excess_cflux_patch                        (begp:endp)) ; this%excess_cflux_patch                        (:) = nan
-    allocate(this%prev_leafc_to_litter_patch                (begp:endp)) ; this%prev_leafc_to_litter_patch                (:) = nan
-    allocate(this%prev_frootc_to_litter_patch               (begp:endp)) ; this%prev_frootc_to_litter_patch               (:) = nan
-    allocate(this%gpp_before_downreg_patch                  (begp:endp)) ; this%gpp_before_downreg_patch                  (:) = nan
-    allocate(this%availc_patch                              (begp:endp)) ; this%availc_patch                              (:) = nan
-    allocate(this%xsmrpool_recover_patch                    (begp:endp)) ; this%xsmrpool_recover_patch                    (:) = nan
-    allocate(this%xsmrpool_c13ratio_patch                   (begp:endp)) ; this%xsmrpool_c13ratio_patch                   (:) = nan
-
-    allocate(this%cpool_to_grainc_patch                     (begp:endp)) ; this%cpool_to_grainc_patch                     (:) = nan
-    allocate(this%cpool_to_grainc_storage_patch             (begp:endp)) ; this%cpool_to_grainc_storage_patch             (:) = nan
-    allocate(this%livestemc_to_litter_patch                 (begp:endp)) ; this%livestemc_to_litter_patch                 (:) = nan
-    allocate(this%grainc_to_food_patch                      (begp:endp)) ; this%grainc_to_food_patch                      (:) = nan
-    allocate(this%grainc_to_seed_patch                      (begp:endp)) ; this%grainc_to_seed_patch                      (:) = nan
-    allocate(this%grainc_xfer_to_grainc_patch               (begp:endp)) ; this%grainc_xfer_to_grainc_patch               (:) = nan
-    allocate(this%cpool_grain_gr_patch                      (begp:endp)) ; this%cpool_grain_gr_patch                      (:) = nan
-    allocate(this%cpool_grain_storage_gr_patch              (begp:endp)) ; this%cpool_grain_storage_gr_patch              (:) = nan
-    allocate(this%transfer_grain_gr_patch                   (begp:endp)) ; this%transfer_grain_gr_patch                   (:) = nan
-    allocate(this%xsmrpool_to_atm_patch                     (begp:endp)) ; this%xsmrpool_to_atm_patch                     (:) = nan
-    allocate(this%grainc_storage_to_xfer_patch              (begp:endp)) ; this%grainc_storage_to_xfer_patch              (:) = nan
-    allocate(this%frootc_alloc_patch                        (begp:endp)) ; this%frootc_alloc_patch                        (:) = nan
-    allocate(this%frootc_loss_patch                         (begp:endp)) ; this%frootc_loss_patch                         (:) = nan
-    allocate(this%leafc_alloc_patch                         (begp:endp)) ; this%leafc_alloc_patch                         (:) = nan
-    allocate(this%leafc_loss_patch                          (begp:endp)) ; this%leafc_loss_patch                          (:) = nan
-    allocate(this%woodc_alloc_patch                         (begp:endp)) ; this%woodc_alloc_patch                         (:) = nan
-    allocate(this%woodc_loss_patch                          (begp:endp)) ; this%woodc_loss_patch                          (:) = nan
-
-    allocate(this%phenology_c_to_litr_met_c_col     (begc:endc,1:nlevdecomp_full)); 
-    this%phenology_c_to_litr_met_c_col (:,:)=nan
-    
-    allocate(this%phenology_c_to_litr_cel_c_col     (begc:endc,1:nlevdecomp_full)); this%phenology_c_to_litr_cel_c_col (:,:)=nan
-    allocate(this%phenology_c_to_litr_lig_c_col     (begc:endc,1:nlevdecomp_full)); this%phenology_c_to_litr_lig_c_col (:,:)=nan
-
-    allocate(this%gap_mortality_c_to_litr_met_c_col (begc:endc,1:nlevdecomp_full)); this%gap_mortality_c_to_litr_met_c_col(:,:)=nan
-    allocate(this%gap_mortality_c_to_litr_cel_c_col (begc:endc,1:nlevdecomp_full)); this%gap_mortality_c_to_litr_cel_c_col(:,:)=nan
-    allocate(this%gap_mortality_c_to_litr_lig_c_col (begc:endc,1:nlevdecomp_full)); this%gap_mortality_c_to_litr_lig_c_col(:,:)=nan
-
-    allocate(this%gap_mortality_c_to_cwdc_col       (begc:endc,1:nlevdecomp_full)); this%gap_mortality_c_to_cwdc_col  (:,:)=nan
-    allocate(this%fire_mortality_c_to_cwdc_col      (begc:endc,1:nlevdecomp_full)); this%fire_mortality_c_to_cwdc_col (:,:)=nan
-    allocate(this%m_c_to_litr_met_fire_col          (begc:endc,1:nlevdecomp_full)); this%m_c_to_litr_met_fire_col     (:,:)=nan
-    allocate(this%m_c_to_litr_cel_fire_col          (begc:endc,1:nlevdecomp_full)); this%m_c_to_litr_cel_fire_col     (:,:)=nan
-    allocate(this%m_c_to_litr_lig_fire_col          (begc:endc,1:nlevdecomp_full)); this%m_c_to_litr_lig_fire_col     (:,:)=nan
-    allocate(this%harvest_c_to_litr_met_c_col       (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_litr_met_c_col  (:,:)=nan
-    allocate(this%harvest_c_to_litr_cel_c_col       (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_litr_cel_c_col  (:,:)=nan
-    allocate(this%harvest_c_to_litr_lig_c_col       (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_litr_lig_c_col  (:,:)=nan
-    allocate(this%harvest_c_to_cwdc_col             (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_cwdc_col        (:,:)=nan
-
-    allocate(this%dwt_slash_cflux_col               (begc:endc))                  ; this%dwt_slash_cflux_col (:) =nan
-    allocate(this%dwt_frootc_to_litr_met_c_col      (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_met_c_col (:,:)=nan
-    allocate(this%dwt_frootc_to_litr_cel_c_col      (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_cel_c_col (:,:)=nan
-    allocate(this%dwt_frootc_to_litr_lig_c_col      (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_lig_c_col (:,:)=nan
-    allocate(this%dwt_livecrootc_to_cwdc_col        (begc:endc,1:nlevdecomp_full)); this%dwt_livecrootc_to_cwdc_col   (:,:)=nan
-    allocate(this%dwt_deadcrootc_to_cwdc_col        (begc:endc,1:nlevdecomp_full)); this%dwt_deadcrootc_to_cwdc_col   (:,:)=nan
-
-    allocate(this%dwt_seedc_to_leaf_patch           (begp:endp))                  ; this%dwt_seedc_to_leaf_patch   (:)  =nan
-    allocate(this%dwt_seedc_to_leaf_grc             (begg:endg))                  ; this%dwt_seedc_to_leaf_grc     (:)  =nan
-    allocate(this%dwt_seedc_to_deadstem_patch       (begp:endp))                  ; this%dwt_seedc_to_deadstem_patch(:)  =nan
-    allocate(this%dwt_seedc_to_deadstem_grc         (begg:endg))                  ; this%dwt_seedc_to_deadstem_grc (:)  =nan
-    allocate(this%dwt_conv_cflux_patch              (begp:endp))                  ; this%dwt_conv_cflux_patch      (:)  =nan
-    allocate(this%dwt_conv_cflux_grc                (begg:endg))                  ; this%dwt_conv_cflux_grc        (:)  =nan
-    allocate(this%dwt_conv_cflux_dribbled_grc       (begg:endg))                  ; this%dwt_conv_cflux_dribbled_grc(:)  =nan
-    allocate(this%dwt_wood_productc_gain_patch      (begp:endp))                  ; this%dwt_wood_productc_gain_patch(:)  =nan
-    allocate(this%dwt_crop_productc_gain_patch      (begp:endp))                  ; this%dwt_crop_productc_gain_patch(:) =nan
-
-    allocate(this%crop_seedc_to_leaf_patch          (begp:endp))                  ; this%crop_seedc_to_leaf_patch  (:)  =nan
-
-    allocate(this%cwdc_hr_col                       (begc:endc))                  ; this%cwdc_hr_col               (:)  =nan
-    allocate(this%cwdc_loss_col                     (begc:endc))                  ; this%cwdc_loss_col             (:)  =nan
-    allocate(this%litterc_loss_col                  (begc:endc))                  ; this%litterc_loss_col          (:)  =nan
-
-    allocate(this%grainc_to_cropprodc_patch(begp:endp))
-    this%grainc_to_cropprodc_patch(:) = nan
-
-    allocate(this%grainc_to_cropprodc_col(begc:endc))
-    this%grainc_to_cropprodc_col(:) = nan
-
-    allocate(this%m_decomp_cpools_to_fire_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))                
-    this%m_decomp_cpools_to_fire_vr_col(:,:,:)= nan
-
-    allocate(this%m_decomp_cpools_to_fire_col(begc:endc,1:ndecomp_pools))                                     
-    this%m_decomp_cpools_to_fire_col(:,:)= nan
-
-    allocate(this%m_decomp_cpools_to_fire_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))                
-    this%m_decomp_cpools_to_fire_vr_col(:,:,:)= nan
-
-    allocate(this%m_decomp_cpools_to_fire_col(begc:endc,1:ndecomp_pools))                                     
-    this%m_decomp_cpools_to_fire_col(:,:)= nan
-
-    allocate(this%rr_patch                (begp:endp)) ; this%rr_patch                (:) = nan
-    allocate(this%mr_patch                (begp:endp)) ; this%mr_patch                (:) = nan
-    allocate(this%gr_patch                (begp:endp)) ; this%gr_patch                (:) = nan
-    allocate(this%ar_patch                (begp:endp)) ; this%ar_patch                (:) = nan
-    allocate(this%npp_patch               (begp:endp)) ; this%npp_patch               (:) = nan
-    allocate(this%agnpp_patch             (begp:endp)) ; this%agnpp_patch             (:) = nan
-    allocate(this%bgnpp_patch             (begp:endp)) ; this%bgnpp_patch             (:) = nan
-    allocate(this%litfall_patch           (begp:endp)) ; this%litfall_patch           (:) = nan
-    allocate(this%wood_harvestc_patch     (begp:endp)) ; this%wood_harvestc_patch     (:) = nan
-    allocate(this%slash_harvestc_patch    (begp:endp)) ; this%slash_harvestc_patch    (:) = nan
-    allocate(this%cinputs_patch           (begp:endp)) ; this%cinputs_patch           (:) = nan
-    allocate(this%coutputs_patch          (begp:endp)) ; this%coutputs_patch          (:) = nan
-    allocate(this%gpp_patch               (begp:endp)) ; this%gpp_patch               (:) = nan
-    allocate(this%fire_closs_patch        (begp:endp)) ; this%fire_closs_patch        (:) = nan
-    allocate(this%sr_col                  (begc:endc)) ; this%sr_col                  (:) = nan
-    allocate(this%er_col                  (begc:endc)) ; this%er_col                  (:) = nan
-    allocate(this%litfire_col             (begc:endc)) ; this%litfire_col             (:) = nan
-    allocate(this%somfire_col             (begc:endc)) ; this%somfire_col             (:) = nan
-    allocate(this%totfire_col             (begc:endc)) ; this%totfire_col             (:) = nan
-    allocate(this%rr_col                  (begc:endc)) ; this%rr_col                  (:) = nan
-    allocate(this%ar_col                  (begc:endc)) ; this%ar_col                  (:) = nan
-    allocate(this%gpp_col                 (begc:endc)) ; this%gpp_col                 (:) = nan
-    allocate(this%npp_col                 (begc:endc)) ; this%npp_col                 (:) = nan
-    allocate(this%fire_closs_p2c_col      (begc:endc)) ; this%fire_closs_p2c_col      (:) = nan
-    allocate(this%fire_closs_col          (begc:endc)) ; this%fire_closs_col          (:) = nan
-    allocate(this%wood_harvestc_col       (begc:endc)) ; this%wood_harvestc_col       (:) = nan
-    allocate(this%hrv_xsmrpool_to_atm_col (begc:endc)) ; this%hrv_xsmrpool_to_atm_col (:) = nan 
-    allocate(this%tempsum_npp_patch       (begp:endp)) ; this%tempsum_npp_patch       (:) = nan
-    allocate(this%annsum_npp_patch        (begp:endp)) ; this%annsum_npp_patch        (:) = nan
-    allocate(this%tempsum_litfall_patch   (begp:endp)) ; this%tempsum_litfall_patch   (:) = nan
-    allocate(this%annsum_litfall_patch    (begp:endp)) ; this%annsum_litfall_patch    (:) = nan
-    allocate(this%annsum_npp_col          (begc:endc)) ; this%annsum_npp_col          (:) = nan
-    allocate(this%lag_npp_col             (begc:endc)) ; this%lag_npp_col             (:) = spval
-
-    allocate(this%nep_col                 (begc:endc)) ; this%nep_col                 (:) = nan
-    allocate(this%nbp_grc                 (begg:endg)) ; this%nbp_grc                 (:) = nan
-    allocate(this%nee_grc                 (begg:endg)) ; this%nee_grc                 (:) = nan
-    allocate(this%landuseflux_grc         (begg:endg)) ; this%landuseflux_grc         (:) = nan
-    allocate(this%npp_Nactive_patch       (begp:endp)) ; this%npp_Nactive_patch       (:) = nan
-    allocate(this%npp_burnedoff_patch     (begp:endp)) ; this%npp_burnedoff_patch     (:) = nan
-    allocate(this%npp_Nnonmyc_patch       (begp:endp)) ; this%npp_Nnonmyc_patch       (:) = nan
-    allocate(this%npp_Nam_patch           (begp:endp)) ; this%npp_Nam_patch           (:) = nan
-    allocate(this%npp_Necm_patch          (begp:endp)) ; this%npp_Necm_patch          (:) = nan
-    allocate(this%npp_Nactive_no3_patch   (begp:endp)) ; this%npp_Nactive_no3_patch   (:) = nan
-    allocate(this%npp_Nactive_nh4_patch   (begp:endp)) ; this%npp_Nactive_nh4_patch   (:) = nan
-    allocate(this%npp_Nnonmyc_no3_patch   (begp:endp)) ; this%npp_Nnonmyc_no3_patch   (:) = nan
-    allocate(this%npp_Nnonmyc_nh4_patch   (begp:endp)) ; this%npp_Nnonmyc_nh4_patch   (:) = nan
-    allocate(this%npp_Nam_no3_patch       (begp:endp)) ; this%npp_Nam_no3_patch       (:) = nan
-    allocate(this%npp_Nam_nh4_patch       (begp:endp)) ; this%npp_Nam_nh4_patch       (:) = nan
-    allocate(this%npp_Necm_no3_patch      (begp:endp)) ; this%npp_Necm_no3_patch      (:) = nan
-    allocate(this%npp_Necm_nh4_patch      (begp:endp)) ; this%npp_Necm_nh4_patch      (:) = nan
-    allocate(this%npp_Nfix_patch          (begp:endp)) ; this%npp_Nfix_patch          (:) = nan
-    allocate(this%npp_Nretrans_patch      (begp:endp)) ; this%npp_Nretrans_patch      (:) = nan
-    allocate(this%npp_Nuptake_patch       (begp:endp)) ; this%npp_Nuptake_patch       (:) = nan
-    allocate(this%npp_growth_patch       (begp:endp)) ; this%npp_growth_patch       (:) = nan
-    allocate(this%leafc_change_patch      (begp:endp)) ; this%leafc_change_patch      (:) = nan
-    allocate(this%soilc_change_patch      (begp:endp)) ; this%soilc_change_patch      (:) = nan
-
-    ! Construct restart field names consistently to what is done in SpeciesNonIsotope &
-    ! SpeciesIsotope, to aid future migration to that infrastructure
-    if (carbon_type == 'c12') then
-       carbon_type_suffix = 'c'
-    else if (carbon_type == 'c13') then
-       carbon_type_suffix = 'c_13'
-    else if (carbon_type == 'c14') then
-       carbon_type_suffix = 'c_14'
-    else
-       write(iulog,*) 'CNVegCarbonFluxType InitAllocate: Unknown carbon_type: ', trim(carbon_type)
-       call endrun(msg='CNVegCarbonFluxType InitAllocate: Unknown carbon_type: ' // &
-            errMsg(sourcefile, __LINE__))
-    end if
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds, carbon_type)
-    !
-    ! !DESCRIPTION:
-    ! add history fields for all CN variables, always set as default='inactive'
-    !
-    ! !USES:
-    use clm_varpar , only : nlevdecomp, nlevdecomp_full, nlevgrnd
-    use clm_varctl , only : hist_wrtch4diag
-    use CNSharedParamsMod, only: use_fun
-    use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
-    !
-    ! !ARGUMENTS:
-    class(cnveg_carbonflux_type) :: this    
-    type(bounds_type)         , intent(in) :: bounds 
-    character(len=3)          , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: k,l,ii,jj 
-    character(8)      :: vr_suffix
-    character(10)     :: active
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    character(24)     :: fieldname
-    character(100)    :: longname
-    real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    if (nlevdecomp > 1) then
-       vr_suffix = "_vr"
-    else 
-       vr_suffix = ""
-    endif
-
-    !-------------------------------
-    ! C flux variables - patch
-    !-------------------------------
-
-    if (carbon_type == 'c12') then
-
-       if (use_crop) then
-          this%grainc_to_food_patch(begp:endp) = spval
-          call hist_addfld1d (fname='GRAINC_TO_FOOD', units='gC/m^2/s', &
-               avgflag='A', long_name='grain C to food', &
-               ptr_patch=this%grainc_to_food_patch, default='inactive')
-
-          this%grainc_to_seed_patch(begp:endp) = spval
-          call hist_addfld1d (fname='GRAINC_TO_SEED', units='gC/m^2/s', &
-               avgflag='A', long_name='grain C to seed', &
-               ptr_patch=this%grainc_to_seed_patch, default='inactive')
-       end if
-
-       this%litterc_loss_col(begc:endc) = spval
-       call hist_addfld1d (fname='LITTERC_LOSS', units='gC/m^2/s', &
-            avgflag='A', long_name='litter C loss', &
-            ptr_col=this%litterc_loss_col, default='inactive')
-
-       this%woodc_alloc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='WOODC_ALLOC', units='gC/m^2/s', &
-            avgflag='A', long_name='wood C eallocation', &
-            ptr_patch=this%woodc_alloc_patch, default='inactive')
-
-       this%woodc_loss_patch(begp:endp) = spval
-       call hist_addfld1d (fname='WOODC_LOSS', units='gC/m^2/s', &
-            avgflag='A', long_name='wood C loss', &
-            ptr_patch=this%woodc_loss_patch, default='inactive')
-
-       this%leafc_loss_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_LOSS', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C loss', &
-            ptr_patch=this%leafc_loss_patch, default='inactive')
-
-       this%leafc_alloc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_ALLOC', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C allocation', &
-            ptr_patch=this%leafc_alloc_patch, default='inactive')
-
-       this%frootc_loss_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_LOSS', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C loss', &
-            ptr_patch=this%frootc_loss_patch, default='inactive')
-
-       this%frootc_alloc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_ALLOC', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C allocation', &
-            ptr_patch=this%frootc_alloc_patch, default='inactive')
-
-       this%m_leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C mortality', &
-            ptr_patch=this%m_leafc_to_litter_patch, default='inactive')
-
-       this%m_frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C mortality', &
-            ptr_patch=this%m_frootc_to_litter_patch, default='inactive')
-
-       this%m_leafc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C storage mortality', &
-            ptr_patch=this%m_leafc_storage_to_litter_patch, default='inactive')
-
-       this%m_frootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C storage mortality', &
-            ptr_patch=this%m_frootc_storage_to_litter_patch, default='inactive')
-
-       this%m_livestemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C storage mortality', &
-            ptr_patch=this%m_livestemc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C storage mortality', &
-            ptr_patch=this%m_deadstemc_storage_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVECROOTC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C storage mortality', &
-            ptr_patch=this%m_livecrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADCROOTC_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C storage mortality', &
-            ptr_patch=this%m_deadcrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_leafc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C transfer mortality', &
-            ptr_patch=this%m_leafc_xfer_to_litter_patch, default='inactive')
-
-       this%m_frootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C transfer mortality', &
-            ptr_patch=this%m_frootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C transfer mortality', &
-            ptr_patch=this%m_livestemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C transfer mortality', &
-            ptr_patch=this%m_deadstemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVECROOTC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C transfer mortality', &
-            ptr_patch=this%m_livecrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADCROOTC_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C transfer mortality', &
-            ptr_patch=this%m_deadcrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C mortality', &
-            ptr_patch=this%m_livestemc_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C mortality', &
-            ptr_patch=this%m_deadstemc_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVECROOTC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C mortality', &
-            ptr_patch=this%m_livecrootc_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADCROOTC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C mortality', &
-            ptr_patch=this%m_deadcrootc_to_litter_patch, default='inactive')
-
-       this%m_gresp_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_STORAGE_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration storage mortality', &
-            ptr_patch=this%m_gresp_storage_to_litter_patch, default='inactive')
-
-       this%m_gresp_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_XFER_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration transfer mortality', &
-            ptr_patch=this%m_gresp_xfer_to_litter_patch, default='inactive')
-
-       this%m_leafc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C fire loss', &
-            ptr_patch=this%m_leafc_to_fire_patch, default='inactive')
-
-       this%m_leafc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C storage fire loss', &
-            ptr_patch=this%m_leafc_storage_to_fire_patch, default='inactive')
-
-       this%m_leafc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C transfer fire loss', &
-            ptr_patch=this%m_leafc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livestemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C fire loss', &
-            ptr_patch=this%m_livestemc_to_fire_patch, default='inactive')
-
-       this%m_livestemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C storage fire loss', &
-            ptr_patch=this%m_livestemc_storage_to_fire_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C transfer fire loss', &
-            ptr_patch=this%m_livestemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C fire loss', &
-            ptr_patch=this%m_deadstemc_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C storage fire loss', &
-            ptr_patch=this%m_deadstemc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C transfer fire loss', &
-            ptr_patch=this%m_deadstemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_frootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C fire loss', &
-            ptr_patch=this%m_frootc_to_fire_patch, default='inactive')
-
-       this%m_frootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C storage fire loss', &
-            ptr_patch=this%m_frootc_storage_to_fire_patch, default='inactive')
-
-       this%m_frootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C transfer fire loss', &
-            ptr_patch=this%m_frootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C fire loss', &
-            ptr_patch=this%m_livecrootc_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C storage fire loss', &
-            ptr_patch=this%m_livecrootc_storage_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C transfer fire loss', &
-            ptr_patch=this%m_livecrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C fire loss', &
-            ptr_patch=this%m_deadcrootc_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C storage fire loss', &
-            ptr_patch=this%m_deadcrootc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C transfer fire loss', &
-            ptr_patch=this%m_deadcrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_gresp_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_STORAGE_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration storage fire loss', &
-            ptr_patch=this%m_gresp_storage_to_fire_patch, default='inactive')
-
-       this%m_gresp_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_XFER_TO_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration transfer fire loss', &
-            ptr_patch=this%m_gresp_xfer_to_fire_patch, default='inactive')
-
-       this%m_leafc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C fire mortality to litter', &
-            ptr_patch=this%m_leafc_to_litter_fire_patch, default='inactive')
-
-       ! add by F. Li and S. Levis
-       this%m_leafc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C fire mortality to litter', &
-            ptr_patch=this%m_leafc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_leafc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LEAFC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C transfer fire mortality to litter', &
-            ptr_patch=this%m_leafc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_livestemc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C fire mortality to litter', &
-            ptr_patch=this%m_livestemc_to_litter_fire_patch, default='inactive')
-
-       this%m_livestemc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C storage fire mortality to litter', &
-            ptr_patch=this%m_livestemc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C transfer fire mortality to litter', &
-            ptr_patch=this%m_livestemc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_livestemc_to_deadstemc_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVESTEMC_TO_DEADSTEMC_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C fire mortality to dead stem C', &
-            ptr_patch=this%m_livestemc_to_deadstemc_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C fire mortality to litter', &
-            ptr_patch=this%m_deadstemc_to_litter_fire_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C storage fire mortality to litter', &
-            ptr_patch=this%m_deadstemc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADSTEMC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C transfer fire mortality to litter', &
-            ptr_patch=this%m_deadstemc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_frootc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C fire mortality to litter', &
-            ptr_patch=this%m_frootc_to_litter_fire_patch, default='inactive')
-
-       this%m_frootc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C storage fire mortality to litter', &
-            ptr_patch=this%m_frootc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_frootc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_FROOTC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C transfer fire mortality to litter', &
-            ptr_patch=this%m_frootc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C fire mortality to litter', &
-            ptr_patch=this%m_livecrootc_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C storage fire mortality to litter', &
-            ptr_patch=this%m_livecrootc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C transfer fire mortality to litter', &
-            ptr_patch=this%m_livecrootc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_to_deadcrootc_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVEROOTC_TO_DEADROOTC_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live root C fire mortality to dead root C', &
-            ptr_patch=this%m_livecrootc_to_deadcrootc_fire_patch, default='inactive')
-
-
-       this%m_deadcrootc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_to_litter_fire_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C storage fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADROOTC_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead root C transfer fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_xfer_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_LIVECROOTC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C fire mortality to litter', &
-            ptr_patch=this%m_livecrootc_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_DEADCROOTC_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C storage fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_storage_to_litter_fire_patch,  default='inactive')
-
-       this%m_gresp_storage_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_STORAGE_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration storage fire mortality to litter', &
-            ptr_patch=this%m_gresp_storage_to_litter_fire_patch, default='inactive')
-
-       this%m_gresp_xfer_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='M_GRESP_XFER_TO_LITTER_FIRE', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration transfer fire mortality to litter', &
-            ptr_patch=this%m_gresp_xfer_to_litter_fire_patch, default='inactive')   
-
-       this%leafc_xfer_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_XFER_TO_LEAFC', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C growth from storage', &
-            ptr_patch=this%leafc_xfer_to_leafc_patch, default='inactive')
-
-       this%frootc_xfer_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_XFER_TO_FROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C growth from storage', &
-            ptr_patch=this%frootc_xfer_to_frootc_patch, default='inactive')
-
-       this%livestemc_xfer_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC_XFER_TO_LIVESTEMC', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C growth from storage', &
-            ptr_patch=this%livestemc_xfer_to_livestemc_patch, default='inactive')
-
-       this%deadstemc_xfer_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADSTEMC_XFER_TO_DEADSTEMC', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C growth from storage', &
-            ptr_patch=this%deadstemc_xfer_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_xfer_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC_XFER_TO_LIVECROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C growth from storage', &
-            ptr_patch=this%livecrootc_xfer_to_livecrootc_patch, default='inactive')
-
-       this%deadcrootc_xfer_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADCROOTC_XFER_TO_DEADCROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C growth from storage', &
-            ptr_patch=this%deadcrootc_xfer_to_deadcrootc_patch, default='inactive')
-
-       this%leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C litterfall', &
-            ptr_patch=this%leafc_to_litter_patch, default='inactive')
-
-       if ( use_fun ) then
-          this%leafc_to_litter_fun_patch(begp:endp) = spval
-          call hist_addfld1d (fname='LEAFC_TO_LITTER_FUN', units='gC/m^2/s', &
-               avgflag='A', long_name='leaf C litterfall used by FUN', &
-               ptr_patch=this%leafc_to_litter_fun_patch, default='inactive')
-       end if
-
-       this%frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C litterfall', &
-            ptr_patch=this%frootc_to_litter_patch, default='inactive')
-            
-       this%cpool_to_resp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='EXCESSC_MR', units='gC/m^2/s', &
-            avgflag='A', long_name='excess C maintenance respiration', &
-            ptr_patch=this%cpool_to_resp_patch, default='inactive')
-       this%leaf_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAF_MR', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf maintenance respiration', &
-            ptr_patch=this%leaf_mr_patch, default='inactive')
-
-       this%froot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOT_MR', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root maintenance respiration', &
-            ptr_patch=this%froot_mr_patch, default='inactive')
-
-       this%livestem_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEM_MR', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem maintenance respiration', &
-            ptr_patch=this%livestem_mr_patch, default='inactive')
-
-       this%livecroot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOT_MR', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root maintenance respiration', &
-            ptr_patch=this%livecroot_mr_patch, default='inactive')
-
-       this%psnsun_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PSNSUN_TO_CPOOL', units='gC/m^2/s', &
-            avgflag='A', long_name='C fixation from sunlit canopy', &
-            ptr_patch=this%psnsun_to_cpool_patch, default='inactive')
-
-       this%psnshade_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PSNSHADE_TO_CPOOL', units='gC/m^2/s', &
-            avgflag='A', long_name='C fixation from shaded canopy', &
-            ptr_patch=this%psnshade_to_cpool_patch, default='inactive')
-
-       this%cpool_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LEAFC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to leaf C', &
-            ptr_patch=this%cpool_to_leafc_patch, default='inactive')
-
-       this%cpool_to_leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LEAFC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to leaf C storage', &
-            ptr_patch=this%cpool_to_leafc_storage_patch, default='inactive')
-
-       this%cpool_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_FROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to fine root C', &
-            ptr_patch=this%cpool_to_frootc_patch, default='inactive')
-
-       this%cpool_to_frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_FROOTC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to fine root C storage', &
-            ptr_patch=this%cpool_to_frootc_storage_patch, default='inactive')
-
-       this%cpool_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LIVESTEMC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to live stem C', &
-            ptr_patch=this%cpool_to_livestemc_patch, default='inactive')
-
-       this%cpool_to_livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LIVESTEMC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to live stem C storage', &
-            ptr_patch=this%cpool_to_livestemc_storage_patch, default='inactive')
-
-       this%cpool_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_DEADSTEMC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to dead stem C', &
-            ptr_patch=this%cpool_to_deadstemc_patch, default='inactive')
-
-       this%cpool_to_deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_DEADSTEMC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to dead stem C storage', &
-            ptr_patch=this%cpool_to_deadstemc_storage_patch, default='inactive')
-
-       this%cpool_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LIVECROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to live coarse root C', &
-            ptr_patch=this%cpool_to_livecrootc_patch, default='inactive')
-
-       this%cpool_to_livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_LIVECROOTC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to live coarse root C storage', &
-            ptr_patch=this%cpool_to_livecrootc_storage_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_DEADCROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to dead coarse root C', &
-            ptr_patch=this%cpool_to_deadcrootc_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_DEADCROOTC_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to dead coarse root C storage', &
-            ptr_patch=this%cpool_to_deadcrootc_storage_patch, default='inactive')
-
-       this%cpool_to_gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_TO_GRESP_STORAGE', units='gC/m^2/s', &
-            avgflag='A', long_name='allocation to growth respiration storage', &
-            ptr_patch=this%cpool_to_gresp_storage_patch, default='inactive')
-
-       this%cpool_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LEAF_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf growth respiration', &
-            ptr_patch=this%cpool_leaf_gr_patch, default='inactive')
-
-       this%cpool_leaf_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LEAF_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf growth respiration to storage', &
-            ptr_patch=this%cpool_leaf_storage_gr_patch, default='inactive')
-
-       this%transfer_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_LEAF_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf growth respiration from storage', &
-            ptr_patch=this%transfer_leaf_gr_patch, default='inactive')
-
-       this%cpool_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_FROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root growth respiration', &
-            ptr_patch=this%cpool_froot_gr_patch, default='inactive')
-
-       this%cpool_froot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_FROOT_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root  growth respiration to storage', &
-            ptr_patch=this%cpool_froot_storage_gr_patch, default='inactive')
-
-       this%transfer_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_FROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root  growth respiration from storage', &
-            ptr_patch=this%transfer_froot_gr_patch, default='inactive')
-
-       this%cpool_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LIVESTEM_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem growth respiration', &
-            ptr_patch=this%cpool_livestem_gr_patch, default='inactive')
-
-       this%cpool_livestem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LIVESTEM_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem growth respiration to storage', &
-            ptr_patch=this%cpool_livestem_storage_gr_patch, default='inactive')
-
-       this%transfer_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_LIVESTEM_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem growth respiration from storage', &
-            ptr_patch=this%transfer_livestem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_DEADSTEM_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem growth respiration', &
-            ptr_patch=this%cpool_deadstem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_DEADSTEM_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem growth respiration to storage', &
-            ptr_patch=this%cpool_deadstem_storage_gr_patch, default='inactive')
-
-       this%transfer_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_DEADSTEM_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem growth respiration from storage', &
-            ptr_patch=this%transfer_deadstem_gr_patch, default='inactive')
-
-       this%cpool_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LIVECROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root growth respiration', &
-            ptr_patch=this%cpool_livecroot_gr_patch, default='inactive')
-
-       this%cpool_livecroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_LIVECROOT_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_livecroot_storage_gr_patch, default='inactive')
-
-       this%transfer_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_LIVECROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_livecroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_DEADCROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root growth respiration', &
-            ptr_patch=this%cpool_deadcroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL_DEADCROOT_STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_deadcroot_storage_gr_patch, default='inactive')
-
-       this%transfer_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_DEADCROOT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_deadcroot_gr_patch, default='inactive')
-
-       this%leafc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='leaf C shift storage to transfer', &
-            ptr_patch=this%leafc_storage_to_xfer_patch, default='inactive')
-
-       this%frootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='fine root C shift storage to transfer', &
-            ptr_patch=this%frootc_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C shift storage to transfer', &
-            ptr_patch=this%livestemc_storage_to_xfer_patch, default='inactive')
-
-       this%deadstemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADSTEMC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead stem C shift storage to transfer', &
-            ptr_patch=this%deadstemc_storage_to_xfer_patch, default='inactive')
-
-       this%livecrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C shift storage to transfer', &
-            ptr_patch=this%livecrootc_storage_to_xfer_patch, default='inactive')
-
-       this%deadcrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADCROOTC_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='dead coarse root C shift storage to transfer', &
-            ptr_patch=this%deadcrootc_storage_to_xfer_patch, default='inactive')
-
-       this%gresp_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GRESP_STORAGE_TO_XFER', units='gC/m^2/s', &
-            avgflag='A', long_name='growth respiration shift storage to transfer', &
-            ptr_patch=this%gresp_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC_TO_DEADSTEMC', units='gC/m^2/s', &
-            avgflag='A', long_name='live stem C turnover', &
-            ptr_patch=this%livestemc_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC_TO_DEADCROOTC', units='gC/m^2/s', &
-            avgflag='A', long_name='live coarse root C turnover', &
-            ptr_patch=this%livecrootc_to_deadcrootc_patch, default='inactive')
-
-       this%gpp_before_downreg_patch(begp:endp) = spval
-       call hist_addfld1d (fname='INIT_GPP', units='gC/m^2/s', &
-            avgflag='A', long_name='GPP flux before downregulation', &
-            ptr_patch=this%gpp_before_downreg_patch, default='inactive')
-
-       this%current_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CURRENT_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='growth resp for new growth displayed in this timestep', &
-            ptr_patch=this%current_gr_patch, default='inactive')
-
-       this%transfer_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TRANSFER_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='growth resp for transfer growth displayed in this timestep', &
-            ptr_patch=this%transfer_gr_patch, default='inactive')
-
-       this%storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='STORAGE_GR', units='gC/m^2/s', &
-            avgflag='A', long_name='growth resp for growth sent to storage for later display', &
-            ptr_patch=this%storage_gr_patch, default='inactive')
-
-       this%availc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='AVAILC', units='gC/m^2/s', &
-            avgflag='A', long_name='C flux available for allocation', &
-            ptr_patch=this%availc_patch, default='inactive')
-
-       this%plant_calloc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PLANT_CALLOC', units='gC/m^2/s', &
-            avgflag='A', long_name='total allocated C flux', &
-            ptr_patch=this%plant_calloc_patch, default='inactive')
-
-       this%excess_cflux_patch(begp:endp) = spval
-       call hist_addfld1d (fname='EXCESS_CFLUX', units='gC/m^2/s', &
-            avgflag='A', long_name='C flux not allocated due to downregulation', &
-            ptr_patch=this%excess_cflux_patch, default='inactive')
-
-       this%prev_leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PREV_LEAFC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='previous timestep leaf C litterfall flux', &
-            ptr_patch=this%prev_leafc_to_litter_patch, default='inactive')
-
-       this%prev_frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PREV_FROOTC_TO_LITTER', units='gC/m^2/s', &
-            avgflag='A', long_name='previous timestep froot C litterfall flux', &
-            ptr_patch=this%prev_frootc_to_litter_patch, default='inactive')
-
-       this%xsmrpool_recover_patch(begp:endp) = spval
-       call hist_addfld1d (fname='XSMRPOOL_RECOVER', units='gC/m^2/s', &
-            avgflag='A', long_name='C flux assigned to recovery of negative xsmrpool', &
-            ptr_patch=this%xsmrpool_recover_patch, default='inactive')
-
-        this%gpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='GPP', units='gC/m^2/s', &
-             avgflag='A', long_name='gross primary production', &
-             ptr_patch=this%gpp_patch, default='inactive')
-
-        this%rr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='RR', units='gC/m^2/s', &
-             avgflag='A', long_name='root respiration (fine root MR + total root GR)', &
-             ptr_patch=this%rr_patch, default='inactive')
-
-        this%mr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='MR', units='gC/m^2/s', &
-             avgflag='A', long_name='maintenance respiration', &
-             ptr_patch=this%mr_patch, default='inactive')
-
-        this%gr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='GR', units='gC/m^2/s', &
-             avgflag='A', long_name='total growth respiration', &
-             ptr_patch=this%gr_patch, default='inactive')
-
-        this%ar_patch(begp:endp) = spval
-        call hist_addfld1d (fname='AR', units='gC/m^2/s', &
-             avgflag='A', long_name='autotrophic respiration (MR + GR)', &
-             ptr_patch=this%ar_patch, default='inactive')
-
-        this%npp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='NPP', units='gC/m^2/s', &
-             avgflag='A', long_name='net primary production', &
-             ptr_patch=this%npp_patch, default='inactive')
-
-        this%agnpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='AGNPP', units='gC/m^2/s', &
-             avgflag='A', long_name='aboveground NPP', &
-             ptr_patch=this%agnpp_patch, default='inactive')
-
-        this%bgnpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='BGNPP', units='gC/m^2/s', &
-             avgflag='A', long_name='belowground NPP', &
-             ptr_patch=this%bgnpp_patch, default='inactive')
-
-        this%litfall_patch(begp:endp) = spval
-        call hist_addfld1d (fname='LITFALL', units='gC/m^2/s', &
-             avgflag='A', long_name='litterfall (leaves and fine roots)', &
-             ptr_patch=this%litfall_patch, default='inactive')
-
-        this%wood_harvestc_patch(begp:endp) = spval
-        call hist_addfld1d (fname='WOOD_HARVESTC', units='gC/m^2/s', &
-             avgflag='A', long_name='wood harvest carbon (to product pools)', &
-             ptr_patch=this%wood_harvestc_patch, default='inactive')
-
-        this%slash_harvestc_patch(begp:endp) = spval
-        call hist_addfld1d (fname='SLASH_HARVESTC', units='gC/m^2/s', &
-             avgflag='A', long_name='slash harvest carbon (to litter)', &
-             ptr_patch=this%slash_harvestc_patch, default='inactive')
-
-        this%fire_closs_patch(begp:endp) = spval
-        call hist_addfld1d (fname='PFT_FIRE_CLOSS', units='gC/m^2/s', &
-             avgflag='A', long_name='total patch-level fire C loss for non-peat fires outside land-type converted region', &
-             ptr_patch=this%fire_closs_patch, default='inactive')
-
-        if ( use_fun ) then
-          this%npp_Nactive_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NPP_NACTIVE', units='gC/m^2/s',     &
-               avgflag='A', long_name='Mycorrhizal N uptake used C',     &
-               ptr_patch=this%npp_Nactive_patch, default='inactive')
-
-          ! BUG(wjs, 2016-04-13, bugz 2292) This field has a threading bug. Making it
-          ! inactive for now.
-          this%npp_burnedoff_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NPP_BURNEDOFF', units='gC/m^2/s',     &
-               avgflag='A', long_name='C that cannot be used for N uptake',     &
-               ptr_patch=this%npp_burnedoff_patch, default='inactive')
-  
-          this%npp_Nnonmyc_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NPP_NNONMYC', units='gC/m^2/s',     &
-               avgflag='A', long_name='Non-mycorrhizal N uptake used C', &
-               ptr_patch=this%npp_Nnonmyc_patch, default='inactive')
-
-          this%npp_Nam_patch(begp:endp)      = spval
-          call hist_addfld1d (fname='NPP_NAM', units='gC/m^2/s',         &
-               avgflag='A', long_name='AM-associated N uptake used C',   &
-               ptr_patch=this%npp_Nam_patch, default='inactive')
-
-          this%npp_Necm_patch(begp:endp)     = spval
-          call hist_addfld1d (fname='NPP_NECM', units='gC/m^2/s',        &
-               avgflag='A', long_name='ECM-associated N uptake used C',  &
-               ptr_patch=this%npp_Necm_patch, default='inactive')
-
-          if (use_nitrif_denitrif) then
-             this%npp_Nactive_no3_patch(begp:endp)  = spval
-             call hist_addfld1d (fname='NPP_NACTIVE_NO3', units='gC/m^2/s', &
-                  avgflag='A', long_name='Mycorrhizal N uptake used C',     &
-                  ptr_patch=this%npp_Nactive_no3_patch, default='inactive')
-
-             this%npp_Nactive_nh4_patch(begp:endp)  = spval
-             call hist_addfld1d (fname='NPP_NACTIVE_NH4', units='gC/m^2/s', &
-                  avgflag='A', long_name='Mycorrhizal N uptake use C',      &
-                  ptr_patch=this%npp_Nactive_nh4_patch, default='inactive')
-
-             this%npp_Nnonmyc_no3_patch(begp:endp)  = spval
-             call hist_addfld1d (fname='NPP_NNONMYC_NO3', units='gC/m^2/s', &
-                  avgflag='A', long_name='Non-mycorrhizal N uptake use C',  &
-                  ptr_patch=this%npp_Nnonmyc_no3_patch, default='inactive')
-
-             this%npp_Nnonmyc_nh4_patch(begp:endp)  = spval
-             call hist_addfld1d (fname='NPP_NNONMYC_NH4', units='gC/m^2/s', &
-                  avgflag='A', long_name='Non-mycorrhizal N uptake use C',  &
-                  ptr_patch=this%npp_Nnonmyc_nh4_patch, default='inactive')
-
-             this%npp_Nam_no3_patch(begp:endp)      = spval
-             call hist_addfld1d (fname='NPP_NAM_NO3', units='gC/m^2/s',     &
-                  avgflag='A', long_name='AM-associated N uptake use C',    &
-                  ptr_patch=this%npp_Nam_no3_patch, default='inactive')
-
-             this%npp_Nam_nh4_patch(begp:endp)      = spval
-             call hist_addfld1d (fname='NPP_NAM_NH4', units='gC/m^2/s',     &
-                  avgflag='A', long_name='AM-associated N uptake use C',    &
-                  ptr_patch=this%npp_Nam_nh4_patch, default='inactive')
-
-             this%npp_Necm_no3_patch(begp:endp)     = spval
-             call hist_addfld1d (fname='NPP_NECM_NO3', units='gC/m^2/s',    &
-                  avgflag='A', long_name='ECM-associated N uptake used C',  &
-                  ptr_patch=this%npp_Necm_no3_patch, default='inactive')
-
-             this%npp_Necm_nh4_patch(begp:endp)     = spval
-             call hist_addfld1d (fname='NPP_NECM_NH4', units='gC/m^2/s',     &
-                  avgflag='A', long_name='ECM-associated N uptake use C',    &
-                  ptr_patch=this%npp_Necm_nh4_patch, default='inactive')
-          end if
-
-          this%npp_Nfix_patch(begp:endp)     = spval
-          call hist_addfld1d (fname='NPP_NFIX', units='gC/m^2/s',         &
-               avgflag='A', long_name='Symbiotic BNF uptake used C',      &
-               ptr_patch=this%npp_Nfix_patch, default='inactive')
-
-          this%npp_Nretrans_patch(begp:endp) = spval
-          call hist_addfld1d (fname='NPP_NRETRANS', units='gC/m^2/s',     &
-              avgflag='A', long_name='Retranslocated N uptake flux',      &
-              ptr_patch=this%npp_Nretrans_patch, default='inactive')
-
-          this%npp_Nuptake_patch(begp:endp) = spval
-          call hist_addfld1d (fname='NPP_NUPTAKE', units='gC/m^2/s',      &
-               avgflag='A', long_name='Total C used by N uptake in FUN',  &
-               ptr_patch=this%npp_Nuptake_patch, default='inactive')
-
-    this%npp_growth_patch(begp:endp) = spval
-          call hist_addfld1d (fname='NPP_GROWTH', units='gC/m^2/s',      &
-               avgflag='A', long_name='Total C used for growth in FUN',  &
-               ptr_patch=this%npp_growth_patch, default='inactive')
-
-
-
-          this%leafc_change_patch(begp:endp) = spval
-          call hist_addfld1d (fname='LEAFC_CHANGE', units='gC/m^2/s',     &
-               avgflag='A', long_name='C change in leaf',                 &
-               ptr_patch=this%leafc_change_patch, default='inactive')
-
-          this%soilc_change_patch(begp:endp) = spval
-          call hist_addfld1d (fname='SOILC_CHANGE', units='gC/m^2/s',     &
-               avgflag='A', long_name='C change in soil',                 &
-               ptr_patch=this%soilc_change_patch, default='inactive')
-      end if
-! FUN Ends 
-
-    end if  ! end of if-c12
-
-    !-------------------------------
-    ! C13 flux variables - patch
-    !-------------------------------
-
-    if ( carbon_type == 'c13') then
-
-        this%gpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_GPP', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 gross primary production', &
-             ptr_patch=this%gpp_patch, default='inactive')
-
-        this%rr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_RR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 root respiration (fine root MR + total root GR)', &
-             ptr_patch=this%rr_patch, default='inactive')
-
-        this%mr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_MR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 maintenance respiration', &
-             ptr_patch=this%mr_patch, default='inactive')
-
-        this%gr_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_GR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total growth respiration', &
-             ptr_patch=this%gr_patch, default='inactive')
-
-        this%ar_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_AR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 autotrophic respiration (MR + GR)', &
-             ptr_patch=this%ar_patch, default='inactive')
-
-        this%npp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_NPP', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 net primary production', &
-             ptr_patch=this%npp_patch, default='inactive')
-
-        this%agnpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_AGNPP', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 aboveground NPP', &
-             ptr_patch=this%agnpp_patch, default='inactive')
-
-        this%bgnpp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_BGNPP', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 belowground NPP', &
-             ptr_patch=this%bgnpp_patch, default='inactive')
-
-        this%litfall_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_LITFALL', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 litterfall (leaves and fine roots)', &
-             ptr_patch=this%litfall_patch, default='inactive')
-
-        this%fire_closs_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C13_PFT_FIRE_CLOSS', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total patch-level fire C loss', &
-             ptr_patch=this%fire_closs_patch, default='inactive')
-
-       this%m_leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C mortality', &
-            ptr_patch=this%m_leafc_to_litter_patch, default='inactive')
-
-       this%m_frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C mortality', &
-            ptr_patch=this%m_frootc_to_litter_patch, default='inactive')
-
-       this%m_leafc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C storage mortality', &
-            ptr_patch=this%m_leafc_storage_to_litter_patch, default='inactive')
-
-       this%m_frootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C storage mortality', &
-            ptr_patch=this%m_frootc_storage_to_litter_patch, default='inactive')
-
-       this%m_livestemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C storage mortality', &
-            ptr_patch=this%m_livestemc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C storage mortality', &
-            ptr_patch=this%m_deadstemc_storage_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C storage mortality', &
-            ptr_patch=this%m_livecrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C storage mortality', &
-            ptr_patch=this%m_deadcrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_leafc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C transfer mortality', &
-            ptr_patch=this%m_leafc_xfer_to_litter_patch, default='inactive')
-
-       this%m_frootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C transfer mortality', &
-            ptr_patch=this%m_frootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C transfer mortality', &
-            ptr_patch=this%m_livestemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C transfer mortality', &
-            ptr_patch=this%m_deadstemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C transfer mortality', &
-            ptr_patch=this%m_livecrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C transfer mortality', &
-            ptr_patch=this%m_deadcrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C mortality', &
-            ptr_patch=this%m_livestemc_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C mortality', &
-            ptr_patch=this%m_deadstemc_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C mortality', &
-            ptr_patch=this%m_livecrootc_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C mortality', &
-            ptr_patch=this%m_deadcrootc_to_litter_patch, default='inactive')
-
-       this%m_gresp_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_GRESP_STORAGE_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth respiration storage mortality', &
-            ptr_patch=this%m_gresp_storage_to_litter_patch, default='inactive')
-
-       this%m_gresp_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_GRESP_XFER_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth respiration transfer mortality', &
-            ptr_patch=this%m_gresp_xfer_to_litter_patch, default='inactive')
-
-       this%m_leafc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C fire loss', &
-            ptr_patch=this%m_leafc_to_fire_patch, default='inactive')
-
-       this%m_frootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C fire loss', &
-            ptr_patch=this%m_frootc_to_fire_patch, default='inactive')
-
-       this%m_leafc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C storage fire loss', &
-            ptr_patch=this%m_leafc_storage_to_fire_patch, default='inactive')
-
-       this%m_frootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C storage fire loss', &
-            ptr_patch=this%m_frootc_storage_to_fire_patch, default='inactive')
-
-       this%m_livestemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C storage fire loss', &
-            ptr_patch=this%m_livestemc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C storage fire loss', &
-            ptr_patch=this%m_deadstemc_storage_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C storage fire loss', &
-            ptr_patch=this%m_livecrootc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C storage fire loss', &
-            ptr_patch=this%m_deadcrootc_storage_to_fire_patch,  default='inactive')
-
-       this%m_leafc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LEAFC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C transfer fire loss', &
-            ptr_patch=this%m_leafc_xfer_to_fire_patch, default='inactive')
-
-       this%m_frootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_FROOTC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C transfer fire loss', &
-            ptr_patch=this%m_frootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C transfer fire loss', &
-            ptr_patch=this%m_livestemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C transfer fire loss', &
-            ptr_patch=this%m_deadstemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C transfer fire loss', &
-            ptr_patch=this%m_livecrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C transfer fire loss', &
-            ptr_patch=this%m_deadcrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livestemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVESTEMC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C fire loss', &
-            ptr_patch=this%m_livestemc_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C fire loss', &
-            ptr_patch=this%m_deadstemc_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADSTEMC_TO_LITTER_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C fire mortality to litter', &
-            ptr_patch=this%m_deadstemc_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_LIVECROOTC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C fire loss', &
-            ptr_patch=this%m_livecrootc_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C fire loss', &
-            ptr_patch=this%m_deadcrootc_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_DEADCROOTC_TO_LITTER_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_to_litter_fire_patch, default='inactive')
-
-       this%m_gresp_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_GRESP_STORAGE_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth respiration storage fire loss', &
-            ptr_patch=this%m_gresp_storage_to_fire_patch, default='inactive')
-
-       this%m_gresp_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_M_GRESP_XFER_TO_FIRE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth respiration transfer fire loss', &
-            ptr_patch=this%m_gresp_xfer_to_fire_patch, default='inactive')
-
-       this%leafc_xfer_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_XFER_TO_LEAFC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C growth from storage', &
-            ptr_patch=this%leafc_xfer_to_leafc_patch, default='inactive')
-
-       this%frootc_xfer_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC_XFER_TO_FROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C growth from storage', &
-            ptr_patch=this%frootc_xfer_to_frootc_patch, default='inactive')
-
-       this%livestemc_xfer_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC_XFER_TO_LIVESTEMC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C growth from storage', &
-            ptr_patch=this%livestemc_xfer_to_livestemc_patch, default='inactive')
-
-       this%deadstemc_xfer_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADSTEMC_XFER_TO_DEADSTEMC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C growth from storage', &
-            ptr_patch=this%deadstemc_xfer_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_xfer_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC_XFER_TO_LIVECROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C growth from storage', &
-            ptr_patch=this%livecrootc_xfer_to_livecrootc_patch, default='inactive')
-
-       this%deadcrootc_xfer_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADCROOTC_XFER_TO_DEADCROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C growth from storage', &
-            ptr_patch=this%deadcrootc_xfer_to_deadcrootc_patch, default='inactive')
-
-       this%leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C litterfall', &
-            ptr_patch=this%leafc_to_litter_patch, default='inactive')
-
-       this%frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC_TO_LITTER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C litterfall', &
-            ptr_patch=this%frootc_to_litter_patch, default='inactive')
-
-       this%leaf_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAF_MR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf maintenance respiration', &
-            ptr_patch=this%leaf_mr_patch, default='inactive')
-
-       this%froot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOT_MR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root maintenance respiration', &
-            ptr_patch=this%froot_mr_patch, default='inactive')
-
-       this%livestem_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEM_MR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem maintenance respiration', &
-            ptr_patch=this%livestem_mr_patch, default='inactive')
-
-       this%livecroot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOT_MR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root maintenance respiration', &
-            ptr_patch=this%livecroot_mr_patch, default='inactive')
-
-       this%psnsun_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_PSNSUN_TO_CPOOL', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 C fixation from sunlit canopy', &
-            ptr_patch=this%psnsun_to_cpool_patch, default='inactive')
-
-       this%psnshade_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_PSNSHADE_TO_CPOOL', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 C fixation from shaded canopy', &
-            ptr_patch=this%psnshade_to_cpool_patch, default='inactive')
-
-       this%cpool_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LEAFC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to leaf C', &
-            ptr_patch=this%cpool_to_leafc_patch, default='inactive')
-
-       this%cpool_to_leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LEAFC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to leaf C storage', &
-            ptr_patch=this%cpool_to_leafc_storage_patch, default='inactive')
-
-       this%cpool_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_FROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to fine root C', &
-            ptr_patch=this%cpool_to_frootc_patch, default='inactive')
-
-       this%cpool_to_frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_FROOTC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to fine root C storage', &
-            ptr_patch=this%cpool_to_frootc_storage_patch, default='inactive')
-
-       this%cpool_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LIVESTEMC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to live stem C', &
-            ptr_patch=this%cpool_to_livestemc_patch, default='inactive')
-
-       this%cpool_to_livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LIVESTEMC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to live stem C storage', &
-            ptr_patch=this%cpool_to_livestemc_storage_patch, default='inactive')
-
-       this%cpool_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_DEADSTEMC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to dead stem C', &
-            ptr_patch=this%cpool_to_deadstemc_patch, default='inactive')
-
-       this%cpool_to_deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_DEADSTEMC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to dead stem C storage', &
-            ptr_patch=this%cpool_to_deadstemc_storage_patch, default='inactive')
-
-       this%cpool_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LIVECROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to live coarse root C', &
-            ptr_patch=this%cpool_to_livecrootc_patch, default='inactive')
-
-       this%cpool_to_livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_LIVECROOTC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to live coarse root C storage', &
-            ptr_patch=this%cpool_to_livecrootc_storage_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_DEADCROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to dead coarse root C', &
-            ptr_patch=this%cpool_to_deadcrootc_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_DEADCROOTC_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to dead coarse root C storage', &
-            ptr_patch=this%cpool_to_deadcrootc_storage_patch, default='inactive')
-
-       this%cpool_to_gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_TO_GRESP_STORAGE', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 allocation to growth respiration storage', &
-            ptr_patch=this%cpool_to_gresp_storage_patch, default='inactive')
-
-       this%cpool_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LEAF_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf growth respiration', &
-            ptr_patch=this%cpool_leaf_gr_patch, default='inactive')
-
-       this%cpool_leaf_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LEAF_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf growth respiration to storage', &
-            ptr_patch=this%cpool_leaf_storage_gr_patch, default='inactive')
-
-       this%transfer_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_LEAF_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf growth respiration from storage', &
-            ptr_patch=this%transfer_leaf_gr_patch, default='inactive')
-
-       this%cpool_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_FROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root growth respiration', &
-            ptr_patch=this%cpool_froot_gr_patch, default='inactive')
-
-       this%cpool_froot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_FROOT_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root  growth respiration to storage', &
-            ptr_patch=this%cpool_froot_storage_gr_patch, default='inactive')
-
-       this%transfer_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_FROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root  growth respiration from storage', &
-            ptr_patch=this%transfer_froot_gr_patch, default='inactive')
-
-       this%cpool_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LIVESTEM_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem growth respiration', &
-            ptr_patch=this%cpool_livestem_gr_patch, default='inactive')
-
-       this%cpool_livestem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LIVESTEM_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem growth respiration to storage', &
-            ptr_patch=this%cpool_livestem_storage_gr_patch, default='inactive')
-
-       this%transfer_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_LIVESTEM_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem growth respiration from storage', &
-            ptr_patch=this%transfer_livestem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_DEADSTEM_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem growth respiration', &
-            ptr_patch=this%cpool_deadstem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_DEADSTEM_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem growth respiration to storage', &
-            ptr_patch=this%cpool_deadstem_storage_gr_patch, default='inactive')
-
-       this%transfer_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_DEADSTEM_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem growth respiration from storage', &
-            ptr_patch=this%transfer_deadstem_gr_patch, default='inactive')
-
-       this%cpool_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LIVECROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root growth respiration', &
-            ptr_patch=this%cpool_livecroot_gr_patch, default='inactive')
-
-       this%cpool_livecroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_LIVECROOT_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_livecroot_storage_gr_patch, default='inactive')
-
-       this%transfer_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_LIVECROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_livecroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_DEADCROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root growth respiration', &
-            ptr_patch=this%cpool_deadcroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL_DEADCROOT_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_deadcroot_storage_gr_patch, default='inactive')
-
-       this%transfer_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_DEADCROOT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_deadcroot_gr_patch, default='inactive')
-
-       this%leafc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 leaf C shift storage to transfer', &
-            ptr_patch=this%leafc_storage_to_xfer_patch, default='inactive')
-
-       this%frootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 fine root C shift storage to transfer', &
-            ptr_patch=this%frootc_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C shift storage to transfer', &
-            ptr_patch=this%livestemc_storage_to_xfer_patch, default='inactive')
-
-       this%deadstemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADSTEMC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead stem C shift storage to transfer', &
-            ptr_patch=this%deadstemc_storage_to_xfer_patch, default='inactive')
-
-       this%livecrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C shift storage to transfer', &
-            ptr_patch=this%livecrootc_storage_to_xfer_patch, default='inactive')
-
-       this%deadcrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADCROOTC_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 dead coarse root C shift storage to transfer', &
-            ptr_patch=this%deadcrootc_storage_to_xfer_patch, default='inactive')
-
-       this%gresp_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_GRESP_STORAGE_TO_XFER', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth respiration shift storage to transfer', &
-            ptr_patch=this%gresp_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC_TO_DEADSTEMC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live stem C turnover', &
-            ptr_patch=this%livestemc_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC_TO_DEADCROOTC', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 live coarse root C turnover', &
-            ptr_patch=this%livecrootc_to_deadcrootc_patch, default='inactive')
-
-       this%current_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CURRENT_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth resp for new growth displayed in this timestep', &
-            ptr_patch=this%current_gr_patch, default='inactive')
-
-       this%transfer_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TRANSFER_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth resp for transfer growth displayed in this timestep', &
-            ptr_patch=this%transfer_gr_patch, default='inactive')
-
-       this%storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_STORAGE_GR', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 growth resp for growth sent to storage for later display', &
-            ptr_patch=this%storage_gr_patch, default='inactive')
-
-       this%xsmrpool_c13ratio_patch(begp:endp) = spval
-       call hist_addfld1d (fname='XSMRPOOL_C13RATIO', units='proportion', &
-            avgflag='A', long_name='C13/C(12+13) ratio for xsmrpool', &
-            ptr_patch=this%xsmrpool_c13ratio_patch, default='inactive')
-
-    endif
-
-    !-------------------------------
-    ! C14 flux variables - patch
-    !-------------------------------
-
-    if ( carbon_type == 'c14' ) then
-
-       this%m_leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C mortality', &
-            ptr_patch=this%m_leafc_to_litter_patch, default='inactive')
-
-       this%m_frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C mortality', &
-            ptr_patch=this%m_frootc_to_litter_patch, default='inactive')
-
-       this%m_leafc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C storage mortality', &
-            ptr_patch=this%m_leafc_storage_to_litter_patch, default='inactive')
-
-       this%m_frootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C storage mortality', &
-            ptr_patch=this%m_frootc_storage_to_litter_patch, default='inactive')
-
-       this%m_livestemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C storage mortality', &
-            ptr_patch=this%m_livestemc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C storage mortality', &
-            ptr_patch=this%m_deadstemc_storage_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C storage mortality', &
-            ptr_patch=this%m_livecrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C storage mortality', &
-            ptr_patch=this%m_deadcrootc_storage_to_litter_patch, default='inactive')
-
-       this%m_leafc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C transfer mortality', &
-            ptr_patch=this%m_leafc_xfer_to_litter_patch, default='inactive')
-
-       this%m_frootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C transfer mortality', &
-            ptr_patch=this%m_frootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C transfer mortality', &
-            ptr_patch=this%m_livestemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C transfer mortality', &
-            ptr_patch=this%m_deadstemc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C transfer mortality', &
-            ptr_patch=this%m_livecrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C transfer mortality', &
-            ptr_patch=this%m_deadcrootc_xfer_to_litter_patch, default='inactive')
-
-       this%m_livestemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C mortality', &
-            ptr_patch=this%m_livestemc_to_litter_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C mortality', &
-            ptr_patch=this%m_deadstemc_to_litter_patch, default='inactive')
-
-       this%m_livecrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C mortality', &
-            ptr_patch=this%m_livecrootc_to_litter_patch, default='inactive')
-
-       this%m_deadcrootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C mortality', &
-            ptr_patch=this%m_deadcrootc_to_litter_patch, default='inactive')
-
-       this%m_gresp_storage_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_GRESP_STORAGE_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth respiration storage mortality', &
-            ptr_patch=this%m_gresp_storage_to_litter_patch, default='inactive')
-
-       this%m_gresp_xfer_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_GRESP_XFER_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth respiration transfer mortality', &
-            ptr_patch=this%m_gresp_xfer_to_litter_patch, default='inactive')
-
-       this%m_leafc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C fire loss', &
-            ptr_patch=this%m_leafc_to_fire_patch, default='inactive')
-
-       this%m_frootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C fire loss', &
-            ptr_patch=this%m_frootc_to_fire_patch, default='inactive')
-
-       this%m_leafc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C storage fire loss', &
-            ptr_patch=this%m_leafc_storage_to_fire_patch, default='inactive')
-
-       this%m_frootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C storage fire loss', &
-            ptr_patch=this%m_frootc_storage_to_fire_patch, default='inactive')
-
-       this%m_livestemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C storage fire loss', &
-            ptr_patch=this%m_livestemc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C storage fire loss', &
-            ptr_patch=this%m_deadstemc_storage_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C storage fire loss', &
-            ptr_patch=this%m_livecrootc_storage_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C storage fire loss', &
-            ptr_patch=this%m_deadcrootc_storage_to_fire_patch,  default='inactive')
-
-       this%m_leafc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LEAFC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C transfer fire loss', &
-            ptr_patch=this%m_leafc_xfer_to_fire_patch, default='inactive')
-
-       this%m_frootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_FROOTC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C transfer fire loss', &
-            ptr_patch=this%m_frootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livestemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C transfer fire loss', &
-            ptr_patch=this%m_livestemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C transfer fire loss', &
-            ptr_patch=this%m_deadstemc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livecrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C transfer fire loss', &
-            ptr_patch=this%m_livecrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C transfer fire loss', &
-            ptr_patch=this%m_deadcrootc_xfer_to_fire_patch, default='inactive')
-
-       this%m_livestemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVESTEMC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C fire loss', &
-            ptr_patch=this%m_livestemc_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C fire loss', &
-            ptr_patch=this%m_deadstemc_to_fire_patch, default='inactive')
-
-       this%m_deadstemc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADSTEMC_TO_LITTER_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C fire mortality to litter', &
-            ptr_patch=this%m_deadstemc_to_litter_fire_patch, default='inactive')
-
-       this%m_livecrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_LIVECROOTC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C fire loss', &
-            ptr_patch=this%m_livecrootc_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C fire loss', &
-            ptr_patch=this%m_deadcrootc_to_fire_patch, default='inactive')
-
-       this%m_deadcrootc_to_litter_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_DEADCROOTC_TO_LITTER_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C fire mortality to litter', &
-            ptr_patch=this%m_deadcrootc_to_litter_fire_patch, default='inactive')
-
-       this%m_gresp_storage_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_GRESP_STORAGE_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth respiration storage fire loss', &
-            ptr_patch=this%m_gresp_storage_to_fire_patch, default='inactive')
-
-       this%m_gresp_xfer_to_fire_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_M_GRESP_XFER_TO_FIRE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth respiration transfer fire loss', &
-            ptr_patch=this%m_gresp_xfer_to_fire_patch, default='inactive')
-
-       this%leafc_xfer_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC_XFER_TO_LEAFC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C growth from storage', &
-            ptr_patch=this%leafc_xfer_to_leafc_patch, default='inactive')
-
-       this%frootc_xfer_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC_XFER_TO_FROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C growth from storage', &
-            ptr_patch=this%frootc_xfer_to_frootc_patch, default='inactive')
-
-       this%livestemc_xfer_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC_XFER_TO_LIVESTEMC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C growth from storage', &
-            ptr_patch=this%livestemc_xfer_to_livestemc_patch, default='inactive')
-
-       this%deadstemc_xfer_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADSTEMC_XFER_TO_DEADSTEMC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C growth from storage', &
-            ptr_patch=this%deadstemc_xfer_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_xfer_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC_XFER_TO_LIVECROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C growth from storage', &
-            ptr_patch=this%livecrootc_xfer_to_livecrootc_patch, default='inactive')
-
-       this%deadcrootc_xfer_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADCROOTC_XFER_TO_DEADCROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C growth from storage', &
-            ptr_patch=this%deadcrootc_xfer_to_deadcrootc_patch, default='inactive')
-
-       this%leafc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C litterfall', &
-            ptr_patch=this%leafc_to_litter_patch, default='inactive')
-
-       this%frootc_to_litter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC_TO_LITTER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C litterfall', &
-            ptr_patch=this%frootc_to_litter_patch, default='inactive')
-
-       this%leaf_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAF_MR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf maintenance respiration', &
-            ptr_patch=this%leaf_mr_patch, default='inactive')
-
-       this%froot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOT_MR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root maintenance respiration', &
-            ptr_patch=this%froot_mr_patch, default='inactive')
-
-       this%livestem_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEM_MR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem maintenance respiration', &
-            ptr_patch=this%livestem_mr_patch, default='inactive')
-
-       this%livecroot_mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOT_MR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root maintenance respiration', &
-            ptr_patch=this%livecroot_mr_patch, default='inactive')
-
-       this%psnsun_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_PSNSUN_TO_CPOOL', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 C fixation from sunlit canopy', &
-            ptr_patch=this%psnsun_to_cpool_patch, default='inactive')
-
-       this%psnshade_to_cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_PSNSHADE_TO_CPOOL', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 C fixation from shaded canopy', &
-            ptr_patch=this%psnshade_to_cpool_patch, default='inactive')
-
-       this%cpool_to_leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LEAFC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to leaf C', &
-            ptr_patch=this%cpool_to_leafc_patch, default='inactive')
-
-       this%cpool_to_leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LEAFC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to leaf C storage', &
-            ptr_patch=this%cpool_to_leafc_storage_patch, default='inactive')
-
-       this%cpool_to_frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_FROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to fine root C', &
-            ptr_patch=this%cpool_to_frootc_patch, default='inactive')
-
-       this%cpool_to_frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_FROOTC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to fine root C storage', &
-            ptr_patch=this%cpool_to_frootc_storage_patch, default='inactive')
-
-       this%cpool_to_livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LIVESTEMC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to live stem C', &
-            ptr_patch=this%cpool_to_livestemc_patch, default='inactive')
-
-       this%cpool_to_livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LIVESTEMC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to live stem C storage', &
-            ptr_patch=this%cpool_to_livestemc_storage_patch, default='inactive')
-
-       this%cpool_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_DEADSTEMC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to dead stem C', &
-            ptr_patch=this%cpool_to_deadstemc_patch, default='inactive')
-
-       this%cpool_to_deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_DEADSTEMC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to dead stem C storage', &
-            ptr_patch=this%cpool_to_deadstemc_storage_patch, default='inactive')
-
-       this%cpool_to_livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LIVECROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to live coarse root C', &
-            ptr_patch=this%cpool_to_livecrootc_patch, default='inactive')
-
-       this%cpool_to_livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_LIVECROOTC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to live coarse root C storage', &
-            ptr_patch=this%cpool_to_livecrootc_storage_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_DEADCROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to dead coarse root C', &
-            ptr_patch=this%cpool_to_deadcrootc_patch, default='inactive')
-
-       this%cpool_to_deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_DEADCROOTC_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to dead coarse root C storage', &
-            ptr_patch=this%cpool_to_deadcrootc_storage_patch, default='inactive')
-
-       this%cpool_to_gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_TO_GRESP_STORAGE', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 allocation to growth respiration storage', &
-            ptr_patch=this%cpool_to_gresp_storage_patch, default='inactive')
-
-       this%cpool_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LEAF_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf growth respiration', &
-            ptr_patch=this%cpool_leaf_gr_patch, default='inactive')
-
-       this%cpool_leaf_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LEAF_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf growth respiration to storage', &
-            ptr_patch=this%cpool_leaf_storage_gr_patch, default='inactive')
-
-       this%transfer_leaf_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_LEAF_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf growth respiration from storage', &
-            ptr_patch=this%transfer_leaf_gr_patch, default='inactive')
-
-       this%cpool_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_FROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root growth respiration', &
-            ptr_patch=this%cpool_froot_gr_patch, default='inactive')
-
-       this%cpool_froot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_FROOT_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root  growth respiration to storage', &
-            ptr_patch=this%cpool_froot_storage_gr_patch, default='inactive')
-
-       this%transfer_froot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_FROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root  growth respiration from storage', &
-            ptr_patch=this%transfer_froot_gr_patch, default='inactive')
-
-       this%cpool_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LIVESTEM_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem growth respiration', &
-            ptr_patch=this%cpool_livestem_gr_patch, default='inactive')
-
-       this%cpool_livestem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LIVESTEM_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem growth respiration to storage', &
-            ptr_patch=this%cpool_livestem_storage_gr_patch, default='inactive')
-
-       this%transfer_livestem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_LIVESTEM_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem growth respiration from storage', &
-            ptr_patch=this%transfer_livestem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_DEADSTEM_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem growth respiration', &
-            ptr_patch=this%cpool_deadstem_gr_patch, default='inactive')
-
-       this%cpool_deadstem_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_DEADSTEM_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem growth respiration to storage', &
-            ptr_patch=this%cpool_deadstem_storage_gr_patch, default='inactive')
-
-       this%transfer_deadstem_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_DEADSTEM_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem growth respiration from storage', &
-            ptr_patch=this%transfer_deadstem_gr_patch, default='inactive')
-
-       this%cpool_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LIVECROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root growth respiration', &
-            ptr_patch=this%cpool_livecroot_gr_patch, default='inactive')
-
-       this%cpool_livecroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_LIVECROOT_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_livecroot_storage_gr_patch, default='inactive')
-
-       this%transfer_livecroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_LIVECROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_livecroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_DEADCROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root growth respiration', &
-            ptr_patch=this%cpool_deadcroot_gr_patch, default='inactive')
-
-       this%cpool_deadcroot_storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL_DEADCROOT_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root growth respiration to storage', &
-            ptr_patch=this%cpool_deadcroot_storage_gr_patch, default='inactive')
-
-       this%transfer_deadcroot_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_DEADCROOT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root growth respiration from storage', &
-            ptr_patch=this%transfer_deadcroot_gr_patch, default='inactive')
-
-       this%leafc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 leaf C shift storage to transfer', &
-            ptr_patch=this%leafc_storage_to_xfer_patch, default='inactive')
-
-       this%frootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 fine root C shift storage to transfer', &
-            ptr_patch=this%frootc_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C shift storage to transfer', &
-            ptr_patch=this%livestemc_storage_to_xfer_patch, default='inactive')
-
-       this%deadstemc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADSTEMC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead stem C shift storage to transfer', &
-            ptr_patch=this%deadstemc_storage_to_xfer_patch, default='inactive')
-
-       this%livecrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C shift storage to transfer', &
-            ptr_patch=this%livecrootc_storage_to_xfer_patch, default='inactive')
-
-       this%deadcrootc_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADCROOTC_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 dead coarse root C shift storage to transfer', &
-            ptr_patch=this%deadcrootc_storage_to_xfer_patch, default='inactive')
-
-       this%gresp_storage_to_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_GRESP_STORAGE_TO_XFER', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth respiration shift storage to transfer', &
-            ptr_patch=this%gresp_storage_to_xfer_patch, default='inactive')
-
-       this%livestemc_to_deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC_TO_DEADSTEMC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live stem C turnover', &
-            ptr_patch=this%livestemc_to_deadstemc_patch, default='inactive')
-
-       this%livecrootc_to_deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC_TO_DEADCROOTC', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 live coarse root C turnover', &
-            ptr_patch=this%livecrootc_to_deadcrootc_patch, default='inactive')
-
-       this%current_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CURRENT_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth resp for new growth displayed in this timestep', &
-            ptr_patch=this%current_gr_patch, default='inactive')
-
-       this%transfer_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TRANSFER_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth resp for transfer growth displayed in this timestep', &
-            ptr_patch=this%transfer_gr_patch, default='inactive')
-
-       this%storage_gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_STORAGE_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 growth resp for growth sent to storage for later display', &
-            ptr_patch=this%storage_gr_patch, default='inactive')
-
-       this%gpp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_GPP', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 gross primary production', &
-            ptr_patch=this%gpp_patch, default='inactive')
-
-       this%rr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_RR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 root respiration (fine root MR + total root GR)', &
-            ptr_patch=this%rr_patch, default='inactive')
-
-       this%mr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_MR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 maintenance respiration', &
-            ptr_patch=this%mr_patch, default='inactive')
-
-       this%gr_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_GR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 total growth respiration', &
-            ptr_patch=this%gr_patch, default='inactive')
-
-       this%ar_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_AR', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 autotrophic respiration (MR + GR)', &
-            ptr_patch=this%ar_patch, default='inactive')
-
-       this%npp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_NPP', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 net primary production', &
-            ptr_patch=this%npp_patch, default='inactive')
-
-       this%agnpp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_AGNPP', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 aboveground NPP', &
-            ptr_patch=this%agnpp_patch, default='inactive')
-
-       this%bgnpp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_BGNPP', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 belowground NPP', &
-            ptr_patch=this%bgnpp_patch, default='inactive')
-
-       this%litfall_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LITFALL', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 litterfall (leaves and fine roots)', &
-            ptr_patch=this%litfall_patch, default='inactive')
-
-       this%fire_closs_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_PFT_FIRE_CLOSS', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 total patch-level fire C loss', &
-            ptr_patch=this%fire_closs_patch, default='inactive')
-    endif
-
-    !-------------------------------
-    ! C flux variables - column 
-    !-------------------------------
-
-    if (carbon_type == 'c12') then
-
-       this%cwdc_loss_col(begc:endc) = spval
-       call hist_addfld1d (fname='CWDC_LOSS', units='gC/m^2/s', &
-            avgflag='A', long_name='coarse woody debris C loss', &
-            ptr_col=this%cwdc_loss_col)
-
-       this%m_decomp_cpools_to_fire_col(begc:endc,:)      = spval
-       this%m_decomp_cpools_to_fire_vr_col(begc:endc,:,:) = spval
-       do k = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then
-             data1dptr => this%m_decomp_cpools_to_fire_col(:,k)
-             fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'
-             longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-             call hist_addfld1d (fname=fieldname, units='gC/m^2/s',  &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data1dptr, default='inactive')
-
-             if ( nlevdecomp_full > 1 ) then
-                data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k)
-                fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix)
-                longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-                call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s', type2d='levdcmp', &
-                     avgflag='A', long_name=longname, &
-                     ptr_col=data2dptr, default='inactive')
-             endif
-          endif
-       end do
-
-       this%dwt_seedc_to_leaf_grc(begg:endg) = spval
-       call hist_addfld1d (fname='DWT_SEEDC_TO_LEAF', units='gC/m^2/s', &
-            avgflag='A', long_name='seed source to patch-level leaf', &
-            ptr_gcell=this%dwt_seedc_to_leaf_grc, default='inactive')
-
-       this%dwt_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DWT_SEEDC_TO_LEAF_PATCH', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level seed source to patch-level leaf ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_leaf_patch, default='inactive')
-
-       this%dwt_seedc_to_deadstem_grc(begg:endg) = spval
-       call hist_addfld1d (fname='DWT_SEEDC_TO_DEADSTEM', units='gC/m^2/s', &
-            avgflag='A', long_name='seed source to patch-level deadstem', &
-            ptr_gcell=this%dwt_seedc_to_deadstem_grc, default='inactive')
-
-       this%dwt_seedc_to_deadstem_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DWT_SEEDC_TO_DEADSTEM_PATCH', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level seed source to patch-level deadstem ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_deadstem_patch, default='inactive')
-
-       this%dwt_conv_cflux_grc(begg:endg) = spval
-       call hist_addfld1d (fname='DWT_CONV_CFLUX', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='conversion C flux (immediate loss to atm) (0 at all times except first timestep of year)', &
-            ptr_gcell=this%dwt_conv_cflux_grc, default='inactive')
-
-       this%dwt_conv_cflux_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DWT_CONV_CFLUX_PATCH', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level conversion C flux (immediate loss to atm) ' // &
-            '(0 at all times except first timestep of year) ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_conv_cflux_patch, default='inactive')
-
-       this%dwt_conv_cflux_dribbled_grc(begg:endg) = spval
-       call hist_addfld1d (fname='DWT_CONV_CFLUX_DRIBBLED', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='conversion C flux (immediate loss to atm), dribbled throughout the year', &
-            ptr_gcell=this%dwt_conv_cflux_dribbled_grc, default='inactive')
-
-       this%dwt_wood_productc_gain_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DWT_WOOD_PRODUCTC_GAIN_PATCH', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level landcover change-driven addition to wood product pools' // &
-            '(0 at all times except first timestep of year) ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_wood_productc_gain_patch, default='inactive')
-
-        this%dwt_slash_cflux_col(begc:endc) = spval
-        call hist_addfld1d (fname='DWT_SLASH_CFLUX', units='gC/m^2/s', &
-             avgflag='A', long_name='slash C flux to litter and CWD due to land use', &
-             ptr_col=this%dwt_slash_cflux_col, default='inactive')
-
-       this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='DWT_FROOTC_TO_LITR_MET_C', units='gC/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_met_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_cel_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='DWT_FROOTC_TO_LITR_CEL_C', units='gC/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_cel_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_lig_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='DWT_FROOTC_TO_LITR_LIG_C', units='gC/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_lig_c_col, default='inactive')
-
-       this%dwt_livecrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='DWT_LIVECROOTC_TO_CWDC', units='gC/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='live coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_livecrootc_to_cwdc_col, default='inactive')
-
-       this%dwt_deadcrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='DWT_DEADCROOTC_TO_CWDC', units='gC/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='dead coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_deadcrootc_to_cwdc_col, default='inactive')
-
-       this%crop_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CROP_SEEDC_TO_LEAF', units='gC/m^2/s', &
-            avgflag='A', long_name='crop seed source to leaf', &
-            ptr_patch=this%crop_seedc_to_leaf_patch, default='inactive')
-
-        this%sr_col(begc:endc) = spval
-        call hist_addfld1d (fname='SR', units='gC/m^2/s', &
-             avgflag='A', long_name='total soil respiration (HR + root resp)', &
-             ptr_col=this%sr_col, default='inactive')
-
-        this%er_col(begc:endc) = spval
-        call hist_addfld1d (fname='ER', units='gC/m^2/s', &
-             avgflag='A', long_name='total ecosystem respiration, autotrophic + heterotrophic', &
-             ptr_col=this%er_col, default='inactive')
-
-        this%litfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='LITFIRE', units='gC/m^2/s', &
-             avgflag='A', long_name='litter fire losses', &
-             ptr_col=this%litfire_col, default='inactive')
-
-        this%somfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='SOMFIRE', units='gC/m^2/s', &
-             avgflag='A', long_name='soil organic matter fire losses', &
-             ptr_col=this%somfire_col, default='inactive')
-
-        this%totfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='TOTFIRE', units='gC/m^2/s', &
-             avgflag='A', long_name='total ecosystem fire losses', &
-             ptr_col=this%totfire_col, default='inactive')
-
-        this%fire_closs_col(begc:endc) = spval
-        call hist_addfld1d (fname='COL_FIRE_CLOSS', units='gC/m^2/s', &
-             avgflag='A', long_name='total column-level fire C loss for non-peat fires outside land-type converted region', &
-             ptr_col=this%fire_closs_col, default='inactive')
-
-        this%annsum_npp_patch(begp:endp) = spval
-        call hist_addfld1d (fname='ANNSUM_NPP', units='gC/m^2/yr', &
-             avgflag='A', long_name='annual sum of NPP', &
-             ptr_patch=this%annsum_npp_patch, default='inactive')
-
-        this%annsum_npp_col(begc:endc) = spval
-        call hist_addfld1d (fname='CANNSUM_NPP', units='gC/m^2/s', &
-             avgflag='A', long_name='annual sum of column-level NPP', &
-             ptr_col=this%annsum_npp_col, default='inactive')
-
-       this%nep_col(begc:endc) = spval
-       call hist_addfld1d (fname='NEP', units='gC/m^2/s', &
-            avgflag='A', long_name='net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink', &
-            ptr_col=this%nep_col, default='inactive')
-
-       this%nbp_grc(begg:endg) = spval
-       call hist_addfld1d (fname='NBP', units='gC/m^2/s', &
-            avgflag='A', long_name='net biome production, includes fire, landuse,'&
-            //' harvest and hrv_xsmrpool flux (latter smoothed over the year), positive for sink'&
-            //' (same as net carbon exchange between land and atmosphere)', &
-            ptr_gcell=this%nbp_grc, default='inactive')
-
-       this%nee_grc(begg:endg) = spval
-       call hist_addfld1d (fname='NEE', units='gC/m^2/s', &
-            avgflag='A', long_name='net ecosystem exchange of carbon,'&
-            //' includes fire and hrv_xsmrpool (latter smoothed over the year),'&
-            //' excludes landuse and harvest flux, positive for source', &
-            ptr_gcell=this%nee_grc, default='inactive')
-
-       this%landuseflux_grc(begg:endg) = spval
-       call hist_addfld1d (fname='LAND_USE_FLUX', units='gC/m^2/s', &
-            avgflag='A', &
-            long_name='total C emitted from land cover conversion (smoothed over the year)'&
-            //' and wood and grain product pools (NOTE: not a net value)', &
-            ptr_gcell=this%landuseflux_grc, default='inactive')
-
-   end if
-    !-------------------------------
-    ! C13 flux variables - column 
-    !-------------------------------
-
-    if ( carbon_type == 'c13' ) then
-
-       this%m_decomp_cpools_to_fire_col(begc:endc,:) = spval
-       this%m_decomp_cpools_to_fire_vr_col(begc:endc,:,:) = spval
-       do k = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then
-             data1dptr => this%m_decomp_cpools_to_fire_col(:,k)
-             fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'
-             longname =  'C13 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-             call hist_addfld1d (fname=fieldname, units='gC13/m^2',  &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data1dptr, default='inactive')
-
-             if ( nlevdecomp_full > 1 ) then
-                data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k)
-                fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix)
-                longname =  'C13 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-                call hist_addfld_decomp (fname=fieldname, units='gC13/m^3',  type2d='levdcmp', &
-                     avgflag='A', long_name=longname, &
-                     ptr_col=data2dptr, default='inactive')
-             end if
-          endif
-       end do
-
-       this%dwt_seedc_to_leaf_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C13_DWT_SEEDC_TO_LEAF', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 seed source to patch-level leaf', &
-            ptr_gcell=this%dwt_seedc_to_leaf_grc, default='inactive')
-
-       this%dwt_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DWT_SEEDC_TO_LEAF_PATCH', units='gC13/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C13 seed source to patch-level leaf ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_leaf_patch, default='inactive')
-
-       this%dwt_seedc_to_deadstem_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C13_DWT_SEEDC_TO_DEADSTEM', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 seed source to patch-level deadstem', &
-            ptr_gcell=this%dwt_seedc_to_deadstem_grc, default='inactive')
-
-       this%dwt_seedc_to_deadstem_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DWT_SEEDC_TO_DEADSTEM_PATCH', units='gC13/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C13 seed source to patch-level deadstem ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_deadstem_patch, default='inactive')
-
-       this%dwt_conv_cflux_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C13_DWT_CONV_CFLUX', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 conversion C flux (immediate loss to atm) ' // &
-            '(0 at all times except first timestep of year)', &
-            ptr_gcell=this%dwt_conv_cflux_grc, default='inactive')
-
-       this%dwt_conv_cflux_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DWT_CONV_CFLUX_PATCH', units='gC13/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C13 conversion C flux (immediate loss to atm) ' // &
-            '(0 at all times except first timestep of year) ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_conv_cflux_patch, default='inactive')
-
-       this%dwt_conv_cflux_dribbled_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C13_DWT_CONV_CFLUX_DRIBBLED', units='gC13/m^2/s', &
-            avgflag='A', &
-            long_name='C13 conversion C flux (immediate loss to atm), dribbled throughout the year', &
-            ptr_gcell=this%dwt_conv_cflux_dribbled_grc, default='inactive')
-
-       this%dwt_slash_cflux_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_DWT_SLASH_CFLUX', units='gC/m^2/s', &
-            avgflag='A', long_name='C13 slash C flux to litter and CWD due to land use', &
-            ptr_col=this%dwt_slash_cflux_col, default='inactive')
-
-       this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C13_DWT_FROOTC_TO_LITR_MET_C', units='gC13/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C13 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_met_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_cel_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C13_DWT_FROOTC_TO_LITR_CEL_C', units='gC13/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C13 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_cel_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_lig_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C13_DWT_FROOTC_TO_LITR_LIG_C', units='gC13/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C13 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_lig_c_col, default='inactive')
-
-       this%dwt_livecrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C13_DWT_LIVECROOTC_TO_CWDC', units='gC13/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C13 live coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_livecrootc_to_cwdc_col, default='inactive')
-
-       this%dwt_deadcrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C13_DWT_DEADCROOTC_TO_CWDC', units='gC13/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C13 dead coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_deadcrootc_to_cwdc_col, default='inactive')
-
-       this%crop_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CROP_SEEDC_TO_LEAF', units='gC13/m^2/s', &
-            avgflag='A', long_name='C13 crop seed source to leaf', &
-            ptr_patch=this%crop_seedc_to_leaf_patch, default='inactive')
-
-        this%sr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_SR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total soil respiration (HR + root resp)', &
-             ptr_col=this%sr_col, default='inactive')
-
-        this%er_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_ER', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total ecosystem respiration, autotrophic + heterotrophic', &
-             ptr_col=this%er_col, default='inactive')
-
-        this%litfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_LITFIRE', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 litter fire losses', &
-             ptr_col=this%litfire_col, default='inactive')
-
-        this%somfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_SOMFIRE', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 soil organic matter fire losses', &
-             ptr_col=this%somfire_col, default='inactive')
-
-        this%totfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_TOTFIRE', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total ecosystem fire losses', &
-             ptr_col=this%totfire_col, default='inactive')
-
-        this%fire_closs_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_COL_FIRE_CLOSS', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total column-level fire C loss', &
-             ptr_col=this%fire_closs_col, default='inactive')
-
-        this%nep_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_NEP', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 net ecosystem production, excludes fire flux, positive for sink', &
-             ptr_col=this%nep_col, default='inactive')
-
-        this%nee_grc(begg:endg) = spval
-        call hist_addfld1d (fname='C13_NEE', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 net ecosystem exchange of carbon, includes fire flux, positive for source', &
-             ptr_gcell=this%nee_grc, default='inactive')
-
-    endif
-
-    !-------------------------------
-    ! C14 flux variables - column 
-    !-------------------------------
-
-    if (carbon_type == 'c14') then
-
-       this%m_decomp_cpools_to_fire_col(begc:endc,:)      = spval
-       this%m_decomp_cpools_to_fire_vr_col(begc:endc,:,:) = spval
-       do k = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then
-             data1dptr => this%m_decomp_cpools_to_fire_col(:,k)
-             fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'
-             longname =  'C14 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-             call hist_addfld1d (fname=fieldname, units='gC14/m^2',  &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data1dptr, default='inactive')
-
-             if ( nlevdecomp_full > 1 ) then
-                data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k)
-                fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix)
-                longname =  'C14 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss'
-                call hist_addfld_decomp (fname=fieldname, units='gC14/m^3',  type2d='levdcmp', &
-                     avgflag='A', long_name=longname, &
-                     ptr_col=data2dptr, default='inactive')
-             end if
-          endif
-       end do
-
-       this%dwt_seedc_to_leaf_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C14_DWT_SEEDC_TO_LEAF', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 seed source to patch-level leaf', &
-            ptr_gcell=this%dwt_seedc_to_leaf_grc, default='inactive')
-
-       this%dwt_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DWT_SEEDC_TO_LEAF_PATCH', units='gC14/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C14 seed source to patch-level leaf ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_leaf_patch, default='inactive')
-
-       this%dwt_seedc_to_deadstem_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C14_DWT_SEEDC_TO_DEADSTEM', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 seed source to patch-level deadstem', &
-            ptr_gcell=this%dwt_seedc_to_deadstem_grc, default='inactive')
-
-       this%dwt_seedc_to_deadstem_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DWT_SEEDC_TO_DEADSTEM_PATCH', units='gC14/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C14 seed source to patch-level deadstem ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_seedc_to_deadstem_patch, default='inactive')
-
-       this%dwt_conv_cflux_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C14_DWT_CONV_CFLUX', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 conversion C flux (immediate loss to atm) ' // &
-            '(0 at all times except first timestep of year)', &
-            ptr_gcell=this%dwt_conv_cflux_grc, default='inactive')
-
-       this%dwt_conv_cflux_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DWT_CONV_CFLUX_PATCH', units='gC14/m^2/s', &
-            avgflag='A', &
-            long_name='patch-level C14 conversion C flux (immediate loss to atm) ' // &
-            '(0 at all times except first timestep of year) ' // &
-            '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-            ptr_patch=this%dwt_conv_cflux_patch, default='inactive')
-
-       this%dwt_conv_cflux_dribbled_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C14_DWT_CONV_CFLUX_DRIBBLED', units='gC14/m^2/s', &
-            avgflag='A', &
-            long_name='C14 conversion C flux (immediate loss to atm), dribbled throughout the year', &
-            ptr_gcell=this%dwt_conv_cflux_dribbled_grc, default='inactive')
-
-       this%dwt_slash_cflux_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_DWT_SLASH_CFLUX', units='gC/m^2/s', &
-            avgflag='A', long_name='C14 slash C flux to litter and CWD due to land use', &
-            ptr_col=this%dwt_slash_cflux_col, default='inactive')
-
-       this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C14_DWT_FROOTC_TO_LITR_MET_C', units='gC14/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C14 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_met_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_cel_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C14_DWT_FROOTC_TO_LITR_CEL_C', units='gC14/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C14 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_cel_c_col, default='inactive')
-
-       this%dwt_frootc_to_litr_lig_c_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C14_DWT_FROOTC_TO_LITR_LIG_C', units='gC14/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C14 fine root to litter due to landcover change', &
-            ptr_col=this%dwt_frootc_to_litr_lig_c_col, default='inactive')
-
-       this%dwt_livecrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C14_DWT_LIVECROOTC_TO_CWDC', units='gC14/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C14 live coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_livecrootc_to_cwdc_col, default='inactive')
-
-       this%dwt_deadcrootc_to_cwdc_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='C14_DWT_DEADCROOTC_TO_CWDC', units='gC14/m^2/s',  type2d='levdcmp', &
-            avgflag='A', long_name='C14 dead coarse root to CWD due to landcover change', &
-            ptr_col=this%dwt_deadcrootc_to_cwdc_col, default='inactive')
-
-       this%crop_seedc_to_leaf_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CROP_SEEDC_TO_LEAF', units='gC14/m^2/s', &
-            avgflag='A', long_name='C14 crop seed source to leaf', &
-            ptr_patch=this%crop_seedc_to_leaf_patch, default='inactive')
-
-        this%sr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_SR', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 total soil respiration (HR + root resp)', &
-             ptr_col=this%sr_col, default='inactive')
-
-        this%er_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_ER', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 total ecosystem respiration, autotrophic + heterotrophic', &
-             ptr_col=this%er_col, default='inactive')
-
-        this%litfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_LITFIRE', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 litter fire losses', &
-             ptr_col=this%litfire_col, default='inactive')
-
-        this%somfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_SOMFIRE', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 soil organic matter fire losses', &
-             ptr_col=this%somfire_col, default='inactive')
-
-        this%totfire_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_TOTFIRE', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 total ecosystem fire losses', &
-             ptr_col=this%totfire_col, default='inactive')
-
-        this%fire_closs_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_COL_FIRE_CLOSS', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 total column-level fire C loss', &
-             ptr_col=this%fire_closs_col, default='inactive')
-
-        this%nep_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_NEP', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 net ecosystem production, excludes fire flux, positive for sink', &
-             ptr_col=this%nep_col, default='inactive')
-
-        this%nee_grc(begg:endg) = spval
-        call hist_addfld1d (fname='C14_NEE', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 net ecosystem exchange of carbon, includes fire flux, positive for source', &
-             ptr_gcell=this%nee_grc, default='inactive')
-
-    endif
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(cnveg_carbonflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p, c, l, j
-    integer :: fc                                        ! filter index
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: num_special_patch                         ! number of good values in special_patch filter
-    integer :: special_col(bounds%endc-bounds%begc+1)    ! special landunit filter - columns
-    integer :: special_patch(bounds%endp-bounds%begp+1)  ! special landunit filter - patches
-    !-----------------------------------------------------------------------
-
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    ! Set patch filters
-
-    num_special_patch = 0
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-
-       if (lun%ifspecial(l)) then
-          num_special_patch = num_special_patch + 1
-          special_patch(num_special_patch) = p
-       end if
-    end do
-
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-       this%gpp_before_downreg_patch(p)       = 0._r8
-
-       if (lun%ifspecial(l)) then
-          this%availc_patch(p)                = spval
-          this%xsmrpool_recover_patch(p)      = spval
-          this%excess_cflux_patch(p)          = spval
-          this%plant_calloc_patch(p)          = spval
-          this%prev_leafc_to_litter_patch(p)  = spval
-          this%prev_frootc_to_litter_patch(p) = spval
-          this%leafc_to_litter_fun_patch(p)   = spval
-       end if
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%availc_patch(p)                = 0._r8
-          this%xsmrpool_recover_patch(p)      = 0._r8
-          this%excess_cflux_patch(p)          = 0._r8
-          this%prev_leafc_to_litter_patch(p)  = 0._r8
-          this%leafc_to_litter_fun_patch(p)   = 0._r8 
-          this%prev_frootc_to_litter_patch(p) = 0._r8
-          this%plant_calloc_patch(p)          = 0._r8
-       end if
-    end do
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       ! also initialize dynamic landcover fluxes so that they have
-       ! real values on first timestep, prior to calling pftdyn_cnbal
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%dwt_slash_cflux_col(c) = 0._r8
-          do j = 1, nlevdecomp_full
-             this%dwt_frootc_to_litr_met_c_col(c,j) = 0._r8
-             this%dwt_frootc_to_litr_cel_c_col(c,j) = 0._r8
-             this%dwt_frootc_to_litr_lig_c_col(c,j) = 0._r8
-             this%dwt_livecrootc_to_cwdc_col(c,j)   = 0._r8
-             this%dwt_deadcrootc_to_cwdc_col(c,j)   = 0._r8
-          end do
-       end if
-    end do
-
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-
-       this%gpp_patch(p)                 = 0._r8
-       if (lun%ifspecial(l)) then
-          this%tempsum_npp_patch(p)      = spval
-          this%annsum_npp_patch(p)       = spval
-          this%tempsum_litfall_patch(p)  = spval
-          this%annsum_litfall_patch(p)   = spval
-       end if
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%tempsum_npp_patch(p)      = 0._r8
-          this%annsum_npp_patch(p)       = 0._r8
-          this%tempsum_litfall_patch(p)  = 0._r8
-          this%annsum_litfall_patch(p)   = 0._r8
-       end if
-    end do
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       if (lun%ifspecial(l)) then
-          this%annsum_npp_col(c) = spval
-       end if
-
-       ! also initialize dynamic landcover fluxes so that they have
-       ! real values on first timestep, prior to calling pftdyn_cnbal
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%annsum_npp_col(c) = 0._r8   
-       end if
-    end do
-
-    ! initialize fields for special filters
-
-    call this%SetValues (&
-         num_patch=num_special_patch, filter_patch=special_patch, value_patch=0._r8, &
-         num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart ( this, bounds, ncid, flag, carbon_type )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon fluxes
-    !
-    ! !USES:
-    use ncdio_pio, only : file_desc_t
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonflux_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   !'read' or 'write'
-    character(len=*)  , intent(in)    :: carbon_type ! 'c12' or 'c13' or 'c14'
-    !------------------------------------------------------------------------
-
-    if (carbon_type == 'c12') then
-       call this%RestartBulkOnly(bounds, ncid, flag)
-    end if
-
-    call this%RestartAllIsotopes(bounds, ncid, flag)
-
-  end subroutine Restart
-
-
-  !-----------------------------------------------------------------------
-  subroutine RestartBulkOnly ( this, bounds, ncid, flag )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon fluxes - fields only present for bulk C
-    !
-    ! !USES:
-    use shr_infnan_mod   , only : isnan => shr_infnan_isnan, nan => shr_infnan_nan, assignment(=)
-    use clm_time_manager , only : is_restart
-    use clm_varcon       , only : c13ratio, c14ratio
-    use CNSharedParamsMod, only : use_fun
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonflux_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   !'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    !------------------------------------------------------------------------
-
-    if (use_crop) then
-
-       call restartvar(ncid=ncid, flag=flag,  varname='grainc_xfer_to_grainc', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain C growth from storage', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainc_xfer_to_grainc_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='livestemc_to_litter', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='live stem C litterfall', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_to_litter_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='grainc_to_food', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain C to food', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainc_to_food_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cpool_to_grainc', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='allocation to grain C', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_to_grainc_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cpool_to_grainc_storage', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='allocation to grain C storage', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_to_grainc_storage_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cpool_grain_gr', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain growth respiration', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_grain_gr_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cpool_grain_storage_gr', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain growth respiration to storage', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_grain_storage_gr_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='transfer_grain_gr', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain growth respiration from storage', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%transfer_grain_gr_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='grainc_storage_to_xfer', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain C shift storage to transfer', units='gC/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainc_storage_to_xfer_patch)
-
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='gpp_pepv', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%gpp_before_downreg_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='availc', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%availc_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='xsmrpool_recover', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%xsmrpool_recover_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='plant_calloc', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%plant_calloc_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='excess_cflux', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%excess_cflux_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='prev_leafc_to_litter', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%prev_leafc_to_litter_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='prev_frootc_to_litter', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%prev_frootc_to_litter_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='tempsum_npp', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tempsum_npp_patch) 
- 
-    call restartvar(ncid=ncid, flag=flag, varname='annsum_npp', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annsum_npp_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='col_lag_npp', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%lag_npp_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='cannsum_npp', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annsum_npp_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='tempsum_litfall', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tempsum_litfall_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='annsum_litfall', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annsum_litfall_patch)
-
-    if ( use_fun ) then
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_to_litter_fun', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_to_litter_fun_patch)
-    end if
-
-  end subroutine RestartBulkOnly
-
-
-  !-----------------------------------------------------------------------
-  subroutine RestartAllIsotopes ( this, bounds, ncid, flag )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon fluxes - fields present for both bulk C and isotopes
-    !
-    ! !USES:
-    use ncdio_pio, only : file_desc_t
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonflux_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   !'read' or 'write'
-    !-----------------------------------------------------------------------
-
-  end subroutine RestartAllIsotopes
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, &
-       num_patch, filter_patch, value_patch, &
-       num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set carbon state fluxes
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonflux_type) :: this
-    integer , intent(in) :: num_patch
-    integer , intent(in) :: filter_patch(:)
-    real(r8), intent(in) :: value_patch
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i     ! loop index
-    integer :: j,k,l    ! indices
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_patch
-       i = filter_patch(fi)
-
-       this%m_leafc_to_litter_patch(i)                   = value_patch
-       this%m_frootc_to_litter_patch(i)                  = value_patch
-       this%m_leafc_storage_to_litter_patch(i)           = value_patch
-       this%m_frootc_storage_to_litter_patch(i)          = value_patch
-       this%m_livestemc_storage_to_litter_patch(i)       = value_patch
-       this%m_deadstemc_storage_to_litter_patch(i)       = value_patch
-       this%m_livecrootc_storage_to_litter_patch(i)      = value_patch
-       this%m_deadcrootc_storage_to_litter_patch(i)      = value_patch
-       this%m_leafc_xfer_to_litter_patch(i)              = value_patch
-       this%m_frootc_xfer_to_litter_patch(i)             = value_patch
-       this%m_livestemc_xfer_to_litter_patch(i)          = value_patch
-       this%m_deadstemc_xfer_to_litter_patch(i)          = value_patch
-       this%m_livecrootc_xfer_to_litter_patch(i)         = value_patch
-       this%m_deadcrootc_xfer_to_litter_patch(i)         = value_patch
-       this%m_livestemc_to_litter_patch(i)               = value_patch
-       this%m_deadstemc_to_litter_patch(i)               = value_patch
-       this%m_livecrootc_to_litter_patch(i)              = value_patch
-       this%m_deadcrootc_to_litter_patch(i)              = value_patch
-       this%m_gresp_storage_to_litter_patch(i)           = value_patch
-       this%m_gresp_xfer_to_litter_patch(i)              = value_patch
-       this%hrv_leafc_to_litter_patch(i)                 = value_patch             
-       this%hrv_leafc_storage_to_litter_patch(i)         = value_patch     
-       this%hrv_leafc_xfer_to_litter_patch(i)            = value_patch        
-       this%hrv_frootc_to_litter_patch(i)                = value_patch            
-       this%hrv_frootc_storage_to_litter_patch(i)        = value_patch    
-       this%hrv_frootc_xfer_to_litter_patch(i)           = value_patch       
-       this%hrv_livestemc_to_litter_patch(i)             = value_patch         
-       this%hrv_livestemc_storage_to_litter_patch(i)     = value_patch 
-       this%hrv_livestemc_xfer_to_litter_patch(i)        = value_patch    
-       this%hrv_deadstemc_storage_to_litter_patch(i)     = value_patch 
-       this%hrv_deadstemc_xfer_to_litter_patch(i)        = value_patch    
-       this%hrv_livecrootc_to_litter_patch(i)            = value_patch        
-       this%hrv_livecrootc_storage_to_litter_patch(i)    = value_patch
-       this%hrv_livecrootc_xfer_to_litter_patch(i)       = value_patch   
-       this%hrv_deadcrootc_to_litter_patch(i)            = value_patch        
-       this%hrv_deadcrootc_storage_to_litter_patch(i)    = value_patch
-       this%hrv_deadcrootc_xfer_to_litter_patch(i)       = value_patch   
-       this%hrv_gresp_storage_to_litter_patch(i)         = value_patch     
-       this%hrv_gresp_xfer_to_litter_patch(i)            = value_patch        
-       this%hrv_xsmrpool_to_atm_patch(i)                 = value_patch
-
-       this%m_leafc_to_fire_patch(i)                     = value_patch
-       this%m_leafc_storage_to_fire_patch(i)             = value_patch
-       this%m_leafc_xfer_to_fire_patch(i)                = value_patch
-       this%m_livestemc_to_fire_patch(i)                 = value_patch
-       this%m_livestemc_storage_to_fire_patch(i)         = value_patch
-       this%m_livestemc_xfer_to_fire_patch(i)            = value_patch
-       this%m_deadstemc_to_fire_patch(i)                 = value_patch
-       this%m_deadstemc_storage_to_fire_patch(i)         = value_patch
-       this%m_deadstemc_xfer_to_fire_patch(i)            = value_patch
-       this%m_frootc_to_fire_patch(i)                    = value_patch
-       this%m_frootc_storage_to_fire_patch(i)            = value_patch
-       this%m_frootc_xfer_to_fire_patch(i)               = value_patch
-       this%m_livecrootc_to_fire_patch(i)                = value_patch
-       this%m_livecrootc_storage_to_fire_patch(i)        = value_patch
-       this%m_livecrootc_xfer_to_fire_patch(i)           = value_patch
-       this%m_deadcrootc_to_fire_patch(i)                = value_patch
-       this%m_deadcrootc_storage_to_fire_patch(i)        = value_patch
-       this%m_deadcrootc_xfer_to_fire_patch(i)           = value_patch
-       this%m_gresp_storage_to_fire_patch(i)             = value_patch
-       this%m_gresp_xfer_to_fire_patch(i)                = value_patch
-
-       this%m_leafc_to_litter_fire_patch(i)              = value_patch
-       this%m_leafc_storage_to_litter_fire_patch(i)      = value_patch
-       this%m_leafc_xfer_to_litter_fire_patch(i)         = value_patch
-       this%m_livestemc_to_litter_fire_patch(i)          = value_patch
-       this%m_livestemc_storage_to_litter_fire_patch(i)  = value_patch
-       this%m_livestemc_xfer_to_litter_fire_patch(i)     = value_patch
-       this%m_livestemc_to_deadstemc_fire_patch(i)       = value_patch
-       this%m_deadstemc_to_litter_fire_patch(i)          = value_patch
-       this%m_deadstemc_storage_to_litter_fire_patch(i)  = value_patch
-       this%m_deadstemc_xfer_to_litter_fire_patch(i)     = value_patch
-       this%m_frootc_to_litter_fire_patch(i)             = value_patch
-       this%m_frootc_storage_to_litter_fire_patch(i)     = value_patch
-       this%m_frootc_xfer_to_litter_fire_patch(i)        = value_patch
-       this%m_livecrootc_to_litter_fire_patch(i)         = value_patch
-       this%m_livecrootc_storage_to_litter_fire_patch(i) = value_patch
-       this%m_livecrootc_xfer_to_litter_fire_patch(i)    = value_patch
-       this%m_livecrootc_to_deadcrootc_fire_patch(i)     = value_patch
-       this%m_deadcrootc_to_litter_fire_patch(i)         = value_patch
-       this%m_deadcrootc_storage_to_litter_fire_patch(i) = value_patch
-       this%m_deadcrootc_xfer_to_litter_fire_patch(i)    = value_patch
-       this%m_gresp_storage_to_litter_fire_patch(i)      = value_patch
-       this%m_gresp_xfer_to_litter_fire_patch(i)         = value_patch
-
-       this%leafc_xfer_to_leafc_patch(i)                 = value_patch
-       this%frootc_xfer_to_frootc_patch(i)               = value_patch
-       this%livestemc_xfer_to_livestemc_patch(i)         = value_patch
-       this%deadstemc_xfer_to_deadstemc_patch(i)         = value_patch
-       this%livecrootc_xfer_to_livecrootc_patch(i)       = value_patch
-       this%deadcrootc_xfer_to_deadcrootc_patch(i)       = value_patch
-       this%leafc_to_litter_patch(i)                     = value_patch
-       this%frootc_to_litter_patch(i)                    = value_patch
-       this%cpool_to_resp_patch(i)                       = value_patch
-       this%cpool_to_leafc_resp_patch(i)                 = value_patch
-       this%cpool_to_leafc_storage_resp_patch(i)         = value_patch
-       this%cpool_to_frootc_resp_patch(i)                = value_patch
-       this%cpool_to_frootc_storage_resp_patch(i)        = value_patch
-       this%cpool_to_livecrootc_resp_patch(i)            = value_patch
-       this%cpool_to_livecrootc_storage_resp_patch(i)    = value_patch
-       this%cpool_to_livestemc_resp_patch(i)             = value_patch
-       this%cpool_to_livestemc_storage_resp_patch(i)     = value_patch
-       this%leaf_mr_patch(i)                             = value_patch
-       this%froot_mr_patch(i)                            = value_patch
-       this%livestem_mr_patch(i)                         = value_patch
-       this%livecroot_mr_patch(i)                        = value_patch
-       this%grain_mr_patch(i)                            = value_patch
-       this%leaf_curmr_patch(i)                          = value_patch
-       this%froot_curmr_patch(i)                         = value_patch
-       this%livestem_curmr_patch(i)                      = value_patch
-       this%livecroot_curmr_patch(i)                     = value_patch
-       this%grain_curmr_patch(i)                         = value_patch
-       this%leaf_xsmr_patch(i)                           = value_patch
-       this%froot_xsmr_patch(i)                          = value_patch
-       this%livestem_xsmr_patch(i)                       = value_patch
-       this%livecroot_xsmr_patch(i)                      = value_patch
-       this%grain_xsmr_patch(i)                          = value_patch
-       this%psnsun_to_cpool_patch(i)                     = value_patch
-       this%psnshade_to_cpool_patch(i)                   = value_patch
-       this%cpool_to_xsmrpool_patch(i)                   = value_patch
-       this%cpool_to_leafc_patch(i)                      = value_patch
-       this%cpool_to_leafc_storage_patch(i)              = value_patch
-       this%cpool_to_frootc_patch(i)                     = value_patch
-       this%cpool_to_frootc_storage_patch(i)             = value_patch
-       this%cpool_to_livestemc_patch(i)                  = value_patch
-       this%cpool_to_livestemc_storage_patch(i)          = value_patch
-       this%cpool_to_deadstemc_patch(i)                  = value_patch
-       this%cpool_to_deadstemc_storage_patch(i)          = value_patch
-       this%cpool_to_livecrootc_patch(i)                 = value_patch
-       this%cpool_to_livecrootc_storage_patch(i)         = value_patch
-       this%cpool_to_deadcrootc_patch(i)                 = value_patch
-       this%cpool_to_deadcrootc_storage_patch(i)         = value_patch
-       this%cpool_to_gresp_storage_patch(i)              = value_patch
-       this%cpool_leaf_gr_patch(i)                       = value_patch
-       this%cpool_leaf_storage_gr_patch(i)               = value_patch
-       this%transfer_leaf_gr_patch(i)                    = value_patch
-       this%cpool_froot_gr_patch(i)                      = value_patch
-       this%cpool_froot_storage_gr_patch(i)              = value_patch
-       this%transfer_froot_gr_patch(i)                   = value_patch
-       this%cpool_livestem_gr_patch(i)                   = value_patch
-       this%cpool_livestem_storage_gr_patch(i)           = value_patch
-       this%transfer_livestem_gr_patch(i)                = value_patch
-       this%cpool_deadstem_gr_patch(i)                   = value_patch
-       this%cpool_deadstem_storage_gr_patch(i)           = value_patch
-       this%transfer_deadstem_gr_patch(i)                = value_patch
-       this%cpool_livecroot_gr_patch(i)                  = value_patch
-       this%cpool_livecroot_storage_gr_patch(i)          = value_patch
-       this%transfer_livecroot_gr_patch(i)               = value_patch
-       this%cpool_deadcroot_gr_patch(i)                  = value_patch
-       this%cpool_deadcroot_storage_gr_patch(i)          = value_patch
-       this%transfer_deadcroot_gr_patch(i)               = value_patch
-       this%leafc_storage_to_xfer_patch(i)               = value_patch
-       this%frootc_storage_to_xfer_patch(i)              = value_patch
-       this%livestemc_storage_to_xfer_patch(i)           = value_patch
-       this%deadstemc_storage_to_xfer_patch(i)           = value_patch
-       this%livecrootc_storage_to_xfer_patch(i)          = value_patch
-       this%deadcrootc_storage_to_xfer_patch(i)          = value_patch
-       this%gresp_storage_to_xfer_patch(i)               = value_patch
-       this%livestemc_to_deadstemc_patch(i)              = value_patch
-       this%livecrootc_to_deadcrootc_patch(i)            = value_patch
-
-       this%current_gr_patch(i)                          = value_patch
-       this%transfer_gr_patch(i)                         = value_patch
-       this%storage_gr_patch(i)                          = value_patch
-       this%frootc_alloc_patch(i)                        = value_patch
-       this%frootc_loss_patch(i)                         = value_patch
-       this%leafc_alloc_patch(i)                         = value_patch
-       this%leafc_loss_patch(i)                          = value_patch
-       this%woodc_alloc_patch(i)                         = value_patch
-       this%woodc_loss_patch(i)                          = value_patch
-
-       this%crop_seedc_to_leaf_patch(i)                  = value_patch
-       this%grainc_to_cropprodc_patch(i)                 = value_patch
-    end do
-
-    if ( use_crop )then
-       do fi = 1,num_patch
-          i = filter_patch(fi)
-          this%xsmrpool_to_atm_patch(i)         = value_patch
-          this%livestemc_to_litter_patch(i)     = value_patch
-          this%grainc_to_food_patch(i)          = value_patch
-          this%grainc_to_seed_patch(i)          = value_patch
-          this%grainc_xfer_to_grainc_patch(i)   = value_patch
-          this%cpool_to_grainc_patch(i)         = value_patch
-          this%cpool_to_grainc_storage_patch(i) = value_patch
-          this%cpool_grain_gr_patch(i)          = value_patch
-          this%cpool_grain_storage_gr_patch(i)  = value_patch
-          this%transfer_grain_gr_patch(i)       = value_patch
-          this%grainc_storage_to_xfer_patch(i)  = value_patch
-       end do
-    end if
-
-    do j = 1, nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-
-          this%phenology_c_to_litr_met_c_col(i,j)     = value_column
-          this%phenology_c_to_litr_cel_c_col(i,j)     = value_column
-          this%phenology_c_to_litr_lig_c_col(i,j)     = value_column
-
-          this%gap_mortality_c_to_litr_met_c_col(i,j) = value_column
-          this%gap_mortality_c_to_litr_cel_c_col(i,j) = value_column
-          this%gap_mortality_c_to_litr_lig_c_col(i,j) = value_column
-          this%gap_mortality_c_to_cwdc_col(i,j)       = value_column
-
-          this%fire_mortality_c_to_cwdc_col(i,j)      = value_column
-          this%m_c_to_litr_met_fire_col(i,j)          = value_column
-          this%m_c_to_litr_cel_fire_col(i,j)          = value_column  
-          this%m_c_to_litr_lig_fire_col(i,j)          = value_column
-
-          this%harvest_c_to_litr_met_c_col(i,j)       = value_column             
-          this%harvest_c_to_litr_cel_c_col(i,j)       = value_column             
-          this%harvest_c_to_litr_lig_c_col(i,j)       = value_column             
-          this%harvest_c_to_cwdc_col(i,j)             = value_column          
-
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%m_decomp_cpools_to_fire_vr_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%m_decomp_cpools_to_fire_col(i,k) = value_column
-       end do
-    end do
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-
-       this%grainc_to_cropprodc_col(i)       = value_column
-       this%cwdc_hr_col(i)                   = value_column
-       this%cwdc_loss_col(i)                 = value_column
-       this%litterc_loss_col(i)              = value_column
-    end do
-
-    do fi = 1,num_patch
-       i = filter_patch(fi)
-
-       this%gpp_patch(i)           = value_patch
-       this%mr_patch(i)            = value_patch
-       this%gr_patch(i)            = value_patch
-       this%ar_patch(i)            = value_patch
-       this%rr_patch(i)            = value_patch 
-       this%npp_patch(i)           = value_patch 
-       this%agnpp_patch(i)         = value_patch
-       this%bgnpp_patch(i)         = value_patch
-       this%litfall_patch(i)       = value_patch
-       this%wood_harvestc_patch(i) = value_patch
-       this%slash_harvestc_patch(i) = value_patch
-       this%cinputs_patch(i)       = value_patch
-       this%coutputs_patch(i)      = value_patch
-       this%fire_closs_patch(i)    = value_patch
-       this%npp_Nactive_patch(i)     = value_patch
-       this%npp_burnedoff_patch(i)     = value_patch
-       this%npp_Nnonmyc_patch(i)     = value_patch
-       this%npp_Nam_patch(i)         = value_patch
-       this%npp_Necm_patch(i)        = value_patch
-       this%npp_Nactive_no3_patch(i) = value_patch
-       this%npp_Nactive_nh4_patch(i) = value_patch
-       this%npp_Nnonmyc_no3_patch(i) = value_patch
-       this%npp_Nnonmyc_nh4_patch(i) = value_patch
-       this%npp_Nam_no3_patch(i)     = value_patch
-       this%npp_Nam_nh4_patch(i)     = value_patch
-       this%npp_Necm_no3_patch(i)    = value_patch
-       this%npp_Necm_nh4_patch(i)    = value_patch
-       this%npp_Nfix_patch(i)        = value_patch
-       this%npp_Nretrans_patch(i)    = value_patch
-       this%npp_Nuptake_patch(i)     = value_patch
-       this%npp_growth_patch(i)      = value_patch
-       this%leafc_change_patch(i)    = value_patch
-       this%soilc_change_patch(i)    = value_patch
-    end do
-
-    do fi = 1,num_column
-       i  = filter_column(fi)
-
-       this%sr_col(i)                  = value_column
-       this%er_col(i)                  = value_column
-       this%litfire_col(i)             = value_column
-       this%somfire_col(i)             = value_column
-       this%totfire_col(i)             = value_column
-       this%fire_closs_col(i)          = value_column
-
-       ! Zero p2c column fluxes
-       this%rr_col(i)                  = value_column  
-       this%ar_col(i)                  = value_column  
-       this%gpp_col(i)                 = value_column 
-       this%npp_col(i)                 = value_column 
-       this%fire_closs_col(i)          = value_column 
-       this%wood_harvestc_col(i)       = value_column 
-       this%hrv_xsmrpool_to_atm_col(i) = value_column
-
-       this%nep_col(i)                 = value_column
-
-    end do
-
-  end subroutine SetValues
-
-end module CNVegCarbonFluxType
-
-
diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90
deleted file mode 100644
index a580047944..0000000000
--- a/src/biogeochem/CNVegCarbonStateType.F90
+++ /dev/null
@@ -1,2346 +0,0 @@
-module CNVegCarbonStateType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  !
-  ! !USES:
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use shr_const_mod  , only : SHR_CONST_PDB
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use pftconMod	     , only : noveg, npcropmin, pftcon
-  use clm_varcon     , only : spval, c3_r2, c4_r2, c14ratio
-  use clm_varctl     , only : iulog, use_cndv, use_crop
-  use decompMod      , only : bounds_type
-  use abortutils     , only : endrun
-  use spmdMod        , only : masterproc 
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col                
-  use PatchType      , only : patch
-  use CNSpeciesMod   , only : species_from_string, CN_SPECIES_C12
-  use CNVegComputeSeedMod, only : ComputeSeedAmounts
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-
-  type, public :: cnveg_carbonstate_type
-
-     integer :: species  ! c12, c13, c14
-
-     real(r8), pointer :: grainc_patch             (:) ! (gC/m2) grain C (crop model)
-     real(r8), pointer :: grainc_storage_patch     (:) ! (gC/m2) grain C storage (crop model)
-     real(r8), pointer :: grainc_xfer_patch        (:) ! (gC/m2) grain C transfer (crop model)
-     real(r8), pointer :: leafc_patch              (:) ! (gC/m2) leaf C
-     real(r8), pointer :: leafc_storage_patch      (:) ! (gC/m2) leaf C storage
-     real(r8), pointer :: leafc_xfer_patch         (:) ! (gC/m2) leaf C transfer
-     real(r8), pointer :: leafc_storage_xfer_acc_patch   (:) ! (gC/m2) Accmulated leaf C transfer
-     real(r8), pointer :: storage_cdemand_patch          (:) ! (gC/m2)       C use from the C storage pool 
-     real(r8), pointer :: frootc_patch             (:) ! (gC/m2) fine root C
-     real(r8), pointer :: frootc_storage_patch     (:) ! (gC/m2) fine root C storage
-     real(r8), pointer :: frootc_xfer_patch        (:) ! (gC/m2) fine root C transfer
-     real(r8), pointer :: livestemc_patch          (:) ! (gC/m2) live stem C
-     real(r8), pointer :: livestemc_storage_patch  (:) ! (gC/m2) live stem C storage
-     real(r8), pointer :: livestemc_xfer_patch     (:) ! (gC/m2) live stem C transfer
-     real(r8), pointer :: deadstemc_patch          (:) ! (gC/m2) dead stem C
-     real(r8), pointer :: deadstemc_storage_patch  (:) ! (gC/m2) dead stem C storage
-     real(r8), pointer :: deadstemc_xfer_patch     (:) ! (gC/m2) dead stem C transfer
-     real(r8), pointer :: livecrootc_patch         (:) ! (gC/m2) live coarse root C
-     real(r8), pointer :: livecrootc_storage_patch (:) ! (gC/m2) live coarse root C storage
-     real(r8), pointer :: livecrootc_xfer_patch    (:) ! (gC/m2) live coarse root C transfer
-     real(r8), pointer :: deadcrootc_patch         (:) ! (gC/m2) dead coarse root C
-     real(r8), pointer :: deadcrootc_storage_patch (:) ! (gC/m2) dead coarse root C storage
-     real(r8), pointer :: deadcrootc_xfer_patch    (:) ! (gC/m2) dead coarse root C transfer
-     real(r8), pointer :: gresp_storage_patch      (:) ! (gC/m2) growth respiration storage
-     real(r8), pointer :: gresp_xfer_patch         (:) ! (gC/m2) growth respiration transfer
-     real(r8), pointer :: cpool_patch              (:) ! (gC/m2) temporary photosynthate C pool
-     real(r8), pointer :: xsmrpool_patch           (:) ! (gC/m2) abstract C pool to meet excess MR demand
-     real(r8), pointer :: ctrunc_patch             (:) ! (gC/m2) patch-level sink for C truncation
-     real(r8), pointer :: woodc_patch              (:) ! (gC/m2) wood C
-     real(r8), pointer :: leafcmax_patch           (:) ! (gC/m2) ann max leaf C
-     real(r8), pointer :: totc_patch               (:) ! (gC/m2) total patch-level carbon, including cpool
-     real(r8), pointer :: rootc_col                (:) ! (gC/m2) root carbon at column level (fire)
-     real(r8), pointer :: leafc_col                (:) ! (gC/m2) column-level leafc (fire)
-     real(r8), pointer :: deadstemc_col            (:) ! (gC/m2) column-level deadstemc (fire)
-     real(r8), pointer :: fuelc_col                (:) ! fuel load outside cropland
-     real(r8), pointer :: fuelc_crop_col           (:) ! fuel load for cropland
-     real(r8), pointer :: cropseedc_deficit_patch  (:) ! (gC/m2) pool for seeding new crop growth; this is a NEGATIVE term, indicating the amount of seed usage that needs to be repaid
-
-     ! pools for dynamic landcover
-     real(r8), pointer :: seedc_grc                (:) ! (gC/m2) gridcell-level pool for seeding new PFTs via dynamic landcover
-
-     ! summary (diagnostic) state variables, not involved in mass balance
-     real(r8), pointer :: dispvegc_patch           (:) ! (gC/m2) displayed veg carbon, excluding storage and cpool
-     real(r8), pointer :: storvegc_patch           (:) ! (gC/m2) stored vegetation carbon, excluding cpool
-     real(r8), pointer :: totvegc_patch            (:) ! (gC/m2) total vegetation carbon, excluding cpool
-     real(r8), pointer :: totvegc_col              (:) ! (gC/m2) total vegetation carbon, excluding cpool averaged to column (p2c)
-
-     ! Total C pools       
-     real(r8), pointer :: totc_p2c_col             (:) ! (gC/m2) totc_patch averaged to col
-     real(r8), pointer :: totc_col                 (:) ! (gC/m2) total column carbon, incl veg and cpool
-     real(r8), pointer :: totecosysc_col           (:) ! (gC/m2) total ecosystem carbon, incl veg but excl cpool 
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: SetValues
-     procedure , public  :: Restart
-     
-     procedure , private :: InitAllocate    ! Allocate arrays
-     procedure , private :: InitReadNML     ! Read in namelist
-     procedure , private :: InitHistory     ! Initialize history
-     procedure , private :: InitCold        ! Initialize arrays for a cold-start
-
-  end type cnveg_carbonstate_type
-
-  ! !PRIVATE DATA:
-
-  type, private :: cnvegcarbonstate_const_type
-      ! !PRIVATE MEMBER DATA:
-      real(r8) :: initial_vegC = 20._r8    ! Initial vegetation carbon for leafc/frootc and storage
-  end type
-  type(cnvegcarbonstate_const_type), private :: cnvegcstate_const    ! Constants used here
-  character(len=*), parameter :: sourcefile = &
-       __FILE__
-
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, carbon_type, ratio, NLFilename, &
-                  c12_cnveg_carbonstate_inst)
-
-    class(cnveg_carbonstate_type)                       :: this
-    type(bounds_type)            , intent(in)           :: bounds  
-    real(r8)                     , intent(in)           :: ratio
-    character(len=*)             , intent(in)           :: carbon_type                ! Carbon isotope type C12, C13 or C1
-    character(len=*)             , intent(in)           :: NLFilename                 ! Namelist filename
-    type(cnveg_carbonstate_type) , intent(in), optional :: c12_cnveg_carbonstate_inst ! cnveg_carbonstate for C12 (if C13 or C14)
-    !-----------------------------------------------------------------------
-
-    this%species = species_from_string(carbon_type)
-
-    call this%InitAllocate ( bounds)
-    call this%InitReadNML  ( NLFilename )
-    call this%InitHistory ( bounds, carbon_type)
-    if (present(c12_cnveg_carbonstate_inst)) then
-       call this%InitCold  ( bounds, ratio, carbon_type, c12_cnveg_carbonstate_inst )
-    else
-       call this%InitCold  ( bounds, ratio, carbon_type )
-    end if
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitReadNML(this, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Read the namelist for CNVegCarbonState
-    !
-    !USES:
-    use fileutils      , only : getavu, relavu, opnfil
-    use shr_nl_mod     , only : shr_nl_find_group_name
-    use spmdMod        , only : masterproc, mpicom
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    use clm_varctl     , only : iulog
-    !
-    ! !ARGUMENTS:
-    class(cnveg_carbonstate_type)                       :: this
-    character(len=*)             , intent(in)           :: NLFilename                 ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-
-    character(len=*), parameter :: subname = 'InitReadNML'
-    character(len=*), parameter :: nmlname = 'cnvegcarbonstate'   ! MUST match what is in namelist below
-    !-----------------------------------------------------------------------
-    real(r8) :: initial_vegC
-    namelist /cnvegcarbonstate/ initial_vegC
-
-    initial_vegC = cnvegcstate_const%initial_vegC
-
-    if (masterproc) then
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nmlname//'  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
-       if (ierr == 0) then
-          read(unitn, nml=cnvegcarbonstate, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-    end if
-
-    call shr_mpi_bcast (initial_vegC            , mpicom)
-
-    cnvegcstate_const%initial_vegC = initial_vegC
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) nmlname//' settings:'
-       write(iulog,nml=cnvegcarbonstate)    ! Name here MUST be the same as in nmlname above!
-       write(iulog,*) ' '
-    end if
-
-    !-----------------------------------------------------------------------
-
-  end subroutine InitReadNML
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%leafc_patch              (begp:endp)) ; this%leafc_patch              (:) = nan
-    allocate(this%leafc_storage_patch      (begp:endp)) ; this%leafc_storage_patch      (:) = nan
-    allocate(this%leafc_xfer_patch         (begp:endp)) ; this%leafc_xfer_patch         (:) = nan
-    allocate(this%leafc_storage_xfer_acc_patch (begp:endp)) ; this%leafc_storage_xfer_acc_patch (:) = nan
-    allocate(this%storage_cdemand_patch        (begp:endp)) ; this%storage_cdemand_patch        (:) = nan
-    allocate(this%frootc_patch             (begp:endp)) ; this%frootc_patch             (:) = nan
-    allocate(this%frootc_storage_patch     (begp:endp)) ; this%frootc_storage_patch     (:) = nan
-    allocate(this%frootc_xfer_patch        (begp:endp)) ; this%frootc_xfer_patch        (:) = nan
-    allocate(this%livestemc_patch          (begp:endp)) ; this%livestemc_patch          (:) = nan
-    allocate(this%livestemc_storage_patch  (begp:endp)) ; this%livestemc_storage_patch  (:) = nan
-    allocate(this%livestemc_xfer_patch     (begp:endp)) ; this%livestemc_xfer_patch     (:) = nan
-    allocate(this%deadstemc_patch          (begp:endp)) ; this%deadstemc_patch          (:) = nan
-    allocate(this%deadstemc_storage_patch  (begp:endp)) ; this%deadstemc_storage_patch  (:) = nan
-    allocate(this%deadstemc_xfer_patch     (begp:endp)) ; this%deadstemc_xfer_patch     (:) = nan
-    allocate(this%livecrootc_patch         (begp:endp)) ; this%livecrootc_patch         (:) = nan
-    allocate(this%livecrootc_storage_patch (begp:endp)) ; this%livecrootc_storage_patch (:) = nan
-    allocate(this%livecrootc_xfer_patch    (begp:endp)) ; this%livecrootc_xfer_patch    (:) = nan
-    allocate(this%deadcrootc_patch         (begp:endp)) ; this%deadcrootc_patch         (:) = nan
-    allocate(this%deadcrootc_storage_patch (begp:endp)) ; this%deadcrootc_storage_patch (:) = nan
-    allocate(this%deadcrootc_xfer_patch    (begp:endp)) ; this%deadcrootc_xfer_patch    (:) = nan
-    allocate(this%gresp_storage_patch      (begp:endp)) ; this%gresp_storage_patch      (:) = nan
-    allocate(this%gresp_xfer_patch         (begp:endp)) ; this%gresp_xfer_patch         (:) = nan
-    allocate(this%cpool_patch              (begp:endp)) ; this%cpool_patch              (:) = nan
-    allocate(this%xsmrpool_patch           (begp:endp)) ; this%xsmrpool_patch           (:) = nan
-    allocate(this%ctrunc_patch             (begp:endp)) ; this%ctrunc_patch             (:) = nan
-    allocate(this%dispvegc_patch           (begp:endp)) ; this%dispvegc_patch           (:) = nan
-    allocate(this%storvegc_patch           (begp:endp)) ; this%storvegc_patch           (:) = nan
-    allocate(this%leafcmax_patch           (begp:endp)) ; this%leafcmax_patch           (:) = nan
-    allocate(this%totc_patch               (begp:endp))  ; this%totc_patch               (:) = nan
-    allocate(this%grainc_patch             (begp:endp)) ; this%grainc_patch             (:) = nan
-    allocate(this%grainc_storage_patch     (begp:endp)) ; this%grainc_storage_patch     (:) = nan
-    allocate(this%grainc_xfer_patch        (begp:endp)) ; this%grainc_xfer_patch        (:) = nan
-    allocate(this%woodc_patch              (begp:endp)) ; this%woodc_patch              (:) = nan     
-
-    allocate(this%cropseedc_deficit_patch  (begp:endp)) ; this%cropseedc_deficit_patch  (:) = nan
-    allocate(this%seedc_grc                (begg:endg)) ; this%seedc_grc                (:) = nan
-    allocate(this%rootc_col                (begc:endc)) ; this%rootc_col                (:) = nan
-    allocate(this%leafc_col                (begc:endc)) ; this%leafc_col                (:) = nan
-    allocate(this%deadstemc_col            (begc:endc)) ; this%deadstemc_col            (:) = nan
-    allocate(this%fuelc_col                (begc:endc)) ; this%fuelc_col                (:) = nan
-    allocate(this%fuelc_crop_col           (begc:endc)) ; this%fuelc_crop_col           (:) = nan
-
-    allocate(this%totvegc_patch            (begp:endp)) ; this%totvegc_patch            (:) = nan
-    allocate(this%totvegc_col              (begc:endc)) ; this%totvegc_col              (:) = nan
-
-    allocate(this%totc_p2c_col             (begc:endc)) ; this%totc_p2c_col             (:) = nan
-    allocate(this%totc_col                 (begc:endc)) ; this%totc_col                 (:) = nan
-    allocate(this%totecosysc_col           (begc:endc)) ; this%totecosysc_col           (:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds, carbon_type)
-    !
-    ! !DESCRIPTION:
-    ! add history fields for all CN variables, always set as default='inactive'
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonstate_type) :: this
-    type(bounds_type)         , intent(in) :: bounds 
-    character(len=*)          , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: k,l,ii,jj 
-    character(10)     :: active
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg 
-    character(24)     :: fieldname
-    character(100)    :: longname
-    real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    !-------------------------------
-    ! C12 state variables
-    !-------------------------------
-
-    if (carbon_type == 'c12') then
-
-       if (use_crop) then
-          this%grainc_patch(begp:endp) = spval
-          call hist_addfld1d (fname='GRAINC', units='gC/m^2', &
-               avgflag='A', long_name='grain C (does not equal yield)', &
-               ptr_patch=this%grainc_patch, default='inactive')
-          this%cropseedc_deficit_patch(begp:endp) = spval
-          call hist_addfld1d (fname='CROPSEEDC_DEFICIT', units='gC/m^2', &
-               avgflag='A', long_name='C used for crop seed that needs to be repaid', &
-               ptr_patch=this%cropseedc_deficit_patch, default='inactive')
-       end if
-       
-       this%woodc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='WOODC', units='gC/m^2', &
-            avgflag='A', long_name='wood C', &
-            ptr_patch=this%woodc_patch, default='inactive')
-
-       this%leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC', units='gC/m^2', &
-            avgflag='A', long_name='leaf C', &
-            ptr_patch=this%leafc_patch, default='inactive')
-
-       this%leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='leaf C storage', &
-            ptr_patch=this%leafc_storage_patch, default='inactive')    
-
-       this%leafc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='leaf C transfer', &
-            ptr_patch=this%leafc_xfer_patch, default='inactive')    
-
-       this%leafc_storage_xfer_acc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFC_STORAGE_XFER_ACC', units='gC/m^2', &
-            avgflag='A', long_name='Accumulated leaf C transfer', &
-            ptr_patch=this%leafc_storage_xfer_acc_patch, default='inactive')
-
-       this%storage_cdemand_patch(begp:endp) = spval
-       call hist_addfld1d (fname='STORAGE_CDEMAND', units='gC/m^2', &
-            avgflag='A', long_name='C use from the C storage pool', &
-            ptr_patch=this%storage_cdemand_patch, default='inactive')
-
-       this%frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC', units='gC/m^2', &
-            avgflag='A', long_name='fine root C', &
-            ptr_patch=this%frootc_patch, default='inactive')
-
-       this%frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='fine root C storage', &
-            ptr_patch=this%frootc_storage_patch, default='inactive')   
-
-       this%frootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FROOTC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='fine root C transfer', &
-            ptr_patch=this%frootc_xfer_patch, default='inactive')    
-
-       this%livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC', units='gC/m^2', &
-            avgflag='A', long_name='live stem C', &
-            ptr_patch=this%livestemc_patch, default='inactive')
-
-       this%livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='live stem C storage', &
-            ptr_patch=this%livestemc_storage_patch, default='inactive')    
-
-       this%livestemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVESTEMC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='live stem C transfer', &
-            ptr_patch=this%livestemc_xfer_patch, default='inactive')     
-
-       this%deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADSTEMC', units='gC/m^2', &
-            avgflag='A', long_name='dead stem C', &
-            ptr_patch=this%deadstemc_patch, default='inactive')
-
-       this%deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADSTEMC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='dead stem C storage', &
-            ptr_patch=this%deadstemc_storage_patch, default='inactive')    
-
-       this%deadstemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADSTEMC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='dead stem C transfer', &
-            ptr_patch=this%deadstemc_xfer_patch, default='inactive')    
-
-       this%livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC', units='gC/m^2', &
-            avgflag='A', long_name='live coarse root C', &
-            ptr_patch=this%livecrootc_patch, default='inactive')
-
-       this%livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='live coarse root C storage', &
-            ptr_patch=this%livecrootc_storage_patch, default='inactive')     
-
-       this%livecrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LIVECROOTC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='live coarse root C transfer', &
-            ptr_patch=this%livecrootc_xfer_patch, default='inactive')    
-
-       this%deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADCROOTC', units='gC/m^2', &
-            avgflag='A', long_name='dead coarse root C', &
-            ptr_patch=this%deadcrootc_patch, default='inactive')
-
-       this%deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADCROOTC_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='dead coarse root C storage', &
-            ptr_patch=this%deadcrootc_storage_patch, default='inactive')   
-
-       this%deadcrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEADCROOTC_XFER', units='gC/m^2', &
-            avgflag='A', long_name='dead coarse root C transfer', &
-            ptr_patch=this%deadcrootc_xfer_patch, default='inactive')   
-
-       this%gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GRESP_STORAGE', units='gC/m^2', &
-            avgflag='A', long_name='growth respiration storage', &
-            ptr_patch=this%gresp_storage_patch, default='inactive')    
-
-       this%gresp_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GRESP_XFER', units='gC/m^2', &
-            avgflag='A', long_name='growth respiration transfer', &
-            ptr_patch=this%gresp_xfer_patch, default='inactive')     
-
-       this%cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CPOOL', units='gC/m^2', &
-            avgflag='A', long_name='temporary photosynthate C pool', &
-            ptr_patch=this%cpool_patch, default='inactive')
-
-       this%xsmrpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='XSMRPOOL', units='gC/m^2', &
-            avgflag='A', long_name='temporary photosynthate C pool', &
-            ptr_patch=this%xsmrpool_patch, default='inactive')
-
-       this%ctrunc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PFT_CTRUNC', units='gC/m^2', &
-            avgflag='A', long_name='patch-level sink for C truncation', &
-            ptr_patch=this%ctrunc_patch, default='inactive')
-
-       this%dispvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DISPVEGC', units='gC/m^2', &
-            avgflag='A', long_name='displayed veg carbon, excluding storage and cpool', &
-            ptr_patch=this%dispvegc_patch, default='inactive')
-
-       this%storvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='STORVEGC', units='gC/m^2', &
-            avgflag='A', long_name='stored vegetation carbon, excluding cpool', &
-            ptr_patch=this%storvegc_patch, default='inactive')
-
-       this%totvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TOTVEGC', units='gC/m^2', &
-            avgflag='A', long_name='total vegetation carbon, excluding cpool', &
-            ptr_patch=this%totvegc_patch, default='inactive')
-
-       this%totc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='TOTPFTC', units='gC/m^2', &
-            avgflag='A', long_name='total patch-level carbon, including cpool', &
-            ptr_patch=this%totc_patch, default='inactive')
-
-       this%seedc_grc(begg:endg) = spval
-       call hist_addfld1d (fname='SEEDC', units='gC/m^2', &
-            avgflag='A', long_name='pool for seeding new PFTs via dynamic landcover', &
-            ptr_gcell=this%seedc_grc, default='inactive')
-
-       this%fuelc_col(begc:endc) = spval
-       call hist_addfld1d (fname='FUELC', units='gC/m^2', &
-            avgflag='A', long_name='fuel load', &
-            ptr_col=this%fuelc_col, default='inactive')
-
-       this%totc_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTCOLC', units='gC/m^2', &
-            avgflag='A', long_name='total column carbon, incl veg and cpool but excl product pools', &
-            ptr_col=this%totc_col, default='inactive')
-
-       this%totecosysc_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTECOSYSC', units='gC/m^2', &
-            avgflag='A', long_name='total ecosystem carbon, incl veg but excl cpool and product pools', &
-            ptr_col=this%totecosysc_col, default='inactive')
-
-    end if
-
-    !-------------------------------
-    ! C13 state variables 
-    !-------------------------------
-
-    if ( carbon_type == 'c13' ) then
-
-       this%leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 leaf C', &
-            ptr_patch=this%leafc_patch, default='inactive')
-
-       this%leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 leaf C storage', &
-            ptr_patch=this%leafc_storage_patch, default='inactive')
-
-       this%leafc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 leaf C transfer', &
-            ptr_patch=this%leafc_xfer_patch, default='inactive')
-
-       this%leafc_storage_xfer_acc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LEAFC_STORAGE_XFER_ACC', units='gC13/m^2', &
-            avgflag='A', long_name='Accumulated C13 leaf C transfer', &
-            ptr_patch=this%leafc_storage_xfer_acc_patch, default='inactive')
-
-       this%frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 fine root C', &
-            ptr_patch=this%frootc_patch, default='inactive')
-
-       this%frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 fine root C storage', &
-            ptr_patch=this%frootc_storage_patch, default='inactive')
-
-       this%frootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_FROOTC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 fine root C transfer', &
-            ptr_patch=this%frootc_xfer_patch, default='inactive')
-
-       this%livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live stem C', &
-            ptr_patch=this%livestemc_patch, default='inactive')
-
-       this%livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live stem C storage', &
-            ptr_patch=this%livestemc_storage_patch, default='inactive')
-
-       this%livestemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVESTEMC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live stem C transfer', &
-            ptr_patch=this%livestemc_xfer_patch, default='inactive')
-
-       this%deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADSTEMC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead stem C', &
-            ptr_patch=this%deadstemc_patch, default='inactive')
-
-       this%deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADSTEMC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead stem C storage', &
-            ptr_patch=this%deadstemc_storage_patch, default='inactive')
-
-       this%deadstemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADSTEMC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead stem C transfer', &
-            ptr_patch=this%deadstemc_xfer_patch, default='inactive')
-
-       this%livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live coarse root C', &
-            ptr_patch=this%livecrootc_patch, default='inactive')
-
-       this%livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live coarse root C storage', &
-            ptr_patch=this%livecrootc_storage_patch, default='inactive')
-
-       this%livecrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_LIVECROOTC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 live coarse root C transfer', &
-            ptr_patch=this%livecrootc_xfer_patch, default='inactive')
-
-       this%deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADCROOTC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead coarse root C', &
-            ptr_patch=this%deadcrootc_patch, default='inactive')
-
-       this%deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADCROOTC_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead coarse root C storage', &
-            ptr_patch=this%deadcrootc_storage_patch,  default='inactive')
-
-       this%deadcrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DEADCROOTC_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 dead coarse root C transfer', &
-            ptr_patch=this%deadcrootc_xfer_patch, default='inactive')
-
-       this%gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_GRESP_STORAGE', units='gC13/m^2', &
-            avgflag='A', long_name='C13 growth respiration storage', &
-            ptr_patch=this%gresp_storage_patch, default='inactive')
-
-       this%gresp_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_GRESP_XFER', units='gC13/m^2', &
-            avgflag='A', long_name='C13 growth respiration transfer', &
-            ptr_patch=this%gresp_xfer_patch, default='inactive')
-
-       this%cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_CPOOL', units='gC13/m^2', &
-            avgflag='A', long_name='C13 temporary photosynthate C pool', &
-            ptr_patch=this%cpool_patch, default='inactive')
-
-       this%xsmrpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_XSMRPOOL', units='gC13/m^2', &
-            avgflag='A', long_name='C13 temporary photosynthate C pool', &
-            ptr_patch=this%xsmrpool_patch, default='inactive')
-
-       this%ctrunc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_PFT_CTRUNC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 patch-level sink for C truncation', &
-            ptr_patch=this%ctrunc_patch, default='inactive')
-
-       this%dispvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_DISPVEGC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 displayed veg carbon, excluding storage and cpool', &
-            ptr_patch=this%dispvegc_patch, default='inactive')
-
-       this%storvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_STORVEGC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 stored vegetation carbon, excluding cpool', &
-            ptr_patch=this%storvegc_patch, default='inactive')
-
-       this%totvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TOTVEGC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total vegetation carbon, excluding cpool', &
-            ptr_patch=this%totvegc_patch, default='inactive')
-
-       this%totc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C13_TOTPFTC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total patch-level carbon, including cpool', &
-            ptr_patch=this%totc_patch, default='inactive')
-
-       this%seedc_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C13_SEEDC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 pool for seeding new PFTs via dynamic landcover', &
-            ptr_gcell=this%seedc_grc, default='inactive')
-
-       this%totc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_TOTCOLC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total column carbon, incl veg and cpool but excl product pools', &
-            ptr_col=this%totc_col, default='inactive')
-
-       this%totecosysc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_TOTECOSYSC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total ecosystem carbon, incl veg but excl cpool and product pools', &
-            ptr_col=this%totecosysc_col, default='inactive')
-
-       if (use_crop) then
-          this%grainc_patch(begp:endp) = spval
-          call hist_addfld1d (fname='C13_GRAINC', units='gC/m^2', &
-               avgflag='A', long_name='C13 grain C (does not equal yield)', &
-               ptr_patch=this%grainc_patch, default='inactive')
-          this%cropseedc_deficit_patch(begp:endp) = spval
-          call hist_addfld1d (fname='C13_CROPSEEDC_DEFICIT', units='gC/m^2', &
-               avgflag='A', long_name='C13 C used for crop seed that needs to be repaid', &
-               ptr_patch=this%cropseedc_deficit_patch, default='inactive')
-       end if
-
-
-    endif
-
-    !-------------------------------
-    ! C14 state variables 
-    !-------------------------------
-
-    if ( carbon_type == 'c14') then
-
-       this%leafc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 leaf C', &
-            ptr_patch=this%leafc_patch, default='inactive')
-
-       this%leafc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 leaf C storage', &
-            ptr_patch=this%leafc_storage_patch, default='inactive')
-
-       this%leafc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LEAFC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 leaf C transfer', &
-            ptr_patch=this%leafc_xfer_patch, default='inactive')
-
-        this%leafc_storage_xfer_acc_patch(begp:endp) = spval
-        call hist_addfld1d (fname='C14_LEAFC_STORAGE_XFER_ACC', units='gC14/m^2', &
-             avgflag='A', long_name='Accumulated C14 leaf C transfer', &
-             ptr_patch=this%leafc_storage_xfer_acc_patch, default='inactive')
-
-       this%frootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 fine root C', &
-            ptr_patch=this%frootc_patch, default='inactive')
-
-       this%frootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 fine root C storage', &
-            ptr_patch=this%frootc_storage_patch, default='inactive')
-
-       this%frootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_FROOTC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 fine root C transfer', &
-            ptr_patch=this%frootc_xfer_patch, default='inactive')
-
-       this%livestemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live stem C', &
-            ptr_patch=this%livestemc_patch, default='inactive')
-
-       this%livestemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live stem C storage', &
-            ptr_patch=this%livestemc_storage_patch, default='inactive')
-
-       this%livestemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVESTEMC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live stem C transfer', &
-            ptr_patch=this%livestemc_xfer_patch, default='inactive')
-
-       this%deadstemc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADSTEMC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead stem C', &
-            ptr_patch=this%deadstemc_patch, default='inactive')
-
-       this%deadstemc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADSTEMC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead stem C storage', &
-            ptr_patch=this%deadstemc_storage_patch, default='inactive')
-
-       this%deadstemc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADSTEMC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead stem C transfer', &
-            ptr_patch=this%deadstemc_xfer_patch, default='inactive')
-
-       this%livecrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live coarse root C', &
-            ptr_patch=this%livecrootc_patch, default='inactive')
-
-       this%livecrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live coarse root C storage', &
-            ptr_patch=this%livecrootc_storage_patch, default='inactive')
-
-       this%livecrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_LIVECROOTC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 live coarse root C transfer', &
-            ptr_patch=this%livecrootc_xfer_patch, default='inactive')
-
-       this%deadcrootc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADCROOTC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead coarse root C', &
-            ptr_patch=this%deadcrootc_patch, default='inactive')
-
-       this%deadcrootc_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADCROOTC_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead coarse root C storage', &
-            ptr_patch=this%deadcrootc_storage_patch,  default='inactive')
-
-       this%deadcrootc_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DEADCROOTC_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 dead coarse root C transfer', &
-            ptr_patch=this%deadcrootc_xfer_patch, default='inactive')
-
-       this%gresp_storage_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_GRESP_STORAGE', units='gC14/m^2', &
-            avgflag='A', long_name='C14 growth respiration storage', &
-            ptr_patch=this%gresp_storage_patch, default='inactive')
-
-       this%gresp_xfer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_GRESP_XFER', units='gC14/m^2', &
-            avgflag='A', long_name='C14 growth respiration transfer', &
-            ptr_patch=this%gresp_xfer_patch, default='inactive')
-
-       this%cpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_CPOOL', units='gC14/m^2', &
-            avgflag='A', long_name='C14 temporary photosynthate C pool', &
-            ptr_patch=this%cpool_patch, default='inactive')
-
-       this%xsmrpool_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_XSMRPOOL', units='gC14/m^2', &
-            avgflag='A', long_name='C14 temporary photosynthate C pool', &
-            ptr_patch=this%xsmrpool_patch, default='inactive')
-
-       this%ctrunc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_PFT_CTRUNC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 patch-level sink for C truncation', &
-            ptr_patch=this%ctrunc_patch, default='inactive')
-
-       this%dispvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_DISPVEGC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 displayed veg carbon, excluding storage and cpool', &
-            ptr_patch=this%dispvegc_patch, default='inactive')
-
-       this%storvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_STORVEGC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 stored vegetation carbon, excluding cpool', &
-            ptr_patch=this%storvegc_patch, default='inactive')
-
-       this%totvegc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TOTVEGC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total vegetation carbon, excluding cpool', &
-            ptr_patch=this%totvegc_patch, default='inactive')
-
-       this%totc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='C14_TOTPFTC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total patch-level carbon, including cpool', &
-            ptr_patch=this%totc_patch, default='inactive')
-
-       this%seedc_grc(begg:endg) = spval
-       call hist_addfld1d (fname='C14_SEEDC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 pool for seeding new PFTs via dynamic landcover', &
-            ptr_gcell=this%seedc_grc, default='inactive')
-
-       this%totc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_TOTCOLC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total column carbon, incl veg and cpool but excl product pools', &
-            ptr_col=this%totc_col, default='inactive')
-
-       this%totecosysc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_TOTECOSYSC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total ecosystem carbon, incl veg but excl cpool and product pools', &
-            ptr_col=this%totecosysc_col, default='inactive')
-
-       if (use_crop) then
-          this%grainc_patch(begp:endp) = spval
-          call hist_addfld1d (fname='C14_GRAINC', units='gC/m^2', &
-               avgflag='A', long_name='C14 grain C (does not equal yield)', &
-               ptr_patch=this%grainc_patch, default='inactive')
-          this%cropseedc_deficit_patch(begp:endp) = spval
-          call hist_addfld1d (fname='C14_CROPSEEDC_DEFICIT', units='gC/m^2', &
-               avgflag='A', long_name='C14 C used for crop seed that needs to be repaid', &
-               ptr_patch=this%cropseedc_deficit_patch, default='inactive')
-       end if
-
-
-    endif
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, ratio, carbon_type, c12_cnveg_carbonstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    ! !USES, default='inactive':
-    use landunit_varcon	 , only : istsoil, istcrop 
-    use clm_time_manager , only : is_restart, get_nstep
-    use clm_varctl, only : MM_Nuptake_opt    
-    !
-    ! !ARGUMENTS:
-    class(cnveg_carbonstate_type)                       :: this 
-    type(bounds_type)            , intent(in)           :: bounds  
-    real(r8)                     , intent(in)           :: ratio              ! Standard isotope ratio
-    character(len=*)             , intent(in)           :: carbon_type        ! 'c12' or 'c13' or 'c14'
-    type(cnveg_carbonstate_type) , optional, intent(in) :: c12_cnveg_carbonstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: p,c,l,g,j,k,i
-    integer  :: fc                                       ! filter index
-    integer  :: num_special_col                          ! number of good values in special_col filter
-    integer  :: num_special_patch                        ! number of good values in special_patch filter
-    integer  :: special_col(bounds%endc-bounds%begc+1)   ! special landunit filter - columns
-    integer  :: special_patch(bounds%endp-bounds%begp+1) ! special landunit filter - patches
-    !-----------------------------------------------------------------------
-
-    if (carbon_type == 'c13' .or. carbon_type == 'c14') then
-       if (.not. present(c12_cnveg_carbonstate_inst)) then
-          call endrun(msg=' ERROR: for C13 or C14 must pass in c12_cnveg_carbonstate_inst as argument' //&
-               errMsg(sourcefile, __LINE__))
-       end if
-    end if
-
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    ! Set patch filters
-
-    num_special_patch = 0
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-       if (lun%ifspecial(l)) then
-          num_special_patch = num_special_patch + 1
-          special_patch(num_special_patch) = p
-       end if
-    end do
-
-    !-----------------------------------------------
-    ! initialize patch-level carbon state variables
-    !-----------------------------------------------
-
-    do p = bounds%begp,bounds%endp
-
-       this%leafcmax_patch(p) = 0._r8
-
-       l = patch%landunit(p)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-
-          if (patch%itype(p) == noveg) then
-             this%leafc_patch(p)          = 0._r8
-             this%leafc_storage_patch(p)  = 0._r8
-             this%frootc_patch(p)         = 0._r8            
-             this%frootc_storage_patch(p) = 0._r8    
-          else
-             if (pftcon%evergreen(patch%itype(p)) == 1._r8) then
-                this%leafc_patch(p)          = cnvegcstate_const%initial_vegC * ratio     
-                this%leafc_storage_patch(p)  = 0._r8
-                this%frootc_patch(p)         = cnvegcstate_const%initial_vegC * ratio           
-                this%frootc_storage_patch(p) = 0._r8    
-             else if (patch%itype(p) >= npcropmin) then ! prognostic crop types
-                this%leafc_patch(p)          = 0._r8
-                this%leafc_storage_patch(p)  = 0._r8
-                this%frootc_patch(p)         = 0._r8            
-                this%frootc_storage_patch(p) = 0._r8    
-             else
-                this%leafc_patch(p)          = 0._r8
-                this%leafc_storage_patch(p)  = cnvegcstate_const%initial_vegC * ratio   
-                this%frootc_patch(p)         = 0._r8            
-                this%frootc_storage_patch(p) = cnvegcstate_const%initial_vegC * ratio   
-             end if
-          end if
-          this%leafc_xfer_patch(p) = 0._r8
-          this%leafc_storage_xfer_acc_patch(p)  = 0._r8
-          this%storage_cdemand_patch(p)         = 0._r8
-
-          if (MM_Nuptake_opt .eqv. .false.) then  ! if not running in floating CN ratio option 
-             this%frootc_patch(p)            = 0._r8 
-             this%frootc_storage_patch(p)    = 0._r8 
-          end if     
-          this%frootc_xfer_patch(p)       = 0._r8 
-
-          this%livestemc_patch(p)         = 0._r8 
-          this%livestemc_storage_patch(p) = 0._r8 
-          this%livestemc_xfer_patch(p)    = 0._r8 
-
-          if (pftcon%woody(patch%itype(p)) == 1._r8) then
-             this%deadstemc_patch(p) = 0.1_r8 * ratio
-          else
-             this%deadstemc_patch(p) = 0._r8 
-          end if
-          this%deadstemc_storage_patch(p)  = 0._r8 
-          this%deadstemc_xfer_patch(p)     = 0._r8 
-
-          this%livecrootc_patch(p)         = 0._r8 
-          this%livecrootc_storage_patch(p) = 0._r8 
-          this%livecrootc_xfer_patch(p)    = 0._r8 
-
-          this%deadcrootc_patch(p)         = 0._r8 
-          this%deadcrootc_storage_patch(p) = 0._r8 
-          this%deadcrootc_xfer_patch(p)    = 0._r8 
-
-          this%gresp_storage_patch(p)      = 0._r8 
-          this%gresp_xfer_patch(p)         = 0._r8 
-
-          this%cpool_patch(p)              = 0._r8 
-          this%xsmrpool_patch(p)           = 0._r8 
-          this%ctrunc_patch(p)             = 0._r8 
-          this%dispvegc_patch(p)           = 0._r8 
-          this%storvegc_patch(p)           = 0._r8 
-          this%woodc_patch(p)              = 0._r8
-          this%totc_patch(p)               = 0._r8 
-
-          if ( use_crop )then
-             this%grainc_patch(p)         = 0._r8 
-             this%grainc_storage_patch(p) = 0._r8 
-             this%grainc_xfer_patch(p)    = 0._r8 
-             this%cropseedc_deficit_patch(p)  = 0._r8
-          end if
-
-       endif
-
-    end do
-
-    ! -----------------------------------------------
-    ! initialize column-level variables
-    ! -----------------------------------------------
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-!          this%totgrainc_col(c)  = 0._r8
-
-          ! total carbon pools
-          this%totecosysc_col(c) = 0._r8
-          this%totc_p2c_col(c)   = 0._r8
-          this%totc_col(c)       = 0._r8
-       end if
-    end do
-
-
-    do g = bounds%begg, bounds%endg
-       this%seedc_grc(g) = 0._r8
-    end do
-
-    if ( .not. is_restart() .and. get_nstep() == 1 ) then
-
-       do p = bounds%begp,bounds%endp
-          if (pftcon%c3psn(patch%itype(p)) == 1._r8) then
-             this%grainc_patch(p)            = c12_cnveg_carbonstate_inst%grainc_patch(p)         * c3_r2
-             this%grainc_storage_patch(p)    = c12_cnveg_carbonstate_inst%grainc_storage_patch(p) * c3_r2
-             this%grainc_xfer_patch(p)       = c12_cnveg_carbonstate_inst%grainc_xfer_patch(p)    * c3_r2
-             this%dispvegc_patch(p)          = c12_cnveg_carbonstate_inst%dispvegc_patch(p)       * c3_r2
-             this%storvegc_patch(p)          = c12_cnveg_carbonstate_inst%storvegc_patch(p)       * c3_r2
-             this%totvegc_patch(p)           = c12_cnveg_carbonstate_inst%totvegc_patch(p)        * c3_r2
-             this%totc_patch(p)              = c12_cnveg_carbonstate_inst%totc_patch(p)           * c3_r2
-             this%woodc_patch(p)             = c12_cnveg_carbonstate_inst%woodc_patch(p)          * c3_r2
-          else
-             this%grainc_patch(p)            = c12_cnveg_carbonstate_inst%grainc_patch(p)         * c4_r2
-             this%grainc_storage_patch(p)    = c12_cnveg_carbonstate_inst%grainc_storage_patch(p) * c4_r2
-             this%grainc_xfer_patch(p)       = c12_cnveg_carbonstate_inst%grainc_xfer_patch(p)    * c4_r2
-             this%dispvegc_patch(p)          = c12_cnveg_carbonstate_inst%dispvegc_patch(p)       * c4_r2
-             this%storvegc_patch(p)          = c12_cnveg_carbonstate_inst%storvegc_patch(p)       * c4_r2
-             this%totvegc_patch(p)           = c12_cnveg_carbonstate_inst%totvegc_patch(p)        * c4_r2
-             this%totc_patch(p)              = c12_cnveg_carbonstate_inst%totc_patch(p)           * c4_r2
-             this%woodc_patch(p)             = c12_cnveg_carbonstate_inst%woodc_patch(p)          * c4_r2
-          end if
-       end do
-    end if
-
-    ! initialize fields for special filters
-
-    call this%SetValues (&
-         num_patch=num_special_patch, filter_patch=special_patch, value_patch=0._r8, &
-         num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart ( this,  bounds, ncid, flag, carbon_type, reseed_dead_plants, &
-                       c12_cnveg_carbonstate_inst, filter_reseed_patch, &
-                       num_reseed_patch)
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon state
-    !
-    ! !USES:
-    use shr_infnan_mod   , only : isnan => shr_infnan_isnan, nan => shr_infnan_nan, assignment(=)
-    use clm_varcon       , only : c13ratio, c14ratio
-    use clm_varctl       , only : spinup_state, use_cndv, MM_Nuptake_opt
-    use clm_time_manager , only : get_nstep, is_restart, get_nstep
-    use landunit_varcon	 , only : istsoil, istcrop 
-    use spmdMod          , only : mpicom
-    use shr_mpi_mod      , only : shr_mpi_sum
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonstate_type)                               :: this
-    type(bounds_type)                     , intent(in)           :: bounds 
-    type(file_desc_t)                     , intent(inout)        :: ncid   ! netcdf id
-    character(len=*)                      , intent(in)           :: flag   !'read' or 'write'
-    character(len=*)                      , intent(in)           :: carbon_type ! 'c12' or 'c13' or 'c14'
-    logical                               , intent(in)           :: reseed_dead_plants
-    type (cnveg_carbonstate_type)         , intent(in), optional :: c12_cnveg_carbonstate_inst 
-    integer                               , intent(out), optional :: filter_reseed_patch(:)
-    integer                               , intent(out), optional :: num_reseed_patch
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i,j,k,l,c,p
-    real(r8)           :: ratio
-    character(len=128) :: varname   ! temporary
-    logical            :: readvar
-    integer            :: idata
-    logical            :: exit_spinup  = .false.
-    logical            :: enter_spinup = .false.
-    ! flags for comparing the model and restart decomposition cascades
-    integer            :: decomp_cascade_state, restart_file_decomp_cascade_state 
-    ! spinup state as read from restart file, for determining whether to enter or exit spinup mode.
-    integer            :: restart_file_spinup_state
-    integer            :: total_num_reseed_patch      ! Total number of patches to reseed across all processors
-
-    !------------------------------------------------------------------------
-
-    if (carbon_type == 'c13' .or. carbon_type == 'c14') then
-       if (.not. present(c12_cnveg_carbonstate_inst)) then
-          call endrun(msg=' ERROR: for C14 must pass in c12_cnveg_carbonstate_inst as argument' //&
-               errMsg(sourcefile, __LINE__))
-       end if
-    end if
-    if (carbon_type == 'c12') then
-       ratio = 1._r8
-    else if (carbon_type == 'c13') then
-       ratio = c13ratio
-    else if (carbon_type == 'c14') then
-       ratio = c14ratio
-    end if
-
-    if ( (      present(num_reseed_patch) .and. .not. present(filter_reseed_patch)) &
-    .or. (.not. present(num_reseed_patch) .and.       present(filter_reseed_patch) ) )then
-       call endrun(msg=' ERROR: filter_reseed_patch and num_reseed_patch both need to be entered ' //&
-       errMsg(sourcefile, __LINE__))
-    end if
-    if ( present(num_reseed_patch) )then
-       num_reseed_patch = 0
-       filter_reseed_patch(:) = -1
-    end if
-
-    !--------------------------------
-    ! patch carbon state variables (c12)
-    !--------------------------------
-
-    if (carbon_type == 'c12') then
-       call restartvar(ncid=ncid, flag=flag, varname='leafc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_storage_xfer_acc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_storage_xfer_acc_patch)
- 
-       call restartvar(ncid=ncid, flag=flag, varname='storage_cdemand', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%storage_cdemand_patch)
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_storage', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_storage_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_xfer', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_xfer_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='cpool', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='xsmrpool', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%xsmrpool_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='pft_ctrunc', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%ctrunc_patch) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafcmax', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafcmax_patch)
-
-       if (flag == 'read') then
-          call restartvar(ncid=ncid, flag=flag, varname='spinup_state', xtype=ncd_int, &
-            long_name='Spinup state of the model that wrote this restart file: ' &
-            // ' 0 = normal model mode, 1 = AD spinup, 2 = AAD spinup', units='', &
-            interpinic_flag='copy', readvar=readvar,  data=idata)
-
-          if (readvar) then
-             restart_file_spinup_state = idata
-          else
-             restart_file_spinup_state = spinup_state
-             if ( masterproc ) then
-                write(iulog,*) ' CNRest: WARNING!  Restart file does not contain info ' &
-                      // ' on spinup state used to generate the restart file. '
-                 write(iulog,*) '   Assuming the same as current setting: ', spinup_state
-             end if
-          end if
-       end if
-
-       if (flag == 'read' .and. spinup_state /= restart_file_spinup_state .and. .not. use_cndv) then
-          if ( masterproc ) write(iulog, *) 'exit_spinup ',exit_spinup,' restart_file_spinup_state ',restart_file_spinup_state
-          if (spinup_state <= 1 .and. restart_file_spinup_state == 2 ) then
-             if ( masterproc ) write(iulog,*) ' CNRest: taking Dead wood C pools out of AD spinup mode'
-             exit_spinup = .true.
-             if ( masterproc ) write(iulog, *) 'Multiplying stemc and crootc by 10 for exit spinup'
-             do i = bounds%begp,bounds%endp
-                this%deadstemc_patch(i) = this%deadstemc_patch(i) * 10._r8
-                this%deadcrootc_patch(i) = this%deadcrootc_patch(i) * 10._r8
-             end do
-          else if (spinup_state == 2 .and. restart_file_spinup_state <= 1 )then
-             if (spinup_state == 2 .and. restart_file_spinup_state <= 1 )then
-                if ( masterproc ) write(iulog,*) ' CNRest: taking Dead wood C pools into AD spinup mode'
-                enter_spinup = .true.
-                if ( masterproc ) write(iulog, *) 'Dividing stemc and crootc by 10 for enter spinup '
-                do i = bounds%begp,bounds%endp
-                   this%deadstemc_patch(i) = this%deadstemc_patch(i) / 10._r8
-                   this%deadcrootc_patch(i) = this%deadcrootc_patch(i) / 10._r8
-                end do
-             end if
-          end if
-       end if
-       !--------------------------------
-       ! C12 carbon state variables
-       !--------------------------------
-
-       if (carbon_type == 'c12') then
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc', xtype=ncd_double,  &
-               dim1name='pft', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) 
-          ! totvegc_col needed for resetting soil carbon stocks during AD spinup exit
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc_col', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_col)
-       end if
-
-       !--------------------------------
-       ! C13 carbon state variables 
-       !--------------------------------
-
-       if ( carbon_type == 'c13')  then
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc_13', xtype=ncd_double,  &
-               dim1name='pft', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) 
-          if (flag=='read' .and. .not. readvar) then
-             if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c13 value'
-             do i = bounds%begp,bounds%endp
-                if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                   this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c3_r2
-                else
-                   this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c4_r2
-                endif
-             end do
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_13', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_col)
-          if (flag=='read' .and. .not. readvar) then
-             if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c13 value'
-             do i = bounds%begc,bounds%endc
-                if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                   this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c3_r2
-                else
-                   this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c4_r2
-                endif
-             end do
-          end if
-
-       end if
-
-       !--------------------------------
-       ! C14 patch carbon state variables 
-       !--------------------------------
-
-       if ( carbon_type == 'c14')  then
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc_14', xtype=ncd_double,  &
-               dim1name='pft', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) 
-          if (flag=='read' .and. .not. readvar) then
-             if ( masterproc ) write(iulog,*) 'initializing this%totvegc_patch with atmospheric c14 value'
-             do i = bounds%begp,bounds%endp
-                if (this%totvegc_patch(i) /= spval .and. &
-                    .not. isnan(this%totvegc_patch(i)) ) then
-                   this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c14ratio
-                endif
-             end do
-          endif
-
-          call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_14', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=this%totvegc_col)
-          if (flag=='read' .and. .not. readvar) then
-             if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c14 value'
-             do i = bounds%begc,bounds%endc
-                if (this%totvegc_col(i) /= spval .and. &
-                    .not. isnan(this%totvegc_col(i)) ) then
-                   this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c14ratio
-                endif
-             end do
-          end if
-       end if
-
-
-       if (  flag == 'read' .and. (enter_spinup .or. (reseed_dead_plants .and. .not. is_restart())) .and. .not. use_cndv) then
-             if ( masterproc ) write(iulog, *) 'Reseeding dead plants for CNVegCarbonState'
-             ! If a pft is dead (indicated by totvegc = 0) then we reseed that
-             ! pft according to the cold start protocol in the InitCold subroutine.
-             ! Thus, the variable totvegc is required to be read before here
-             ! so that if it is zero for a given pft, the pft can be reseeded.
-             do i = bounds%begp,bounds%endp
-                if (this%totvegc_patch(i) .le. 0.0_r8) then
-                   !-----------------------------------------------
-                   ! initialize patch-level carbon state variables
-                   !-----------------------------------------------
-
-                   this%leafcmax_patch(i) = 0._r8
-
-                   l = patch%landunit(i)
-                   if (lun%itype(l) == istsoil )then
-                      if ( present(num_reseed_patch) ) then
-                         num_reseed_patch = num_reseed_patch + 1
-                         filter_reseed_patch(num_reseed_patch) = i
-                      end if
-
-                      if (patch%itype(i) == noveg) then
-                         this%leafc_patch(i)          = 0._r8
-                         this%leafc_storage_patch(i)  = 0._r8
-                         this%frootc_patch(i)         = 0._r8            
-                         this%frootc_storage_patch(i) = 0._r8    
-                      else
-                         if (pftcon%evergreen(patch%itype(i)) == 1._r8) then
-                            this%leafc_patch(i)          = cnvegcstate_const%initial_vegC * ratio     
-                            this%leafc_storage_patch(i)  = 0._r8
-                            this%frootc_patch(i)         = cnvegcstate_const%initial_vegC * ratio           
-                            this%frootc_storage_patch(i) = 0._r8    
-                         else
-                            this%leafc_patch(i)          = 0._r8
-                            this%leafc_storage_patch(i)  = cnvegcstate_const%initial_vegC * ratio   
-                            this%frootc_patch(i)         = 0._r8            
-                            this%frootc_storage_patch(i) = cnvegcstate_const%initial_vegC * ratio   
-                         end if
-                      end if
-                      this%leafc_xfer_patch(i) = 0._r8
-                      this%leafc_storage_xfer_acc_patch(i)  = 0._r8
-                      this%storage_cdemand_patch(i)         = 0._r8
-
-                      if (MM_Nuptake_opt .eqv. .false.) then  ! if not running in floating CN ratio option 
-                         this%frootc_patch(i)            = 0._r8 
-                         this%frootc_storage_patch(i)    = 0._r8 
-                      end if     
-                      this%frootc_xfer_patch(i)       = 0._r8 
-
-                      this%livestemc_patch(i)         = 0._r8 
-                      this%livestemc_storage_patch(i) = 0._r8 
-                      this%livestemc_xfer_patch(i)    = 0._r8 
-
-                      if (pftcon%woody(patch%itype(i)) == 1._r8) then
-                         this%deadstemc_patch(i) = 0.1_r8 * ratio
-                      else
-                         this%deadstemc_patch(i) = 0._r8 
-                      end if
-                      this%deadstemc_storage_patch(i)  = 0._r8 
-                      this%deadstemc_xfer_patch(i)     = 0._r8 
-
-                      this%livecrootc_patch(i)         = 0._r8 
-                      this%livecrootc_storage_patch(i) = 0._r8 
-                      this%livecrootc_xfer_patch(i)    = 0._r8 
-
-                      this%deadcrootc_patch(i)         = 0._r8 
-                      this%deadcrootc_storage_patch(i) = 0._r8 
-                      this%deadcrootc_xfer_patch(i)    = 0._r8 
-
-                      this%gresp_storage_patch(i)      = 0._r8 
-                      this%gresp_xfer_patch(i)         = 0._r8 
-
-                      this%cpool_patch(i)              = 0._r8 
-                      this%xsmrpool_patch(i)           = 0._r8 
-                      this%ctrunc_patch(i)             = 0._r8 
-                      this%dispvegc_patch(i)           = 0._r8 
-                      this%storvegc_patch(i)           = 0._r8 
-                      this%woodc_patch(i)              = 0._r8
-                      this%totc_patch(i)               = 0._r8 
-
-                      if ( use_crop )then
-                         this%grainc_patch(i)         = 0._r8 
-                         this%grainc_storage_patch(i) = 0._r8 
-                         this%grainc_xfer_patch(i)    = 0._r8 
-                         this%cropseedc_deficit_patch(i)  = 0._r8
-                      end if
-
-                      ! calculate totvegc explicitly so that it is available for the isotope 
-                      ! code on the first time step.
-
-                      this%totvegc_patch(i) = &
-                           this%leafc_patch(i)              + &
-                           this%leafc_storage_patch(i)      + &
-                           this%leafc_xfer_patch(i)         + &
-                           this%frootc_patch(i)             + &
-                           this%frootc_storage_patch(i)     + &
-                           this%frootc_xfer_patch(i)        + &
-                           this%livestemc_patch(i)          + &
-                           this%livestemc_storage_patch(i)  + &
-                           this%livestemc_xfer_patch(i)     + &
-                           this%deadstemc_patch(i)          + &
-                           this%deadstemc_storage_patch(i)  + &
-                           this%deadstemc_xfer_patch(i)     + &
-                           this%livecrootc_patch(i)         + &
-                           this%livecrootc_storage_patch(i) + &
-                           this%livecrootc_xfer_patch(i)    + &
-                           this%deadcrootc_patch(i)         + &
-                           this%deadcrootc_storage_patch(i) + &
-                           this%deadcrootc_xfer_patch(i)    + &
-                           this%gresp_storage_patch(i)      + &
-                           this%gresp_xfer_patch(i)         + &
-                           this%cpool_patch(i)
-
-                      if ( use_crop )then
-                         this%totvegc_patch(i) =         &
-                              this%totvegc_patch(i)    + &
-                              this%grainc_patch(i)         + &
-                              this%grainc_storage_patch(i) + &
-                              this%grainc_xfer_patch(i)
-                      end if
-
-                   endif
-                end if
-             end do
-             if ( .not. is_restart() .and. get_nstep() == 1 ) then
-
-                do p = bounds%begp,bounds%endp
-                  if (this%leafc_patch(p) .lt. 0.01_r8) then
-                   if (pftcon%c3psn(patch%itype(p)) == 1._r8) then
-                      this%grainc_patch(p)         = c12_cnveg_carbonstate_inst%grainc_patch(p)         * c3_r2
-                      this%grainc_storage_patch(p) = c12_cnveg_carbonstate_inst%grainc_storage_patch(p) * c3_r2
-                      this%grainc_xfer_patch(p)    = c12_cnveg_carbonstate_inst%grainc_xfer_patch(p)    * c3_r2
-                      this%dispvegc_patch(p)       = c12_cnveg_carbonstate_inst%dispvegc_patch(p)       * c3_r2
-                      this%storvegc_patch(p)       = c12_cnveg_carbonstate_inst%storvegc_patch(p)       * c3_r2
-                      this%totvegc_patch(p)        = c12_cnveg_carbonstate_inst%totvegc_patch(p)        * c3_r2
-                      this%totc_patch(p)           = c12_cnveg_carbonstate_inst%totc_patch(p)           * c3_r2
-                      this%woodc_patch(p)          = c12_cnveg_carbonstate_inst%woodc_patch(p)          * c3_r2
-                   else
-                      this%grainc_patch(p)         = c12_cnveg_carbonstate_inst%grainc_patch(p)         * c4_r2
-                      this%grainc_storage_patch(p) = c12_cnveg_carbonstate_inst%grainc_storage_patch(p) * c4_r2
-                      this%grainc_xfer_patch(p)    = c12_cnveg_carbonstate_inst%grainc_xfer_patch(p)    * c4_r2
-                      this%dispvegc_patch(p)       = c12_cnveg_carbonstate_inst%dispvegc_patch(p)       * c4_r2
-                      this%storvegc_patch(p)       = c12_cnveg_carbonstate_inst%storvegc_patch(p)       * c4_r2
-                      this%totvegc_patch(p)        = c12_cnveg_carbonstate_inst%totvegc_patch(p)        * c4_r2
-                      this%totc_patch(p)           = c12_cnveg_carbonstate_inst%totc_patch(p)           * c4_r2
-                      this%woodc_patch(p)          = c12_cnveg_carbonstate_inst%woodc_patch(p)          * c4_r2
-                   end if
-                  end if
-                end do
-             end if
-             if ( present(num_reseed_patch) ) then
-                call shr_mpi_sum( num_reseed_patch, total_num_reseed_patch, mpicom )
-                if ( masterproc ) write(iulog,*) 'Total num_reseed, over all tasks = ', total_num_reseed_patch
-             end if
-       end if
-
-    end if
-
-    !--------------------------------
-    ! C13 patch carbon state variables 
-    !--------------------------------
-
-    if ( carbon_type == 'c13')  then
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_patch)
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%leafc_patch(i) = c12_cnveg_carbonstate_inst%leafc_patch(i) * c3_r2
-             else
-                this%leafc_patch(i) = c12_cnveg_carbonstate_inst%leafc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c3_r2
-             else
-                this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c4_r2
-                this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%leafc_xfer_patch(i) = c12_cnveg_carbonstate_inst%leafc_xfer_patch(i) * c3_r2
-             else
-                this%leafc_xfer_patch(i) = c12_cnveg_carbonstate_inst%leafc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%frootc_patch(i) = c12_cnveg_carbonstate_inst%frootc_patch(i) * c3_r2
-             else
-                this%frootc_patch(i) = c12_cnveg_carbonstate_inst%frootc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%frootc_storage_patch(i) = c12_cnveg_carbonstate_inst%frootc_storage_patch(i) * c3_r2
-             else
-                this%frootc_storage_patch(i) = c12_cnveg_carbonstate_inst%frootc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%frootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%frootc_xfer_patch(i) * c3_r2
-             else
-                this%frootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%frootc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livestemc_patch(i) = c12_cnveg_carbonstate_inst%livestemc_patch(i) * c3_r2
-             else
-                this%livestemc_patch(i) = c12_cnveg_carbonstate_inst%livestemc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livestemc_storage_patch(i) = c12_cnveg_carbonstate_inst%livestemc_storage_patch(i) * c3_r2
-             else
-                this%livestemc_storage_patch(i) = c12_cnveg_carbonstate_inst%livestemc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livestemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livestemc_xfer_patch(i) * c3_r2
-             else
-                this%livestemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livestemc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadstemc_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_patch(i) * c3_r2
-             else
-                this%deadstemc_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadstemc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_storage_patch(i) * c3_r2
-             else
-                this%deadstemc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadstemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_xfer_patch(i) * c3_r2
-             else
-                this%deadstemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livecrootc_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_patch(i) * c3_r2
-             else
-                this%livecrootc_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livecrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_storage_patch(i) * c3_r2
-             else
-                this%livecrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%livecrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_xfer_patch(i) * c3_r2
-             else
-                this%livecrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadcrootc_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_patch(i) * c3_r2
-             else
-                this%deadcrootc_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadcrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_storage_patch(i) * c3_r2
-             else
-                this%deadcrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%deadcrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_xfer_patch(i) * c3_r2
-             else
-                this%deadcrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_storage_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%gresp_storage with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%gresp_storage_patch(i) = c12_cnveg_carbonstate_inst%gresp_storage_patch(i) * c3_r2
-             else
-                this%gresp_storage_patch(i) = c12_cnveg_carbonstate_inst%gresp_storage_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_xfer_13', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%gresp_xfer with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%gresp_xfer_patch(i) = c12_cnveg_carbonstate_inst%gresp_xfer_patch(i) * c3_r2
-             else
-                this%gresp_xfer_patch(i) = c12_cnveg_carbonstate_inst%gresp_xfer_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='cpool_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%cpool with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%cpool_patch(i) = c12_cnveg_carbonstate_inst%cpool_patch(i) * c3_r2
-             else
-                this%cpool_patch(i) = c12_cnveg_carbonstate_inst%cpool_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='xsmrpool_13', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%xsmrpool_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%xsmrpool with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%xsmrpool_patch(i) = c12_cnveg_carbonstate_inst%xsmrpool_patch(i) * c3_r2
-             else
-                this%xsmrpool_patch(i) = c12_cnveg_carbonstate_inst%xsmrpool_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='pft_ctrunc_13', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%ctrunc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%ctrunc with atmospheric c13 value'
-          do i = bounds%begp,bounds%endp
-             if (pftcon%c3psn(patch%itype(i)) == 1._r8) then
-                this%ctrunc_patch(i) = c12_cnveg_carbonstate_inst%ctrunc_patch(i) * c3_r2
-             else
-                this%ctrunc_patch(i) = c12_cnveg_carbonstate_inst%ctrunc_patch(i) * c4_r2
-             endif
-          end do
-       end if
-
-    end if
-
-    !--------------------------------
-    ! C14 patch carbon state variables 
-    !--------------------------------
-
-    if ( carbon_type == 'c14')  then
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%leafc_patch(i) /= spval .and. &
-                  .not. isnan(this%leafc_patch(i)) ) then
-                this%leafc_patch(i) = c12_cnveg_carbonstate_inst%leafc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%leafc_storage_patch(i) /= spval .and. &
-                  .not. isnan(this%leafc_storage_patch(i)) ) then
-                this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='leafc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft',    long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%leafc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%leafc_xfer_patch(i) /= spval .and. .not. isnan(this%leafc_xfer_patch(i)) ) then
-                this%leafc_xfer_patch(i) = c12_cnveg_carbonstate_inst%leafc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%frootc_patch(i) /= spval .and. &
-                  .not. isnan(this%frootc_patch(i)) ) then
-                this%frootc_patch(i) = c12_cnveg_carbonstate_inst%frootc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%frootc_storage_patch(i) /= spval .and. &
-                  .not. isnan(this%frootc_storage_patch(i)) ) then
-                this%frootc_storage_patch(i) = c12_cnveg_carbonstate_inst%frootc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='frootc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%frootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%frootc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%frootc_xfer_patch(i) /= spval .and. &
-                  .not. isnan(this%frootc_xfer_patch(i)) ) then
-                this%frootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%frootc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livestemc_patch(i) /= spval .and. .not. isnan(this%livestemc_patch(i)) ) then
-                this%livestemc_patch(i) = c12_cnveg_carbonstate_inst%livestemc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livestemc_storage_patch(i) /= spval .and. .not. isnan(this%livestemc_storage_patch(i)) ) then
-                this%livestemc_storage_patch(i) = c12_cnveg_carbonstate_inst%livestemc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livestemc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livestemc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livestemc_xfer_patch(i) /= spval .and. .not. isnan(this%livestemc_xfer_patch(i)) ) then
-                this%livestemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livestemc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadstemc_patch(i) /= spval .and. .not. isnan(this%deadstemc_patch(i)) ) then
-                this%deadstemc_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadstemc_storage_patch(i) /= spval .and. .not. isnan(this%deadstemc_storage_patch(i)) ) then
-                this%deadstemc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadstemc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadstemc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadstemc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadstemc_xfer_patch(i) /= spval .and. .not. isnan(this%deadstemc_xfer_patch(i)) ) then
-                this%deadstemc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadstemc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livecrootc_patch(i) /= spval .and. .not. isnan(this%livecrootc_patch(i)) ) then
-                this%livecrootc_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livecrootc_storage_patch(i) /= spval .and. .not. isnan(this%livecrootc_storage_patch(i)) ) then
-                this%livecrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='livecrootc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%livecrootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%livecrootc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%livecrootc_xfer_patch(i) /= spval .and. .not. isnan(this%livecrootc_xfer_patch(i)) ) then
-                this%livecrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%livecrootc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadcrootc_patch(i) /= spval .and. .not. isnan(this%deadcrootc_patch(i)) ) then
-                this%deadcrootc_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadcrootc_storage_patch(i) /= spval .and. .not. isnan(this%deadcrootc_storage_patch(i)) ) then
-                this%deadcrootc_storage_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='deadcrootc_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%deadcrootc_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%deadcrootc_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%deadcrootc_xfer_patch(i) /= spval .and. .not. isnan(this%deadcrootc_xfer_patch(i)) ) then
-                this%deadcrootc_xfer_patch(i) = c12_cnveg_carbonstate_inst%deadcrootc_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_storage_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_storage_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%gresp_storage_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%gresp_storage_patch(i) /= spval .and. .not. isnan(this%gresp_storage_patch(i)) ) then
-                this%gresp_storage_patch(i) = c12_cnveg_carbonstate_inst%gresp_storage_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='gresp_xfer_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%gresp_xfer_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%gresp_xfer_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%gresp_xfer_patch(i) /= spval .and. .not. isnan(this%gresp_xfer_patch(i)) ) then
-                this%gresp_xfer_patch(i) = c12_cnveg_carbonstate_inst%gresp_xfer_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='cpool_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%cpool_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%cpool_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%cpool_patch(i) /= spval .and. .not. isnan(this%cpool_patch(i)) ) then
-                this%cpool_patch(i) = c12_cnveg_carbonstate_inst%cpool_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='xsmrpool_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%xsmrpool_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%xsmrpool_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%xsmrpool_patch(i) /= spval .and. .not. isnan(this%xsmrpool_patch(i)) ) then
-                this%xsmrpool_patch(i) = c12_cnveg_carbonstate_inst%xsmrpool_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='pft_ctrunc_14', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%ctrunc_patch) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%ctrunc_patch with atmospheric c14 value'
-          do i = bounds%begp,bounds%endp
-             if (this%ctrunc_patch(i) /= spval .and. .not. isnan(this%ctrunc_patch(i)) ) then
-                this%ctrunc_patch(i) = c12_cnveg_carbonstate_inst%ctrunc_patch(i) * c14ratio
-             endif
-          end do
-       end if
-
-    end if
-
-    !--------------------------------
-    ! patch prognostic crop variables
-    !--------------------------------
-
-    if (use_crop) then
-       if (carbon_type == 'c12') then
-          call restartvar(ncid=ncid, flag=flag,  varname='grainc', xtype=ncd_double,  &
-               dim1name='pft', long_name='grain C', units='gC/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_patch)
-
-          call restartvar(ncid=ncid, flag=flag,  varname='grainc_storage', xtype=ncd_double,  &
-               dim1name='pft', long_name='grain C storage', units='gC/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_storage_patch)
-
-          call restartvar(ncid=ncid, flag=flag,  varname='grainc_xfer', xtype=ncd_double,  &
-               dim1name='pft', long_name='grain C transfer', units='gC/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_xfer_patch)
-
-          call restartvar(ncid=ncid, flag=flag, varname='cropseedc_deficit', xtype=ncd_double,  &
-               dim1name='pft', long_name='pool for seeding new crop growth', units='gC/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%cropseedc_deficit_patch)
-       end if
-
-       if (carbon_type == 'c13') then
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_13', xtype=ncd_double,  &
-               dim1name='pft', long_name='c13 grain C', units='gC13/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_13_storage', xtype=ncd_double,  &
-               dim1name='pft', long_name='c13 grain C storage', units='gC13/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_storage_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_storage_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_storage_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_13_xfer', xtype=ncd_double,  &
-               dim1name='pft', long_name='c13 grain C transfer', units='gC13/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_xfer_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_xfer_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_xfer_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='cropseedc_13_deficit', xtype=ncd_double,  &
-               dim1name='pft', long_name='pool for seeding new crop growth', units='gC13/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%cropseedc_deficit_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%cropseedc_deficit_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%cropseedc_deficit_patch, &
-                  multiplier = c3_r2)
-          end if
-       end if
-
-       if ( carbon_type == 'c14' ) then
-
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_14', xtype=ncd_double,  &
-               dim1name='pft', long_name='c14 grain C', units='gC14/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_14_storage', xtype=ncd_double,  &
-               dim1name='pft', long_name='c14 grain C storage', units='gC14/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_storage_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_storage_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_storage_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='grainc_14_xfer', xtype=ncd_double,  &
-               dim1name='pft', long_name='c14 grain C transfer', units='gC14/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%grainc_xfer_patch)
-          if (flag=='read' .and. .not. readvar) then
-             call set_missing_from_template( &
-                  my_var = this%grainc_xfer_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%grainc_xfer_patch, &
-                  multiplier = c3_r2)
-          end if
-
-          call restartvar(ncid=ncid, flag=flag, varname='cropseedc_14_deficit', xtype=ncd_double,  &
-               dim1name='pft', long_name='pool for seeding new crop growth', units='gC14/m2', &
-               interpinic_flag='interp', readvar=readvar, data=this%cropseedc_deficit_patch)
-          if (flag=='read' .and. .not. readvar) then
-             if ( masterproc ) write(iulog,*) 'initializing this%cropseedc_deficit_patch with atmospheric c14 value'
-             call set_missing_from_template( &
-                  my_var = this%cropseedc_deficit_patch, &
-                  template_var = c12_cnveg_carbonstate_inst%cropseedc_deficit_patch, &
-                  multiplier = c14ratio)
-          end if
-       end if
-    end if
-
-    !--------------------------------
-    ! gridcell carbon state variables
-    !--------------------------------
-
-    if (carbon_type == 'c12') then
-       ! BACKWARDS_COMPATIBILITY(wjs, 2017-01-12) Naming this with a _g suffix in order
-       ! to distinguish it from the old column-level seedc restart variable
-       call restartvar(ncid=ncid, flag=flag, varname='seedc_g', xtype=ncd_double,  &
-            dim1name='gridcell', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%seedc_grc) 
-    end if
-
-    !--------------------------------
-    ! C13 gridcell carbon state variables
-    !--------------------------------
-
-    if (carbon_type == 'c13') then
-       call restartvar(ncid=ncid, flag=flag, varname='seedc_13_g', xtype=ncd_double,  &
-            dim1name='gridcell', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%seedc_grc) 
-       if (flag=='read' .and. .not. readvar) then
-          call set_missing_from_template( &
-               my_var = this%seedc_grc, &
-               template_var = c12_cnveg_carbonstate_inst%seedc_grc, &
-               multiplier = c3_r2)
-       end if
-    end if
-
-    !--------------------------------
-    ! C14 column carbon state variables
-    !--------------------------------
-
-    if ( carbon_type == 'c14' ) then
-       call restartvar(ncid=ncid, flag=flag, varname='seedc_14_g', xtype=ncd_double,  &
-            dim1name='gridcell', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%seedc_grc) 
-       if (flag=='read' .and. .not. readvar) then
-          if ( masterproc ) write(iulog,*) 'initializing this%seedc_grc with atmospheric c14 value'
-          call set_missing_from_template( &
-               my_var = this%seedc_grc, &
-               template_var = c12_cnveg_carbonstate_inst%seedc_grc, &
-               multiplier = c14ratio)
-       end if
-    end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, &
-       num_patch, filter_patch, value_patch, &
-       num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set carbon state variables
-    !
-    ! !ARGUMENTS:
-    class (cnveg_carbonstate_type) :: this
-    integer , intent(in) :: num_patch
-    integer , intent(in) :: filter_patch(:)
-    real(r8), intent(in) :: value_patch
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i,j,k,l     ! loop index
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_patch
-       i  = filter_patch(fi)
-       this%leafc_patch(i)              = value_patch
-       this%leafc_storage_patch(i)      = value_patch
-       this%leafc_xfer_patch(i)         = value_patch
-       this%leafc_storage_xfer_acc_patch(i) = value_patch
-       this%storage_cdemand_patch(i)        = value_patch        
-       this%frootc_patch(i)             = value_patch
-       this%frootc_storage_patch(i)     = value_patch
-       this%frootc_xfer_patch(i)        = value_patch
-       this%livestemc_patch(i)          = value_patch
-       this%livestemc_storage_patch(i)  = value_patch
-       this%livestemc_xfer_patch(i)     = value_patch
-       this%deadstemc_patch(i)          = value_patch
-       this%deadstemc_storage_patch(i)  = value_patch
-       this%deadstemc_xfer_patch(i)     = value_patch
-       this%livecrootc_patch(i)         = value_patch
-       this%livecrootc_storage_patch(i) = value_patch
-       this%livecrootc_xfer_patch(i)    = value_patch
-       this%deadcrootc_patch(i)         = value_patch
-       this%deadcrootc_storage_patch(i) = value_patch
-       this%deadcrootc_xfer_patch(i)    = value_patch
-       this%gresp_storage_patch(i)      = value_patch
-       this%gresp_xfer_patch(i)         = value_patch
-       this%cpool_patch(i)              = value_patch
-       this%xsmrpool_patch(i)           = value_patch
-       this%ctrunc_patch(i)             = value_patch
-       this%dispvegc_patch(i)           = value_patch
-       this%storvegc_patch(i)           = value_patch
-       this%woodc_patch(i)              = value_patch
-       this%totvegc_patch(i)            = value_patch
-       this%totc_patch(i)               = value_patch
-       if ( use_crop ) then
-          this%grainc_patch(i)          = value_patch
-          this%grainc_storage_patch(i)  = value_patch
-          this%grainc_xfer_patch(i)     = value_patch
-          this%cropseedc_deficit_patch(i)  = value_patch
-       end if
-    end do
-
-    do fi = 1,num_column
-       i  = filter_column(fi)
-       this%rootc_col(i)                = value_column
-       this%leafc_col(i)                = value_column
-       this%deadstemc_col(i)            = value_column
-       this%fuelc_col(i)                = value_column
-       this%fuelc_crop_col(i)           = value_column
-       this%totvegc_col(i)              = value_column
-       this%totc_p2c_col(i)             = value_column
-       this%totc_col(i)                 = value_column
-       this%totecosysc_col(i)           = value_column
-    end do
-
-  end subroutine SetValues
-
-end module CNVegCarbonStateType
diff --git a/src/biogeochem/CNVegComputeSeedMod.F90 b/src/biogeochem/CNVegComputeSeedMod.F90
deleted file mode 100644
index 01cf471e20..0000000000
--- a/src/biogeochem/CNVegComputeSeedMod.F90
+++ /dev/null
@@ -1,259 +0,0 @@
-module CNVegComputeSeedMod
-
-  !-----------------------------------------------------------------------
-  ! Module to compute seed amounts for new patch areas
-  !
-  ! !USES:
-#include "shr_assert.h"
-
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use decompMod      , only : bounds_type
-  use pftconMod      , only : pftcon, noveg
-  use clm_varcon     , only : c3_r2, c4_r2, c14ratio
-  use clm_varctl     , only : iulog
-  use PatchType      , only : patch
-  use abortutils     , only : endrun
-  use CNSpeciesMod   , only : CN_SPECIES_C12, CN_SPECIES_C13, CN_SPECIES_C14, CN_SPECIES_N
-  !
-  ! !PUBLIC ROUTINES:
-  implicit none
-  private
-
-  public :: ComputeSeedAmounts
-
-  ! !PRIVATE ROUTINES:
-
-  private :: SpeciesTypeMultiplier
-  private :: LeafProportions  ! compute leaf proportions (leaf, storage and xfer)
-
-  ! !PRIVATE DATA:
-
-  integer, parameter :: COMPONENT_LEAF = 1
-  integer, parameter :: COMPONENT_DEADWOOD = 2
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine ComputeSeedAmounts(bounds, &
-       num_soilp_with_inactive, filter_soilp_with_inactive, &
-       species, &
-       leafc_seed, deadstemc_seed, &
-       leaf_patch, leaf_storage_patch, leaf_xfer_patch, &
-       compute_here_patch, ignore_current_state_patch, &
-       seed_leaf_patch, seed_leaf_storage_patch, seed_leaf_xfer_patch, &
-       seed_deadstem_patch)
-    !
-    ! !DESCRIPTION:
-    ! Compute seed amounts for patches that increase in area, for various variables, for
-    ! the given species (c12, c13, c14 or n).
-    !
-    ! The output variables are only set for patches inside the filter, where
-    ! compute_here_patch is true; for other patches, they remain at their original values.
-    !
-    ! Note that, regardless of the species, leafc_seed and deadstemc_seed are specified
-    ! in terms of gC/m2; these amounts are converted to the amount of the given species
-    ! here.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)              , intent(in) :: bounds
-    integer                        , intent(in) :: num_soilp_with_inactive       ! number of points in filter
-    integer                        , intent(in) :: filter_soilp_with_inactive(:) ! soil patch filter that includes inactive points
-    integer                        , intent(in) :: species                       ! which C/N species we're operating on; should be one of the values in CNSpeciesMod
-    real(r8)                       , intent(in) :: leafc_seed                    ! seed amount for leaf C
-    real(r8)                       , intent(in) :: deadstemc_seed                ! seed amount for deadstem C
-    real(r8)                       , intent(in) :: leaf_patch( bounds%begp: )   ! current leaf C or N content (g/m2)
-    real(r8)                       , intent(in) :: leaf_storage_patch( bounds%begp: ) ! current leaf C or N storage content (g/m2)
-    real(r8)                       , intent(in) :: leaf_xfer_patch( bounds%begp: )    ! current leaf C or N xfer content (g/m2)
-
-    ! whether to compute outputs for each patch
-    logical, intent(in) :: compute_here_patch( bounds%begp: )
-
-    ! If ignore_current_state is true, then use default leaf proportions rather than
-    ! proportions based on current state.
-    logical, intent(in) :: ignore_current_state_patch( bounds%begp: )
-
-    real(r8), intent(inout) :: seed_leaf_patch( bounds%begp: ) ! seed amount for leaf itself for this species (g/m2)
-    real(r8), intent(inout) :: seed_leaf_storage_patch( bounds%begp: ) ! seed amount for leaf storage for this species (g/m2)
-    real(r8), intent(inout) :: seed_leaf_xfer_patch( bounds%begp: ) ! seed amount for leaf xfer for this species (g/m2)
-    real(r8), intent(inout) :: seed_deadstem_patch( bounds%begp: ) ! seed amount for deadstem for this species (g/m2)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fp, p
-    integer :: begp, endp
-    real(r8) :: my_leaf_seed
-    real(r8) :: my_deadstem_seed
-    integer  :: pft_type
-    real(r8) :: pleaf
-    real(r8) :: pstor
-    real(r8) :: pxfer
-
-    character(len=*), parameter :: subname = 'ComputeSeedAmounts'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    SHR_ASSERT_ALL((ubound(leaf_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(leaf_storage_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(leaf_xfer_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(compute_here_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(ignore_current_state_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(seed_leaf_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(seed_leaf_storage_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(seed_leaf_xfer_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(seed_deadstem_patch) == (/endp/)), errMsg(sourcefile, __LINE__))
-
-
-    do fp = 1, num_soilp_with_inactive
-       p = filter_soilp_with_inactive(fp)
-
-       if (compute_here_patch(p)) then
-
-          my_leaf_seed = 0._r8
-          my_deadstem_seed = 0._r8
-
-          pft_type = patch%itype(p)
-
-          call LeafProportions( &
-               ignore_current_state = ignore_current_state_patch(p), &
-               pft_type = pft_type, &
-               leaf = leaf_patch(p), &
-               leaf_storage = leaf_storage_patch(p), &
-               leaf_xfer = leaf_xfer_patch(p), &
-               pleaf = pleaf, &
-               pstorage = pstor, &
-               pxfer = pxfer)
-
-          if (pft_type /= noveg) then
-             my_leaf_seed = leafc_seed * &
-                  SpeciesTypeMultiplier(species, pft_type, COMPONENT_LEAF)
-             if (pftcon%woody(pft_type) == 1._r8) then
-                my_deadstem_seed = deadstemc_seed * &
-                     SpeciesTypeMultiplier(species, pft_type, COMPONENT_DEADWOOD)
-             end if
-          end if
-
-          seed_leaf_patch(p) = my_leaf_seed * pleaf
-          seed_leaf_storage_patch(p) = my_leaf_seed * pstor
-          seed_leaf_xfer_patch(p) = my_leaf_seed * pxfer
-          seed_deadstem_patch(p) = my_deadstem_seed
-       end if
-
-    end do
-
-  end subroutine ComputeSeedAmounts
-
-
-  !-----------------------------------------------------------------------
-  function SpeciesTypeMultiplier(species, pft_type, component) result(multiplier)
-    !
-    ! !DESCRIPTION:
-    ! Returns a multiplier based on the species type. This multiplier is
-    ! meant to be applied to some state variable expressed in terms of g C, translating
-    ! this value into an appropriate value for c13, c14 or n.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    real(r8) :: multiplier  ! function result
-    integer, intent(in) :: species ! which C/N species we're operating on; should be one of the values in CNSpeciesMod
-    integer, intent(in) :: pft_type
-    integer, intent(in) :: component ! which plant component; should be one of the COMPONENT_* parameters defined in this module
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'SpeciesTypeMultiplier'
-    !-----------------------------------------------------------------------
-
-    select case (species)
-    case (CN_SPECIES_C12)
-       multiplier = 1._r8
-
-    case (CN_SPECIES_C13)
-       if (pftcon%c3psn(pft_type) == 1._r8) then
-          multiplier = c3_r2
-       else
-          multiplier = c4_r2
-       end if
-
-    case (CN_SPECIES_C14)
-       ! 14c state is initialized assuming initial "modern" 14C of 1.e-12
-       multiplier = c14ratio
-
-    case (CN_SPECIES_N)
-       select case (component)
-       case (COMPONENT_LEAF)
-          multiplier = 1._r8 / pftcon%leafcn(pft_type)
-       case (COMPONENT_DEADWOOD)
-          multiplier = 1._r8 / pftcon%deadwdcn(pft_type)
-       case default
-          write(iulog,*) subname//' ERROR: unknown component: ', component
-          call endrun(subname//': unknown component')
-       end select
-
-    case default
-       write(iulog,*) subname//' ERROR: unknown species: ', species
-       call endrun(subname//': unknown species')
-    end select
-
-  end function SpeciesTypeMultiplier
-
-
-  !-----------------------------------------------------------------------
-  subroutine LeafProportions(ignore_current_state, &
-       pft_type, &
-       leaf, leaf_storage, leaf_xfer, &
-       pleaf, pstorage, pxfer)
-    !
-    ! !DESCRIPTION:
-    ! Compute leaf proportions (leaf, storage and xfer)
-    !
-    ! If ignore_current_state is true, then use default proportions rather than
-    ! proportions based on current state. (Also use default proportions if total leaf mass
-    ! is 0 for this patch.)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    logical, intent(in) :: ignore_current_state  ! see comment above
-    integer , intent(in) :: pft_type
-    real(r8), intent(in) :: leaf  ! g/m2 leaf C or N
-    real(r8), intent(in) :: leaf_storage ! g/m2 leaf C or N storage
-    real(r8), intent(in) :: leaf_xfer ! g/m2 leaf C or N transfer
-
-    real(r8), intent(out) :: pleaf  ! proportion in leaf itself
-    real(r8), intent(out) :: pstorage ! proportion in leaf storage
-    real(r8), intent(out) :: pxfer ! proportion in leaf xfer
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: tot_leaf
-
-    character(len=*), parameter :: subname = 'LeafProportions'
-    !-----------------------------------------------------------------------
-
-    tot_leaf = leaf + leaf_storage + leaf_xfer
-    pleaf = 0._r8
-    pstorage = 0._r8
-    pxfer = 0._r8
-
-    if (tot_leaf == 0._r8 .or. ignore_current_state) then
-       if (pftcon%evergreen(pft_type) == 1._r8) then
-          pleaf = 1._r8
-       else
-          pstorage = 1._r8
-       end if
-    else
-       pleaf = leaf/tot_leaf
-       pstorage = leaf_storage/tot_leaf
-       pxfer = leaf_xfer/tot_leaf
-    end if
-
-  end subroutine LeafProportions
-
-end module CNVegComputeSeedMod
diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90
deleted file mode 100644
index 65727f5c62..0000000000
--- a/src/biogeochem/CNVegNitrogenFluxType.F90
+++ /dev/null
@@ -1,1737 +0,0 @@
-module CNVegNitrogenFluxType
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp
-  use clm_varcon                         , only : spval, ispval, dzsoi_decomp
-  use clm_varctl                         , only : use_nitrif_denitrif, use_vertsoilc, use_crop
-  use CNSharedParamsMod                  , only : use_fun
-  use decompMod                          , only : bounds_type
-  use abortutils                         , only : endrun
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  use PatchType                          , only : patch                
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  type, public :: cnveg_nitrogenflux_type
-
-     ! gap mortality fluxes
-     real(r8), pointer :: m_leafn_to_litter_patch                   (:)     ! patch leaf N mortality (gN/m2/s)
-     real(r8), pointer :: m_frootn_to_litter_patch                  (:)     ! patch fine root N mortality (gN/m2/s)
-     real(r8), pointer :: m_leafn_storage_to_litter_patch           (:)     ! patch leaf N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_frootn_storage_to_litter_patch          (:)     ! patch fine root N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_livestemn_storage_to_litter_patch       (:)     ! patch live stem N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_deadstemn_storage_to_litter_patch       (:)     ! patch dead stem N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_livecrootn_storage_to_litter_patch      (:)     ! patch live coarse root N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_deadcrootn_storage_to_litter_patch      (:)     ! patch dead coarse root N storage mortality (gN/m2/s)
-     real(r8), pointer :: m_leafn_xfer_to_litter_patch              (:)     ! patch leaf N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_frootn_xfer_to_litter_patch             (:)     ! patch fine root N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_livestemn_xfer_to_litter_patch          (:)     ! patch live stem N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_deadstemn_xfer_to_litter_patch          (:)     ! patch dead stem N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_livecrootn_xfer_to_litter_patch         (:)     ! patch live coarse root N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_deadcrootn_xfer_to_litter_patch         (:)     ! patch dead coarse root N transfer mortality (gN/m2/s)
-     real(r8), pointer :: m_livestemn_to_litter_patch               (:)     ! patch live stem N mortality (gN/m2/s)
-     real(r8), pointer :: m_deadstemn_to_litter_patch               (:)     ! patch dead stem N mortality (gN/m2/s)
-     real(r8), pointer :: m_livecrootn_to_litter_patch              (:)     ! patch live coarse root N mortality (gN/m2/s)
-     real(r8), pointer :: m_deadcrootn_to_litter_patch              (:)     ! patch dead coarse root N mortality (gN/m2/s)
-     real(r8), pointer :: m_retransn_to_litter_patch                (:)     ! patch retranslocated N pool mortality (gN/m2/s)
-
-     ! harvest fluxes
-     real(r8), pointer :: hrv_leafn_to_litter_patch                 (:)     ! patch leaf N harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_frootn_to_litter_patch                (:)     ! patch fine root N harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_leafn_storage_to_litter_patch         (:)     ! patch leaf N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_frootn_storage_to_litter_patch        (:)     ! patch fine root N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livestemn_storage_to_litter_patch     (:)     ! patch live stem N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_deadstemn_storage_to_litter_patch     (:)     ! patch dead stem N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livecrootn_storage_to_litter_patch    (:)     ! patch live coarse root N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_deadcrootn_storage_to_litter_patch    (:)     ! patch dead coarse root N storage harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_leafn_xfer_to_litter_patch            (:)     ! patch leaf N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_frootn_xfer_to_litter_patch           (:)     ! patch fine root N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livestemn_xfer_to_litter_patch        (:)     ! patch live stem N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_deadstemn_xfer_to_litter_patch        (:)     ! patch dead stem N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livecrootn_xfer_to_litter_patch       (:)     ! patch live coarse root N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_deadcrootn_xfer_to_litter_patch       (:)     ! patch dead coarse root N transfer harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livestemn_to_litter_patch             (:)     ! patch live stem N harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_livecrootn_to_litter_patch            (:)     ! patch live coarse root N harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_deadcrootn_to_litter_patch            (:)     ! patch dead coarse root N harvest mortality (gN/m2/s)
-     real(r8), pointer :: hrv_retransn_to_litter_patch              (:)     ! patch retranslocated N pool harvest mortality (gN/m2/s)
-     real(r8), pointer :: grainn_to_cropprodn_patch                 (:)     ! patch grain N to crop product pool (gN/m2/s)
-     real(r8), pointer :: grainn_to_cropprodn_col                   (:)     ! col grain N to crop product pool (gN/m2/s)
-     real(r8), pointer :: m_n_to_litr_met_fire_col                  (:,:)   ! col N from leaf, froot, xfer and storage N to litter labile N by fire (gN/m3/s)
-     real(r8), pointer :: m_n_to_litr_cel_fire_col                  (:,:)   ! col N from leaf, froot, xfer and storage N to litter cellulose N by fire (gN/m3/s) 
-     real(r8), pointer :: m_n_to_litr_lig_fire_col                  (:,:)   ! col N from leaf, froot, xfer and storage N to litter lignin N by fire (gN/m3/s) 
-     real(r8), pointer :: harvest_n_to_litr_met_n_col               (:,:)   ! col N fluxes associated with harvest to litter metabolic pool (gN/m3/s)
-     real(r8), pointer :: harvest_n_to_litr_cel_n_col               (:,:)   ! col N fluxes associated with harvest to litter cellulose pool (gN/m3/s)
-     real(r8), pointer :: harvest_n_to_litr_lig_n_col               (:,:)   ! col N fluxes associated with harvest to litter lignin pool (gN/m3/s)
-     real(r8), pointer :: harvest_n_to_cwdn_col                     (:,:)   ! col N fluxes associated with harvest to CWD pool (gN/m3/s)
-
-     ! fire N fluxes 
-     real(r8), pointer :: m_decomp_npools_to_fire_vr_col            (:,:,:) ! col vertically-resolved decomposing N fire loss (gN/m3/s)
-     real(r8), pointer :: m_decomp_npools_to_fire_col               (:,:)   ! col vertically-integrated (diagnostic) decomposing N fire loss (gN/m2/s)
-     real(r8), pointer :: m_leafn_to_fire_patch                     (:)     ! patch (gN/m2/s) fire N emissions from leafn 
-     real(r8), pointer :: m_leafn_storage_to_fire_patch             (:)     ! patch (gN/m2/s) fire N emissions from leafn_storage            
-     real(r8), pointer :: m_leafn_xfer_to_fire_patch                (:)     ! patch (gN/m2/s) fire N emissions from leafn_xfer     
-     real(r8), pointer :: m_livestemn_to_fire_patch                 (:)     ! patch (gN/m2/s) fire N emissions from livestemn 
-     real(r8), pointer :: m_livestemn_storage_to_fire_patch         (:)     ! patch (gN/m2/s) fire N emissions from livestemn_storage      
-     real(r8), pointer :: m_livestemn_xfer_to_fire_patch            (:)     ! patch (gN/m2/s) fire N emissions from livestemn_xfer
-     real(r8), pointer :: m_deadstemn_to_fire_patch                 (:)     ! patch (gN/m2/s) fire N emissions from deadstemn
-     real(r8), pointer :: m_deadstemn_storage_to_fire_patch         (:)     ! patch (gN/m2/s) fire N emissions from deadstemn_storage         
-     real(r8), pointer :: m_deadstemn_xfer_to_fire_patch            (:)     ! patch (gN/m2/s) fire N emissions from deadstemn_xfer
-     real(r8), pointer :: m_frootn_to_fire_patch                    (:)     ! patch (gN/m2/s) fire N emissions from frootn
-     real(r8), pointer :: m_frootn_storage_to_fire_patch            (:)     ! patch (gN/m2/s) fire N emissions from frootn_storage
-     real(r8), pointer :: m_frootn_xfer_to_fire_patch               (:)     ! patch (gN/m2/s) fire N emissions from frootn_xfer
-     real(r8), pointer :: m_livecrootn_to_fire_patch                (:)     ! patch (gN/m2/s) fire N emissions from m_livecrootn_to_fire
-     real(r8), pointer :: m_livecrootn_storage_to_fire_patch        (:)     ! patch (gN/m2/s) fire N emissions from livecrootn_storage     
-     real(r8), pointer :: m_livecrootn_xfer_to_fire_patch           (:)     ! patch (gN/m2/s) fire N emissions from livecrootn_xfer
-     real(r8), pointer :: m_deadcrootn_to_fire_patch                (:)     ! patch (gN/m2/s) fire N emissions from deadcrootn
-     real(r8), pointer :: m_deadcrootn_storage_to_fire_patch        (:)     ! patch (gN/m2/s) fire N emissions from deadcrootn_storage  
-     real(r8), pointer :: m_deadcrootn_xfer_to_fire_patch           (:)     ! patch (gN/m2/s) fire N emissions from deadcrootn_xfer
-     real(r8), pointer :: m_retransn_to_fire_patch                  (:)     ! patch (gN/m2/s) fire N emissions from retransn
-     real(r8), pointer :: m_leafn_to_litter_fire_patch              (:)     ! patch (gN/m2/s) from leafn to litter N  due to fire               
-     real(r8), pointer :: m_leafn_storage_to_litter_fire_patch      (:)     ! patch (gN/m2/s) from leafn_storage to litter N  due to fire                              
-     real(r8), pointer :: m_leafn_xfer_to_litter_fire_patch         (:)     ! patch (gN/m2/s) from leafn_xfer to litter N  due to fire                              
-     real(r8), pointer :: m_livestemn_to_litter_fire_patch          (:)     ! patch (gN/m2/s) from livestemn to litter N  due to fire                              
-     real(r8), pointer :: m_livestemn_storage_to_litter_fire_patch  (:)     ! patch (gN/m2/s) from livestemn_storage to litter N  due to fire                                     
-     real(r8), pointer :: m_livestemn_xfer_to_litter_fire_patch     (:)     ! patch (gN/m2/s) from livestemn_xfer to litter N  due to fire                                     
-     real(r8), pointer :: m_livestemn_to_deadstemn_fire_patch       (:)     ! patch (gN/m2/s) from livestemn to deadstemn N  due to fire                                     
-     real(r8), pointer :: m_deadstemn_to_litter_fire_patch          (:)     ! patch (gN/m2/s) from deadstemn to litter N  due to fire                                     
-     real(r8), pointer :: m_deadstemn_storage_to_litter_fire_patch  (:)     ! patch (gN/m2/s) from deadstemn_storage to litter N  due to fire                                               
-     real(r8), pointer :: m_deadstemn_xfer_to_litter_fire_patch     (:)     ! patch (gN/m2/s) from deadstemn_xfer to litter N  due to fire                                               
-     real(r8), pointer :: m_frootn_to_litter_fire_patch             (:)     ! patch (gN/m2/s) from frootn to litter N  due to fire                                               
-     real(r8), pointer :: m_frootn_storage_to_litter_fire_patch     (:)     ! patch (gN/m2/s) from frootn_storage to litter N  due to fire                                               
-     real(r8), pointer :: m_frootn_xfer_to_litter_fire_patch        (:)     ! patch (gN/m2/s) from frootn_xfer to litter N  due to fire                                               
-     real(r8), pointer :: m_livecrootn_to_litter_fire_patch         (:)     ! patch (gN/m2/s) from livecrootn to litter N  due to fire                                               
-     real(r8), pointer :: m_livecrootn_storage_to_litter_fire_patch (:)     ! patch (gN/m2/s) from livecrootn_storage to litter N  due to fire                                                     
-     real(r8), pointer :: m_livecrootn_xfer_to_litter_fire_patch    (:)     ! patch (gN/m2/s) from livecrootn_xfer to litter N  due to fire                                                     
-     real(r8), pointer :: m_livecrootn_to_deadcrootn_fire_patch     (:)     ! patch (gN/m2/s) from livecrootn_xfer to deadcrootn due to fire                                                     
-     real(r8), pointer :: m_deadcrootn_to_litter_fire_patch         (:)     ! patch (gN/m2/s) from deadcrootn to deadcrootn due to fire                                                       
-     real(r8), pointer :: m_deadcrootn_storage_to_litter_fire_patch (:)     ! patch (gN/m2/s) from deadcrootn_storage to deadcrootn due to fire                                                        
-     real(r8), pointer :: m_deadcrootn_xfer_to_litter_fire_patch    (:)     ! patch (gN/m2/s) from deadcrootn_xfer to deadcrootn due to fire                                                         
-     real(r8), pointer :: m_retransn_to_litter_fire_patch           (:)     ! patch (gN/m2/s) from retransn to deadcrootn due to fire                                                         
-     real(r8), pointer :: fire_nloss_patch                          (:)     ! patch total patch-level fire N loss (gN/m2/s) 
-     real(r8), pointer :: fire_nloss_col                            (:)     ! col total column-level fire N loss (gN/m2/s)
-     real(r8), pointer :: fire_nloss_p2c_col                        (:)     ! col patch2col column-level fire N loss (gN/m2/s) (p2c)
-     real(r8), pointer :: fire_mortality_n_to_cwdn_col              (:,:)   ! col N fluxes associated with fire mortality to CWD pool (gN/m3/s)
-
-     ! phenology fluxes from transfer pool
-     real(r8), pointer :: grainn_xfer_to_grainn_patch               (:)     ! patch grain N growth from storage for prognostic crop model (gN/m2/s)
-     real(r8), pointer :: leafn_xfer_to_leafn_patch                 (:)     ! patch leaf N growth from storage (gN/m2/s)
-     real(r8), pointer :: frootn_xfer_to_frootn_patch               (:)     ! patch fine root N growth from storage (gN/m2/s)
-     real(r8), pointer :: livestemn_xfer_to_livestemn_patch         (:)     ! patch live stem N growth from storage (gN/m2/s)
-     real(r8), pointer :: deadstemn_xfer_to_deadstemn_patch         (:)     ! patch dead stem N growth from storage (gN/m2/s)
-     real(r8), pointer :: livecrootn_xfer_to_livecrootn_patch       (:)     ! patch live coarse root N growth from storage (gN/m2/s)
-     real(r8), pointer :: deadcrootn_xfer_to_deadcrootn_patch       (:)     ! patch dead coarse root N growth from storage (gN/m2/s)
-
-     ! litterfall fluxes
-     real(r8), pointer :: livestemn_to_litter_patch                 (:)     ! patch livestem N to litter (gN/m2/s)
-     real(r8), pointer :: grainn_to_food_patch                      (:)     ! patch grain N to food for prognostic crop (gN/m2/s)
-     real(r8), pointer :: grainn_to_seed_patch                      (:)     ! patch grain N to seed for prognostic crop (gN/m2/s)
-     real(r8), pointer :: leafn_to_litter_patch                     (:)     ! patch leaf N litterfall (gN/m2/s)
-     real(r8), pointer :: leafn_to_retransn_patch                   (:)     ! patch leaf N to retranslocated N pool (gN/m2/s)
-     real(r8), pointer :: frootn_to_retransn_patch                  (:)     ! patch fine root N to retranslocated N pool (gN/m2/s)
-     real(r8), pointer :: frootn_to_litter_patch                    (:)     ! patch fine root N litterfall (gN/m2/s)
-
-     ! allocation fluxes
-     real(r8), pointer :: retransn_to_npool_patch                   (:)     ! patch deployment of retranslocated N (gN/m2/s)  
-     real(r8), pointer :: free_retransn_to_npool_patch              (:)     ! patch deployment of free retranslocated N (gN/m2/s)           
-     real(r8), pointer :: sminn_to_npool_patch                      (:)     ! patch deployment of soil mineral N uptake (gN/m2/s)
-     real(r8), pointer :: npool_to_grainn_patch                     (:)     ! patch allocation to grain N for prognostic crop (gN/m2/s)
-     real(r8), pointer :: npool_to_grainn_storage_patch             (:)     ! patch allocation to grain N storage for prognostic crop (gN/m2/s)
-     real(r8), pointer :: npool_to_leafn_patch                      (:)     ! patch allocation to leaf N (gN/m2/s)
-     real(r8), pointer :: npool_to_leafn_storage_patch              (:)     ! patch allocation to leaf N storage (gN/m2/s)
-     real(r8), pointer :: npool_to_frootn_patch                     (:)     ! patch allocation to fine root N (gN/m2/s)
-     real(r8), pointer :: npool_to_frootn_storage_patch             (:)     ! patch allocation to fine root N storage (gN/m2/s)
-     real(r8), pointer :: npool_to_livestemn_patch                  (:)     ! patch allocation to live stem N (gN/m2/s)
-     real(r8), pointer :: npool_to_livestemn_storage_patch          (:)     ! patch allocation to live stem N storage (gN/m2/s)
-     real(r8), pointer :: npool_to_deadstemn_patch                  (:)     ! patch allocation to dead stem N (gN/m2/s)
-     real(r8), pointer :: npool_to_deadstemn_storage_patch          (:)     ! patch allocation to dead stem N storage (gN/m2/s)
-     real(r8), pointer :: npool_to_livecrootn_patch                 (:)     ! patch allocation to live coarse root N (gN/m2/s)
-     real(r8), pointer :: npool_to_livecrootn_storage_patch         (:)     ! patch allocation to live coarse root N storage (gN/m2/s)
-     real(r8), pointer :: npool_to_deadcrootn_patch                 (:)     ! patch allocation to dead coarse root N (gN/m2/s)
-     real(r8), pointer :: npool_to_deadcrootn_storage_patch         (:)     ! patch allocation to dead coarse root N storage (gN/m2/s)
-
-     ! annual turnover of storage to transfer pools           
-     real(r8), pointer :: grainn_storage_to_xfer_patch              (:)     ! patch grain N shift storage to transfer for prognostic crop (gN/m2/s)
-     real(r8), pointer :: leafn_storage_to_xfer_patch               (:)     ! patch leaf N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: frootn_storage_to_xfer_patch              (:)     ! patch fine root N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: livestemn_storage_to_xfer_patch           (:)     ! patch live stem N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: deadstemn_storage_to_xfer_patch           (:)     ! patch dead stem N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: livecrootn_storage_to_xfer_patch          (:)     ! patch live coarse root N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: deadcrootn_storage_to_xfer_patch          (:)     ! patch dead coarse root N shift storage to transfer (gN/m2/s)
-     real(r8), pointer :: fert_patch                                (:)     ! patch applied fertilizer (gN/m2/s)
-     real(r8), pointer :: fert_counter_patch                        (:)     ! patch >0 fertilize; <=0 not
-     real(r8), pointer :: soyfixn_patch                             (:)     ! patch soybean fixed N (gN/m2/s)
-
-     ! turnover of livewood to deadwood, with retranslocation 
-     real(r8), pointer :: livestemn_to_deadstemn_patch              (:)     ! patch live stem N turnover (gN/m2/s)
-     real(r8), pointer :: livestemn_to_retransn_patch               (:)     ! patch live stem N to retranslocated N pool (gN/m2/s)
-     real(r8), pointer :: livecrootn_to_deadcrootn_patch            (:)     ! patch live coarse root N turnover (gN/m2/s)
-     real(r8), pointer :: livecrootn_to_retransn_patch              (:)     ! patch live coarse root N to retranslocated N pool (gN/m2/s)
-
-     ! summary (diagnostic) flux variables, not involved in mass balance
-     real(r8), pointer :: ndeploy_patch                             (:)     ! patch total N deployed to growth and storage (gN/m2/s)
-     real(r8), pointer :: wood_harvestn_patch                       (:)     ! patch total N losses to wood product pools (gN/m2/s)
-     real(r8), pointer :: wood_harvestn_col                         (:)     ! col total N losses to wood product pools (gN/m2/s) (p2c)
-
-     ! phenology: litterfall and crop fluxes
-     real(r8), pointer :: phenology_n_to_litr_met_n_col             (:,:)   ! col N fluxes associated with phenology (litterfall and crop) to litter metabolic pool (gN/m3/s)
-     real(r8), pointer :: phenology_n_to_litr_cel_n_col             (:,:)   ! col N fluxes associated with phenology (litterfall and crop) to litter cellulose pool (gN/m3/s)
-     real(r8), pointer :: phenology_n_to_litr_lig_n_col             (:,:)   ! col N fluxes associated with phenology (litterfall and crop) to litter lignin pool (gN/m3/s)
-
-     ! gap mortality fluxes
-     real(r8), pointer :: gap_mortality_n_to_litr_met_n_col         (:,:)   ! col N fluxes associated with gap mortality to litter metabolic pool (gN/m3/s)
-     real(r8), pointer :: gap_mortality_n_to_litr_cel_n_col         (:,:)   ! col N fluxes associated with gap mortality to litter cellulose pool (gN/m3/s)
-     real(r8), pointer :: gap_mortality_n_to_litr_lig_n_col         (:,:)   ! col N fluxes associated with gap mortality to litter lignin pool (gN/m3/s)
-     real(r8), pointer :: gap_mortality_n_to_cwdn_col               (:,:)   ! col N fluxes associated with gap mortality to CWD pool (gN/m3/s)
-
-     ! dynamic landcover fluxes
-     real(r8), pointer :: dwt_seedn_to_leaf_patch                   (:)     ! (gN/m2/s) seed source to patch-level; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_seedn_to_leaf_grc                     (:)     ! (gN/m2/s) dwt_seedn_to_leaf_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_seedn_to_deadstem_patch               (:)     ! (gN/m2/s) seed source to patch-level; although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_seedn_to_deadstem_grc                 (:)     ! (gN/m2/s) dwt_seedn_to_deadstem_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_conv_nflux_patch                      (:)     ! (gN/m2/s) conversion N flux (immediate loss to atm); although this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_conv_nflux_grc                        (:)     ! (gN/m2/s) dwt_conv_nflux_patch summed to the gridcell-level
-     real(r8), pointer :: dwt_wood_productn_gain_patch              (:)     ! patch (gN/m2/s) addition to wood product pools from landcover change; even though this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_crop_productn_gain_patch              (:)     ! patch (gN/m2/s) addition to crop product pool from landcover change; even though this is a patch-level flux, it is expressed per unit GRIDCELL area
-     real(r8), pointer :: dwt_frootn_to_litr_met_n_col              (:,:)   ! col (gN/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_frootn_to_litr_cel_n_col              (:,:)   ! col (gN/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_frootn_to_litr_lig_n_col              (:,:)   ! col (gN/m3/s) fine root to litter due to landcover change
-     real(r8), pointer :: dwt_livecrootn_to_cwdn_col                (:,:)   ! col (gN/m3/s) live coarse root to CWD due to landcover change
-     real(r8), pointer :: dwt_deadcrootn_to_cwdn_col                (:,:)   ! col (gN/m3/s) dead coarse root to CWD due to landcover change
-
-     ! crop fluxes
-     real(r8), pointer :: crop_seedn_to_leaf_patch                  (:)     ! patch (gN/m2/s) seed source to leaf, for crops
-     
-     ! Misc
-     real(r8), pointer :: plant_ndemand_patch                       (:)     ! N flux required to support initial GPP (gN/m2/s)
-     real(r8), pointer :: avail_retransn_patch                      (:)     ! N flux available from retranslocation pool (gN/m2/s)
-     real(r8), pointer :: plant_nalloc_patch                        (:)     ! total allocated N flux (gN/m2/s)
-     real(r8), pointer :: plant_ndemand_retrans_patch               (:)     ! The N demand pool generated for FUN2.0; mainly used for deciduous trees (gN/m2/s)
-     real(r8), pointer :: plant_ndemand_season_patch                (:)     ! The N demand pool for seasonal deciduous (gN/m2/s)
-     real(r8), pointer :: plant_ndemand_stress_patch                (:)     ! The N demand pool for stress deciduous   (gN/m2/s)
-     real(r8), pointer :: Nactive_patch                             (:)     ! N acquired by mycorrhizal uptake  (gN/m2/s)
-     real(r8), pointer :: Nnonmyc_patch                             (:)     ! N acquired by non-myc uptake      (gN/m2/s)
-     real(r8), pointer :: Nam_patch                                 (:)     ! N acquired by AM plant            (gN/m2/s)
-     real(r8), pointer :: Necm_patch                                (:)     ! N acquired by ECM plant           (gN/m2/s)
-     real(r8), pointer :: Nactive_no3_patch                         (:)     ! N acquired by mycorrhizal uptake  (gN/m2/s)
-     real(r8), pointer :: Nactive_nh4_patch                         (:)     ! N acquired by mycorrhizal uptake  (gN/m2/s)
-     real(r8), pointer :: Nnonmyc_no3_patch                         (:)     ! N acquired by non-myc             (gN/m2/s)
-     real(r8), pointer :: Nnonmyc_nh4_patch                         (:)     ! N acquired by non-myc             (gN/m2/s)
-     real(r8), pointer :: Nam_no3_patch                             (:)     ! N acquired by AM plant            (gN/m2/s)
-     real(r8), pointer :: Nam_nh4_patch                             (:)     ! N acquired by AM plant            (gN/m2/s)
-     real(r8), pointer :: Necm_no3_patch                            (:)     ! N acquired by ECM plant           (gN/m2/s)
-     real(r8), pointer :: Necm_nh4_patch                            (:)     ! N acquired by ECM plant           (gN/m2/s)
-     real(r8), pointer :: Nfix_patch                                (:)     ! N acquired by Symbiotic BNF       (gN/m2/s)
-     real(r8), pointer :: Npassive_patch                            (:)     ! N acquired by passive uptake      (gN/m2/s)
-     real(r8), pointer :: Nretrans_patch                            (:)     ! N acquired by retranslocation     (gN/m2/s)
-     real(r8), pointer :: Nretrans_org_patch                        (:)     ! N acquired by retranslocation     (gN/m2/s)
-     real(r8), pointer :: Nretrans_season_patch                     (:)     ! N acquired by retranslocation     (gN/m2/s)
-     real(r8), pointer :: Nretrans_stress_patch                     (:)     ! N acquired by retranslocation     (gN/m2/s)
-     real(r8), pointer :: Nuptake_patch                             (:)     ! Total N uptake of FUN             (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_patch                  (:)     ! Total soil N uptake of FUN        (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_vr_patch               (:,:)   ! Total layer soil N uptake of FUN  (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_no3_vr_patch           (:,:)   ! Total layer no3 uptake of FUN     (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_nh4_vr_patch           (:,:)   ! Total layer nh4 uptake of FUN     (gN/m2/s)
-     real(r8), pointer :: cost_nfix_patch                           (:)     ! Average cost of fixation          (gN/m2/s)
-     real(r8), pointer :: cost_nactive_patch                        (:)     ! Average cost of active uptake     (gN/m2/s)
-     real(r8), pointer :: cost_nretrans_patch                       (:)     ! Average cost of retranslocation   (gN/m2/s)
-     real(r8), pointer :: nuptake_npp_fraction_patch                (:)    ! frac of npp spent on N acquisition   (gN/m2/s)
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: Restart
-     procedure , public  :: SetValues
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory
-     procedure , private :: InitCold
-
-  end type cnveg_nitrogenflux_type
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(cnveg_nitrogenflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate (bounds)
-    call this%InitHistory (bounds)
-    call this%InitCold (bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize patch nitrogen flux
-    !
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenflux_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%m_leafn_to_litter_patch                   (begp:endp)) ; this%m_leafn_to_litter_patch                   (:) = nan
-    allocate(this%m_frootn_to_litter_patch                  (begp:endp)) ; this%m_frootn_to_litter_patch                  (:) = nan
-    allocate(this%m_leafn_storage_to_litter_patch           (begp:endp)) ; this%m_leafn_storage_to_litter_patch           (:) = nan
-    allocate(this%m_frootn_storage_to_litter_patch          (begp:endp)) ; this%m_frootn_storage_to_litter_patch          (:) = nan
-    allocate(this%m_livestemn_storage_to_litter_patch       (begp:endp)) ; this%m_livestemn_storage_to_litter_patch       (:) = nan
-    allocate(this%m_deadstemn_storage_to_litter_patch       (begp:endp)) ; this%m_deadstemn_storage_to_litter_patch       (:) = nan
-    allocate(this%m_livecrootn_storage_to_litter_patch      (begp:endp)) ; this%m_livecrootn_storage_to_litter_patch      (:) = nan
-    allocate(this%m_deadcrootn_storage_to_litter_patch      (begp:endp)) ; this%m_deadcrootn_storage_to_litter_patch      (:) = nan
-    allocate(this%m_leafn_xfer_to_litter_patch              (begp:endp)) ; this%m_leafn_xfer_to_litter_patch              (:) = nan
-    allocate(this%m_frootn_xfer_to_litter_patch             (begp:endp)) ; this%m_frootn_xfer_to_litter_patch             (:) = nan
-    allocate(this%m_livestemn_xfer_to_litter_patch          (begp:endp)) ; this%m_livestemn_xfer_to_litter_patch          (:) = nan
-    allocate(this%m_deadstemn_xfer_to_litter_patch          (begp:endp)) ; this%m_deadstemn_xfer_to_litter_patch          (:) = nan
-    allocate(this%m_livecrootn_xfer_to_litter_patch         (begp:endp)) ; this%m_livecrootn_xfer_to_litter_patch         (:) = nan
-    allocate(this%m_deadcrootn_xfer_to_litter_patch         (begp:endp)) ; this%m_deadcrootn_xfer_to_litter_patch         (:) = nan
-    allocate(this%m_livestemn_to_litter_patch               (begp:endp)) ; this%m_livestemn_to_litter_patch               (:) = nan
-    allocate(this%m_deadstemn_to_litter_patch               (begp:endp)) ; this%m_deadstemn_to_litter_patch               (:) = nan
-    allocate(this%m_livecrootn_to_litter_patch              (begp:endp)) ; this%m_livecrootn_to_litter_patch              (:) = nan
-    allocate(this%m_deadcrootn_to_litter_patch              (begp:endp)) ; this%m_deadcrootn_to_litter_patch              (:) = nan
-    allocate(this%m_retransn_to_litter_patch                (begp:endp)) ; this%m_retransn_to_litter_patch                (:) = nan
-    allocate(this%hrv_leafn_to_litter_patch                 (begp:endp)) ; this%hrv_leafn_to_litter_patch                 (:) = nan
-    allocate(this%hrv_frootn_to_litter_patch                (begp:endp)) ; this%hrv_frootn_to_litter_patch                (:) = nan
-    allocate(this%hrv_leafn_storage_to_litter_patch         (begp:endp)) ; this%hrv_leafn_storage_to_litter_patch         (:) = nan
-    allocate(this%hrv_frootn_storage_to_litter_patch        (begp:endp)) ; this%hrv_frootn_storage_to_litter_patch        (:) = nan
-    allocate(this%hrv_livestemn_storage_to_litter_patch     (begp:endp)) ; this%hrv_livestemn_storage_to_litter_patch     (:) = nan
-    allocate(this%hrv_deadstemn_storage_to_litter_patch     (begp:endp)) ; this%hrv_deadstemn_storage_to_litter_patch     (:) = nan
-    allocate(this%hrv_livecrootn_storage_to_litter_patch    (begp:endp)) ; this%hrv_livecrootn_storage_to_litter_patch    (:) = nan
-    allocate(this%hrv_deadcrootn_storage_to_litter_patch    (begp:endp)) ; this%hrv_deadcrootn_storage_to_litter_patch    (:) = nan
-    allocate(this%hrv_leafn_xfer_to_litter_patch            (begp:endp)) ; this%hrv_leafn_xfer_to_litter_patch            (:) = nan
-    allocate(this%hrv_frootn_xfer_to_litter_patch           (begp:endp)) ; this%hrv_frootn_xfer_to_litter_patch           (:) = nan
-    allocate(this%hrv_livestemn_xfer_to_litter_patch        (begp:endp)) ; this%hrv_livestemn_xfer_to_litter_patch        (:) = nan
-    allocate(this%hrv_deadstemn_xfer_to_litter_patch        (begp:endp)) ; this%hrv_deadstemn_xfer_to_litter_patch        (:) = nan
-    allocate(this%hrv_livecrootn_xfer_to_litter_patch       (begp:endp)) ; this%hrv_livecrootn_xfer_to_litter_patch       (:) = nan
-    allocate(this%hrv_deadcrootn_xfer_to_litter_patch       (begp:endp)) ; this%hrv_deadcrootn_xfer_to_litter_patch       (:) = nan
-    allocate(this%hrv_livestemn_to_litter_patch             (begp:endp)) ; this%hrv_livestemn_to_litter_patch             (:) = nan
-    allocate(this%hrv_livecrootn_to_litter_patch            (begp:endp)) ; this%hrv_livecrootn_to_litter_patch            (:) = nan
-    allocate(this%hrv_deadcrootn_to_litter_patch            (begp:endp)) ; this%hrv_deadcrootn_to_litter_patch            (:) = nan
-    allocate(this%hrv_retransn_to_litter_patch              (begp:endp)) ; this%hrv_retransn_to_litter_patch              (:) = nan
-
-    allocate(this%m_leafn_to_fire_patch                     (begp:endp)) ; this%m_leafn_to_fire_patch                     (:) = nan
-    allocate(this%m_leafn_storage_to_fire_patch             (begp:endp)) ; this%m_leafn_storage_to_fire_patch             (:) = nan
-    allocate(this%m_leafn_xfer_to_fire_patch                (begp:endp)) ; this%m_leafn_xfer_to_fire_patch                (:) = nan
-    allocate(this%m_livestemn_to_fire_patch                 (begp:endp)) ; this%m_livestemn_to_fire_patch                 (:) = nan
-    allocate(this%m_livestemn_storage_to_fire_patch         (begp:endp)) ; this%m_livestemn_storage_to_fire_patch         (:) = nan
-    allocate(this%m_livestemn_xfer_to_fire_patch            (begp:endp)) ; this%m_livestemn_xfer_to_fire_patch            (:) = nan
-    allocate(this%m_deadstemn_to_fire_patch                 (begp:endp)) ; this%m_deadstemn_to_fire_patch                 (:) = nan
-    allocate(this%m_deadstemn_storage_to_fire_patch         (begp:endp)) ; this%m_deadstemn_storage_to_fire_patch         (:) = nan
-    allocate(this%m_deadstemn_xfer_to_fire_patch            (begp:endp)) ; this%m_deadstemn_xfer_to_fire_patch            (:) = nan
-    allocate(this%m_frootn_to_fire_patch                    (begp:endp)) ; this%m_frootn_to_fire_patch                    (:) = nan
-    allocate(this%m_frootn_storage_to_fire_patch            (begp:endp)) ; this%m_frootn_storage_to_fire_patch            (:) = nan
-    allocate(this%m_frootn_xfer_to_fire_patch               (begp:endp)) ; this%m_frootn_xfer_to_fire_patch               (:) = nan
-    allocate(this%m_livecrootn_to_fire_patch                (begp:endp)) ;     
-    allocate(this%m_livecrootn_storage_to_fire_patch        (begp:endp)) ; this%m_livecrootn_storage_to_fire_patch        (:) = nan
-    allocate(this%m_livecrootn_xfer_to_fire_patch           (begp:endp)) ; this%m_livecrootn_xfer_to_fire_patch           (:) = nan
-    allocate(this%m_deadcrootn_to_fire_patch                (begp:endp)) ; this%m_deadcrootn_to_fire_patch                (:) = nan
-    allocate(this%m_deadcrootn_storage_to_fire_patch        (begp:endp)) ; this%m_deadcrootn_storage_to_fire_patch        (:) = nan
-    allocate(this%m_deadcrootn_xfer_to_fire_patch           (begp:endp)) ; this%m_deadcrootn_xfer_to_fire_patch           (:) = nan
-    allocate(this%m_retransn_to_fire_patch                  (begp:endp)) ; this%m_retransn_to_fire_patch                  (:) = nan
-
-    allocate(this%m_leafn_to_litter_fire_patch              (begp:endp)) ; this%m_leafn_to_litter_fire_patch              (:) = nan
-    allocate(this%m_leafn_storage_to_litter_fire_patch      (begp:endp)) ; this%m_leafn_storage_to_litter_fire_patch      (:) = nan
-    allocate(this%m_leafn_xfer_to_litter_fire_patch         (begp:endp)) ; this%m_leafn_xfer_to_litter_fire_patch         (:) = nan
-    allocate(this%m_livestemn_to_litter_fire_patch          (begp:endp)) ; this%m_livestemn_to_litter_fire_patch          (:) = nan
-    allocate(this%m_livestemn_storage_to_litter_fire_patch  (begp:endp)) ; this%m_livestemn_storage_to_litter_fire_patch  (:) = nan
-    allocate(this%m_livestemn_xfer_to_litter_fire_patch     (begp:endp)) ; this%m_livestemn_xfer_to_litter_fire_patch     (:) = nan
-    allocate(this%m_livestemn_to_deadstemn_fire_patch       (begp:endp)) ; this%m_livestemn_to_deadstemn_fire_patch       (:) = nan
-    allocate(this%m_deadstemn_to_litter_fire_patch          (begp:endp)) ; this%m_deadstemn_to_litter_fire_patch          (:) = nan
-    allocate(this%m_deadstemn_storage_to_litter_fire_patch  (begp:endp)) ; this%m_deadstemn_storage_to_litter_fire_patch  (:) = nan
-    allocate(this%m_deadstemn_xfer_to_litter_fire_patch     (begp:endp)) ; this%m_deadstemn_xfer_to_litter_fire_patch     (:) = nan
-    allocate(this%m_frootn_to_litter_fire_patch             (begp:endp)) ; this%m_frootn_to_litter_fire_patch             (:) = nan
-    allocate(this%m_frootn_storage_to_litter_fire_patch     (begp:endp)) ; this%m_frootn_storage_to_litter_fire_patch     (:) = nan
-    allocate(this%m_frootn_xfer_to_litter_fire_patch        (begp:endp)) ; this%m_frootn_xfer_to_litter_fire_patch        (:) = nan
-    allocate(this%m_livecrootn_to_litter_fire_patch         (begp:endp)) ; this%m_livecrootn_to_litter_fire_patch         (:) = nan
-    allocate(this%m_livecrootn_storage_to_litter_fire_patch (begp:endp)) ; this%m_livecrootn_storage_to_litter_fire_patch (:) = nan
-    allocate(this%m_livecrootn_xfer_to_litter_fire_patch    (begp:endp)) ; this%m_livecrootn_xfer_to_litter_fire_patch    (:) = nan
-    allocate(this%m_livecrootn_to_deadcrootn_fire_patch     (begp:endp)) ; this%m_livecrootn_to_deadcrootn_fire_patch     (:) = nan
-    allocate(this%m_deadcrootn_to_litter_fire_patch         (begp:endp)) ; this%m_deadcrootn_to_litter_fire_patch         (:) = nan
-    allocate(this%m_deadcrootn_storage_to_litter_fire_patch (begp:endp)) ; this%m_deadcrootn_storage_to_litter_fire_patch (:) = nan
-    allocate(this%m_deadcrootn_xfer_to_litter_fire_patch    (begp:endp)) ; this%m_deadcrootn_xfer_to_litter_fire_patch    (:) = nan
-    allocate(this%m_retransn_to_litter_fire_patch           (begp:endp)) ; this%m_retransn_to_litter_fire_patch           (:) = nan
-
-    allocate(this%leafn_xfer_to_leafn_patch                 (begp:endp)) ; this%leafn_xfer_to_leafn_patch                 (:) = nan
-    allocate(this%frootn_xfer_to_frootn_patch               (begp:endp)) ; this%frootn_xfer_to_frootn_patch               (:) = nan
-    allocate(this%livestemn_xfer_to_livestemn_patch         (begp:endp)) ; this%livestemn_xfer_to_livestemn_patch         (:) = nan
-    allocate(this%deadstemn_xfer_to_deadstemn_patch         (begp:endp)) ; this%deadstemn_xfer_to_deadstemn_patch         (:) = nan
-    allocate(this%livecrootn_xfer_to_livecrootn_patch       (begp:endp)) ; this%livecrootn_xfer_to_livecrootn_patch       (:) = nan
-    allocate(this%deadcrootn_xfer_to_deadcrootn_patch       (begp:endp)) ; this%deadcrootn_xfer_to_deadcrootn_patch       (:) = nan
-    allocate(this%leafn_to_litter_patch                     (begp:endp)) ; this%leafn_to_litter_patch                     (:) = nan
-    allocate(this%leafn_to_retransn_patch                   (begp:endp)) ; this%leafn_to_retransn_patch                   (:) = nan
-    allocate(this%frootn_to_retransn_patch                  (begp:endp)) ; this%frootn_to_retransn_patch                  (:) = nan
-    allocate(this%frootn_to_litter_patch                    (begp:endp)) ; this%frootn_to_litter_patch                    (:) = nan
-    allocate(this%retransn_to_npool_patch                   (begp:endp)) ; this%retransn_to_npool_patch                   (:) = nan
-    allocate(this%free_retransn_to_npool_patch              (begp:endp)) ; this%free_retransn_to_npool_patch              (:) = nan
-    allocate(this%sminn_to_npool_patch                      (begp:endp)) ; this%sminn_to_npool_patch                      (:) = nan
-
-    allocate(this%npool_to_leafn_patch                      (begp:endp)) ; this%npool_to_leafn_patch                      (:) = nan
-    allocate(this%npool_to_leafn_storage_patch              (begp:endp)) ; this%npool_to_leafn_storage_patch              (:) = nan
-    allocate(this%npool_to_frootn_patch                     (begp:endp)) ; this%npool_to_frootn_patch                     (:) = nan
-    allocate(this%npool_to_frootn_storage_patch             (begp:endp)) ; this%npool_to_frootn_storage_patch             (:) = nan
-    allocate(this%npool_to_livestemn_patch                  (begp:endp)) ; this%npool_to_livestemn_patch                  (:) = nan
-    allocate(this%npool_to_livestemn_storage_patch          (begp:endp)) ; this%npool_to_livestemn_storage_patch          (:) = nan
-    allocate(this%npool_to_deadstemn_patch                  (begp:endp)) ; this%npool_to_deadstemn_patch                  (:) = nan
-    allocate(this%npool_to_deadstemn_storage_patch          (begp:endp)) ; this%npool_to_deadstemn_storage_patch          (:) = nan
-    allocate(this%npool_to_livecrootn_patch                 (begp:endp)) ; this%npool_to_livecrootn_patch                 (:) = nan
-    allocate(this%npool_to_livecrootn_storage_patch         (begp:endp)) ; this%npool_to_livecrootn_storage_patch         (:) = nan
-    allocate(this%npool_to_deadcrootn_patch                 (begp:endp)) ; this%npool_to_deadcrootn_patch                 (:) = nan
-    allocate(this%npool_to_deadcrootn_storage_patch         (begp:endp)) ; this%npool_to_deadcrootn_storage_patch         (:) = nan
-    allocate(this%leafn_storage_to_xfer_patch               (begp:endp)) ; this%leafn_storage_to_xfer_patch               (:) = nan
-    allocate(this%frootn_storage_to_xfer_patch              (begp:endp)) ; this%frootn_storage_to_xfer_patch              (:) = nan
-    allocate(this%livestemn_storage_to_xfer_patch           (begp:endp)) ; this%livestemn_storage_to_xfer_patch           (:) = nan
-    allocate(this%deadstemn_storage_to_xfer_patch           (begp:endp)) ; this%deadstemn_storage_to_xfer_patch           (:) = nan
-    allocate(this%livecrootn_storage_to_xfer_patch          (begp:endp)) ; this%livecrootn_storage_to_xfer_patch          (:) = nan
-    allocate(this%deadcrootn_storage_to_xfer_patch          (begp:endp)) ; this%deadcrootn_storage_to_xfer_patch          (:) = nan
-    allocate(this%livestemn_to_deadstemn_patch              (begp:endp)) ; this%livestemn_to_deadstemn_patch              (:) = nan
-    allocate(this%livestemn_to_retransn_patch               (begp:endp)) ; this%livestemn_to_retransn_patch               (:) = nan
-    allocate(this%livecrootn_to_deadcrootn_patch            (begp:endp)) ; this%livecrootn_to_deadcrootn_patch            (:) = nan
-    allocate(this%livecrootn_to_retransn_patch              (begp:endp)) ; this%livecrootn_to_retransn_patch              (:) = nan
-    allocate(this%ndeploy_patch                             (begp:endp)) ; this%ndeploy_patch                             (:) = nan
-    allocate(this%wood_harvestn_patch                       (begp:endp)) ; this%wood_harvestn_patch                       (:) = nan
-    allocate(this%fire_nloss_patch                          (begp:endp)) ; this%fire_nloss_patch                          (:) = nan
-    allocate(this%npool_to_grainn_patch                     (begp:endp)) ; this%npool_to_grainn_patch                     (:) = nan
-    allocate(this%npool_to_grainn_storage_patch             (begp:endp)) ; this%npool_to_grainn_storage_patch             (:) = nan
-    allocate(this%livestemn_to_litter_patch                 (begp:endp)) ; this%livestemn_to_litter_patch                 (:) = nan
-    allocate(this%grainn_to_food_patch                      (begp:endp)) ; this%grainn_to_food_patch                      (:) = nan
-    allocate(this%grainn_to_seed_patch                      (begp:endp)) ; this%grainn_to_seed_patch                      (:) = nan
-    allocate(this%grainn_xfer_to_grainn_patch               (begp:endp)) ; this%grainn_xfer_to_grainn_patch               (:) = nan
-    allocate(this%grainn_storage_to_xfer_patch              (begp:endp)) ; this%grainn_storage_to_xfer_patch              (:) = nan
-    allocate(this%fert_patch                                (begp:endp)) ; this%fert_patch                                (:) = nan
-    allocate(this%fert_counter_patch                        (begp:endp)) ; this%fert_counter_patch                        (:) = nan
-    allocate(this%soyfixn_patch                             (begp:endp)) ; this%soyfixn_patch                             (:) = nan
-
-    allocate(this%grainn_to_cropprodn_patch                 (begp:endp)) ; this%grainn_to_cropprodn_patch                 (:) = nan
-    allocate(this%grainn_to_cropprodn_col                   (begc:endc)) ; this%grainn_to_cropprodn_col                   (:) = nan
-
-    allocate(this%fire_nloss_col                            (begc:endc)) ; this%fire_nloss_col                            (:) = nan
-    allocate(this%fire_nloss_p2c_col                        (begc:endc)) ; this%fire_nloss_p2c_col                        (:) = nan
-
-    allocate(this%m_n_to_litr_met_fire_col     (begc:endc,1:nlevdecomp_full)) ; this%m_n_to_litr_met_fire_col     (:,:) = nan
-    allocate(this%m_n_to_litr_cel_fire_col     (begc:endc,1:nlevdecomp_full)) ; this%m_n_to_litr_cel_fire_col     (:,:) = nan
-    allocate(this%m_n_to_litr_lig_fire_col     (begc:endc,1:nlevdecomp_full)) ; this%m_n_to_litr_lig_fire_col     (:,:) = nan
-
-    allocate(this%dwt_seedn_to_leaf_patch      (begp:endp))                   ; this%dwt_seedn_to_leaf_patch      (:)   = nan
-    allocate(this%dwt_seedn_to_leaf_grc        (begg:endg))                   ; this%dwt_seedn_to_leaf_grc        (:)   = nan
-    allocate(this%dwt_seedn_to_deadstem_patch  (begp:endp))                   ; this%dwt_seedn_to_deadstem_patch  (:)   = nan
-    allocate(this%dwt_seedn_to_deadstem_grc    (begg:endg))                   ; this%dwt_seedn_to_deadstem_grc    (:)   = nan
-    allocate(this%dwt_conv_nflux_patch         (begp:endp))                   ; this%dwt_conv_nflux_patch         (:)   = nan
-    allocate(this%dwt_conv_nflux_grc           (begg:endg))                   ; this%dwt_conv_nflux_grc           (:)   = nan
-    allocate(this%dwt_wood_productn_gain_patch (begp:endp))                   ; this%dwt_wood_productn_gain_patch (:)   = nan
-    allocate(this%dwt_crop_productn_gain_patch (begp:endp))                   ; this%dwt_crop_productn_gain_patch (:)   = nan
-    allocate(this%wood_harvestn_col            (begc:endc))                   ; this%wood_harvestn_col            (:)   = nan
-
-    allocate(this%dwt_frootn_to_litr_met_n_col (begc:endc,1:nlevdecomp_full)) ; this%dwt_frootn_to_litr_met_n_col (:,:) = nan
-    allocate(this%dwt_frootn_to_litr_cel_n_col (begc:endc,1:nlevdecomp_full)) ; this%dwt_frootn_to_litr_cel_n_col (:,:) = nan
-    allocate(this%dwt_frootn_to_litr_lig_n_col (begc:endc,1:nlevdecomp_full)) ; this%dwt_frootn_to_litr_lig_n_col (:,:) = nan
-    allocate(this%dwt_livecrootn_to_cwdn_col   (begc:endc,1:nlevdecomp_full)) ; this%dwt_livecrootn_to_cwdn_col   (:,:) = nan
-    allocate(this%dwt_deadcrootn_to_cwdn_col   (begc:endc,1:nlevdecomp_full)) ; this%dwt_deadcrootn_to_cwdn_col   (:,:) = nan
-
-    allocate(this%crop_seedn_to_leaf_patch     (begp:endp))                   ; this%crop_seedn_to_leaf_patch     (:)   = nan
-
-    allocate(this%m_decomp_npools_to_fire_vr_col    (begc:endc,1:nlevdecomp_full,1:ndecomp_pools))
-    allocate(this%m_decomp_npools_to_fire_col       (begc:endc,1:ndecomp_pools                  ))
-
-    this%m_decomp_npools_to_fire_vr_col   (:,:,:) = nan
-    this%m_decomp_npools_to_fire_col      (:,:)   = nan
-
-    allocate(this%phenology_n_to_litr_met_n_col     (begc:endc, 1:nlevdecomp_full))
-    allocate(this%phenology_n_to_litr_cel_n_col     (begc:endc, 1:nlevdecomp_full))
-    allocate(this%phenology_n_to_litr_lig_n_col     (begc:endc, 1:nlevdecomp_full))
-    allocate(this%gap_mortality_n_to_litr_met_n_col (begc:endc, 1:nlevdecomp_full))
-    allocate(this%gap_mortality_n_to_litr_cel_n_col (begc:endc, 1:nlevdecomp_full))
-    allocate(this%gap_mortality_n_to_litr_lig_n_col (begc:endc, 1:nlevdecomp_full))
-    allocate(this%gap_mortality_n_to_cwdn_col       (begc:endc, 1:nlevdecomp_full))
-    allocate(this%fire_mortality_n_to_cwdn_col      (begc:endc, 1:nlevdecomp_full))
-    allocate(this%harvest_n_to_litr_met_n_col       (begc:endc, 1:nlevdecomp_full))
-    allocate(this%harvest_n_to_litr_cel_n_col       (begc:endc, 1:nlevdecomp_full))
-    allocate(this%harvest_n_to_litr_lig_n_col       (begc:endc, 1:nlevdecomp_full))
-    allocate(this%harvest_n_to_cwdn_col             (begc:endc, 1:nlevdecomp_full))
-
-    this%phenology_n_to_litr_met_n_col     (:,:) = nan
-    this%phenology_n_to_litr_cel_n_col     (:,:) = nan
-    this%phenology_n_to_litr_lig_n_col     (:,:) = nan
-    this%gap_mortality_n_to_litr_met_n_col (:,:) = nan
-    this%gap_mortality_n_to_litr_cel_n_col (:,:) = nan
-    this%gap_mortality_n_to_litr_lig_n_col (:,:) = nan
-    this%gap_mortality_n_to_cwdn_col       (:,:) = nan
-    this%fire_mortality_n_to_cwdn_col      (:,:) = nan
-    this%harvest_n_to_litr_met_n_col       (:,:) = nan
-    this%harvest_n_to_litr_cel_n_col       (:,:) = nan
-    this%harvest_n_to_litr_lig_n_col       (:,:) = nan
-    this%harvest_n_to_cwdn_col             (:,:) = nan
-
-    allocate(this%plant_ndemand_patch         (begp:endp)) ;    this%plant_ndemand_patch         (:) = nan
-    allocate(this%avail_retransn_patch        (begp:endp)) ;    this%avail_retransn_patch        (:) = nan
-    allocate(this%plant_nalloc_patch          (begp:endp)) ;    this%plant_nalloc_patch          (:) = nan
-
-    allocate(this%plant_ndemand_retrans_patch (begp:endp)) ;    this%plant_ndemand_retrans_patch (:) = nan
-    allocate(this%plant_ndemand_season_patch  (begp:endp)) ;    this%plant_ndemand_season_patch  (:) = nan
-    allocate(this%plant_ndemand_stress_patch  (begp:endp)) ;    this%plant_ndemand_stress_patch  (:) = nan
-    allocate(this%Nactive_patch               (begp:endp)) ;    this%Nactive_patch               (:) = nan 
-    allocate(this%Nnonmyc_patch               (begp:endp)) ;    this%Nnonmyc_patch               (:) = nan
-    allocate(this%Nam_patch                   (begp:endp)) ;    this%Nam_patch                   (:) = nan
-    allocate(this%Necm_patch                  (begp:endp)) ;    this%Necm_patch                  (:) = nan
-    allocate(this%Nactive_no3_patch           (begp:endp)) ;    this%Nactive_no3_patch           (:) = nan
-    allocate(this%Nactive_nh4_patch           (begp:endp)) ;    this%Nactive_nh4_patch           (:) = nan
-    allocate(this%Nnonmyc_no3_patch           (begp:endp)) ;    this%Nnonmyc_no3_patch           (:) = nan
-    allocate(this%Nnonmyc_nh4_patch           (begp:endp)) ;    this%Nnonmyc_nh4_patch           (:) = nan
-    allocate(this%Nam_no3_patch               (begp:endp)) ;    this%Nam_no3_patch               (:) = nan
-    allocate(this%Nam_nh4_patch               (begp:endp)) ;    this%Nam_nh4_patch               (:) = nan
-    allocate(this%Necm_no3_patch              (begp:endp)) ;    this%Necm_no3_patch              (:) = nan
-    allocate(this%Necm_nh4_patch              (begp:endp)) ;    this%Necm_nh4_patch              (:) = nan
-    allocate(this%Npassive_patch              (begp:endp)) ;    this%Npassive_patch              (:) = nan
-    allocate(this%Nfix_patch                  (begp:endp)) ;    this%Nfix_patch                  (:) = nan
-    allocate(this%Nretrans_patch              (begp:endp)) ;    this%Nretrans_patch              (:) = nan
-    allocate(this%Nretrans_org_patch          (begp:endp)) ;    this%Nretrans_org_patch          (:) = nan
-    allocate(this%Nretrans_season_patch       (begp:endp)) ;    this%Nretrans_season_patch       (:) = nan
-    allocate(this%Nretrans_stress_patch       (begp:endp)) ;    this%Nretrans_stress_patch       (:) = nan 
-    allocate(this%Nuptake_patch               (begp:endp)) ;    this%Nuptake_patch               (:) = nan
-    allocate(this%sminn_to_plant_fun_patch    (begp:endp)) ;    this%sminn_to_plant_fun_patch    (:) = nan
-    allocate(this%sminn_to_plant_fun_vr_patch (begp:endp,1:nlevdecomp_full)) 
-    this%sminn_to_plant_fun_vr_patch          (:,:) = nan
-    allocate(this%sminn_to_plant_fun_no3_vr_patch (begp:endp,1:nlevdecomp_full))  
-    this%sminn_to_plant_fun_no3_vr_patch      (:,:) = nan
-    allocate(this%sminn_to_plant_fun_nh4_vr_patch (begp:endp,1:nlevdecomp_full))  
-    this%sminn_to_plant_fun_nh4_vr_patch      (:,:) = nan
-    allocate(this%cost_nfix_patch              (begp:endp)) ;    this%cost_nfix_patch            (:) = nan
-    allocate(this%cost_nactive_patch           (begp:endp)) ;    this%cost_nactive_patch         (:) = nan
-    allocate(this%cost_nretrans_patch          (begp:endp)) ;    this%cost_nretrans_patch        (:) = nan
-    allocate(this%nuptake_npp_fraction_patch   (begp:endp)) ;    this%nuptake_npp_fraction_patch            (:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar     , only : nlevsno, nlevgrnd
-    use histFileMod    , only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp
-    !
-    ! !ARGUMENTS:
-    class(cnveg_nitrogenflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer        :: k,l
-    integer        :: begp, endp
-    integer        :: begc, endc
-    integer        :: begg, endg
-    character(10)  :: active
-    character(24)  :: fieldname
-    character(100) :: longname
-    character(8)   :: vr_suffix
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    ! add suffix if number of soil decomposition depths is greater than 1
-    if (nlevdecomp > 1) then
-       vr_suffix = "_vr"
-    else 
-       vr_suffix = ""
-    endif
-
-    this%m_leafn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N mortality', &
-         ptr_patch=this%m_leafn_to_litter_patch, default='inactive')
-
-    this%m_frootn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N mortality', &
-         ptr_patch=this%m_frootn_to_litter_patch, default='inactive')
-
-    this%m_leafn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N storage mortality', &
-         ptr_patch=this%m_leafn_storage_to_litter_patch, default='inactive')
-
-    this%m_frootn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N storage mortality', &
-         ptr_patch=this%m_frootn_storage_to_litter_patch, default='inactive')
-
-    this%m_livestemn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N storage mortality', &
-         ptr_patch=this%m_livestemn_storage_to_litter_patch, default='inactive')
-
-    this%m_deadstemn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N storage mortality', &
-         ptr_patch=this%m_deadstemn_storage_to_litter_patch, default='inactive')
-
-    this%m_livecrootn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N storage mortality', &
-         ptr_patch=this%m_livecrootn_storage_to_litter_patch, default='inactive')
-
-    this%m_deadcrootn_storage_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_STORAGE_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N storage mortality', &
-         ptr_patch=this%m_deadcrootn_storage_to_litter_patch, default='inactive')
-
-    this%m_leafn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N transfer mortality', &
-         ptr_patch=this%m_leafn_xfer_to_litter_patch, default='inactive')
-
-    this%m_frootn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N transfer mortality', &
-         ptr_patch=this%m_frootn_xfer_to_litter_patch, default='inactive')
-
-    this%m_livestemn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N transfer mortality', &
-         ptr_patch=this%m_livestemn_xfer_to_litter_patch, default='inactive')
-
-    this%m_deadstemn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N transfer mortality', &
-         ptr_patch=this%m_deadstemn_xfer_to_litter_patch, default='inactive')
-
-    this%m_livecrootn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N transfer mortality', &
-         ptr_patch=this%m_livecrootn_xfer_to_litter_patch, default='inactive')
-
-    this%m_deadcrootn_xfer_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_XFER_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N transfer mortality', &
-         ptr_patch=this%m_deadcrootn_xfer_to_litter_patch, default='inactive')
-
-    this%m_livestemn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N mortality', &
-         ptr_patch=this%m_livestemn_to_litter_patch, default='inactive')
-
-    this%m_deadstemn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N mortality', &
-         ptr_patch=this%m_deadstemn_to_litter_patch, default='inactive')
-
-    this%m_livecrootn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N mortality', &
-         ptr_patch=this%m_livecrootn_to_litter_patch, default='inactive')
-
-    this%m_deadcrootn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N mortality', &
-         ptr_patch=this%m_deadcrootn_to_litter_patch, default='inactive')
-
-    this%m_retransn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_RETRANSN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='retranslocated N pool mortality', &
-         ptr_patch=this%m_retransn_to_litter_patch, default='inactive')
-
-    this%m_leafn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N fire loss', &
-         ptr_patch=this%m_leafn_to_fire_patch, default='inactive')
-
-    this%m_frootn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N fire loss ', &
-         ptr_patch=this%m_frootn_to_fire_patch, default='inactive')
-
-    this%m_leafn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N storage fire loss', &
-         ptr_patch=this%m_leafn_storage_to_fire_patch, default='inactive')
-
-    this%m_frootn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N storage fire loss', &
-         ptr_patch=this%m_frootn_storage_to_fire_patch, default='inactive')
-
-    this%m_livestemn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N storage fire loss', &
-         ptr_patch=this%m_livestemn_storage_to_fire_patch, default='inactive')
-
-    this%m_deadstemn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N storage fire loss', &
-         ptr_patch=this%m_deadstemn_storage_to_fire_patch, default='inactive')
-
-    this%m_livecrootn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N storage fire loss', &
-         ptr_patch=this%m_livecrootn_storage_to_fire_patch, default='inactive')
-
-    this%m_deadcrootn_storage_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_STORAGE_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N storage fire loss', &
-         ptr_patch=this%m_deadcrootn_storage_to_fire_patch, default='inactive')
-
-    this%m_leafn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LEAFN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N transfer fire loss', &
-         ptr_patch=this%m_leafn_xfer_to_fire_patch, default='inactive')
-
-    this%m_frootn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_FROOTN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N transfer fire loss', &
-         ptr_patch=this%m_frootn_xfer_to_fire_patch, default='inactive')
-
-    this%m_livestemn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N transfer fire loss', &
-         ptr_patch=this%m_livestemn_xfer_to_fire_patch, default='inactive')
-
-    this%m_deadstemn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N transfer fire loss', &
-         ptr_patch=this%m_deadstemn_xfer_to_fire_patch, default='inactive')
-
-    this%m_livecrootn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N transfer fire loss', &
-         ptr_patch=this%m_livecrootn_xfer_to_fire_patch, default='inactive')
-
-    this%m_deadcrootn_xfer_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_XFER_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N transfer fire loss', &
-         ptr_patch=this%m_deadcrootn_xfer_to_fire_patch, default='inactive')
-
-    this%m_livestemn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVESTEMN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N fire loss', &
-         ptr_patch=this%m_livestemn_to_fire_patch, default='inactive')
-
-    this%m_deadstemn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N fire loss', &
-         ptr_patch=this%m_deadstemn_to_fire_patch, default='inactive')
-
-    this%m_deadstemn_to_litter_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADSTEMN_TO_LITTER_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N fire mortality to litter', &
-         ptr_patch=this%m_deadstemn_to_litter_fire_patch, default='inactive')
-
-    this%m_livecrootn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_LIVECROOTN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N fire loss', &
-         ptr_patch=this%m_livecrootn_to_fire_patch, default='inactive')
-
-    this%m_deadcrootn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N fire loss', &
-         ptr_patch=this%m_deadcrootn_to_fire_patch, default='inactive')
-
-    this%m_deadcrootn_to_litter_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_DEADCROOTN_TO_LITTER_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N fire mortality to litter', &
-         ptr_patch=this%m_deadcrootn_to_litter_fire_patch, default='inactive')
-
-    this%m_retransn_to_fire_patch(begp:endp) = spval
-    call hist_addfld1d (fname='M_RETRANSN_TO_FIRE', units='gN/m^2/s', &
-         avgflag='A', long_name='retranslocated N pool fire loss', &
-         ptr_patch=this%m_retransn_to_fire_patch, default='inactive')
-
-    this%leafn_xfer_to_leafn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_XFER_TO_LEAFN', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N growth from storage', &
-         ptr_patch=this%leafn_xfer_to_leafn_patch, default='inactive')
-
-    this%frootn_xfer_to_frootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN_XFER_TO_FROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N growth from storage', &
-         ptr_patch=this%frootn_xfer_to_frootn_patch, default='inactive')
-
-    this%livestemn_xfer_to_livestemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_XFER_TO_LIVESTEMN', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N growth from storage', &
-         ptr_patch=this%livestemn_xfer_to_livestemn_patch, default='inactive')
-
-    this%deadstemn_xfer_to_deadstemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADSTEMN_XFER_TO_DEADSTEMN', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N growth from storage', &
-         ptr_patch=this%deadstemn_xfer_to_deadstemn_patch, default='inactive')
-
-    this%livecrootn_xfer_to_livecrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_XFER_TO_LIVECROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N growth from storage', &
-         ptr_patch=this%livecrootn_xfer_to_livecrootn_patch, default='inactive')
-
-    this%deadcrootn_xfer_to_deadcrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADCROOTN_XFER_TO_DEADCROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N growth from storage', &
-         ptr_patch=this%deadcrootn_xfer_to_deadcrootn_patch, default='inactive')
-
-    this%leafn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N litterfall', &
-         ptr_patch=this%leafn_to_litter_patch, default='inactive')
-
-    this%leafn_to_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_TO_RETRANSN', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N to retranslocated N pool', &
-         ptr_patch=this%leafn_to_retransn_patch, default='inactive')
-
-    this%frootn_to_litter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN_TO_LITTER', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N litterfall', &
-         ptr_patch=this%frootn_to_litter_patch, default='inactive')
-
-    this%retransn_to_npool_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RETRANSN_TO_NPOOL', units='gN/m^2/s', &
-         avgflag='A', long_name='deployment of retranslocated N', &
-         ptr_patch=this%retransn_to_npool_patch, default='inactive')
-         
-    this%free_retransn_to_npool_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FREE_RETRANSN_TO_NPOOL', units='gN/m^2/s', &
-         avgflag='A', long_name='deployment of retranslocated N', &
-         ptr_patch=this%free_retransn_to_npool_patch, default='inactive')
-
-    this%sminn_to_npool_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SMINN_TO_NPOOL', units='gN/m^2/s', &
-         avgflag='A', long_name='deployment of soil mineral N uptake', &
-         ptr_patch=this%sminn_to_npool_patch, default='inactive')
-
-    this%npool_to_leafn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LEAFN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to leaf N', &
-         ptr_patch=this%npool_to_leafn_patch, default='inactive')
-
-    this%npool_to_leafn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LEAFN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to leaf N storage', &
-         ptr_patch=this%npool_to_leafn_storage_patch, default='inactive')
-
-    this%npool_to_frootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_FROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to fine root N', &
-         ptr_patch=this%npool_to_frootn_patch, default='inactive')
-
-    this%npool_to_frootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_FROOTN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to fine root N storage', &
-         ptr_patch=this%npool_to_frootn_storage_patch, default='inactive')
-
-    this%npool_to_livestemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LIVESTEMN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to live stem N', &
-         ptr_patch=this%npool_to_livestemn_patch, default='inactive')
-
-    this%npool_to_livestemn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LIVESTEMN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to live stem N storage', &
-         ptr_patch=this%npool_to_livestemn_storage_patch, default='inactive')
-
-    this%npool_to_deadstemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_DEADSTEMN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to dead stem N', &
-         ptr_patch=this%npool_to_deadstemn_patch, default='inactive')
-
-    this%npool_to_deadstemn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_DEADSTEMN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to dead stem N storage', &
-         ptr_patch=this%npool_to_deadstemn_storage_patch, default='inactive')
-
-    this%npool_to_livecrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LIVECROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to live coarse root N', &
-         ptr_patch=this%npool_to_livecrootn_patch, default='inactive')
-
-    this%npool_to_livecrootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_LIVECROOTN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to live coarse root N storage', &
-         ptr_patch=this%npool_to_livecrootn_storage_patch, default='inactive')
-
-    this%npool_to_deadcrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_DEADCROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to dead coarse root N', &
-         ptr_patch=this%npool_to_deadcrootn_patch, default='inactive')
-
-    this%npool_to_deadcrootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL_TO_DEADCROOTN_STORAGE', units='gN/m^2/s', &
-         avgflag='A', long_name='allocation to dead coarse root N storage', &
-         ptr_patch=this%npool_to_deadcrootn_storage_patch, default='inactive')
-
-    this%leafn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='leaf N shift storage to transfer', &
-         ptr_patch=this%leafn_storage_to_xfer_patch, default='inactive')
-
-    this%frootn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='fine root N shift storage to transfer', &
-         ptr_patch=this%frootn_storage_to_xfer_patch, default='inactive')
-
-    this%livestemn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N shift storage to transfer', &
-         ptr_patch=this%livestemn_storage_to_xfer_patch, default='inactive')
-
-    this%deadstemn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADSTEMN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead stem N shift storage to transfer', &
-         ptr_patch=this%deadstemn_storage_to_xfer_patch, default='inactive')
-
-    this%livecrootn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N shift storage to transfer', &
-         ptr_patch=this%livecrootn_storage_to_xfer_patch, default='inactive')
-
-    this%deadcrootn_storage_to_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADCROOTN_STORAGE_TO_XFER', units='gN/m^2/s', &
-         avgflag='A', long_name='dead coarse root N shift storage to transfer', &
-         ptr_patch=this%deadcrootn_storage_to_xfer_patch, default='inactive')
-
-    this%livestemn_to_deadstemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_TO_DEADSTEMN', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N turnover', &
-         ptr_patch=this%livestemn_to_deadstemn_patch, default='inactive')
-
-    this%livestemn_to_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_TO_RETRANSN', units='gN/m^2/s', &
-         avgflag='A', long_name='live stem N to retranslocated N pool', &
-         ptr_patch=this%livestemn_to_retransn_patch, default='inactive')
-
-    this%livecrootn_to_deadcrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_TO_DEADCROOTN', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N turnover', &
-         ptr_patch=this%livecrootn_to_deadcrootn_patch, default='inactive')
-
-    this%livecrootn_to_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_TO_RETRANSN', units='gN/m^2/s', &
-         avgflag='A', long_name='live coarse root N to retranslocated N pool', &
-         ptr_patch=this%livecrootn_to_retransn_patch, default='inactive')
-
-    this%ndeploy_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NDEPLOY', units='gN/m^2/s', &
-         avgflag='A', long_name='total N deployed in new growth', &
-         ptr_patch=this%ndeploy_patch, default='inactive')
-
-    this%wood_harvestn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='WOOD_HARVESTN', units='gN/m^2/s', &
-         avgflag='A', long_name='wood harvest N (to product pools)', &
-         ptr_patch=this%wood_harvestn_patch, default='inactive')
-
-    this%fire_nloss_patch(begp:endp) = spval
-    call hist_addfld1d (fname='PFT_FIRE_NLOSS', units='gN/m^2/s', &
-         avgflag='A', long_name='total patch-level fire N loss', &
-         ptr_patch=this%fire_nloss_patch, default='inactive')
-
-    if (use_crop) then
-       this%fert_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NFERTILIZATION', units='gN/m^2/s', &
-            avgflag='A', long_name='fertilizer added', &
-            ptr_patch=this%fert_patch, default='inactive')
-    end if
-
-    if (use_crop) then
-       this%soyfixn_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SOYFIXN', units='gN/m^2/s', &
-            avgflag='A', long_name='soybean fixation', &
-            ptr_patch=this%soyfixn_patch, default='inactive')
-    end if
-
-    if (use_crop) then
-       this%fert_counter_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FERT_COUNTER', units='seconds', &
-            avgflag='A', long_name='time left to fertilize', &
-            ptr_patch=this%fert_counter_patch, default='inactive')
-    end if
-
-    !-------------------------------
-    ! N flux variables - native to column
-    !-------------------------------
-
-    do k = 1, ndecomp_pools
-       if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then
-          this%m_decomp_npools_to_fire_col(begc:endc,k) = spval
-          data1dptr => this%m_decomp_npools_to_fire_col(:,k)
-          fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_FIRE'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' N fire loss'
-          call hist_addfld1d (fname=fieldname, units='gN/m^2',  &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-
-          if ( nlevdecomp_full > 1 ) then
-             this%m_decomp_npools_to_fire_vr_col(begc:endc,:,k) = spval
-             data2dptr => this%m_decomp_npools_to_fire_vr_col(:,:,k)
-             fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_FIRE'//trim(vr_suffix)
-             longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' N fire loss'
-             call hist_addfld_decomp (fname=fieldname, units='gN/m^3',  type2d='levdcmp', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data2dptr, default='inactive')
-          endif
-       endif
-    end do
-
-    this%fire_nloss_col(begc:endc) = spval
-    call hist_addfld1d (fname='COL_FIRE_NLOSS', units='gN/m^2/s', &
-         avgflag='A', long_name='total column-level fire N loss', &
-         ptr_col=this%fire_nloss_col, default='inactive')
-
-    this%dwt_seedn_to_leaf_grc(begg:endg) = spval
-    call hist_addfld1d (fname='DWT_SEEDN_TO_LEAF', units='gN/m^2/s', &
-         avgflag='A', long_name='seed source to patch-level leaf', &
-         ptr_gcell=this%dwt_seedn_to_leaf_grc, default='inactive')
-
-    this%dwt_seedn_to_leaf_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DWT_SEEDN_TO_LEAF_PATCH', units='gN/m^2/s', &
-         avgflag='A', &
-         long_name='patch-level seed source to patch-level leaf ' // &
-         '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-         ptr_patch=this%dwt_seedn_to_leaf_patch, default='inactive')
-
-    this%dwt_seedn_to_deadstem_grc(begg:endg) = spval
-    call hist_addfld1d (fname='DWT_SEEDN_TO_DEADSTEM', units='gN/m^2/s', &
-         avgflag='A', long_name='seed source to patch-level deadstem', &
-         ptr_gcell=this%dwt_seedn_to_deadstem_grc, default='inactive')
-
-    this%dwt_seedn_to_deadstem_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DWT_SEEDN_TO_DEADSTEM_PATCH', units='gN/m^2/s', &
-         avgflag='A', &
-         long_name='patch-level seed source to patch-level deadstem ' // &
-         '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-         ptr_patch=this%dwt_seedn_to_deadstem_patch, default='inactive')
-
-    this%dwt_conv_nflux_grc(begg:endg) = spval
-    call hist_addfld1d (fname='DWT_CONV_NFLUX', units='gN/m^2/s', &
-         avgflag='A', &
-         long_name='conversion N flux (immediate loss to atm) (0 at all times except first timestep of year)', &
-         ptr_gcell=this%dwt_conv_nflux_grc, default='inactive')
-
-    this%dwt_conv_nflux_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DWT_CONV_NFLUX_PATCH', units='gN/m^2/s', &
-         avgflag='A', &
-         long_name='patch-level conversion N flux (immediate loss to atm) ' // &
-         '(0 at all times except first timestep of year) ' // &
-         '(per-area-gridcell; only makes sense with dov2xy=.false.)', &
-         ptr_patch=this%dwt_conv_nflux_patch, default='inactive')
-    
-    this%dwt_frootn_to_litr_met_n_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='DWT_FROOTN_TO_LITR_MET_N', units='gN/m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='fine root to litter due to landcover change', &
-         ptr_col=this%dwt_frootn_to_litr_met_n_col, default='inactive')
-
-    this%dwt_frootn_to_litr_cel_n_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='DWT_FROOTN_TO_LITR_CEL_N', units='gN/m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='fine root to litter due to landcover change', &
-         ptr_col=this%dwt_frootn_to_litr_cel_n_col, default='inactive')
-
-    this%dwt_frootn_to_litr_lig_n_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='DWT_FROOTN_TO_LITR_LIG_N', units='gN/m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='fine root to litter due to landcover change', &
-         ptr_col=this%dwt_frootn_to_litr_lig_n_col, default='inactive')
-
-    this%dwt_livecrootn_to_cwdn_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='DWT_LIVECROOTN_TO_CWDN', units='gN/m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='live coarse root to CWD due to landcover change', &
-         ptr_col=this%dwt_livecrootn_to_cwdn_col, default='inactive')
-
-    this%dwt_deadcrootn_to_cwdn_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='DWT_DEADCROOTN_TO_CWDN', units='gN/m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='dead coarse root to CWD due to landcover change', &
-         ptr_col=this%dwt_deadcrootn_to_cwdn_col, default='inactive')
-
-    this%crop_seedn_to_leaf_patch(begp:endp) = spval
-    call hist_addfld1d (fname='CROP_SEEDN_TO_LEAF', units='gN/m^2/s', &
-         avgflag='A', long_name='crop seed source to leaf', &
-         ptr_patch=this%crop_seedn_to_leaf_patch, default='inactive')
-
-    this%plant_ndemand_patch(begp:endp) = spval
-    call hist_addfld1d (fname='PLANT_NDEMAND', units='gN/m^2/s', &
-         avgflag='A', long_name='N flux required to support initial GPP', &
-         ptr_patch=this%plant_ndemand_patch, default='inactive')
-
-    this%avail_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='AVAIL_RETRANSN', units='gN/m^2/s', &
-         avgflag='A', long_name='N flux available from retranslocation pool', &
-         ptr_patch=this%avail_retransn_patch, default='inactive')
-
-    this%plant_nalloc_patch(begp:endp) = spval
-    call hist_addfld1d (fname='PLANT_NALLOC', units='gN/m^2/s', &
-         avgflag='A', long_name='total allocated N flux', &
-         ptr_patch=this%plant_nalloc_patch, default='inactive')
-    
-    if ( use_fun ) then
-       this%Nactive_patch(begp:endp)  = spval
-       call hist_addfld1d (fname='NACTIVE', units='gN/m^2/s',       &
-            avgflag='A', long_name='Mycorrhizal N uptake flux',     &
-            ptr_patch=this%Nactive_patch, default='inactive')
-   
-       this%Nnonmyc_patch(begp:endp)  = spval
-       call hist_addfld1d (fname='NNONMYC', units='gN/m^2/s',       &
-            avgflag='A', long_name='Non-mycorrhizal N uptake flux', &
-            ptr_patch=this%Nnonmyc_patch, default='inactive')    
-
-       this%Nam_patch(begp:endp)      = spval
-       call hist_addfld1d (fname='NAM', units='gN/m^2/s',           &
-            avgflag='A', long_name='AM-associated N uptake flux',   &
-            ptr_patch=this%Nam_patch, default='inactive')
-
-       this%Necm_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='NECM', units='gN/m^2/s',          &
-            avgflag='A', long_name='ECM-associated N uptake flux',  &
-            ptr_patch=this%Necm_patch, default='inactive')
-
-       if (use_nitrif_denitrif) then
-          this%Nactive_no3_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NACTIVE_NO3', units='gN/m^2/s',   &
-               avgflag='A', long_name='Mycorrhizal N uptake flux',     &
-               ptr_patch=this%Nactive_no3_patch, default='inactive')
-   
-          this%Nactive_nh4_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NACTIVE_NH4', units='gN/m^2/s',   &
-               avgflag='A', long_name='Mycorrhizal N uptake flux',     &
-               ptr_patch=this%Nactive_nh4_patch, default='inactive')
-
-          this%Nnonmyc_no3_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NNONMYC_NO3', units='gN/m^2/s',   &
-               avgflag='A', long_name='Non-mycorrhizal N uptake flux', &
-               ptr_patch=this%Nnonmyc_no3_patch, default='inactive')
-  
-          this%Nnonmyc_nh4_patch(begp:endp)  = spval
-          call hist_addfld1d (fname='NNONMYC_NH4', units='gN/m^2/s',   &
-               avgflag='A', long_name='Non-mycorrhizal N uptake flux', &
-               ptr_patch=this%Nnonmyc_nh4_patch, default='inactive')
-
-          this%Nam_no3_patch(begp:endp)      = spval
-          call hist_addfld1d (fname='NAM_NO3', units='gN/m^2/s',       &
-               avgflag='A', long_name='AM-associated N uptake flux',   &
-               ptr_patch=this%Nam_no3_patch, default='inactive')
- 
-          this%Nam_nh4_patch(begp:endp)      = spval
-          call hist_addfld1d (fname='NAM_NH4', units='gN/m^2/s',       &
-               avgflag='A', long_name='AM-associated N uptake flux',   &
-               ptr_patch=this%Nam_nh4_patch, default='inactive')
-
-          this%Necm_no3_patch(begp:endp)     = spval
-          call hist_addfld1d (fname='NECM_NO3', units='gN/m^2/s',      &
-               avgflag='A', long_name='ECM-associated N uptake flux',  &
-               ptr_patch=this%Necm_no3_patch, default='inactive') 
-  
-          this%Necm_nh4_patch(begp:endp)     = spval
-          call hist_addfld1d (fname='NECM_NH4', units='gN/m^2/s',      &
-               avgflag='A', long_name='ECM-associated N uptake flux',  &
-               ptr_patch=this%Necm_nh4_patch, default='inactive')   
-       end if 
-
-       this%Npassive_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NPASSIVE', units='gN/m^2/s',        &
-            avgflag='A', long_name='Passive N uptake flux',           &
-            ptr_patch=this%Npassive_patch, default='inactive')
-
-       this%Nfix_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='NFIX', units='gN/m^2/s',            &
-            avgflag='A', long_name='Symbiotic BNF uptake flux',       &
-            ptr_patch=this%Nfix_patch, default='inactive')
-
-       this%Nretrans_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NRETRANS', units='gN/m^2/s',        &
-            avgflag='A', long_name='Retranslocated N uptake flux',    &
-            ptr_patch=this%Nretrans_patch, default='inactive')
-  
-       this%Nretrans_org_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NRETRANS_REG', units='gN/m^2/s',    &
-            avgflag='A', long_name='Retranslocated N uptake flux',    &
-            ptr_patch=this%Nretrans_org_patch, default='inactive')
-
-       this%Nretrans_season_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NRETRANS_SEASON', units='gN/m^2/s', &
-            avgflag='A', long_name='Retranslocated N uptake flux',    &
-            ptr_patch=this%Nretrans_season_patch, default='inactive')
-
-       this%Nretrans_stress_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NRETRANS_STRESS', units='gN/m^2/s', &
-            avgflag='A', long_name='Retranslocated N uptake flux',    &
-            ptr_patch=this%Nretrans_stress_patch, default='inactive')
-  
-       this%Nuptake_patch(begp:endp) = spval
-       call hist_addfld1d (fname='NUPTAKE', units='gN/m^2/s',         &
-            avgflag='A', long_name='Total N uptake of FUN',           &
-            ptr_patch=this%Nuptake_patch, default='inactive')
-
-       this%sminn_to_plant_fun_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SMINN_TO_PLANT_FUN', units='gN/m^2/s',&
-            avgflag='A', long_name='Total soil N uptake of FUN',        &
-            ptr_patch=this%sminn_to_plant_fun_patch, default='inactive')      
-       
-       this%cost_nfix_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='COST_NFIX', units='gN/gC',            &
-            avgflag='A', long_name='Cost of fixation',       &
-            ptr_patch=this%cost_nfix_patch, default='inactive')
-            
-       this%cost_nactive_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='COST_NACTIVE', units='gN/gC',            &
-            avgflag='A', long_name='Cost of active uptake',       &
-            ptr_patch=this%cost_nactive_patch, default='inactive')
-            
-       this%cost_nretrans_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='COST_NRETRANS', units='gN/gC',            &
-            avgflag='A', long_name='Cost of retranslocation',       &
-            ptr_patch=this%cost_nretrans_patch, default='inactive')
-            
-      this%nuptake_npp_fraction_patch(begp:endp)     = spval
-       call hist_addfld1d (fname='NUPTAKE_NPP_FRACTION', units='-',            &
-            avgflag='A', long_name='frac of NPP used in N uptake',       &
-            ptr_patch=this%nuptake_npp_fraction_patch, default='inactive')
-                  
-     
-    end if
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    ! !USES:
-    use landunit_varcon , only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    class(cnveg_nitrogenflux_type) :: this 
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,c,l,j
-    integer :: fp, fc                                    ! filter indices
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: num_special_patch                         ! number of good values in special_patch filter
-    integer :: special_col(bounds%endc-bounds%begc+1)    ! special landunit filter - columns
-    integer :: special_patch(bounds%endp-bounds%begp+1)  ! special landunit filter - patches
-    !---------------------------------------------------------------------
-
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    ! Set patch filters
-
-    num_special_patch = 0
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-       if (lun%ifspecial(l)) then
-          num_special_patch = num_special_patch + 1
-          special_patch(num_special_patch) = p
-       end if
-    end do
-
-    !-----------------------------------------------
-    ! initialize nitrogen flux variables
-    !-----------------------------------------------
-
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-
-       if ( use_crop )then
-          this%fert_counter_patch(p)  = spval
-          this%fert_patch(p)          = 0._r8 
-          this%soyfixn_patch(p)       = 0._r8 
-       end if
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%fert_counter_patch(p)  = 0._r8
-       end if
-       if ( use_fun ) then
-          if (lun%ifspecial(l)) then
-             this%plant_ndemand_patch(p)        = spval
-             this%avail_retransn_patch(p)       = spval
-             this%plant_nalloc_patch(p)         = spval
-             this%Npassive_patch(p)             = spval
-             this%Nactive_patch(p)              = spval
-             this%Nnonmyc_patch(p)              = spval
-             this%Nam_patch(p)                  = spval
-             this%Necm_patch(p)                 = spval
-             if (use_nitrif_denitrif) then
-                this%Nactive_no3_patch(p)       = spval
-                this%Nactive_nh4_patch(p)       = spval
-                this%Nnonmyc_no3_patch(p)       = spval
-                this%Nnonmyc_nh4_patch(p)       = spval
-                this%Nam_no3_patch(p)           = spval
-                this%Nam_nh4_patch(p)           = spval
-                this%Necm_no3_patch(p)          = spval
-                this%Necm_nh4_patch(p)          = spval
-             end if
-             this%Nfix_patch(p)                      = spval
-             this%Nretrans_patch(p)             = spval
-             this%Nretrans_org_patch(p)         = spval
-             this%Nretrans_season_patch(p)      = spval
-             this%Nretrans_stress_patch(p)      = spval
-             this%Nuptake_patch(p)              = spval
-             this%sminn_to_plant_fun_patch(p)   = spval
-             this%cost_nfix_patch               = spval
-             this%cost_nactive_patch            = spval
-             this%cost_nretrans_patch           = spval          
-             this%nuptake_npp_fraction_patch    = spval
-                             
-             do j = 1, nlevdecomp
-                this%sminn_to_plant_fun_vr_patch(p,j)       = spval
-                this%sminn_to_plant_fun_no3_vr_patch(p,j)   = spval
-                this%sminn_to_plant_fun_nh4_vr_patch(p,j)   = spval
-             end do 
-          end if
-       end if
-    end do
-
-    ! initialize fields for special filters
-
-    call this%SetValues (&
-         num_patch=num_special_patch, filter_patch=special_patch, value_patch=0._r8, &
-         num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart (this,  bounds, ncid, flag )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon state
-    !
-    ! !USES:
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenflux_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   !'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag, varname='fert_counter', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%fert_counter_patch)
-
-       call restartvar(ncid=ncid, flag=flag, varname='fert', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%fert_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='grainn_xfer_to_grainn', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain N growth from storage', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_xfer_to_grainn_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='livestemn_to_litter', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='livestem N to litter', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%livestemn_to_litter_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='grainn_to_food', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain N to food', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_to_food_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='npool_to_grainn', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='allocation to grain N', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%npool_to_grainn_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='npool_to_grainn_storage', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='allocation to grain N storage', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%npool_to_grainn_storage_patch)
-    end if
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag, varname='grainn_storage_to_xfer', xtype=ncd_double,  &
-            dim1name='pft', &
-            long_name='grain N shift storage to transfer', units='gN/m2/s', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_storage_to_xfer_patch)
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='plant_ndemand', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%plant_ndemand_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='avail_retransn', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%avail_retransn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='plant_nalloc', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%plant_nalloc_patch) 
-
-     if ( use_fun ) then
-        call restartvar(ncid=ncid, flag=flag, varname='Nactive', xtype=ncd_double,       &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nactive_patch) 
-!    
-        call restartvar(ncid=ncid, flag=flag, varname='Nnonmyc', xtype=ncd_double,       &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nnonmyc_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nam', xtype=ncd_double,           &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nam_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Necm', xtype=ncd_double,          &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Necm_patch)
- 
-        if (use_nitrif_denitrif) then
-           call restartvar(ncid=ncid, flag=flag, varname='Nactive_no3', xtype=ncd_double,   &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nactive_no3_patch)
-    
-           call restartvar(ncid=ncid, flag=flag, varname='Nactive_nh4', xtype=ncd_double,   &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nactive_nh4_patch)   
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Nnonmyc_no3', xtype=ncd_double,    &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nnonmyc_no3_patch)
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Nnonmyc_nh4', xtype=ncd_double,    &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nnonmyc_nh4_patch)
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Nam_no3', xtype=ncd_double,         &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nam_no3_patch)
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Nam_nh4', xtype=ncd_double,         &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Nam_nh4_patch)
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Necm_no3', xtype=ncd_double,        &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Necm_no3_patch)
- 
-           call restartvar(ncid=ncid, flag=flag, varname='Necm_nh4', xtype=ncd_double,        &
-                dim1name='pft', &
-                long_name='', units='', &
-                interpinic_flag='interp', readvar=readvar, data=this%Necm_nh4_patch)
-        end if
-!
-        call restartvar(ncid=ncid, flag=flag, varname='Npassive', xtype=ncd_double,      &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Npassive_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nfix', xtype=ncd_double,          &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nfix_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nretrans', xtype=ncd_double,       &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nretrans_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nretrans_org', xtype=ncd_double,   &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nretrans_org_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nretrans_season', xtype=ncd_double, &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nretrans_season_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nretrans_stress', xtype=ncd_double, &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nretrans_stress_patch)
- 
-        call restartvar(ncid=ncid, flag=flag, varname='Nuptake', xtype=ncd_double,            &
-             dim1name='pft', &
-             long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%Nuptake_patch)
-
-        call restartvar(ncid=ncid, flag=flag, varname='sminn_to_plant_fun', xtype=ncd_double,            &
-             dim1name='pft', &
-             long_name='Total soil N uptake of FUN', units='gN/m2/s', &
-             interpinic_flag='interp', readvar=readvar, data=this%sminn_to_plant_fun_patch)
-     end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, &
-       num_patch, filter_patch, value_patch, &
-       num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set nitrogen flux variables
-    !
-    ! !ARGUMENTS:
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenflux_type) :: this
-    integer , intent(in) :: num_patch
-    integer , intent(in) :: filter_patch(:)
-    real(r8), intent(in) :: value_patch
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i,j,k,l     ! loop index
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_patch
-       i=filter_patch(fi)
-
-       this%m_leafn_to_litter_patch(i)                   = value_patch
-       this%m_frootn_to_litter_patch(i)                  = value_patch
-       this%m_leafn_storage_to_litter_patch(i)           = value_patch
-       this%m_frootn_storage_to_litter_patch(i)          = value_patch
-       this%m_livestemn_storage_to_litter_patch(i)       = value_patch
-       this%m_deadstemn_storage_to_litter_patch(i)       = value_patch
-       this%m_livecrootn_storage_to_litter_patch(i)      = value_patch
-       this%m_deadcrootn_storage_to_litter_patch(i)      = value_patch
-       this%m_leafn_xfer_to_litter_patch(i)              = value_patch
-       this%m_frootn_xfer_to_litter_patch(i)             = value_patch
-       this%m_livestemn_xfer_to_litter_patch(i)          = value_patch
-       this%m_deadstemn_xfer_to_litter_patch(i)          = value_patch
-       this%m_livecrootn_xfer_to_litter_patch(i)         = value_patch
-       this%m_deadcrootn_xfer_to_litter_patch(i)         = value_patch
-       this%m_livestemn_to_litter_patch(i)               = value_patch
-       this%m_deadstemn_to_litter_patch(i)               = value_patch
-       this%m_livecrootn_to_litter_patch(i)              = value_patch
-       this%m_deadcrootn_to_litter_patch(i)              = value_patch
-       this%m_retransn_to_litter_patch(i)                = value_patch
-       this%hrv_leafn_to_litter_patch(i)                 = value_patch             
-       this%hrv_frootn_to_litter_patch(i)                = value_patch            
-       this%hrv_leafn_storage_to_litter_patch(i)         = value_patch     
-       this%hrv_frootn_storage_to_litter_patch(i)        = value_patch    
-       this%hrv_livestemn_storage_to_litter_patch(i)     = value_patch 
-       this%hrv_deadstemn_storage_to_litter_patch(i)     = value_patch 
-       this%hrv_livecrootn_storage_to_litter_patch(i)    = value_patch
-       this%hrv_deadcrootn_storage_to_litter_patch(i)    = value_patch
-       this%hrv_leafn_xfer_to_litter_patch(i)            = value_patch        
-       this%hrv_frootn_xfer_to_litter_patch(i)           = value_patch       
-       this%hrv_livestemn_xfer_to_litter_patch(i)        = value_patch    
-       this%hrv_deadstemn_xfer_to_litter_patch(i)        = value_patch    
-       this%hrv_livecrootn_xfer_to_litter_patch(i)       = value_patch   
-       this%hrv_deadcrootn_xfer_to_litter_patch(i)       = value_patch   
-       this%hrv_livestemn_to_litter_patch(i)             = value_patch         
-       this%hrv_livecrootn_to_litter_patch(i)            = value_patch        
-       this%hrv_deadcrootn_to_litter_patch(i)            = value_patch        
-       this%hrv_retransn_to_litter_patch(i)              = value_patch    
-
-       this%m_leafn_to_fire_patch(i)                     = value_patch
-       this%m_leafn_storage_to_fire_patch(i)             = value_patch
-       this%m_leafn_xfer_to_fire_patch(i)                = value_patch
-       this%m_livestemn_to_fire_patch(i)                 = value_patch
-       this%m_livestemn_storage_to_fire_patch(i)         = value_patch
-       this%m_livestemn_xfer_to_fire_patch(i)            = value_patch
-       this%m_deadstemn_to_fire_patch(i)                 = value_patch
-       this%m_deadstemn_storage_to_fire_patch(i)         = value_patch
-       this%m_deadstemn_xfer_to_fire_patch(i)            = value_patch
-       this%m_frootn_to_fire_patch(i)                    = value_patch
-       this%m_frootn_storage_to_fire_patch(i)            = value_patch
-       this%m_frootn_xfer_to_fire_patch(i)               = value_patch
-       this%m_livecrootn_to_fire_patch(i)                = value_patch
-       this%m_livecrootn_storage_to_fire_patch(i)        = value_patch
-       this%m_livecrootn_xfer_to_fire_patch(i)           = value_patch
-       this%m_deadcrootn_to_fire_patch(i)                = value_patch
-       this%m_deadcrootn_storage_to_fire_patch(i)        = value_patch
-       this%m_deadcrootn_xfer_to_fire_patch(i)           = value_patch
-       this%m_retransn_to_fire_patch(i)                  = value_patch
-
-
-       this%m_leafn_to_litter_fire_patch(i)              = value_patch
-       this%m_leafn_storage_to_litter_fire_patch(i)      = value_patch
-       this%m_leafn_xfer_to_litter_fire_patch(i)         = value_patch
-       this%m_livestemn_to_litter_fire_patch(i)          = value_patch
-       this%m_livestemn_storage_to_litter_fire_patch(i)  = value_patch
-       this%m_livestemn_xfer_to_litter_fire_patch(i)     = value_patch
-       this%m_livestemn_to_deadstemn_fire_patch(i)       = value_patch
-       this%m_deadstemn_to_litter_fire_patch(i)          = value_patch
-       this%m_deadstemn_storage_to_litter_fire_patch(i)  = value_patch
-       this%m_deadstemn_xfer_to_litter_fire_patch(i)     = value_patch
-       this%m_frootn_to_litter_fire_patch(i)             = value_patch
-       this%m_frootn_storage_to_litter_fire_patch(i)     = value_patch
-       this%m_frootn_xfer_to_litter_fire_patch(i)        = value_patch
-       this%m_livecrootn_to_litter_fire_patch(i)         = value_patch
-       this%m_livecrootn_storage_to_litter_fire_patch(i) = value_patch
-       this%m_livecrootn_xfer_to_litter_fire_patch(i)    = value_patch
-       this%m_livecrootn_to_deadcrootn_fire_patch(i)     = value_patch
-       this%m_deadcrootn_to_litter_fire_patch(i)         = value_patch
-       this%m_deadcrootn_storage_to_litter_fire_patch(i) = value_patch
-       this%m_deadcrootn_xfer_to_litter_fire_patch(i)    = value_patch
-       this%m_retransn_to_litter_fire_patch(i)           = value_patch
-
-       this%leafn_xfer_to_leafn_patch(i)                 = value_patch
-       this%frootn_xfer_to_frootn_patch(i)               = value_patch
-       this%livestemn_xfer_to_livestemn_patch(i)         = value_patch
-       this%deadstemn_xfer_to_deadstemn_patch(i)         = value_patch
-       this%livecrootn_xfer_to_livecrootn_patch(i)       = value_patch
-       this%deadcrootn_xfer_to_deadcrootn_patch(i)       = value_patch
-       this%leafn_to_litter_patch(i)                     = value_patch
-       this%leafn_to_retransn_patch(i)                   = value_patch
-       this%frootn_to_litter_patch(i)                    = value_patch
-       this%retransn_to_npool_patch(i)                   = value_patch
-       this%free_retransn_to_npool_patch(i)              = value_patch
-       this%sminn_to_npool_patch(i)                      = value_patch
-       this%npool_to_leafn_patch(i)                      = value_patch
-       this%npool_to_leafn_storage_patch(i)              = value_patch
-       this%npool_to_frootn_patch(i)                     = value_patch
-       this%npool_to_frootn_storage_patch(i)             = value_patch
-       this%npool_to_livestemn_patch(i)                  = value_patch
-       this%npool_to_livestemn_storage_patch(i)          = value_patch
-       this%npool_to_deadstemn_patch(i)                  = value_patch
-       this%npool_to_deadstemn_storage_patch(i)          = value_patch
-       this%npool_to_livecrootn_patch(i)                 = value_patch
-       this%npool_to_livecrootn_storage_patch(i)         = value_patch
-       this%npool_to_deadcrootn_patch(i)                 = value_patch
-       this%npool_to_deadcrootn_storage_patch(i)         = value_patch
-       this%leafn_storage_to_xfer_patch(i)               = value_patch
-       this%frootn_storage_to_xfer_patch(i)              = value_patch
-       this%livestemn_storage_to_xfer_patch(i)           = value_patch
-       this%deadstemn_storage_to_xfer_patch(i)           = value_patch
-       this%livecrootn_storage_to_xfer_patch(i)          = value_patch
-       this%deadcrootn_storage_to_xfer_patch(i)          = value_patch
-       this%livestemn_to_deadstemn_patch(i)              = value_patch
-       this%livestemn_to_retransn_patch(i)               = value_patch
-       this%livecrootn_to_deadcrootn_patch(i)            = value_patch
-       this%livecrootn_to_retransn_patch(i)              = value_patch
-       this%ndeploy_patch(i)                             = value_patch
-       this%wood_harvestn_patch(i)                       = value_patch
-       this%fire_nloss_patch(i)                          = value_patch
-
-       this%crop_seedn_to_leaf_patch(i)                  = value_patch
-       this%grainn_to_cropprodn_patch(i)                 = value_patch
-    end do
-
-    if ( use_crop )then
-       do fi = 1,num_patch
-          i = filter_patch(fi)
-          this%livestemn_to_litter_patch(i)              = value_patch
-          this%grainn_to_food_patch(i)                   = value_patch
-          this%grainn_to_seed_patch(i)                   = value_patch
-          this%grainn_xfer_to_grainn_patch(i)            = value_patch
-          this%npool_to_grainn_patch(i)                  = value_patch
-          this%npool_to_grainn_storage_patch(i)          = value_patch
-          this%grainn_storage_to_xfer_patch(i)           = value_patch
-          this%soyfixn_patch(i)                          = value_patch
-          this%frootn_to_retransn_patch(i)               = value_patch
-       end do
-    end if
-
-    do j = 1, nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-
-          ! phenology: litterfall and crop fluxes associated wit
-          this%phenology_n_to_litr_met_n_col(i,j)        = value_column
-          this%phenology_n_to_litr_cel_n_col(i,j)        = value_column
-          this%phenology_n_to_litr_lig_n_col(i,j)        = value_column
-
-          ! gap mortality
-          this%gap_mortality_n_to_litr_met_n_col(i,j)    = value_column
-          this%gap_mortality_n_to_litr_cel_n_col(i,j)    = value_column
-          this%gap_mortality_n_to_litr_lig_n_col(i,j)    = value_column
-          this%gap_mortality_n_to_cwdn_col(i,j)          = value_column
-
-          ! fire
-          this%fire_mortality_n_to_cwdn_col(i,j)         = value_column
-          this%m_n_to_litr_met_fire_col(i,j)             = value_column
-          this%m_n_to_litr_cel_fire_col(i,j)             = value_column  
-          this%m_n_to_litr_lig_fire_col(i,j)             = value_column
-
-          ! harvest
-          this%harvest_n_to_litr_met_n_col(i,j)          = value_column             
-          this%harvest_n_to_litr_cel_n_col(i,j)          = value_column             
-          this%harvest_n_to_litr_lig_n_col(i,j)          = value_column             
-          this%harvest_n_to_cwdn_col(i,j)                = value_column  
-       end do
-    end do
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-
-       this%grainn_to_cropprodn_col(i)       = value_column
-       this%fire_nloss_col(i)                = value_column
-
-       ! Zero p2c column fluxes
-       this%fire_nloss_col(i) = value_column
-       this%wood_harvestn_col(i) = value_column
-    end do
-
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%m_decomp_npools_to_fire_col(i,k) = value_column
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%m_decomp_npools_to_fire_vr_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-  end subroutine SetValues
-
-end module CNVegNitrogenFluxType
-
diff --git a/src/biogeochem/CNVegNitrogenStateType.F90 b/src/biogeochem/CNVegNitrogenStateType.F90
deleted file mode 100644
index 5910caadb5..0000000000
--- a/src/biogeochem/CNVegNitrogenStateType.F90
+++ /dev/null
@@ -1,911 +0,0 @@
-module CNVegNitrogenStateType
-
-#include "shr_assert.h"
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : isnan => shr_infnan_isnan, nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp
-  use clm_varcon                         , only : spval, ispval, dzsoi_decomp, zisoi
-  use landunit_varcon                    , only : istcrop, istsoil 
-  use clm_varctl                         , only : use_nitrif_denitrif, use_vertsoilc, use_century_decomp
-  use clm_varctl                         , only : iulog, override_bgc_restart_mismatch_dump
-  use clm_varctl                         , only : use_crop
-  use CNSharedParamsMod                  , only : use_fun
-  use decompMod                          , only : bounds_type
-  use pftconMod                          , only : npcropmin, noveg, pftcon
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use abortutils                         , only : endrun
-  use spmdMod                            , only : masterproc 
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  use PatchType                          , only : patch                
-  use CNSpeciesMod   , only : CN_SPECIES_N
-  use CNVegComputeSeedMod, only : ComputeSeedAmounts
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-
-  private
-
-
-  !
-  type, public :: cnveg_nitrogenstate_type
-
-     real(r8), pointer :: grainn_patch             (:) ! (gN/m2) grain N (crop)
-     real(r8), pointer :: grainn_storage_patch     (:) ! (gN/m2) grain N storage (crop)
-     real(r8), pointer :: grainn_xfer_patch        (:) ! (gN/m2) grain N transfer (crop)
-     real(r8), pointer :: leafn_patch              (:) ! (gN/m2) leaf N 
-     real(r8), pointer :: leafn_storage_patch      (:) ! (gN/m2) leaf N storage
-     real(r8), pointer :: leafn_xfer_patch         (:) ! (gN/m2) leaf N transfer
-     real(r8), pointer :: leafn_storage_xfer_acc_patch (:) ! (gN/m2) Accmulated leaf N transfer
-     real(r8), pointer :: storage_ndemand_patch        (:) ! (gN/m2) N demand during the offset period 
-     real(r8), pointer :: frootn_patch             (:) ! (gN/m2) fine root N
-     real(r8), pointer :: frootn_storage_patch     (:) ! (gN/m2) fine root N storage
-     real(r8), pointer :: frootn_xfer_patch        (:) ! (gN/m2) fine root N transfer
-     real(r8), pointer :: livestemn_patch          (:) ! (gN/m2) live stem N
-     real(r8), pointer :: livestemn_storage_patch  (:) ! (gN/m2) live stem N storage
-     real(r8), pointer :: livestemn_xfer_patch     (:) ! (gN/m2) live stem N transfer
-     real(r8), pointer :: deadstemn_patch          (:) ! (gN/m2) dead stem N
-     real(r8), pointer :: deadstemn_storage_patch  (:) ! (gN/m2) dead stem N storage
-     real(r8), pointer :: deadstemn_xfer_patch     (:) ! (gN/m2) dead stem N transfer
-     real(r8), pointer :: livecrootn_patch         (:) ! (gN/m2) live coarse root N
-     real(r8), pointer :: livecrootn_storage_patch (:) ! (gN/m2) live coarse root N storage
-     real(r8), pointer :: livecrootn_xfer_patch    (:) ! (gN/m2) live coarse root N transfer
-     real(r8), pointer :: deadcrootn_patch         (:) ! (gN/m2) dead coarse root N
-     real(r8), pointer :: deadcrootn_storage_patch (:) ! (gN/m2) dead coarse root N storage
-     real(r8), pointer :: deadcrootn_xfer_patch    (:) ! (gN/m2) dead coarse root N transfer
-     real(r8), pointer :: retransn_patch           (:) ! (gN/m2) plant pool of retranslocated N
-     real(r8), pointer :: npool_patch              (:) ! (gN/m2) temporary plant N pool
-     real(r8), pointer :: ntrunc_patch             (:) ! (gN/m2) patch-level sink for N truncation
-     real(r8), pointer :: cropseedn_deficit_patch  (:) ! (gN/m2) pool for seeding new crop growth; this is a NEGATIVE term, indicating the amount of seed usage that needs to be repaid
-     real(r8), pointer :: seedn_grc                (:) ! (gN/m2) gridcell-level pool for seeding new pFTs via dynamic landcover
-
-     ! summary (diagnostic) state variables, not involved in mass balance
-     real(r8), pointer :: dispvegn_patch           (:) ! (gN/m2) displayed veg nitrogen, excluding storage
-     real(r8), pointer :: storvegn_patch           (:) ! (gN/m2) stored vegetation nitrogen
-     real(r8), pointer :: totvegn_patch            (:) ! (gN/m2) total vegetation nitrogen
-     real(r8), pointer :: totvegn_col              (:) ! (gN/m2) total vegetation nitrogen (p2c)
-     real(r8), pointer :: totn_patch               (:) ! (gN/m2) total patch-level nitrogen
-     real(r8), pointer :: totn_p2c_col             (:) ! (gN/m2) totn_patch averaged to col
-     real(r8), pointer :: totn_col                 (:) ! (gN/m2) total column nitrogen, incl veg
-     real(r8), pointer :: totecosysn_col           (:) ! (gN/m2) total ecosystem nitrogen, incl veg  
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: Restart
-     procedure , public  :: SetValues
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory  
-     procedure , private :: InitCold     
-
-  end type cnveg_nitrogenstate_type
-  !------------------------------------------------------------------------
-
-  ! !PRIVATE DATA:
-  character(len=*), parameter :: sourcefile = &
-       __FILE__
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds,                           &
-       leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch)
-
-    class(cnveg_nitrogenstate_type)   :: this
-    type(bounds_type) , intent(in)    :: bounds  
-    real(r8)          , intent(in)    :: leafc_patch          (bounds%begp:)
-    real(r8)          , intent(in)    :: leafc_storage_patch  (bounds%begp:)
-    real(r8)          , intent(in)    :: frootc_patch         (bounds%begp:)     
-    real(r8)          , intent(in)    :: frootc_storage_patch (bounds%begp:)     
-    real(r8)          , intent(in)    :: deadstemc_patch      (bounds%begp:)
-
-    call this%InitAllocate (bounds )
-    call this%InitHistory (bounds)
-    call this%InitCold ( bounds, &
-         leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenstate_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%grainn_patch             (begp:endp)) ; this%grainn_patch             (:) = nan     
-    allocate(this%grainn_storage_patch     (begp:endp)) ; this%grainn_storage_patch     (:) = nan
-    allocate(this%grainn_xfer_patch        (begp:endp)) ; this%grainn_xfer_patch        (:) = nan     
-    allocate(this%leafn_patch              (begp:endp)) ; this%leafn_patch              (:) = nan
-    allocate(this%leafn_storage_patch      (begp:endp)) ; this%leafn_storage_patch      (:) = nan     
-    allocate(this%leafn_xfer_patch         (begp:endp)) ; this%leafn_xfer_patch         (:) = nan     
-    allocate(this%leafn_storage_xfer_acc_patch  (begp:endp)) ; this%leafn_storage_xfer_acc_patch         (:) = nan
-    allocate(this%storage_ndemand_patch    (begp:endp)) ; this%storage_ndemand_patch    (:) = nan
-    allocate(this%frootn_patch             (begp:endp)) ; this%frootn_patch             (:) = nan
-    allocate(this%frootn_storage_patch     (begp:endp)) ; this%frootn_storage_patch     (:) = nan     
-    allocate(this%frootn_xfer_patch        (begp:endp)) ; this%frootn_xfer_patch        (:) = nan     
-    allocate(this%livestemn_patch          (begp:endp)) ; this%livestemn_patch          (:) = nan
-    allocate(this%livestemn_storage_patch  (begp:endp)) ; this%livestemn_storage_patch  (:) = nan
-    allocate(this%livestemn_xfer_patch     (begp:endp)) ; this%livestemn_xfer_patch     (:) = nan
-    allocate(this%deadstemn_patch          (begp:endp)) ; this%deadstemn_patch          (:) = nan
-    allocate(this%deadstemn_storage_patch  (begp:endp)) ; this%deadstemn_storage_patch  (:) = nan
-    allocate(this%deadstemn_xfer_patch     (begp:endp)) ; this%deadstemn_xfer_patch     (:) = nan
-    allocate(this%livecrootn_patch         (begp:endp)) ; this%livecrootn_patch         (:) = nan
-    allocate(this%livecrootn_storage_patch (begp:endp)) ; this%livecrootn_storage_patch (:) = nan
-    allocate(this%livecrootn_xfer_patch    (begp:endp)) ; this%livecrootn_xfer_patch    (:) = nan
-    allocate(this%deadcrootn_patch         (begp:endp)) ; this%deadcrootn_patch         (:) = nan
-    allocate(this%deadcrootn_storage_patch (begp:endp)) ; this%deadcrootn_storage_patch (:) = nan
-    allocate(this%deadcrootn_xfer_patch    (begp:endp)) ; this%deadcrootn_xfer_patch    (:) = nan
-    allocate(this%retransn_patch           (begp:endp)) ; this%retransn_patch           (:) = nan
-    allocate(this%npool_patch              (begp:endp)) ; this%npool_patch              (:) = nan
-    allocate(this%ntrunc_patch             (begp:endp)) ; this%ntrunc_patch             (:) = nan
-    allocate(this%dispvegn_patch           (begp:endp)) ; this%dispvegn_patch           (:) = nan
-    allocate(this%storvegn_patch           (begp:endp)) ; this%storvegn_patch           (:) = nan
-    allocate(this%totvegn_patch            (begp:endp)) ; this%totvegn_patch            (:) = nan
-    allocate(this%totn_patch               (begp:endp)) ; this%totn_patch               (:) = nan
-
-    allocate(this%cropseedn_deficit_patch  (begp:endp)) ; this%cropseedn_deficit_patch  (:) = nan
-    allocate(this%seedn_grc                (begg:endg)) ; this%seedn_grc                (:) = nan
-    allocate(this%totvegn_col              (begc:endc)) ; this%totvegn_col              (:) = nan
-    allocate(this%totn_p2c_col             (begc:endc)) ; this%totn_p2c_col             (:) = nan
-    allocate(this%totn_col                 (begc:endc)) ; this%totn_col                 (:) = nan
-    allocate(this%totecosysn_col           (begc:endc)) ; this%totecosysn_col           (:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! add history fields for all CN variables, always set as default='inactive'
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(cnveg_nitrogenstate_type) :: this
-    type(bounds_type)         , intent(in) :: bounds 
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: k,l,ii,jj 
-    integer           :: begp,endp
-    integer           :: begc,endc
-    integer           :: begg,endg
-    character(24)     :: fieldname
-    character(100)    :: longname
-    real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begg = bounds%begg; endg = bounds%endg
-
-    !-------------------------------
-    ! patch state variables 
-    !-------------------------------
-    
-    if (use_crop) then
-       this%grainn_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GRAINN', units='gN/m^2', &
-            avgflag='A', long_name='grain N', &
-            ptr_patch=this%grainn_patch, default='inactive')
-       call hist_addfld1d (fname='CROPSEEDN_DEFICIT', units='gN/m^2', &
-            avgflag='A', long_name='N used for crop seed that needs to be repaid', &
-            ptr_patch=this%cropseedn_deficit_patch, default='inactive')
-    end if
-
-    this%leafn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN', units='gN/m^2', &
-         avgflag='A', long_name='leaf N', &
-         ptr_patch=this%leafn_patch, default='inactive')
-
-    this%leafn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='leaf N storage', &
-         ptr_patch=this%leafn_storage_patch, default='inactive')     
-
-    this%leafn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='leaf N transfer', &
-         ptr_patch=this%leafn_xfer_patch, default='inactive')     
-
-    if ( use_fun ) then
-       this%leafn_storage_xfer_acc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LEAFN_STORAGE_XFER_ACC', units='gN/m^2', &
-            avgflag='A', long_name='Accmulated leaf N transfer', &
-            ptr_patch=this%leafn_storage_xfer_acc_patch, default='inactive')
-
-       this%storage_ndemand_patch(begp:endp)        = spval
-       call hist_addfld1d (fname='STORAGE_NDEMAND', units='gN/m^2', &
-            avgflag='A', long_name='N demand during the offset period', &
-            ptr_patch=this%storage_ndemand_patch, default='inactive')
-    end if
-
-    this%frootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN', units='gN/m^2', &
-         avgflag='A', long_name='fine root N', &
-         ptr_patch=this%frootn_patch, default='inactive')
-
-    this%frootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='fine root N storage', &
-         ptr_patch=this%frootn_storage_patch, default='inactive')     
-
-    this%frootn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FROOTN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='fine root N transfer', &
-         ptr_patch=this%frootn_xfer_patch, default='inactive')     
-
-    this%livestemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN', units='gN/m^2', &
-         avgflag='A', long_name='live stem N', &
-         ptr_patch=this%livestemn_patch, default='inactive')
-
-    this%livestemn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='live stem N storage', &
-         ptr_patch=this%livestemn_storage_patch, default='inactive')    
-
-    this%livestemn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVESTEMN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='live stem N transfer', &
-         ptr_patch=this%livestemn_xfer_patch, default='inactive')     
-
-    this%deadstemn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADSTEMN', units='gN/m^2', &
-         avgflag='A', long_name='dead stem N', &
-         ptr_patch=this%deadstemn_patch, default='inactive')
-
-    this%deadstemn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADSTEMN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='dead stem N storage', &
-         ptr_patch=this%deadstemn_storage_patch, default='inactive')    
-
-    this%deadstemn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADSTEMN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='dead stem N transfer', &
-         ptr_patch=this%deadstemn_xfer_patch, default='inactive')    
-
-    this%livecrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN', units='gN/m^2', &
-         avgflag='A', long_name='live coarse root N', &
-         ptr_patch=this%livecrootn_patch, default='inactive')
-
-    this%livecrootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='live coarse root N storage', &
-         ptr_patch=this%livecrootn_storage_patch, default='inactive')    
-
-    this%livecrootn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LIVECROOTN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='live coarse root N transfer', &
-         ptr_patch=this%livecrootn_xfer_patch, default='inactive')    
-
-    this%deadcrootn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADCROOTN', units='gN/m^2', &
-         avgflag='A', long_name='dead coarse root N', &
-         ptr_patch=this%deadcrootn_patch, default='inactive')
-
-    this%deadcrootn_storage_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADCROOTN_STORAGE', units='gN/m^2', &
-         avgflag='A', long_name='dead coarse root N storage', &
-         ptr_patch=this%deadcrootn_storage_patch, default='inactive')    
-
-    this%deadcrootn_xfer_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DEADCROOTN_XFER', units='gN/m^2', &
-         avgflag='A', long_name='dead coarse root N transfer', &
-         ptr_patch=this%deadcrootn_xfer_patch, default='inactive')    
-
-    this%retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RETRANSN', units='gN/m^2', &
-         avgflag='A', long_name='plant pool of retranslocated N', &
-         ptr_patch=this%retransn_patch, default='inactive')
-
-    this%npool_patch(begp:endp) = spval
-    call hist_addfld1d (fname='NPOOL', units='gN/m^2', &
-         avgflag='A', long_name='temporary plant N pool', &
-         ptr_patch=this%npool_patch, default='inactive')     
-
-    this%ntrunc_patch(begp:endp) = spval
-    call hist_addfld1d (fname='PFT_NTRUNC', units='gN/m^2', &
-         avgflag='A', long_name='patch-level sink for N truncation', &
-         ptr_patch=this%ntrunc_patch, default='inactive')
-
-    this%dispvegn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DISPVEGN', units='gN/m^2', &
-         avgflag='A', long_name='displayed vegetation nitrogen', &
-         ptr_patch=this%dispvegn_patch, default='inactive')
-
-    this%storvegn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='STORVEGN', units='gN/m^2', &
-         avgflag='A', long_name='stored vegetation nitrogen', &
-         ptr_patch=this%storvegn_patch, default='inactive')
-
-    this%totvegn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TOTVEGN', units='gN/m^2', &
-         avgflag='A', long_name='total vegetation nitrogen', &
-         ptr_patch=this%totvegn_patch, default='inactive')
-
-    this%totn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TOTPFTN', units='gN/m^2', &
-         avgflag='A', long_name='total patch-level nitrogen', &
-         ptr_patch=this%totn_patch, default='inactive')
-
-    !-------------------------------
-    ! column state variables 
-    !-------------------------------
-
-    this%seedn_grc(begg:endg) = spval
-    call hist_addfld1d (fname='SEEDN', units='gN/m^2', &
-         avgflag='A', long_name='pool for seeding new PFTs via dynamic landcover', &
-         ptr_gcell=this%seedn_grc, default='inactive')
-
-    this%totecosysn_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTECOSYSN', units='gN/m^2', &
-         avgflag='A', long_name='total ecosystem N, excluding product pools', &
-         ptr_col=this%totecosysn_col, default='inactive')
-
-    this%totn_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTCOLN', units='gN/m^2', &
-         avgflag='A', long_name='total column-level N, excluding product pools', &
-         ptr_col=this%totn_col, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, &
-       leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    use clm_varctl     , only : MM_Nuptake_opt   
-    ! !ARGUMENTS:
-    class(cnveg_nitrogenstate_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    real(r8)          , intent(in) :: leafc_patch(bounds%begp:)
-    real(r8)          , intent(in) :: leafc_storage_patch(bounds%begp:)
-    real(r8)          , intent(in) :: frootc_patch(bounds%begp:)            
-    real(r8)          , intent(in) :: frootc_storage_patch(bounds%begp:)    
-    real(r8)          , intent(in) :: deadstemc_patch(bounds%begp:)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc,fp,g,l,c,p,j,k                       ! indices
-    integer :: num_special_col                         ! number of good values in special_col filter
-    integer :: num_special_patch                         ! number of good values in special_patch filter
-    integer :: special_col   (bounds%endc-bounds%begc+1) ! special landunit filter - columns
-    integer :: special_patch (bounds%endp-bounds%begp+1) ! special landunit filter - patches
-    !------------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(leafc_patch)          == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(leafc_storage_patch)  == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(frootc_patch)         == (/bounds%endp/)), errMsg(sourcefile, __LINE__))   
-    SHR_ASSERT_ALL((ubound(frootc_storage_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))   
-    SHR_ASSERT_ALL((ubound(deadstemc_patch)      == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-
-    ! Set column filters
-
-    num_special_patch = 0
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-       if (lun%ifspecial(l)) then
-          num_special_patch = num_special_patch + 1
-          special_patch(num_special_patch) = p
-       end if
-    end do
-
-    ! Set patch filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    !-------------------------------------------
-    ! initialize patch-level variables
-    !-------------------------------------------
-
-    do p = bounds%begp,bounds%endp
-
-       l = patch%landunit(p)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-
-          if (patch%itype(p) == noveg) then
-             this%leafn_patch(p) = 0._r8
-             this%leafn_storage_patch(p) = 0._r8
-             if (MM_Nuptake_opt .eqv. .true.) then   
-                this%frootn_patch(p) = 0._r8            
-                this%frootn_storage_patch(p) = 0._r8    
-             end if 
-          else
-             this%leafn_patch(p)         = leafc_patch(p)         / pftcon%leafcn(patch%itype(p))
-             this%leafn_storage_patch(p) = leafc_storage_patch(p) / pftcon%leafcn(patch%itype(p))
-             if (MM_Nuptake_opt .eqv. .true.) then  
-                this%frootn_patch(p) = frootc_patch(p) / pftcon%frootcn(patch%itype(p))           
-                this%frootn_storage_patch(p) = frootc_storage_patch(p) / pftcon%frootcn(patch%itype(p))   
-             end if 
-          end if
-
-          this%leafn_xfer_patch(p)        = 0._r8
-
-          this%leafn_storage_xfer_acc_patch(p)        = 0._r8
-          this%storage_ndemand_patch(p)   = 0._r8
-
-          if ( use_crop )then
-             this%grainn_patch(p)         = 0._r8
-             this%grainn_storage_patch(p) = 0._r8
-             this%grainn_xfer_patch(p)    = 0._r8
-             this%cropseedn_deficit_patch(p)  = 0._r8
-          end if
-          if (MM_Nuptake_opt .eqv. .false.) then  ! if not running in floating CN ratio option 
-             this%frootn_patch(p)            = 0._r8
-             this%frootn_storage_patch(p)    = 0._r8
-          end if 
-          this%frootn_xfer_patch(p)       = 0._r8
-          this%livestemn_patch(p)         = 0._r8
-          this%livestemn_storage_patch(p) = 0._r8
-          this%livestemn_xfer_patch(p)    = 0._r8
-
-          ! tree types need to be initialized with some stem mass so that
-          ! roughness length is not zero in canopy flux calculation
-
-          if (pftcon%woody(patch%itype(p)) == 1._r8) then
-             this%deadstemn_patch(p) = deadstemc_patch(p) / pftcon%deadwdcn(patch%itype(p))
-          else
-             this%deadstemn_patch(p) = 0._r8
-          end if
-
-          this%deadstemn_storage_patch(p)  = 0._r8
-          this%deadstemn_xfer_patch(p)     = 0._r8
-          this%livecrootn_patch(p)         = 0._r8
-          this%livecrootn_storage_patch(p) = 0._r8
-          this%livecrootn_xfer_patch(p)    = 0._r8
-          this%deadcrootn_patch(p)         = 0._r8
-          this%deadcrootn_storage_patch(p) = 0._r8
-          this%deadcrootn_xfer_patch(p)    = 0._r8
-          this%retransn_patch(p)           = 0._r8
-          this%npool_patch(p)              = 0._r8
-          this%ntrunc_patch(p)             = 0._r8
-          this%dispvegn_patch(p)           = 0._r8
-          this%storvegn_patch(p)           = 0._r8
-          this%totvegn_patch(p)            = 0._r8
-          this%totn_patch(p)               = 0._r8
-       end if
-    end do
-
-    !-------------------------------------------
-    ! initialize column-level variables
-    !-------------------------------------------
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          ! total nitrogen pools
-          this%totecosysn_col(c) = 0._r8
-          this%totn_p2c_col(c)   = 0._r8
-          this%totn_col(c)       = 0._r8
-       end if
-    end do
-
-
-    do g = bounds%begg, bounds%endg
-       this%seedn_grc(g) = 0._r8
-    end do
-
-    ! now loop through special filters and explicitly set the variables that
-    ! have to be in place for biogeophysics
-
-    ! initialize fields for special filters
-
-    call this%SetValues (&
-         num_patch=num_special_patch, filter_patch=special_patch, value_patch=0._r8, &
-         num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart ( this,  bounds, ncid, flag, leafc_patch, &
-                       leafc_storage_patch, frootc_patch, frootc_storage_patch, &
-                       deadstemc_patch, filter_reseed_patch, num_reseed_patch )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write restart data 
-    !
-    ! !USES:
-    use restUtilMod
-    use ncdio_pio
-    use clm_varctl             , only : spinup_state, use_cndv
-    use clm_time_manager       , only : get_nstep, is_restart
-    use clm_varctl             , only : MM_Nuptake_opt   
-
-    !
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenstate_type) :: this
-    type(bounds_type)          , intent(in)    :: bounds 
-    type(file_desc_t)          , intent(inout) :: ncid   
-    character(len=*)           , intent(in)    :: flag   !'read' or 'write' or 'define'
-    real(r8)          , intent(in) :: leafc_patch(bounds%begp:)
-    real(r8)          , intent(in) :: leafc_storage_patch(bounds%begp:)
-    real(r8)          , intent(in) :: frootc_patch(bounds%begp:)            
-    real(r8)          , intent(in) :: frootc_storage_patch(bounds%begp:)    
-    real(r8)          , intent(in) :: deadstemc_patch(bounds%begp:)
-    integer           , intent(in) :: filter_reseed_patch(:)
-    integer           , intent(in) :: num_reseed_patch
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i, p, l
-    logical            :: readvar
-    real(r8), pointer  :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    character(len=128) :: varname    ! temporary
-    logical            :: exit_spinup  = .false.
-    logical            :: enter_spinup = .false.
-    integer            :: idata
-
-    ! spinup state as read from restart file, for determining whether to enter or exit spinup mode.
-    integer            :: restart_file_spinup_state
-
-    !------------------------------------------------------------------------
-
-    !--------------------------------
-    ! patch nitrogen state variables
-    !--------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='leafn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%leafn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='leafn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%leafn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='leafn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%leafn_xfer_patch) 
-
-     if ( use_fun ) then
-        call restartvar(ncid=ncid, flag=flag, varname='leafn_storage_xfer_acc', xtype=ncd_double,  &
-             dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%leafn_storage_xfer_acc_patch)
-    
-        call restartvar(ncid=ncid, flag=flag, varname='storage_ndemand', xtype=ncd_double,  &
-             dim1name='pft', long_name='', units='', &
-             interpinic_flag='interp', readvar=readvar, data=this%storage_ndemand_patch)
-     end if
-
-
-    call restartvar(ncid=ncid, flag=flag, varname='frootn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%frootn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='frootn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%frootn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='frootn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%frootn_xfer_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livestemn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livestemn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livestemn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livestemn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livestemn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livestemn_xfer_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadstemn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadstemn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadstemn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadstemn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadstemn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadstemn_xfer_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livecrootn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livecrootn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livecrootn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livecrootn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='livecrootn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%livecrootn_xfer_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadcrootn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadcrootn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadcrootn_storage', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadcrootn_storage_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='deadcrootn_xfer', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%deadcrootn_xfer_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='retransn', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%retransn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='npool', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%npool_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='pft_ntrunc', xtype=ncd_double,  &
-         dim1name='pft', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%ntrunc_patch) 
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='grainn', xtype=ncd_double,  &
-            dim1name='pft',    long_name='grain N', units='gN/m2', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='grainn_storage', xtype=ncd_double,  &
-            dim1name='pft',    long_name='grain N storage', units='gN/m2', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_storage_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='grainn_xfer', xtype=ncd_double,  &
-            dim1name='pft',    long_name='grain N transfer', units='gN/m2', &
-            interpinic_flag='interp', readvar=readvar, data=this%grainn_xfer_patch)
-
-       call restartvar(ncid=ncid, flag=flag, varname='cropseedn_deficit', xtype=ncd_double,  &
-            dim1name='pft', long_name='pool for seeding new crop growth', units='gN/m2', &
-            interpinic_flag='interp', readvar=readvar, data=this%cropseedn_deficit_patch)
-    end if
-
-    !--------------------------------
-    ! gridcell nitrogen state variables
-    !--------------------------------
-
-    ! BACKWARDS_COMPATIBILITY(wjs, 2017-01-12) Naming this with a _g suffix in order to
-    ! distinguish it from the old column-level seedn restart variable
-    call restartvar(ncid=ncid, flag=flag, varname='seedn_g', xtype=ncd_double,  &
-         dim1name='gridcell', long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%seedn_grc) 
-
-
-    if (flag == 'read') then
-       call restartvar(ncid=ncid, flag=flag, varname='spinup_state', xtype=ncd_int, &
-         long_name='Spinup state of the model that wrote this restart file: ' &
-         // ' 0 = normal model mode, 1 = AD spinup', units='', &
-         interpinic_flag='copy', readvar=readvar,  data=idata)
-
-       if (readvar) then
-          restart_file_spinup_state = idata
-       else
-          restart_file_spinup_state = spinup_state
-          if ( masterproc ) then
-             write(iulog,*) ' CNRest: WARNING!  Restart file does not contain info ' &
-                   // ' on spinup state used to generate the restart file. '
-             write(iulog,*) '   Assuming the same as current setting: ', spinup_state
-          end if
-       end if
-    end if
-
-    if (flag == 'read' .and. spinup_state /= restart_file_spinup_state .and. .not. use_cndv) then
-       if (spinup_state <= 1 .and. restart_file_spinup_state == 2 ) then
-          if ( masterproc ) write(iulog,*) ' CNRest: taking Dead wood N pools out of AD spinup mode'
-          exit_spinup = .true.
-          if ( masterproc ) write(iulog, *) 'Multiplying stemn and crootn by 10 for exit spinup '
-          do i = bounds%begp,bounds%endp
-             this%deadstemn_patch(i) = this%deadstemn_patch(i) * 10._r8
-             this%deadcrootn_patch(i) = this%deadcrootn_patch(i) * 10._r8
-          end do
-       else if (spinup_state == 2 .and. restart_file_spinup_state <= 1 ) then
-          if ( masterproc ) write(iulog,*) ' CNRest: taking Dead wood N pools into AD spinup mode'
-          enter_spinup = .true.
-          if ( masterproc ) write(iulog, *) 'Dividing stemn and crootn by 10 for enter spinup '
-          do i = bounds%begp,bounds%endp
-             this%deadstemn_patch(i) = this%deadstemn_patch(i) / 10._r8
-             this%deadcrootn_patch(i) = this%deadcrootn_patch(i) / 10._r8
-          end do
-       endif
-
-    end if
-    ! Reseed dead plants
-    if ( flag == 'read' .and. num_reseed_patch > 0 )then
-       if ( masterproc ) write(iulog, *) 'Reseed dead plants for CNVegNitrogenState'
-       do i = 1, num_reseed_patch
-          p = filter_reseed_patch(i)
-
-          l = patch%landunit(p)
-
-             if (patch%itype(p) == noveg) then
-                this%leafn_patch(p) = 0._r8
-                this%leafn_storage_patch(p) = 0._r8
-                if (MM_Nuptake_opt .eqv. .true.) then   
-                   this%frootn_patch(p) = 0._r8            
-                   this%frootn_storage_patch(p) = 0._r8    
-                end if 
-             else
-                this%leafn_patch(p)         = leafc_patch(p)         / pftcon%leafcn(patch%itype(p))
-                this%leafn_storage_patch(p) = leafc_storage_patch(p) / pftcon%leafcn(patch%itype(p))
-                if (MM_Nuptake_opt .eqv. .true.) then  
-                   this%frootn_patch(p) = frootc_patch(p) / pftcon%frootcn(patch%itype(p))           
-                   this%frootn_storage_patch(p) = frootc_storage_patch(p) / pftcon%frootcn(patch%itype(p))   
-                end if 
-             end if
-   
-             this%leafn_xfer_patch(p)        = 0._r8
-
-             this%leafn_storage_xfer_acc_patch(p)        = 0._r8
-             this%storage_ndemand_patch(p)   = 0._r8
-   
-             if ( use_crop )then
-                this%grainn_patch(p)         = 0._r8
-                this%grainn_storage_patch(p) = 0._r8
-                this%grainn_xfer_patch(p)    = 0._r8
-                this%cropseedn_deficit_patch(p)  = 0._r8
-             end if
-             if (MM_Nuptake_opt .eqv. .false.) then  ! if not running in floating CN ratio option 
-                this%frootn_patch(p)            = 0._r8
-                this%frootn_storage_patch(p)    = 0._r8
-             end if 
-             this%frootn_xfer_patch(p)       = 0._r8
-             this%livestemn_patch(p)         = 0._r8
-             this%livestemn_storage_patch(p) = 0._r8
-             this%livestemn_xfer_patch(p)    = 0._r8
-   
-             ! tree types need to be initialized with some stem mass so that
-             ! roughness length is not zero in canopy flux calculation
-   
-             if (pftcon%woody(patch%itype(p)) == 1._r8) then
-                this%deadstemn_patch(p) = deadstemc_patch(p) / pftcon%deadwdcn(patch%itype(p))
-             else
-                this%deadstemn_patch(p) = 0._r8
-             end if
-
-             this%deadstemn_storage_patch(p)  = 0._r8
-             this%deadstemn_xfer_patch(p)     = 0._r8
-             this%livecrootn_patch(p)         = 0._r8
-             this%livecrootn_storage_patch(p) = 0._r8
-             this%livecrootn_xfer_patch(p)    = 0._r8
-             this%deadcrootn_patch(p)         = 0._r8
-             this%deadcrootn_storage_patch(p) = 0._r8
-             this%deadcrootn_xfer_patch(p)    = 0._r8
-             this%retransn_patch(p)           = 0._r8
-             this%npool_patch(p)              = 0._r8
-             this%ntrunc_patch(p)             = 0._r8
-             this%dispvegn_patch(p)           = 0._r8
-             this%storvegn_patch(p)           = 0._r8
-             this%totvegn_patch(p)            = 0._r8
-             this%totn_patch(p)               = 0._r8
-
-             ! calculate totvegc explicitly so that it is available for the isotope 
-             ! code on the first time step.
-
-             this%totvegn_patch(p) = &
-                           this%leafn_patch(p)              + &
-                           this%leafn_storage_patch(p)      + &
-                           this%leafn_xfer_patch(p)         + &
-                           this%frootn_patch(p)             + &
-                           this%frootn_storage_patch(p)     + &
-                           this%frootn_xfer_patch(p)        + &
-                           this%livestemn_patch(p)          + &
-                           this%livestemn_storage_patch(p)  + &
-                           this%livestemn_xfer_patch(p)     + &
-                           this%deadstemn_patch(p)          + &
-                           this%deadstemn_storage_patch(p)  + &
-                           this%deadstemn_xfer_patch(p)     + &
-                           this%livecrootn_patch(p)         + &
-                           this%livecrootn_storage_patch(p) + &
-                           this%livecrootn_xfer_patch(p)    + &
-                           this%deadcrootn_patch(p)         + &
-                           this%deadcrootn_storage_patch(p) + &
-                           this%deadcrootn_xfer_patch(p)    + &
-                           this%npool_patch(p)
-
-             if ( use_crop )then
-                 this%totvegn_patch(p) =         &
-                              this%totvegn_patch(p)    + &
-                              this%grainn_patch(p)         + &
-                              this%grainn_storage_patch(p) + &
-                              this%grainn_xfer_patch(p)
-             end if
-       end do
-     end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, &
-       num_patch, filter_patch, value_patch, &
-       num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set nitrogen state variables
-    !
-    ! !ARGUMENTS:
-    class (cnveg_nitrogenstate_type) :: this
-    integer , intent(in) :: num_patch
-    integer , intent(in) :: filter_patch(:)
-    real(r8), intent(in) :: value_patch
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i     ! loop index
-    integer :: j,k      ! indices
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_patch
-       i = filter_patch(fi)
-
-       this%leafn_patch(i)              = value_patch
-       this%leafn_storage_patch(i)      = value_patch
-       this%leafn_xfer_patch(i)         = value_patch
-       this%leafn_storage_xfer_acc_patch(i) = value_patch
-       this%frootn_patch(i)             = value_patch
-       this%frootn_storage_patch(i)     = value_patch
-       this%frootn_xfer_patch(i)        = value_patch
-       this%livestemn_patch(i)          = value_patch
-       this%livestemn_storage_patch(i)  = value_patch
-       this%livestemn_xfer_patch(i)     = value_patch
-       this%deadstemn_patch(i)          = value_patch
-       this%deadstemn_storage_patch(i)  = value_patch
-       this%deadstemn_xfer_patch(i)     = value_patch
-       this%livecrootn_patch(i)         = value_patch
-       this%livecrootn_storage_patch(i) = value_patch
-       this%livecrootn_xfer_patch(i)    = value_patch
-       this%deadcrootn_patch(i)         = value_patch
-       this%deadcrootn_storage_patch(i) = value_patch
-       this%deadcrootn_xfer_patch(i)    = value_patch
-       this%retransn_patch(i)           = value_patch
-       this%npool_patch(i)              = value_patch
-       this%ntrunc_patch(i)             = value_patch
-       this%dispvegn_patch(i)           = value_patch
-       this%storvegn_patch(i)           = value_patch
-       this%totvegn_patch(i)            = value_patch
-       this%totn_patch(i)               = value_patch
-    end do
-
-    if ( use_crop )then
-       do fi = 1,num_patch
-          i = filter_patch(fi)
-          this%grainn_patch(i)          = value_patch
-          this%grainn_storage_patch(i)  = value_patch
-          this%grainn_xfer_patch(i)     = value_patch   
-          this%cropseedn_deficit_patch(i)  = value_patch
-       end do
-    end if
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-
-       this%totecosysn_col(i) = value_column
-       this%totvegn_col(i)    = value_column
-       this%totn_p2c_col(i)   = value_column
-       this%totn_col(i)       = value_column
-    end do
-
-  end subroutine SetValues
-
-end module CNVegNitrogenStateType
diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90
deleted file mode 100644
index 1d78017a52..0000000000
--- a/src/biogeochem/CNVegStateType.F90
+++ /dev/null
@@ -1,905 +0,0 @@
-module CNVegStateType
-
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use decompMod      , only : bounds_type
-  use abortutils     , only : endrun
-  use spmdMod        , only : masterproc
-  use clm_varpar     , only : nlevsno, nlevgrnd, nlevlak, nlevsoi
-  use clm_varctl     , only : use_cn, iulog, fsurdat, use_crop, use_cndv
-  use clm_varcon     , only : spval, ispval, grlnd
-  use landunit_varcon, only : istsoil, istcrop
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col                
-  use PatchType      , only : patch                
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: cnveg_state_type
-
-     integer  , pointer :: burndate_patch              (:)     ! patch crop burn date
-     real(r8) , pointer :: dwt_smoothed_patch          (:)     ! change in patch weight (-1 to 1) on the gridcell in this time step; changes in first time step of year are smoothed (dribbled) over the whole year
-
-     ! Prognostic crop model
-     !
-     ! TODO(wjs, 2016-02-22) Most / all of these crop-specific state variables should be
-     ! moved to CropType
-     real(r8) , pointer :: hdidx_patch                 (:)     ! patch cold hardening index?
-     real(r8) , pointer :: cumvd_patch                 (:)     ! patch cumulative vernalization d?ependence?
-     real(r8) , pointer :: gddmaturity_patch           (:)     ! patch growing degree days (gdd) needed to harvest (ddays)
-     real(r8) , pointer :: huileaf_patch               (:)     ! patch heat unit index needed from planting to leaf emergence
-     real(r8) , pointer :: huigrain_patch              (:)     ! patch heat unit index needed to reach vegetative maturity
-     real(r8) , pointer :: aleafi_patch                (:)     ! patch saved leaf allocation coefficient from phase 2
-     real(r8) , pointer :: astemi_patch                (:)     ! patch saved stem allocation coefficient from phase 2
-     real(r8) , pointer :: aleaf_patch                 (:)     ! patch leaf allocation coefficient
-     real(r8) , pointer :: astem_patch                 (:)     ! patch stem allocation coefficient
-     real(r8) , pointer :: htmx_patch                  (:)     ! patch max hgt attained by a crop during yr (m)
-     integer  , pointer :: peaklai_patch               (:)     ! patch 1: max allowed lai; 0: not at max
-
-     integer  , pointer :: idop_patch                  (:)     ! patch date of planting
-
-     real(r8) , pointer :: gdp_lf_col                  (:)     ! col global real gdp data (k US$/capita)
-     real(r8) , pointer :: peatf_lf_col                (:)     ! col global peatland fraction data (0-1)
-     integer  , pointer :: abm_lf_col                  (:)     ! col global peak month of crop fire emissions 
-
-     real(r8) , pointer :: lgdp_col                    (:)     ! col gdp limitation factor for fire occurrence (0-1)
-     real(r8) , pointer :: lgdp1_col                   (:)     ! col gdp limitation factor for fire spreading (0-1)
-     real(r8) , pointer :: lpop_col                    (:)     ! col pop limitation factor for fire spreading (0-1)
-
-     real(r8) , pointer :: tempavg_t2m_patch           (:)     ! patch temporary average 2m air temperature (K)
-     real(r8) , pointer :: annavg_t2m_patch            (:)     ! patch annual average 2m air temperature (K)
-     real(r8) , pointer :: annavg_t2m_col              (:)     ! col annual average of 2m air temperature, averaged from patch-level (K)
-     real(r8) , pointer :: annsum_counter_col          (:)     ! col seconds since last annual accumulator turnover
-
-     ! Fire
-     real(r8) , pointer :: nfire_col                   (:)     ! col fire counts (count/km2/sec), valid only in Reg. C
-     real(r8) , pointer :: fsr_col                     (:)     ! col fire spread rate at column level (m/s)
-     real(r8) , pointer :: fd_col                      (:)     ! col fire duration at column level (hr)
-     real(r8) , pointer :: lfc_col                     (:)     ! col conversion area fraction of BET and BDT that haven't burned before (/timestep)
-     real(r8) , pointer :: lfc2_col                    (:)     ! col conversion area fraction of BET and BDT that burned (/sec)
-     real(r8) , pointer :: dtrotr_col                  (:)     ! col annual decreased fraction coverage of BET on the gridcell (0-1)
-     real(r8) , pointer :: trotr1_col                  (:)     ! col patch weight of BET on the column (0-1)
-     real(r8) , pointer :: trotr2_col                  (:)     ! col patch weight of BDT on the column (0-1)
-     real(r8) , pointer :: cropf_col                   (:)     ! col crop fraction in veg column (0-1)
-     real(r8) , pointer :: baf_crop_col                (:)     ! col baf for cropland(/sec)
-     real(r8) , pointer :: baf_peatf_col               (:)     ! col baf for peatland (/sec)
-     real(r8) , pointer :: fbac_col                    (:)     ! col total burned area out of conversion (/sec)
-     real(r8) , pointer :: fbac1_col                   (:)     ! col burned area out of conversion region due to land use fire (/sec)
-     real(r8) , pointer :: wtlf_col                    (:)     ! col fractional coverage of non-crop Patches (0-1)
-     real(r8) , pointer :: lfwt_col                    (:)     ! col fractional coverage of non-crop and non-bare-soil Patches (0-1)
-     real(r8) , pointer :: farea_burned_col            (:)     ! col fractional area burned (/sec) 
-
-     real(r8), pointer :: dormant_flag_patch           (:)     ! patch dormancy flag
-     real(r8), pointer :: days_active_patch            (:)     ! patch number of days since last dormancy
-     real(r8), pointer :: onset_flag_patch             (:)     ! patch onset flag
-     real(r8), pointer :: onset_counter_patch          (:)     ! patch onset days counter
-     real(r8), pointer :: onset_gddflag_patch          (:)     ! patch onset flag for growing degree day sum
-     real(r8), pointer :: onset_fdd_patch              (:)     ! patch onset freezing degree days counter
-     real(r8), pointer :: onset_gdd_patch              (:)     ! patch onset growing degree days
-     real(r8), pointer :: onset_swi_patch              (:)     ! patch onset soil water index
-     real(r8), pointer :: offset_flag_patch            (:)     ! patch offset flag
-     real(r8), pointer :: offset_counter_patch         (:)     ! patch offset days counter
-     real(r8), pointer :: offset_fdd_patch             (:)     ! patch offset freezing degree days counter
-     real(r8), pointer :: offset_swi_patch             (:)     ! patch offset soil water index
-     real(r8), pointer :: grain_flag_patch             (:)     ! patch 1: grain fill stage; 0: not
-     real(r8), pointer :: lgsf_patch                   (:)     ! patch long growing season factor [0-1]
-     real(r8), pointer :: bglfr_patch                  (:)     ! patch background litterfall rate (1/s)
-     real(r8), pointer :: bgtr_patch                   (:)     ! patch background transfer growth rate (1/s)
-     real(r8), pointer :: c_allometry_patch            (:)     ! patch C allocation index (DIM)
-     real(r8), pointer :: n_allometry_patch            (:)     ! patch N allocation index (DIM)
-
-     real(r8), pointer :: tempsum_potential_gpp_patch  (:)     ! patch temporary annual sum of potential GPP
-     real(r8), pointer :: annsum_potential_gpp_patch   (:)     ! patch annual sum of potential GPP
-     real(r8), pointer :: tempmax_retransn_patch       (:)     ! patch temporary annual max of retranslocated N pool (gN/m2)
-     real(r8), pointer :: annmax_retransn_patch        (:)     ! patch annual max of retranslocated N pool (gN/m2)
-     real(r8), pointer :: downreg_patch                (:)     ! patch fractional reduction in GPP due to N limitation (DIM)
-     real(r8), pointer :: leafcn_offset_patch          (:)     ! patch leaf C:N used by FUN
-     real(r8), pointer :: plantCN_patch                (:)     ! patch plant C:N used by FUN
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, public  :: Restart      
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type cnveg_state_type
-  !------------------------------------------------------------------------
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(cnveg_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate ( bounds )
-    if (use_cn) then
-       call this%InitHistory ( bounds )
-    end if
-    call this%InitCold ( bounds ) 
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(cnveg_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    logical :: allows_non_annual_delta
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    allocate(this%burndate_patch      (begp:endp))                   ; this%burndate_patch      (:)   = ispval
-    allocate(this%dwt_smoothed_patch  (begp:endp))                   ; this%dwt_smoothed_patch  (:)   = nan
-
-    allocate(this%hdidx_patch         (begp:endp))                   ; this%hdidx_patch         (:)   = nan
-    allocate(this%cumvd_patch         (begp:endp))                   ; this%cumvd_patch         (:)   = nan
-    allocate(this%gddmaturity_patch   (begp:endp))                   ; this%gddmaturity_patch   (:)   = spval
-    allocate(this%huileaf_patch       (begp:endp))                   ; this%huileaf_patch       (:)   = nan
-    allocate(this%huigrain_patch      (begp:endp))                   ; this%huigrain_patch      (:)   = 0.0_r8
-    allocate(this%aleafi_patch        (begp:endp))                   ; this%aleafi_patch        (:)   = nan
-    allocate(this%astemi_patch        (begp:endp))                   ; this%astemi_patch        (:)   = nan
-    allocate(this%aleaf_patch         (begp:endp))                   ; this%aleaf_patch         (:)   = nan
-    allocate(this%astem_patch         (begp:endp))                   ; this%astem_patch         (:)   = nan
-    allocate(this%htmx_patch          (begp:endp))                   ; this%htmx_patch          (:)   = 0.0_r8
-    allocate(this%peaklai_patch       (begp:endp))                   ; this%peaklai_patch       (:)   = 0
-
-    allocate(this%idop_patch          (begp:endp))                   ; this%idop_patch          (:)   = huge(1)
-
-    allocate(this%gdp_lf_col          (begc:endc))                   ;
-    allocate(this%peatf_lf_col        (begc:endc))                   ; 
-    allocate(this%abm_lf_col          (begc:endc))                   ; 
-
-    allocate(this%lgdp_col            (begc:endc))                   ; 
-    allocate(this%lgdp1_col           (begc:endc))                   ; 
-    allocate(this%lpop_col            (begc:endc))                   ;  
-
-    allocate(this%tempavg_t2m_patch   (begp:endp))                   ; this%tempavg_t2m_patch   (:)   = nan
-    allocate(this%annsum_counter_col  (begc:endc))                   ; this%annsum_counter_col  (:)   = nan
-    allocate(this%annavg_t2m_col      (begc:endc))                   ; this%annavg_t2m_col      (:)   = nan
-    allocate(this%annavg_t2m_patch    (begp:endp))                   ; this%annavg_t2m_patch    (:)   = nan
-
-    allocate(this%nfire_col           (begc:endc))                   ; this%nfire_col           (:)   = spval
-    allocate(this%fsr_col             (begc:endc))                   ; this%fsr_col             (:)   = nan
-    allocate(this%fd_col              (begc:endc))                   ; this%fd_col              (:)   = nan
-    allocate(this%lfc_col             (begc:endc))                   ; this%lfc_col             (:)   = spval
-    allocate(this%lfc2_col            (begc:endc))                   ; this%lfc2_col            (:)   = 0._r8
-    allocate(this%dtrotr_col          (begc:endc))                   ; this%dtrotr_col          (:)   = 0._r8
-    allocate(this%trotr1_col          (begc:endc))                   ; this%trotr1_col          (:)   = 0._r8
-    allocate(this%trotr2_col          (begc:endc))                   ; this%trotr2_col          (:)   = 0._r8
-    allocate(this%cropf_col           (begc:endc))                   ; this%cropf_col           (:)   = nan
-    allocate(this%baf_crop_col        (begc:endc))                   ; this%baf_crop_col        (:)   = nan
-    allocate(this%baf_peatf_col       (begc:endc))                   ; this%baf_peatf_col       (:)   = nan
-    allocate(this%fbac_col            (begc:endc))                   ; this%fbac_col            (:)   = nan
-    allocate(this%fbac1_col           (begc:endc))                   ; this%fbac1_col           (:)   = nan
-    allocate(this%wtlf_col            (begc:endc))                   ; this%wtlf_col            (:)   = nan
-    allocate(this%lfwt_col            (begc:endc))                   ; this%lfwt_col            (:)   = nan
-    allocate(this%farea_burned_col    (begc:endc))                   ; this%farea_burned_col    (:)   = nan
-
-    allocate(this%dormant_flag_patch          (begp:endp)) ;    this%dormant_flag_patch          (:) = nan
-    allocate(this%days_active_patch           (begp:endp)) ;    this%days_active_patch           (:) = nan
-    allocate(this%onset_flag_patch            (begp:endp)) ;    this%onset_flag_patch            (:) = nan
-    allocate(this%onset_counter_patch         (begp:endp)) ;    this%onset_counter_patch         (:) = nan
-    allocate(this%onset_gddflag_patch         (begp:endp)) ;    this%onset_gddflag_patch         (:) = nan
-    allocate(this%onset_fdd_patch             (begp:endp)) ;    this%onset_fdd_patch             (:) = nan
-    allocate(this%onset_gdd_patch             (begp:endp)) ;    this%onset_gdd_patch             (:) = nan
-    allocate(this%onset_swi_patch             (begp:endp)) ;    this%onset_swi_patch             (:) = nan
-    allocate(this%offset_flag_patch           (begp:endp)) ;    this%offset_flag_patch           (:) = nan
-    allocate(this%offset_counter_patch        (begp:endp)) ;    this%offset_counter_patch        (:) = nan
-    allocate(this%offset_fdd_patch            (begp:endp)) ;    this%offset_fdd_patch            (:) = nan
-    allocate(this%offset_swi_patch            (begp:endp)) ;    this%offset_swi_patch            (:) = nan
-    allocate(this%grain_flag_patch            (begp:endp)) ;    this%grain_flag_patch            (:) = nan
-    allocate(this%lgsf_patch                  (begp:endp)) ;    this%lgsf_patch                  (:) = nan
-    allocate(this%bglfr_patch                 (begp:endp)) ;    this%bglfr_patch                 (:) = nan
-    allocate(this%bgtr_patch                  (begp:endp)) ;    this%bgtr_patch                  (:) = nan
-    allocate(this%c_allometry_patch           (begp:endp)) ;    this%c_allometry_patch           (:) = nan
-    allocate(this%n_allometry_patch           (begp:endp)) ;    this%n_allometry_patch           (:) = nan
-    allocate(this%tempsum_potential_gpp_patch (begp:endp)) ;    this%tempsum_potential_gpp_patch (:) = nan
-    allocate(this%annsum_potential_gpp_patch  (begp:endp)) ;    this%annsum_potential_gpp_patch  (:) = nan
-    allocate(this%tempmax_retransn_patch      (begp:endp)) ;    this%tempmax_retransn_patch      (:) = nan
-    allocate(this%annmax_retransn_patch       (begp:endp)) ;    this%annmax_retransn_patch       (:) = nan
-    allocate(this%downreg_patch               (begp:endp)) ;    this%downreg_patch               (:) = nan
-    allocate(this%leafcn_offset_patch         (begp:endp)) ;    this%leafcn_offset_patch         (:) = nan
-    allocate(this%plantCN_patch               (begp:endp)) ;    this%plantCN_patch               (:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use histFileMod    , only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp, no_snow_normal
-    !
-    ! !ARGUMENTS:
-    class(cnveg_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    character(8)      :: vr_suffix
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    if ( use_crop) then
-       this%gddmaturity_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDDHARV', units='ddays', &
-            avgflag='A', long_name='Growing degree days (gdd) needed to harvest', &
-            ptr_patch=this%gddmaturity_patch, default='inactive')
-    end if
-
-    this%lfc2_col(begc:endc) = spval
-    call hist_addfld1d (fname='LFC2', units='per sec', &
-         avgflag='A', long_name='conversion area fraction of BET and BDT that burned', &
-         ptr_col=this%lfc2_col, default='inactive')
-
-    this%annsum_counter_col(begc:endc) = spval
-    call hist_addfld1d (fname='ANNSUM_COUNTER', units='s', &
-         avgflag='A', long_name='seconds since last annual accumulator turnover', &
-         ptr_col=this%annsum_counter_col, default='inactive')
-
-    this%annavg_t2m_col(begc:endc) = spval
-    call hist_addfld1d (fname='CANNAVG_T2M', units='K', &
-         avgflag='A', long_name='annual average of 2m air temperature', &
-         ptr_col=this%annavg_t2m_col, default='inactive')
-
-    this%nfire_col(begc:endc) = spval
-    call hist_addfld1d (fname='NFIRE',  units='counts/km2/sec', &
-         avgflag='A', long_name='fire counts valid only in Reg.C', &
-         ptr_col=this%nfire_col, default='inactive')
-
-    this%farea_burned_col(begc:endc) = spval
-    call hist_addfld1d (fname='FAREA_BURNED',  units='proportion/sec', &
-         avgflag='A', long_name='timestep fractional area burned', &
-         ptr_col=this%farea_burned_col, default='inactive')
-
-    this%baf_crop_col(begc:endc) = spval
-    call hist_addfld1d (fname='BAF_CROP',  units='proportion/sec', &
-         avgflag='A', long_name='fractional area burned for crop', &
-         ptr_col=this%baf_crop_col, default='inactive')
-
-    this%baf_peatf_col(begc:endc) = spval
-    call hist_addfld1d (fname='BAF_PEATF',  units='proportion/sec', &
-         avgflag='A', long_name='fractional area burned in peatland', &
-         ptr_col=this%baf_peatf_col, default='inactive')
- 
-    this%annavg_t2m_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ANNAVG_T2M', units='K', &
-         avgflag='A', long_name='annual average 2m air temperature', &
-         ptr_patch=this%annavg_t2m_patch, default='inactive')
-
-    this%tempavg_t2m_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TEMPAVG_T2M', units='K', &
-         avgflag='A', long_name='temporary average 2m air temperature', &
-         ptr_patch=this%tempavg_t2m_patch, default='inactive')
-
-    this%dormant_flag_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DORMANT_FLAG', units='none', &
-         avgflag='A', long_name='dormancy flag', &
-         ptr_patch=this%dormant_flag_patch, default='inactive')
-
-    this%days_active_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DAYS_ACTIVE', units='days', &
-         avgflag='A', long_name='number of days since last dormancy', &
-         ptr_patch=this%days_active_patch, default='inactive')
-
-    this%onset_flag_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_FLAG', units='none', &
-         avgflag='A', long_name='onset flag', &
-         ptr_patch=this%onset_flag_patch, default='inactive')
-
-    this%onset_counter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_COUNTER', units='days', &
-         avgflag='A', long_name='onset days counter', &
-         ptr_patch=this%onset_counter_patch, default='inactive')
-
-    this%onset_gddflag_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_GDDFLAG', units='none', &
-         avgflag='A', long_name='onset flag for growing degree day sum', &
-         ptr_patch=this%onset_gddflag_patch, default='inactive')
-
-    this%onset_fdd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_FDD', units='C degree-days', &
-         avgflag='A', long_name='onset freezing degree days counter', &
-         ptr_patch=this%onset_fdd_patch, default='inactive')
-
-    this%onset_gdd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_GDD', units='C degree-days', &
-         avgflag='A', long_name='onset growing degree days', &
-         ptr_patch=this%onset_gdd_patch, default='inactive')
-
-    this%onset_swi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ONSET_SWI', units='none', &
-         avgflag='A', long_name='onset soil water index', &
-         ptr_patch=this%onset_swi_patch, default='inactive')
-
-    this%offset_flag_patch(begp:endp) = spval
-    call hist_addfld1d (fname='OFFSET_FLAG', units='none', &
-         avgflag='A', long_name='offset flag', &
-         ptr_patch=this%offset_flag_patch, default='inactive')
-
-    this%offset_counter_patch(begp:endp) = spval
-    call hist_addfld1d (fname='OFFSET_COUNTER', units='days', &
-         avgflag='A', long_name='offset days counter', &
-         ptr_patch=this%offset_counter_patch, default='inactive')
-
-    this%offset_fdd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='OFFSET_FDD', units='C degree-days', &
-         avgflag='A', long_name='offset freezing degree days counter', &
-         ptr_patch=this%offset_fdd_patch, default='inactive')
-
-    this%offset_swi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='OFFSET_SWI', units='none', &
-         avgflag='A', long_name='offset soil water index', &
-         ptr_patch=this%offset_swi_patch, default='inactive')
-
-    this%lgsf_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LGSF', units='proportion', &
-         avgflag='A', long_name='long growing season factor', &
-         ptr_patch=this%lgsf_patch, default='inactive')
-
-    this%bglfr_patch(begp:endp) = spval
-    call hist_addfld1d (fname='BGLFR', units='1/s', &
-         avgflag='A', long_name='background litterfall rate', &
-         ptr_patch=this%bglfr_patch, default='inactive')
-
-    this%bgtr_patch(begp:endp) = spval
-    call hist_addfld1d (fname='BGTR', units='1/s', &
-         avgflag='A', long_name='background transfer growth rate', &
-         ptr_patch=this%bgtr_patch, default='inactive')
-
-    this%c_allometry_patch(begp:endp) = spval
-    call hist_addfld1d (fname='C_ALLOMETRY', units='none', &
-         avgflag='A', long_name='C allocation index', &
-         ptr_patch=this%c_allometry_patch, default='inactive')
-
-    this%n_allometry_patch(begp:endp) = spval
-    call hist_addfld1d (fname='N_ALLOMETRY', units='none', &
-         avgflag='A', long_name='N allocation index', &
-         ptr_patch=this%n_allometry_patch, default='inactive')
-
-    this%tempsum_potential_gpp_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TEMPSUM_POTENTIAL_GPP', units='gC/m^2/yr', &
-         avgflag='A', long_name='temporary annual sum of potential GPP', &
-         ptr_patch=this%tempsum_potential_gpp_patch, default='inactive')
-
-    this%annsum_potential_gpp_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ANNSUM_POTENTIAL_GPP', units='gN/m^2/yr', &
-         avgflag='A', long_name='annual sum of potential GPP', &
-         ptr_patch=this%annsum_potential_gpp_patch, default='inactive')
-
-    this%tempmax_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TEMPMAX_RETRANSN', units='gN/m^2', &
-         avgflag='A', long_name='temporary annual max of retranslocated N pool', &
-         ptr_patch=this%tempmax_retransn_patch, default='inactive')
-
-    this%annmax_retransn_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ANNMAX_RETRANSN', units='gN/m^2', &
-         avgflag='A', long_name='annual max of retranslocated N pool', &
-         ptr_patch=this%annmax_retransn_patch, default='inactive')
-
-    this%downreg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DOWNREG', units='proportion', &
-         avgflag='A', long_name='fractional reduction in GPP due to N limitation', &
-         ptr_patch=this%downreg_patch, default='inactive')
-
-    this%leafcn_offset_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LEAFCN_OFFSET', units='unitless', &
-         avgflag='A', long_name='Leaf C:N used by FUN', &
-         ptr_patch=this%leafcn_offset_patch, default='inactive')
-
-    this%plantCN_patch(begp:endp)       = spval
-    call hist_addfld1d (fname='PLANTCN', units='unitless', &
-         avgflag='A', long_name='Plant C:N used by FUN', &
-         ptr_patch=this%plantCN_patch, default='inactive')
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine initCold(this, bounds)
-    !
-    ! !USES:
-    use spmdMod    , only : masterproc
-    use fileutils  , only : getfil
-    use clm_varctl , only : nsrest, nsrStartup
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class(cnveg_state_type) :: this
-    type(bounds_type), intent(in) :: bounds   
-    !
-    ! !LOCAL VARIABLES:
-    integer               :: g,l,c,p,n,j,m            ! indices
-    real(r8) ,pointer     :: gdp (:)                  ! global gdp data (needs to be a pointer for use in ncdio)
-    real(r8) ,pointer     :: peatf (:)                ! global peatf data (needs to be a pointer for use in ncdio)
-    integer  ,pointer     :: abm (:)                  ! global abm data (needs to be a pointer for use in ncdio)
-    real(r8) ,pointer     :: gti (:)                  ! read in - fmax (needs to be a pointer for use in ncdio)
-    integer               :: dimid                    ! dimension id
-    integer               :: ier                      ! error status
-    type(file_desc_t)     :: ncid                     ! netcdf id
-    logical               :: readvar 
-    character(len=256)    :: locfn                    ! local filename
-    integer               :: begc, endc
-    integer               :: begg, endg
-    !-----------------------------------------------------------------------
-
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    ! --------------------------------------------------------------------
-    ! Open surface dataset
-    ! --------------------------------------------------------------------
-
-    call getfil (fsurdat, locfn, 0)
-    call ncd_pio_openfile (ncid, locfn, 0)
-
-    ! --------------------------------------------------------------------
-    ! Read in GDP data 
-    ! --------------------------------------------------------------------
-
-    allocate(gdp(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       this%gdp_lf_col(c) = gdp(g)
-    end do
-    deallocate(gdp)
-
-    ! --------------------------------------------------------------------
-    ! Read in peatf data 
-    ! --------------------------------------------------------------------
-
-    allocate(peatf(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       this%peatf_lf_col(c) = peatf(g)
-    end do
-    deallocate(peatf)
-
-    ! --------------------------------------------------------------------
-    ! Read in ABM data 
-    ! --------------------------------------------------------------------
-
-    allocate(abm(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       this%abm_lf_col(c) = abm(g)
-    end do
-    deallocate(abm)
-
-    ! Close file
-
-    call ncd_pio_closefile(ncid)
-
-    if (masterproc) then
-       write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data'
-       write(iulog,*)
-    endif
-    
-    ! --------------------------------------------------------------------
-    ! Initialize terms needed for dust model
-    ! TODO - move these terms to DUSTMod module variables 
-    ! --------------------------------------------------------------------
-       
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          this%annsum_counter_col (c) = spval
-          this%annavg_t2m_col     (c) = spval
-          this%nfire_col          (c) = spval
-          this%baf_crop_col       (c) = spval
-          this%baf_peatf_col      (c) = spval
-          this%fbac_col           (c) = spval
-          this%fbac1_col          (c) = spval
-          this%farea_burned_col   (c) = spval
-       end if
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%annsum_counter_col(c) = 0._r8   
-          this%annavg_t2m_col(c)     = 280._r8 
-
-          ! fire related variables 
-          this%baf_crop_col(c)       = 0._r8 
-          this%baf_peatf_col(c)      = 0._r8 
-          this%fbac_col(c)           = 0._r8 
-          this%fbac1_col(c)          = 0._r8 
-          this%farea_burned_col(c)   = 0._r8 
-          this%nfire_col(c)          = 0._r8
-       end if
-    end do
-
-    ! ecophysiological and phenology variables
-
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-
-       if (lun%ifspecial(l)) then
-          this%annavg_t2m_patch  (p)          = spval
-          this%tempavg_t2m_patch (p)          = spval
-          this%dormant_flag_patch(p)          = spval
-          this%days_active_patch(p)           = spval
-          this%onset_flag_patch(p)            = spval
-          this%onset_counter_patch(p)         = spval
-          this%onset_gddflag_patch(p)         = spval
-          this%onset_fdd_patch(p)             = spval
-          this%onset_gdd_patch(p)             = spval
-          this%onset_swi_patch(p)             = spval
-          this%offset_flag_patch(p)           = spval
-          this%offset_counter_patch(p)        = spval
-          this%offset_fdd_patch(p)            = spval
-          this%offset_swi_patch(p)            = spval
-          this%grain_flag_patch(p)            = spval
-          this%lgsf_patch(p)                  = spval
-          this%bglfr_patch(p)                 = spval
-          this%bgtr_patch(p)                  = spval
-          this%c_allometry_patch(p)           = spval
-          this%n_allometry_patch(p)           = spval
-          this%tempsum_potential_gpp_patch(p) = spval
-          this%annsum_potential_gpp_patch(p)  = spval
-          this%tempmax_retransn_patch(p)      = spval
-          this%annmax_retransn_patch(p)       = spval
-          this%downreg_patch(p)               = spval
-          this%leafcn_offset_patch(p)         = spval
-          this%plantCN_patch(p)               = spval
-       end if
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          ! phenology variables
-          this%dormant_flag_patch(p)   = 1._r8
-          this%days_active_patch(p)    = 0._r8
-          this%onset_flag_patch(p)     = 0._r8
-          this%onset_counter_patch(p)  = 0._r8
-          this%onset_gddflag_patch(p)  = 0._r8
-          this%onset_fdd_patch(p)      = 0._r8
-          this%onset_gdd_patch(p)      = 0._r8
-          this%onset_swi_patch(p)      = 0._r8
-          this%offset_flag_patch(p)    = 0._r8
-          this%offset_counter_patch(p) = 0._r8
-          this%offset_fdd_patch(p)     = 0._r8
-          this%offset_swi_patch(p)     = 0._r8
-          this%lgsf_patch(p)           = 0._r8
-          this%bglfr_patch(p)          = 0._r8
-          this%bgtr_patch(p)           = 0._r8
-          this%annavg_t2m_patch(p)     = 280._r8
-          this%tempavg_t2m_patch(p)    = 0._r8
-          this%grain_flag_patch(p)     = 0._r8
-
-          ! non-phenology variables
-          this%c_allometry_patch(p)           = 0._r8
-          this%n_allometry_patch(p)           = 0._r8
-          this%tempsum_potential_gpp_patch(p) = 0._r8
-          this%annsum_potential_gpp_patch(p)  = 0._r8
-          this%tempmax_retransn_patch(p)      = 0._r8
-          this%annmax_retransn_patch(p)       = 0._r8
-          this%downreg_patch(p)               = 0._r8
-          this%leafcn_offset_patch(p)         = spval 
-          this%plantCN_patch(p)               = spval 
-       end if
-
-    end do
-
-    ! fire variables
-
-    do c = bounds%begc,bounds%endc
-       this%lfc2_col(c) = 0._r8
-    end do
-
-  end subroutine initCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, &
-             cnveg_nitrogenstate, filter_reseed_patch, num_reseed_patch)
-    !
-    ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use spmdMod    , only : masterproc
-    use abortutils , only : endrun
-    use CNVegNitrogenStateType, only: cnveg_nitrogenstate_type
-    use CNVegCarbonStateType  , only: cnveg_carbonstate_type
-    use restUtilMod
-    use ncdio_pio
-    use pftconMod , only : pftcon
-    !
-    ! !ARGUMENTS:
-    class(cnveg_state_type) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   
-    character(len=*) , intent(in)    :: flag   
-    type(cnveg_nitrogenstate_type), intent(in) :: cnveg_nitrogenstate
-    type(cnveg_carbonstate_type)  , intent(in) :: cnveg_carbonstate
-    integer                       , intent(out), optional :: filter_reseed_patch(:)
-    integer                       , intent(out), optional :: num_reseed_patch
-    !
-    ! !LOCAL VARIABLES:
-    integer          :: j,c,i,p ! indices
-    logical          :: readvar   ! determine if variable is on initial file
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    !-----------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='dormant_flag', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='dormancy flag', units='unitless', &
-         interpinic_flag='interp', readvar=readvar, data=this%dormant_flag_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='days_active', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='number of days since last dormancy', units='days' , &
-         interpinic_flag='interp', readvar=readvar, data=this%days_active_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_flag', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='flag if critical growing degree-day sum is exceeded', units='unitless' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_flag_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_counter', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='onset days counter', units='sec' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_counter_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_gddflag', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='onset flag for growing degree day sum', units='' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_gddflag_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_fdd', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='onset freezing degree days counter', units='days' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_fdd_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_gdd', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='onset growing degree days', units='days' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_gdd_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='onset_swi', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='onset soil water index', units='days' , &
-         interpinic_flag='interp', readvar=readvar, data=this%onset_swi_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='offset_flag', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='offset flag', units='unitless' , &
-         interpinic_flag='interp', readvar=readvar, data=this%offset_flag_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='offset_counter', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='offset days counter', units='sec' , &
-         interpinic_flag='interp', readvar=readvar, data=this%offset_counter_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='offset_fdd', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='offset freezing degree days counter', units='days' , &
-         interpinic_flag='interp', readvar=readvar, data=this%offset_fdd_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='offset_swi', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%offset_swi_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='lgsf', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%lgsf_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='bglfr', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%bglfr_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='bgtr', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%bgtr_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='annavg_t2m', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annavg_t2m_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='tempavg_t2m', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tempavg_t2m_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='c_allometry', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%c_allometry_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='n_allometry', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%n_allometry_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='tempsum_potential_gpp', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tempsum_potential_gpp_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='annsum_potential_gpp', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annsum_potential_gpp_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='tempmax_retransn', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tempmax_retransn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='annmax_retransn', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annmax_retransn_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='downreg', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%downreg_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='leafcn_offset', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%leafcn_offset_patch)
-     
-    call restartvar(ncid=ncid, flag=flag, varname='plantCN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%plantCN_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='annsum_counter', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annsum_counter_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='burndate', xtype=ncd_int,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%burndate_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='lfc', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%lfc_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='cannavg_t2m', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%annavg_t2m_col) 
-
-    if (use_crop) then
-
-       call restartvar(ncid=ncid, flag=flag,  varname='htmx', xtype=ncd_double,  &
-            dim1name='pft', long_name='max height attained by a crop during year', units='m', &
-            interpinic_flag='interp', readvar=readvar, data=this%htmx_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='peaklai', xtype=ncd_int,  &
-            dim1name='pft', long_name='Flag if at max allowed LAI or not', &
-            flag_values=(/0,1/), nvalid_range=(/0,1/), &
-            flag_meanings=(/'NOT-at-peak', 'AT_peak-LAI' /) , &
-            interpinic_flag='interp', readvar=readvar, data=this%peaklai_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='idop', xtype=ncd_int,  &
-            dim1name='pft', long_name='Date of planting', units='jday', nvalid_range=(/1,366/), & 
-            interpinic_flag='interp', readvar=readvar, data=this%idop_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='aleaf', xtype=ncd_double,  &
-            dim1name='pft', long_name='leaf allocation coefficient', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%aleaf_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='aleafi', xtype=ncd_double,  &
-            dim1name='pft', long_name='Saved leaf allocation coefficient from phase 2', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%aleafi_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='astem', xtype=ncd_double,  &
-            dim1name='pft', long_name='stem allocation coefficient', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%astem_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='astemi', xtype=ncd_double,  &
-            dim1name='pft', long_name='Saved stem allocation coefficient from phase 2', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%astemi_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='hdidx', xtype=ncd_double,  &
-            dim1name='pft', long_name='cold hardening index', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%hdidx_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cumvd', xtype=ncd_double,  &
-            dim1name='pft', long_name='cumulative vernalization d', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%cumvd_patch)
-
-      call restartvar(ncid=ncid, flag=flag,  varname='gddmaturity', xtype=ncd_double,  &
-            dim1name='pft', long_name='Growing degree days needed to harvest', units='ddays', &
-            interpinic_flag='interp', readvar=readvar, data=this%gddmaturity_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='huileaf', xtype=ncd_double,  &
-            dim1name='pft', long_name='heat unit index needed from planting to leaf emergence', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%huileaf_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='huigrain', xtype=ncd_double,  &
-            dim1name='pft', long_name='heat unit index needed to reach vegetative maturity', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%huigrain_patch)
-
-       call restartvar(ncid=ncid, flag=flag, varname='grain_flag', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%grain_flag_patch)
-    end if
-    if ( flag == 'read' .and. num_reseed_patch > 0 )then
-       if ( masterproc ) write(iulog, *) 'Reseed dead plants for CNVegState'
-       do i = 1, num_reseed_patch
-          p = filter_reseed_patch(i)
-          ! phenology variables
-          this%dormant_flag_patch(p)   = 1._r8
-          this%days_active_patch(p)    = 0._r8
-          this%onset_flag_patch(p)     = 0._r8
-          this%onset_counter_patch(p)  = 0._r8
-          this%onset_gddflag_patch(p)  = 0._r8
-          this%onset_fdd_patch(p)      = 0._r8
-          this%onset_gdd_patch(p)      = 0._r8
-          this%onset_swi_patch(p)      = 0._r8
-          this%offset_flag_patch(p)    = 0._r8
-          this%offset_counter_patch(p) = 0._r8
-          this%offset_fdd_patch(p)     = 0._r8
-          this%offset_swi_patch(p)     = 0._r8
-          this%lgsf_patch(p)           = 0._r8
-          this%bglfr_patch(p)          = 0._r8
-          this%bgtr_patch(p)           = 0._r8
-          this%annavg_t2m_patch(p)     = 280._r8
-          this%tempavg_t2m_patch(p)    = 0._r8
-          this%grain_flag_patch(p)     = 0._r8
-
-          this%c_allometry_patch(p)           = 0._r8
-          this%n_allometry_patch(p)           = 0._r8
-          this%tempsum_potential_gpp_patch(p) = 0._r8
-          this%annsum_potential_gpp_patch(p)  = 0._r8
-          this%tempmax_retransn_patch(p)      = 0._r8
-          this%annmax_retransn_patch(p)       = 0._r8
-          this%downreg_patch(p)               = 0._r8
-          this%leafcn_offset_patch(p) = spval
-          this%plantCN_patch(p)       = spval
-       end do
-    end if
-
-  end subroutine Restart
-
-end module CNVegStateType
diff --git a/src/biogeochem/CNVegStructUpdateMod.F90 b/src/biogeochem/CNVegStructUpdateMod.F90
deleted file mode 100644
index 27b677b04d..0000000000
--- a/src/biogeochem/CNVegStructUpdateMod.F90
+++ /dev/null
@@ -1,307 +0,0 @@
-module CNVegStructUpdateMod
-
-  !-----------------------------------------------------------------------
-  ! Module for vegetation structure updates (LAI, SAI, htop, hbot)
-  !
-  ! !USES:
-  use shr_kind_mod         , only: r8 => shr_kind_r8
-  use shr_const_mod        , only : SHR_CONST_PI
-  use clm_varctl           , only : iulog, use_cndv
-  use CNDVType             , only : dgv_ecophyscon    
-  use WaterStateType       , only : waterstate_type
-  use FrictionVelocityMod  , only : frictionvel_type
-  use CNDVType             , only : dgvs_type
-  use CNVegStateType       , only : cnveg_state_type
-  use CropType             , only : crop_type
-  use CNVegCarbonStateType , only : cnveg_carbonstate_type
-  use CanopyStateType      , only : canopystate_type
-  use PatchType            , only : patch                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: CNVegStructUpdate
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine CNVegStructUpdate(num_soilp, filter_soilp, &
-       waterstate_inst, frictionvel_inst, dgvs_inst, cnveg_state_inst, crop_inst, &
-       cnveg_carbonstate_inst, canopystate_inst)
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, use C state variables and epc to diagnose
-    ! vegetation structure (LAI, SAI, height)
-    !
-    ! !USES:
-    use pftconMod        , only : noveg, nc3crop, nc3irrig, nbrdlf_evr_shrub, nbrdlf_dcd_brl_shrub
-    use pftconMod        , only : npcropmin 
-    use pftconMod        , only : ntmp_corn, nirrig_tmp_corn
-    use pftconMod        , only : ntrp_corn, nirrig_trp_corn
-    use pftconMod        , only : nsugarcane, nirrig_sugarcane
-    use pftconMod        , only : pftcon
-    use clm_varctl       , only : spinup_state
-    use clm_time_manager , only : get_rad_step_size
-    !
-    ! !ARGUMENTS:
-    integer                      , intent(in)    :: num_soilp       ! number of column soil points in patch filter
-    integer                      , intent(in)    :: filter_soilp(:) ! patch filter for soil points
-    type(waterstate_type)        , intent(in)    :: waterstate_inst
-    type(frictionvel_type)       , intent(in)    :: frictionvel_inst
-    type(dgvs_type)              , intent(in)    :: dgvs_inst
-    type(cnveg_state_type)       , intent(inout) :: cnveg_state_inst
-    type(crop_type)              , intent(in)    :: crop_inst
-    type(cnveg_carbonstate_type) , intent(in)    :: cnveg_carbonstate_inst
-    type(canopystate_type)       , intent(inout) :: canopystate_inst
-    !
-    ! !REVISION HISTORY:
-    ! 10/28/03: Created by Peter Thornton
-    ! 2/29/08, David Lawrence: revised snow burial fraction for short vegetation
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: p,c,g      ! indices
-    integer  :: fp         ! lake filter indices
-    real(r8) :: taper      ! ratio of height:radius_breast_height (tree allometry)
-    real(r8) :: stocking   ! #stems / ha (stocking density)
-    real(r8) :: ol         ! thickness of canopy layer covered by snow (m)
-    real(r8) :: fb         ! fraction of canopy layer covered by snow
-    real(r8) :: tlai_old   ! for use in Zeng tsai formula
-    real(r8) :: tsai_old   ! for use in Zeng tsai formula
-    real(r8) :: tsai_min   ! PATCH derived minimum tsai
-    real(r8) :: tsai_alpha ! monthly decay rate of tsai
-    real(r8) :: dt         ! radiation time step (sec)
-
-    real(r8), parameter :: dtsmonth = 2592000._r8 ! number of seconds in a 30 day month (60x60x24x30)
-    !-----------------------------------------------------------------------
-    ! tsai formula from Zeng et. al. 2002, Journal of Climate, p1835
-    !
-    ! tsai(p) = max( tsai_alpha(ivt(p))*tsai_old + max(tlai_old-tlai(p),0_r8), tsai_min(ivt(p)) )
-    ! notes:
-    ! * RHS tsai & tlai are from previous timestep
-    ! * should create tsai_alpha(ivt(p)) & tsai_min(ivt(p)) in pftconMod.F90 - slevis
-    ! * all non-crop patches use same values:
-    !   crop    tsai_alpha,tsai_min = 0.0,0.1
-    !   noncrop tsai_alpha,tsai_min = 0.5,1.0  (includes bare soil and urban)
-    !-------------------------------------------------------------------------------
-    
-    associate(                                                            & 
-         ivt                =>  patch%itype                               , & ! Input:  [integer  (:) ] patch vegetation type                                
-
-         woody              =>  pftcon%woody                            , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
-         slatop             =>  pftcon%slatop                           , & ! Input:  specific leaf area at top of canopy, projected area basis [m^2/gC]
-         dsladlai           =>  pftcon%dsladlai                         , & ! Input:  dSLA/dLAI, projected area basis [m^2/gC]           
-         z0mr               =>  pftcon%z0mr                             , & ! Input:  ratio of momentum roughness length to canopy top height (-)
-         displar            =>  pftcon%displar                          , & ! Input:  ratio of displacement height to canopy top height (-)
-         dwood              =>  pftcon%dwood                            , & ! Input:  density of wood (gC/m^3)                          
-         ztopmx             =>  pftcon%ztopmx                           , & ! Input:
-         laimx              =>  pftcon%laimx                            , & ! Input:
-         
-         allom2             =>  dgv_ecophyscon%allom2                   , & ! Input:  [real(r8) (:) ] ecophys const                                     
-         allom3             =>  dgv_ecophyscon%allom3                   , & ! Input:  [real(r8) (:) ] ecophys const                                     
-
-         nind               =>  dgvs_inst%nind_patch                    , & ! Input:  [real(r8) (:) ] number of individuals (#/m**2)                    
-         fpcgrid            =>  dgvs_inst%fpcgrid_patch                 , & ! Input:  [real(r8) (:) ] fractional area of patch (pft area/nat veg area)    
-
-         snow_depth         =>  waterstate_inst%snow_depth_col          , & ! Input:  [real(r8) (:) ] snow height (m)                                   
-
-         forc_hgt_u_patch   =>  frictionvel_inst%forc_hgt_u_patch       , & ! Input:  [real(r8) (:) ] observational height of wind at patch-level [m]     
-
-         leafc              =>  cnveg_carbonstate_inst%leafc_patch      , & ! Input:  [real(r8) (:) ] (gC/m2) leaf C                                    
-         deadstemc          =>  cnveg_carbonstate_inst%deadstemc_patch  , & ! Input:  [real(r8) (:) ] (gC/m2) dead stem C                               
-
-         farea_burned       =>  cnveg_state_inst%farea_burned_col       , & ! Input:  [real(r8) (:) ] F. Li and S. Levis                                 
-         htmx               =>  cnveg_state_inst%htmx_patch             , & ! Output: [real(r8) (:) ] max hgt attained by a crop during yr (m)          
-         peaklai            =>  cnveg_state_inst%peaklai_patch          , & ! Output: [integer  (:) ] 1: max allowed lai; 0: not at max                  
-
-         harvdate           =>  crop_inst%harvdate_patch                , & ! Input:  [integer  (:) ] harvest date                                       
-
-         ! *** Key Output from CN***
-         tlai               =>  canopystate_inst%tlai_patch             , & ! Output: [real(r8) (:) ] one-sided leaf area index, no burying by snow      
-         tsai               =>  canopystate_inst%tsai_patch             , & ! Output: [real(r8) (:) ] one-sided stem area index, no burying by snow      
-         htop               =>  canopystate_inst%htop_patch             , & ! Output: [real(r8) (:) ] canopy top (m)                                     
-         hbot               =>  canopystate_inst%hbot_patch             , & ! Output: [real(r8) (:) ] canopy bottom (m)                                  
-         elai               =>  canopystate_inst%elai_patch             , & ! Output: [real(r8) (:) ] one-sided leaf area index with burying by snow    
-         esai               =>  canopystate_inst%esai_patch             , & ! Output: [real(r8) (:) ] one-sided stem area index with burying by snow    
-         frac_veg_nosno_alb =>  canopystate_inst%frac_veg_nosno_alb_patch & ! Output: [integer  (:) ] frac of vegetation not covered by snow [-]         
-         )
-
-      dt = real( get_rad_step_size(), r8 )
-
-      ! constant allometric parameters
-      taper = 200._r8
-      stocking = 1000._r8
-
-      ! convert from stems/ha -> stems/m^2
-      stocking = stocking / 10000._r8
-
-      ! patch loop
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-         c = patch%column(p)
-         g = patch%gridcell(p)
-
-         if (ivt(p) /= noveg) then
-
-            tlai_old = tlai(p) ! n-1 value
-            tsai_old = tsai(p) ! n-1 value
-
-            ! update the leaf area index based on leafC and SLA
-            ! Eq 3 from Thornton and Zimmerman, 2007, J Clim, 20, 3902-3923. 
-            if (dsladlai(ivt(p)) > 0._r8) then
-               tlai(p) = (slatop(ivt(p))*(exp(leafc(p)*dsladlai(ivt(p))) - 1._r8))/dsladlai(ivt(p))
-            else
-               tlai(p) = slatop(ivt(p)) * leafc(p)
-            end if
-            tlai(p) = max(0._r8, tlai(p))
-
-            ! update the stem area index and height based on LAI, stem mass, and veg type.
-            ! With the exception of htop for woody vegetation, this follows the DGVM logic.
-
-            ! tsai formula from Zeng et. al. 2002, Journal of Climate, p1835 (see notes)
-            ! Assumes doalb time step .eq. CLM time step, SAI min and monthly decay factor
-            ! alpha are set by PFT, and alpha is scaled to CLM time step by multiplying by
-            ! dt and dividing by dtsmonth (seconds in average 30 day month)
-            ! tsai_min scaled by 0.5 to match MODIS satellite derived values
-            if (ivt(p) == nc3crop .or. ivt(p) == nc3irrig) then ! generic crops
-
-               tsai_alpha = 1.0_r8-1.0_r8*dt/dtsmonth
-               tsai_min = 0.1_r8
-            else
-               tsai_alpha = 1.0_r8-0.5_r8*dt/dtsmonth
-               tsai_min = 1.0_r8
-            end if
-            tsai_min = tsai_min * 0.5_r8
-            tsai(p) = max(tsai_alpha*tsai_old+max(tlai_old-tlai(p),0._r8),tsai_min)
-
-            if (woody(ivt(p)) == 1._r8) then
-
-               ! trees and shrubs
-
-               ! if shrubs have a squat taper 
-               if (ivt(p) >= nbrdlf_evr_shrub .and. ivt(p) <= nbrdlf_dcd_brl_shrub) then
-                  taper = 10._r8
-                  ! otherwise have a tall taper
-               else
-                  taper = 200._r8
-               end if
-
-               ! trees and shrubs for now have a very simple allometry, with hard-wired
-               ! stem taper (height:radius) and hard-wired stocking density (#individuals/area)
-               if (use_cndv) then
-
-                  if (fpcgrid(p) > 0._r8 .and. nind(p) > 0._r8) then
-
-                     stocking = nind(p)/fpcgrid(p) !#ind/m2 nat veg area -> #ind/m2 patch area
-                     htop(p) = allom2(ivt(p)) * ( (24._r8 * deadstemc(p) / &
-                          (SHR_CONST_PI * stocking * dwood(ivt(p)) * taper))**(1._r8/3._r8) )**allom3(ivt(p)) ! lpj's htop w/ cn's stemdiam
-
-                  else
-                     htop(p) = 0._r8
-                  end if
-
-               else
-                  !correct height calculation if doing accelerated spinup
-                  if (spinup_state == 2) then
-                    htop(p) = ((3._r8 * deadstemc(p) * 10._r8 * taper * taper)/ &
-                         (SHR_CONST_PI * stocking * dwood(ivt(p))))**(1._r8/3._r8)
-                  else
-                    htop(p) = ((3._r8 * deadstemc(p) * taper * taper)/ &
-                         (SHR_CONST_PI * stocking * dwood(ivt(p))))**(1._r8/3._r8)
-                  end if
-
-               endif
-
-               ! Peter Thornton, 5/3/2004
-               ! Adding test to keep htop from getting too close to forcing height for windspeed
-               ! Also added for grass, below, although it is not likely to ever be an issue.
-               htop(p) = min(htop(p),(forc_hgt_u_patch(p)/(displar(ivt(p))+z0mr(ivt(p))))-3._r8)
-
-               ! Peter Thornton, 8/11/2004
-               ! Adding constraint to keep htop from going to 0.0.
-               ! This becomes an issue when fire mortality is pushing deadstemc
-               ! to 0.0.
-               htop(p) = max(htop(p), 0.01_r8)
-
-               hbot(p) = max(0._r8, min(3._r8, htop(p)-1._r8))
-
-            else if (ivt(p) >= npcropmin) then ! prognostic crops
-
-               if (tlai(p) >= laimx(ivt(p))) peaklai(p) = 1 ! used in CNAllocation
-
-               if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. &
-                   ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. &
-                   ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane) then
-                  tsai(p) = 0.1_r8 * tlai(p)
-               else
-                  tsai(p) = 0.2_r8 * tlai(p)
-               end if
-
-               ! "stubble" after harvest
-               if (harvdate(p) < 999 .and. tlai(p) == 0._r8) then
-                  tsai(p) = 0.25_r8*(1._r8-farea_burned(c)*0.90_r8)    !changed by F. Li and S. Levis
-                  htmx(p) = 0._r8
-                  peaklai(p) = 0
-               end if
-               !if (harvdate(p) < 999 .and. tlai(p) > 0._r8) write(iulog,*) 'CNVegStructUpdate: tlai>0 after harvest!' ! remove after initial debugging?
-
-               ! canopy top and bottom heights
-               htop(p) = ztopmx(ivt(p)) * (min(tlai(p)/(laimx(ivt(p))-1._r8),1._r8))**2
-               htmx(p) = max(htmx(p), htop(p))
-               htop(p) = max(0.05_r8, max(htmx(p),htop(p)))
-               hbot(p) = 0.02_r8
-
-            else ! generic crops and ...
-
-               ! grasses
-
-               ! height for grasses depends only on LAI
-               htop(p) = max(0.25_r8, tlai(p) * 0.25_r8)
-
-               htop(p) = min(htop(p),(forc_hgt_u_patch(p)/(displar(ivt(p))+z0mr(ivt(p))))-3._r8)
-
-               ! Peter Thornton, 8/11/2004
-               ! Adding constraint to keep htop from going to 0.0.
-               htop(p) = max(htop(p), 0.01_r8)
-
-               hbot(p) = max(0.0_r8, min(0.05_r8, htop(p)-0.20_r8))
-            end if
-
-         else
-
-            tlai(p) = 0._r8
-            tsai(p) = 0._r8
-            htop(p) = 0._r8
-            hbot(p) = 0._r8
-
-         end if
-
-         ! adjust lai and sai for burying by snow. 
-         ! snow burial fraction for short vegetation (e.g. grasses) as in
-         ! Wang and Zeng, 2007.
-         if (ivt(p) > noveg .and. ivt(p) <= nbrdlf_dcd_brl_shrub ) then
-            ol = min( max(snow_depth(c)-hbot(p), 0._r8), htop(p)-hbot(p))
-            fb = 1._r8 - ol / max(1.e-06_r8, htop(p)-hbot(p))
-         else
-            fb = 1._r8 - max(min(snow_depth(c),0.2_r8),0._r8)/0.2_r8   ! 0.2m is assumed
-            !depth of snow required for complete burial of grasses
-         endif
-
-         elai(p) = max(tlai(p)*fb, 0.0_r8)
-         esai(p) = max(tsai(p)*fb, 0.0_r8)
-
-         ! Fraction of vegetation free of snow
-         if ((elai(p) + esai(p)) > 0._r8) then
-            frac_veg_nosno_alb(p) = 1
-         else
-            frac_veg_nosno_alb(p) = 0
-         end if
-
-      end do
-
-    end associate 
-
- end subroutine CNVegStructUpdate
-
-end module CNVegStructUpdateMod
diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90
deleted file mode 100644
index 02d0f98ab0..0000000000
--- a/src/biogeochem/CNVegetationFacade.F90
+++ /dev/null
@@ -1,422 +0,0 @@
-module CNVegetationFacade
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Facade for the CN Vegetation subsystem.
-  !
-  ! (A "facade", in software engineering terms, is a unified interface to a set of
-  ! interfaces in a subsystem. The facade defines a higher-level interface that makes the
-  ! subsystem easier to use.)
-  !
-  ! NOTE(wjs, 2016-02-19) I envision that we will introduce an abstract base class
-  ! (VegBase). Then both CNVeg and EDVeg will extend VegBase. The rest of the CLM code can
-  ! then have an instance of VegBase, which depending on the run, can be either a CNVeg or
-  ! EDVeg instance.
-  !
-  ! In addition, we probably want an implementation when running without CN or fates - i.e.,
-  ! an SPVeg inst. This would provide implementations for get_leafn_patch,
-  ! get_downreg_patch, etc., so that we don't need to handle the non-cn case here (note
-  ! that, currently, we return NaN for most of these getters, because these arrays are
-  ! invalid and shouldn't be used when running in SP mode). Also, in its EcosystemDynamics
-  ! routine, it would call SatellitePhenology (but note that the desired interface for
-  ! EcosystemDynamics would be quite different... could just pass everything needed by any
-  ! model, and ignore unneeded arguments). Then we can get rid of comments in this module
-  ! like, "only call if use_cn is true", as well as use_cn conditionals in this module.
-  !
-  ! NOTE(wjs, 2016-02-23) Currently, SatellitePhenology is called even when running with
-  ! CN, for the sake of dry deposition. This seems weird to me, and my gut feeling -
-  ! without understanding it well - is that this should be rewritten to depend on LAI from
-  ! CN rather than from satellite phenology. Until that is done, the separation between SP
-  ! and other Veg modes will be messier.
-  !
-  ! NOTE(wjs, 2016-02-23) Currently, this class coordinates calls to soil BGC routines as
-  ! well as veg BGC routines (even though it doesn't contain any soil BGC types). This is
-  ! because CNDriver coordinates both the veg & soil BGC. We should probably split up
-  ! CNDriver so that there is a cleaner separation between veg BGC and soil BGC, to allow
-  ! easier swapping of (for example) CN and ED. At that point, this class could
-  ! coordinate just the calls to veg BGC routines, with a similar facade class
-  ! coordinating the calls to soil BGC routines.
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use shr_infnan_mod                  , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                     , only : errMsg => shr_log_errMsg
-  use perf_mod                        , only : t_startf, t_stopf
-  use decompMod                       , only : bounds_type
-  use clm_varctl                      , only : iulog, use_cn
-  use abortutils                      , only : endrun
-  use spmdMod                         , only : masterproc
-  use CNBalanceCheckMod               , only : cn_balance_type
-  use CNVegStateType                  , only : cnveg_state_type
-  use CNVegCarbonFluxType             , only : cnveg_carbonflux_type
-  use CNVegCarbonStateType            , only : cnveg_carbonstate_type
-  use CNVegNitrogenFluxType           , only : cnveg_nitrogenflux_type
-  use CNVegNitrogenStateType          , only : cnveg_nitrogenstate_type
-  use CNProductsMod                   , only : cn_products_type
-  use SpeciesIsotopeType              , only : species_isotope_type
-  use SpeciesNonIsotopeType           , only : species_non_isotope_type
-  use CNDriverMod                     , only : CNDriverInit
-  !
-  implicit none
-  private
-
-  ! !PUBLIC TYPES:
-
-  type, public :: cn_vegetation_type
-     ! FIXME(bja, 2016-06) These need to be public for use when fates is
-     ! turned on. Should either be moved out of here or create some ED
-     ! version of the facade....
-     type(cnveg_state_type)         :: cnveg_state_inst
-     type(cnveg_carbonstate_type)   :: cnveg_carbonstate_inst
-     type(cnveg_carbonflux_type)    :: cnveg_carbonflux_inst
-
-     !X!private
-
-     type(cnveg_carbonstate_type)   :: c13_cnveg_carbonstate_inst
-     type(cnveg_carbonstate_type)   :: c14_cnveg_carbonstate_inst
-     type(cnveg_carbonflux_type)    :: c13_cnveg_carbonflux_inst
-     type(cnveg_carbonflux_type)    :: c14_cnveg_carbonflux_inst
-     type(cnveg_nitrogenstate_type) :: cnveg_nitrogenstate_inst
-     type(cnveg_nitrogenflux_type)  :: cnveg_nitrogenflux_inst
-
-     type(cn_products_type)         :: c_products_inst
-     type(cn_products_type)         :: c13_products_inst
-     type(cn_products_type)         :: c14_products_inst
-     type(cn_products_type)         :: n_products_inst
-
-     type(cn_balance_type)          :: cn_balance_inst
-
-     ! Control variables
-     logical, private :: reseed_dead_plants    ! Flag to indicate if should reseed dead plants when starting up the model
-
-     ! TODO(wjs, 2016-02-19) Evaluate whether some other variables should be moved in
-     ! here. Whether they should be moved in depends on how tightly they are tied in with
-     ! the other CN Vegetation stuff. A question to ask is: Is this module used when
-     ! running with SP or ED? If so, then it should probably remain outside of CNVeg.
-     !
-     ! From the clm_instMod section on "CN vegetation types":
-     ! - nutrient_competition_method
-     !   - I'm pretty sure this should be moved into here; it's just a little messy to do
-     !     so, because of how it's initialized (specifically, the call to readParameters
-     !     in clm_initializeMod).
-     !
-     ! From the clm_instMod section on "general biogeochem types":
-     ! - ch4_inst
-     !   - probably not: really seems to belong in soilbiogeochem
-     ! - crop_inst
-     ! - dust_inst
-     ! - vocemis_inst
-     ! - fireemis_inst
-     ! - drydepvel_inst
-     
-   contains
-     procedure, public :: Init
-     procedure, public :: InitAccBuffer
-     procedure, public :: InitAccVars
-     procedure, public :: Restart
-
-     procedure, public :: Init2                         ! Do initialization in initialize phase, after subgrid weights are determined
-     procedure, public :: WriteHistory                  ! Do any history writes that are specific to veg dynamics
-
-     procedure, public :: get_totvegc_col               ! Get column-level total vegetation carbon array
-
-     procedure, private :: CNReadNML                    ! Read in the CN general namelist
-  end type cn_vegetation_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Initialize a CNVeg object.
-    !
-    ! Should be called regardless of whether use_cn is true
-    !
-    ! !USES:
-    use clm_varcon       , only : c13ratio, c14ratio
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    character(len=*) , intent(in)    :: NLFilename ! namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-
-    character(len=*), parameter :: subname = 'Init'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    ! Note - always initialize the memory for cnveg_state_inst (used in biogeophys/)
-    call this%cnveg_state_inst%Init(bounds)
-    
-    if (use_cn) then
-
-       ! Read in the general CN namelist
-       call this%CNReadNML( NLFilename )    ! MUST be called first as passes down control information to others
-
-       call this%cnveg_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8, NLFilename=NLFilename)
-       call this%cnveg_carbonflux_inst%Init(bounds, carbon_type='c12')
-       call this%cnveg_nitrogenstate_inst%Init(bounds,                   &
-            this%cnveg_carbonstate_inst%leafc_patch(begp:endp),          &
-            this%cnveg_carbonstate_inst%leafc_storage_patch(begp:endp),  &
-            this%cnveg_carbonstate_inst%frootc_patch(begp:endp),         &
-            this%cnveg_carbonstate_inst%frootc_storage_patch(begp:endp), &
-            this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp) )
-       call this%cnveg_nitrogenflux_inst%Init(bounds) 
-
-       call this%c_products_inst%Init(bounds, species_non_isotope_type('C'))
-       call this%n_products_inst%Init(bounds, species_non_isotope_type('N'))
-
-       call this%cn_balance_inst%Init(bounds)
-
-    end if
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine CNReadNML( this, NLFilename )
-    !
-    ! !DESCRIPTION:
-    ! Read in the general CN control namelist
-    !
-    ! !USES:
-    use fileutils      , only : getavu, relavu, opnfil
-    use shr_nl_mod     , only : shr_nl_find_group_name
-    use spmdMod        , only : masterproc, mpicom
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    use clm_varctl     , only : iulog
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(inout) :: this
-    character(len=*)         , intent(in)    :: NLFilename                 ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-
-    character(len=*), parameter :: subname = 'CNReadNML'
-    character(len=*), parameter :: nmlname = 'cn_general'   ! MUST match what is in namelist below
-    !-----------------------------------------------------------------------
-    logical :: reseed_dead_plants
-    namelist /cn_general/ reseed_dead_plants
-
-    reseed_dead_plants = this%reseed_dead_plants
-
-    if (masterproc) then
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nmlname//'  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
-       if (ierr == 0) then
-          read(unitn, nml=cn_general, iostat=ierr)   ! Namelist name here MUST be the same as in nmlname above!
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-    end if
-
-    call shr_mpi_bcast (reseed_dead_plants      , mpicom)
-
-    this%reseed_dead_plants = reseed_dead_plants
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) nmlname//' settings:'
-       write(iulog,nml=cn_general)    ! Name here MUST be the same as in nmlname above!
-       write(iulog,*) ' '
-    end if
-
-    !-----------------------------------------------------------------------
-
-  end subroutine CNReadNML
-
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccBuffer(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for types contained here 
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'InitAccBuffer'
-    !-----------------------------------------------------------------------
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize variables that are associated with accumulated fields
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'InitAccVars'
-    !-----------------------------------------------------------------------
-
-  end subroutine InitAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !DESCRIPTION:
-    ! Handle restart (read / write) for CNVeg
-    !
-    ! Should be called regardless of whether use_cn is true
-    !
-    ! !USES:
-    use ncdio_pio, only : file_desc_t
-    use clm_varcon, only : c3_r2, c14ratio
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   
-    character(len=*) , intent(in)    :: flag   
-    integer  :: reseed_patch(bounds%endp-bounds%begp+1)
-    integer  :: num_reseed_patch
-    !
-    ! !LOCAL VARIABLES:
-
-    integer :: begp, endp
-
-    character(len=*), parameter :: subname = 'Restart'
-    !-----------------------------------------------------------------------
-
-    if (use_cn) then
-       begp = bounds%begp
-       endp = bounds%endp
-       call this%cnveg_carbonstate_inst%restart(bounds, ncid, flag=flag, carbon_type='c12', &
-               reseed_dead_plants=this%reseed_dead_plants, filter_reseed_patch=reseed_patch, &
-               num_reseed_patch=num_reseed_patch )
-       if ( flag /= 'read' .and. num_reseed_patch /= 0 )then
-          call endrun(msg="ERROR num_reseed should be zero and is not"//errmsg(sourcefile, __LINE__))
-       end if
-       call this%cnveg_carbonflux_inst%restart(bounds, ncid, flag=flag, carbon_type='c12')
-
-       call this%cnveg_nitrogenstate_inst%restart(bounds, ncid, flag=flag,  &
-            leafc_patch=this%cnveg_carbonstate_inst%leafc_patch(begp:endp),         &
-            leafc_storage_patch=this%cnveg_carbonstate_inst%leafc_storage_patch(begp:endp), &
-            frootc_patch=this%cnveg_carbonstate_inst%frootc_patch(begp:endp), &
-            frootc_storage_patch=this%cnveg_carbonstate_inst%frootc_storage_patch(begp:endp), &
-            deadstemc_patch=this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp), &
-            filter_reseed_patch=reseed_patch, num_reseed_patch=num_reseed_patch)
-       call this%cnveg_nitrogenflux_inst%restart(bounds, ncid, flag=flag)
-       call this%cnveg_state_inst%restart(bounds, ncid, flag=flag, &
-            cnveg_carbonstate=this%cnveg_carbonstate_inst, &
-            cnveg_nitrogenstate=this%cnveg_nitrogenstate_inst, &
-            filter_reseed_patch=reseed_patch, num_reseed_patch=num_reseed_patch)
-
-       call this%c_products_inst%restart(bounds, ncid, flag)
-       call this%n_products_inst%restart(bounds, ncid, flag)
-
-    end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine Init2(this, bounds, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Do initialization that is needed in the initialize phase, after subgrid weights are
-    ! determined
-    !
-    ! Should only be called if use_cn is true
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type) , intent(inout) :: this
-    type(bounds_type) , intent(in)    :: bounds
-    character(len=*)  , intent(in)    :: NLFilename ! namelist filename
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'Init2'
-    !-----------------------------------------------------------------------
-
-    call CNDriverInit(bounds, NLFilename )
-
-  end subroutine Init2
-
-
-  !-----------------------------------------------------------------------
-  subroutine WriteHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Do any history writes that are specific to vegetation dynamics
-    !
-    ! NOTE(wjs, 2016-02-23) This could probably be combined with
-    ! EndOfTimeStepVegDynamics, except for the fact that (currently) history writes are
-    ! done with proc bounds rather than clump bounds. If that were changed, then the body
-    ! of this could be moved into EndOfTimeStepVegDynamics, inside a "if (.not.
-    ! use_noio)" conditional.
-    !
-    ! Should only be called if use_cn is true
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(in) :: this
-    type(bounds_type)  , intent(in) :: bounds                  
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'WriteHistory'
-    !-----------------------------------------------------------------------
-
-  end subroutine WriteHistory
-
-  !-----------------------------------------------------------------------
-  function get_totvegc_col(this, bounds) result(totvegc_col)
-    !
-    ! !DESCRIPTION:
-    ! Get column-level total vegetation carbon array
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(cn_vegetation_type), intent(in) :: this
-    type(bounds_type), intent(in) :: bounds
-    real(r8) :: totvegc_col(bounds%begc:bounds%endc)  ! function result: (gC/m2)
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'get_totvegc_col'
-    !-----------------------------------------------------------------------
-
-    if (use_cn) then
-       totvegc_col(bounds%begc:bounds%endc) = &
-            this%cnveg_carbonstate_inst%totvegc_col(bounds%begc:bounds%endc)
-    else
-       totvegc_col(bounds%begc:bounds%endc) = nan
-    end if
-
-  end function get_totvegc_col
-
-
-end module CNVegetationFacade
diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
deleted file mode 100644
index 1b28927b35..0000000000
--- a/src/biogeochem/CropType.F90
+++ /dev/null
@@ -1,644 +0,0 @@
-module CropType
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module containing variables needed for the crop model
-  !
-  ! TODO(wjs, 2014-08-05) Move more crop-specific variables into here - many are
-  ! currently in CNVegStateType
-  !
-  ! !USES:
-  use shr_kind_mod        , only : r8 => shr_kind_r8
-  use shr_log_mod         , only : errMsg => shr_log_errMsg
-  use spmdMod             , only : masterproc
-  use abortutils          , only : endrun
-  use decompMod           , only : bounds_type
-  use clm_varcon          , only : spval
-  use clm_varctl          , only : iulog, use_crop
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC DATA TYPES:
-  !
-  ! Crop state variables structure
-  type, public :: crop_type
-
-     ! Note that cropplant and harvdate could be 2D to facilitate rotation
-     integer , pointer :: nyrs_crop_active_patch  (:)   ! number of years this crop patch has been active (0 for non-crop patches)
-     logical , pointer :: croplive_patch          (:)   ! patch Flag, true if planted, not harvested
-     logical , pointer :: cropplant_patch         (:)   ! patch Flag, true if planted
-     integer , pointer :: harvdate_patch          (:)   ! patch harvest date
-     real(r8), pointer :: fertnitro_patch         (:)   ! patch fertilizer nitrogen
-     real(r8), pointer :: gddplant_patch          (:)   ! patch accum gdd past planting date for crop       (ddays)
-     real(r8), pointer :: gddtsoi_patch           (:)   ! patch growing degree-days from planting (top two soil layers) (ddays)
-     real(r8), pointer :: vf_patch                (:)   ! patch vernalization factor for cereal
-     real(r8), pointer :: cphase_patch            (:)   ! phenology phase
-     real(r8), pointer :: latbaset_patch          (:)   ! Latitude vary baset for gddplant (degree C)
-     character(len=20) :: baset_mapping
-     real(r8) :: baset_latvary_intercept
-     real(r8) :: baset_latvary_slope
-
-   contains
-     ! Public routines
-     procedure, public  :: Init               ! Initialize the crop type
-     procedure, public  :: InitAccBuffer
-     procedure, public  :: InitAccVars
-     procedure, public  :: Restart
-     ! NOTE(wjs, 2014-09-29) need to rename this from UpdateAccVars to CropUpdateAccVars
-     ! to prevent cryptic error messages with pgi (v. 13.9 on yellowstone)
-     ! This is probably related to this bug
-     ! <http://www.pgroup.com/userforum/viewtopic.php?t=4285>, which was fixed in pgi 14.7.
-     procedure, public  :: CropUpdateAccVars
-
-     procedure, public  :: CropIncrementYear
-
-     ! Private routines
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-     procedure, private, nopass :: checkDates
-
-  end type crop_type
-
-  character(len=*), parameter, private :: baset_map_constant = 'constant'
-  character(len=*), parameter, private :: baset_map_latvary  = 'varytropicsbylat'
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !------------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(crop_type) , intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'Init'
-    !-----------------------------------------------------------------------
-    
-    call this%InitAllocate(bounds)
-
-    if (use_crop) then
-       call this%InitHistory(bounds)
-       call this%InitCold(bounds)
-    end if
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(crop_type) , intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitAllocate'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0
-    allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false.
-    allocate(this%cropplant_patch(begp:endp)) ; this%cropplant_patch(:) = .false.
-    allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) 
-    allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval
-    allocate(this%gddplant_patch (begp:endp)) ; this%gddplant_patch (:) = spval
-    allocate(this%gddtsoi_patch  (begp:endp)) ; this%gddtsoi_patch  (:) = spval
-    allocate(this%vf_patch       (begp:endp)) ; this%vf_patch       (:) = 0.0_r8
-    allocate(this%cphase_patch   (begp:endp)) ; this%cphase_patch   (:) = 0.0_r8
-    allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod    , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(crop_type),  intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-    
-    begp = bounds%begp; endp = bounds%endp
-
-    this%fertnitro_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FERTNITRO', units='gN/m2/yr', &
-         avgflag='A', long_name='Nitrogen fertilizer for each crop', &
-         ptr_patch=this%fertnitro_patch, default='inactive')
-
-    this%gddplant_patch(begp:endp) = spval
-    call hist_addfld1d (fname='GDDPLANT', units='ddays', &
-         avgflag='A', long_name='Accumulated growing degree days past planting date for crop', &
-         ptr_patch=this%gddplant_patch, default='inactive')
-
-    this%gddtsoi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='GDDTSOI', units='ddays', &
-         avgflag='A', long_name='Growing degree-days from planting (top two soil layers)', &
-         ptr_patch=this%gddtsoi_patch, default='inactive')
-
-    this%cphase_patch(begp:endp) = spval
-    call hist_addfld1d (fname='CPHASE', units='0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest', &
-         avgflag='A', long_name='crop phenology phase', &
-         ptr_patch=this%cphase_patch, default='inactive')
-
-    if ( (trim(this%baset_mapping) == baset_map_latvary) )then
-       this%latbaset_patch(begp:endp) = spval
-       call hist_addfld1d (fname='LATBASET', units='degree C', &
-            avgflag='A', long_name='latitude vary base temperature for gddplant', &
-            ptr_patch=this%latbaset_patch, default='inactive')
-    end if
-
-  end subroutine InitHistory
-
-  subroutine InitCold(this, bounds)
-    ! !USES:
-    use LandunitType, only : lun                
-    use landunit_varcon, only : istcrop
-    use PatchType, only : patch
-    use clm_instur, only : fert_cft
-    use pftconMod        , only : pftcon 
-    use GridcellType     , only : grc
-    use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
-    ! !ARGUMENTS:
-    class(crop_type),  intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c, l, g, p, m, ivt ! indices
-
-    character(len=*), parameter :: subname = 'InitCold'
-    !-----------------------------------------------------------------------
-
-!DLL - added wheat & sugarcane restrictions to base T vary by lat
-    do p= bounds%begp,bounds%endp
-       g   = patch%gridcell(p)
-       ivt = patch%itype(p)
-
-       this%nyrs_crop_active_patch(p) = 0
-
-       if ( grc%latdeg(g) >= 0.0_r8 .and. grc%latdeg(g) <= 30.0_r8) then
-          this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8-0.4_r8*grc%latdeg(g)
-       else if (grc%latdeg(g) < 0.0_r8 .and. grc%latdeg(g) >= -30.0_r8) then
-          this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8+0.4_r8*grc%latdeg(g)
-       else
-          this%latbaset_patch(p)=pftcon%baset(ivt)
-       end if
-       if ( trim(this%baset_mapping) == baset_map_constant ) then
-          this%latbaset_patch(p) = nan
-       end if
-    end do
-!DLL -- end of mods
-
-    if (use_crop) then
-       do p= bounds%begp,bounds%endp
-          g = patch%gridcell(p)
-          l = patch%landunit(p)
-          c = patch%column(p)
-
-          if (lun%itype(l) == istcrop) then
-             m = patch%itype(p)
-             this%fertnitro_patch(p) = fert_cft(g,m)
-          end if
-       end do
-    end if
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-
-    !-----------------------------------------------------------------------
-  subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    ! Each interval and accumulation type is unique to each field processed.
-    ! Routine [initAccBuffer] defines the fields to be processed
-    ! and the type of accumulation. 
-    ! Routine [updateAccVars] does the actual accumulation for a given field.
-    ! Fields are accumulated by calls to subroutine [update_accum_field]. 
-    ! To accumulate a field, it must first be defined in subroutine [initAccVars] 
-    ! and then accumulated by calls to [updateAccVars].
-    !
-    ! Should only be called if use_crop is true
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field
-    !
-    ! !ARGUMENTS:
-    class(crop_type) , intent(in) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    !
-    ! !LOCAL VARIABLES:
-    integer, parameter :: not_used = huge(1)
-
-    !---------------------------------------------------------------------
-
-    call init_accum_field (name='GDDPLANT', units='K', &
-         desc='growing degree-days from planting', accum_type='runaccum', accum_period=not_used,  &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    call init_accum_field (name='GDDTSOI', units='K', &
-         desc='growing degree-days from planting (top two soil layers)', accum_type='runaccum', accum_period=not_used,  &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! !USES:
-    use accumulMod       , only : extract_accum_field
-    use clm_time_manager , only : get_nstep
-    !
-    ! !ARGUMENTS:
-    class(crop_type),  intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begp, endp
-    integer  :: nstep
-    integer  :: ier
-    real(r8), pointer :: rbufslp(:)  ! temporary
-    
-    character(len=*), parameter :: subname = 'InitAccVars'
-    !-----------------------------------------------------------------------
-    
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Allocate needed dynamic memory for single level patch field
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)' in '
-       call endrun(msg=" allocation error for rbufslp"//&
-            errMsg(sourcefile, __LINE__))
-    endif
-
-    nstep = get_nstep()
-
-    call extract_accum_field ('GDDPLANT', rbufslp, nstep) 
-    this%gddplant_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('GDDTSOI', rbufslp, nstep) 
-    this%gddtsoi_patch(begp:endp)  = rbufslp(begp:endp)
-
-    deallocate(rbufslp)
-
-  end subroutine InitAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !USES:
-    use restUtilMod
-    use ncdio_pio
-    use PatchType, only : patch
-    use pftconMod, only : npcropmin, npcropmax
-    !
-    ! !ARGUMENTS:
-    class(crop_type), intent(inout)  :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   
-    character(len=*) , intent(in)    :: flag   
-    !
-    ! !LOCAL VARIABLES:
-    integer, pointer :: temp1d(:) ! temporary
-    integer :: restyear
-    integer :: p
-    logical :: readvar   ! determine if variable is on initial file
-
-    character(len=*), parameter :: subname = 'Restart'
-    !-----------------------------------------------------------------------
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag, varname='nyrs_crop_active', xtype=ncd_int, &
-            dim1name='pft', &
-            long_name='Number of years this crop patch has been active (0 for non-crop patches)', &
-            units='years', &
-            interpinic_flag='interp', readvar=readvar, data=this%nyrs_crop_active_patch)
-       if (flag == 'read' .and. .not. readvar) then
-          ! BACKWARDS_COMPATIBILITY(wjs, 2017-02-17) Old restart files did not have this
-          ! patch-level variable. Instead, they had a single scalar tracking the number
-          ! of years the crop model ran. Copy this scalar onto all *active* crop patches.
-
-          ! Some arguments in the following restartvar call are irrelevant, because we
-          ! only call this for 'read'. I'm simply maintaining the old restartvar call.
-          call restartvar(ncid=ncid, flag=flag,  varname='restyear', xtype=ncd_int,  &
-               long_name='Number of years prognostic crop ran', units="years", &
-               interpinic_flag='copy', readvar=readvar, data=restyear)
-          if (readvar) then
-             do p = bounds%begp, bounds%endp
-                if (patch%itype(p) >= npcropmin .and. patch%itype(p) <= npcropmax .and. &
-                     patch%active(p)) then
-                   this%nyrs_crop_active_patch(p) = restyear
-                end if
-             end do
-          end if
-       end if
-
-       allocate(temp1d(bounds%begp:bounds%endp))
-       if (flag == 'write') then 
-          do p= bounds%begp,bounds%endp
-             if (this%croplive_patch(p)) then
-                temp1d(p) = 1
-             else
-                temp1d(p) = 0
-             end if
-          end do
-       end if
-       call restartvar(ncid=ncid, flag=flag,  varname='croplive', xtype=ncd_log,  &
-            dim1name='pft', &
-            long_name='Flag that crop is alive, but not harvested', &
-            interpinic_flag='interp', readvar=readvar, data=temp1d)
-       if (flag == 'read') then 
-          do p= bounds%begp,bounds%endp
-             if (temp1d(p) == 1) then
-                this%croplive_patch(p) = .true.
-             else
-                this%croplive_patch(p) = .false.
-             end if
-          end do
-       end if
-       deallocate(temp1d)
-
-       allocate(temp1d(bounds%begp:bounds%endp))
-       if (flag == 'write') then 
-          do p= bounds%begp,bounds%endp
-             if (this%cropplant_patch(p)) then
-                temp1d(p) = 1
-             else
-                temp1d(p) = 0
-             end if
-          end do
-       end if
-       call restartvar(ncid=ncid, flag=flag,  varname='cropplant', xtype=ncd_log,  &
-            dim1name='pft', &
-            long_name='Flag that crop is planted, but not harvested' , &
-            interpinic_flag='interp', readvar=readvar, data=temp1d)
-       if (flag == 'read') then 
-          do p= bounds%begp,bounds%endp
-             if (temp1d(p) == 1) then
-                this%cropplant_patch(p) = .true.
-             else
-                this%cropplant_patch(p) = .false.
-             end if
-          end do
-       end if
-       deallocate(temp1d)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='harvdate', xtype=ncd_int,  &
-            dim1name='pft', long_name='harvest date', units='jday', nvalid_range=(/1,366/), & 
-            interpinic_flag='interp', readvar=readvar, data=this%harvdate_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='vf', xtype=ncd_double,  &
-            dim1name='pft', long_name='vernalization factor', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%vf_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='cphase',xtype=ncd_double, &
-            dim1name='pft', long_name='crop phenology phase', &
-            units='0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest', &
-            interpinic_flag='interp', readvar=readvar, data=this%cphase_patch)
-       if (flag=='read' )then
-          call this%checkDates( )  ! Check that restart date is same calendar date (even if year is different)
-                                   ! This is so that it properly goes through
-                                   ! the crop phases
-       end if
-    end if
-
-  end subroutine Restart
-
-
-  !-----------------------------------------------------------------------
-  subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col)
-    !
-    ! !DESCRIPTION:
-    ! Update accumulated variables. Should be called every time step.
-    ! Should only be called if use_crop is true.
-    !
-    ! !USES:
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    use clm_time_manager , only : get_step_size, get_nstep
-    use clm_varpar       , only : nlevsno, nlevgrnd
-    use pftconMod        , only : nswheat, nirrig_swheat, pftcon
-    use pftconMod        , only : nwwheat, nirrig_wwheat
-    use pftconMod        , only : nsugarcane, nirrig_sugarcane
-    use ColumnType       , only : col
-    use PatchType        , only : patch
-    !
-    ! !ARGUMENTS:
-    implicit none
-    class(crop_type)       , intent(inout) :: this
-    type(bounds_type)      , intent(in)    :: bounds
-    real(r8)               , intent(in)    :: t_ref2m_patch( bounds%begp:)
-    real(r8)               , intent(inout) :: t_soisno_col(bounds%begc:, -nlevsno+1:)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,c,g ! indices
-    integer :: ivt   ! vegetation type
-    integer :: dtime ! timestep size [seconds]
-    integer :: nstep ! timestep number
-    integer :: ier   ! error status
-    integer :: begp, endp
-    integer :: begc, endc
-    real(r8), pointer :: rbufslp(:)      ! temporary single level - patch level
-    character(len=*), parameter :: subname = 'CropUpdateAccVars'
-    !-----------------------------------------------------------------------
-    
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(t_ref2m_patch)  == (/endp/))          , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(t_soisno_col)   == (/endc,nlevgrnd/)) , errMsg(sourcefile, __LINE__))
-
-    dtime = get_step_size()
-    nstep = get_nstep()
-
-    ! Allocate needed dynamic memory for single level patch field
-
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'update_accum_hist allocation error for rbuf1dp'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Accumulate and extract GDDPLANT
-    
-    call extract_accum_field ('GDDPLANT', rbufslp, nstep)
-    do p = begp,endp
-      rbufslp(p) = max(0.,this%gddplant_patch(p)-rbufslp(p))
-    end do
-    call update_accum_field  ('GDDPLANT', rbufslp, nstep)
-    do p = begp,endp
-       if (this%croplive_patch(p)) then ! relative to planting date
-          ivt = patch%itype(p)
-          if ( (trim(this%baset_mapping) == baset_map_latvary) .and. &
-             ((ivt == nswheat) .or. (ivt == nirrig_swheat) .or. &
-              (ivt == nsugarcane) .or. (ivt == nirrig_sugarcane)) ) then
-             rbufslp(p) = max(0._r8, min(pftcon%mxtmp(ivt), &
-             t_ref2m_patch(p)-(SHR_CONST_TKFRZ + this%latbaset_patch(p)))) &
-             * dtime/SHR_CONST_CDAY
-          else
-             rbufslp(p) = max(0._r8, min(pftcon%mxtmp(ivt), &
-             t_ref2m_patch(p)-(SHR_CONST_TKFRZ + pftcon%baset(ivt)))) &
-             * dtime/SHR_CONST_CDAY
-          end if
-          if (ivt == nwwheat .or. ivt == nirrig_wwheat) then
-             rbufslp(p) = rbufslp(p) * this%vf_patch(p)
-          end if
-       else
-          rbufslp(p) = accumResetVal
-       end if
-    end do
-    call update_accum_field  ('GDDPLANT', rbufslp, nstep)
-    call extract_accum_field ('GDDPLANT', this%gddplant_patch, nstep)
-
-    ! Accumulate and extract GDDTSOI
-    ! In agroibis this variable is calculated
-    ! to 0.05 m, so here we use the top two soil layers
-
-    do p = begp,endp
-       if (this%croplive_patch(p)) then ! relative to planting date
-          ivt = patch%itype(p)
-          c   = patch%column(p)
-          rbufslp(p) = max(0._r8, min(pftcon%mxtmp(ivt), &
-               ((t_soisno_col(c,1)*col%dz(c,1) + &
-               t_soisno_col(c,2)*col%dz(c,2))/(col%dz(c,1)+col%dz(c,2))) - &
-               (SHR_CONST_TKFRZ + pftcon%baset(ivt)))) * dtime/SHR_CONST_CDAY
-          if (ivt == nwwheat .or. ivt == nwwheat) then
-             rbufslp(p) = rbufslp(p) * this%vf_patch(p)
-          end if
-       else
-          rbufslp(p) = accumResetVal
-       end if
-    end do
-    call update_accum_field  ('GDDTSOI', rbufslp, nstep)
-    call extract_accum_field ('GDDTSOI', this%gddtsoi_patch, nstep)
-
-    deallocate(rbufslp)
-
-  end subroutine CropUpdateAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine CropIncrementYear (this, num_pcropp, filter_pcropp)
-    !
-    ! !DESCRIPTION: 
-    ! Increment the crop year, if appropriate
-    !
-    ! This routine should be called every time step
-    !
-    ! !USES:
-    use clm_time_manager , only : get_curr_date, is_first_step
-    !
-    ! !ARGUMENTS:
-    class(crop_type) :: this
-    integer , intent(in) :: num_pcropp       ! number of prog. crop patches in filter
-    integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches
-    !
-    ! !LOCAL VARIABLES:
-    integer kyr   ! current year
-    integer kmo   ! month of year  (1, ..., 12)
-    integer kda   ! day of month   (1, ..., 31)
-    integer mcsec ! seconds of day (0, ..., seconds/day)
-    integer :: fp, p
-    !-----------------------------------------------------------------------
-
-    call get_curr_date (   kyr, kmo, kda, mcsec)
-    ! Update nyrs when it's the end of the year (unless it's the very start of the
-    ! run). This assumes that, if this patch is active at the end of the year, then it was
-    ! active for the whole year.
-    if ((kmo == 1 .and. kda == 1 .and. mcsec == 0) .and. .not. is_first_step()) then
-       do fp = 1, num_pcropp
-          p = filter_pcropp(fp)
-
-          this%nyrs_crop_active_patch(p) = this%nyrs_crop_active_patch(p) + 1
-       end do
-    end if
-
-  end subroutine CropIncrementYear
-
-  !-----------------------------------------------------------------------
-  subroutine checkDates( )
-    !
-    ! !DESCRIPTION: 
-    ! Make sure the dates are compatible. The date given to startup the model
-    ! and the date on the restart file must be the same although years can be
-    ! different. The dates need to be checked when the restart file is being
-    ! read in for a startup or branch case (they are NOT allowed to be different
-    ! for a restart case).
-    !
-    ! For the prognostic crop model the date of planting is tracked and growing
-    ! degree days is tracked (with a 20 year mean) -- so shifting the start dates
-    ! messes up these bits of saved information.
-    !
-    ! !ARGUMENTS:
-    use clm_time_manager, only : get_driver_start_ymd, get_start_date
-    use clm_varctl      , only : iulog
-    use clm_varctl      , only : nsrest, nsrBranch, nsrStartup
-    !
-    ! !LOCAL VARIABLES:
-    integer :: stymd       ! Start date YYYYMMDD from driver
-    integer :: styr        ! Start year from driver
-    integer :: stmon_day   ! Start date MMDD from driver
-    integer :: rsmon_day   ! Restart date MMDD from restart file
-    integer :: rsyr        ! Restart year from restart file
-    integer :: rsmon       ! Restart month from restart file
-    integer :: rsday       ! Restart day from restart file
-    integer :: tod         ! Restart time of day from restart file
-    character(len=*), parameter :: formDate = '(A,i4.4,"/",i2.2,"/",i2.2)' ! log output format
-    character(len=32) :: subname = 'CropRest::checkDates'
-    !-----------------------------------------------------------------------
-    !
-    ! If branch or startup make sure the startdate is compatible with the date
-    ! on the restart file.
-    !
-    if ( nsrest == nsrBranch .or. nsrest == nsrStartup )then
-       stymd       = get_driver_start_ymd()
-       styr        = stymd / 10000
-       stmon_day   = stymd - styr*10000
-       call get_start_date( rsyr, rsmon, rsday, tod )
-       rsmon_day = rsmon*100 + rsday
-       if ( masterproc ) &
-            write(iulog,formDate) 'Date on the restart file is: ', rsyr, rsmon, rsday
-       if ( stmon_day /= rsmon_day )then
-          write(iulog,formDate) 'Start date is: ', styr, stmon_day/100, &
-               (stmon_day - stmon_day/100)
-          call endrun(msg=' ERROR: For prognostic crop to work correctly, the start date (month and day)'// &
-               ' and the date on the restart file needs to match (years can be different)'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-    end if
-
-  end subroutine checkDates
-
-end module CropType
-
diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90
deleted file mode 100644
index 6a906e41ea..0000000000
--- a/src/biogeochem/DUSTMod.F90
+++ /dev/null
@@ -1,925 +0,0 @@
-module DUSTMod
-
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION: 
-  ! Routines in this module calculate Dust mobilization and dry deposition for dust.
-  ! Simulates dust mobilization due to wind from the surface into the 
-  ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust 
-  ! emission (kg/m**2/s) [ + = to atm].
-  ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition 
-  ! velocity through the lowest atmospheric layer). CAM will calculate the settling 
-  ! velocity through the whole atmospheric column. The two calculations will determine 
-  ! the dust dry deposition flux to the surface.
-  !                              
-  ! !USES:
-  use shr_kind_mod         , only : r8 => shr_kind_r8 
-  use shr_log_mod          , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar           , only : dst_src_nbr, ndst, sz_nbr
-  use clm_varcon           , only : grav, spval
-  use landunit_varcon      , only : istcrop, istsoil
-  use clm_varctl           , only : iulog
-  use abortutils           , only : endrun
-  use subgridAveMod        , only : p2l_1d
-  use decompMod            , only : bounds_type
-  use atm2lndType          , only : atm2lnd_type
-  use SoilStateType        , only : soilstate_type
-  use CanopyStateType      , only : canopystate_type
-  use WaterstateType       , only : waterstate_type
-  use FrictionVelocityMod  , only : frictionvel_type
-  use LandunitType         , only : lun
-  use ColumnType           , only : col
-  use PatchType            , only : patch
-  !  
-  ! !PUBLIC TYPES
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  !
-  public DustEmission   ! Dust mobilization 
-  public DustDryDep     ! Turbulent dry deposition for dust
-  !
-  ! !PUBLIC DATA:
-  !
-  real(r8) , allocatable :: ovr_src_snk_mss(:,:)
-  real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved
-  real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity
-  real(r8) tmp1                        !Factor in saltation computation (named as in Charlie's code)
-  real(r8) dns_aer                     ![kg m-3] Aerosol density
-  !
-  ! !PUBLIC DATA TYPES:
-  !
-  type, public :: dust_type
-
-     real(r8), pointer, PUBLIC  :: flx_mss_vrt_dst_patch     (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) 
-     real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:)   ! total dust flux into atmosphere
-     real(r8), pointer, private :: vlc_trb_patch             (:,:) ! turbulent deposition velocity  (m/s) (ndst) 
-     real(r8), pointer, private :: vlc_trb_1_patch           (:)   ! turbulent deposition velocity 1(m/s)
-     real(r8), pointer, private :: vlc_trb_2_patch           (:)   ! turbulent deposition velocity 2(m/s)
-     real(r8), pointer, private :: vlc_trb_3_patch           (:)   ! turbulent deposition velocity 3(m/s)
-     real(r8), pointer, private :: vlc_trb_4_patch           (:)   ! turbulent deposition velocity 4(m/s)
-     real(r8), pointer, private :: mbl_bsn_fct_col           (:)   ! basin factor
-
-   contains
-
-     procedure , public  :: Init
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory  
-     procedure , private :: InitCold     
-     procedure , private :: InitDustVars ! Initialize variables used in subroutine Dust
-
-  end type dust_type
-  !------------------------------------------------------------------------
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate (bounds)
-    call this%InitHistory  (bounds)
-    call this%InitCold     (bounds)
-    call this%InitDustVars (bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp,endp
-    integer :: begc,endc
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp ; endp = bounds%endp
-    begc = bounds%begc ; endc = bounds%endc
-
-    allocate(this%flx_mss_vrt_dst_patch     (begp:endp,1:ndst)) ; this%flx_mss_vrt_dst_patch     (:,:) = nan
-    allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp))        ; this%flx_mss_vrt_dst_tot_patch (:)   = nan
-    allocate(this%vlc_trb_patch             (begp:endp,1:ndst)) ; this%vlc_trb_patch             (:,:) = nan
-    allocate(this%vlc_trb_1_patch           (begp:endp))        ; this%vlc_trb_1_patch           (:)   = nan
-    allocate(this%vlc_trb_2_patch           (begp:endp))        ; this%vlc_trb_2_patch           (:)   = nan 
-    allocate(this%vlc_trb_3_patch           (begp:endp))        ; this%vlc_trb_3_patch           (:)   = nan
-    allocate(this%vlc_trb_4_patch           (begp:endp))        ; this%vlc_trb_4_patch           (:)   = nan
-    allocate(this%mbl_bsn_fct_col           (begc:endc))        ; this%mbl_bsn_fct_col     (:)   = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d
-    !
-    !
-    ! !ARGUMENTS:
-    class (dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp,endp
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    this%flx_mss_vrt_dst_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DSTFLXT', units='kg/m2/s',  &
-         avgflag='A', long_name='total surface dust emission', &
-         ptr_patch=this%flx_mss_vrt_dst_tot_patch, set_lake=0._r8, set_urb=0._r8, default='inactive')
-
-    this%vlc_trb_1_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB1', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 1', &
-         ptr_patch=this%vlc_trb_1_patch, default='inactive')
-
-    this%vlc_trb_2_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB2', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 2', &
-         ptr_patch=this%vlc_trb_2_patch, default='inactive')
-
-    this%vlc_trb_3_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB3', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 3', &
-         ptr_patch=this%vlc_trb_3_patch, default='inactive')
-
-    this%vlc_trb_4_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DPVLTRB4', units='m/s',  &
-         avgflag='A', long_name='turbulent deposition velocity 4', &
-         ptr_patch=this%vlc_trb_4_patch, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (dust_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,l
-    !-----------------------------------------------------------------------
-
-    ! Set basin factor to 1 for now
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       if (.not.lun%lakpoi(l)) then
-          this%mbl_bsn_fct_col(c) = 1.0_r8
-       end if
-    end do
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine DustEmission (bounds, &
-       num_nolakep, filter_nolakep, &
-       atm2lnd_inst, soilstate_inst, canopystate_inst, waterstate_inst, &
-       frictionvel_inst, dust_inst)
-    !
-    ! !DESCRIPTION: 
-    ! Dust mobilization. This code simulates dust mobilization due to wind
-    ! from the surface into the lowest atmospheric layer
-    ! On output flx_mss_vrt_dst(ndst) is the surface dust emission 
-    ! (kg/m**2/s) [ + = to atm]
-    ! Source: C. Zender's dust model
-    !
-    ! !USES
-    use shr_const_mod, only : SHR_CONST_RHOFW
-    use subgridaveMod, only : p2g
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)      , intent(in)    :: bounds                      
-    integer                , intent(in)    :: num_nolakep                 ! number of column non-lake points in patch filter
-    integer                , intent(in)    :: filter_nolakep(num_nolakep) ! patch filter for non-lake points
-    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
-    type(soilstate_type)   , intent(in)    :: soilstate_inst
-    type(canopystate_type) , intent(in)    :: canopystate_inst
-    type(waterstate_type)  , intent(in)    :: waterstate_inst
-    type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    type(dust_type)        , intent(inout) :: dust_inst
-
-    !
-    ! !LOCAL VARIABLES
-    integer  :: fp,p,c,l,g,m,n      ! indices
-    real(r8) :: liqfrac             ! fraction of total water that is liquid
-    real(r8) :: wnd_frc_rat         ! [frc] Wind friction threshold over wind friction
-    real(r8) :: wnd_frc_slt_dlt     ! [m s-1] Friction velocity increase from saltatn
-    real(r8) :: wnd_rfr_dlt         ! [m s-1] Reference windspeed excess over threshld
-    real(r8) :: dst_slt_flx_rat_ttl
-    real(r8) :: flx_mss_hrz_slt_ttl
-    real(r8) :: flx_mss_vrt_dst_ttl(bounds%begp:bounds%endp)
-    real(r8) :: frc_thr_wet_fct
-    real(r8) :: frc_thr_rgh_fct
-    real(r8) :: wnd_frc_thr_slt
-    real(r8) :: wnd_rfr_thr_slt
-    real(r8) :: wnd_frc_slt
-    real(r8) :: lnd_frc_mbl(bounds%begp:bounds%endp)
-    real(r8) :: bd
-    real(r8) :: gwc_sfc
-    real(r8) :: ttlai(bounds%begp:bounds%endp)
-    real(r8) :: tlai_lu(bounds%begl:bounds%endl)
-    real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights
-    logical  :: found                          ! temporary for error check
-    integer  :: index
-    !    
-    ! constants
-    !
-    real(r8), parameter :: cst_slt = 2.61_r8           ! [frc] Saltation constant
-    real(r8), parameter :: flx_mss_fdg_fct = 5.0e-4_r8 ! [frc] Empir. mass flx tuning eflx_lh_vegt
-    real(r8), parameter :: vai_mbl_thr = 0.3_r8        ! [m2 m-2] VAI threshold quenching dust mobilization
-    !------------------------------------------------------------------------
-
-    associate(                                                         & 
-         forc_rho            => atm2lnd_inst%forc_rho_downscaled_col , & ! Input:  [real(r8) (:)   ]  downscaled density (kg/m**3)                                 
-         
-         gwc_thr             => soilstate_inst%gwc_thr_col           , & ! Input:  [real(r8) (:)   ]  threshold gravimetric soil moisture based on clay content
-         mss_frc_cly_vld     => soilstate_inst%mss_frc_cly_vld_col   , & ! Input:  [real(r8) (:)   ]  [frc] Mass fraction clay limited to 0.20          
-         watsat              => soilstate_inst%watsat_col            , & ! Input:  [real(r8) (:,:) ]  saturated volumetric soil water                 
-         
-         tlai                => canopystate_inst%tlai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided leaf area index, no burying by snow     
-         tsai                => canopystate_inst%tsai_patch          , & ! Input:  [real(r8) (:)   ]  one-sided stem area index, no burying by snow     
-         
-         frac_sno            => waterstate_inst%frac_sno_col         , & ! Input:  [real(r8) (:)   ]  fraction of ground covered by snow (0 to 1)       
-         h2osoi_vol          => waterstate_inst%h2osoi_vol_col       , & ! Input:  [real(r8) (:,:) ]  volumetric soil water (0<=h2osoi_vol<=watsat)   
-         h2osoi_liq          => waterstate_inst%h2osoi_liq_col       , & ! Input:  [real(r8) (:,:) ]  liquid soil water (kg/m2)                       
-         h2osoi_ice          => waterstate_inst%h2osoi_ice_col       , & ! Input:  [real(r8) (:,:) ]  frozen soil water (kg/m2)                       
-         
-         fv                  => frictionvel_inst%fv_patch            , & ! Input:  [real(r8) (:)   ]  friction velocity (m/s) (for dust model)          
-         u10                 => frictionvel_inst%u10_patch           , & ! Input:  [real(r8) (:)   ]  10-m wind (m/s) (created for dust model)          
-         
-         mbl_bsn_fct         => dust_inst%mbl_bsn_fct_col            , & ! Input:  [real(r8) (:)   ]  basin factor                                      
-         flx_mss_vrt_dst     => dust_inst%flx_mss_vrt_dst_patch      , & ! Output: [real(r8) (:,:) ]  surface dust emission (kg/m**2/s)               
-         flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch    & ! Output: [real(r8) (:)   ]  total dust flux back to atmosphere (pft)
-         )
-
-      ttlai(bounds%begp : bounds%endp) = 0._r8
-      ! make lai average at landunit level
-      do fp = 1,num_nolakep
-         p = filter_nolakep(fp)
-         ttlai(p) = tlai(p)+tsai(p)
-      enddo
-
-      tlai_lu(bounds%begl : bounds%endl) = spval
-      sumwt(bounds%begl : bounds%endl) = 0._r8
-      do p = bounds%begp,bounds%endp
-         if (ttlai(p) /= spval .and. patch%active(p) .and. patch%wtlunit(p) /= 0._r8) then
-            c = patch%column(p)
-            l = patch%landunit(p)
-            if (sumwt(l) == 0._r8) tlai_lu(l) = 0._r8
-            tlai_lu(l) = tlai_lu(l) + ttlai(p) * patch%wtlunit(p)
-            sumwt(l) = sumwt(l) + patch%wtlunit(p)
-         end if
-      end do
-      found = .false.
-      do l = bounds%begl,bounds%endl
-         if (sumwt(l) > 1.0_r8 + 1.e-6_r8) then
-            found = .true.
-            index = l
-            exit
-         else if (sumwt(l) /= 0._r8) then
-            tlai_lu(l) = tlai_lu(l)/sumwt(l)
-         end if
-      end do
-      if (found) then
-         write(iulog,*) 'p2l_1d error: sumwt is greater than 1.0 at l= ',index
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-      end if
-
-      ! Loop through patches
-
-      ! initialize variables which get passed to the atmosphere
-      flx_mss_vrt_dst(bounds%begp:bounds%endp,:)=0._r8
-
-      do fp = 1,num_nolakep
-         p = filter_nolakep(fp)
-         c = patch%column(p)
-         l = patch%landunit(p)
-
-         ! the following code from subr. lnd_frc_mbl_get was adapted for lsm use
-         ! purpose: return fraction of each gridcell suitable for dust mobilization
-
-         ! the "bare ground" fraction of the current sub-gridscale cell decreases
-         ! linearly from 1 to 0 as VAI(=tlai+tsai) increases from 0 to vai_mbl_thr
-         ! if ice sheet, wetland, or lake, no dust allowed
-
-         if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-            if (tlai_lu(l) < vai_mbl_thr) then
-               lnd_frc_mbl(p) = 1.0_r8 - (tlai_lu(l))/vai_mbl_thr
-            else
-               lnd_frc_mbl(p) = 0.0_r8
-            endif
-            lnd_frc_mbl(p) = lnd_frc_mbl(p) * (1.0_r8 - frac_sno(c))
-         else          
-            lnd_frc_mbl(p) = 0.0_r8   
-         end if
-      end do
-
-      do fp = 1,num_nolakep
-         p = filter_nolakep(fp)
-         if (lnd_frc_mbl(p)>1.0_r8 .or. lnd_frc_mbl(p)<0.0_r8) then
-            write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p)
-            call endrun(msg=errMsg(sourcefile, __LINE__))
-         end if
-      end do
-
-      ! reset history output variables before next if-statement to avoid output = inf
-
-      do fp = 1,num_nolakep
-         p = filter_nolakep(fp)
-         flx_mss_vrt_dst_tot(p) = 0.0_r8
-      end do
-      do n = 1, ndst
-         do fp = 1,num_nolakep
-            p = filter_nolakep(fp)
-            flx_mss_vrt_dst(p,n) = 0.0_r8
-         end do
-      end do
-
-      do fp = 1,num_nolakep
-         p = filter_nolakep(fp)
-         c = patch%column(p)
-         l = patch%landunit(p)
-         g = patch%gridcell(p)
-
-         ! only perform the following calculations if lnd_frc_mbl is non-zero 
-
-         if (lnd_frc_mbl(p) > 0.0_r8) then
-
-            ! the following comes from subr. frc_thr_rgh_fct_get
-            ! purpose: compute factor by which surface roughness increases threshold
-            !          friction velocity (currently a constant)
-
-            frc_thr_rgh_fct = 1.0_r8
-
-            ! the following comes from subr. frc_thr_wet_fct_get
-            ! purpose: compute factor by which soil moisture increases threshold friction velocity
-            ! adjust threshold velocity for inhibition by moisture
-            ! modified 4/5/2002 (slevis) to use gravimetric instead of volumetric
-            ! water content
-
-            bd = (1._r8-watsat(c,1))*2.7e3_r8      ![kg m-3] Bulk density of dry surface soil
-            gwc_sfc = h2osoi_vol(c,1)*SHR_CONST_RHOFW/bd    ![kg kg-1] Gravimetric H2O cont
-            if (gwc_sfc > gwc_thr(c)) then
-               frc_thr_wet_fct = sqrt(1.0_r8 + 1.21_r8 * (100.0_r8*(gwc_sfc - gwc_thr(c)))**0.68_r8)
-            else
-               frc_thr_wet_fct = 1.0_r8
-            end if
-
-            ! slevis: adding liqfrac here, because related to effects from soil water
-
-            liqfrac = max( 0.0_r8, min( 1.0_r8, h2osoi_liq(c,1) / (h2osoi_ice(c,1)+h2osoi_liq(c,1)+1.0e-6_r8) ) )
-
-            ! the following lines come from subr. dst_mbl
-            ! purpose: adjust threshold friction velocity to acct for moisture and
-            !          roughness. The ratio tmp1 / sqrt(forc_rho) comes from
-            !          subr. wnd_frc_thr_slt_get which computes dry threshold
-            !          friction velocity for saltation
-
-            wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct
-
-            ! reset these variables which will be updated in the following if-block
-
-            wnd_frc_slt = fv(p)
-            flx_mss_hrz_slt_ttl = 0.0_r8
-            flx_mss_vrt_dst_ttl(p) = 0.0_r8
-
-            ! the following line comes from subr. dst_mbl
-            ! purpose: threshold saltation wind speed
-
-            wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p)
-
-            ! the following if-block comes from subr. wnd_frc_slt_get 
-            ! purpose: compute the saltating friction velocity
-            ! theory: saltation roughens the boundary layer, AKA "Owen's effect"
-
-            if (u10(p) >= wnd_rfr_thr_slt) then
-               wnd_rfr_dlt = u10(p) - wnd_rfr_thr_slt
-               wnd_frc_slt_dlt = 0.003_r8 * wnd_rfr_dlt * wnd_rfr_dlt
-               wnd_frc_slt = fv(p) + wnd_frc_slt_dlt
-            end if
-
-            ! the following comes from subr. flx_mss_hrz_slt_ttl_Whi79_get
-            ! purpose: compute vertically integrated streamwise mass flux of particles
-
-            if (wnd_frc_slt > wnd_frc_thr_slt) then
-               wnd_frc_rat = wnd_frc_thr_slt / wnd_frc_slt
-               flx_mss_hrz_slt_ttl = cst_slt * forc_rho(c) * (wnd_frc_slt**3.0_r8) * &
-                    (1.0_r8 - wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) * (1.0_r8 + wnd_frc_rat) / grav
-
-               ! the following loop originates from subr. dst_mbl
-               ! purpose: apply land sfc and veg limitations and global tuning factor
-               ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect 
-               ! of frozen soil
-
-               flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * &
-                    flx_mss_fdg_fct * liqfrac
-            end if
-
-            ! the following comes from subr. flx_mss_vrt_dst_ttl_MaB95_get
-            ! purpose: diagnose total vertical mass flux of dust from vertically
-            !          integrated streamwise mass flux
-
-            dst_slt_flx_rat_ttl = 100.0_r8 * exp( log(10.0_r8) * (13.4_r8 * mss_frc_cly_vld(c) - 6.0_r8) )
-            flx_mss_vrt_dst_ttl(p) = flx_mss_hrz_slt_ttl * dst_slt_flx_rat_ttl
-
-         end if   ! lnd_frc_mbl > 0.0
-
-      end do
-
-      ! the following comes from subr. flx_mss_vrt_dst_prt in C. Zender's code
-      ! purpose: partition total vertical mass flux of dust into transport bins
-
-      do n = 1, ndst
-         do m = 1, dst_src_nbr
-            do fp = 1,num_nolakep
-               p = filter_nolakep(fp)
-               if (lnd_frc_mbl(p) > 0.0_r8) then
-                  flx_mss_vrt_dst(p,n) = flx_mss_vrt_dst(p,n) +  ovr_src_snk_mss(m,n) * flx_mss_vrt_dst_ttl(p)
-               end if
-            end do
-         end do
-      end do
-
-      do n = 1, ndst
-         do fp = 1,num_nolakep
-            p = filter_nolakep(fp)
-            if (lnd_frc_mbl(p) > 0.0_r8) then
-               flx_mss_vrt_dst_tot(p) = flx_mss_vrt_dst_tot(p) + flx_mss_vrt_dst(p,n)
-            end if
-         end do
-      end do
-
-    end associate
-
-  end subroutine DustEmission
-
-   !------------------------------------------------------------------------
-  subroutine DustDryDep (bounds, &
-       atm2lnd_inst, frictionvel_inst, dust_inst)
-    !
-    ! !DESCRIPTION: 
-    !
-    ! Determine Turbulent dry deposition for dust. Calculate the turbulent 
-    ! component of dust dry deposition, (the turbulent deposition velocity 
-    ! through the lowest atmospheric layer. CAM will calculate the settling 
-    ! velocity through the whole atmospheric column. The two calculations 
-    ! will determine the dust dry deposition flux to the surface.
-    ! Note: Same process should occur over oceans. For the coupled CESM,
-    ! we may find it more efficient to let CAM calculate the turbulent dep
-    ! velocity over all surfaces. This would require passing the
-    ! aerodynamic resistance, ram(1), and the friction velocity, fv, from
-    ! the land to the atmosphere component. In that case, dustini need not
-    ! calculate particle diamter (dmt_vwr) and particle density (dns_aer).
-    ! Source: C. Zender's dry deposition code
-    !
-    ! !USES
-    use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)      , intent(in)    :: bounds 
-    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
-    type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    type(dust_type)        , intent(inout) :: dust_inst
-    !
-    ! !LOCAL VARIABLES
-    integer  :: p,c,g,m,n                             ! indices
-    real(r8) :: vsc_dyn_atm(bounds%begp:bounds%endp)  ! [kg m-1 s-1] Dynamic viscosity of air
-    real(r8) :: vsc_knm_atm(bounds%begp:bounds%endp)  ! [m2 s-1] Kinematic viscosity of atmosphere
-    real(r8) :: shm_nbr_xpn                           ! [frc] Sfc-dep exponent for aerosol-diffusion dependence on Schmidt number
-    real(r8) :: shm_nbr                               ! [frc] Schmidt number
-    real(r8) :: stk_nbr                               ! [frc] Stokes number
-    real(r8) :: mfp_atm                               ! [m] Mean free path of air
-    real(r8) :: dff_aer                               ! [m2 s-1] Brownian diffusivity of particle
-    real(r8) :: rss_trb                               ! [s m-1] Resistance to turbulent deposition
-    real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor
-    real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity
-    real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance
-    real(r8) :: tmp                                   ! temporary 
-    real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land
-    !------------------------------------------------------------------------
-
-    associate(                                                   & 
-         forc_pbot =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8)  (:)   ]  atm pressure (Pa)                                 
-         forc_rho  =>    atm2lnd_inst%forc_rho_downscaled_col  , & ! Input:  [real(r8)  (:)   ]  atm density (kg/m**3)                             
-         forc_t    =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8)  (:)   ]  atm temperature (K)                               
-         
-         ram1      =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8)  (:)   ]  aerodynamical resistance (s/m)                    
-         fv        =>    frictionvel_inst%fv_patch             , & ! Input:  [real(r8)  (:)   ]  friction velocity (m/s)                           
-         
-         vlc_trb   =>    dust_inst%vlc_trb_patch               , & ! Output:  [real(r8) (:,:) ]  Turbulent deposn velocity (m/s)                 
-         vlc_trb_1 =>    dust_inst%vlc_trb_1_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 1                   
-         vlc_trb_2 =>    dust_inst%vlc_trb_2_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 2                   
-         vlc_trb_3 =>    dust_inst%vlc_trb_3_patch             , & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 3                   
-         vlc_trb_4 =>    dust_inst%vlc_trb_4_patch               & ! Output:  [real(r8) (:)   ]  Turbulent deposition velocity 4                   
-         )
-
-      do p = bounds%begp,bounds%endp
-         if (patch%active(p)) then
-            g = patch%gridcell(p)
-            c = patch%column(p)
-
-            ! from subroutine dst_dps_dry (consider adding sanity checks from line 212)
-            ! when code asks to use midlayer density, pressure, temperature,
-            ! I use the data coming in from the atmosphere, ie forc_t, forc_pbot, forc_rho
-
-            ! Quasi-laminar layer resistance: call rss_lmn_get
-            ! Size-independent thermokinetic properties
-
-            vsc_dyn_atm(p) = 1.72e-5_r8 * ((forc_t(c)/273.0_r8)**1.5_r8) * 393.0_r8 / &
-                 (forc_t(c)+120.0_r8)      ![kg m-1 s-1] RoY94 p. 102
-            mfp_atm = 2.0_r8 * vsc_dyn_atm(p) / &   ![m] SeP97 p. 455
-                 (forc_pbot(c)*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*forc_t(c))))
-            vsc_knm_atm(p) = vsc_dyn_atm(p) / forc_rho(c) ![m2 s-1] Kinematic viscosity of air
-
-            do m = 1, ndst
-               slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * &
-                    (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-                    dmt_vwr(m)   ![frc] Slip correction factor SeP97 p. 464
-               vlc_grv(p,m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * &
-                    grav * slp_crc(p,m) / vsc_dyn_atm(p)   ![m s-1] Stokes' settling velocity SeP97 p. 466
-               vlc_grv(p,m) = vlc_grv(p,m) * stk_crc(m)    ![m s-1] Correction to Stokes settling velocity
-            end do
-         end if
-      end do
-
-      do m = 1, ndst
-         do p = bounds%begp,bounds%endp
-            if (patch%active(p)) then
-               g = patch%gridcell(p)
-               c = patch%column(p)
-
-               stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p))  ![frc] SeP97 p.965
-               dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / &          ![m2 s-1]
-                    (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * dmt_vwr(m))          !SeP97 p.474
-               shm_nbr = vsc_knm_atm(p) / dff_aer                                ![frc] SeP97 p.972
-               shm_nbr_xpn = shm_nbr_xpn_lnd                                     ![frc]
-
-               ! fxm: Turning this on dramatically reduces
-               ! deposition velocity in low wind regimes
-               ! Schmidt number exponent is -2/3 over solid surfaces and
-               ! -1/2 over liquid surfaces SlS80 p. 1014
-               ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd
-               ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # 
-
-               tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr)
-               rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965
-            end if
-         end do
-      end do
-
-      ! Lowest layer: Turbulent deposition (CAM will calc. gravitational dep)
-
-      do m = 1, ndst
-         do p = bounds%begp,bounds%endp
-            if (patch%active(p)) then
-               rss_trb = ram1(p) + rss_lmn(p,m) + ram1(p) * rss_lmn(p,m) * vlc_grv(p,m) ![s m-1]
-               vlc_trb(p,m) = 1.0_r8 / rss_trb                                          ![m s-1]
-            end if
-         end do
-      end do
-
-      do p = bounds%begp,bounds%endp
-         if (patch%active(p)) then
-            vlc_trb_1(p) = vlc_trb(p,1)
-            vlc_trb_2(p) = vlc_trb(p,2)
-            vlc_trb_3(p) = vlc_trb(p,3)
-            vlc_trb_4(p) = vlc_trb(p,4)
-         end if
-      end do
-
-    end associate
-
-  end subroutine DustDryDep
-
-   !------------------------------------------------------------------------
-   subroutine InitDustVars(this, bounds)
-     !
-     ! !DESCRIPTION: 
-     !
-     ! Compute source efficiency factor from topography
-     ! Initialize other variables used in subroutine Dust:
-     ! ovr_src_snk_mss(m,n) and tmp1.
-     ! Define particle diameter and density needed by atm model
-     ! as well as by dry dep model
-     ! Source: Paul Ginoux (for source efficiency factor)
-     ! Modifications by C. Zender and later by S. Levis
-     ! Rest of subroutine from C. Zender's dust model
-     !
-     ! !USES
-     use shr_const_mod , only: SHR_CONST_PI, SHR_CONST_RDAIR
-     use shr_spfn_mod  , only: erf => shr_spfn_erf
-     use decompMod     , only : get_proc_bounds
-     !
-     ! !ARGUMENTS:
-     class(dust_type)  :: this
-     type(bounds_type), intent(in) :: bounds  
-     !
-     ! !LOCAL VARIABLES
-    integer  :: fc,c,l,m,n              ! indices
-    real(r8) :: ovr_src_snk_frc
-    real(r8) :: sqrt2lngsdi             ! [frc] Factor in erf argument
-    real(r8) :: lndmaxjovrdmdni         ! [frc] Factor in erf argument
-    real(r8) :: lndminjovrdmdni         ! [frc] Factor in erf argument
-    real(r8) :: ryn_nbr_frc_thr_prx_opt ! [frc] Threshold friction Reynolds number approximation for optimal size
-    real(r8) :: ryn_nbr_frc_thr_opt_fnc ! [frc] Threshold friction Reynolds factor for saltation calculation
-    real(r8) :: icf_fct                 ! Interpartical cohesive forces factor for saltation calc
-    real(r8) :: dns_fct                 ! Density ratio factor for saltation calculation
-    real(r8) :: dmt_min(ndst)           ! [m] Size grid minimum
-    real(r8) :: dmt_max(ndst)           ! [m] Size grid maximum
-    real(r8) :: dmt_ctr(ndst)           ! [m] Diameter at bin center
-    real(r8) :: dmt_dlt(ndst)           ! [m] Width of size bin
-    real(r8) :: slp_crc(ndst)           ! [frc] Slip correction factor
-    real(r8) :: vlm_rsl(ndst)           ! [m3 m-3] Volume concentration resolved
-    real(r8) :: vlc_stk(ndst)           ! [m s-1] Stokes settling velocity
-    real(r8) :: vlc_grv(ndst)           ! [m s-1] Settling velocity
-    real(r8) :: ryn_nbr_grv(ndst)       ! [frc] Reynolds number at terminal velocity
-    real(r8) :: cff_drg_grv(ndst)       ! [frc] Drag coefficient at terminal velocity
-    real(r8) :: tmp                     ! temporary 
-    real(r8) :: ln_gsd                  ! [frc] ln(gsd)
-    real(r8) :: gsd_anl                 ! [frc] Geometric standard deviation
-    real(r8) :: dmt_vma                 ! [m] Mass median diameter analytic She84 p.75 Tabl.1
-    real(r8) :: dmt_nma                 ! [m] Number median particle diameter
-    real(r8) :: lgn_dst                 ! Lognormal distribution at sz_ctr
-    real(r8) :: eps_max                 ! [frc] Relative accuracy for convergence
-    real(r8) :: eps_crr                 ! [frc] Current relative accuracy
-    real(r8) :: itr_idx                 ! [idx] Counting index
-    real(r8) :: dns_mdp                 ! [kg m-3] Midlayer density
-    real(r8) :: mfp_atm                 ! [m] Mean free path of air
-    real(r8) :: vsc_dyn_atm             ! [kg m-1 s-1] Dynamic viscosity of air
-    real(r8) :: vsc_knm_atm             ! [kg m-1 s-1] Kinematic viscosity of air
-    real(r8) :: vlc_grv_old             ! [m s-1] Previous gravitational settling velocity
-    real(r8) :: series_ratio            ! Factor for logarithmic grid
-    real(r8) :: lngsdsqrttwopi_rcp      ! Factor in lognormal distribution
-    real(r8) :: sz_min(sz_nbr)          ! [m] Size Bin minima
-    real(r8) :: sz_max(sz_nbr)          ! [m] Size Bin maxima
-    real(r8) :: sz_ctr(sz_nbr)          ! [m] Size Bin centers
-    real(r8) :: sz_dlt(sz_nbr)          ! [m] Size Bin widths
-    
-    ! constants
-    real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter       BSM96 p. 73 Table 2
-    real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation  BSM96 p. 73 Table 2
-    real(r8), allocatable :: mss_frc_src(:) ! [frc] Mass fraction            BSM96 p. 73 Table 2
-
-    real(r8) :: dmt_grd(5) =                  &     ! [m] Particle diameter grid
-         (/ 0.1e-6_r8, 1.0e-6_r8, 2.5e-6_r8, 5.0e-6_r8, 10.0e-6_r8 /)
-    real(r8), parameter :: dmt_slt_opt = 75.0e-6_r8    ! [m] Optim diam for saltation
-    real(r8), parameter :: dns_slt = 2650.0_r8         ! [kg m-3] Density of optimal saltation particles
-    !------------------------------------------------------------------------
-
-    associate(& 
-         mbl_bsn_fct  =>  this%mbl_bsn_fct_col   & ! Output:  [real(r8) (:)] basin factor                                       
-         )
-
-      ! allocate module variable
-      allocate (ovr_src_snk_mss(dst_src_nbr,ndst))  
-      allocate (dmt_vwr(ndst))
-      allocate (stk_crc(ndst))
-
-      ! allocate local variable
-      allocate (dmt_vma_src(dst_src_nbr))  
-      allocate (gsd_anl_src(dst_src_nbr))  
-      allocate (mss_frc_src(dst_src_nbr))  
-
-      dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /)        
-      gsd_anl_src(:) = (/ 2.10_r8     , 1.90_r8    , 1.60_r8     /)        
-      mss_frc_src(:) = (/ 0.036_r8    , 0.957_r8   , 0.007_r8 /)                  
-
-      ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get
-      !                      and (2) dstszdst.F subroutine dst_szdst_ini
-      ! purpose(1): given one set (the "source") of lognormal distributions,
-      !             and one set of bin boundaries (the "sink"), compute and return
-      !             the overlap factors between the source and sink distributions
-      ! purpose(2): set important statistics of size distributions
-
-      do m = 1, dst_src_nbr
-         sqrt2lngsdi = sqrt(2.0_r8) * log(gsd_anl_src(m))
-         do n = 1, ndst
-            lndmaxjovrdmdni = log(dmt_grd(n+1)/dmt_vma_src(m))
-            lndminjovrdmdni = log(dmt_grd(n  )/dmt_vma_src(m))
-            ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - &
-                 erf(lndminjovrdmdni/sqrt2lngsdi))
-            ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m)
-         end do
-      end do
-
-      ! The following code from subroutine wnd_frc_thr_slt_get was placed 
-      ! here because tmp1 needs to be defined just once
-
-      ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8
-
-      if (ryn_nbr_frc_thr_prx_opt < 0.03_r8) then
-         write(iulog,*) 'dstmbl: ryn_nbr_frc_thr_prx_opt < 0.03'
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-      else if (ryn_nbr_frc_thr_prx_opt < 10.0_r8) then
-         ryn_nbr_frc_thr_opt_fnc = -1.0_r8 + 1.928_r8 * (ryn_nbr_frc_thr_prx_opt**0.0922_r8)
-         ryn_nbr_frc_thr_opt_fnc = 0.1291_r8 * 0.1291_r8 / ryn_nbr_frc_thr_opt_fnc
-      else
-         ryn_nbr_frc_thr_opt_fnc = 1.0_r8 - 0.0858_r8 * exp(-0.0617_r8*(ryn_nbr_frc_thr_prx_opt-10.0_r8))
-         ryn_nbr_frc_thr_opt_fnc = 0.120_r8 * 0.120_r8 * ryn_nbr_frc_thr_opt_fnc * ryn_nbr_frc_thr_opt_fnc
-      end if
-
-      icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8))
-      dns_fct = dns_slt * grav * dmt_slt_opt
-      tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc)
-
-      ! Introducing particle diameter. Needed by atm model and by dry dep model.
-      ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl,
-      ! grd_mk (dstpsd.F90) and subroutine lgn_evl (psdlgn.F90)
-
-      ! Charlie allows logarithmic or linear option for size distribution
-      ! however, he hardwires the distribution to logarithmic in his code
-      ! therefore, I take his logarithmic code only
-      ! furthermore, if dst_nbr == 4, he overrides the automatic grid calculation
-      ! he currently works with dst_nbr = 4, so I only take the relevant code
-      ! if ndst ever becomes different from 4, must add call grd_mk (dstpsd.F90)
-      ! as done in subroutine dst_psd_ini
-      ! note that here ndst = dst_nbr
-
-      ! Override automatic grid with preset grid if available
-
-      if (ndst == 4) then
-         do n = 1, ndst
-            dmt_min(n) = dmt_grd(n)                       ![m] Max diameter in bin
-            dmt_max(n) = dmt_grd(n+1)                     ![m] Min diameter in bin
-            dmt_ctr(n) = 0.5_r8 * (dmt_min(n)+dmt_max(n)) ![m] Diameter at bin ctr
-            dmt_dlt(n) = dmt_max(n)-dmt_min(n)            ![m] Width of size bin
-         end do
-      else
-         write(iulog,*) 'Dustini error: ndst must equal to 4 with current code'
-         call endrun(msg=errMsg(sourcefile, __LINE__))
-         !see more comments above end if ndst == 4
-      end if
-
-      ! Bin physical properties
-
-      gsd_anl = 2.0_r8      ! [frc] Geometric std dev PaG77 p. 2080 Table1
-      ln_gsd = log(gsd_anl)
-      dns_aer = 2.5e+3_r8   ! [kg m-3] Aerosol density
-
-      ! Set a fundamental statistic for each bin
-
-      dmt_vma = 3.5000e-6_r8 ! [m] Mass median diameter analytic She84 p.75 Table1
-
-      ! Compute analytic size statistics
-      ! Convert mass median diameter to number median diameter (call vma2nma)
-
-      dmt_nma = dmt_vma * exp(-3.0_r8*ln_gsd*ln_gsd) ! [m]
-
-      ! Compute resolved size statistics for each size distribution
-      ! In C. Zender's code call dst_sz_rsl
-
-      do n = 1, ndst
-
-         series_ratio = (dmt_max(n)/dmt_min(n))**(1.0_r8/sz_nbr)
-         sz_min(1) = dmt_min(n)
-         do m = 2, sz_nbr                            ! Loop starts at 2
-            sz_min(m) = sz_min(m-1) * series_ratio
-         end do
-
-         ! Derived grid values
-         do m = 1, sz_nbr-1                          ! Loop ends at sz_nbr-1
-            sz_max(m) = sz_min(m+1)                  ! [m]
-         end do
-         sz_max(sz_nbr) = dmt_max(n)                 ! [m]
-
-         ! Final derived grid values
-         do m = 1, sz_nbr
-            sz_ctr(m) = 0.5_r8 * (sz_min(m)+sz_max(m))
-            sz_dlt(m) = sz_max(m)-sz_min(m)
-         end do
-
-         lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI))
-         dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved
-         vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved
-
-         do m = 1, sz_nbr
-
-            ! Evaluate lognormal distribution for these sizes (call lgn_evl)
-            tmp = log(sz_ctr(m)/dmt_nma) / ln_gsd
-            lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m)
-
-            ! Integrate moments of size distribution
-            dmt_vwr(n) = dmt_vwr(n) + sz_ctr(m) *                    &
-                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
-                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
-            vlm_rsl(n) = vlm_rsl(n) +                                &
-                 SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume
-                 lgn_dst * sz_dlt(m)                ![# m-3] Number concentrn
-
-         end do
-
-         dmt_vwr(n) = dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved
-
-      end do
-
-      ! calculate correction to Stokes' settling velocity (subroutine stk_crc_get)
-
-      eps_max = 1.0e-4_r8
-      dns_mdp = 100000._r8 / (295.0_r8*SHR_CONST_RDAIR) ![kg m-3] const prs_mdp & tpt_vrt
-
-      ! Size-independent thermokinetic properties
-
-      vsc_dyn_atm = 1.72e-5_r8 * ((295.0_r8/273.0_r8)**1.5_r8) * 393.0_r8 / &
-           (295.0_r8+120.0_r8)      ![kg m-1 s-1] RoY94 p.102 tpt_mdp=295.0
-      mfp_atm = 2.0_r8 * vsc_dyn_atm / &  !SeP97 p. 455 constant prs_mdp, tpt_mdp
-           (100000._r8*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*295.0_r8)))
-      vsc_knm_atm = vsc_dyn_atm / dns_mdp ![m2 s-1] Kinematic viscosity of air
-
-      do m = 1, ndst
-         slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm *                      &
-              (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / &
-              dmt_vwr(m)                      ! [frc] Slip correction factor SeP97 p.464
-         vlc_stk(m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * &
-              grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466
-      end do
-
-      ! For Reynolds number flows Re < 0.1 Stokes' velocity is valid for
-      ! vlc_grv SeP97 p. 466 (8.42). For larger Re, inertial effects become
-      ! important and empirical drag coefficients must be employed
-      ! Implicit equation for Re, Cd, and Vt is SeP97 p. 467 (8.44)
-      ! Using Stokes' velocity rather than iterative solution with empirical
-      ! drag coefficient causes 60% errors for D = 200 um SeP97 p. 468
-
-      ! Iterative solution for drag coefficient, Reynolds number, and terminal veloc
-      do m = 1, ndst
-
-         ! Initialize accuracy and counter
-         eps_crr = eps_max + 1.0_r8  ![frc] Current relative accuracy
-         itr_idx = 0                 ![idx] Counting index
-
-         ! Initial guess for vlc_grv is exact for Re < 0.1
-         vlc_grv(m) = vlc_stk(m)     ![m s-1]
-
-         do while(eps_crr > eps_max)
-
-            ! Save terminal velocity for convergence test
-            vlc_grv_old = vlc_grv(m) ![m s-1]
-            ryn_nbr_grv(m) = vlc_grv(m) * dmt_vwr(m) / vsc_knm_atm !SeP97 p.460
-
-            ! Update drag coefficient based on new Reynolds number
-            if (ryn_nbr_grv(m) < 0.1_r8) then
-               cff_drg_grv(m) = 24.0_r8 / ryn_nbr_grv(m) !Stokes' law Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 2.0_r8) then
-               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) *    &
-                    (1.0_r8 + 3.0_r8*ryn_nbr_grv(m)/16.0_r8 + &
-                    9.0_r8*ryn_nbr_grv(m)*ryn_nbr_grv(m)*     &
-                    log(2.0_r8*ryn_nbr_grv(m))/160.0_r8)        !Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 500.0_r8) then
-               cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * &
-                    (1.0_r8 + 0.15_r8*ryn_nbr_grv(m)**0.687_r8) !Sep97 p.463 (8.32)
-            else if (ryn_nbr_grv(m) < 2.0e5_r8) then
-               cff_drg_grv(m) = 0.44_r8                         !Sep97 p.463 (8.32)
-            else
-               write(iulog,'(a,es9.2)') "ryn_nbr_grv(m) = ",ryn_nbr_grv(m)
-               write(iulog,*)'Dustini error: Reynolds number too large in stk_crc_get()'
-               call endrun(msg=errMsg(sourcefile, __LINE__))
-            end if
-
-            ! Update terminal velocity based on new Reynolds number and drag coeff
-            ! [m s-1] Terminal veloc SeP97 p.467 (8.44)
-
-            vlc_grv(m) = sqrt(4.0_r8 * grav * dmt_vwr(m) * slp_crc(m) * dns_aer / &
-                 (3.0_r8*cff_drg_grv(m)*dns_mdp))   
-            eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence
-            if (itr_idx == 12) then
-               ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0
-               ! due to discontinuities in derivative of drag coefficient
-               vlc_grv(m) = 0.5_r8 * (vlc_grv(m)+vlc_grv_old)  ! [m s-1]
-            end if
-            if (itr_idx > 20) then
-               write(iulog,*) 'Dustini error: Terminal velocity not converging ',&
-                    ' in stk_crc_get(), breaking loop...'
-               goto 100                                        !to next iteration
-            end if
-            itr_idx = itr_idx + 1
-
-         end do                                                !end while
-
-100      continue   !Label to jump to when iteration does not converge
-      end do   !end loop over size
-
-      ! Compute factors to convert Stokes' settling velocities to
-      ! actual settling velocities
-
-      do m = 1, ndst
-         stk_crc(m) = vlc_grv(m) / vlc_stk(m)
-      end do
-
-    end associate 
-
-  end subroutine InitDustVars
-
-end module DUSTMod
diff --git a/src/biogeochem/DryDepVelocity.F90 b/src/biogeochem/DryDepVelocity.F90
deleted file mode 100644
index 603e9d24c4..0000000000
--- a/src/biogeochem/DryDepVelocity.F90
+++ /dev/null
@@ -1,678 +0,0 @@
-Module DryDepVelocity                                              
-
-  !-----------------------------------------------------------------------  
-  !  
-  ! Purpose:  
-  ! Deposition velocity (m/s) 
-  !  
-  ! Method:  
-  ! This code simulates dry deposition velocities using the Wesely scheme.   
-  ! Details of this method can be found in:  
-  ! 
-  ! M.L Wesely. Parameterization of surface resistances to gaseous dry deposition 
-  ! in regional-scale numericl models. 1989. Atmospheric Environment vol.23 No.6  
-  ! pp. 1293-1304. 
-  ! 
-  ! In Wesely (1998) "the magnitude of the dry deposition velocity can be found 
-  ! as: 
-  ! 
-  !  |vd|=(ra+rb+rc)^-1 
-  ! 
-  ! where ra is the aerodynamic resistance (common to all gases) between a  
-  ! specific height and the surface, rb is the quasilaminar sublayer resistance 
-  ! (whose only dependence on the porperties of the gas of interest is its 
-  ! molecular diffusivity in air), and rc is the bulk surface resistance". 
-  ! 
-  ! In this subroutine both ra and rb are calculated elsewhere in CLM.  
-  ! 
-  ! In Wesely (1989) rc is estimated for five seasonal categories and 11 landuse 
-  ! types.  For each season and landuse type, Wesely compiled data into a  
-  ! look-up-table for several parameters used to calculate rc. In this subroutine 
-  ! the same values are used as found in wesely's look-up-tables, the only  
-  ! difference is that this subroutine uses a CLM generated LAI to select values 
-  ! from the look-up-table instead of seasonality.  Inaddition, Wesely(1989)  
-  ! land use types are "mapped" into CLM patch types.
-  ! 
-  ! Subroutine written to operate at the patch level. 
-  ! 
-  ! Output: 
-  ! 
-  ! vd(n_species) !Dry deposition velocity [m s-1] for each molecule or species 
-  !  
-  ! Author: Beth Holland and  James Sulzman 
-  ! 
-  ! Modified: Francis Vitt -- 30 Mar 2007
-  ! Modified: Maria Val Martin -- 15 Jan 2014
-  !  Corrected major bugs in the leaf and stomatal resitances. The code is now
-  !  coupled to LAI and Rs uses the Ball-Berry Scheme. Also, corrected minor 
-  !  bugs in rlu and rcl calculations. Added 
-  !  no vegetation removal for CO. See README for details and 
-  !     Val Martin et al., 2014 GRL for major corrections
-  ! Modified: Louisa Emmons -- 30 November 2017
-  !  Corrected the equation calculating stomatal resistance from rssun and rssha,
-  !     and removed factor that scaled Rs to match observations
-  !
-  !----------------------------------------------------------------------- 
-
-  use shr_log_mod          , only : errMsg => shr_log_errMsg
-  use shr_kind_mod         , only : r8 => shr_kind_r8 
-  use abortutils           , only : endrun
-  use clm_time_manager     , only : get_nstep, get_curr_date, get_curr_time 
-  use spmdMod              , only : masterproc
-  use seq_drydep_mod       , only : n_drydep, drydep_list 
-  use seq_drydep_mod       , only : drydep_method, DD_XLND
-  use seq_drydep_mod       , only : index_o3=>o3_ndx, index_o3a=>o3a_ndx, index_so2=>so2_ndx, index_h2=>h2_ndx
-  use seq_drydep_mod       , only : index_co=>co_ndx, index_ch4=>ch4_ndx, index_pan=>pan_ndx
-  use seq_drydep_mod       , only : index_xpan=>xpan_ndx
-  use decompMod            , only : bounds_type
-  use clm_varcon           , only : namep
-  use atm2lndType          , only : atm2lnd_type
-  use CanopyStateType      , only : canopystate_type
-  use FrictionVelocityMod  , only : frictionvel_type
-  use PhotosynthesisMod    , only : photosyns_type
-  use WaterstateType       , only : waterstate_type
-  use GridcellType         , only : grc                
-  use LandunitType         , only : lun                
-  use PatchType            , only : patch                
-  !
-  implicit none 
-  private
-  !
-  public :: depvel_compute
-  !
-  type, public :: drydepvel_type
-
-     real(r8), pointer, public  :: velocity_patch (:,:) ! Dry Deposition Velocity
-     real(r8), pointer, private :: rs_drydep_patch (:)  ! Stomatal resistance associated with dry deposition velocity for Ozone
-
-   contains
-
-     procedure , public  :: Init 
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory
-
-  end type drydepvel_type
-  !----------------------------------------------------------------------- 
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-CONTAINS 
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(drydepvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use seq_drydep_mod , only : n_drydep, drydep_method, DD_XLND
-    !
-    ! !ARGUMENTS:
-    class(drydepvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-
-    ! Dry Deposition Velocity 
-    if ( n_drydep > 0 .and. drydep_method == DD_XLND )then
-       allocate(this%velocity_patch(begp:endp, n_drydep));  this%velocity_patch(:,:) = nan 
-       allocate(this%rs_drydep_patch(begp:endp))         ;  this%rs_drydep_patch(:)  = nan 
-    end if
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize history output fields for dry deposition diagnositics
-    !
-    ! !USES 
-    use clm_varcon     , only : spval
-    use histFileMod    , only : hist_addfld1d
-    use seq_drydep_mod , only : mapping
-    !
-    ! !ARGUMENTS:
-    class(drydepvel_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    real(r8), pointer  :: ptr_1d(:)  ! pointer to 1d patch array
-    !
-    ! !LOCAL VARIABLES
-    integer :: ispec 
-    integer :: begp, endp
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    if ( n_drydep == 0 .or. drydep_method /= DD_XLND ) return
-
-    do ispec=1,n_drydep 
-       if(mapping(ispec) <= 0) cycle 
-
-       this%velocity_patch(begp:endp,ispec)= spval
-       ptr_1d => this%velocity_patch(begp:endp,ispec)
-       call hist_addfld1d ( fname='DRYDEPV_'//trim(drydep_list(ispec)), units='cm/sec',  &
-            avgflag='A', long_name='Dry Deposition Velocity', &
-            ptr_patch=ptr_1d, default='inactive' )
-    end do
-
-    this%rs_drydep_patch(begp:endp)= spval
-    call hist_addfld1d ( fname='RS_DRYDEP_O3', units='s/m',  &
-         avgflag='A', long_name='Stomatal Resistance Associated with Ozone Dry Deposition Velocity', &
-         ptr_patch=this%rs_drydep_patch, default='inactive' )
-
-  end subroutine InitHistory
-
-  !----------------------------------------------------------------------- 
-  subroutine depvel_compute( bounds, &
-       atm2lnd_inst, canopystate_inst, waterstate_inst, frictionvel_inst, &
-       photosyns_inst, drydepvel_inst)
-    !
-    ! !DESCRIPTION:
-    ! computes the dry deposition velocity of tracers
-    !
-    ! !USES:
-    use shr_const_mod  , only : tmelt => shr_const_tkfrz
-    use seq_drydep_mod , only : seq_drydep_setHCoeff, mapping, drat, foxd
-    use seq_drydep_mod , only : rcls, h2_a, h2_b, h2_c, ri, rac, rclo, rlu, rgss, rgso
-    use landunit_varcon, only : istsoil, istice_mec, istdlak, istwet
-    use clm_varctl     , only : iulog
-    use pftconMod      , only : noveg, ndllf_evr_tmp_tree, ndllf_evr_brl_tree
-    use pftconMod      , only : ndllf_dcd_brl_tree, nbrdlf_evr_trp_tree
-    use pftconMod      , only : nbrdlf_evr_tmp_tree, nbrdlf_dcd_trp_tree
-    use pftconMod      , only : nbrdlf_dcd_tmp_tree, nbrdlf_dcd_brl_tree
-    use pftconMod      , only : nbrdlf_evr_shrub, nbrdlf_dcd_tmp_shrub
-    use pftconMod      , only : nbrdlf_dcd_brl_shrub,nc3_arctic_grass
-    use pftconMod      , only : nc3_nonarctic_grass, nc4_grass, nc3crop
-    use pftconMod      , only : nc3irrig, npcropmin, npcropmax
-    use clm_varcon     , only : spval
-
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)      , intent(in)    :: bounds  
-    type(atm2lnd_type)     , intent(in)    :: atm2lnd_inst
-    type(canopystate_type) , intent(in)    :: canopystate_inst
-    type(waterstate_type)  , intent(in)    :: waterstate_inst
-    type(frictionvel_type) , intent(in)    :: frictionvel_inst
-    type(photosyns_type)   , intent(in)    :: photosyns_inst
-    type(drydepvel_type)   , intent(inout) :: drydepvel_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c
-    real(r8) :: soilw, var_soilw, fact_h2, dv_soil_h2
-    integer  :: pi,g, l
-    integer  :: ispec 
-    integer  :: length 
-    integer  :: wesveg       !wesely vegegation index  
-    integer  :: clmveg       !clm veg index from ivegtype 
-    integer  :: i 
-    integer  :: index_season !seasonal index based on LAI.  This indexs wesely data tables 
-    integer  :: nstep        !current step 
-    integer  :: indexp 
-
-    real(r8) :: pg           ! surface pressure 
-    real(r8) :: tc           ! temperature in celsius  
-    real(r8) :: es           ! saturation vapor pressur 
-    real(r8) :: ws           ! saturation mixing ratio 
-    real(r8) :: rmx          ! resistance by vegetation 
-    real(r8) :: qs           ! saturation specific humidity 
-    real(r8) :: dewm         ! multiplier for rs when dew occurs 
-    real(r8) :: crs          ! multiplier to calculate crs 
-    real(r8) :: rdc          ! part of lower canopy resistance 
-    real(r8) :: rain         ! rain fall 
-    real(r8) :: spec_hum     ! specific humidity 
-    real(r8) :: solar_flux   ! solar radiation(direct beam) W/m2 
-    real(r8) :: lat          ! latitude in degrees 
-    real(r8) :: lon          ! longitude in degrees 
-    real(r8) :: sfc_temp     ! surface temp 
-    real(r8) :: minlai       ! minimum of monthly lai 
-    real(r8) :: maxlai       ! maximum of monthly lai 
-    real(r8) :: rds         ! resistance for aerosols
-
-    !mvm 11/30/2013
-    real(r8) :: rlu_lai      ! constant to calculate rlu over bulk canopy
-    
-    logical  :: has_dew
-    logical  :: has_rain
-    real(r8), parameter :: rain_threshold      = 1.e-7_r8  ! of the order of 1cm/day expressed in m/s
-
-    ! local arrays: dependent on species only 
-    real(r8), dimension(n_drydep) :: rsmx  !vegetative resistance (plant mesophyll) 
-    real(r8), dimension(n_drydep) :: rclx !lower canopy resistance  
-    real(r8), dimension(n_drydep) :: rlux !vegetative resistance (upper canopy) 
-    real(r8), dimension(n_drydep) :: rgsx !gournd resistance 
-    real(r8), dimension(n_drydep) :: heff   
-    real(r8) :: rs    ! stomatal resistance associated with dry deposition velocity (s/m)
-    real(r8) :: rc    !combined surface resistance 
-    real(r8) :: cts   !correction to flu rcl and rgs for frost 
-    real(r8) :: rlux_o3 !to calculate O3 leaf resistance in dew/rain conditions
-
-    ! constants 
-    real(r8), parameter :: slope = 0._r8      ! Used to calculate  rdc in (lower canopy resistance) 
-    integer, parameter :: wveg_unset = -1     ! Unset Wesley vegetation type
-    character(len=32), parameter :: subname = "depvel_compute"
-
-    ! jfl : mods for PAN
-    real(r8)                  :: dv_pan
-    real(r8) :: c0_pan(11) = (/ 0.000_r8, 0.006_r8, 0.002_r8, 0.009_r8, 0.015_r8, &
-                                0.006_r8, 0.000_r8, 0.000_r8, 0.000_r8, 0.002_r8, 0.002_r8 /)
-    real(r8) :: k_pan (11) = (/ 0.000_r8, 0.010_r8, 0.005_r8, 0.004_r8, 0.003_r8, &
-                                0.005_r8, 0.000_r8, 0.000_r8, 0.000_r8, 0.075_r8, 0.002_r8 /)
-    !----------------------------------------------------------------------- 
-
-    if ( n_drydep == 0 .or. drydep_method /= DD_XLND ) return
-
-    associate(                                                    & 
-         forc_solai =>    atm2lnd_inst%forc_solai_grc           , & ! Input:  [real(r8) (:,:) ] direct beam radiation (visible only)             
-         forc_solad =>    atm2lnd_inst%forc_solad_grc           , & ! Input:  [real(r8) (:,:) ] direct beam radiation (visible only)             
-         forc_t     =>    atm2lnd_inst%forc_t_downscaled_col    , & ! Input:  [real(r8) (:)   ] downscaled atmospheric temperature (Kelvin)                   
-         forc_q     =>    atm2lnd_inst%forc_q_downscaled_col    , & ! Input:  [real(r8) (:)   ] downscaled atmospheric specific humidity (kg/kg)              
-         forc_psrf  =>    atm2lnd_inst%forc_pbot_downscaled_col , & ! Input:  [real(r8) (:)   ] downscaled surface pressure (Pa)                              
-         forc_rain  =>    atm2lnd_inst%forc_rain_downscaled_col , & ! Input:  [real(r8) (:)   ] downscaled rain rate [mm/s]                                   
-
-         h2osoi_vol =>    waterstate_inst%h2osoi_vol_col        , & ! Input:  [real(r8) (:,:) ] volumetric soil water (0<=h2osoi_vol<=watsat)   
-         snow_depth =>    waterstate_inst%snow_depth_col        , & ! Input:  [real(r8) (:)   ] snow height (m)                                   
-
-         ram1       =>    frictionvel_inst%ram1_patch           , & ! Input:  [real(r8) (:)   ] aerodynamical resistance                           
-         rb1        =>    frictionvel_inst%rb1_patch            , & ! Input:  [real(r8) (:)   ] leaf boundary layer resistance [s/m]               
-         vds        =>    frictionvel_inst%vds_patch            , & ! Input:  [real(r8) (:)   ] aerodynamical resistance                           
-
-         rssun      =>    photosyns_inst%rssun_patch            , & ! Input:  [real(r8) (:)   ] stomatal resistance                                
-         rssha      =>    photosyns_inst%rssha_patch            , & ! Input:  [real(r8) (:)   ] shaded stomatal resistance (s/m)                   
-
-         fsun       =>    canopystate_inst%fsun_patch           , & ! Input:  [real(r8) (:)   ] sunlit fraction of canopy                          
-         elai       =>    canopystate_inst%elai_patch           , & ! Input:  [real(r8) (:)   ] one-sided leaf area index with burying by snow     
-         mlaidiff   =>    canopystate_inst%mlaidiff_patch       , & ! Input:  [real(r8) (:)   ] difference in lai between month one and month two  
-         annlai     =>    canopystate_inst%annlai_patch         , & ! Input:  [real(r8) (:,:) ] 12 months of monthly lai from input data set     
-         
-         velocity   =>    drydepvel_inst%velocity_patch         , & ! Output: [real(r8) (:,:) ] cm/sec
-         rs_drydep  =>    drydepvel_inst%rs_drydep_patch          & ! Output: [real(r8) (:)   ]  stomatal resistance associated with Ozone dry deposition velocity (s/m)
-         )
-
-      !_________________________________________________________________ 
-      ! Begin loop through patches
-
-      pft_loop: do pi = bounds%begp,bounds%endp
-         l = patch%landunit(pi)
-         
-         active: if (patch%active(pi)) then
-
-            c = patch%column(pi)
-            g = patch%gridcell(pi)
-            pg         = forc_psrf(c)  
-            spec_hum   = forc_q(c)
-            rain       = forc_rain(c) 
-            sfc_temp   = forc_t(c) 
-            solar_flux = forc_solad(g,1) 
-            lat        = grc%latdeg(g) 
-            lon        = grc%londeg(g) 
-            clmveg     = patch%itype(pi) 
-            soilw      = h2osoi_vol(c,1)
-
-            !map CLM veg type into Wesely veg type  
-            wesveg = wveg_unset 
-            if (clmveg == noveg                               ) wesveg = 8 
-            if (clmveg == ndllf_evr_tmp_tree                  ) wesveg = 5 
-            if (clmveg == ndllf_evr_brl_tree                  ) wesveg = 5 
-            if (clmveg == ndllf_dcd_brl_tree                  ) wesveg = 5 
-            if (clmveg == nbrdlf_evr_trp_tree                 ) wesveg = 4 
-            if (clmveg == nbrdlf_evr_tmp_tree                 ) wesveg = 4 
-            if (clmveg == nbrdlf_dcd_trp_tree                 ) wesveg = 4 
-            if (clmveg == nbrdlf_dcd_tmp_tree                 ) wesveg = 4 
-            if (clmveg == nbrdlf_dcd_brl_tree                 ) wesveg = 4 
-            if (clmveg == nbrdlf_evr_shrub                    ) wesveg = 11 
-            if (clmveg == nbrdlf_dcd_tmp_shrub                ) wesveg = 11 
-            if (clmveg == nbrdlf_dcd_brl_shrub                ) wesveg = 11 
-            if (clmveg == nc3_arctic_grass                    ) wesveg = 3 
-            if (clmveg == nc3_nonarctic_grass                 ) wesveg = 3 
-            if (clmveg == nc4_grass                           ) wesveg = 3 
-            if (clmveg == nc3crop                             ) wesveg = 2 
-            if (clmveg == nc3irrig                            ) wesveg = 2 
-            if (clmveg >= npcropmin .and. clmveg <= npcropmax ) wesveg = 2 
-            if (wesveg == wveg_unset )then
-               write(iulog,*) 'clmveg = ', clmveg, 'lun%itype = ', lun%itype(l)
-               call endrun(decomp_index=pi, clmlevel=namep, &
-                    msg='ERROR: Not able to determine Wesley vegetation type'//&
-                    errMsg(sourcefile, __LINE__))
-            end if
-
-            ! create seasonality index used to index wesely data tables from LAI,  Bascially 
-            !if elai is between max lai from input data and half that max the index_season=1 
-
-
-            !mail1j and mlai2j are the two monthly lai values pulled from a CLM input data set 
-            !/fs/cgd/csm/inputdata/lnd/clm2/rawdata/mksrf_lai.nc.  lai for dates in the middle  
-            !of the month are interpolated using using these values and stored in the variable  
-            !elai (done elsewhere).  If the difference between mlai1j and mlai2j is greater 
-            !than zero it is assumed to be fall and less than zero it is assumed to be spring. 
-
-            !wesely seasonal "index_season" 
-            ! 1 - midsummer with lush vegetation 
-            ! 2 - Autumn with unharvested cropland 
-            ! 3 - Late autumn after frost, no snow 
-            ! 4 - Winter, snow on ground and subfreezing 
-            ! 5 - Transitional spring with partially green short annuals 
-
-
-            !mlaidiff=jan-feb 
-            minlai=minval(annlai(:,pi)) 
-            maxlai=maxval(annlai(:,pi)) 
-
-            index_season = -1
-
-            if ( lun%itype(l) /= istsoil )then
-               if ( lun%itype(l) == istice_mec ) then
-                  wesveg       = 8
-                  index_season = 4
-               elseif ( lun%itype(l) == istdlak ) then
-                  wesveg       = 7
-                  index_season = 4
-               elseif ( lun%itype(l) == istwet ) then
-                  wesveg       = 9
-                  index_season = 2
-               elseif ( lun%urbpoi(l) ) then
-                  wesveg       = 1
-                  index_season = 2
-               end if
-            else if ( snow_depth(c) > 0 ) then
-               index_season = 4
-            else if(elai(pi) > 0.5_r8*maxlai) then  
-               index_season = 1  
-            endif
-
-            if (index_season<0) then 
-               if (elai(pi) < (minlai+0.05*(maxlai-minlai))) then  
-                  index_season = 3 
-               endif
-            endif
-
-            if (index_season<0) then 
-               if (mlaidiff(pi) > 0.0_r8) then 
-                  index_season = 2 
-               elseif (mlaidiff(pi) < 0.0_r8) then 
-                  index_season = 5 
-               elseif (mlaidiff(pi).eq.0.0_r8) then 
-                  index_season = 3 
-               endif
-            endif
-
-            if (index_season<0) then 
-               call endrun('ERROR: not able to determine season'//errmsg(sourcefile, __LINE__))
-            endif
-
-            ! saturation specific humidity 
-            ! 
-            es = 611_r8*exp(5414.77_r8*((1._r8/tmelt)-(1._r8/sfc_temp))) 
-            ws = .622_r8*es/(pg-es) 
-            qs = ws/(1._r8+ws) 
-
-            has_dew = .false.
-            if( qs <= spec_hum ) then
-               has_dew = .true.
-            end if
-            if( sfc_temp < tmelt ) then
-               has_dew = .false.
-            end if
-
-            has_rain = rain > rain_threshold
-
-            if ( has_dew .or. has_rain ) then
-               dewm = 3._r8
-            else
-               dewm = 1._r8
-            end if
-
-            !Define tc
-            tc = sfc_temp - tmelt
-
-            ! 
-            ! rdc (lower canopy res) 
-            ! 
-            rdc=100._r8*(1._r8+1000._r8/(solar_flux+10._r8))/(1._r8+1000._r8*slope) 
-
-            ! surface resistance : depends on both land type and species 
-            ! land types are computed seperately, then resistance is computed as average of values 
-            ! following wesely rc=(1/(rs+rm) + 1/rlu +1/(rdc+rcl) + 1/(rac+rgs))**-1 
-
-            !******************************************************* 
-            call seq_drydep_setHCoeff( sfc_temp, heff(:n_drydep) )
-            !********************************************************* 
-
-            species_loop1: do ispec=1, n_drydep
-               if(mapping(ispec) <= 0) cycle 
-
-               if(ispec.eq.index_o3.or.ispec.eq.index_o3a.or.ispec.eq.index_so2) then 
-                  rmx=0._r8
-               else 
-                  rmx=1._r8/((heff(ispec)/3000._r8)+(100._r8*foxd(ispec))) 
-               endif
-
-               ! correction for frost 
-               cts = 1000._r8*exp( -tc - 4._r8 ) 
-
-               !ground resistance  
-               rgsx(ispec) = 1._r8/((heff(ispec)/(1.e5_r8*(rgss(index_season,wesveg)+cts))) + & 
-                    (foxd(ispec)/(rgso(index_season,wesveg)+cts))) 
-
-               !-------------------------------------------------------------------------------------
-               ! special case for H2 and CO;; CH4 is set ot a fraction of dv(H2)
-               !-------------------------------------------------------------------------------------
-               if( ispec == index_h2 .or. ispec == index_co .or. ispec == index_ch4 ) then
-
-                  if( ispec == index_co ) then
-                     fact_h2 = 1.0_r8
-                  elseif ( ispec == index_h2 ) then
-                     fact_h2 = 0.5_r8
-                  elseif ( ispec == index_ch4 ) then
-                     fact_h2 = 50.0_r8
-                  end if
-
-                  !-------------------------------------------------------------------------------------
-                  ! no deposition on snow, ice, desert, and water
-                  !-------------------------------------------------------------------------------------
-                  if( wesveg == 1 .or. wesveg == 7 .or. wesveg == 8 .or. index_season == 4 ) then
-                     rgsx(ispec) = spval
-                  else
-                     var_soilw = max( .1_r8,min( soilw,.3_r8 ) )
-                     if( wesveg == 3 ) then
-                        var_soilw = log( var_soilw )
-                     end if
-                     dv_soil_h2 = h2_c(wesveg) + var_soilw*(h2_b(wesveg) + var_soilw*h2_a(wesveg))
-                     if( dv_soil_h2 > 0._r8 ) then
-                        rgsx(ispec) = fact_h2/(dv_soil_h2*1.e-4_r8)
-                     end if
-                  end if
-               end if
-
-               !-------------------------------------------------------------------------------------
-               ! no deposition on water or no vegetation or snow (elai<=0)
-               !-------------------------------------------------------------------------------------
-
-               no_dep: if( wesveg == 7 .or. elai(pi).le.0_r8 ) then !mvm 11/26/2013
-                  rclx(ispec)  = spval
-                  rsmx(ispec)  = spval
-                  rlux(ispec)  = spval
-                  rs           = spval
-               else
-                  
-                  !Stomatal resistance  
-                  
-                  ! fvitt -- at midnight rssun and/or rssha can be zero in some places which sets rs to zero 
-                  ! --- this fix prevents divide by zero error (when rsmx is zero)
-                  if (rssun(pi)>0._r8 .and. rssun(pi)<1.e30 .and. rssha(pi)>0._r8 .and. rssha(pi)<1.e30 ) then
-                     !LKE: corrected rs to add rssun and rssha in parallel (11/30/2017)
-                     rs=1._r8/(fsun(pi)*elai(pi)/rssun(pi) + (1.-fsun(pi))*elai(pi)/rssha(pi))
-                  else
-                     rs=spval
-                  endif
-
-                  rsmx(ispec) = rs*drat(ispec)+rmx 
-
-                  ! Leaf resistance
-                  !MVM: adjusted rlu by LAI to get leaf resistance over bulk canopy (gao and wesely, 1995)
-                  rlu_lai=cts+rlu(index_season,wesveg)/elai(pi)
-                  rlux(ispec) = rlu_lai/(1.e-5_r8*heff(ispec)+foxd(ispec))      
-
-                  !Lower canopy resistance 
-                  rclx(ispec) = 1._r8/((heff(ispec)/(1.e5_r8*(rcls(index_season,wesveg)+cts))) + &
-                       (foxd(ispec)/(rclo(index_season,wesveg)+cts)))
-
-                  !-----------------------------------
-                  !mvm 11/30/2013: special case for CO
-                  !Dry deposition of CO and hydrocarbons is negligibly 
-                  !small in vegetation [Mueller and Brasseur, 1995].
-                  !------------------------------------
-                  if( ispec == index_co ) then
-                     rclx(ispec)   = spval
-                     rsmx(ispec)   = spval
-                     rlux(ispec)   = spval
-                  endif
-
-                  !--------------------------------------------
-                  ! jfl : special case for PAN
-                  !--------------------------------------------
-                  if( ispec == index_pan ) then
-                     dv_pan =  c0_pan(wesveg) * (1._r8 - exp(-k_pan(wesveg)*(rs*drat(ispec))*1.e-2_r8 ))
-
-                     if( dv_pan > 0._r8 .and. index_season /= 4 ) then
-                        rsmx(ispec) = ( 1._r8/dv_pan )
-                     end if
-                  end if
-
-               endif no_dep
-               if ( ispec == index_o3 )then
-                  rs_drydep(pi) = rs
-               end if
-
-            end do species_loop1
-
-
-            !----------------------------------------------
-            !Adjustment for dew and rain in leaf resitances
-            !---------------------------------------------
-            ! no effect over water            
-            no_water: if( wesveg.ne.7 ) then
-               !MVM: effect only on vegetated areas (elai> 0)
-               with_LAI: if (elai(pi).gt.0._r8) then
-
-                  ! 
-                  ! no effect if sfc_temp < O C 
-                  ! 
-                  non_freezing: if(sfc_temp.gt.tmelt) then
-                     if( has_dew ) then 
-                        rlu_lai=cts+rlu(index_season,wesveg)/elai(pi)
-                        rlux_o3 = 1._r8/((1._r8/3000._r8)+(1._r8/(3._r8*rlu_lai))) 
-
-                        if (index_o3 > 0) then
-                           rlux(index_o3) = rlux_o3
-                        endif
-                        if (index_o3a > 0) then
-                           rlux(index_o3a) = rlux_o3
-                        endif
-                     endif
-
-                     if(has_rain) then 
-                        rlu_lai=cts+rlu(index_season,wesveg)/elai(pi)
-                        rlux_o3 = 1._r8/((1._r8/1000._r8)+(1._r8/(3._r8*rlu_lai)))
-
-                        if (index_o3 > 0) then
-                           rlux(index_o3) = rlux_o3
-                        endif
-                        if (index_o3a > 0) then
-                           rlux(index_o3a) = rlux_o3
-                        endif
-                     endif
-
-                     species_loop2: do ispec=1,n_drydep 
-                        if(mapping(ispec).le.0) cycle 
-                        if(ispec.ne.index_o3.and.ispec.ne.index_o3a.and.ispec.ne.index_so2) then 
-
-                           if( has_dew .or. has_rain) then
-                              rlu_lai=cts+rlu(index_season,wesveg)/elai(pi)
-                              rlux(ispec)=1._r8/((1._r8/(3._r8*rlu_lai))+ & 
-                                   (1.e-7_r8*heff(ispec))+(foxd(ispec)/rlux_o3))
-                           endif
-
-                        elseif(ispec.eq.index_so2) then 
-
-                           if( has_dew ) then
-                              rlux(ispec) = 100._r8
-                           endif
-
-                           if(has_rain) then 
-                              rlu_lai=cts+rlu(index_season,wesveg)/elai(pi)
-                              rlux(ispec) = 1._r8/((1._r8/5000._r8)+(1._r8/(3._r8*rlu_lai))) 
-                           endif
-
-                           if( has_dew .or. has_rain ) then
-                              !MVM:rlux=50 for SO2 in dew or rain only for *urban land* type surfaces.
-                              if (wesveg.eq.1) then
-                                 rlux(ispec)=50._r8
-                              endif
-                           endif
-                        end if
-                        !mvm 11/30/2013: special case for CO
-                        if( ispec.eq.index_co ) then
-                           rlux(ispec) = spval
-                        endif
-                     end do species_loop2
-                  endif non_freezing
-               endif with_LAI
-            endif no_water
-
-            ! resistance for aerosols 
-            rds = 1._r8/vds(pi)
-
-            species_loop3: do ispec=1,n_drydep 
-               if(mapping(ispec) <= 0) cycle 
-
-               ! 
-               ! compute rc 
-               ! 
-               rc = 1._r8/((1._r8/rsmx(ispec))+(1._r8/rlux(ispec)) + & 
-                    (1._r8/(rdc+rclx(ispec)))+(1._r8/(rac(index_season,wesveg)+rgsx(ispec))))
-               rc = max( 10._r8, rc)
-               !
-               ! assume no surface resistance for SO2 over water
-               !
-               if ( drydep_list(ispec) == 'SO2' .and. wesveg == 7 ) then
-                  rc = 0._r8
-               end if
-
-               select case( drydep_list(ispec) )
-               case ( 'SO4' )
-                  velocity(pi,ispec) = (1._r8/(ram1(pi)+rds))*100._r8
-               case ( 'NH4','NH4NO3','XNH4NO3' )
-                  velocity(pi,ispec) = (1._r8/(ram1(pi)+0.5_r8*rds))*100._r8
-               case ( 'Pb' )
-                  velocity(pi,ispec) = 0.2_r8
-               case ( 'CB1', 'CB2', 'OC1', 'OC2', 'SOAM', 'SOAI', 'SOAT', 'SOAB', 'SOAX' )
-                  velocity(pi,ispec) = 0.10_r8
-               case ( 'SO2' )
-                  velocity(pi,ispec) = (1._r8/(ram1(pi)+rb1(pi)+rc))*200._r8
-               case default
-                  velocity(pi,ispec) = (1._r8/(ram1(pi)+rb1(pi)+rc))*100._r8
-               end select
-            end do species_loop3
-         endif active
-      end do pft_loop
-
-     end associate 
-
-  end subroutine depvel_compute
-
-end module DryDepVelocity
diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90
deleted file mode 100644
index 78b2cf0e24..0000000000
--- a/src/biogeochem/SatellitePhenologyMod.F90
+++ /dev/null
@@ -1,684 +0,0 @@
-module SatellitePhenologyMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! CLM Satelitte Phenology model (SP) ecosystem dynamics (phenology, vegetation). 
-  ! Allow some subroutines to be used by the CLM Carbon Nitrogen model (CLMCN) 
-  ! so that DryDeposition code can get estimates of LAI differences between months.
-  !
-  ! !USES:
-  use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create
-  use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_kind_mod    , only : CL => shr_kind_CL
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use decompMod       , only : bounds_type
-  use abortutils      , only : endrun
-  use clm_varctl      , only : scmlat,scmlon,single_column
-  use clm_varctl      , only : iulog, use_lai_streams
-  use clm_varcon      , only : grlnd
-  use controlMod      , only : NLFilename
-  use decompMod       , only : gsmap_lnd_gdc2glo
-  use domainMod       , only : ldomain
-  use fileutils       , only : getavu, relavu
-  use PatchType       , only : patch                
-  use CanopyStateType , only : canopystate_type
-  use WaterstateType  , only : waterstate_type
-  use perf_mod        , only : t_startf, t_stopf
-  use spmdMod         , only : masterproc
-  use spmdMod         , only : mpicom, comp_id
-  use mct_mod
-  use ncdio_pio   
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: SatellitePhenology     ! CLMSP Ecosystem dynamics: phenology, vegetation
-  public :: SatellitePhenologyInit ! Dynamically allocate memory
-  public :: interpMonthlyVeg       ! interpolate monthly vegetation data
-  public :: readAnnualVegetation   ! Read in annual vegetation (needed for Dry-deposition)
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: readMonthlyVegetation   ! read monthly vegetation data for two months
-  private :: lai_init    ! position datasets for LAI
-  private :: lai_interp  ! interpolates between two years of LAI data
-
-  ! !PRIVATE MEMBER DATA:
-  type(shr_strdata_type) :: sdat_lai           ! LAI input data stream
-  !
-  ! !PRIVATE TYPES:
-  integer , private :: InterpMonths1            ! saved month index
-  real(r8), private :: timwt(2)                 ! time weights for month 1 and month 2
-  real(r8), private, allocatable :: mlai2t(:,:) ! lai for interpolation (2 months)
-  real(r8), private, allocatable :: msai2t(:,:) ! sai for interpolation (2 months)
-  real(r8), private, allocatable :: mhvt2t(:,:) ! top vegetation height for interpolation (2 months)
-  real(r8), private, allocatable :: mhvb2t(:,:) ! bottom vegetation height for interpolation(2 months)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-  
-  !-----------------------------------------------------------------------
-  !
-  ! lai_init
-  !
-  !-----------------------------------------------------------------------
-  subroutine lai_init(bounds)
-    !
-    ! Initialize data stream information for LAI.
-    !
-    !
-    ! !USES:
-    use clm_varctl       , only : inst_name
-    use clm_time_manager , only : get_calendar
-    use ncdio_pio        , only : pio_subsystem
-    use shr_pio_mod      , only : shr_pio_getiotype
-    use clm_nlUtilsMod   , only : find_nlgroup_name
-    use ndepStreamMod    , only : clm_domain_mct
-    use histFileMod      , only : hist_addfld1d
-    use shr_stream_mod   , only : shr_stream_file_null
-    use shr_string_mod   , only : shr_string_listCreateField
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds          ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i                          ! index
-    integer            :: stream_year_first_lai      ! first year in Lai stream to use
-    integer            :: stream_year_last_lai       ! last year in Lai stream to use
-    integer            :: model_year_align_lai       ! align stream_year_first_lai with 
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    type(mct_ggrid)    :: dom_clm                    ! domain information 
-    character(len=CL)  :: stream_fldFileName_lai     ! lai stream filename to read
-    character(len=CL)  :: lai_mapalgo = 'bilinear'   ! Mapping alogrithm
-
-    character(*), parameter    :: subName = "('laidyn_init')"
-    character(*), parameter    :: F00 = "('(laidyn_init) ',4a)"
-    character(*), parameter    :: laiString = "LAI"  ! base string for field string
-    integer     , parameter    :: numLaiFields = 16  ! number of fields to build field string
-    character(SHR_KIND_CXX)    :: fldList            ! field string
-    !-----------------------------------------------------------------------
-    !
-    ! deal with namelist variables here in init
-    !
-    namelist /lai_streams/         &
-         stream_year_first_lai,    &
-         stream_year_last_lai,     &
-         model_year_align_lai,     &
-         lai_mapalgo,              &
-         stream_fldFileName_lai
-
-    ! Default values for namelist
-    stream_year_first_lai     = 1      ! first year in stream to use
-    stream_year_last_lai      = 1      ! last  year in stream to use
-    model_year_align_lai      = 1      ! align stream_year_first_lai with this model year
-    stream_fldFileName_lai    = shr_stream_file_null
-
-    ! Read lai_streams namelist
-    if (masterproc) then
-       nu_nml = getavu()
-       open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=lai_streams,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading lai_streams namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding lai_streams namelist')
-       end if
-       close(nu_nml)
-       call relavu( nu_nml )
-    endif
-
-    call shr_mpi_bcast(stream_year_first_lai, mpicom)
-    call shr_mpi_bcast(stream_year_last_lai, mpicom)
-    call shr_mpi_bcast(model_year_align_lai, mpicom)
-    call shr_mpi_bcast(stream_fldFileName_lai, mpicom)
-
-    if (masterproc) then
-
-       write(iulog,*) ' '
-       write(iulog,*) 'lai_stream settings:'
-       write(iulog,*) '  stream_year_first_lai  = ',stream_year_first_lai  
-       write(iulog,*) '  stream_year_last_lai   = ',stream_year_last_lai   
-       write(iulog,*) '  model_year_align_lai   = ',model_year_align_lai   
-       write(iulog,*) '  stream_fldFileName_lai = ',trim(stream_fldFileName_lai)
-
-    endif
-
-    call clm_domain_mct (bounds, dom_clm)
-
-    !
-    ! create the field list for these lai fields...use in shr_strdata_create
-    !
-    fldList = shr_string_listCreateField( numLaiFields, laiString )
-
-    call shr_strdata_create(sdat_lai,name="laidyn",    &
-         pio_subsystem=pio_subsystem,                  & 
-         pio_iotype=shr_pio_getiotype(inst_name),      &
-         mpicom=mpicom, compid=comp_id,                &
-         gsmap=gsmap_lnd_gdc2glo, ggrid=dom_clm,       &
-         nxg=ldomain%ni, nyg=ldomain%nj,               &
-         yearFirst=stream_year_first_lai,              &
-         yearLast=stream_year_last_lai,                &
-         yearAlign=model_year_align_lai,               &
-         offset=0,                                     &
-         domFilePath='',                               &
-         domFileName=trim(stream_fldFileName_lai),  &
-         domTvarName='time',                           &
-         domXvarName='lon' ,                           &
-         domYvarName='lat' ,                           &  
-         domAreaName='area',                           &
-         domMaskName='mask',                           &
-         filePath='',                                  &
-         filename=(/stream_fldFileName_lai/),          &
-         fldListFile=fldList,                          &
-         fldListModel=fldList,                         &
-         fillalgo='none',                              &
-         mapalgo=lai_mapalgo,                          &
-         calendar=get_calendar(),                      &
-         taxmode='cycle'                               )
-
-    if (masterproc) then
-       call shr_strdata_print(sdat_lai,'LAI data')
-    endif
-
-  end subroutine lai_init
-
-  !-----------------------------------------------------------------------
-  !
-  ! lai_interp
-  !
-  !-----------------------------------------------------------------------
-  subroutine lai_interp(bounds, canopystate_inst)
-    !
-    ! Interpolate data stream information for Lai.
-    !
-    ! !USES:
-    use clm_time_manager, only : get_curr_date
-    use pftconMod       , only : noveg
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type)      , intent(in)    :: bounds                          
-    type(canopystate_type) , intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ivt, p, g, ip, ig, gpft
-    integer :: year    ! year (0, ...) for nstep+1
-    integer :: mon     ! month (1, ..., 12) for nstep+1
-    integer :: day     ! day of month (1, ..., 31) for nstep+1
-    integer :: sec     ! seconds into current date for nstep+1
-    integer :: mcdate  ! Current model date (yyyymmdd)
-    character(len=CL)  :: stream_var_name
-    !-----------------------------------------------------------------------
-
-    call get_curr_date(year, mon, day, sec)
-    mcdate = year*10000 + mon*100 + day
-
-    call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn')
-
-    do p = bounds%begp, bounds%endp
-       ivt = patch%itype(p)
-       if (ivt /= noveg) then     ! vegetated pft
-          write(stream_var_name,"(i6)") ivt
-          stream_var_name = 'LAI_'//trim(adjustl(stream_var_name))
-          ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name))
-       endif
-       gpft = patch%gridcell(p)
-
-       !
-       ! Determine vector index corresponding to gpft
-       !
-       ig = 0
-       do g = bounds%begg,bounds%endg
-          ig = ig+1
-          if (g == gpft) exit
-       end do
-
-       !
-       ! Set lai for each gridcell/patch combination
-       !
-       if (ivt /= noveg) then     ! vegetated pft
-          canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig)
-       else                       ! non-vegetated pft
-          canopystate_inst%tlai_patch(p) = 0._r8
-       endif
-    end do
-
-  end subroutine lai_interp
-
-  !-----------------------------------------------------------------------
-  subroutine SatellitePhenologyInit (bounds)
-    !
-    ! !DESCRIPTION:
-    ! Dynamically allocate memory and set to signaling NaN.
-    !
-    ! !USES:
-    use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ier    ! error code
-    !-----------------------------------------------------------------------
-
-    InterpMonths1 = -999  ! saved month index
-
-    ier = 0
-    if(.not.allocated(mlai2t)) then
-       allocate (mlai2t(bounds%begp:bounds%endp,2), &
-            msai2t(bounds%begp:bounds%endp,2), &
-            mhvt2t(bounds%begp:bounds%endp,2), &
-            mhvb2t(bounds%begp:bounds%endp,2), stat=ier)
-    end if
-    if (ier /= 0) then
-       write(iulog,*) 'EcosystemDynini allocation error'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-
-    mlai2t(bounds%begp : bounds%endp, :) = nan
-    msai2t(bounds%begp : bounds%endp, :) = nan
-    mhvt2t(bounds%begp : bounds%endp, :) = nan
-    mhvb2t(bounds%begp : bounds%endp, :) = nan
-
-    if (use_lai_streams) then
-       call lai_init(bounds)
-    endif
-
-  end subroutine SatellitePhenologyInit
-
-  !-----------------------------------------------------------------------
-  subroutine SatellitePhenology(bounds, num_nolakep, filter_nolakep, &
-       waterstate_inst, canopystate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Ecosystem dynamics: phenology, vegetation
-    ! Calculates leaf areas (tlai, elai),  stem areas (tsai, esai) and height (htop).
-    !
-    ! !USES:
-    use pftconMod, only : noveg, nbrdlf_dcd_brl_shrub
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)      , intent(in)    :: bounds                          
-    integer                , intent(in)    :: num_nolakep                               ! number of column non-lake points in patch filter
-    integer                , intent(in)    :: filter_nolakep(bounds%endp-bounds%begp+1) ! patch filter for non-lake points
-    type(waterstate_type)  , intent(in)    :: waterstate_inst
-    type(canopystate_type) , intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: fp,p,c                            ! indices
-    real(r8) :: ol                                ! thickness of canopy layer covered by snow (m)
-    real(r8) :: fb                                ! fraction of canopy layer covered by snow
-    !-----------------------------------------------------------------------
-
-    associate(                                                           &
-         frac_sno           => waterstate_inst%frac_sno_col   ,          & ! Input:  [real(r8) (:) ] fraction of ground covered by snow (0 to 1)       
-         snow_depth         => waterstate_inst%snow_depth_col ,          & ! Input:  [real(r8) (:) ] snow height (m)                                                       
-         tlai               => canopystate_inst%tlai_patch    ,          & ! Output: [real(r8) (:) ] one-sided leaf area index, no burying by snow 
-         tsai               => canopystate_inst%tsai_patch    ,          & ! Output: [real(r8) (:) ] one-sided stem area index, no burying by snow
-         elai               => canopystate_inst%elai_patch    ,          & ! Output: [real(r8) (:) ] one-sided leaf area index with burying by snow
-         esai               => canopystate_inst%esai_patch    ,          & ! Output: [real(r8) (:) ] one-sided stem area index with burying by snow
-         htop               => canopystate_inst%htop_patch    ,          & ! Output: [real(r8) (:) ] canopy top (m)                           
-         hbot               => canopystate_inst%hbot_patch    ,          & ! Output: [real(r8) (:) ] canopy bottom (m)                           
-         frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch & ! Output: [integer  (:) ] fraction of vegetation not covered by snow (0 OR 1) [-]
-         )
-
-      if (use_lai_streams) then
-         call lai_interp(bounds, canopystate_inst)
-      endif
-
-      do fp = 1, num_nolakep
-         p = filter_nolakep(fp)
-         c = patch%column(p)
-
-         ! need to update elai and esai only every albedo time step so do not
-         ! have any inconsistency in lai and sai between SurfaceAlbedo calls (i.e.,
-         ! if albedos are not done every time step).
-         ! leaf phenology
-         ! Set leaf and stem areas based on day of year
-         ! Interpolate leaf area index, stem area index, and vegetation heights
-         ! between two monthly
-         ! The weights below (timwt(1) and timwt(2)) were obtained by a call to
-         ! routine InterpMonthlyVeg in subroutine NCARlsm.
-         !                 Field   Monthly Values
-         !                -------------------------
-         ! leaf area index LAI  <- mlai1 and mlai2
-         ! leaf area index SAI  <- msai1 and msai2
-         ! top height      HTOP <- mhvt1 and mhvt2
-         ! bottom height   HBOT <- mhvb1 and mhvb2
-
-         if (.not. use_lai_streams) then
-            tlai(p) = timwt(1)*mlai2t(p,1) + timwt(2)*mlai2t(p,2)
-         endif
-
-         tsai(p) = timwt(1)*msai2t(p,1) + timwt(2)*msai2t(p,2)
-         htop(p) = timwt(1)*mhvt2t(p,1) + timwt(2)*mhvt2t(p,2)
-         hbot(p) = timwt(1)*mhvb2t(p,1) + timwt(2)*mhvb2t(p,2)
-
-         ! adjust lai and sai for burying by snow. if exposed lai and sai
-         ! are less than 0.05, set equal to zero to prevent numerical
-         ! problems associated with very small lai and sai.
-
-         ! snow burial fraction for short vegetation (e.g. grasses) as in
-         ! Wang and Zeng, 2007. 
-
-         if (patch%itype(p) > noveg .and. patch%itype(p) <= nbrdlf_dcd_brl_shrub ) then
-            ol = min( max(snow_depth(c)-hbot(p), 0._r8), htop(p)-hbot(p))
-            fb = 1._r8 - ol / max(1.e-06_r8, htop(p)-hbot(p))
-         else
-            fb = 1._r8 - max(min(snow_depth(c),0.2_r8),0._r8)/0.2_r8   ! 0.2m is assumed
-            !depth of snow required for complete burial of grasses
-         endif
-
-         ! area weight by snow covered fraction
-
-         elai(p) = max(tlai(p)*(1.0_r8 - frac_sno(c)) + tlai(p)*fb*frac_sno(c), 0.0_r8)
-         esai(p) = max(tsai(p)*(1.0_r8 - frac_sno(c)) + tsai(p)*fb*frac_sno(c), 0.0_r8)
-         if (elai(p) < 0.05_r8) elai(p) = 0._r8
-         if (esai(p) < 0.05_r8) esai(p) = 0._r8
-
-         ! Fraction of vegetation free of snow
-
-         if ((elai(p) + esai(p)) >= 0.05_r8) then
-            frac_veg_nosno_alb(p) = 1
-         else
-            frac_veg_nosno_alb(p) = 0
-         end if
-
-      end do ! end of patch loop
-
-    end associate
-
-  end subroutine SatellitePhenology
-
-  !-----------------------------------------------------------------------
-  subroutine interpMonthlyVeg (bounds, canopystate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Determine if 2 new months of data are to be read.
-    !
-    ! !USES:
-    use clm_varctl      , only : fsurdat
-    use clm_time_manager, only : get_curr_date, get_step_size, get_nstep
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds  
-    type(canopystate_type), intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: kyr         ! year (0, ...) for nstep+1
-    integer :: kmo         ! month (1, ..., 12)
-    integer :: kda         ! day of month (1, ..., 31)
-    integer :: ksec        ! seconds into current date for nstep+1
-    real(r8):: dtime       ! land model time step (sec)
-    real(r8):: t           ! a fraction: kda/ndaypm
-    integer :: it(2)       ! month 1 and month 2 (step 1)
-    integer :: months(2)   ! months to be interpolated (1 to 12)
-    integer, dimension(12) :: ndaypm= &
-         (/31,28,31,30,31,30,31,31,30,31,30,31/) !days per month
-    !-----------------------------------------------------------------------
-
-    dtime = get_step_size()
-
-    call get_curr_date(kyr, kmo, kda, ksec, offset=int(dtime))
-
-    t = (kda-0.5_r8) / ndaypm(kmo)
-    it(1) = t + 0.5_r8
-    it(2) = it(1) + 1
-    months(1) = kmo + it(1) - 1
-    months(2) = kmo + it(2) - 1
-    if (months(1) <  1) months(1) = 12
-    if (months(2) > 12) months(2) = 1
-    timwt(1) = (it(1)+0.5_r8) - t
-    timwt(2) = 1._r8-timwt(1)
-
-    if (InterpMonths1 /= months(1)) then
-       if (masterproc) then
-          write(iulog,*) 'Attempting to read monthly vegetation data .....'
-          write(iulog,*) 'nstep = ',get_nstep(),' month = ',kmo,' day = ',kda
-       end if
-       call t_startf('readMonthlyVeg')
-       call readMonthlyVegetation (bounds, fsurdat, months, canopystate_inst)
-       InterpMonths1 = months(1)
-       call t_stopf('readMonthlyVeg')
-    end if
-
-  end subroutine interpMonthlyVeg
-
-  !-----------------------------------------------------------------------
-  subroutine readAnnualVegetation (bounds, canopystate_inst)
-    !
-    ! !DESCRIPTION:
-    ! read 12 months of veg data for dry deposition
-    !
-    ! !USES:
-    use clm_varpar  , only : numpft
-    use pftconMod   , only : noveg
-    use domainMod   , only : ldomain
-    use fileutils   , only : getfil
-    use clm_varctl  , only : fsurdat
-    use shr_scam_mod, only : shr_scam_getCloseLatLon
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds  
-    type(canopystate_type), intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    type(file_desc_t) :: ncid             ! netcdf id
-    real(r8), pointer :: annlai(:,:)      ! 12 months of monthly lai from input data set 
-    real(r8), pointer :: mlai(:,:)        ! lai read from input files
-    real(r8):: closelat,closelon          ! single column vars
-    integer :: ier                        ! error code
-    integer :: g,k,l,m,n,p                ! indices
-    integer :: ni,nj,ns                   ! indices
-    integer :: dimid,varid                ! input netCDF id's
-    integer :: ntim                       ! number of input data time samples
-    integer :: nlon_i                     ! number of input data longitudes
-    integer :: nlat_i                     ! number of input data latitudes
-    integer :: npft_i                     ! number of input data patch types
-    integer :: closelatidx,closelonidx    ! single column vars
-    logical :: isgrid2d                   ! true => file is 2d
-    character(len=256) :: locfn           ! local file name
-    character(len=32) :: subname = 'readAnnualVegetation'
-    !-----------------------------------------------------------------------
-
-    annlai    => canopystate_inst%annlai_patch 
-
-    ! Determine necessary indices
-
-    allocate(mlai(bounds%begg:bounds%endg,0:numpft), stat=ier)
-    if (ier /= 0) then
-       write(iulog,*)subname, 'allocation error ' 
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-
-    if (masterproc) then
-       write (iulog,*) 'Attempting to read annual vegetation data .....'
-    end if
-
-    call getfil(fsurdat, locfn, 0)
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-    call ncd_inqfdims (ncid, isgrid2d, ni, nj, ns)
-
-    if (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj) then
-       write(iulog,*)trim(subname), 'ldomain and input file do not match dims '
-       write(iulog,*)trim(subname), 'ldomain%ni,ni,= ',ldomain%ni,ni
-       write(iulog,*)trim(subname), 'ldomain%nj,nj,= ',ldomain%nj,nj
-       write(iulog,*)trim(subname), 'ldomain%ns,ns,= ',ldomain%ns,ns
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-    call check_dim(ncid, 'lsmpft', numpft+1)
-
-    if (single_column) then
-       call shr_scam_getCloseLatLon(locfn, scmlat, scmlon, &
-            closelat, closelon, closelatidx, closelonidx)
-    endif
-
-    do k=1,12   !! loop over months and read vegetated data
-
-       call ncd_io(ncid=ncid, varname='MONTHLY_LAI', flag='read', data=mlai, &
-            dim1name=grlnd, nt=k)
-
-       !! only vegetated patches have nonzero values
-       !! Assign lai/sai/hgtt/hgtb to the top [maxpatch_pft] patches
-       !! as determined in subroutine surfrd
-
-       do p = bounds%begp,bounds%endp
-          g =patch%gridcell(p)
-          if (patch%itype(p) /= noveg) then     !! vegetated pft
-             do l = 0, numpft
-                if (l == patch%itype(p)) then
-                   annlai(k,p) = mlai(g,l)
-                end if
-             end do
-          else                       !! non-vegetated pft
-             annlai(k,p) = 0._r8
-          end if
-       end do   ! end of loop over patches  
-
-    enddo ! months loop
-
-    call ncd_pio_closefile(ncid)
-
-    deallocate(mlai)
-
-  endsubroutine readAnnualVegetation
-
-  !-----------------------------------------------------------------------
-  subroutine readMonthlyVegetation (bounds, &
-       fveg, months, canopystate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Read monthly vegetation data for two consec. months.
-    !
-    ! !USES:
-    use clm_varpar       , only : numpft
-    use pftconMod        , only : noveg
-    use fileutils        , only : getfil
-    use spmdMod          , only : masterproc, mpicom, MPI_REAL8, MPI_INTEGER
-    use shr_scam_mod     , only : shr_scam_getCloseLatLon
-    use clm_time_manager , only : get_nstep
-    use netcdf
-    !
-    ! !ARGUMENTS:
-    type(bounds_type) , intent(in) :: bounds  
-    character(len=*)  , intent(in) :: fveg      ! file with monthly vegetation data
-    integer           , intent(in) :: months(2) ! months to be interpolated (1 to 12)
-    type(canopystate_type), intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    character(len=256) :: locfn           ! local file name
-    type(file_desc_t)  :: ncid            ! netcdf id
-    integer :: g,n,k,l,m,p,ni,nj,ns       ! indices
-    integer :: dimid,varid                ! input netCDF id's
-    integer :: ntim                       ! number of input data time samples
-    integer :: nlon_i                     ! number of input data longitudes
-    integer :: nlat_i                     ! number of input data latitudes
-    integer :: npft_i                     ! number of input data patch types
-    integer :: ier                        ! error code
-    integer :: closelatidx,closelonidx
-    real(r8):: closelat,closelon
-    logical :: readvar
-    real(r8), pointer :: mlai(:,:)        ! lai read from input files
-    real(r8), pointer :: msai(:,:)        ! sai read from input files
-    real(r8), pointer :: mhgtt(:,:)       ! top vegetation height
-    real(r8), pointer :: mhgtb(:,:)       ! bottom vegetation height
-    character(len=32) :: subname = 'readMonthlyVegetation'
-    !-----------------------------------------------------------------------
-
-    ! Determine necessary indices
-
-    allocate(&
-         mlai(bounds%begg:bounds%endg,0:numpft), &
-         msai(bounds%begg:bounds%endg,0:numpft), &
-         mhgtt(bounds%begg:bounds%endg,0:numpft), &
-         mhgtb(bounds%begg:bounds%endg,0:numpft), &
-         stat=ier)
-    if (ier /= 0) then
-       write(iulog,*)subname, 'allocation big error '
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-
-    ! ----------------------------------------------------------------------
-    ! Open monthly vegetation file
-    ! Read data and convert from gridcell to patch data
-    ! ----------------------------------------------------------------------
-
-    call getfil(fveg, locfn, 0)
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-
-    if (single_column) then
-       call shr_scam_getCloseLatLon (ncid, scmlat, scmlon, closelat, closelon,&
-            closelatidx, closelonidx)
-    endif
-
-    do k=1,2   !loop over months and read vegetated data
-
-       call ncd_io(ncid=ncid, varname='MONTHLY_LAI', flag='read', data=mlai, dim1name=grlnd, &
-            nt=months(k), readvar=readvar)
-       if (.not. readvar) call endrun(msg=' ERROR: MONTHLY_LAI NOT on fveg file'//errMsg(sourcefile, __LINE__))
-
-       call ncd_io(ncid=ncid, varname='MONTHLY_SAI', flag='read', data=msai, dim1name=grlnd, &
-            nt=months(k), readvar=readvar)
-       if (.not. readvar) call endrun(msg=' ERROR: MONTHLY_SAI NOT on fveg file'//errMsg(sourcefile, __LINE__))
-
-       call ncd_io(ncid=ncid, varname='MONTHLY_HEIGHT_TOP', flag='read', data=mhgtt, dim1name=grlnd, &
-            nt=months(k), readvar=readvar)
-       if (.not. readvar) call endrun(msg=' ERROR: MONTHLY_HEIGHT_TOP NOT on fveg file'//errMsg(sourcefile, __LINE__))
-
-       call ncd_io(ncid=ncid, varname='MONTHLY_HEIGHT_BOT', flag='read', data=mhgtb, dim1name=grlnd, &
-            nt=months(k), readvar=readvar)
-       if (.not. readvar) call endrun(msg=' ERROR: MONTHLY_HEIGHT_TOP NOT on fveg file'//errMsg(sourcefile, __LINE__))
-
-       ! Only vegetated patches have nonzero values
-       ! Assign lai/sai/hgtt/hgtb to the top [maxpatch_pft] patches
-       ! as determined in subroutine surfrd
-
-       do p = bounds%begp,bounds%endp
-          g =patch%gridcell(p)
-          if (patch%itype(p) /= noveg) then     ! vegetated pft
-             do l = 0, numpft
-                if (l == patch%itype(p)) then
-                   mlai2t(p,k) = mlai(g,l)
-                   msai2t(p,k) = msai(g,l)
-                   mhvt2t(p,k) = mhgtt(g,l)
-                   mhvb2t(p,k) = mhgtb(g,l)
-                end if
-             end do
-          else                        ! non-vegetated pft
-             mlai2t(p,k) = 0._r8
-             msai2t(p,k) = 0._r8
-             mhvt2t(p,k) = 0._r8
-             mhvb2t(p,k) = 0._r8
-          end if
-       end do   ! end of loop over patches
-
-    end do   ! end of loop over months
-
-    call ncd_pio_closefile(ncid)
-
-    if (masterproc) then
-       k = 2
-       write(iulog,*) 'Successfully read monthly vegetation data for'
-       write(iulog,*) 'month ', months(k)
-       write(iulog,*)
-    end if
-
-    deallocate(mlai, msai, mhgtt, mhgtb)
-
-    do p = bounds%begp,bounds%endp
-       canopystate_inst%mlaidiff_patch(p) = mlai2t(p,1)-mlai2t(p,2)
-    enddo
-
-  end subroutine readMonthlyVegetation
-
-end module SatellitePhenologyMod
diff --git a/src/biogeochem/SpeciesBaseType.F90 b/src/biogeochem/SpeciesBaseType.F90
deleted file mode 100644
index 239ca91fe3..0000000000
--- a/src/biogeochem/SpeciesBaseType.F90
+++ /dev/null
@@ -1,67 +0,0 @@
-module SpeciesBaseType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Defines a base class for working with chemical species, such as building history and
-  ! restart field names.
-  !
-  ! !USES:
-  !
-  implicit none
-  private
-
-  ! !PUBLIC TYPES:
-
-  type, abstract, public :: species_base_type
-   contains
-     ! Get a history field name for this species
-     procedure(hist_fname_interface), public, deferred :: hist_fname
-
-     ! Get a restart field name for this species
-     procedure(rest_fname_interface), public, deferred :: rest_fname
-
-     ! Get the full species name
-     procedure(get_species_interface), public, deferred :: get_species
-  end type species_base_type
-
-  abstract interface
-     pure function hist_fname_interface(this, basename, suffix) result(fname)
-       ! Get a history field name for this species
-       !
-       ! basename gives the base name of the history field
-       !
-       ! suffix, if provided, gives a suffix that appears after all species information
-       ! in the field name
-       import :: species_base_type
-
-       character(len=:)         , allocatable :: fname  ! function result
-       class(species_base_type) , intent(in)  :: this
-       character(len=*)         , intent(in)  :: basename
-       character(len=*)         , optional, intent(in) :: suffix
-     end function hist_fname_interface
-
-     function rest_fname_interface(this, basename, suffix) result(fname)
-       ! Get a restart field name for this species
-       !
-       ! basename gives the base name of the restart field
-       !
-       ! suffix, if provided, gives a suffix that appears after all species information
-       ! in the field name
-       import :: species_base_type
-
-       character(len=:)         , allocatable :: fname  ! function result
-       class(species_base_type) , intent(in)  :: this
-       character(len=*)         , intent(in)  :: basename
-       character(len=*)         , optional, intent(in) :: suffix
-     end function rest_fname_interface
-
-     pure function get_species_interface(this) result(species_name)
-       ! Get the full species name
-       import :: species_base_type
-
-       character(len=:), allocatable :: species_name
-       class(species_base_type) , intent(in)  :: this
-     end function get_species_interface
-  end interface
-
-end module SpeciesBaseType
diff --git a/src/biogeochem/SpeciesIsotopeType.F90 b/src/biogeochem/SpeciesIsotopeType.F90
deleted file mode 100644
index b5fb749823..0000000000
--- a/src/biogeochem/SpeciesIsotopeType.F90
+++ /dev/null
@@ -1,136 +0,0 @@
-module SpeciesIsotopeType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Defines a class for working with chemical species, such as building history and
-  ! restart field names.
-  !
-  ! This version is used for isotopic species
-  !
-  ! !USES:
-  !
-  use SpeciesBaseType, only : species_base_type
-  use abortutils, only : endrun
-  use shr_log_mod, only : errMsg => shr_log_errMsg
-  use clm_varctl, only : iulog
-
-  implicit none
-  save
-  private
-
-  ! COMPILER_BUG(wjs, 2016-03-16, pgi 15.10) Ideally, we would use allocatable characters
-  ! for species_name and isotope_name. However, this causes problems for pgi: it seems
-  ! that these allocatable characters randomly get changed. So, for now, using
-  ! fixed-length character variables. (It's possible that this was programmer error on my
-  ! part, although using allocatable character variables worked with other compilers.)
-  !
-  ! If species_name and isotope_name were changed back to allocatable-length characters,
-  ! then we could remove the error checking in the constructor as well as various 'trim'
-  ! statements scattered throughout the code (because this%species_name and
-  ! this%isotope_name would already be trimmed).
-  integer, parameter :: species_name_maxlen = 8
-  integer, parameter :: isotope_name_maxlen = 8
-
-  type, extends(species_base_type), public :: species_isotope_type
-     private
-     character(len=species_name_maxlen) :: species_name  ! does not contain the isotope number
-     character(len=isotope_name_maxlen) :: isotope_name  ! e.g., just the 13 for C13
-   contains
-     procedure, public :: hist_fname
-     procedure, public :: rest_fname
-     procedure, public :: get_species
-  end type species_isotope_type
-
-  interface species_isotope_type
-     module procedure constructor
-  end interface species_isotope_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  function constructor(species_name, isotope_name) result(this)
-    ! Create a species_isotope_type object
-
-    type(species_isotope_type) :: this  ! function result
-    character(len=*), intent(in) :: species_name  ! e.g., 'C' or 'N' - without the isotope number
-    character(len=*), intent(in) :: isotope_name  ! e.g., '13' for C13
-    !-----------------------------------------------------------------------
-
-    if (len_trim(species_name) > species_name_maxlen) then
-       write(iulog,*) 'species_isotope_type constructor: species_name too long'
-       write(iulog,*) trim(species_name) // ' exceeds max length: ', species_name_maxlen
-       call endrun(msg='species_isotope_type constructor: species_name too long: '// &
-            errMsg(sourcefile, __LINE__))
-    end if
-    if (len_trim(isotope_name) > isotope_name_maxlen) then
-       write(iulog,*) 'species_isotope_type constructor: isotope_name too long'
-       write(iulog,*) trim(isotope_name) // ' exceeds max length: ', isotope_name_maxlen
-       call endrun(msg='species_isotope_type constructor: isotope_name too long: '// &
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    this%species_name = trim(species_name)
-    this%isotope_name = trim(isotope_name)
-  end function constructor
-
-  pure function hist_fname(this, basename, suffix) result(fname)
-    ! Get a history field name for this species
-    !
-    ! basename gives the base name of the history field
-    !
-    ! suffix, if provided, gives a suffix that appears after all species information
-    ! in the field name
-
-    character(len=:), allocatable :: fname  ! function result
-    class(species_isotope_type) , intent(in)  :: this
-    character(len=*), intent(in)  :: basename
-    character(len=*), optional, intent(in) :: suffix
-    !-----------------------------------------------------------------------
-
-    fname = trim(this%species_name) // trim(this%isotope_name) // '_' // &
-         trim(basename) // trim(this%species_name)
-    if (present(suffix)) then
-       fname = trim(fname) // trim(suffix)
-    end if
-
-  end function hist_fname
-
-  function rest_fname(this, basename, suffix) result(fname)
-    ! Get a restart field name for this species
-    !
-    ! basename gives the base name of the restart field
-    !
-    ! suffix, if provided, gives a suffix that appears after all species information in
-    ! the field name
-    use shr_string_mod, only : shr_string_toLower
-
-    character(len=:), allocatable :: fname  ! function result
-    class(species_isotope_type) , intent(in)  :: this
-    character(len=*), intent(in)  :: basename
-    character(len=*), optional, intent(in) :: suffix
-
-    character(len=:), allocatable :: species_name_lcase
-    !-----------------------------------------------------------------------
-
-    species_name_lcase = shr_string_toLower(trim(this%species_name))
-    fname = trim(basename) // species_name_lcase // '_' // trim(this%isotope_name)
-    if (present(suffix)) then
-       fname = trim(fname) // trim(suffix)
-    end if
-
-  end function rest_fname
-
-  pure function get_species(this) result(species_name)
-    ! Get the full species name (e.g., 'C13')
-
-    character(len=:), allocatable :: species_name
-    class(species_isotope_type) , intent(in)  :: this
-    !-----------------------------------------------------------------------
-
-    species_name = trim(this%species_name) // trim(this%isotope_name)
-
-  end function get_species
-
-end module SpeciesIsotopeType
diff --git a/src/biogeochem/SpeciesNonIsotopeType.F90 b/src/biogeochem/SpeciesNonIsotopeType.F90
deleted file mode 100644
index 0daf6b3f72..0000000000
--- a/src/biogeochem/SpeciesNonIsotopeType.F90
+++ /dev/null
@@ -1,125 +0,0 @@
-module SpeciesNonIsotopeType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Defines a class for working with chemical species, such as building history and
-  ! restart field names.
-  !
-  ! This version is used for non-isotopic species
-  !
-  ! !USES:
-  !
-  use SpeciesBaseType, only : species_base_type
-  use abortutils, only : endrun
-  use shr_log_mod, only : errMsg => shr_log_errMsg
-  use clm_varctl, only : iulog
-
-  implicit none
-  save
-  private
-
-  ! COMPILER_BUG(wjs, 2016-03-16, pgi 15.10) Ideally, we would use an allocatable
-  ! character variable for species_name. However, this causes problems for pgi: it seems
-  ! that this allocatable character variable randomly gets changed. So, for now, using a
-  ! fixed-length character variable. (It's possible that this was programmer error on my
-  ! part, although using allocatable character variables worked with other compilers.)
-  !
-  ! If species_name was changed back to an allocatable-length character variable, then we
-  ! could remove the error checking in the constructor as well as various 'trim'
-  ! statements scattered throughout the code (because this%species_name would already be
-  ! trimmed).
-  integer, parameter :: species_name_maxlen = 8
-
-  type, extends(species_base_type), public :: species_non_isotope_type
-     private
-     character(len=species_name_maxlen) :: species_name
-   contains
-     procedure, public :: hist_fname
-     procedure, public :: rest_fname
-     procedure, public :: get_species
-  end type species_non_isotope_type
-
-  interface species_non_isotope_type
-     module procedure constructor
-  end interface species_non_isotope_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  function constructor(species_name) result(this)
-    ! Create a species_non_isotope_type object
-
-    type(species_non_isotope_type) :: this  ! function result
-    character(len=*), intent(in) :: species_name  ! e.g., 'C' or 'N'
-    !-----------------------------------------------------------------------
-
-    if (len_trim(species_name) > species_name_maxlen) then
-       write(iulog,*) 'species_isotope_type constructor: species_name too long'
-       write(iulog,*) trim(species_name) // ' exceeds max length: ', species_name_maxlen
-       call endrun(msg='species_isotope_type constructor: species_name too long: '// &
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    this%species_name = trim(species_name)
-  end function constructor
-
-  pure function hist_fname(this, basename, suffix) result(fname)
-    ! Get a history field name for this species
-    !
-    ! basename gives the base name of the history field
-    !
-    ! suffix, if provided, gives a suffix that appears after all species information
-    ! in the field name
-
-    character(len=:), allocatable :: fname  ! function result
-    class(species_non_isotope_type) , intent(in)  :: this
-    character(len=*), intent(in)  :: basename
-    character(len=*), optional, intent(in) :: suffix
-    !-----------------------------------------------------------------------
-
-    fname = trim(basename) // trim(this%species_name)
-    if (present(suffix)) then
-       fname = trim(fname) // trim(suffix)
-    end if
-
-  end function hist_fname
-
-  function rest_fname(this, basename, suffix) result(fname)
-    ! Get a restart field name for this species
-    !
-    ! basename gives the base name of the restart field
-    !
-    ! suffix, if provided, gives a suffix that appears after all species information in
-    ! the field name
-    use shr_string_mod, only : shr_string_toLower
-
-    character(len=:), allocatable :: fname  ! function result
-    class(species_non_isotope_type) , intent(in)  :: this
-    character(len=*), intent(in)  :: basename
-    character(len=*), optional, intent(in) :: suffix
-
-    character(len=:), allocatable :: species_name_lcase
-    !-----------------------------------------------------------------------
-
-    species_name_lcase = shr_string_toLower(trim(this%species_name))
-    fname = trim(basename) // trim(species_name_lcase)
-    if (present(suffix)) then
-       fname = trim(fname) // trim(suffix)
-    end if
-
-  end function rest_fname
-
-  pure function get_species(this) result(species_name)
-    ! Get the full species name
-
-    character(len=:), allocatable :: species_name
-    class(species_non_isotope_type) , intent(in)  :: this
-    !-----------------------------------------------------------------------
-
-    species_name = trim(this%species_name)
-
-  end function get_species
-
-end module SpeciesNonIsotopeType
diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
deleted file mode 100644
index 1c9a0e58f6..0000000000
--- a/src/biogeochem/VOCEmissionMod.F90
+++ /dev/null
@@ -1,26 +0,0 @@
-module VOCEmissionMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Volatile organic compound emission
-  !
-  ! !USES:
-  use shr_kind_mod       , only : r8 => shr_kind_r8
-  use shr_log_mod        , only : errMsg => shr_log_errMsg
-  !
-  implicit none
-  private 
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  !
-  ! !PUBLIC TYPES:
-  type, public :: vocemis_type
-  end type vocemis_type
-  !
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-end module VOCEmissionMod
-
-
diff --git a/src/biogeochem/ch4Mod.F90 b/src/biogeochem/ch4Mod.F90
deleted file mode 100644
index 81978bf6dd..0000000000
--- a/src/biogeochem/ch4Mod.F90
+++ /dev/null
@@ -1,123 +0,0 @@
-module ch4Mod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding routines to calculate methane fluxes
-  ! The driver averages up to gridcell, weighting by finundated, and checks for balance errors.
-  ! Sources, sinks, "competition" for CH4 & O2, & transport are resolved in ch4_tran.
-  !
-  ! !USES:
-  use shr_kind_mod                   , only : r8 => shr_kind_r8
-  use shr_infnan_mod                 , only : nan => shr_infnan_nan, assignment(=), shr_infnan_isnan
-  use shr_log_mod                    , only : errMsg => shr_log_errMsg
-  use abortutils                     , only : endrun
-  !
-  implicit none
-  private
-
-  ! Non-tunable constants
-  real(r8) :: rgasm  ! J/mol.K; rgas / 1000; will be set below
-  real(r8), parameter :: rgasLatm = 0.0821_r8 ! L.atm/mol.K
-
-  type, public :: ch4_type
-     real(r8), pointer, private :: ch4_prod_depth_sat_col     (:,:) ! col CH4 production rate from methanotrophs (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_prod_depth_unsat_col   (:,:) ! col CH4 production rate from methanotrophs (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_prod_depth_lake_col    (:,:) ! col CH4 production rate from methanotrophs (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_oxid_depth_sat_col     (:,:) ! col CH4 consumption rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_oxid_depth_unsat_col   (:,:) ! col CH4 consumption rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_oxid_depth_lake_col    (:,:) ! col CH4 consumption rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_aere_depth_sat_col     (:,:) ! col CH4 loss rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_aere_depth_unsat_col   (:,:) ! col CH4 loss rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_tran_depth_sat_col     (:,:) ! col CH4 loss rate via transpiration in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_tran_depth_unsat_col   (:,:) ! col CH4 loss rate via transpiration in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_ebul_depth_sat_col     (:,:) ! col CH4 loss rate via ebullition in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_ebul_depth_unsat_col   (:,:) ! col CH4 loss rate via ebullition in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: ch4_ebul_total_sat_col     (:)   ! col Total col CH4 ebullition (mol/m2/s)
-     real(r8), pointer, private :: ch4_ebul_total_unsat_col   (:)   ! col Total col CH4 ebullition (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_aere_sat_col      (:)   ! col CH4 aerenchyma flux to atmosphere (after oxidation) (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_aere_unsat_col    (:)   ! col CH4 aerenchyma flux to atmosphere (after oxidation) (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_ebul_sat_col      (:)   ! col CH4 ebullition flux to atmosphere (after oxidation) (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_ebul_unsat_col    (:)   ! col CH4 ebullition flux to atmosphere (after oxidation) (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_ebul_lake_col     (:)   ! col CH4 ebullition flux to atmosphere (after oxidation) (mol/m2/s)
-     real(r8), pointer, private :: co2_aere_depth_sat_col     (:,:) ! col CO2 loss rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: co2_aere_depth_unsat_col   (:,:) ! col CO2 loss rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: o2_oxid_depth_sat_col      (:,:) ! col O2 consumption rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: o2_oxid_depth_unsat_col    (:,:) ! col O2 consumption rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: o2_aere_depth_sat_col      (:,:) ! col O2 gain rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: o2_aere_depth_unsat_col    (:,:) ! col O2 gain rate via aerenchyma in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: co2_decomp_depth_sat_col   (:,:) ! col CO2 production during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-     real(r8), pointer, private :: co2_decomp_depth_unsat_col (:,:) ! col CO2 production during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-     real(r8), pointer, private :: co2_oxid_depth_sat_col     (:,:) ! col CO2 production rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: co2_oxid_depth_unsat_col   (:,:) ! col CO2 production rate via oxidation in each soil layer (mol/m3/s) (nlevsoi)
-     real(r8), pointer, private :: conc_o2_lake_col           (:,:) ! col O2 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, private :: conc_ch4_sat_col           (:,:) ! col CH4 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, private :: conc_ch4_unsat_col         (:,:) ! col CH4 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, private :: conc_ch4_lake_col          (:,:) ! col CH4 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, private :: ch4_surf_diff_sat_col      (:)   ! col CH4 surface flux (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_diff_unsat_col    (:)   ! col CH4 surface flux (mol/m2/s)
-     real(r8), pointer, private :: ch4_surf_diff_lake_col     (:)   ! col CH4 surface flux (mol/m2/s)
-     real(r8), pointer, private :: ch4_dfsat_flux_col         (:)   ! col CH4 flux to atm due to decreasing fsat (kg C/m^2/s) [+]
-
-     real(r8), pointer, private :: zwt_ch4_unsat_col          (:)   ! col depth of water table for unsaturated fraction (m)
-     real(r8), pointer, private :: lake_soilc_col             (:,:) ! col total soil organic matter found in level (g C / m^3) (nlevsoi)
-     real(r8), pointer, private :: totcolch4_col              (:)   ! col total methane found in soil col (g C / m^2)
-     real(r8), pointer, private :: totcolch4_bef_col          (:)   ! col total methane found in soil col, start of timestep (g C / m^2)
-     real(r8), pointer, private :: annsum_counter_col         (:)   ! col seconds since last annual accumulator turnover
-     real(r8), pointer, private :: tempavg_somhr_col          (:)   ! col temporary average SOM heterotrophic resp. (gC/m2/s)
-     real(r8), pointer, private :: annavg_somhr_col           (:)   ! col annual average SOM heterotrophic resp. (gC/m2/s)
-     real(r8), pointer, private :: tempavg_finrw_col          (:)   ! col respiration-weighted annual average of finundated
-     real(r8), pointer, private :: annavg_finrw_col           (:)   ! col respiration-weighted annual average of finundated
-     real(r8), pointer, private :: sif_col                    (:)   ! col (unitless) ratio applied to sat. prod. to account for seasonal inundation
-     real(r8), pointer, private :: ch4stress_unsat_col        (:,:) ! col Ratio of methane available to the total per-timestep methane sinks (nlevsoi)
-     real(r8), pointer, private :: ch4stress_sat_col          (:,:) ! col Ratio of methane available to the total per-timestep methane sinks (nlevsoi)
-     real(r8), pointer, private :: qflx_surf_lag_col          (:)   ! col time-lagged surface runoff (mm H2O /s)
-     real(r8), pointer, private :: finundated_lag_col         (:)   ! col time-lagged fractional inundated area
-     real(r8), pointer, private :: layer_sat_lag_col          (:,:) ! col Lagged saturation status of soil layer in the unsaturated zone (1 = sat)
-     real(r8), pointer, private :: zwt0_col                   (:)   ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: f0_col                     (:)   ! col maximum inundated fraction for a gridcell (for methane code)
-     real(r8), pointer, private :: p3_col                     (:)   ! col coefficient for determining finundated (m)
-     real(r8), pointer, private :: pH_col                     (:)   ! col pH values for methane production
-     !
-     real(r8), pointer, private :: dyn_ch4bal_adjustments_col (:)   ! adjustments to each column made in this timestep via dynamic column area adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) (g C / m^2)
-     !
-     real(r8), pointer, private :: c_atm_grc                  (:,:) ! grc atmospheric conc of CH4, O2, CO2 (mol/m3)
-     real(r8), pointer, private :: ch4co2f_grc                (:)   ! grc CO2 production from CH4 oxidation (g C/m**2/s)
-     real(r8), pointer, private :: ch4prodg_grc               (:)   ! grc average CH4 production (g C/m^2/s)
-     !
-     ! for aerenchyma calculations 
-     real(r8), pointer, private :: annavg_agnpp_patch         (:)   ! patch (gC/m2/s) annual average aboveground NPP
-     real(r8), pointer, private :: annavg_bgnpp_patch         (:)   ! patch (gC/m2/s) annual average belowground NPP
-     real(r8), pointer, private :: tempavg_agnpp_patch        (:)   ! patch (gC/m2/s) temp. average aboveground NPP
-     real(r8), pointer, private :: tempavg_bgnpp_patch        (:)   ! patch (gC/m2/s) temp. average belowground NPP
-     !
-     ! The following variable reports whether this is the first timestep that includes
-     ! ch4. It is true in the first timestep of the run, and remains true until the
-     ! methane code is first run - at which point it becomes false, and remains
-     ! false. This could be a scalar, but scalars cause problems with threading, so we use
-     ! a column-level array (column-level for convenience, because it is referenced in
-     ! column-level loops).
-     logical , pointer, private :: ch4_first_time_col         (:)   ! col whether this is the first time step that includes ch4
-     !
-     real(r8), pointer, public :: finundated_col             (:)   ! col fractional inundated area (excluding dedicated wetland cols)
-     real(r8), pointer, public :: finundated_pre_snow_col    (:)   ! col fractional inundated area (excluding dedicated wetland cols) before snow
-     real(r8), pointer, public :: o2stress_unsat_col         (:,:) ! col Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
-     real(r8), pointer, public :: o2stress_sat_col           (:,:) ! col Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
-     real(r8), pointer, public :: conc_o2_sat_col            (:,:) ! col O2 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, public :: conc_o2_unsat_col          (:,:) ! col O2 conc in each soil layer (mol/m3) (nlevsoi)
-     real(r8), pointer, public :: o2_decomp_depth_sat_col    (:,:) ! col O2 consumption during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-     real(r8), pointer, public :: o2_decomp_depth_unsat_col  (:,:) ! col O2 consumption during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-     real(r8), pointer, public :: ch4_surf_flux_tot_col      (:)   ! col CH4 surface flux (to atm) (kg C/m**2/s)
-
-     real(r8), pointer, public :: grnd_ch4_cond_patch        (:)   ! patch tracer conductance for boundary layer [m/s]
-     real(r8), pointer, public :: grnd_ch4_cond_col          (:)   ! col tracer conductance for boundary layer [m/s]
-
-  end type ch4_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-end module ch4Mod
-
diff --git a/src/biogeophys/ActiveLayerMod.F90 b/src/biogeophys/ActiveLayerMod.F90
deleted file mode 100644
index a1b871829c..0000000000
--- a/src/biogeophys/ActiveLayerMod.F90
+++ /dev/null
@@ -1,155 +0,0 @@
-module ActiveLayerMod
-  
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding routines for calculation of active layer dynamics
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_const_mod   , only : SHR_CONST_TKFRZ
-  use clm_varctl      , only : iulog
-  use TemperatureType , only : temperature_type
-  use CanopyStateType , only : canopystate_type
-  use GridcellType    , only : grc       
-  use ColumnType      , only : col       
-  !
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public:: alt_calc
-  !-----------------------------------------------------------------------
-  
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine alt_calc(num_soilc, filter_soilc, &
-       temperature_inst, canopystate_inst) 
-    !
-    ! !DESCRIPTION:
-    !  define active layer thickness similarly to frost_table, except set as deepest thawed layer and define on nlevgrnd
-    !  also update annual maxima, and keep track of prior year for rooting memory
-    !
-    ! BUG(wjs, 2014-12-15, bugz 2107) Because of this routine's placement in the driver
-    ! sequence (it is called very early in each timestep, before weights are adjusted and
-    ! filters are updated), it may be necessary for this routine to compute values over
-    ! inactive as well as active points (since some inactive points may soon become
-    ! active) - so that's what is done now. Currently, it seems to be okay to do this,
-    ! because the variables computed here seem to only depend on quantities that are valid
-    ! over inactive as well as active points.
-    !
-    ! !USES:
-    use shr_const_mod    , only : SHR_CONST_TKFRZ
-    use clm_varpar       , only : nlevgrnd
-    use clm_time_manager , only : get_curr_date, get_step_size
-    use clm_varctl       , only : iulog
-    use clm_varcon       , only : zsoi
-    !
-    ! !ARGUMENTS:
-    integer                , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(temperature_type) , intent(in)    :: temperature_inst
-    type(canopystate_type) , intent(inout) :: canopystate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c, j, fc, g                     ! counters
-    integer  :: alt_ind                         ! index of base of activel layer
-    integer  :: year                            ! year (0, ...) for nstep+1
-    integer  :: mon                             ! month (1, ..., 12) for nstep+1
-    integer  :: day                             ! day of month (1, ..., 31) for nstep+1
-    integer  :: sec                             ! seconds into current date for nstep+1
-    integer  :: dtime                           ! time step length in seconds
-    integer  :: k_frz                           ! index of first nonfrozen soil layer
-    logical  :: found_thawlayer                 ! used to break loop when first unfrozen layer reached
-    real(r8) :: t1, t2, z1, z2                  ! temporary variables
-    !-----------------------------------------------------------------------
-
-    associate(                                                                & 
-         t_soisno             =>    temperature_inst%t_soisno_col        ,    & ! Input:   [real(r8) (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)                    
-         
-         alt                  =>    canopystate_inst%alt_col             ,    & ! Output:  [real(r8) (:)   ]  current depth of thaw                                                 
-         altmax               =>    canopystate_inst%altmax_col          ,    & ! Output:  [real(r8) (:)   ]  maximum annual depth of thaw                                          
-         altmax_lastyear      =>    canopystate_inst%altmax_lastyear_col ,    & ! Output:  [real(r8) (:)   ]  prior year maximum annual depth of thaw                               
-         alt_indx             =>    canopystate_inst%alt_indx_col        ,    & ! Output:  [integer  (:)   ]  current depth of thaw                                                  
-         altmax_indx          =>    canopystate_inst%altmax_indx_col     ,    & ! Output:  [integer  (:)   ]  maximum annual depth of thaw                                           
-         altmax_lastyear_indx =>    canopystate_inst%altmax_lastyear_indx_col & ! Output:  [integer  (:)   ]  prior year maximum annual depth of thaw                                
-         )
-
-      ! on a set annual timestep, update annual maxima
-      ! make this 1 January for NH columns, 1 July for SH columns
-      call get_curr_date(year, mon, day, sec)
-      dtime =  get_step_size()
-      if ( (mon .eq. 1) .and. (day .eq. 1) .and. ( sec / dtime .eq. 1) ) then
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            g = col%gridcell(c)
-            if ( grc%lat(g) > 0. ) then 
-               altmax_lastyear(c) = altmax(c)
-               altmax_lastyear_indx(c) = altmax_indx(c)
-               altmax(c) = 0.
-               altmax_indx(c) = 0
-            endif
-         end do
-      endif
-      if ( (mon .eq. 7) .and. (day .eq. 1) .and. ( sec / dtime .eq. 1) ) then
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            g = col%gridcell(c)
-            if ( grc%lat(g) <= 0. ) then 
-               altmax_lastyear(c) = altmax(c)
-               altmax_lastyear_indx(c) = altmax_indx(c)
-               altmax(c) = 0.
-               altmax_indx(c) = 0
-            endif
-         end do
-      endif
-
-      do fc = 1,num_soilc
-         c = filter_soilc(fc)
-
-         ! calculate alt for a given timestep
-         ! start from base of soil and search upwards for first thawed layer.
-         ! note that this will put talik in with active layer
-         ! a different way of doing this could be to keep track of how long a given layer has ben frozen for, and define ALT as the first layer that has been frozen for less than 2 years.
-         if (t_soisno(c,nlevgrnd) > SHR_CONST_TKFRZ ) then
-            alt(c) = zsoi(nlevgrnd)
-            alt_indx(c) = nlevgrnd
-         else
-            k_frz=0
-            found_thawlayer = .false.
-            do j=nlevgrnd-1,1,-1
-               if ( ( t_soisno(c,j) > SHR_CONST_TKFRZ ) .and. .not. found_thawlayer ) then
-                  k_frz=j
-                  found_thawlayer = .true.
-               endif
-            end do
-
-            if ( k_frz > 0 ) then
-               ! define active layer as the depth at which the linearly interpolated temperature line intersects with zero
-               z1 = zsoi(k_frz)
-               z2 = zsoi(k_frz+1)
-               t1 = t_soisno(c,k_frz)
-               t2 = t_soisno(c,k_frz+1)
-               alt(c) = z1 + (t1-SHR_CONST_TKFRZ)*(z2-z1)/(t1-t2)
-               alt_indx(c) = k_frz
-            else
-               alt(c)=0._r8
-               alt_indx(c) = 0
-            endif
-         endif
-
-
-         ! if appropriate, update maximum annual active layer thickness
-         if (alt(c) > altmax(c)) then
-            altmax(c) = alt(c)
-            altmax_indx(c) = alt_indx(c)
-         endif
-
-      end do
-
-    end associate 
-
-  end subroutine alt_calc
-  
-end module ActiveLayerMod
diff --git a/src/biogeophys/AerosolMod.F90 b/src/biogeophys/AerosolMod.F90
deleted file mode 100644
index 06111cd1d0..0000000000
--- a/src/biogeophys/AerosolMod.F90
+++ /dev/null
@@ -1,29 +0,0 @@
-module AerosolMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  use shr_kind_mod     , only : r8 => shr_kind_r8
-  use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
-  use abortutils       , only : endrun
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  !
-  ! !PUBLIC DATA MEMBERS:
-  real(r8), public, parameter :: snw_rds_min = 54.526_r8          ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns]
-  real(r8), public            :: fresh_snw_rds_max = 204.526_r8   ! maximum warm fresh snow effective radius [microns]
-  !
-  type, public :: aerosol_type
-
-  end type aerosol_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-end module AerosolMod
diff --git a/src/biogeophys/BandDiagonalMod.F90 b/src/biogeophys/BandDiagonalMod.F90
deleted file mode 100644
index 5065ea59b5..0000000000
--- a/src/biogeophys/BandDiagonalMod.F90
+++ /dev/null
@@ -1,224 +0,0 @@
-module BandDiagonalMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Band Diagonal matrix solution
-  !
-  ! !USES:
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use decompMod      , only : bounds_type
-  use abortutils     , only : endrun
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use clm_varctl     , only : iulog
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: BandDiagonal
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine BandDiagonal(bounds, lbj, ubj, jtop, jbot, numf, filter, nband, b, r, u)
-    !
-    ! !DESCRIPTION:
-    ! Tridiagonal matrix solution
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds                    
-    integer , intent(in)    :: lbj, ubj                        ! lbinning and ubing level indices
-    integer , intent(in)    :: jtop( bounds%begc: )            ! top level for each column [col]
-    integer , intent(in)    :: jbot( bounds%begc: )            ! bottom level for each column [col]
-    integer , intent(in)    :: numf                            ! filter dimension
-    integer , intent(in)    :: nband                           ! band width
-    integer , intent(in)    :: filter(:)                       ! filter
-    real(r8), intent(in)    :: b( bounds%begc: , 1:   , lbj: ) ! compact band matrix [col, nband, j]
-    real(r8), intent(in)    :: r( bounds%begc: , lbj: )        ! "r" rhs of linear system [col, j]
-    real(r8), intent(inout) :: u( bounds%begc: , lbj: )        ! solution [col, j]
-    !
-    ! ! LOCAL VARIABLES:
-    integer  :: j,ci,fc,info,m,n              !indices
-    integer  :: kl,ku                         !number of sub/super diagonals
-    integer, allocatable :: ipiv(:)           !temporary
-    real(r8),allocatable :: ab(:,:),temp(:,:) !compact storage array
-    real(r8),allocatable :: result(:)
-
-    !-----------------------------------------------------------------------
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(jtop) == (/bounds%endc/)),             errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(jbot) == (/bounds%endc/)),             errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(b)    == (/bounds%endc, nband, ubj/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(r)    == (/bounds%endc, ubj/)),        errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(u)    == (/bounds%endc, ubj/)),        errMsg(sourcefile, __LINE__))
-
-
-!!$     SUBROUTINE SGBSV( N, KL, KU, NRHS, AB, LDAB, IPIV, B, LDB, INFO )
-!!$*
-!!$*  -- LAPACK driver routine (version 3.1) --
-!!$*     Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd..
-!!$*     November 2006
-!!$*
-!!$*     .. Scalar Arguments ..
-!!$      INTEGER            INFO, KL, KU, LDAB, LDB, N, NRHS
-!!$*     ..
-!!$*     .. Array Arguments ..
-!!$      INTEGER            IPIV( * )
-!!$      REAL               AB( LDAB, * ), B( LDB, * )
-!!$*     ..
-!!$*
-!!$*  Purpose
-!!$*  =======
-!!$*
-!!$*  SGBSV computes the solution to a real system of linear equations
-!!$*  A * X = B, where A is a band matrix of order N with KL subdiagonals
-!!$*  and KU superdiagonals, and X and B are N-by-NRHS matrices.
-!!$*
-!!$*  The LU decomposition with partial pivoting and row interchanges is
-!!$*  used to factor A as A = L * U, where L is a product of permutation
-!!$*  and unit lower triangular matrices with KL subdiagonals, and U is
-!!$*  upper triangular with KL+KU superdiagonals.  The factored form of A
-!!$*  is then used to solve the system of equations A * X = B.
-!!$*
-!!$*  Arguments
-!!$*  =========
-!!$*
-!!$*  N       (input) INTEGER
-!!$*          The number of linear equations, i.e., the order of the
-!!$*          matrix A.  N >= 0.
-!!$*
-!!$*  KL      (input) INTEGER
-!!$*          The number of subdiagonals within the band of A.  KL >= 0.
-!!$*
-!!$*  KU      (input) INTEGER
-!!$*          The number of superdiagonals within the band of A.  KU >= 0.
-!!$*
-!!$*  NRHS    (input) INTEGER
-!!$*          The number of right hand sides, i.e., the number of columns
-!!$*          of the matrix B.  NRHS >= 0.
-!!$*
-!!$*  AB      (input/output) REAL array, dimension (LDAB,N)
-!!$*          On entry, the matrix A in band storage, in rows KL+1 to
-!!$*          2*KL+KU+1; rows 1 to KL of the array need not be set.
-!!$*          The j-th column of A is stored in the j-th column of the
-!!$*          array AB as follows:
-!!$*          AB(KL+KU+1+i-j,j) = A(i,j) for max(1,j-KU)<=i<=min(N,j+KL)
-!!$*          On exit, details of the factorization: U is stored as an
-!!$*          upper triangular band matrix with KL+KU superdiagonals in
-!!$*          rows 1 to KL+KU+1, and the multipliers used during the
-!!$*          factorization are stored in rows KL+KU+2 to 2*KL+KU+1.
-!!$*          See below for further details.
-!!$*
-!!$*  LDAB    (input) INTEGER
-!!$*          The leading dimension of the array AB.  LDAB >= 2*KL+KU+1.
-!!$*
-!!$*  IPIV    (output) INTEGER array, dimension (N)
-!!$*          The pivot indices that define the permutation matrix P;
-!!$*          row i of the matrix was interchanged with row IPIV(i).
-!!$*
-!!$*  B       (input/output) REAL array, dimension (LDB,NRHS)
-!!$*          On entry, the N-by-NRHS right hand side matrix B.
-!!$*          On exit, if INFO = 0, the N-by-NRHS solution matrix X.
-!!$*
-!!$*  LDB     (input) INTEGER
-!!$*          The leading dimension of the array B.  LDB >= max(1,N).
-!!$*
-!!$*  INFO    (output) INTEGER
-!!$*          = 0:  successful exit
-!!$*          < 0:  if INFO = -i, the i-th argument had an illegal value
-!!$*          > 0:  if INFO = i, U(i,i) is exactly zero.  The factorization
-!!$*                has been completed, but the factor U is exactly
-!!$*                singular, and the solution has not been computed.
-!!$*
-!!$*  Further Details
-!!$*  ===============
-!!$*
-!!$*  The band storage scheme is illustrated by the following example, when
-!!$*  M = N = 6, KL = 2, KU = 1:
-!!$*
-!!$*  On entry:                       On exit:
-!!$*
-!!$*      *    *    *    +    +    +       *    *    *   u14  u25  u36
-!!$*      *    *    +    +    +    +       *    *   u13  u24  u35  u46
-!!$*      *   a12  a23  a34  a45  a56      *   u12  u23  u34  u45  u56
-!!$*     a11  a22  a33  a44  a55  a66     u11  u22  u33  u44  u55  u66
-!!$*     a21  a32  a43  a54  a65   *      m21  m32  m43  m54  m65   *
-!!$*     a31  a42  a53  a64   *    *      m31  m42  m53  m64   *    *
-!!$*
-!!$*  Array elements marked * are not used by the routine; elements marked
-!!$*  + need not be set on entry, but are required by the routine to store
-!!$*  elements of U because of fill-in resulting from the row interchanges.
-
-
-!Set up input matrix AB
-!An m-by-n band matrix with kl subdiagonals and ku superdiagonals 
-!may be stored compactly in a two-dimensional array with 
-!kl+ku+1 rows and n columns
-!AB(KL+KU+1+i-j,j) = A(i,j)
-
-    do fc = 1,numf
-       ci = filter(fc)
-
-       kl=(nband-1)/2
-       ku=kl
-! m is the number of rows required for storage space by dgbsv
-       m=2*kl+ku+1
-! n is the number of levels (snow/soil)
-!scs: replace ubj with jbot
-       n=jbot(ci)-jtop(ci)+1
-
-       allocate(ab(m,n))
-       ab=0.0
-
-       ab(kl+ku-1,3:n)=b(ci,1,jtop(ci):jbot(ci)-2)   ! 2nd superdiagonal
-       ab(kl+ku+0,2:n)=b(ci,2,jtop(ci):jbot(ci)-1)   ! 1st superdiagonal
-       ab(kl+ku+1,1:n)=b(ci,3,jtop(ci):jbot(ci))     ! diagonal
-       ab(kl+ku+2,1:n-1)=b(ci,4,jtop(ci)+1:jbot(ci)) ! 1st subdiagonal
-       ab(kl+ku+3,1:n-2)=b(ci,5,jtop(ci)+2:jbot(ci)) ! 2nd subdiagonal
-
-       allocate(temp(m,n))
-       temp=ab
-
-       allocate(ipiv(n))
-       allocate(result(n))
-
-! on input result is rhs, on output result is solution vector
-       result(:)=r(ci,jtop(ci):jbot(ci))
-
-!       DGBSV( N, KL, KU, NRHS, AB, LDAB, IPIV, B, LDB, INFO )
-       call dgbsv( n, kl, ku, 1, ab, m, ipiv, result, n, info )
-       u(ci,jtop(ci):jbot(ci))=result(:)
-
-       if(info /= 0) then 
-          write(iulog,*)'index: ', ci
-          write(iulog,*)'n,kl,ku,m ',n,kl,ku,m
-          write(iulog,*)'dgbsv info: ',ci,info
-          
-          write(iulog,*) ''
-          write(iulog,*) 'ab matrix'
-          do j=1,n
-             !             write(iulog,'(i2,7f18.7)') j,temp(:,j)
-             write(iulog,'(i2,5f18.7)') j,temp(3:7,j)
-          enddo
-          write(iulog,*) ''
-          call endrun( 'BandDiagonal ERROR: dgbsv returned error code' )
-       endif
-       deallocate(temp)
-
-       deallocate(ab)
-       deallocate(ipiv)
-       deallocate(result)
-    end do
-
-  end subroutine BandDiagonal
-
-end module BandDiagonalMod
diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90
deleted file mode 100644
index beef9527d5..0000000000
--- a/src/biogeophys/CanopyStateType.F90
+++ /dev/null
@@ -1,640 +0,0 @@
-module CanopyStateType
-
-  !------------------------------------------------------------------------------
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_infnan_mod  , only : nan => shr_infnan_nan, shr_infnan_isnan, assignment(=)
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type
-  use landunit_varcon , only : istsoil, istcrop
-  use clm_varpar      , only : nlevcan, nvegwcs
-  use clm_varcon      , only : spval  
-  use clm_varctl      , only : iulog, use_cn, use_fates, use_hydrstress
-  use LandunitType    , only : lun                
-  use ColumnType      , only : col                
-  use PatchType       , only : patch                
-  !
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: CanopyState_type
-
-     integer  , pointer :: frac_veg_nosno_patch     (:)   ! patch fraction of vegetation not covered by snow (0 OR 1) [-] 
-     integer  , pointer :: frac_veg_nosno_alb_patch (:)   ! patch fraction of vegetation not covered by snow (0 OR 1) [-] 
-
-     real(r8) , pointer :: tlai_patch               (:)   ! patch canopy one-sided leaf area index, no burying by snow
-     real(r8) , pointer :: tsai_patch               (:)   ! patch canopy one-sided stem area index, no burying by snow
-     real(r8) , pointer :: elai_patch               (:)   ! patch canopy one-sided leaf area index with burying by snow
-     real(r8) , pointer :: esai_patch               (:)   ! patch canopy one-sided stem area index with burying by snow
-     real(r8) , pointer :: elai240_patch            (:)   ! patch canopy one-sided leaf area index with burying by snow average over 10days 
-     real(r8) , pointer :: laisun_patch             (:)   ! patch patch sunlit projected leaf area index  
-     real(r8) , pointer :: laisha_patch             (:)   ! patch patch shaded projected leaf area index  
-     real(r8) , pointer :: laisun_z_patch           (:,:) ! patch patch sunlit leaf area for canopy layer 
-     real(r8) , pointer :: laisha_z_patch           (:,:) ! patch patch shaded leaf area for canopy layer 
-     real(r8) , pointer :: mlaidiff_patch           (:)   ! patch difference between lai month one and month two (for dry deposition of chemical tracers)
-     real(r8) , pointer :: annlai_patch             (:,:) ! patch 12 months of monthly lai from input data set (for dry deposition of chemical tracers) 
-     real(r8) , pointer :: htop_patch               (:)   ! patch canopy top (m)
-     real(r8) , pointer :: hbot_patch               (:)   ! patch canopy bottom (m)
-     real(r8) , pointer :: displa_patch             (:)   ! patch displacement height (m)
-     real(r8) , pointer :: fsun_patch               (:)   ! patch sunlit fraction of canopy         
-     real(r8) , pointer :: fsun24_patch             (:)   ! patch 24hr average of sunlit fraction of canopy 
-     real(r8) , pointer :: fsun240_patch            (:)   ! patch 240hr average of sunlit fraction of canopy
-
-     real(r8) , pointer :: alt_col                  (:)   ! col current depth of thaw 
-     integer  , pointer :: alt_indx_col             (:)   ! col current depth of thaw 
-     real(r8) , pointer :: altmax_col               (:)   ! col maximum annual depth of thaw 
-     real(r8) , pointer :: altmax_lastyear_col      (:)   ! col prior year maximum annual depth of thaw 
-     integer  , pointer :: altmax_indx_col          (:)   ! col maximum annual depth of thaw 
-     integer  , pointer :: altmax_lastyear_indx_col (:)   ! col prior year maximum annual depth of thaw 
-
-     real(r8) , pointer :: dewmx_patch              (:)   ! patch maximum allowed dew [mm] 
-     real(r8) , pointer :: dleaf_patch              (:)   ! patch characteristic leaf width (diameter) [m]
-                                                          ! for non-ED/FATES this is the same as pftcon%dleaf()
-     real(r8) , pointer :: rscanopy_patch           (:)   ! patch canopy stomatal resistance (s/m) (ED specific)
-
-     real(r8) , pointer :: vegwp_patch              (:,:) ! patch vegetation water matric potential (mm)
-
-     real(r8)           :: leaf_mr_vcm = spval            ! Scalar constant of leaf respiration with Vcmax
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-     procedure, public  :: ReadNML
-     procedure, public  :: InitAccBuffer
-     procedure, public  :: InitAccVars
-     procedure, public  :: UpdateAccVars
-     procedure, public  :: Restart      
-
-  end type CanopyState_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains   
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-    if ( this%leaf_mr_vcm == spval ) then
-       call endrun(msg="ERROR canopystate Init called before ReadNML"//errmsg(sourcefile, __LINE__))
-    end if
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    integer :: begg, endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate(this%frac_veg_nosno_patch     (begp:endp))           ; this%frac_veg_nosno_patch     (:)   = huge(1)
-    allocate(this%frac_veg_nosno_alb_patch (begp:endp))           ; this%frac_veg_nosno_alb_patch (:)   = 0
-    allocate(this%tlai_patch               (begp:endp))           ; this%tlai_patch               (:)   = nan
-    allocate(this%tsai_patch               (begp:endp))           ; this%tsai_patch               (:)   = nan
-    allocate(this%elai_patch               (begp:endp))           ; this%elai_patch               (:)   = nan
-    allocate(this%elai240_patch            (begp:endp))           ; this%elai240_patch            (:)   = nan
-    allocate(this%esai_patch               (begp:endp))           ; this%esai_patch               (:)   = nan
-    allocate(this%laisun_patch             (begp:endp))           ; this%laisun_patch             (:)   = nan
-    allocate(this%laisha_patch             (begp:endp))           ; this%laisha_patch             (:)   = nan
-    allocate(this%laisun_z_patch           (begp:endp,1:nlevcan)) ; this%laisun_z_patch           (:,:) = nan
-    allocate(this%laisha_z_patch           (begp:endp,1:nlevcan)) ; this%laisha_z_patch           (:,:) = nan
-    allocate(this%mlaidiff_patch           (begp:endp))           ; this%mlaidiff_patch           (:)   = nan
-    allocate(this%annlai_patch          (12,begp:endp))           ; this%annlai_patch             (:,:) = nan
-    allocate(this%htop_patch               (begp:endp))           ; this%htop_patch               (:)   = nan
-    allocate(this%hbot_patch               (begp:endp))           ; this%hbot_patch               (:)   = nan
-    allocate(this%displa_patch             (begp:endp))           ; this%displa_patch             (:)   = nan
-    allocate(this%fsun_patch               (begp:endp))           ; this%fsun_patch               (:)   = nan
-    allocate(this%fsun24_patch             (begp:endp))           ; this%fsun24_patch             (:)   = nan
-    allocate(this%fsun240_patch            (begp:endp))           ; this%fsun240_patch            (:)   = nan
-
-    allocate(this%alt_col                  (begc:endc))           ; this%alt_col                  (:)   = spval     
-    allocate(this%altmax_col               (begc:endc))           ; this%altmax_col               (:)   = spval
-    allocate(this%altmax_lastyear_col      (begc:endc))           ; this%altmax_lastyear_col      (:)   = spval
-    allocate(this%alt_indx_col             (begc:endc))           ; this%alt_indx_col             (:)   = huge(1)
-    allocate(this%altmax_indx_col          (begc:endc))           ; this%altmax_indx_col          (:)   = huge(1)
-    allocate(this%altmax_lastyear_indx_col (begc:endc))           ; this%altmax_lastyear_indx_col (:)   = huge(1)
-
-    allocate(this%dewmx_patch              (begp:endp))           ; this%dewmx_patch              (:)   = nan
-    allocate(this%dleaf_patch              (begp:endp))           ; this%dleaf_patch              (:)   = nan
-    allocate(this%rscanopy_patch           (begp:endp))           ; this%rscanopy_patch           (:)   = nan
-!    allocate(this%gccanopy_patch           (begp:endp))           ; this%gccanopy_patch           (:)   = 0.0_r8     
-    allocate(this%vegwp_patch              (begp:endp,1:nvegwcs)) ; this%vegwp_patch              (:,:) = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begc, endc
-    integer :: begp, endp
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    this%elai_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ELAI', units='m^2/m^2', &
-        avgflag='A', long_name='exposed one-sided leaf area index', &
-         ptr_patch=this%elai_patch, default='inactive')
-
-    this%esai_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ESAI', units='m^2/m^2', &
-         avgflag='A', long_name='exposed one-sided stem area index', &
-         ptr_patch=this%esai_patch, default='inactive')
-
-    this%tlai_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TLAI', units='none', &
-         avgflag='A', long_name='total projected leaf area index', &
-         ptr_patch=this%tlai_patch, default='inactive')
-
-    this%tsai_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TSAI', units='none', &
-         avgflag='A', long_name='total projected stem area index', &
-         ptr_patch=this%tsai_patch, default='inactive')
-
-    this%laisun_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LAISUN', units='none', &
-         avgflag='A', long_name='sunlit projected leaf area index', &
-         ptr_patch=this%laisun_patch, set_urb=0._r8, default='inactive')
-
-    this%laisha_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LAISHA', units='none', &
-         avgflag='A', long_name='shaded projected leaf area index', &
-         ptr_patch=this%laisha_patch, set_urb=0._r8, default='inactive')
-
-    if (use_cn .or. use_fates) then
-       this%fsun_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FSUN', units='proportion', &
-            avgflag='A', long_name='sunlit fraction of canopy', &
-            ptr_patch=this%fsun_patch, default='inactive')
-
-       this%dewmx_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DEWMX', units='mm', &
-            avgflag='A', long_name='Maximum allowed dew', &
-            ptr_patch=this%dewmx_patch, default='inactive')
-
-       this%htop_patch(begp:endp) = spval
-       call hist_addfld1d (fname='HTOP', units='m', &
-            avgflag='A', long_name='canopy top', &
-            ptr_patch=this%htop_patch, default='inactive')
-
-       this%hbot_patch(begp:endp) = spval
-       call hist_addfld1d (fname='HBOT', units='m', &
-            avgflag='A', long_name='canopy bottom', &
-            ptr_patch=this%hbot_patch, default='inactive')
-
-       this%displa_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DISPLA', units='m', &
-            avgflag='A', long_name='displacement height', &
-            ptr_patch=this%displa_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%alt_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALT', units='m', &
-            avgflag='A', long_name='current active layer thickness', &
-            ptr_col=this%alt_col, default='inactive')
-
-       this%altmax_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALTMAX', units='m', &
-            avgflag='A', long_name='maximum annual active layer thickness', &
-            ptr_col=this%altmax_col, default='inactive')
-
-       this%altmax_lastyear_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALTMAX_LASTYEAR', units='m', &
-            avgflag='A', long_name='maximum prior year active layer thickness', &
-            ptr_col=this%altmax_lastyear_col, default='inactive')
-    end if
-
-    ! Allow active layer fields to be optionally output even if not running CN
-
-    if (.not. use_cn) then
-       this%alt_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALT', units='m', &
-            avgflag='A', long_name='current active layer thickness', &
-            ptr_col=this%alt_col, default='inactive')
-
-       this%altmax_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALTMAX', units='m', &
-            avgflag='A', long_name='maximum annual active layer thickness', &
-            ptr_col=this%altmax_col, default='inactive')
-
-       this%altmax_lastyear_col(begc:endc) = spval
-       call hist_addfld1d (fname='ALTMAX_LASTYEAR', units='m', &
-            avgflag='A', long_name='maximum prior year active layer thickness', &
-            ptr_col=this%altmax_lastyear_col, default='inactive')
-    end if
-
-
-
-    ! Accumulated fields
-    this%fsun24_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSUN24', units='K',  &
-         avgflag='A', long_name='fraction sunlit (last 24hrs)', &
-         ptr_patch=this%fsun24_patch, default='inactive')
-
-    this%fsun240_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSUN240', units='K',  &
-         avgflag='A', long_name='fraction sunlit (last 240hrs)', &
-         ptr_patch=this%fsun240_patch, default='inactive')
-
-    this%elai240_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LAI240', units='m^2/m^2', &
-         avgflag='A', long_name='240hr average of leaf area index', &
-         ptr_patch=this%elai240_patch, default='inactive')
-
-    ! Ed specific field
-    if ( use_fates ) then
-       this%rscanopy_patch(begp:endp) = spval
-       call hist_addfld1d (fname='RSCANOPY', units=' s m-1',  &
-            avgflag='A', long_name='canopy resistance', &
-            ptr_patch=this%rscanopy_patch, set_lake=0._r8, set_urb=0._r8, default='inactive')
-    end if
-
-!    call hist_addfld1d (fname='GCCANOPY', units='none',  &
-!         avgflag='A', long_name='Canopy Conductance: mmol m-2 s-1', &
-!         ptr_patch=this%GCcanopy_patch, set_lake=0._r8, set_urb=0._r8)  
-
-    if ( use_hydrstress ) then
-       this%vegwp_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='VEGWP',  units='mm', type2d='nvegwcs', &
-            avgflag='A', long_name='vegetation water matric potential for sun/sha canopy,xyl,root segments', &
-            ptr_patch=this%vegwp_patch, default='inactive')
-    end if
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    !
-    ! !USES 
-    use accumulMod  , only : init_accum_field
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !---------------------------------------------------------------------
-
-    this%fsun24_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='FSUN24', units='fraction',                                        &
-         desc='24hr average of diffuse solar radiation',  accum_type='runmean', accum_period=-1,   &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    this%fsun240_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='FSUN240', units='fraction',                                       &
-         desc='240hr average of diffuse solar radiation',  accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    this%elai240_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='LAI240', units='m2/m2',                                             &
-         desc='240hr average of leaf area index',  accum_type='runmean', accum_period=-10,      &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! !USES 
-    use accumulMod       , only : extract_accum_field
-    use clm_time_manager , only : get_nstep
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begp, endp
-    integer  :: nstep
-    integer  :: ier
-    real(r8), pointer :: rbufslp(:)  ! temporary
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Allocate needed dynamic memory for single level patch field
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)' in '
-       call endrun(msg="extract_accum_hist allocation error for rbufslp"//&
-            errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Determine time step
-    nstep = get_nstep()
-
-    call extract_accum_field ('FSUN24', rbufslp, nstep)
-    this%fsun24_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('FSUN240', rbufslp, nstep)
-    this%fsun240_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('LAI240', rbufslp, nstep)
-    this%elai240_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('FSUN24', rbufslp, nstep)
-    this%fsun24_patch(begp:endp) = rbufslp(begp:endp)
-
-    deallocate(rbufslp)
-
-  end subroutine InitAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine ReadNML( this, NLFilename )
-    !
-    ! Read in canopy parameter namelist
-    !       
-    ! USES:
-    use shr_mpi_mod   , only : shr_mpi_bcast
-    use abortutils    , only : endrun
-    use spmdMod       , only : masterproc, mpicom
-    use fileutils     , only : getavu, relavu, opnfil
-    use shr_nl_mod    , only : shr_nl_find_group_name
-    use shr_mpi_mod   , only : shr_mpi_bcast
-    use clm_varctl    , only : iulog
-    use shr_log_mod   , only : errMsg => shr_log_errMsg
-    !
-    ! ARGUMENTS:
-    implicit none
-    class(canopystate_type)      :: this
-    character(len=*), intent(IN) :: NLFilename ! Namelist filename
-    ! LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    real(r8) :: leaf_mr_vcm         ! Scalar of leaf respiration to vcmax
-    character(len=32) :: subname = 'CanopyStateType::ReadNML'  ! subroutine name
-    !-----------------------------------------------------------------------
-    namelist / clm_canopy_inparm / leaf_mr_vcm
-
-    ! ----------------------------------------------------------------------
-    ! Read namelist from input namelist filename
-    ! ----------------------------------------------------------------------
-
-    if ( masterproc )then
-
-       unitn = getavu()
-       write(iulog,*) 'Read in clm_canopy_inparm  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, 'clm_canopy_inparm', status=ierr)
-       if (ierr == 0) then
-          read(unitn, clm_canopy_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading clm_canopy_inparm namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR finding clm_canopy_inparm namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-
-    end if
-
-    ! Broadcast namelist variables read in
-    call shr_mpi_bcast(leaf_mr_vcm, mpicom)
-    this%leaf_mr_vcm = leaf_mr_vcm
-
-  end subroutine ReadNML
-
-  !-----------------------------------------------------------------------
-  subroutine UpdateAccVars (this, bounds)
-    !
-    ! USES
-    use clm_time_manager, only : get_nstep
-    use accumulMod      , only : update_accum_field, extract_accum_field
-    use abortutils      , only : endrun
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type)             :: this
-    type(bounds_type)      , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g,p                       ! indices
-    integer :: dtime                     ! timestep size [seconds]
-    integer :: nstep                     ! timestep number
-    integer :: ier                       ! error status
-    integer :: begp, endp
-    real(r8), pointer :: rbufslp(:)      ! temporary single level - patch level
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    nstep = get_nstep()
-
-    ! Allocate needed dynamic memory for single level patch field
-
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'update_accum_hist allocation error for rbuf1dp'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Accumulate and extract fsun24 & fsun240   
-    do p = begp,endp
-       rbufslp(p) = this%fsun_patch(p)
-    end do
-    call update_accum_field  ('FSUN24' , rbufslp              , nstep)
-    call extract_accum_field ('FSUN24' , this%fsun24_patch    , nstep)
-    call update_accum_field  ('FSUN240', rbufslp              , nstep)
-    call extract_accum_field ('FSUN240', this%fsun240_patch   , nstep)
-
-    ! Accumulate and extract elai240
-    do p = begp,endp
-       rbufslp(p) = this%elai_patch(p)
-    end do
-    call update_accum_field  ('LAI240', rbufslp               , nstep)
-    call extract_accum_field ('LAI240', this%elai240_patch    , nstep)
-
-    deallocate(rbufslp)
-
-  end subroutine UpdateAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: p,l,c,g 
-    !-----------------------------------------------------------------------
-
-    do p = bounds%begp, bounds%endp
-       l = patch%landunit(p)
-
-       this%frac_veg_nosno_patch(p) = 0._r8
-       this%tlai_patch(p)       = 0._r8
-       this%tsai_patch(p)       = 0._r8
-       this%elai_patch(p)       = 0._r8
-       this%esai_patch(p)       = 0._r8
-       this%htop_patch(p)       = 0._r8
-       this%hbot_patch(p)       = 0._r8
-       this%dewmx_patch(p)      = 0.1_r8
-       this%vegwp_patch(p,:)    = -2.5e4_r8
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%laisun_patch(p) = 0._r8
-          this%laisha_patch(p) = 0._r8
-       end if
-
-       ! needs to be initialized to spval to avoid problems when averaging for the accum
-       ! field
-       this%fsun_patch(p) = spval
-    end do
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%alt_col(c)               = 0._r8 !iniitialized to spval for all columns
-          this%altmax_col(c)            = 0._r8 !iniitialized to spval for all columns
-          this%altmax_lastyear_col(c)   = 0._r8 !iniitialized to spval for all columns
-          this%alt_indx_col(c)          = 0     !initiialized to huge  for all columns
-          this%altmax_indx_col(c)       = 0     !initiialized to huge  for all columns
-          this%altmax_lastyear_indx_col = 0     !initiialized to huge  for all columns
-       end if
-    end do
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !USES:
-    use spmdMod    , only : masterproc
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(canopystate_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,p,c,iv ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    integer :: begp, endp
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    call restartvar(ncid=ncid, flag=flag, varname='FRAC_VEG_NOSNO_ALB', xtype=ncd_int,  &
-         dim1name='pft', long_name='fraction of vegetation not covered by snow (0 or 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%frac_veg_nosno_alb_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='tlai', xtype=ncd_double,  &
-         dim1name='pft', long_name='one-sided leaf area index, no burying by snow', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tlai_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='tsai', xtype=ncd_double,  &
-         dim1name='pft', long_name='one-sided stem area index, no burying by snow', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tsai_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='elai', xtype=ncd_double,  &
-         dim1name='pft', long_name='one-sided leaf area index, with burying by snow', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%elai_patch)
-    
-    call restartvar(ncid=ncid, flag=flag, varname='esai', xtype=ncd_double,  &
-         dim1name='pft', long_name='one-sided stem area index, with burying by snow', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%esai_patch)
-    
-    call restartvar(ncid=ncid, flag=flag, varname='htop', xtype=ncd_double,  &
-         dim1name='pft', long_name='canopy top', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%htop_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='hbot', xtype=ncd_double,  &
-         dim1name='pft', long_name='canopy botton', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%hbot_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='mlaidiff', xtype=ncd_double,  &
-         dim1name='pft', long_name='difference between lai month one and month two', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%mlaidiff_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='fsun', xtype=ncd_double,  &
-         dim1name='pft', long_name='sunlit fraction of canopy', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fsun_patch)
-
-    if (flag=='read' )then
-       do p = bounds%begp,bounds%endp
-          if (shr_infnan_isnan(this%fsun_patch(p)) ) then
-             this%fsun_patch(p) = spval
-          end if
-       end do
-    end if
-
-    if (use_cn .or. use_fates) then
-       call restartvar(ncid=ncid, flag=flag, varname='altmax', xtype=ncd_double,  &
-            dim1name='column', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%altmax_col) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='altmax_lastyear', xtype=ncd_double,  &
-            dim1name='column', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%altmax_lastyear_col) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='altmax_indx', xtype=ncd_int,  &
-            dim1name='column', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%altmax_indx_col) 
-
-       call restartvar(ncid=ncid, flag=flag, varname='altmax_lastyear_indx', xtype=ncd_int,  &
-            dim1name='column', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%altmax_lastyear_indx_col) 
-    end if
-
-    if ( use_hydrstress ) then
-       call restartvar(ncid=ncid, flag=flag, varname='vegwp', xtype=ncd_double,  &
-            dim1name='pft', dim2name='vegwcs', switchdim=.true., &
-            long_name='vegetation water matric potential', units='mm', &
-            interpinic_flag='interp', readvar=readvar, data=this%vegwp_patch) 
-
-    end if
-
-  end subroutine Restart
-
-end module CanopyStateType
diff --git a/src/biogeophys/EnergyFluxType.F90 b/src/biogeophys/EnergyFluxType.F90
index 83b5281e80..940783766d 100644
--- a/src/biogeophys/EnergyFluxType.F90
+++ b/src/biogeophys/EnergyFluxType.F90
@@ -7,9 +7,7 @@ module EnergyFluxType
   !
   use shr_kind_mod   , only : r8 => shr_kind_r8
   use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use clm_varcon     , only : spval
   use decompMod      , only : bounds_type
-  use LandunitType   , only : lun                
   use ColumnType     , only : col                
   use PatchType      , only : patch                
   !
@@ -20,105 +18,14 @@ module EnergyFluxType
   type, public :: energyflux_type
 
      ! Fluxes
-     real(r8), pointer :: eflx_sh_grnd_patch      (:)   ! patch sensible heat flux from ground (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_veg_patch       (:)   ! patch sensible heat flux from leaves (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_snow_patch      (:)   ! patch sensible heat flux from snow (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_soil_patch      (:)   ! patch sensible heat flux from soil  (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_h2osfc_patch    (:)   ! patch sensible heat flux from surface water (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_tot_patch       (:)   ! patch total sensible heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_tot_u_patch     (:)   ! patch urban total sensible heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_tot_r_patch     (:)   ! patch rural total sensible heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_precip_conversion_col(:) ! col sensible heat flux from precipitation conversion (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_tot_patch       (:)   ! patch total latent heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_tot_u_patch     (:)   ! patch urban total latent heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_tot_r_patch     (:)   ! patch rural total latent heat flux (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_vegt_patch      (:)   ! patch transpiration heat flux from veg (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_vege_patch      (:)   ! patch evaporation heat flux from veg (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_lh_grnd_patch      (:)   ! patch evaporation heat flux from ground (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_soil_grnd_patch    (:)   ! patch soil heat flux (W/m**2) [+ = into soil] 
-     real(r8), pointer :: eflx_soil_grnd_u_patch  (:)   ! patch urban soil heat flux (W/m**2) [+ = into soil]
-     real(r8), pointer :: eflx_soil_grnd_r_patch  (:)   ! patch rural soil heat flux (W/m**2) [+ = into soil]
-     real(r8), pointer :: eflx_lwrad_net_patch    (:)   ! patch net infrared (longwave) rad (W/m**2) [+ = to atm]
-     real(r8), pointer :: eflx_lwrad_net_r_patch  (:)   ! patch rural net infrared (longwave) rad (W/m**2) [+ = to atm]
-     real(r8), pointer :: eflx_lwrad_net_u_patch  (:)   ! patch urban net infrared (longwave) rad (W/m**2) [+ = to atm]
      real(r8), pointer :: eflx_lwrad_out_patch    (:)   ! patch emitted infrared (longwave) radiation (W/m**2)
-     real(r8), pointer :: eflx_lwrad_out_r_patch  (:)   ! patch rural emitted infrared (longwave) rad (W/m**2)
-     real(r8), pointer :: eflx_lwrad_out_u_patch  (:)   ! patch urban emitted infrared (longwave) rad (W/m**2)
-     real(r8), pointer :: eflx_snomelt_col        (:)   ! col snow melt heat flux (W/m**2)
-     real(r8), pointer :: eflx_snomelt_r_col      (:)   ! col rural snow melt heat flux (W/m**2)
-     real(r8), pointer :: eflx_snomelt_u_col      (:)   ! col urban snow melt heat flux (W/m**2)
-     real(r8), pointer :: eflx_gnet_patch         (:)   ! patch net heat flux into ground  (W/m**2)
-     real(r8), pointer :: eflx_grnd_lake_patch    (:)   ! patch net heat flux into lake / snow surface, excluding light transmission (W/m**2)
-     real(r8), pointer :: eflx_dynbal_grc         (:)   ! grc dynamic land cover change conversion energy flux (W/m**2)
-     real(r8), pointer :: eflx_bot_col            (:)   ! col heat flux from beneath the soil or ice column (W/m**2)
-     real(r8), pointer :: eflx_fgr12_col          (:)   ! col ground heat flux between soil layers 1 and 2 (W/m**2)
-     real(r8), pointer :: eflx_fgr_col            (:,:) ! col (rural) soil downward heat flux (W/m2) (1:nlevgrnd)  (pos upward; usually eflx_bot >= 0)
-     real(r8), pointer :: eflx_building_heat_errsoi_col(:) ! col heat flux to interior surface of walls and roof for errsoi check (W m-2)
-     real(r8), pointer :: eflx_urban_ac_col       (:)   ! col urban air conditioning flux (W/m**2)
-     real(r8), pointer :: eflx_urban_heat_col     (:)   ! col urban heating flux (W/m**2)
-     real(r8), pointer :: eflx_anthro_patch       (:)   ! patch total anthropogenic heat flux (W/m**2)
-     real(r8), pointer :: eflx_traffic_patch      (:)   ! patch traffic sensible heat flux (W/m**2)
-     real(r8), pointer :: eflx_wasteheat_patch    (:)   ! patch sensible heat flux from domestic heating/cooling sources of waste heat (W/m**2)
-     real(r8), pointer :: eflx_heat_from_ac_patch (:)   ! patch sensible heat flux put back into canyon due to removal by AC (W/m**2)
-     real(r8), pointer :: eflx_traffic_lun        (:)   ! lun traffic sensible heat flux (W/m**2)
-     real(r8), pointer :: eflx_wasteheat_lun      (:)   ! lun sensible heat flux from domestic heating/cooling sources of waste heat (W/m**2)
-     real(r8), pointer :: eflx_heat_from_ac_lun   (:)   ! lun sensible heat flux to be put back into canyon due to removal by AC (W/m**2)
-     real(r8), pointer :: eflx_building_lun       (:)   ! lun building heat flux from change in interior building air temperature (W/m**2)
-     real(r8), pointer :: eflx_urban_ac_lun       (:)   ! lun urban air conditioning flux (W/m**2)
-     real(r8), pointer :: eflx_urban_heat_lun     (:)   ! lun urban heating flux (W/m**2)
-
-     ! Derivatives of energy fluxes
-     real(r8), pointer :: dgnetdT_patch           (:)   ! patch derivative of net ground heat flux wrt soil temp  (W/m**2 K)
-     real(r8), pointer :: netrad_patch            (:)   ! col net radiation (W/m**2) [+ = to sfc]
-     real(r8), pointer :: cgrnd_patch             (:)   ! col deriv. of soil energy flux wrt to soil temp [W/m2/k]
-     real(r8), pointer :: cgrndl_patch            (:)   ! col deriv. of soil latent heat flux wrt soil temp  [W/m**2/k]
-     real(r8), pointer :: cgrnds_patch            (:)   ! col deriv. of soil sensible heat flux wrt soil temp [W/m2/k]
-
-     ! Canopy radiation
-     real(r8), pointer :: dlrad_patch             (:)   ! col downward longwave radiation below the canopy [W/m2]
-     real(r8), pointer :: ulrad_patch             (:)   ! col upward longwave radiation above the canopy [W/m2]
-
-     ! Wind Stress
-     real(r8), pointer :: taux_patch              (:)   ! patch wind (shear) stress: e-w (kg/m/s**2)
-     real(r8), pointer :: tauy_patch              (:)   ! patch wind (shear) stress: n-s (kg/m/s**2)
-
-     ! Conductance
-     real(r8), pointer :: canopy_cond_patch       (:)   ! patch tracer conductance for canopy [m/s] 
-
-     ! Transpiration
-     real(r8), pointer :: btran_patch             (:)   ! patch transpiration wetness factor (0 to 1)
-     real(r8), pointer :: btran_min_patch         (:)   ! patch daily minimum transpiration wetness factor (0 to 1)
-     real(r8), pointer :: btran_min_inst_patch    (:)   ! patch instantaneous daily minimum transpiration wetness factor (0 to 1)
-     real(r8), pointer :: bsun_patch              (:)   ! patch sunlit canopy transpiration wetness factor (0 to 1)
-     real(r8), pointer :: bsha_patch              (:)   ! patch shaded canopy transpiration wetness factor (0 to 1)
-
-     ! Roots
-     real(r8), pointer :: btran2_patch            (:)   ! patch root zone soil wetness factor (0 to 1) 
-     real(r8), pointer :: rresis_patch            (:,:) ! patch root resistance by layer (0-1)  (nlevgrnd)
-
-     ! Latent heat
-     real(r8), pointer :: htvp_col                (:)   ! latent heat of vapor of water (or sublimation) [j/kg]
-
-     ! Balance Checks
-     real(r8), pointer :: errsoi_patch            (:)   ! soil/lake energy conservation error   (W/m**2)
-     real(r8), pointer :: errsoi_col              (:)   ! soil/lake energy conservation error   (W/m**2)
-     real(r8), pointer :: errseb_patch            (:)   ! surface energy conservation error     (W/m**2)
-     real(r8), pointer :: errseb_col              (:)   ! surface energy conservation error     (W/m**2)
-     real(r8), pointer :: errsol_patch            (:)   ! solar radiation conservation error    (W/m**2)
-     real(r8), pointer :: errsol_col              (:)   ! solar radiation conservation error    (W/m**2)
-     real(r8), pointer :: errlon_patch            (:)   ! longwave radiation conservation error (W/m**2)
-     real(r8), pointer :: errlon_col              (:)   ! longwave radiation conservation error (W/m**2)
 
    contains
 
      procedure, public  :: Init            ! Public initialization method
      procedure, private :: InitAllocate    ! initialize/allocate
-     procedure, private :: InitHistory     ! setup history fields
      procedure, private :: InitCold        ! initialize for cold start
      procedure, public  :: Restart         ! setup restart fields
-     procedure, public  :: InitAccBuffer
-     procedure, public  :: InitAccVars
-     procedure, public  :: UpdateAccVars
 
   end type energyflux_type
 
@@ -129,7 +36,7 @@ module EnergyFluxType
 contains
 
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, t_grnd_col, is_simple_buildtemp, is_prog_buildtemp )
+  subroutine Init(this, bounds, t_grnd_col)
     !
     ! !DESCRIPTION:
     !    Allocate and initialize the data type and setup history, and initialize for cold-start.
@@ -139,14 +46,11 @@ subroutine Init(this, bounds, t_grnd_col, is_simple_buildtemp, is_prog_buildtemp
     class(energyflux_type)         :: this
     type(bounds_type) , intent(in) :: bounds  
     real(r8)          , intent(in) :: t_grnd_col( bounds%begc: )
-    logical           , intent(in) :: is_simple_buildtemp        ! If using simple building temp method
-    logical           , intent(in) :: is_prog_buildtemp          ! If using prognostic building temp method
 
     SHR_ASSERT_ALL((ubound(t_grnd_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
 
     call this%InitAllocate ( bounds )
-    call this%InitHistory ( bounds, is_simple_buildtemp )
-    call this%InitCold ( bounds, t_grnd_col, is_simple_buildtemp, is_prog_buildtemp ) 
+    call this%InitCold ( bounds, t_grnd_col) 
 
   end subroutine Init
 
@@ -158,7 +62,6 @@ subroutine InitAllocate(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar     , only : nlevsno, nlevgrnd, nlevlak
     implicit none
     !
     ! !ARGUMENTS:
@@ -167,610 +70,52 @@ subroutine InitAllocate(this, bounds)
     !
     ! !LOCAL VARIABLES:
     integer :: begp, endp
-    integer :: begc, endc
-    integer :: begl, endl
-    integer :: begg, endg
     !------------------------------------------------------------------------
 
     begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begl = bounds%begl; endl= bounds%endl
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate( this%eflx_sh_snow_patch      (begp:endp))             ; this%eflx_sh_snow_patch      (:)   = nan
-    allocate( this%eflx_sh_soil_patch      (begp:endp))             ; this%eflx_sh_soil_patch      (:)   = nan
-    allocate( this%eflx_sh_h2osfc_patch    (begp:endp))             ; this%eflx_sh_h2osfc_patch    (:)   = nan
-    allocate( this%eflx_sh_tot_patch       (begp:endp))             ; this%eflx_sh_tot_patch       (:)   = nan
-    allocate( this%eflx_sh_tot_u_patch     (begp:endp))             ; this%eflx_sh_tot_u_patch     (:)   = nan
-    allocate( this%eflx_sh_tot_r_patch     (begp:endp))             ; this%eflx_sh_tot_r_patch     (:)   = nan
-    allocate( this%eflx_sh_grnd_patch      (begp:endp))             ; this%eflx_sh_grnd_patch      (:)   = nan
-    allocate( this%eflx_sh_veg_patch       (begp:endp))             ; this%eflx_sh_veg_patch       (:)   = nan
-    allocate( this%eflx_sh_precip_conversion_col(begc:endc))        ; this%eflx_sh_precip_conversion_col(:) = nan
-    allocate( this%eflx_lh_tot_u_patch     (begp:endp))             ; this%eflx_lh_tot_u_patch     (:)   = nan
-    allocate( this%eflx_lh_tot_patch       (begp:endp))             ; this%eflx_lh_tot_patch       (:)   = nan
-    allocate( this%eflx_lh_tot_r_patch     (begp:endp))             ; this%eflx_lh_tot_r_patch     (:)   = nan
-    allocate( this%eflx_lh_grnd_patch      (begp:endp))             ; this%eflx_lh_grnd_patch      (:)   = nan
-    allocate( this%eflx_lh_vege_patch      (begp:endp))             ; this%eflx_lh_vege_patch      (:)   = nan
-    allocate( this%eflx_lh_vegt_patch      (begp:endp))             ; this%eflx_lh_vegt_patch      (:)   = nan
-    allocate( this%eflx_soil_grnd_patch    (begp:endp))             ; this%eflx_soil_grnd_patch    (:)   = nan
-    allocate( this%eflx_soil_grnd_u_patch  (begp:endp))             ; this%eflx_soil_grnd_u_patch  (:)   = nan
-    allocate( this%eflx_soil_grnd_r_patch  (begp:endp))             ; this%eflx_soil_grnd_r_patch  (:)   = nan
-    allocate( this%eflx_lwrad_net_patch    (begp:endp))             ; this%eflx_lwrad_net_patch    (:)   = nan
-    allocate( this%eflx_lwrad_net_u_patch  (begp:endp))             ; this%eflx_lwrad_net_u_patch  (:)   = nan
-    allocate( this%eflx_lwrad_net_r_patch  (begp:endp))             ; this%eflx_lwrad_net_r_patch  (:)   = nan
     allocate( this%eflx_lwrad_out_patch    (begp:endp))             ; this%eflx_lwrad_out_patch    (:)   = nan
-    allocate( this%eflx_lwrad_out_u_patch  (begp:endp))             ; this%eflx_lwrad_out_u_patch  (:)   = nan
-    allocate( this%eflx_lwrad_out_r_patch  (begp:endp))             ; this%eflx_lwrad_out_r_patch  (:)   = nan
-    allocate( this%eflx_gnet_patch         (begp:endp))             ; this%eflx_gnet_patch         (:)   = nan
-    allocate( this%eflx_grnd_lake_patch    (begp:endp))             ; this%eflx_grnd_lake_patch    (:)   = nan
-    allocate( this%eflx_dynbal_grc         (begg:endg))             ; this%eflx_dynbal_grc         (:)   = nan
-    allocate( this%eflx_bot_col            (begc:endc))             ; this%eflx_bot_col            (:)   = nan
-    allocate( this%eflx_snomelt_col        (begc:endc))             ; this%eflx_snomelt_col        (:)   = nan
-    allocate( this%eflx_snomelt_r_col      (begc:endc))             ; this%eflx_snomelt_r_col      (:)   = nan
-    allocate( this%eflx_snomelt_u_col      (begc:endc))             ; this%eflx_snomelt_u_col      (:)   = nan
-    allocate( this%eflx_fgr12_col          (begc:endc))             ; this%eflx_fgr12_col          (:)   = nan
-    allocate( this%eflx_fgr_col            (begc:endc, 1:nlevgrnd)) ; this%eflx_fgr_col            (:,:) = nan
-    allocate( this%eflx_building_heat_errsoi_col  (begc:endc))      ; this%eflx_building_heat_errsoi_col(:)= nan
-    allocate( this%eflx_urban_ac_col       (begc:endc))             ; this%eflx_urban_ac_col       (:)   = nan
-    allocate( this%eflx_urban_heat_col     (begc:endc))             ; this%eflx_urban_heat_col     (:)   = nan
-    allocate( this%eflx_wasteheat_patch    (begp:endp))             ; this%eflx_wasteheat_patch    (:)   = nan
-    allocate( this%eflx_traffic_patch      (begp:endp))             ; this%eflx_traffic_patch      (:)   = nan
-    allocate( this%eflx_heat_from_ac_patch (begp:endp))             ; this%eflx_heat_from_ac_patch (:)   = nan
-    allocate( this%eflx_heat_from_ac_lun   (begl:endl))             ; this%eflx_heat_from_ac_lun   (:)   = nan
-    allocate( this%eflx_building_lun       (begl:endl))             ; this%eflx_building_lun       (:)   = nan
-    allocate( this%eflx_urban_ac_lun       (begl:endl))             ; this%eflx_urban_ac_lun       (:)   = nan
-    allocate( this%eflx_urban_heat_lun     (begl:endl))             ; this%eflx_urban_heat_lun     (:)   = nan
-    allocate( this%eflx_traffic_lun        (begl:endl))             ; this%eflx_traffic_lun        (:)   = nan
-    allocate( this%eflx_wasteheat_lun      (begl:endl))             ; this%eflx_wasteheat_lun      (:)   = nan
-    allocate( this%eflx_anthro_patch       (begp:endp))             ; this%eflx_anthro_patch       (:)   = nan
-
-    allocate( this%dgnetdT_patch           (begp:endp))             ; this%dgnetdT_patch           (:)   = nan
-    allocate( this%cgrnd_patch             (begp:endp))             ; this%cgrnd_patch             (:)   = nan
-    allocate( this%cgrndl_patch            (begp:endp))             ; this%cgrndl_patch            (:)   = nan
-    allocate( this%cgrnds_patch            (begp:endp))             ; this%cgrnds_patch            (:)   = nan
-    allocate( this%dlrad_patch             (begp:endp))             ; this%dlrad_patch             (:)   = nan
-    allocate( this%ulrad_patch             (begp:endp))             ; this%ulrad_patch             (:)   = nan
-    allocate( this%netrad_patch            (begp:endp))             ; this%netrad_patch            (:)   = nan  
-
-    allocate( this%taux_patch              (begp:endp))             ; this%taux_patch              (:)   = nan
-    allocate( this%tauy_patch              (begp:endp))             ; this%tauy_patch              (:)   = nan
-
-    allocate( this%canopy_cond_patch       (begp:endp))             ; this%canopy_cond_patch       (:)   = nan
-
-    allocate( this%htvp_col                (begc:endc))             ; this%htvp_col                (:)   = nan
-
-    allocate(this%rresis_patch             (begp:endp,1:nlevgrnd))  ; this%rresis_patch            (:,:) = nan
-    allocate(this%btran_patch              (begp:endp))             ; this%btran_patch             (:)   = nan
-    allocate(this%btran_min_patch          (begp:endp))             ; this%btran_min_patch         (:)   = nan
-    allocate(this%btran_min_inst_patch     (begp:endp))             ; this%btran_min_inst_patch    (:)   = nan
-    allocate(this%btran2_patch             (begp:endp))             ; this%btran2_patch            (:)   = nan
-    allocate( this%bsun_patch              (begp:endp))             ; this%bsun_patch              (:)   = nan
-    allocate( this%bsha_patch              (begp:endp))             ; this%bsha_patch              (:)   = nan
-    allocate( this%errsoi_patch            (begp:endp))             ; this%errsoi_patch            (:)   = nan
-    allocate( this%errsoi_col              (begc:endc))             ; this%errsoi_col              (:)   = nan
-    allocate( this%errseb_patch            (begp:endp))             ; this%errseb_patch            (:)   = nan
-    allocate( this%errseb_col              (begc:endc))             ; this%errseb_col              (:)   = nan
-    allocate( this%errsol_patch            (begp:endp))             ; this%errsol_patch            (:)   = nan
-    allocate( this%errsol_col              (begc:endc))             ; this%errsol_col              (:)   = nan
-    allocate( this%errlon_patch            (begp:endp))             ; this%errlon_patch            (:)   = nan
-    allocate( this%errlon_col              (begc:endc))             ; this%errlon_col              (:)   = nan
 
   end subroutine InitAllocate
     
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds, is_simple_buildtemp)
-    !
-    ! !DESCRIPTION:
-    ! Setup fields that can be output to history files
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar     , only : nlevsno, nlevgrnd
-    use clm_varctl     , only : use_cn, use_hydrstress
-    use histFileMod    , only : hist_addfld1d, hist_addfld2d, no_snow_normal
-    use ncdio_pio      , only : ncd_inqvdlen
-    implicit none
-    !
-    ! !ARGUMENTS:
-    class(energyflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    logical          , intent(in) :: is_simple_buildtemp ! If using simple building temp method
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    integer           :: begl, endl
-    integer           :: begg, endg
-    integer           :: dimlen
-    integer           :: err_code
-    logical           :: do_io
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begl = bounds%begl; endl= bounds%endl
-    begg = bounds%begg; endg= bounds%endg
-
-
-    this%eflx_dynbal_grc(begg:endg) = spval 
-    call hist_addfld1d (fname='EFLX_DYNBAL',  units='W/m^2',  &
-         avgflag='A', long_name='dynamic land cover change conversion energy flux', &
-         ptr_lnd=this%eflx_dynbal_grc, default='inactive')
-
-    this%eflx_snomelt_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSM',  units='W/m^2',  &
-         avgflag='A', long_name='snow melt heat flux', &
-         ptr_col=this%eflx_snomelt_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FSM_ICE', units='W/m^2',  &
-         avgflag='A', long_name='snow melt heat flux (ice landunits only)', &
-         ptr_col=this%eflx_snomelt_col, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%eflx_snomelt_r_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSM_R',  units='W/m^2',  &
-         avgflag='A', long_name='Rural snow melt heat flux', &
-         ptr_col=this%eflx_snomelt_r_col, set_spec=spval, default='inactive')
-
-    this%eflx_snomelt_u_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSM_U',  units='W/m^2',  &
-         avgflag='A', long_name='Urban snow melt heat flux', &
-         ptr_col=this%eflx_snomelt_u_col, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%eflx_lwrad_net_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FIRA', units='W/m^2',  &
-         avgflag='A', long_name='net infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_net_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FIRA_ICE', units='W/m^2',  &
-         avgflag='A', long_name='net infrared (longwave) radiation (ice landunits only)', &
-         ptr_patch=this%eflx_lwrad_net_patch, c2l_scale_type='urbanf', l2g_scale_type='ice',&
-         default='inactive')
-
-    this%eflx_lwrad_net_r_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='FIRA_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural net infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_net_r_patch, set_spec=spval, default='inactive')
-
-    this%eflx_lwrad_out_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='FIRE', units='W/m^2',  &
-         avgflag='A', long_name='emitted infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_out_patch, c2l_scale_type='urbanf', default='inactive')
-    ! Rename of FIRE for Urban intercomparision project
-    call hist_addfld1d (fname='LWup', units='W/m^2',  &
-         avgflag='A', long_name='upwelling longwave radiation', &
-         ptr_patch=this%eflx_lwrad_out_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FIRE_ICE', units='W/m^2',  &
-         avgflag='A', long_name='emitted infrared (longwave) radiation (ice landunits only)', &
-         ptr_patch=this%eflx_lwrad_out_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%eflx_lwrad_out_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FIRE_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural emitted infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_out_r_patch, set_spec=spval, default='inactive')
-
-    this%eflx_lh_vegt_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FCTR', units='W/m^2',  &
-         avgflag='A', long_name='canopy transpiration', &
-         ptr_patch=this%eflx_lh_vegt_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_lh_vege_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FCEV', units='W/m^2',  &
-         avgflag='A', long_name='canopy evaporation', &
-         ptr_patch=this%eflx_lh_vege_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_lh_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FGEV', units='W/m^2',  &
-         avgflag='A', long_name='ground evaporation', &
-         ptr_patch=this%eflx_lh_grnd_patch, c2l_scale_type='urbanf', default='inactive') 
-
-    this%eflx_sh_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSH', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat not including correction for land use change and rain/snow conversion', &
-         ptr_patch=this%eflx_sh_tot_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FSH_ICE', units='W/m^2',  &
-         avgflag='A', &
-         long_name='sensible heat not including correction for land use change and rain/snow conversion (ice landunits only)', &
-         ptr_patch=this%eflx_sh_tot_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%eflx_sh_tot_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSH_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural sensible heat', &
-         ptr_patch=this%eflx_sh_tot_r_patch, set_spec=spval, default='inactive')
-
-    this%eflx_sh_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='Qh', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat', &
-         ptr_patch=this%eflx_sh_tot_patch, c2l_scale_type='urbanf', &
-         default = 'inactive')
-
-    this%eflx_lh_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='Qle', units='W/m^2',  &
-         avgflag='A', long_name='total evaporation', &
-         ptr_patch=this%eflx_lh_tot_patch, c2l_scale_type='urbanf', &
-         default = 'inactive')
-
-    this%eflx_lh_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='EFLX_LH_TOT', units='W/m^2', &
-         avgflag='A', long_name='total latent heat flux [+ to atm]', &
-         ptr_patch=this%eflx_lh_tot_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='EFLX_LH_TOT_ICE', units='W/m^2',  &
-         avgflag='A', long_name='total latent heat flux [+ to atm] (ice landunits only)', &
-         ptr_patch=this%eflx_lh_tot_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%eflx_lh_tot_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='EFLX_LH_TOT_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural total evaporation', &
-         ptr_patch=this%eflx_lh_tot_r_patch, set_spec=spval, default='inactive')
-
-    this%eflx_soil_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='Qstor', units='W/m^2',  &
-         avgflag='A', long_name='storage heat flux (includes snowmelt)', &
-         ptr_patch=this%eflx_soil_grnd_patch, c2l_scale_type='urbanf', &
-         default = 'inactive')
-    this%eflx_sh_veg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSH_V', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat from veg', &
-         ptr_patch=this%eflx_sh_veg_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_sh_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSH_G', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat from ground', &
-         ptr_patch=this%eflx_sh_grnd_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_soil_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FGR', units='W/m^2',  &
-         avgflag='A', long_name='heat flux into soil/snow including snow melt and lake / snow light transmission', &
-         ptr_patch=this%eflx_soil_grnd_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FGR_ICE', units='W/m^2',  &
-         avgflag='A', &
-         long_name='heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits only)', &
-         ptr_patch=this%eflx_soil_grnd_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%eflx_soil_grnd_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FGR_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural heat flux into soil/snow including snow melt and snow light transmission', &
-         ptr_patch=this%eflx_soil_grnd_r_patch, set_spec=spval, default='inactive')
-
-    this%eflx_lwrad_net_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FIRA_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban net infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_net_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%eflx_soil_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='EFLX_SOIL_GRND', units='W/m^2', &
-         avgflag='A', long_name='soil heat flux [+ into soil]', &
-         ptr_patch=this%eflx_soil_grnd_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%eflx_lwrad_out_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FIRE_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban emitted infrared (longwave) radiation', &
-         ptr_patch=this%eflx_lwrad_out_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%eflx_sh_tot_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSH_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban sensible heat', &
-         ptr_patch=this%eflx_sh_tot_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%eflx_sh_precip_conversion_col(begc:endc) = spval
-    call hist_addfld1d (fname = 'FSH_PRECIP_CONVERSION', units='W/m^2', &
-         avgflag='A', long_name='Sensible heat flux from conversion of rain/snow atm forcing', &
-         ptr_col=this%eflx_sh_precip_conversion_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_lh_tot_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='EFLX_LH_TOT_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban total evaporation', &
-         ptr_patch=this%eflx_lh_tot_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%eflx_soil_grnd_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FGR_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban heat flux into soil/snow including snow melt', &
-         ptr_patch=this%eflx_soil_grnd_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%netrad_patch(begp:endp) = spval
-    call hist_addfld1d (fname='Rnet', units='W/m^2',  &
-         avgflag='A', long_name='net radiation', &
-         ptr_patch=this%netrad_patch, c2l_scale_type='urbanf', &
-         default='inactive')
-
-    if (use_cn) then
-       this%dlrad_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DLRAD', units='W/m^2', &
-            avgflag='A', long_name='downward longwave radiation below the canopy', &
-            ptr_patch=this%dlrad_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    if (use_cn) then
-       this%ulrad_patch(begp:endp) = spval
-       call hist_addfld1d (fname='ULRAD', units='W/m^2', &
-            avgflag='A', long_name='upward longwave radiation above the canopy', &
-            ptr_patch=this%ulrad_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    if (use_cn) then
-       this%cgrnd_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CGRND', units='W/m^2/K', &
-            avgflag='A', long_name='deriv. of soil energy flux wrt to soil temp', &
-            ptr_patch=this%cgrnd_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    if (use_cn) then
-       this%cgrndl_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CGRNDL', units='W/m^2/K', &
-            avgflag='A', long_name='deriv. of soil latent heat flux wrt soil temp', &
-            ptr_patch=this%cgrndl_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    if (use_cn) then
-       this%cgrnds_patch(begp:endp) = spval
-       call hist_addfld1d (fname='CGRNDS', units='W/m^2/K', &
-            avgflag='A', long_name='deriv. of soil sensible heat flux wrt soil temp', &
-            ptr_patch=this%cgrnds_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    if (use_cn) then
-       this%eflx_gnet_patch(begp:endp) = spval
-       call hist_addfld1d (fname='EFLX_GNET', units='W/m^2', &
-            avgflag='A', long_name='net heat flux into ground', &
-            ptr_patch=this%eflx_gnet_patch, default='inactive', c2l_scale_type='urbanf')
-    end if 
-
-    this%eflx_grnd_lake_patch(begp:endp) = spval
-    call hist_addfld1d (fname='EFLX_GRND_LAKE', units='W/m^2', &
-         avgflag='A', long_name='net heat flux into lake/snow surface, excluding light transmission', &
-         ptr_patch=this%eflx_grnd_lake_patch, set_nolake=spval, default='inactive')
-
-    if (      is_simple_buildtemp )then
-       this%eflx_building_heat_errsoi_col(begc:endc) = spval
-       call hist_addfld1d (fname='BUILDHEAT', units='W/m^2',  &
-            avgflag='A', long_name='heat flux from urban building interior to walls and roof', &
-            ptr_col=this%eflx_building_heat_errsoi_col, set_nourb=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-       this%eflx_urban_ac_col(begc:endc) = spval
-       call hist_addfld1d (fname='URBAN_AC', units='W/m^2',  &
-            avgflag='A', long_name='urban air conditioning flux', &
-            ptr_col=this%eflx_urban_ac_col, set_nourb=0._r8, c2l_scale_type='urbanf', default='inactive')
-   
-       this%eflx_urban_heat_col(begc:endc) = spval
-       call hist_addfld1d (fname='URBAN_HEAT', units='W/m^2',  &
-            avgflag='A', long_name='urban heating flux', &
-            ptr_col=this%eflx_urban_heat_col, set_nourb=0._r8, c2l_scale_type='urbanf', default='inactive')
-    else
-       this%eflx_urban_ac_lun(begl:endl) = spval
-       call hist_addfld1d (fname='EFLXBUILD', units='W/m^2',  &
-            avgflag='A', long_name='building heat flux from change in interior building air temperature', &
-            ptr_lunit=this%eflx_building_lun, set_nourb=0._r8, l2g_scale_type='unity', default='inactive')
-
-       this%eflx_urban_ac_lun(begl:endl) = spval
-       call hist_addfld1d (fname='URBAN_AC', units='W/m^2',  &
-            avgflag='A', long_name='urban air conditioning flux', &
-            ptr_lunit=this%eflx_urban_ac_lun, set_nourb=0._r8, l2g_scale_type='unity', default='inactive')
-
-       this%eflx_urban_heat_lun(begl:endl) = spval
-       call hist_addfld1d (fname='URBAN_HEAT', units='W/m^2',  &
-            avgflag='A', long_name='urban heating flux', &
-            ptr_lunit=this%eflx_urban_heat_lun, set_nourb=0._r8, l2g_scale_type='unity', default='inactive')
-    end if
-
-
-    this%dgnetdT_patch(begp:endp) = spval
-    call hist_addfld1d (fname='DGNETDT', units='W/m^2/K', &
-         avgflag='A', long_name='derivative of net ground heat flux wrt soil temp', &
-         ptr_patch=this%dgnetdT_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%eflx_fgr12_col(begc:endc) = spval
-    call hist_addfld1d (fname='FGR12',  units='W/m^2',  &
-         avgflag='A', long_name='heat flux between soil layers 1 and 2', &
-         ptr_col=this%eflx_fgr12_col, set_lake=spval, default='inactive')
-
-    this%eflx_fgr_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='FGR_SOIL_R', units='watt/m^2', type2d='levgrnd', &
-         avgflag='A', long_name='Rural downward heat flux at interface below each soil layer', &
-         ptr_col=this%eflx_fgr_col, set_spec=spval, default='inactive')
-
-    this%eflx_traffic_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TRAFFICFLUX', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat flux from urban traffic', &
-         ptr_patch=this%eflx_traffic_patch, set_nourb=0._r8, c2l_scale_type='urbanf', &
-         default='inactive')
-
-    this%eflx_wasteheat_patch(begp:endp) = spval
-    call hist_addfld1d (fname='WASTEHEAT', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat flux from heating/cooling sources of urban waste heat', &
-         ptr_patch=this%eflx_wasteheat_patch, set_nourb=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%eflx_heat_from_ac_patch(begp:endp) = spval
-    call hist_addfld1d (fname='HEAT_FROM_AC', units='W/m^2',  &
-         avgflag='A', long_name='sensible heat flux put into canyon due to heat removed from air conditioning', &
-         ptr_patch=this%eflx_heat_from_ac_patch, set_nourb=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    if ( is_simple_buildtemp )then
-       this%eflx_anthro_patch(begp:endp) = spval
-       call hist_addfld1d (fname='Qanth', units='W/m^2',  &
-            avgflag='A', long_name='anthropogenic heat flux', &
-            ptr_patch=this%eflx_anthro_patch, set_nourb=0._r8, c2l_scale_type='urbanf', &
-            default='inactive')
-    end if
-
-    this%taux_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TAUX', units='kg/m/s^2',  &
-         avgflag='A', long_name='zonal surface stress', &
-         ptr_patch=this%taux_patch, default='inactive')
-    ! Rename of TAUX for Urban intercomparision project (when U=V)    
-    call hist_addfld1d (fname='Qtau', units='kg/m/s^2',  &  
-         avgflag='A', long_name='momentum flux', &
-         ptr_patch=this%taux_patch, default='inactive')
-
-    this%tauy_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TAUY', units='kg/m/s^2',  &
-         avgflag='A', long_name='meridional surface stress', &
-         ptr_patch=this%tauy_patch, default='inactive')
-
-    this%btran_patch(begp:endp) = spval
-    if (.not. use_hydrstress) then
-       call hist_addfld1d (fname='BTRAN', units='unitless',  &
-            avgflag='A', long_name='transpiration beta factor', &
-            ptr_patch=this%btran_patch, set_lake=spval, set_urb=spval, default='inactive')
-    end if
-
-    this%btran_min_patch(begp:endp) = spval
-    call hist_addfld1d (fname='BTRANMN', units='unitless',  &
-         avgflag='A', long_name='daily minimum of transpiration beta factor', &
-         ptr_patch=this%btran_min_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-    this%btran2_patch(begp:endp) = spval
-    call hist_addfld1d (fname='BTRAN2', units='unitless',  &
-         avgflag='A', long_name='root zone soil wetness factor', &
-         ptr_patch=this%btran2_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-    if (use_cn) then
-       this%rresis_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='RRESIS', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='root resistance in each soil layer', &
-            ptr_patch=this%rresis_patch, default='inactive')
-    end if
-
-    this%errsoi_col(begc:endc) = spval
-    call hist_addfld1d (fname='ERRSOI',  units='W/m^2',  &
-         avgflag='A', long_name='soil/lake energy conservation error', &
-         ptr_col=this%errsoi_col, default='inactive')
-
-    this%errseb_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ERRSEB',  units='W/m^2',  &
-         avgflag='A', long_name='surface energy conservation error', &
-         ptr_patch=this%errseb_patch, default='inactive')
-
-    this%errsol_patch(begp:endp) = spval
-    call hist_addfld1d (fname='ERRSOL',  units='W/m^2',  &
-         avgflag='A', long_name='solar radiation conservation error', &
-         ptr_patch=this%errsol_patch, set_urb=spval, default='inactive')
-
-  end subroutine InitHistory
-
   !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, t_grnd_col, is_simple_buildtemp, is_prog_buildtemp)
+  subroutine InitCold(this, bounds, t_grnd_col)
     !
     ! !DESCRIPTION:
     ! Initialize cold start conditions for module variables
     !
     ! !USES:
     use shr_kind_mod    , only : r8 => shr_kind_r8
-    use shr_const_mod   , only : SHR_CONST_TKFRZ
-    use clm_varpar      , only : nlevsoi, nlevgrnd, nlevsno, nlevlak, nlevurb
-    use clm_varcon      , only : denice, denh2o, sb
-    use landunit_varcon , only : istwet, istsoil, istdlak
-    use column_varcon   , only : icol_road_imperv, icol_roof, icol_sunwall
-    use column_varcon   , only : icol_shadewall, icol_road_perv
-    use clm_varctl      , only : iulog, use_vancouver, use_mexicocity
+    use clm_varcon      , only : sb
     implicit none
     !
     ! !ARGUMENTS:
     class(energyflux_type)         :: this
     type(bounds_type) , intent(in) :: bounds  
     real(r8)          , intent(in) :: t_grnd_col( bounds%begc: )
-    logical           , intent(in) :: is_simple_buildtemp ! If using simple building temp method
-    logical           , intent(in) :: is_prog_buildtemp   ! If using prognostic building temp method
     !
     ! !LOCAL VARIABLES:
-    integer  :: j,l,c,p,levs,lev
+    integer  :: c,p
     !-----------------------------------------------------------------------
 
     SHR_ASSERT_ALL((ubound(t_grnd_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
 
-    ! Columns
-    if ( is_simple_buildtemp )then
-       do c = bounds%begc, bounds%endc
-          l = col%landunit(c)
-
-          if (lun%urbpoi(l)) then
-             this%eflx_building_heat_errsoi_col(c) = 0._r8
-             this%eflx_urban_ac_col(c)             = 0._r8
-             this%eflx_urban_heat_col(c)           = 0._r8
-          else
-             this%eflx_building_heat_errsoi_col(c) = 0._r8
-             this%eflx_urban_ac_col(c)             = 0._r8
-             this%eflx_urban_heat_col(c)           = 0._r8
-          end if
-
-       end do
-    end if
-
     ! Patches
     do p = bounds%begp, bounds%endp 
        c = patch%column(p)
-       l = patch%landunit(p)
-
-       if (.not. lun%urbpoi(l)) then ! non-urban
-          this%eflx_lwrad_net_u_patch(p) = spval
-          this%eflx_lwrad_out_u_patch(p) = spval
-          this%eflx_lh_tot_u_patch(p)    = spval
-          this%eflx_sh_tot_u_patch(p)    = spval
-          this%eflx_soil_grnd_u_patch(p) = spval
-       end if
-
        this%eflx_lwrad_out_patch(p) = sb * (t_grnd_col(c))**4
     end do
 
-    ! patches
-    do p = bounds%begp, bounds%endp 
-       l = patch%landunit(p)
-
-       if (.not. lun%urbpoi(l)) then
-          this%eflx_traffic_lun(l)        = spval
-          this%eflx_wasteheat_lun(l)      = spval
-          if ( is_prog_buildtemp )then
-             this%eflx_building_lun(l)   = 0._r8
-             this%eflx_urban_ac_lun(l)   = 0._r8
-             this%eflx_urban_heat_lun(l) = 0._r8
-          end if
-
-          this%eflx_wasteheat_patch(p)    = 0._r8
-          this%eflx_heat_from_ac_patch(p) = 0._r8
-          this%eflx_traffic_patch(p)      = 0._r8
-          if ( is_simple_buildtemp) &
-             this%eflx_anthro_patch(p)    = 0._r8
-       else
-          if ( is_prog_buildtemp )then
-             this%eflx_building_lun(l)   = 0._r8
-             this%eflx_urban_ac_lun(l)   = 0._r8
-             this%eflx_urban_heat_lun(l) = 0._r8
-          end if
-       end if
-    end do
-
-    ! initialize rresis, for use in ecosystemdyn
-    do p = bounds%begp,bounds%endp
-       do lev = 1,nlevgrnd
-          this%rresis_patch(p,lev) = 0._r8
-       end do
-    end do 
-
   end subroutine InitCold
 
   !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildtemp)
+  subroutine Restart(this, bounds, ncid, flag)
     ! 
     ! !DESCRIPTION:
     ! Read/Write module information to/from restart file.
     !
     ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use spmdMod    , only : masterproc
-    use abortutils , only : endrun
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, &
-                            ncd_inqvdlen
+    use ncdio_pio  , only : file_desc_t, ncd_double
     use restUtilMod
-    use decompMod      , only : get_proc_global
     implicit none
     !
     ! !ARGUMENTS:
@@ -778,245 +123,16 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     type(bounds_type), intent(in)    :: bounds 
     type(file_desc_t), intent(inout) :: ncid   
     character(len=*) , intent(in)    :: flag   
-    logical          , intent(in)    :: is_simple_buildtemp ! If using simple building temp method
-    logical          , intent(in)    :: is_prog_buildtemp   ! If using prognostic building temp method
     !
     ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    integer :: dimlen
-    integer :: err_code
-    integer :: numl_global
     logical :: readvar      ! determine if variable is on initial file
-    logical :: do_io
     !-----------------------------------------------------------------------
 
-    call get_proc_global(nl=numl_global)
     call restartvar(ncid=ncid, flag=flag, varname='EFLX_LWRAD_OUT', xtype=ncd_double,  & 
          dim1name='pft', &
          long_name='emitted infrared (longwave) radiation', units='watt/m^2', &
          interpinic_flag='interp', readvar=readvar, data=this%eflx_lwrad_out_patch)
 
-    ! Restart for building air temperature method
-    if ( is_prog_buildtemp )then
-       ! landunit urban energy state variable - eflx_urban_ac
-       do_io = .true.
-       ! On a read, confirm that this variable has the expected size (landunit-level); if not, 
-       ! don't read it (instead give it a default value). This is needed to support older initial
-       ! conditions for which this variable had a different size (column-level).
-       if (flag == 'read') then
-          call ncd_inqvdlen(ncid, 'URBAN_AC_L', 1, dimlen, err_code)
-          if (dimlen /= numl_global) then
-             do_io = .false.
-             readvar = .false.
-          end if
-       end if
-       if (do_io) then
-          call restartvar(ncid=ncid, flag=flag, varname='URBAN_AC_L', xtype=ncd_double,  &
-               dim1name='landunit',&
-               long_name='urban air conditioning flux', units='watt/m^2', &
-               interpinic_flag='interp', readvar=readvar, data=this%eflx_urban_ac_lun)
-       else
-          this%eflx_urban_ac_lun = 0.0_r8
-       end if
-       ! landunit urban energy state variable - eflx_urban_heat
-       do_io = .true.
-       ! On a read, confirm that this variable has the expected size (landunit-level); if not, 
-       ! don't read it (instead give it a default value). This is needed to support older initial
-       ! conditions for which this variable had a different size (column-level).
-       if (flag == 'read') then
-          call ncd_inqvdlen(ncid, 'URBAN_HEAT_L', 1, dimlen, err_code)
-          if (dimlen /= numl_global) then
-             do_io = .false.
-             readvar = .false.
-          end if
-       end if
-       if (do_io) then
-          call restartvar(ncid=ncid, flag=flag, varname='URBAN_HEAT_L', xtype=ncd_double,  &
-               dim1name='landunit',&
-               long_name='urban heating flux', units='watt/m^2', &
-               interpinic_flag='interp', readvar=readvar, data=this%eflx_urban_heat_lun)
-       else
-          this%eflx_urban_heat_lun = 0.0_r8
-       end if
-    else if ( is_simple_buildtemp )then
-        call restartvar(ncid=ncid, flag=flag, varname='URBAN_AC', xtype=ncd_double, &
-            dim1name='column', &
-            long_name='urban air conditioning flux', units='watt/m^2', &
-            interpinic_flag='interp', readvar=readvar, data=this%eflx_urban_ac_col)
-        call restartvar(ncid=ncid, flag=flag, varname='URBAN_HEAT', xtype=ncd_double,  &
-            dim1name='column', &
-            long_name='urban heating flux', units='watt/m^2', &
-            interpinic_flag='interp', readvar=readvar, data=this%eflx_urban_heat_col)
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='btran2', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%btran2_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='BTRAN_MIN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='daily minimum of transpiration wetness factor', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%btran_min_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='BTRAN_MIN_INST', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='instantaneous daily minimum of transpiration wetness factor', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%btran_min_inst_patch) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='eflx_grnd_lake', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='net heat flux into lake/snow surface, excluding light transmission', units='W/m^2', &
-         interpinic_flag='interp', readvar=readvar, data=this%eflx_grnd_lake_patch)
-
   end subroutine Restart
-  !-----------------------------------------------------------------------
-  subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    ! Each interval and accumulation type is unique to each field processed.
-    ! Routine [initAccBuffer] defines the fields to be processed
-    ! and the type of accumulation. 
-    ! Routine [updateAccVars] does the actual accumulation for a given field.
-    ! Fields are accumulated by calls to subroutine [update_accum_field]. 
-    ! To accumulate a field, it must first be defined in subroutine [initAccVars] 
-    ! and then accumulated by calls to [updateAccVars].
-    ! Four types of accumulations are possible:
-    !   o average over time interval
-    !   o running mean over time interval
-    !   o running accumulation over time interval
-    ! Time average fields are only valid at the end of the averaging interval.
-    ! Running means are valid once the length of the simulation exceeds the
-    ! averaging interval. Accumulated fields are continuously accumulated.
-    ! The trigger value "-99999." resets the accumulation to zero.
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field
-    use clm_time_manager , only : get_step_size
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    !
-    ! !ARGUMENTS:
-    class(energyflux_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES: 
-    real(r8) :: dtime
-    integer, parameter :: not_used = huge(1)
-    !---------------------------------------------------------------------
-
-    dtime = get_step_size()
-
-    call init_accum_field(name='BTRANAV', units='-', &
-         desc='average over an hour of btran', accum_type='timeavg', accum_period=nint(3600._r8/dtime), &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-  end subroutine InitAccBuffer
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field, extract_accum_field
-    use clm_time_manager , only : get_nstep
-    use clm_varctl       , only : nsrest, nsrStartup
-    use abortutils       , only : endrun
-    !
-    ! !ARGUMENTS:
-    class(energyflux_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begp, endp
-    integer  :: nstep
-    integer  :: ier
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Initialize variables that are to be time accumulated
-    ! Initialize btran min values
-    if (nsrest == nsrStartup) then
-       this%btran_min_patch(begp:endp)        =  spval
-
-       this%btran_min_inst_patch(begp:endp)   =  spval
-    end if
-
-  end subroutine InitAccVars
-  !-----------------------------------------------------------------------
-  subroutine UpdateAccVars (this, bounds)
-    !
-    ! USES
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
-    use clm_varctl       , only : iulog
-    use abortutils       , only : endrun
-    !
-    ! !ARGUMENTS:
-    class(energyflux_type)                :: this
-    type(bounds_type)      , intent(in)    :: bounds
-
-    !
-    ! !LOCAL VARIABLES:
-    integer :: m,g,l,c,p                 ! indices
-    integer :: ier                       ! error status
-    integer :: dtime                     ! timestep size [seconds]
-    integer :: nstep                     ! timestep number
-    integer :: year                      ! year (0, ...) for nstep
-    integer :: month                     ! month (1, ..., 12) for nstep
-    integer :: day                       ! day of month (1, ..., 31) for nstep
-    integer :: secs                      ! seconds into current date for nstep
-    logical :: end_cd                    ! temporary for is_end_curr_day() value
-    integer :: begp, endp
-    real(r8), pointer :: rbufslp(:)      ! temporary single level - pft level
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    dtime = get_step_size()
-    nstep = get_nstep()
-    call get_curr_date (year, month, day, secs)
-
-    ! Allocate needed dynamic memory for single level pft field
-
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'update_accum_hist allocation error for rbuf1dp'
-       call endrun(msg=errMsg(__FILE__, __LINE__))
-    endif
-
-    ! Accumulate and extract BTRANAV - hourly average btran
-    ! Used to compute minimum of hourly averaged btran
-    ! over a day. Note that "spval" is returned by the call to
-    ! accext if the time step does not correspond to the end of an
-    ! accumulation interval. First, initialize the necessary values for
-    ! an initial run at the first time step the accumulator is called
-
-    call update_accum_field  ('BTRANAV', this%btran_patch, nstep)
-    call extract_accum_field ('BTRANAV', rbufslp, nstep)
-    end_cd = is_end_curr_day()
-    do p = begp,endp
-       if (rbufslp(p) /= spval) then
-          this%btran_min_inst_patch(p) = min(rbufslp(p), this%btran_min_inst_patch(p))
-       endif
-       if (end_cd) then
-          this%btran_min_patch(p) = this%btran_min_inst_patch(p)
-          this%btran_min_inst_patch(p) =  spval
-       else if (secs == dtime) then
-          this%btran_min_patch(p) = spval
-       endif
-    end do
-
-    deallocate(rbufslp)
-
-  end subroutine UpdateAccVars
 
 end module EnergyFluxType
diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90
deleted file mode 100644
index 46ce60875a..0000000000
--- a/src/biogeophys/FrictionVelocityMod.F90
+++ /dev/null
@@ -1,772 +0,0 @@
-module FrictionVelocityMod
-
-#include "shr_assert.h"
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculation of the friction velocity, relation for potential
-  ! temperature and humidity profiles of surface boundary layer.
-  !
-  ! !USES:
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use shr_log_mod  , only : errMsg => shr_log_errMsg
-  use decompMod    , only : bounds_type
-  use clm_varcon   , only : spval
-  use clm_varctl   , only : use_cn, use_luna
-  use LandunitType , only : lun                
-  use ColumnType   , only : col
-  use PatchType    , only : patch                
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: FrictionVelocity       ! Calculate friction velocity
-  public :: MoninObukIni           ! Initialization of the Monin-Obukhov length
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: StabilityFunc1        ! Stability function for rib < 0.
-  private :: StabilityFunc2        ! Stability function for rib < 0.
-
-  type, public :: frictionvel_type
-
-     ! Roughness length/resistance for friction velocity calculation
-
-     real(r8), pointer, public :: forc_hgt_u_patch (:)   ! patch wind forcing height (10m+z0m+d) (m)
-     real(r8), pointer, public :: forc_hgt_t_patch (:)   ! patch temperature forcing height (10m+z0m+d) (m)
-     real(r8), pointer, public :: forc_hgt_q_patch (:)   ! patch specific humidity forcing height (10m+z0m+d) (m)
-     real(r8), pointer, public :: u10_patch        (:)   ! patch 10-m wind (m/s) (for dust model)
-     real(r8), pointer, public :: u10_clm_patch    (:)   ! patch 10-m wind (m/s) (for clm_map2gcell)
-     real(r8), pointer, public :: va_patch         (:)   ! patch atmospheric wind speed plus convective velocity (m/s)
-     real(r8), pointer, public :: vds_patch        (:)   ! patch deposition velocity term (m/s) (for dry dep SO4, NH4NO3)
-     real(r8), pointer, public :: fv_patch         (:)   ! patch friction velocity (m/s) (for dust model)
-     real(r8), pointer, public :: rb1_patch        (:)   ! patch aerodynamical resistance (s/m) (for dry deposition of chemical tracers)
-     real(r8), pointer, public :: rb10_patch       (:)   ! 10-day mean patch aerodynamical resistance (s/m) (for LUNA model)
-     real(r8), pointer, public :: ram1_patch       (:)   ! patch aerodynamical resistance (s/m)
-     real(r8), pointer, public :: z0m_patch        (:)   ! patch momentum roughness length (m)
-     real(r8), pointer, public :: z0mv_patch       (:)   ! patch roughness length over vegetation, momentum [m]
-     real(r8), pointer, public :: z0hv_patch       (:)   ! patch roughness length over vegetation, sensible heat [m]
-     real(r8), pointer, public :: z0qv_patch       (:)   ! patch roughness length over vegetation, latent heat [m]
-     real(r8), pointer, public :: z0mg_col         (:)   ! col roughness length over ground, momentum  [m] 
-     real(r8), pointer, public :: z0hg_col         (:)   ! col roughness length over ground, sensible heat [m]
-     real(r8), pointer, public :: z0qg_col         (:)   ! col roughness length over ground, latent heat [m]
-
-   contains
-
-     ! Public procedures
-     procedure, public  :: Init         
-     procedure, public  :: Restart      
-
-     ! Private procedures
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type frictionvel_type
-
-  type, public :: frictionvel_parms_type
-     real(r8) :: zetamaxstable            ! Max value zeta ("height" used in Monin-Obukhov theory) can go to under stable conditions
-  end type frictionvel_parms_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------------
-
-  type(frictionvel_parms_type), public, protected :: frictionvel_parms_inst
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(frictionvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(frictionvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    allocate(this%forc_hgt_u_patch (begp:endp)) ; this%forc_hgt_u_patch (:)   = nan
-    allocate(this%forc_hgt_t_patch (begp:endp)) ; this%forc_hgt_t_patch (:)   = nan
-    allocate(this%forc_hgt_q_patch (begp:endp)) ; this%forc_hgt_q_patch (:)   = nan
-    allocate(this%u10_patch        (begp:endp)) ; this%u10_patch        (:)   = nan
-    allocate(this%u10_clm_patch    (begp:endp)) ; this%u10_clm_patch    (:)   = nan
-    allocate(this%va_patch         (begp:endp)) ; this%va_patch         (:)   = nan
-    allocate(this%vds_patch        (begp:endp)) ; this%vds_patch        (:)   = nan
-    allocate(this%fv_patch         (begp:endp)) ; this%fv_patch         (:)   = nan
-    allocate(this%rb1_patch        (begp:endp)) ; this%rb1_patch        (:)   = nan
-    allocate(this%rb10_patch       (begp:endp)) ; this%rb10_patch       (:)   = spval
-    allocate(this%ram1_patch       (begp:endp)) ; this%ram1_patch       (:)   = nan
-    allocate(this%z0m_patch        (begp:endp)) ; this%z0m_patch        (:)   = nan
-    allocate(this%z0mv_patch       (begp:endp)) ; this%z0mv_patch       (:)   = nan
-    allocate(this%z0hv_patch       (begp:endp)) ; this%z0hv_patch       (:)   = nan
-    allocate(this%z0qv_patch       (begp:endp)) ; this%z0qv_patch       (:)   = nan
-    allocate(this%z0mg_col         (begc:endc)) ; this%z0mg_col         (:)   = nan
-    allocate(this%z0qg_col         (begc:endc)) ; this%z0qg_col         (:)   = nan
-    allocate(this%z0hg_col         (begc:endc)) ; this%z0hg_col         (:)   = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(frictionvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begc, endc
-    integer :: begp, endp
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    this%z0mg_col(begc:endc) = spval
-    call hist_addfld1d (fname='Z0MG', units='m', &
-         avgflag='A', long_name='roughness length over ground, momentum', &
-         ptr_col=this%z0mg_col, default='inactive')
-
-    this%z0hg_col(begc:endc) = spval
-    call hist_addfld1d (fname='Z0HG', units='m', &
-         avgflag='A', long_name='roughness length over ground, sensible heat', &
-         ptr_col=this%z0hg_col, default='inactive')
-
-    this%z0qg_col(begc:endc) = spval
-    call hist_addfld1d (fname='Z0QG', units='m', &
-         avgflag='A', long_name='roughness length over ground, latent heat', &
-         ptr_col=this%z0qg_col, default='inactive')
-
-    this%va_patch(begp:endp) = spval
-    call hist_addfld1d (fname='VA', units='m/s', &
-         avgflag='A', long_name='atmospheric wind speed plus convective velocity', &
-         ptr_patch=this%va_patch, default='inactive')
-
-    this%u10_clm_patch(begp:endp) = spval
-    call hist_addfld1d (fname='U10', units='m/s', &
-         avgflag='A', long_name='10-m wind', &
-         ptr_patch=this%u10_clm_patch, default='inactive')
-
-    call hist_addfld1d (fname='U10_ICE', units='m/s',  &
-         avgflag='A', long_name='10-m wind (ice landunits only)', &
-         ptr_patch=this%u10_clm_patch, l2g_scale_type='ice', default='inactive')
-
-    this%u10_patch(begp:endp) = spval
-    call hist_addfld1d (fname='U10_DUST', units='m/s', &
-         avgflag='A', long_name='10-m wind for dust model', &
-         ptr_patch=this%u10_patch, default='inactive')
-
-    if (use_cn) then
-       this%ram1_patch(begp:endp) = spval
-       call hist_addfld1d (fname='RAM1', units='s/m', &
-            avgflag='A', long_name='aerodynamical resistance ', &
-            ptr_patch=this%ram1_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%fv_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FV', units='m/s', &
-            avgflag='A', long_name='friction velocity for dust model', &
-            ptr_patch=this%fv_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%z0hv_patch(begp:endp) = spval
-       call hist_addfld1d (fname='Z0HV', units='m', &
-            avgflag='A', long_name='roughness length over vegetation, sensible heat', &
-            ptr_patch=this%z0hv_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%z0m_patch(begp:endp) = spval
-       call hist_addfld1d (fname='Z0M', units='m', &
-            avgflag='A', long_name='momentum roughness length', &
-            ptr_patch=this%z0m_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%z0mv_patch(begp:endp) = spval
-       call hist_addfld1d (fname='Z0MV', units='m', &
-            avgflag='A', long_name='roughness length over vegetation, momentum', &
-            ptr_patch=this%z0mv_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%z0qv_patch(begp:endp) = spval
-       call hist_addfld1d (fname='Z0QV', units='m', &
-            avgflag='A', long_name='roughness length over vegetation, latent heat', &
-            ptr_patch=this%z0qv_patch, default='inactive')
-    end if
-
-    if (use_luna) then
-       call hist_addfld1d (fname='RB10', units='s/m', &
-            avgflag='A', long_name='10 day running mean boundary layer resistance', &
-            ptr_patch=this%rb10_patch, default='inactive')
-    end if
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! Initialize module surface albedos to reasonable values
-    !
-    ! !ARGUMENTS:
-    class(frictionvel_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p, c, l                         ! indices
-    !-----------------------------------------------------------------------
-
-    ! Added 5/4/04, PET: initialize forc_hgt_u (gridcell-level),
-    ! since this is not initialized before first call to CNVegStructUpdate,
-    ! and it is required to set the upper bound for canopy top height.
-    ! Changed 3/21/08, KO: still needed but don't have sufficient information 
-    ! to set this properly (e.g., patch-level displacement height and roughness 
-    ! length). So leave at 30m.
-
-    if (use_cn) then
-       do p = bounds%begp, bounds%endp
-          this%forc_hgt_u_patch(p) = 30._r8
-       end do
-    end if
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%lakpoi(l)) then !lake
-          this%z0mg_col(c) = 0.0004_r8
-       end if
-    end do
-   
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !DESCRIPTION:
-    ! Read/Write module information to/from restart file.
-    !
-    ! !USES:
-    use spmdMod    , only : masterproc
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(frictionvel_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    !-----------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='Z0MG', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='ground momentum roughness length', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%z0mg_col)
-
-    if(use_luna)then
-       call restartvar(ncid=ncid, flag=flag, varname='rb10', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean boundary layer resistance at the pacth', units='s/m', &
-            interpinic_flag='interp', readvar=readvar, data=this%rb10_patch)
-    endif
-
-  end subroutine Restart
-
-  !------------------------------------------------------------------------------
-  subroutine FrictionVelocity(lbn, ubn, fn, filtern, &
-       displa, z0m, z0h, z0q, &
-       obu, iter, ur, um, ustar, &
-       temp1, temp2, temp12m, temp22m, fm, frictionvel_inst, landunit_index)
-    !
-    ! !DESCRIPTION:
-    ! Calculation of the friction velocity, relation for potential
-    ! temperature and humidity profiles of surface boundary layer.
-    ! The scheme is based on the work of Zeng et al. (1998):
-    ! Intercomparison of bulk aerodynamic algorithms for the computation
-    ! of sea surface fluxes using TOGA CORE and TAO data. J. Climate,
-    ! Vol. 11, 2628-2644.
-    !
-    ! !USES:
-    use clm_varcon, only : vkc
-    use clm_varctl, only : iulog
-    !
-    ! !ARGUMENTS:
-    integer  , intent(in)    :: lbn, ubn                 ! pft/landunit array bounds
-    integer  , intent(in)    :: fn                       ! number of filtered pft/landunit elements
-    integer  , intent(in)    :: filtern(fn)              ! pft/landunit filter
-    real(r8) , intent(in)    :: displa  ( lbn: )         ! displacement height (m) [lbn:ubn]
-    real(r8) , intent(in)    :: z0m     ( lbn: )         ! roughness length over vegetation, momentum [m] [lbn:ubn]
-    real(r8) , intent(in)    :: z0h     ( lbn: )         ! roughness length over vegetation, sensible heat [m] [lbn:ubn]
-    real(r8) , intent(in)    :: z0q     ( lbn: )         ! roughness length over vegetation, latent heat [m] [lbn:ubn]
-    real(r8) , intent(in)    :: obu     ( lbn: )         ! monin-obukhov length (m) [lbn:ubn]
-    integer  , intent(in)    :: iter                     ! iteration number
-    real(r8) , intent(in)    :: ur      ( lbn: )         ! wind speed at reference height [m/s] [lbn:ubn]
-    real(r8) , intent(in)    :: um      ( lbn: )         ! wind speed including the stablity effect [m/s] [lbn:ubn]
-    real(r8) , intent(out)   :: ustar   ( lbn: )         ! friction velocity [m/s] [lbn:ubn]
-    real(r8) , intent(out)   :: temp1   ( lbn: )         ! relation for potential temperature profile [lbn:ubn]
-    real(r8) , intent(out)   :: temp12m ( lbn: )         ! relation for potential temperature profile applied at 2-m [lbn:ubn]
-    real(r8) , intent(out)   :: temp2   ( lbn: )         ! relation for specific humidity profile [lbn:ubn]
-    real(r8) , intent(out)   :: temp22m ( lbn: )         ! relation for specific humidity profile applied at 2-m [lbn:ubn]
-    real(r8) , intent(inout) :: fm      ( lbn: )         ! diagnose 10m wind (DUST only) [lbn:ubn]
-    type(frictionvel_type) , intent(inout) :: frictionvel_inst
-    logical  , intent(in), optional :: landunit_index   ! optional argument that defines landunit or pft level
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), parameter :: zetam = 1.574_r8 ! transition point of flux-gradient relation (wind profile)
-    real(r8), parameter :: zetat = 0.465_r8 ! transition point of flux-gradient relation (temp. profile)
-    integer  :: f                           ! pft/landunit filter index
-    integer  :: n                           ! pft/landunit index
-    integer  :: g                           ! gridcell index
-    integer  :: pp                          ! pfti,pftf index
-    real(r8) :: zldis(lbn:ubn)              ! reference height "minus" zero displacement heght [m]
-    real(r8) :: zeta(lbn:ubn)               ! dimensionless height used in Monin-Obukhov theory
-    real(r8) :: tmp1,tmp2,tmp3,tmp4         ! Used to diagnose the 10 meter wind
-    real(r8) :: fmnew                       ! Used to diagnose the 10 meter wind
-    real(r8) :: fm10                        ! Used to diagnose the 10 meter wind
-    real(r8) :: zeta10                      ! Used to diagnose the 10 meter wind
-    real(r8) :: vds_tmp                     ! Temporary for dry deposition velocity
-    !------------------------------------------------------------------------------
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(displa)  == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(z0m)     == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(z0h)     == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(z0q)     == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(obu)     == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(ur)      == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(um)      == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(ustar)   == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(temp1)   == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(temp12m) == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(temp2)   == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(temp22m) == (/ubn/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(fm)      == (/ubn/)), errMsg(sourcefile, __LINE__))
-
-    associate(                                                   & 
-         pfti             => lun%patchi                          , & ! Input:  [integer  (:) ] beginning pfti index for landunit         
-         pftf             => lun%patchf                          , & ! Input:  [integer  (:) ] final pft index for landunit              
-         
-         forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Input:  [real(r8) (:) ] observational height of wind at pft level [m]
-         forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Input:  [real(r8) (:) ] observational height of temperature at pft level [m]
-         forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Input:  [real(r8) (:) ] observational height of specific humidity at pft level [m]
-         vds              => frictionvel_inst%vds_patch        , & ! Output: [real(r8) (:) ] dry deposition velocity term (m/s) (for SO4 NH4NO3)
-         u10              => frictionvel_inst%u10_patch        , & ! Output: [real(r8) (:) ] 10-m wind (m/s) (for dust model)        
-         u10_clm          => frictionvel_inst%u10_clm_patch    , & ! Output: [real(r8) (:) ] 10-m wind (m/s)                         
-         va               => frictionvel_inst%va_patch         , & ! Output: [real(r8) (:) ] atmospheric wind speed plus convective velocity (m/s)
-         fv               => frictionvel_inst%fv_patch           & ! Output: [real(r8) (:) ] friction velocity (m/s) (for dust model)
-         )
-
-      ! Adjustment factors for unstable (moz < 0) or stable (moz > 0) conditions.
-
-      do f = 1, fn
-         n = filtern(f)
-         if (present(landunit_index)) then
-            g = lun%gridcell(n) 
-         else
-            g = patch%gridcell(n)  
-         end if
-
-         ! Wind profile
-
-         if (present(landunit_index)) then
-            zldis(n) = forc_hgt_u_patch(pfti(n))-displa(n)
-         else
-            zldis(n) = forc_hgt_u_patch(n)-displa(n)
-         end if
-         zeta(n) = zldis(n)/obu(n)
-         if (zeta(n) < -zetam) then
-            ustar(n) = vkc*um(n)/(log(-zetam*obu(n)/z0m(n))&
-                 - StabilityFunc1(-zetam) &
-                 + StabilityFunc1(z0m(n)/obu(n)) &
-                 + 1.14_r8*((-zeta(n))**0.333_r8-(zetam)**0.333_r8))
-         else if (zeta(n) < 0._r8) then
-            ustar(n) = vkc*um(n)/(log(zldis(n)/z0m(n))&
-                 - StabilityFunc1(zeta(n))&
-                 + StabilityFunc1(z0m(n)/obu(n)))
-         else if (zeta(n) <=  1._r8) then
-            ustar(n) = vkc*um(n)/(log(zldis(n)/z0m(n)) + 5._r8*zeta(n) -5._r8*z0m(n)/obu(n))
-         else
-            ustar(n) = vkc*um(n)/(log(obu(n)/z0m(n))+5._r8-5._r8*z0m(n)/obu(n) &
-                 +(5._r8*log(zeta(n))+zeta(n)-1._r8))
-         end if
-
-         if (zeta(n) < 0._r8) then
-            vds_tmp = 2.e-3_r8*ustar(n) * ( 1._r8 + (300._r8/(-obu(n)))**0.666_r8)
-         else
-            vds_tmp = 2.e-3_r8*ustar(n)
-         endif
-
-         if (present(landunit_index)) then
-            do pp = pfti(n),pftf(n)
-               vds(pp) = vds_tmp
-            end do
-         else
-            vds(n) = vds_tmp
-         end if
-
-         ! Calculate a 10-m wind (10m + z0m + d)
-         ! For now, this will not be the same as the 10-m wind calculated for the dust 
-         ! model because the CLM stability functions are used here, not the LSM stability
-         ! functions used in the dust model. We will eventually change the dust model to be 
-         ! consistent with the following formulation.
-         ! Note that the 10-m wind calculated this way could actually be larger than the
-         ! atmospheric forcing wind because 1) this includes the convective velocity, 2)
-         ! this includes the 1 m/s minimum wind threshold
-
-         ! If forcing height is less than or equal to 10m, then set 10-m wind to um
-         if (present(landunit_index)) then
-            do pp = pfti(n),pftf(n)
-               if (zldis(n)-z0m(n) <= 10._r8) then
-                  u10_clm(pp) = um(n)
-               else
-                  if (zeta(n) < -zetam) then
-                     u10_clm(pp) = um(n) - ( ustar(n)/vkc*(log(-zetam*obu(n)/(10._r8+z0m(n)))      &
-                          - StabilityFunc1(-zetam)                              &
-                          + StabilityFunc1((10._r8+z0m(n))/obu(n))              &
-                          + 1.14_r8*((-zeta(n))**0.333_r8-(zetam)**0.333_r8)) )
-                  else if (zeta(n) < 0._r8) then
-                     u10_clm(pp) = um(n) - ( ustar(n)/vkc*(log(zldis(n)/(10._r8+z0m(n)))           &
-                          - StabilityFunc1(zeta(n))                             &
-                          + StabilityFunc1((10._r8+z0m(n))/obu(n))) )
-                  else if (zeta(n) <=  1._r8) then
-                     u10_clm(pp) = um(n) - ( ustar(n)/vkc*(log(zldis(n)/(10._r8+z0m(n)))           &
-                          + 5._r8*zeta(n) - 5._r8*(10._r8+z0m(n))/obu(n)) )
-                  else
-                     u10_clm(pp) = um(n) - ( ustar(n)/vkc*(log(obu(n)/(10._r8+z0m(n)))             &
-                          + 5._r8 - 5._r8*(10._r8+z0m(n))/obu(n)                &
-                          + (5._r8*log(zeta(n))+zeta(n)-1._r8)) )
-
-                  end if
-               end if
-               va(pp) = um(n)
-            end do
-         else
-            if (zldis(n)-z0m(n) <= 10._r8) then
-               u10_clm(n) = um(n)
-            else
-               if (zeta(n) < -zetam) then
-                  u10_clm(n) = um(n) - ( ustar(n)/vkc*(log(-zetam*obu(n)/(10._r8+z0m(n)))         &
-                       - StabilityFunc1(-zetam)                                 &
-                       + StabilityFunc1((10._r8+z0m(n))/obu(n))                 &
-                       + 1.14_r8*((-zeta(n))**0.333_r8-(zetam)**0.333_r8)) )
-               else if (zeta(n) < 0._r8) then
-                  u10_clm(n) = um(n) - ( ustar(n)/vkc*(log(zldis(n)/(10._r8+z0m(n)))              &
-                       - StabilityFunc1(zeta(n))                                &
-                       + StabilityFunc1((10._r8+z0m(n))/obu(n))) )
-               else if (zeta(n) <=  1._r8) then
-                  u10_clm(n) = um(n) - ( ustar(n)/vkc*(log(zldis(n)/(10._r8+z0m(n)))              &
-                       + 5._r8*zeta(n) - 5._r8*(10._r8+z0m(n))/obu(n)) )
-               else
-                  u10_clm(n) = um(n) - ( ustar(n)/vkc*(log(obu(n)/(10._r8+z0m(n)))                &
-                       + 5._r8 - 5._r8*(10._r8+z0m(n))/obu(n)                   &
-                       + (5._r8*log(zeta(n))+zeta(n)-1._r8)) )
-               end if
-            end if
-            va(n) = um(n)
-         end if
-
-         ! Temperature profile
-
-         if (present(landunit_index)) then
-            zldis(n) = forc_hgt_t_patch(pfti(n))-displa(n)
-         else
-            zldis(n) = forc_hgt_t_patch(n)-displa(n)
-         end if
-         zeta(n) = zldis(n)/obu(n)
-         if (zeta(n) < -zetat) then
-            temp1(n) = vkc/(log(-zetat*obu(n)/z0h(n))&
-                 - StabilityFunc2(-zetat) &
-                 + StabilityFunc2(z0h(n)/obu(n)) &
-                 + 0.8_r8*((zetat)**(-0.333_r8)-(-zeta(n))**(-0.333_r8)))
-         else if (zeta(n) < 0._r8) then
-            temp1(n) = vkc/(log(zldis(n)/z0h(n)) &
-                 - StabilityFunc2(zeta(n)) &
-                 + StabilityFunc2(z0h(n)/obu(n)))
-         else if (zeta(n) <=  1._r8) then
-            temp1(n) = vkc/(log(zldis(n)/z0h(n)) + 5._r8*zeta(n) - 5._r8*z0h(n)/obu(n))
-         else
-            temp1(n) = vkc/(log(obu(n)/z0h(n)) + 5._r8 - 5._r8*z0h(n)/obu(n) &
-                 + (5._r8*log(zeta(n))+zeta(n)-1._r8))
-         end if
-
-         ! Humidity profile
-
-         if (present(landunit_index)) then
-            if (forc_hgt_q_patch(pfti(n)) == forc_hgt_t_patch(pfti(n)) .and. z0q(n) == z0h(n)) then
-               temp2(n) = temp1(n)
-            else
-               zldis(n) = forc_hgt_q_patch(pfti(n))-displa(n)
-               zeta(n) = zldis(n)/obu(n)
-               if (zeta(n) < -zetat) then
-                  temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) &
-                       - StabilityFunc2(-zetat) &
-                       + StabilityFunc2(z0q(n)/obu(n)) &
-                       + 0.8_r8*((zetat)**(-0.333_r8)-(-zeta(n))**(-0.333_r8)))
-               else if (zeta(n) < 0._r8) then
-                  temp2(n) = vkc/(log(zldis(n)/z0q(n)) &
-                       - StabilityFunc2(zeta(n)) &
-                       + StabilityFunc2(z0q(n)/obu(n)))
-               else if (zeta(n) <=  1._r8) then
-                  temp2(n) = vkc/(log(zldis(n)/z0q(n)) + 5._r8*zeta(n)-5._r8*z0q(n)/obu(n))
-               else
-                  temp2(n) = vkc/(log(obu(n)/z0q(n)) + 5._r8 - 5._r8*z0q(n)/obu(n) &
-                       + (5._r8*log(zeta(n))+zeta(n)-1._r8))
-               end if
-            end if
-         else
-            if (forc_hgt_q_patch(n) == forc_hgt_t_patch(n) .and. z0q(n) == z0h(n)) then
-               temp2(n) = temp1(n)
-            else
-               zldis(n) = forc_hgt_q_patch(n)-displa(n)
-               zeta(n) = zldis(n)/obu(n)
-               if (zeta(n) < -zetat) then
-                  temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) &
-                       - StabilityFunc2(-zetat) &
-                       + StabilityFunc2(z0q(n)/obu(n)) &
-                       + 0.8_r8*((zetat)**(-0.333_r8)-(-zeta(n))**(-0.333_r8)))
-               else if (zeta(n) < 0._r8) then
-                  temp2(n) = vkc/(log(zldis(n)/z0q(n)) &
-                       - StabilityFunc2(zeta(n)) &
-                       + StabilityFunc2(z0q(n)/obu(n)))
-               else if (zeta(n) <=  1._r8) then
-                  temp2(n) = vkc/(log(zldis(n)/z0q(n)) + 5._r8*zeta(n)-5._r8*z0q(n)/obu(n))
-               else
-                  temp2(n) = vkc/(log(obu(n)/z0q(n)) + 5._r8 - 5._r8*z0q(n)/obu(n) &
-                       + (5._r8*log(zeta(n))+zeta(n)-1._r8))
-               end if
-            endif
-         endif
-
-         ! Temperature profile applied at 2-m
-
-         zldis(n) = 2.0_r8 + z0h(n)
-         zeta(n) = zldis(n)/obu(n)
-         if (zeta(n) < -zetat) then
-            temp12m(n) = vkc/(log(-zetat*obu(n)/z0h(n))&
-                 - StabilityFunc2(-zetat) &
-                 + StabilityFunc2(z0h(n)/obu(n)) &
-                 + 0.8_r8*((zetat)**(-0.333_r8)-(-zeta(n))**(-0.333_r8)))
-         else if (zeta(n) < 0._r8) then
-            temp12m(n) = vkc/(log(zldis(n)/z0h(n)) &
-                 - StabilityFunc2(zeta(n))  &
-                 + StabilityFunc2(z0h(n)/obu(n)))
-         else if (zeta(n) <=  1._r8) then
-            temp12m(n) = vkc/(log(zldis(n)/z0h(n)) + 5._r8*zeta(n) - 5._r8*z0h(n)/obu(n))
-         else
-            temp12m(n) = vkc/(log(obu(n)/z0h(n)) + 5._r8 - 5._r8*z0h(n)/obu(n) &
-                 + (5._r8*log(zeta(n))+zeta(n)-1._r8))
-         end if
-
-         ! Humidity profile applied at 2-m
-
-         if (z0q(n) == z0h(n)) then
-            temp22m(n) = temp12m(n)
-         else
-            zldis(n) = 2.0_r8 + z0q(n)
-            zeta(n) = zldis(n)/obu(n)
-            if (zeta(n) < -zetat) then
-               temp22m(n) = vkc/(log(-zetat*obu(n)/z0q(n)) - &
-                    StabilityFunc2(-zetat) + StabilityFunc2(z0q(n)/obu(n)) &
-                    + 0.8_r8*((zetat)**(-0.333_r8)-(-zeta(n))**(-0.333_r8)))
-            else if (zeta(n) < 0._r8) then
-               temp22m(n) = vkc/(log(zldis(n)/z0q(n)) - &
-                    StabilityFunc2(zeta(n))+StabilityFunc2(z0q(n)/obu(n)))
-            else if (zeta(n) <=  1._r8) then
-               temp22m(n) = vkc/(log(zldis(n)/z0q(n)) + 5._r8*zeta(n)-5._r8*z0q(n)/obu(n))
-            else
-               temp22m(n) = vkc/(log(obu(n)/z0q(n)) + 5._r8 - 5._r8*z0q(n)/obu(n) &
-                    + (5._r8*log(zeta(n))+zeta(n)-1._r8))
-            end if
-         end if
-
-         ! diagnose 10-m wind for dust model (dstmbl.F)
-         ! Notes from C. Zender's dst.F:
-         ! According to Bon96 p. 62, the displacement height d (here displa) is
-         ! 0.0 <= d <= 0.34 m in dust source regions (i.e., regions w/o trees).
-         ! Therefore d <= 0.034*z1 and may safely be neglected.
-         ! Code from LSM routine SurfaceTemperature was used to obtain u10
-
-         if (present(landunit_index)) then
-            zldis(n) = forc_hgt_u_patch(pfti(n))-displa(n)
-         else
-            zldis(n) = forc_hgt_u_patch(n)-displa(n)
-         end if
-         zeta(n) = zldis(n)/obu(n)
-         if (min(zeta(n), 1._r8) < 0._r8) then
-            tmp1 = (1._r8 - 16._r8*min(zeta(n),1._r8))**0.25_r8
-            tmp2 = log((1._r8+tmp1*tmp1)/2._r8)
-            tmp3 = log((1._r8+tmp1)/2._r8)
-            fmnew = 2._r8*tmp3 + tmp2 - 2._r8*atan(tmp1) + 1.5707963_r8
-         else
-            fmnew = -5._r8*min(zeta(n),1._r8)
-         endif
-         if (iter == 1) then
-            fm(n) = fmnew
-         else
-            fm(n) = 0.5_r8 * (fm(n)+fmnew)
-         end if
-         zeta10 = min(10._r8/obu(n), 1._r8)
-         if (zeta(n) == 0._r8) zeta10 = 0._r8
-         if (zeta10 < 0._r8) then
-            tmp1 = (1.0_r8 - 16.0_r8 * zeta10)**0.25_r8
-            tmp2 = log((1.0_r8 + tmp1*tmp1)/2.0_r8)
-            tmp3 = log((1.0_r8 + tmp1)/2.0_r8)
-            fm10 = 2.0_r8*tmp3 + tmp2 - 2.0_r8*atan(tmp1) + 1.5707963_r8
-         else                ! not stable
-            fm10 = -5.0_r8 * zeta10
-         end if
-         if (present(landunit_index)) then
-            tmp4 = log( max( 1.0_r8, forc_hgt_u_patch(pfti(n)) / 10._r8) )
-         else 
-            tmp4 = log( max( 1.0_r8, forc_hgt_u_patch(n) / 10._r8) )
-         end if
-         if (present(landunit_index)) then
-            do pp = pfti(n),pftf(n)
-               u10(pp) = ur(n) - ustar(n)/vkc * (tmp4 - fm(n) + fm10)
-               fv(pp)  = ustar(n)
-            end do
-         else
-            u10(n) = ur(n) - ustar(n)/vkc * (tmp4 - fm(n) + fm10)
-            fv(n)  = ustar(n)
-         end if
-
-      end do
-
-    end associate
-  end subroutine FrictionVelocity
-
-  !------------------------------------------------------------------------------
-  real(r8) function StabilityFunc1(zeta)
-    !
-    ! !DESCRIPTION:
-    ! Stability function for rib < 0.
-    !
-    ! !USES:
-    use shr_const_mod, only: SHR_CONST_PI
-    !
-    ! !ARGUMENTS:
-    implicit none
-    real(r8), intent(in) :: zeta  ! dimensionless height used in Monin-Obukhov theory
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: chik, chik2
-    !------------------------------------------------------------------------------
-
-    chik2 = sqrt(1._r8-16._r8*zeta)
-    chik = sqrt(chik2)
-    StabilityFunc1 = 2._r8*log((1._r8+chik)*0.5_r8) &
-         + log((1._r8+chik2)*0.5_r8)-2._r8*atan(chik)+SHR_CONST_PI*0.5_r8
-
-  end function StabilityFunc1
-
-  !------------------------------------------------------------------------------
-  real(r8) function StabilityFunc2(zeta)
-    !
-    ! !DESCRIPTION:
-    ! Stability function for rib < 0.
-    !
-    ! !USES:
-    use shr_const_mod, only: SHR_CONST_PI
-    !
-    ! !ARGUMENTS:
-    implicit none
-    real(r8), intent(in) :: zeta  ! dimensionless height used in Monin-Obukhov theory
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: chik2
-    !------------------------------------------------------------------------------
-
-    chik2 = sqrt(1._r8-16._r8*zeta)
-    StabilityFunc2 = 2._r8*log((1._r8+chik2)*0.5_r8)
-
-  end function StabilityFunc2
-
-  !-----------------------------------------------------------------------
-  subroutine MoninObukIni (ur, thv, dthv, zldis, z0m, um, obu)
-    !
-    ! !DESCRIPTION:
-    ! Initialization of the Monin-Obukhov length.
-    ! The scheme is based on the work of Zeng et al. (1998):
-    ! Intercomparison of bulk aerodynamic algorithms for the computation
-    ! of sea surface fluxes using TOGA CORE and TAO data. J. Climate,
-    ! Vol. 11, 2628-2644.
-    !
-    ! !USES:
-    use clm_varcon, only : grav
-    !
-    ! !ARGUMENTS:
-    implicit none
-    real(r8), intent(in)  :: ur    ! wind speed at reference height [m/s]
-    real(r8), intent(in)  :: thv   ! virtual potential temperature (kelvin)
-    real(r8), intent(in)  :: dthv  ! diff of vir. poten. temp. between ref. height and surface
-    real(r8), intent(in)  :: zldis ! reference height "minus" zero displacement heght [m]
-    real(r8), intent(in)  :: z0m   ! roughness length, momentum [m]
-    real(r8), intent(out) :: um    ! wind speed including the stability effect [m/s]
-    real(r8), intent(out) :: obu   ! monin-obukhov length (m)
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: wc    ! convective velocity [m/s]
-    real(r8) :: rib   ! bulk Richardson number
-    real(r8) :: zeta  ! dimensionless height used in Monin-Obukhov theory
-    real(r8) :: ustar ! friction velocity [m/s]
-    !-----------------------------------------------------------------------
-
-    ! Initial values of u* and convective velocity
-
-    ustar=0.06_r8
-    wc=0.5_r8
-    if (dthv >= 0._r8) then
-       um=max(ur,0.1_r8)
-    else
-       um=sqrt(ur*ur+wc*wc)
-    endif
-
-    rib=grav*zldis*dthv/(thv*um*um)
-
-    if (rib >= 0._r8) then      ! neutral or stable
-       zeta = rib*log(zldis/z0m)/(1._r8-5._r8*min(rib,0.19_r8))
-       zeta = min(frictionvel_parms_inst%zetamaxstable,max(zeta,0.01_r8 ))
-    else                     ! unstable
-       zeta=rib*log(zldis/z0m)
-       zeta = max(-100._r8,min(zeta,-0.01_r8 ))
-    endif
-
-    obu=zldis/zeta
-
-  end subroutine MoninObukIni
-
-end module FrictionVelocityMod
diff --git a/src/biogeophys/GlacierSurfaceMassBalanceMod.F90 b/src/biogeophys/GlacierSurfaceMassBalanceMod.F90
deleted file mode 100644
index adaa6ceec4..0000000000
--- a/src/biogeophys/GlacierSurfaceMassBalanceMod.F90
+++ /dev/null
@@ -1,452 +0,0 @@
-module GlacierSurfaceMassBalanceMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Computes fluxes that are specific to glaciers
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use decompMod      , only : bounds_type
-  use clm_varcon     , only : spval, secspday
-  use clm_varpar     , only : nlevgrnd
-  use clm_varctl     , only : glc_snow_persistence_max_days
-  use clm_time_manager, only : get_step_size
-  use landunit_varcon, only : istice_mec
-  use ColumnType     , only : col                
-  use LandunitType   , only : lun
-  use glc2lndMod     , only : glc2lnd_type
-  use WaterstateType , only : waterstate_type
-  use WaterfluxType  , only : waterflux_type
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  type, public :: glacier_smb_type
-     private
-
-     ! ------------------------------------------------------------------------
-     ! Public data
-     ! ------------------------------------------------------------------------
-
-     real(r8), pointer, public :: qflx_glcice_col(:) ! col net flux of new glacial ice (growth - melt) (mm H2O/s), passed to GLC; only valid inside the do_smb_c filter
-     real(r8), pointer, public :: qflx_glcice_dyn_water_flux_col(:) ! col water flux needed for balance check due to glc_dyn_runoff_routing (mm H2O/s) (positive means addition of water to the system); valid for all columns
-
-     ! ------------------------------------------------------------------------
-     ! Private data
-     ! ------------------------------------------------------------------------
-
-     real(r8), pointer :: qflx_glcice_frz_col (:)   ! col ice growth (positive definite) (mm H2O/s); only valid inside the do_smb_c filter
-     real(r8), pointer :: qflx_glcice_melt_col(:)   ! col ice melt (positive definite) (mm H2O/s); only valid inside the do_smb_c filter
-
-   contains
-
-     ! ------------------------------------------------------------------------
-     ! Public routines
-     ! ------------------------------------------------------------------------
-
-     procedure, public :: Init
-
-     ! The science routines need to be separated into a few pieces so they can be
-     ! sequenced properly based on what variables they depend on, and what they affect
-     procedure, public :: HandleIceMelt        ! compute ice melt in glacier columns, and convert liquid back to ice
-     procedure, public :: ComputeSurfaceMassBalance ! compute fluxes other than ice melt
-     procedure, public :: AdjustRunoffTerms    ! adjust liquid and ice runoff fluxes due to glacier fluxes
-
-     ! ------------------------------------------------------------------------
-     ! Private routines
-     ! ------------------------------------------------------------------------
-
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-
-  end type glacier_smb_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  ! ========================================================================
-  ! Infrastructure routines
-  ! ========================================================================
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds)
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !-----------------------------------------------------------------------
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-
-    integer :: begc, endc
-    !-----------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    allocate(this%qflx_glcice_col               (begc:endc)) ; this%qflx_glcice_col                (:) = nan
-    allocate(this%qflx_glcice_dyn_water_flux_col(begc:endc)) ; this%qflx_glcice_dyn_water_flux_col (:) = nan
-    allocate(this%qflx_glcice_frz_col           (begc:endc)) ; this%qflx_glcice_frz_col            (:) = nan
-    allocate(this%qflx_glcice_melt_col          (begc:endc)) ; this%qflx_glcice_melt_col           (:) = nan
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begc, endc
-    !-----------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    this%qflx_glcice_col(begc:endc) = spval
-    call hist_addfld1d (fname='QICE',  units='mm/s',  &
-         avgflag='A', long_name='ice growth/melt', &
-         ptr_col=this%qflx_glcice_col, l2g_scale_type='ice', default='inactive')
-
-    this%qflx_glcice_frz_col(begc:endc) = spval
-    call hist_addfld1d (fname='QICE_FRZ',  units='mm/s',  &
-         avgflag='A', long_name='ice growth', &
-         ptr_col=this%qflx_glcice_frz_col, l2g_scale_type='ice', default='inactive')
-
-    this%qflx_glcice_melt_col(begc:endc) = spval
-    call hist_addfld1d (fname='QICE_MELT',  units='mm/s',  &
-         avgflag='A', long_name='ice melt', &
-         ptr_col=this%qflx_glcice_melt_col, l2g_scale_type='ice', default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-
-    integer :: c
-    !-----------------------------------------------------------------------
-
-    ! Initialize qflx_glcice_dyn_water_flux_col to 0 for all columns because we want this
-    ! flux to remain 0 for columns where is is never set, including non-glacier columns.
-    !
-    ! Other fluxes intentionally remain unset (spval) outside the do_smb filter, so that
-    ! they are flagged as missing value outside that filter.
-    do c = bounds%begc, bounds%endc
-       this%qflx_glcice_dyn_water_flux_col(c) = 0._r8
-    end do
-
-  end subroutine InitCold
-
-  ! ========================================================================
-  ! Science routines
-  ! ========================================================================
-
-  !-----------------------------------------------------------------------
-  subroutine HandleIceMelt(this, bounds, num_do_smb_c, filter_do_smb_c, &
-       waterstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Compute ice melt in glacier columns, and convert liquid back to ice
-    !
-    ! Ideally this should be called immediately after ice is melted, so that liquid is
-    ! converted back to ice as soon as possible.
-    !
-    ! NOTE(wjs, 2016-06-29) Currently this is separated from the main ComputeSurfaceMassBalance
-    ! routine so that it can be called from the same place in the driver loop where it was
-    ! done before the introduction of GlacierSurfaceMassBalanceMod. This was needed to maintain
-    ! identical answers, due to the adjustment of h2osoi_ice and h2osoi_liq in this
-    ! routine. In principle we should be able to do these adjustments of h2osoi_ice and
-    ! h2osoi_liq later in the driver loop: this would just mean that some intervening
-    ! science code is operating on the temporarily-thawed state, before the water runs off
-    ! and is replaced by ice from below. The main reason to make this change would be to
-    ! simplify the driver logic, consolidating calls to this module. On the other hand,
-    ! having a period when there is liquid water at the top of the glacier column could
-    ! defeat some of the purpose of converting it immediately back to ice (i.e., so that
-    ! the surface fluxes are always generated based on an ice-covered surface) - so it
-    ! may be best to keep this separate.
-    !
-    ! !ARGUMENTS:
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    integer, intent(in) :: num_do_smb_c        ! number of column points in filter_do_smb_c
-    integer, intent(in) :: filter_do_smb_c(:)  ! column filter for points where SMB is calculated
-    type(waterstate_type), intent(inout) :: waterstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j
-    integer :: fc, c, l
-    real(r8) :: dtime ! land model time step (sec)
-
-    character(len=*), parameter :: subname = 'HandleIceMelt'
-    !-----------------------------------------------------------------------
-
-    associate( &
-         qflx_glcice_melt => this%qflx_glcice_melt_col , & ! Output: [real(r8) (:)   ] ice melt (positive definite) (mm H2O/s)
-         h2osoi_liq       => waterstate_inst%h2osoi_liq_col      , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2)
-         h2osoi_ice       => waterstate_inst%h2osoi_ice_col        & ! Output: [real(r8) (:,:) ] ice lens (kg/m2)
-         )
-
-    dtime = get_step_size()
-
-    do fc = 1, num_do_smb_c
-       c = filter_do_smb_c(fc)
-       qflx_glcice_melt(c) = 0._r8
-    end do
-
-    ! Note that, because the following code only operates over the do_smb filter, that
-    ! means that the conversion of water back to ice only happens for glacier columns
-    ! where we're computing SMB.
-
-    do j = 1, nlevgrnd
-       do fc = 1, num_do_smb_c
-          c = filter_do_smb_c(fc)
-          l = col%landunit(c)
-
-          if (lun%itype(l) == istice_mec) then
-             if (h2osoi_liq(c,j) > 0._r8) then   ! ice layer with meltwater
-                qflx_glcice_melt(c) = qflx_glcice_melt(c) + h2osoi_liq(c,j)/dtime
-                
-                ! convert layer back to pure ice by "borrowing" ice from below the column
-                h2osoi_ice(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j)
-                h2osoi_liq(c,j) = 0._r8
-             end if  ! liquid water is present
-          end if  ! istice_mec
-       end do
-    end do
-
-    end associate
-
-  end subroutine HandleIceMelt
-
-  !-----------------------------------------------------------------------
-  subroutine ComputeSurfaceMassBalance(this, bounds, num_allc, filter_allc, &
-       num_do_smb_c, filter_do_smb_c, glc2lnd_inst, waterstate_inst, waterflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! Compute glacier fluxes other than ice melt.
-    !
-    ! This sets the public fields qflx_glcice_col and qflx_glcice_dyn_water_flux_col to
-    ! their final values.
-    !
-    ! Should be called after HandleIceMelt, and after waterflux_inst%qflx_snwcp_ice_col is
-    ! computed
-    !
-    ! !ARGUMENTS:
-    class(glacier_smb_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    integer, intent(in) :: num_allc        ! number of column points in filter_allc
-    integer, intent(in) :: filter_allc(:)  ! column filter for all points
-    integer, intent(in) :: num_do_smb_c        ! number of column points in filter_do_smb_c
-    integer, intent(in) :: filter_do_smb_c(:)  ! column filter for points where SMB is calculated
-    type(glc2lnd_type), intent(in) :: glc2lnd_inst
-    type(waterstate_type), intent(in) :: waterstate_inst
-    type(waterflux_type), intent(in) :: waterflux_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc, c, l, g
-
-    character(len=*), parameter :: subname = 'ComputeSurfaceMassBalance'
-    !-----------------------------------------------------------------------
-
-    associate( &
-         qflx_glcice                => this%qflx_glcice_col                    , & ! Output: [real(r8) (:)] net flux of new glacial ice (growth - melt) (mm H2O/s)
-         qflx_glcice_frz            => this%qflx_glcice_frz_col                , & ! Output: [real(r8) (:)] ice growth (positive definite) (mm H2O/s)
-         qflx_glcice_dyn_water_flux => this%qflx_glcice_dyn_water_flux_col     , & ! Output: [real(r8) (:)] water flux needed for balance check due to glc_dyn_runoff_routing (mm H2O/s) (positive means addition of water to the system)
-         qflx_glcice_melt           => this%qflx_glcice_melt_col               , & ! Input: [real(r8) (:)] ice melt (positive definite) (mm H2O/s)
-         glc_dyn_runoff_routing     => glc2lnd_inst%glc_dyn_runoff_routing_grc , & ! Input:  [real(r8) (:)]  whether we're doing runoff routing appropriate for having a dynamic icesheet
-         snow_persistence           => waterstate_inst%snow_persistence_col    , & ! Input: [real(r8) (:)]  counter for length of time snow-covered
-         qflx_snwcp_ice             => waterflux_inst%qflx_snwcp_ice_col         & ! Input: [real(r8) (:)]  excess solid h2o due to snow capping (outgoing) (mm H2O /s) [+]
-         )
-
-    ! NOTE(wjs, 2016-06-29) The following initialization is done in case the columns
-    ! included / excluded in the do_smb_c filter can change mid-run (besides just being
-    ! active vs. inactive): If an active column was inside this filter in the previous
-    ! timestep, but is no longer inside this filter in this timestep, we want this flux to
-    ! be 0 (rather than remaining at its previous value). (Currently, the set of active
-    ! columns included in the do_smb filter cannot change mid-run, but the logic is
-    ! complex enough that I don't want to assume that that will always remain true.) This
-    ! initialization also handles the case where glc_dyn_runoff_routing may change
-    ! mid-run, so that a point previously inside that mask no longer is.
-    do fc = 1, num_allc
-       c = filter_allc(fc)
-       qflx_glcice_dyn_water_flux(c) = 0._r8
-    end do
-
-
-    ! Calculate positive surface mass balance to ice sheets, both from already-glaciated
-    ! landunits and from non-glaciated landunits (glacial inception)
-    do fc = 1, num_do_smb_c
-       c = filter_do_smb_c(fc)
-       l = col%landunit(c)
-       g = col%gridcell(c)
-       ! In the following, we convert glc_snow_persistence_max_days to r8 to avoid overflow
-       if ( (snow_persistence(c) >= (real(glc_snow_persistence_max_days, r8) * secspday)) &
-            .or. lun%itype(l) == istice_mec) then
-          qflx_glcice_frz(c) = qflx_snwcp_ice(c)
-       else
-          qflx_glcice_frz(c) = 0._r8
-       end if
-
-       qflx_glcice(c) = qflx_glcice_frz(c) - qflx_glcice_melt(c)
-
-       ! For glc_dyn_runoff_routing > 0::
-       ! (1) All or part of the excess snow (from snow capping) has been incorporated in
-       !     qflx_glcice_frz.  This flux must be included here to complete the water
-       !     balance, because it is a sink of water as far as CLM is concerned (this water
-       !     will now be owned by CISM).
-       ! (2) Meltwater from ice (qflx_glcice_melt) is allowed to run off and is included
-       !     in qflx_qrgwl, but the water content of the ice column has not changed
-       !     because an equivalent ice mass has been "borrowed" from the base of the
-       !     column. So this borrowing is a source of water as far as CLM is concerned.
-       !   
-       ! For glc_dyn_runoff_routing = 0: Point (2) is the same as for the
-       ! glc_dyn_runoff_routing > 0 case: there is a source of water equal to
-       ! qflx_glcice_melt. However, in this case, the sink of water is also equal to
-       ! qflx_glcice_melt: We have simply replaced some liquid water with an equal amount
-       ! of solid ice. Another way to think about this is:
-       ! (1) qflx_ice_runoff_snwcp is reduced by an amount equal to qflx_glcice_melt (done
-       !     elsewhere in this module). The amount of snow removal is therefore given by
-       !     (qflx_ice_runoff_snwcp + qflx_glcice_melt), meaning that there is an
-       !     additional sink of water equal to qflx_glcice_melt.
-       ! (2) Meltwater from ice (qflx_glcice_melt) is allowed to run off and is included
-       !     in qflx_qrgwl, but the water content of the ice column has not changed
-       !     because an equivalent ice mass has been "borrowed" from the base of the
-       !     column. So this borrowing is a source of water as far as CLM is concerned.
-       ! These two corrections cancel out, so nothing is done here.
-       qflx_glcice_dyn_water_flux(c) = glc_dyn_runoff_routing(g) * (qflx_glcice_melt(c) - qflx_glcice_frz(c))
-    end do
-
-    end associate
-
-  end subroutine ComputeSurfaceMassBalance
-
-  !-----------------------------------------------------------------------
-  subroutine AdjustRunoffTerms(this, bounds, num_do_smb_c, filter_do_smb_c, &
-       glc2lnd_inst, qflx_qrgwl, qflx_ice_runoff_snwcp)
-    !
-    ! !DESCRIPTION:
-    ! Adjust liquid and ice runoff fluxes due to glacier fluxes
-    !
-    ! Should be called after ComputeSurfaceMassBalance, and after qflx_qrgwl and
-    ! qflx_ice_runoff_snwcp have been given their initial values
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(glacier_smb_type), intent(in) :: this
-    type(bounds_type), intent(in) :: bounds
-    integer, intent(in) :: num_do_smb_c        ! number of column points in filter_do_smb_c
-    integer, intent(in) :: filter_do_smb_c(:)  ! column filter for points where SMB is calculated
-    type(glc2lnd_type), intent(in) :: glc2lnd_inst
-    real(r8), intent(inout) :: qflx_qrgwl( bounds%begc: ) ! col qflx_surf at glaciers, wetlands, lakes
-    real(r8), intent(inout) :: qflx_ice_runoff_snwcp( bounds%begc: ) ! col solid runoff from snow capping (mm H2O /s)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc, c, g
-
-    character(len=*), parameter :: subname = 'AdjustRunoffTerms'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(qflx_qrgwl) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(qflx_ice_runoff_snwcp) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-    associate( &
-         qflx_glcice_frz        => this%qflx_glcice_frz_col                   , & ! Input: [real(r8) (:)] ice growth (positive definite) (mm H2O/s)
-         qflx_glcice_melt       => this%qflx_glcice_melt_col                  , & ! Input: [real(r8) (:)] ice melt (positive definite) (mm H2O/s)
-         glc_dyn_runoff_routing =>    glc2lnd_inst%glc_dyn_runoff_routing_grc   & ! Input: [real(r8) (:)]  gridcell fraction coupled to dynamic ice sheet
-         )
-
-    ! Note that, because the following code only operates over the do_smb filter, that
-    ! means that the adjustments here are only applied for glacier columns where we're
-    ! computing SMB. This is consistent with the use of the do_smb filter in
-    ! HandleIceMelt.
-
-    do fc = 1, num_do_smb_c
-       c = filter_do_smb_c(fc)
-       g = col%gridcell(c)
-
-       ! Melt is only generated for glacier columns. But it doesn't hurt to do this for
-       ! all columns in the do_smb filter: this melt term will be 0 for other columns.
-       ! Note: Ice melt is added to the runoff whether or not the column is coupled
-       ! to a dynamic glacier model.
-
-       qflx_qrgwl(c) = qflx_qrgwl(c) + qflx_glcice_melt(c)
-
-       ! For the part of the column that is coupled to a dynamic glacier model,
-       ! the glacier model handles the fate of capped snow, so we do not want it sent to runoff.
-       qflx_ice_runoff_snwcp(c) = qflx_ice_runoff_snwcp(c) - glc_dyn_runoff_routing(g)*qflx_glcice_frz(c)
-
-       ! In places where we are not coupled to a dynamic glacier model, CLM sends all of
-       ! the snow capping to the ocean as an ice runoff term. (This is essentially a crude
-       ! parameterization of calving, assuming steady state - i.e., all ice gain is
-       ! balanced by an ice loss.) But each unit of melt that happens is an indication
-       ! that 1 unit of the ice shouldn't have made it to the ocean - but instead melted
-       ! before it got there. So we need to correct for that by removing 1 unit of ice
-       ! runoff for each unit of melt. Note that, for a given point in space & time, this
-       ! can result in negative ice runoff. However, we expect that, in a temporally and
-       ! spatially-integrated sense (if we're near equilibrium), this will just serve to
-       ! decrease the too-high positive ice runoff.
-       !
-       ! Another way to think about this is: ice melt removes mass; the snow capping flux
-       ! also removes mass. If both the accumulation and melt remove mass, there is a
-       ! double-counting. So we need to correct that by: for each unit of ice melt
-       ! (resulting in 1 unit of liquid runoff), remove 1 unit of ice runoff. (This is not
-       ! an issue for parts of the column coupled to the dynamic glacier model, because
-       ! then the snow capping mass is retained in the LND-GLC coupled system.)
-       !
-       ! The alternative of simply not adding ice melt to the runoff stream where
-       ! glc_dyn_runoff_routing = 0 conserves mass, but fails to conserve energy, for a
-       ! similar reason: Ice melt in CLM removes energy; also, the ocean's melting of the
-       ! snow capping flux removes energy. If both the accumulation and melting remove
-       ! energy, there is a double-counting.
-       !
-       ! Yet another way to think about this is: When ice melted, we let the liquid run
-       ! off, and replaced it with new ice from below. But that new ice needed to come
-       ! from somewhere to keep the system in water balance. We "request" the new ice from
-       ! the ocean by generating a negataive ice runoff equivalent to the amount we have
-       ! melted (i.e., equivalent to the amount of new ice that we created from below).
-       
-       ! As above: Melt is only generated for glacier columns. But it doesn't hurt to do
-       ! this for all columns in the do_smb filter: this melt term will be 0 for other
-       ! columns.
-       
-       qflx_ice_runoff_snwcp(c) = qflx_ice_runoff_snwcp(c) - (1.0_r8 - glc_dyn_runoff_routing(g)) * qflx_glcice_melt(c)
-
-       ! Recall that glc_dyn_runoff_routing = min(lfrac, Sg_icemask_coupled_fluxes_l) / lfrac.
-       !
-       ! Consider a cell with lfrac = 0.8 and Sg_icemask_coupled_fluxes_l = 0.4. (For
-       ! instance, the cell might have half its land coverage in Greenland and the other
-       ! half in Ellemere.)  Given qflx_ice_runoff_snwcp(c) = 1 m/yr, half the flux (0.5
-       ! m/yr) will be sent to the runoff model, where it will be multiplied by lfrac to
-       ! give a net flux of 0.4 m/yr times the cell area.
-       !
-       ! The full SMB of 1 m/yr will be sent to the coupler's prep_glc_mod, but it will be
-       ! weighted by 0.4 when integrating over the whole ice sheet. So a net flux of 0.4
-       ! m/yr will also be applied to the ice sheet model.  The total flux of 0.8 m/yr,
-       ! split evenly between runoff and ice sheet, is what we want.
-
-    end do
-
-    end associate
-
-  end subroutine AdjustRunoffTerms
-
-end module GlacierSurfaceMassBalanceMod
diff --git a/src/biogeophys/LakeCon.F90 b/src/biogeophys/LakeCon.F90
deleted file mode 100644
index a42a3d0137..0000000000
--- a/src/biogeophys/LakeCon.F90
+++ /dev/null
@@ -1,178 +0,0 @@
-module LakeCon
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module containing constants and parameters for the Lake code 
-  ! (CLM4-LISSS, documented in Subin et al. 2011, JAMES)
-  ! Also contains time constant variables for Lake code
-  ! Created by Zack Subin, 2011
-  !
-  ! !USES:
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use decompMod    , only : bounds_type
-  use clm_varctl   , only : iulog
-  use spmdMod      , only : masterproc
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: LakeConInit
-  !-----------------------------------------------------------------------
-
-  !------------------------------------------------------------------
-  ! Lake Model non-tuneable constants 
-  !------------------------------------------------------------------
-
-  ! temperature of maximum water density (K)
-  ! This is from Hostetler and Bartlein (1990); more updated sources suggest 277.13 K.
-  real(r8), parameter :: tdmax = 277._r8   
-
-  !------------------------------------------------------------------
-  ! Lake Model tuneable constants 
-  !------------------------------------------------------------------
-
-  ! lake emissivity. This is used for both frozen and unfrozen lakes. 
-  ! This is pulled in from CLM4 and the reference is unclear.
-  real(r8), parameter :: emg_lake = 0.97_r8
-
-  ! The fraction of the visible (e.g. vis not nir from atm) sunlight
-  ! absorbed in ~1 m of water (the surface layer za_lake).
-  ! This is roughly the fraction over 700 nm but may depend on the details
-  ! of atmospheric radiative transfer. As long as NIR = 700 nm and up, this can be zero.
-  real(r8) :: betavis = 0.0_r8            
-
-  ! Momentum Roughness length over frozen lakes without snow  (m)
-  ! Typical value found in the literature, and consistent with Mironov expressions.
-  ! See e.g. Morris EM 1989, Andreas EL 1987, Guest & Davidson 1991 (as cited in Vavrus 1996)
-  real(r8), parameter :: z0frzlake = 0.001_r8  
-
-  ! Base of surface light absorption layer for lakes (m)
-  real(r8), parameter :: za_lake = 0.6_r8           
-
-  ! For calculating prognostic roughness length
-  real(r8), parameter :: cur0    = 0.01_r8  ! min. Charnock parameter
-  real(r8), parameter :: cus     = 0.1_r8   ! empirical constant for roughness under smooth flow
-  real(r8), parameter :: curm    = 0.1_r8   ! maximum Charnock parameter
-
-  ! The following will be set in initLake based on namelists. !TODO - fix this commend
-  real(r8)            :: fcrit              ! critical dimensionless fetch for Charnock parameter.
-  real(r8)            :: minz0lake          ! (m) Minimum allowed roughness length for unfrozen lakes.
-
-  ! For calculating enhanced diffusivity
-  real(r8), parameter :: n2min = 7.5e-5_r8 ! (s^-2) (yields diffusivity about 6 times km) ! Fang & Stefan 1996
-
-  ! Note, this will be adjusted in initLake if the timestep is not 1800 s.
-  ! Lake top numerics can oscillate with 0.01m top layer and 1800 s timestep.
-  ! The problem is that the surface flux is fixed during the calculation of the top
-  ! layer temperature in the diffusion and not corrected for the tendency of the top layer.
-  ! This thickness will be added to all minimum and maximum snow layer thicknesses compared to that used over non-lakes.
-  ! Analysis of the CFL condition suggests that the minimum snow layer thickness for 1800 s needs
-  ! to be at least ~1.2 cm for the bulk snow values of conductivity and heat capacity
-  ! and as much as 2.3 cm for pure ice.
-  ! Alternatively, a check could be done in LakeTemperature in case
-  ! t_grnd(c) - t_soisno(c,snl(c)+1) changed sign after the Crank-Nicholson step.
-  ! Such an approach, while perhaps allowing additional snow layer resolution, has not been tested.
-  ! The approach used over non-lakes is to have a first-order surface flux correction.
-  ! We choose not to do that here because t_grnd can vary independently of the top model
-  ! layer temperature, while it is fixed to the top layer temperature if tbot > tfrz and
-  ! the lake is frozen, or if there is an unstable density gradient in the top unfrozen lake layer.
-  real(r8)            :: lsadz = 0.03_r8 ! m
-
-  !! The following will be set in initLake based on namelists.
-  real(r8)            :: pudz          ! (m) Optional minimum total ice thickness required to allow lake puddling.
-  ! Currently used for sensitivity tests only.
-  real(r8)            :: depthcrit     ! (m) Depth beneath which to increase mixing. See discussion in Subin et al. 2011
-  real(r8)            :: mixfact       ! Mixing increase factor.
-
-  !!!!!!!!!!!
-  ! Namelists (some of these have not been extensively tested and are hardwired to default values currently).
-  !!!!!!!!!!!
-
-  ! used in LakeFluxes
-  ! true => use old fcrit & minz0 as per Subin et al 2011 form
-  ! See initLakeMod for details. Difference is very small for
-  ! small lakes and negligible for large lakes. Currently hardwired off.
-  logical,  public :: lake_use_old_fcrit_minz0 = .false. 
-
-  ! used in LakeTemperature
-  ! Increase mixing by a large factor for deep lakes
-  ! Crude but enhanced performance at all 4 deep lakes tested.
-  ! See Subin et al 2011 (JAMES) for details
-
-  ! (m) minimum lake depth to invoke deepmixing
-  real(r8), public :: deepmixing_depthcrit = 25._r8     
-
-  ! factor to increase mixing by
-  real(r8), public :: deepmixing_mixfact   = 10._r8     
-
-  ! true => Suppress enhanced diffusion. Small differences.
-  ! Currently hardwired .false.
-  ! See Subin et al 2011 for details.
-  ! Enhanced diffusion is intended for under ice and at large depths.
-  ! It is a much smaller change on its own than the "deepmixing"
-  ! above, but it increases the effect of deepmixing under ice and for large depths.
-  logical,  public :: lake_no_ed = .false.              
-
-  ! puddling (not extensively tested and currently hardwired off)
-  ! used in LakeTemperature and SurfaceAlbedo
-
-  ! true => suppress convection when greater than minimum amount
-  ! of ice is present. This also effectively sets lake_no_melt_icealb.
-  logical,  public :: lakepuddling = .false.            
-
-  ! (m) minimum amount of total ice nominal thickness before
-  ! convection is suppressed
-  real(r8), public :: lake_puddle_thick = 0.2_r8        
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine LakeConInit()
-    !
-    ! !DESCRIPTION:
-    ! Initialize time invariant variables for S Lake code 
-    !------------------------------------------------------------------------
-
-    if (masterproc) write (iulog,*) 'Attempting to initialize time invariant variables for lakes'
-
-    ! Set LakeCon constants according to namelist fields
-    if (lake_use_old_fcrit_minz0) then
-       ! critical dimensionless fetch for Charnock parameter. From Vickers & Mahrt 1997
-       ! but converted to use u instead of u* (Form used in Subin et al. 2011)
-       fcrit   = 22._r8 
-
-       ! (m) Minimum allowed roughness length for unfrozen lakes.
-       ! (Used in Subin et al. 2011)
-       minz0lake = 1.e-5_r8        
-    else
-       ! Vickers & Mahrt 1997
-       fcrit   = 100._r8  
-
-       ! (m) Minimum allowed roughness length for unfrozen lakes.
-       ! Now set low so it is only to avoid floating point exceptions.
-       minz0lake = 1.e-10_r8       
-    end if
-
-    if (lakepuddling) then
-       ! (m) Minimum total ice thickness required to allow lake puddling. Default is 0.2m.
-       ! This option has not been extensively tested.
-       ! This option turns on lake_no_melt_icealb, as the decrease in albedo will be based
-       ! on whether there is water over nice, not purely a function of ice top temperature.
-       pudz = lake_puddle_thick    
-    end if
-
-    ! (m) Depth beneath which to increase mixing. See discussion in Subin et al. 2011
-    depthcrit = deepmixing_depthcrit 
-
-    ! Mixing increase factor. ! Defaults are 25 m, increase by 10.
-    ! Note some other namelists will be used directly in lake physics during model integration.
-    mixfact = deepmixing_mixfact 
-
-    if (masterproc) write (iulog,*) 'Successfully initialized time invariant variables for lakes'
-
-  end subroutine LakeConInit
-
-end module LakeCon
diff --git a/src/biogeophys/LakeStateType.F90 b/src/biogeophys/LakeStateType.F90
deleted file mode 100644
index f440a81957..0000000000
--- a/src/biogeophys/LakeStateType.F90
+++ /dev/null
@@ -1,296 +0,0 @@
-module LakeStateType
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Lake data types and associated procesures
-  !
-  ! !USES:
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use shr_log_mod  , only : errMsg => shr_log_errMsg
-  use clm_varcon   , only : spval, grlnd
-  use decompMod    , only : bounds_type
-  use spmdMod      , only : masterproc
-  use abortUtils   , only : endrun
-  use LandunitType , only : lun                
-  use ColumnType   , only : col                
-  !
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: lakestate_type
-     ! Time constant variables
-     real(r8), pointer :: lakefetch_col     (:)   ! col lake fetch from surface data (m)                    
-     real(r8), pointer :: etal_col          (:)   ! col lake extinction coefficient from surface data (1/m) 
-
-     ! Time varying variables
-     real(r8), pointer :: lake_raw_col      (:)   ! col aerodynamic resistance for moisture (s/m)
-     real(r8), pointer :: ks_col            (:)   ! col coefficient for calculation of decay of eddy diffusivity with depth
-     real(r8), pointer :: ws_col            (:)   ! col surface friction velocity (m/s)
-     real(r8), pointer :: ust_lake_col      (:)   ! col friction velocity (m/s)          
-     real(r8), pointer :: betaprime_col     (:)   ! col effective beta: sabg_lyr(p,jtop) for snow layers, beta otherwise
-     real(r8), pointer :: savedtke1_col     (:)   ! col top level eddy conductivity from previous timestep (W/mK)
-     real(r8), pointer :: lake_icefrac_col  (:,:) ! col mass fraction of lake layer that is frozen
-     real(r8), pointer :: lake_icefracsurf_col(:) ! col mass fraction of surface lake layer that is frozen
-     real(r8), pointer :: lake_icethick_col (:)   ! col ice thickness (m) (integrated if lakepuddling)
-     real(r8), pointer :: lakeresist_col    (:)   ! col [s/m] (Needed for calc. of grnd_ch4_cond)
-     real(r8), pointer :: ram1_lake_patch   (:)   ! patch aerodynamical resistance (s/m)
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, public  :: Restart      
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type lakestate_type
-  !-----------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(lakestate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate ( bounds )
-    call this%InitHistory ( bounds )
-    call this%InitCold ( bounds ) 
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use clm_varpar    , only: nlevlak, nlevsno
-    !
-    ! !ARGUMENTS:
-    class(lakestate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !---------------------------------------------------------------------
-
-    ! Initialize savedtke1 to spval so that c->g averaging will be done correctly
-    ! TODO: can this be now be set to nan???
-    ! Initialize ust_lake to spval to detect input from restart file if not arbinit 
-    ! TODO: can this be removed now???
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    allocate(this%etal_col           (begc:endc))           ; this%etal_col           (:)   = nan
-    allocate(this%lakefetch_col      (begc:endc))           ; this%lakefetch_col      (:)   = nan
-    allocate(this%lakeresist_col     (begc:endc))           ; this%lakeresist_col     (:)   = nan
-    allocate(this%savedtke1_col      (begc:endc))           ; this%savedtke1_col      (:)   = spval  
-    allocate(this%lake_icefrac_col   (begc:endc,1:nlevlak)) ; this%lake_icefrac_col   (:,:) = nan
-    allocate(this%lake_icefracsurf_col (begc:endc))         ; this%lake_icefracsurf_col (:)   = nan
-    allocate(this%lake_icethick_col  (begc:endc))           ; this%lake_icethick_col  (:)   = nan
-    allocate(this%ust_lake_col       (begc:endc))           ; this%ust_lake_col       (:)   = spval   
-    allocate(this%ram1_lake_patch    (begp:endp))           ; this%ram1_lake_patch      (:)   = nan
-    allocate(this%lake_raw_col       (begc:endc))           ; this%lake_raw_col       (:)   = nan
-    allocate(this%ks_col             (begc:endc))           ; this%ks_col             (:)   = nan
-    allocate(this%ws_col             (begc:endc))           ; this%ws_col             (:)   = nan
-    allocate(this%betaprime_col      (begc:endc))           ; this%betaprime_col      (:)   = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(lakestate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    this%lake_icefrac_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='LAKEICEFRAC',  units='unitless', type2d='levlak', &
-         avgflag='A', long_name='lake layer ice mass fraction', &
-         ptr_col=this%lake_icefrac_col, default='inactive')
-
-    this%lake_icefracsurf_col(begc:endc) = spval
-    call hist_addfld1d (fname='LAKEICEFRAC_SURF',  units='unitless', &
-         avgflag='A', long_name='surface lake layer ice mass fraction', &
-         ptr_col=this%lake_icefracsurf_col, set_nolake=spval, default='inactive')
-    
-    this%lake_icethick_col(begc:endc) = spval ! This will be more useful than LAKEICEFRAC for many users.
-    call hist_addfld1d (fname='LAKEICETHICK', units='m', &
-         avgflag='A', long_name='thickness of lake ice (including physical expansion on freezing)', &
-         ptr_col=this%lake_icethick_col, set_nolake=spval, default='inactive')
-
-    this%savedtke1_col(begc:endc) = spval
-    call hist_addfld1d (fname='TKE1',  units='W/(mK)', &
-         avgflag='A', long_name='top lake level eddy thermal conductivity', &
-         ptr_col=this%savedtke1_col, default='inactive')
-
-    this%ram1_lake_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RAM_LAKE', units='s/m', &
-         avgflag='A', long_name='aerodynamic resistance for momentum (lakes only)', &
-         ptr_patch=this%ram1_lake_patch, set_nolake=spval, default='inactive')
-
-    this%ust_lake_col(begc:endc) = spval
-    call hist_addfld1d (fname='UST_LAKE', units='m/s', &
-         avgflag='A', long_name='friction velocity (lakes only)', &
-         ptr_col=this%ust_lake_col, set_nolake=spval, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize time constant and time varying module variables
-    !
-    ! !USES:
-    use clm_varctl , only : fsurdat
-    use clm_varctl , only : iulog
-    use clm_varpar , only : nlevlak
-    use clm_varcon , only : tkwat 
-    use fileutils  , only : getfil
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use ncdio_pio  , only : ncd_pio_openfile, ncd_inqfdims, ncd_pio_closefile, ncd_inqdid, ncd_inqdlen
-    !
-    ! !ARGUMENTS:
-    class(lakestate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer             :: c,g,i,j,l,lev
-    logical             :: readvar 
-    type(file_desc_t)   :: ncid                   ! netcdf id
-    character(len=256)  :: locfn                  ! local filename
-    real(r8)            :: depthratio             ! ratio of lake depth to standard deep lake depth
-    real(r8) ,pointer   :: lakefetch_in (:)       ! read in - lakefetch 
-    real(r8) ,pointer   :: etal_in (:)            ! read in - etal 
-    !-----------------------------------------------------------------------
-
-    !-------------------------------------------------
-    ! Initialize time constant variables
-    !-------------------------------------------------
-
-    call getfil (fsurdat, locfn, 0)
-    call ncd_pio_openfile (ncid, locfn, 0)
-
-    ! Read lake eta
-    allocate(etal_in(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='ETALAKE', flag='read', data=etal_in, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       if (masterproc) then
-          write(iulog,*) 'WARNING:: ETALAKE not found on surface data set. All lake columns will have eta', &
-               ' set equal to default value as a function of depth.'
-       end if
-       etal_in(:) = -1._r8
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       this%etal_col(c) = etal_in(g)
-    end do
-    deallocate(etal_in)
-
-    ! Read lake fetch
-    allocate(lakefetch_in(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='LAKEFETCH', flag='read', data=lakefetch_in, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       if (masterproc) then
-          write(iulog,*) 'WARNING:: LAKEFETCH not found on surface data set. All lake columns will have fetch', &
-               ' set equal to default value as a function of depth.'
-       end if
-       lakefetch_in(:) = -1._r8
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       this%lakefetch_col(c) = lakefetch_in(g)
-    end do
-    deallocate(lakefetch_in)
-
-    call ncd_pio_closefile(ncid)
-
-    !-------------------------------------------------
-    ! Initialize time varying variables
-    !-------------------------------------------------
-         
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%lakpoi(l)) then
-
-          ! Set lake ice fraction and top eddy conductivity from previous timestep
-          ! Always initialize with no ice to prevent excessive ice sheets from forming when
-          ! starting with old lake model that has unrealistically cold lake conseratures.
-          ! Keep lake temperature as is, and the energy deficit below freezing (which is no smaller
-          ! than it would have been with prognostic ice, as the temperature would then have been higher
-          ! and more heat would have flowed out of the lake) will be converted to ice in the first timestep.
-          this%lake_icefrac_col(c,1:nlevlak) = 0._r8
-
-          ! Set lake top eddy conductivity from previous timestep
-          this%savedtke1_col(c) = tkwat
-
-          ! Set column friction vlocity 
-          this%ust_lake_col(c)  = 0.1_r8
-       end if
-    end do
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !DESCRIPTION:
-    ! Read/Write module information to/from restart file.
-    !
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(lakestate_type) :: this
-    type(bounds_type), intent(in)    :: bounds  
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    !-----------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='LAKE_ICEFRAC', xtype=ncd_double,  &
-         dim1name='column', dim2name='levlak', switchdim=.true., &
-         long_name='lake layer ice fraction', units='kg/kg', &
-         interpinic_flag='interp', readvar=readvar, data=this%lake_icefrac_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='SAVEDTKE1', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='top lake layer eddy conductivity', units='W/(m K)', &
-         interpinic_flag='interp', readvar=readvar, data=this%savedtke1_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='USTLAKE', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='friction velocity for lakes', units='m/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%ust_lake_col)
-
-  end subroutine Restart
-
-end module LakeStateType
-
diff --git a/src/biogeophys/OzoneBaseMod.F90 b/src/biogeophys/OzoneBaseMod.F90
deleted file mode 100644
index c50818f380..0000000000
--- a/src/biogeophys/OzoneBaseMod.F90
+++ /dev/null
@@ -1,146 +0,0 @@
-module OzoneBaseMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Define the interface for ozone_type, which calculates ozone-induced stress. The type
-  ! defined here is abstract; it will get instantiated as a concrete type that extends
-  ! this base type (e.g., an ozone-off or ozone-on version).
-  !
-  ! !USES:
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use decompMod   , only : bounds_type
-
-  implicit none
-  save
-  private
-
-  ! !PUBLIC TYPES:
-  type, abstract, public :: ozone_base_type
-     private
-
-     ! Public data members
-     ! These should be treated as read-only by other modules (except that they can be
-     ! modified by extensions of the ozone_base_type)
-     real(r8), pointer, public :: o3coefvsha_patch(:)  ! ozone coefficient for photosynthesis, shaded leaves (0 - 1)
-     real(r8), pointer, public :: o3coefvsun_patch(:)  ! ozone coefficient for photosynthesis, sunlit leaves (0 - 1)
-     real(r8), pointer, public :: o3coefgsha_patch(:)  ! ozone coefficient for conductance, shaded leaves (0 - 1)
-     real(r8), pointer, public :: o3coefgsun_patch(:)  ! ozone coefficient for conductance, sunlit leaves (0 - 1)
-     
-     
-   contains
-     ! The following routines need to be implemented by all type extensions
-     procedure(Init_interface)            , public, deferred :: Init
-     procedure(Restart_interface)         , public, deferred :: Restart
-     procedure(CalcOzoneStress_interface) , public, deferred :: CalcOzoneStress
-
-     ! The following routines should only be called by extensions of the ozone_base_type
-     procedure, public :: InitAllocateBase
-     procedure, public :: InitColdBase
-
-  end type ozone_base_type
-
-  abstract interface
-
-     subroutine Init_interface(this, bounds)
-       use decompMod, only : bounds_type
-       import :: ozone_base_type
-
-       class(ozone_base_type), intent(inout) :: this
-       type(bounds_type), intent(in) :: bounds
-     end subroutine Init_interface
-  
-     subroutine Restart_interface(this, bounds, ncid, flag)
-       use decompMod , only : bounds_type
-       use ncdio_pio , only : file_desc_t       
-       import :: ozone_base_type
-
-       class(ozone_base_type)            :: this
-       type(bounds_type) , intent(in)    :: bounds
-       type(file_desc_t) , intent(inout) :: ncid ! netcdf id
-       character(len=*)  , intent(in)    :: flag ! 'read', 'write' or 'define'
-     end subroutine Restart_interface
-       
-     subroutine CalcOzoneStress_interface(this, bounds, num_exposedvegp, filter_exposedvegp, &
-          forc_pbot, forc_th, rssun, rssha, rb, ram, tlai)
-       use decompMod    , only : bounds_type
-       use shr_kind_mod , only : r8 => shr_kind_r8
-       import :: ozone_base_type
-
-       class(ozone_base_type) , intent(inout) :: this
-       type(bounds_type)      , intent(in)    :: bounds
-       integer  , intent(in) :: num_exposedvegp           ! number of points in filter_exposedvegp
-       integer  , intent(in) :: filter_exposedvegp(:)     ! patch filter for non-snow-covered veg
-       real(r8) , intent(in) :: forc_pbot( bounds%begc: ) ! atmospheric pressure (Pa)
-       real(r8) , intent(in) :: forc_th( bounds%begc: )   ! atmospheric potential temperature (K)
-       real(r8) , intent(in) :: rssun( bounds%begp: )     ! leaf stomatal resistance, sunlit leaves (s/m)
-       real(r8) , intent(in) :: rssha( bounds%begp: )     ! leaf stomatal resistance, shaded leaves (s/m)
-       real(r8) , intent(in) :: rb( bounds%begp: )        ! boundary layer resistance (s/m)
-       real(r8) , intent(in) :: ram( bounds%begp: )       ! aerodynamical resistance (s/m)
-       real(r8) , intent(in) :: tlai( bounds%begp: )      ! one-sided leaf area index, no burying by snow
-     end subroutine CalcOzoneStress_interface
-
-  end interface
-     
-contains
-  
-  !-----------------------------------------------------------------------
-  subroutine InitAllocateBase(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Allocate variables in the base class
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(ozone_base_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitAllocateBase'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    allocate(this%o3coefvsha_patch(begp:endp))  ; this%o3coefvsha_patch(:) = nan
-    allocate(this%o3coefvsun_patch(begp:endp))  ; this%o3coefvsun_patch(:) = nan
-    allocate(this%o3coefgsha_patch(begp:endp))  ; this%o3coefgsha_patch(:) = nan
-    allocate(this%o3coefgsun_patch(begp:endp))  ; this%o3coefgsun_patch(:) = nan
-    
-  end subroutine InitAllocateBase
-
-
-  !-----------------------------------------------------------------------
-  subroutine InitColdBase(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Do cold start initialization for variables in the base class. Note that this
-    ! initialization will be the same for all ozone implementations, including the
-    ! ozone-off implementation.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(ozone_base_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitColdBase'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    this%o3coefvsha_patch(begp:endp) = 1._r8
-    this%o3coefvsun_patch(begp:endp) = 1._r8
-    this%o3coefgsha_patch(begp:endp) = 1._r8
-    this%o3coefgsun_patch(begp:endp) = 1._r8
-
-  end subroutine InitColdBase
-
-end module OzoneBaseMod
diff --git a/src/biogeophys/OzoneFactoryMod.F90 b/src/biogeophys/OzoneFactoryMod.F90
deleted file mode 100644
index 2b28587a99..0000000000
--- a/src/biogeophys/OzoneFactoryMod.F90
+++ /dev/null
@@ -1,53 +0,0 @@
-module OzoneFactoryMod
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Factory to create an instance of ozone_base_type. This module figures out the
-  ! particular type to return.
-  !
-  ! !USES:
-  use decompMod   , only : bounds_type
-
-  implicit none
-  save
-  private
-
-  !
-  ! !PUBLIC ROUTINES:
-  public :: create_and_init_ozone_type  ! create an object of class ozone_base_type
-
-contains
-
-  !-----------------------------------------------------------------------
-  function create_and_init_ozone_type(bounds) result(ozone)
-    !
-    ! !DESCRIPTION:
-    ! Create and initialize an object of ozone_base_type, and return this object. The
-    ! particular type is determined based on the use_ozone namelist parameter.
-    !
-    ! !USES:
-    use clm_varctl   , only : use_ozone
-    use OzoneBaseMod , only : ozone_base_type
-    use OzoneOffMod  , only : ozone_off_type
-    use OzoneMod     , only : ozone_type
-    !
-    ! !ARGUMENTS:
-    class(ozone_base_type), allocatable :: ozone  ! function result
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'create_and_init_ozone_type'
-    !-----------------------------------------------------------------------
-
-    if (use_ozone) then
-       allocate(ozone, source = ozone_type())
-    else
-       allocate(ozone, source = ozone_off_type())
-    end if
-
-    call ozone%Init(bounds)
-    
-  end function create_and_init_ozone_type
-
-end module OzoneFactoryMod
diff --git a/src/biogeophys/OzoneMod.F90 b/src/biogeophys/OzoneMod.F90
deleted file mode 100644
index 6c0e35779a..0000000000
--- a/src/biogeophys/OzoneMod.F90
+++ /dev/null
@@ -1,543 +0,0 @@
-module OzoneMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculates ozone-induced stress.
-  !
-  ! Note that the ozone calculations need to happen AFTER rssun and rsshade are computed
-  ! by the Photosynthesis routine. However, Photosynthesis also uses the ozone stress
-  ! computed here. Thus, the ozone stress computed in timestep i is applied in timestep
-  ! (i+1), requiring these stresses to be saved on the restart file.
-  !
-  ! Developed by Danica Lombardozzi.
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use decompMod   , only : bounds_type
-  use clm_varcon  , only : spval
-  use shr_log_mod , only : errMsg => shr_log_errMsg
-  use OzoneBaseMod, only : ozone_base_type
-  use abortutils  , only : endrun
-
-  implicit none
-  save
-  private
-
-  ! !PUBLIC TYPES:
-  type, extends(ozone_base_type), public :: ozone_type
-     private
-     ! Private data members
-     real(r8), pointer :: o3uptakesha_patch(:) ! ozone dose, shaded leaves (mmol O3/m^2)
-     real(r8), pointer :: o3uptakesun_patch(:) ! ozone dose, sunlit leaves (mmol O3/m^2)
-
-     ! NOTE(wjs, 2014-09-29) tlai_old_patch really belongs alongside tlai_patch in
-     ! CanopyStateType.  But there are problems with any way I can think to implement
-     ! that:
-     ! 
-     ! - Updating tlai_old from a call in clm_driver, just before tlai is updated: This
-     !   is problematic to do correctly because tlai is updated in different places
-     !   depending on whether you're using SP, CN or ED.
-     ! 
-     ! - Updating tlai_old within each routine that updates tlai: This feels fragile,
-     !   since it depends on each scheme remembering to do this update at the correct
-     !   time.
-     !
-     ! - Making tlai a private member of CanopyFluxes, with getter and setter methods.
-     !   Then the setter method would also set tlai_old. This feels like the most robust
-     !   solution, but we don't have any precedent for using getters and setters for data
-     !   arrays.
-     real(r8), pointer :: tlai_old_patch(:)  ! tlai from last time step
-
-   contains
-     ! Public routines
-     procedure, public :: Init
-     procedure, public :: Restart
-     procedure, public :: CalcOzoneStress
-
-     ! Private routines
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-
-     ! Calculate ozone stress for a single point, for just sunlit or shaded leaves
-     procedure, private, nopass :: CalcOzoneStressOnePoint
-  end type ozone_type
-
-  interface ozone_type
-     module procedure constructor
-  end interface ozone_type
-
-  ! !PRIVATE TYPES:
-  
-  ! TODO(wjs, 2014-09-29) This parameter will eventually become a spatially-varying
-  ! value, obtained from ATM
-  real(r8), parameter :: forc_ozone = 100._r8 * 1.e-9_r8  ! ozone partial pressure [mol/mol]
-
-  ! TODO(wjs, 2014-09-29) The following parameters should eventually be moved to the
-  ! params file. Parameters differentiated on veg type should be put on the params file
-  ! with a pft dimension.
-
-  ! o3:h2o resistance ratio defined by Sitch et al. 2007
-  real(r8), parameter :: ko3 = 1.67_r8
-
-  ! LAI threshold for LAIs that asymptote and don't reach 0
-  real(r8), parameter :: lai_thresh = 0.5_r8
-
-  ! threshold below which o3flux is set to 0 (nmol m^-2 s^-1)
-  real(r8), parameter :: o3_flux_threshold = 0.8_r8
-
-  ! o3 intercepts and slopes for photosynthesis
-  real(r8), parameter :: needleleafPhotoInt   = 0.8390_r8  ! units = unitless 
-  real(r8), parameter :: needleleafPhotoSlope = 0._r8      ! units = per mmol m^-2
-  real(r8), parameter :: broadleafPhotoInt    = 0.8752_r8  ! units = unitless  
-  real(r8), parameter :: broadleafPhotoSlope  = 0._r8      ! units = per mmol m^-2
-  real(r8), parameter :: nonwoodyPhotoInt     = 0.8021_r8  ! units = unitless
-  real(r8), parameter :: nonwoodyPhotoSlope   = -0.0009_r8 ! units = per mmol m^-2
-
-  ! o3 intercepts and slopes for conductance
-  real(r8), parameter :: needleleafCondInt    = 0.7823_r8  ! units = unitless
-  real(r8), parameter :: needleleafCondSlope  = 0.0048_r8  ! units = per mmol m^-2
-  real(r8), parameter :: broadleafCondInt     = 0.9125_r8  ! units = unitless
-  real(r8), parameter :: broadleafCondSlope   = 0._r8      ! units = per mmol m^-2
-  real(r8), parameter :: nonwoodyCondInt      = 0.7511_r8  ! units = unitless
-  real(r8), parameter :: nonwoodyCondSlope    = 0._r8      ! units = per mmol m^-2
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-  
-  ! ========================================================================
-  ! Infrastructure routines (initialization, restart, etc.)
-  ! ========================================================================
-
-  !-----------------------------------------------------------------------
-  function constructor() result(ozone)
-    !
-    ! !DESCRIPTION:
-    ! Return an instance of ozone_type
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(ozone_type) :: ozone  ! function result
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'constructor'
-    !-----------------------------------------------------------------------
-
-    ! DO NOTHING (simply return a variable of the appropriate type)
-
-    ! Eventually this should call the Init routine (or replace the Init routine
-    ! entirely). But I think it would be confusing to do that until we switch everything
-    ! to use a constructor rather than the init routine.
-    
-  end function constructor
-
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize ozone data structure
-    !
-    ! !ARGUMENTS:
-    class(ozone_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !-----------------------------------------------------------------------
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-    
-  end subroutine Init
-
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Allocate memory for ozone data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(ozone_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    call this%InitAllocateBase(bounds)
-
-    allocate(this%o3uptakesha_patch(begp:endp)) ; this%o3uptakesha_patch(:) = nan
-    allocate(this%o3uptakesun_patch(begp:endp)) ; this%o3uptakesun_patch(:) = nan
-    allocate(this%tlai_old_patch(begp:endp))    ; this%tlai_old_patch(:) = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize ozone history variables
-    !
-    ! !USES:
-    use histFileMod  , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(ozone_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-    
-    begp = bounds%begp
-    endp = bounds%endp
-
-    this%o3uptakesun_patch(begp:endp) = spval
-    call hist_addfld1d (fname='O3UPTAKESUN', units='mmol/m^2', &
-         avgflag='A', long_name='total ozone flux into sunlit leaves', &
-         ptr_patch=this%o3uptakesun_patch, default='inactive')
-
-    this%o3uptakesha_patch(begp:endp) = spval
-    call hist_addfld1d (fname='O3UPTAKESHA', units='mmol/m^2', &
-         avgflag='A', long_name='total ozone flux into shaded leaves', &
-         ptr_patch=this%o3uptakesha_patch, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Perform cold-start initialization for ozone
-    !
-    ! !ARGUMENTS:
-    class(ozone_type), intent(inout) :: this
-    type(bounds_type), intent(in)    :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    
-    character(len=*), parameter :: subname = 'InitCold'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp
-    endp = bounds%endp
-
-    call this%InitColdBase(bounds)
-
-    this%o3uptakesha_patch(begp:endp) = 0._r8
-    this%o3uptakesun_patch(begp:endp) = 0._r8
-    this%tlai_old_patch(begp:endp) = 0._r8
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !DESCRIPTION:
-    ! Handle restart of ozone variables.
-    !
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t, ncd_inqvdlen, ncd_double
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(ozone_type) :: this
-    type(bounds_type), intent(in)    :: bounds
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read', 'write' or 'define'
-    !
-    ! !LOCAL VARIABLES:
-    logical :: readvar
-
-    character(len=*), parameter :: subname = 'Restart'
-    !-----------------------------------------------------------------------
-    
-    call restartvar(ncid=ncid, flag=flag, varname='o3_tlaiold', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='one-sided leaf area index, from previous timestep, for ozone calculations', units='', &
-         readvar=readvar, interpinic_flag='interp', data=this%tlai_old_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3uptakesha', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone uptake for shaded leaves', units='mmol m^-3', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3uptakesha_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3uptakesun', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone uptake for sunlit leaves', units='mmol m^-3', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3uptakesun_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3coefvsun', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone coefficient for photosynthesis for sunlit leaves', units='unitless', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3coefvsun_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3coefgsun', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone coefficient for stomatal conductance for sunlit leaves', units='unitless', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3coefgsun_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3coefvsha', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone coefficient for photosynthesis for shaded leaves', units='unitless', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3coefvsha_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='o3coefgsha', xtype=ncd_double, &
-         dim1name='pft', &
-         long_name='ozone coefficient for stomatal conductance for shaded leaves', units='unitless', &
-         readvar=readvar, interpinic_flag='interp', data=this%o3coefgsha_patch)
-
-  end subroutine Restart
-
-  ! ========================================================================
-  ! Science routines
-  ! ========================================================================
-
-  !-----------------------------------------------------------------------
-  subroutine CalcOzoneStress(this, bounds, num_exposedvegp, filter_exposedvegp, &
-       forc_pbot, forc_th, rssun, rssha, rb, ram, tlai)
-    !
-    ! !DESCRIPTION:
-    ! Calculate ozone stress.
-    !
-    ! !USES:
-    use PatchType            , only : patch
-    !
-    ! !ARGUMENTS:
-    class(ozone_type)      , intent(inout) :: this
-    type(bounds_type)      , intent(in)    :: bounds
-    integer  , intent(in) :: num_exposedvegp           ! number of points in filter_exposedvegp
-    integer  , intent(in) :: filter_exposedvegp(:)     ! patch filter for non-snow-covered veg
-    real(r8) , intent(in) :: forc_pbot( bounds%begc: ) ! atmospheric pressure (Pa)
-    real(r8) , intent(in) :: forc_th( bounds%begc: )   ! atmospheric potential temperature (K)
-    real(r8) , intent(in) :: rssun( bounds%begp: )     ! leaf stomatal resistance, sunlit leaves (s/m)
-    real(r8) , intent(in) :: rssha( bounds%begp: )     ! leaf stomatal resistance, shaded leaves (s/m)
-    real(r8) , intent(in) :: rb( bounds%begp: )        ! boundary layer resistance (s/m)
-    real(r8) , intent(in) :: ram( bounds%begp: )       ! aerodynamical resistance (s/m)
-    real(r8) , intent(in) :: tlai( bounds%begp: )      ! one-sided leaf area index, no burying by snow
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: fp             ! filter index
-    integer  :: p              ! patch index
-    integer  :: c              ! column index
-
-    character(len=*), parameter :: subname = 'CalcOzoneStress'
-    !-----------------------------------------------------------------------
-    
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(forc_pbot) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(forc_th) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rssun) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rssha) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rb) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(ram) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(tlai) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-
-    associate( &
-         o3coefvsha  => this%o3coefvsha_patch                 , & ! Output: [real(r8) (:)] ozone coef
-         o3coefvsun  => this%o3coefvsun_patch                 , & ! Output: [real(r8) (:)] ozone coef
-         o3coefgsha  => this%o3coefgsha_patch                 , & ! Output: [real(r8) (:)] ozone coef
-         o3coefgsun  => this%o3coefgsun_patch                 , & ! Output: [real(r8) (:)] ozone coef
-         o3uptakesha => this%o3uptakesha_patch                , & ! Output: [real(r8) (:)] ozone dose
-         o3uptakesun => this%o3uptakesun_patch                , & ! Output: [real(r8) (:)] ozone dose
-         tlai_old    => this%tlai_old_patch                     & ! Output: [real(r8) (:)] tlai from last time step
-         )
-         
-    do fp = 1, num_exposedvegp
-       p = filter_exposedvegp(fp)
-       c = patch%column(p)
-
-!       if (.not.patch%is_fates(p)) then   ! When FATES coexists with other vegetation,
-                                     ! or when it has an ozone compatible module,  this
-                                     ! logic will likely come into play
-          
-          ! Ozone stress for shaded leaves
-          call CalcOzoneStressOnePoint( &
-               forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
-               rs=rssha(p), rb=rb(p), ram=ram(p), &
-               tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
-               o3uptake=o3uptakesha(p), o3coefv=o3coefvsha(p), o3coefg=o3coefgsha(p))
-          
-          ! Ozone stress for sunlit leaves
-          call CalcOzoneStressOnePoint( &
-               forc_ozone=forc_ozone, forc_pbot=forc_pbot(c), forc_th=forc_th(c), &
-               rs=rssun(p), rb=rb(p), ram=ram(p), &
-               tlai=tlai(p), tlai_old=tlai_old(p), pft_type=patch%itype(p), &
-               o3uptake=o3uptakesun(p), o3coefv=o3coefvsun(p), o3coefg=o3coefgsun(p))
-          
-          tlai_old(p) = tlai(p)
-
-!       else
-!          ! FATES is fundamentlaly incompatible with this type of patch-level
-!          ! association with plant functional type, so for the time
-!          ! being, fates patches will just push these values to invalid
-!          o3uptakesha(p) = spval
-!          o3coefvsha(p)  = spval
-!          o3coefgsha(p)  = spval
-!          o3uptakesun(p) = spval
-!          o3coefvsun(p)  = spval
-!          o3coefgsun(p)  = spval 
-!
-!       end if
-
-!       else
-!          ! FATES is fundamentlaly incompatible with this type of patch-level
-!          ! association with plant functional type, so for the time
-!          ! being, fates patches will just push these values to invalid
-!          o3uptakesha(p) = spval
-!          o3coefvsha(p)  = spval
-!          o3coefgsha(p)  = spval
-!          o3uptakesun(p) = spval
-!          o3coefvsun(p)  = spval
-!          o3coefgsun(p)  = spval 
-!
-!       end if
-
-    end do
-
-    end associate
-
-  end subroutine CalcOzoneStress
-
-  !-----------------------------------------------------------------------
-  subroutine CalcOzoneStressOnePoint( &
-       forc_ozone, forc_pbot, forc_th, &
-       rs, rb, ram, &
-       tlai, tlai_old, pft_type, &
-       o3uptake, o3coefv, o3coefg)
-    !
-    ! !DESCRIPTION:
-    ! Calculates ozone stress for a single point, for just sunlit or shaded leaves
-    !
-    ! !USES:
-    use shr_const_mod        , only : SHR_CONST_RGAS
-    use pftconMod            , only : pftcon
-    use clm_time_manager     , only : get_step_size
-    !
-    ! !ARGUMENTS:
-    real(r8) , intent(in)    :: forc_ozone ! ozone partial pressure (mol/mol)
-    real(r8) , intent(in)    :: forc_pbot  ! atmospheric pressure (Pa)
-    real(r8) , intent(in)    :: forc_th    ! atmospheric potential temperature (K)
-    real(r8) , intent(in)    :: rs         ! leaf stomatal resistance (s/m)
-    real(r8) , intent(in)    :: rb         ! boundary layer resistance (s/m)
-    real(r8) , intent(in)    :: ram        ! aerodynamical resistance (s/m)
-    real(r8) , intent(in)    :: tlai       ! one-sided leaf area index, no burying by snow
-    real(r8) , intent(in)    :: tlai_old   ! tlai from last time step
-    integer  , intent(in)    :: pft_type   ! vegetation type, for indexing into pftvarcon arrays
-    real(r8) , intent(inout) :: o3uptake   ! ozone entering the leaf
-    real(r8) , intent(out)   :: o3coefv    ! ozone coefficient for photosynthesis (0 - 1)
-    real(r8) , intent(out)   :: o3coefg    ! ozone coefficient for conductance (0 - 1)
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: dtime          ! land model time step (sec)
-    real(r8) :: dtimeh         ! time step in hours
-    real(r8) :: o3concnmolm3   ! o3 concentration (nmol/m^3)
-    real(r8) :: o3flux         ! instantaneous o3 flux (nmol m^-2 s^-1)
-    real(r8) :: o3fluxcrit     ! instantaneous o3 flux beyond threshold (nmol m^-2 s^-1)
-    real(r8) :: o3fluxperdt    ! o3 flux per timestep (mmol m^-2)
-    real(r8) :: heal           ! o3uptake healing rate based on % of new leaves growing (mmol m^-2)
-    real(r8) :: leafturn       ! leaf turnover time / mortality rate (per hour)
-    real(r8) :: decay          ! o3uptake decay rate based on leaf lifetime (mmol m^-2)
-    real(r8) :: photoInt       ! intercept for photosynthesis
-    real(r8) :: photoSlope     ! slope for photosynthesis
-    real(r8) :: condInt        ! intercept for conductance
-    real(r8) :: condSlope      ! slope for conductance
-
-    character(len=*), parameter :: subname = 'CalcOzoneStressOnePoint'
-    !-----------------------------------------------------------------------
-
-    ! convert o3 from mol/mol to nmol m^-3
-    o3concnmolm3 = forc_ozone * 1.e9_r8 * (forc_pbot/(forc_th*SHR_CONST_RGAS*0.001_r8))
-
-    ! calculate instantaneous flux
-    o3flux = o3concnmolm3/ (ko3*rs+ rb + ram)
-
-    ! apply o3 flux threshold 
-    if (o3flux < o3_flux_threshold) then
-       o3fluxcrit = 0._r8
-    else
-       o3fluxcrit = o3flux - o3_flux_threshold
-    endif
-
-    dtime  = get_step_size()
-    dtimeh = dtime / 3600._r8
-
-    ! calculate o3 flux per timestep
-    o3fluxperdt = o3fluxcrit * dtime * 0.000001_r8
-
-    if (tlai > lai_thresh) then
-       ! checking if new leaf area was added
-       if (tlai - tlai_old > 0) then
-          ! minimizing o3 damage to new leaves
-          heal = max(0._r8,(((tlai-tlai_old)/tlai)*o3fluxperdt))
-       else
-          heal = 0._r8
-       endif
-
-       if (pftcon%evergreen(pft_type) == 1) then
-          leafturn = 1._r8/(pftcon%leaf_long(pft_type)*365._r8*24._r8)
-       else
-          leafturn = 0._r8
-       endif
-
-       ! o3 uptake decay based on leaf lifetime for evergreen plants
-       decay = o3uptake * leafturn * dtimeh
-       !cumulative uptake (mmol m^-2)
-       o3uptake = max(0._r8, o3uptake + o3fluxperdt - decay - heal)
-
-    else
-       o3uptake = 0._r8
-    end if
-
-
-    if (o3uptake == 0._r8) then
-       ! No o3 damage if no o3 uptake
-       o3coefv = 1._r8
-       o3coefg = 1._r8
-    else
-       ! Determine parameter values for this pft
-       ! TODO(wjs, 2014-10-01) Once these parameters are moved into the params file, this
-       ! logic can be removed.
-       if (pft_type>3) then
-          if (pftcon%woody(pft_type)==0) then
-             photoInt   = nonwoodyPhotoInt
-             photoSlope = nonwoodyPhotoSlope
-             condInt    = nonwoodyCondInt
-             condSlope  = nonwoodyCondSlope
-          else
-             photoInt   = broadleafPhotoInt
-             photoSlope = broadleafPhotoSlope
-             condInt    = broadleafCondInt
-             condSlope  = broadleafCondSlope
-          end if
-       else
-          photoInt   = needleleafPhotoInt
-          photoSlope = needleleafPhotoSlope
-          condInt    = needleleafCondInt
-          condSlope  = needleleafCondSlope
-       end if
-
-       ! Apply parameter values to compute o3 coefficients
-       o3coefv = max(0._r8, min(1._r8, photoInt + photoSlope * o3uptake))
-       o3coefg = max(0._r8, min(1._r8, condInt  + condSlope  * o3uptake))
-
-    end if
-
-  end subroutine CalcOzoneStressOnePoint
-
-
-end module OzoneMod
diff --git a/src/biogeophys/OzoneOffMod.F90 b/src/biogeophys/OzoneOffMod.F90
deleted file mode 100644
index 8d0df71fd3..0000000000
--- a/src/biogeophys/OzoneOffMod.F90
+++ /dev/null
@@ -1,118 +0,0 @@
-module OzoneOffMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Provides an implementatio of ozone_base_type for the ozone-off case. Note that very
-  ! little needs to be done in this case, so this module mainly provides empty
-  ! implementations to satisfy the interface.
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use shr_log_mod , only : errMsg => shr_log_errMsg
-  use decompMod   , only : bounds_type
-  use OzoneBaseMod, only : ozone_base_type
-
-  implicit none
-  save
-  private
-
-  ! !PUBLIC TYPES:
-  type, extends(ozone_base_type), public :: ozone_off_type
-     private
-   contains
-     procedure, public :: Init
-     procedure, public :: Restart
-     procedure, public :: CalcOzoneStress
-  end type ozone_off_type
-
-  interface ozone_off_type
-     module procedure constructor
-  end interface ozone_off_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-  
-  !-----------------------------------------------------------------------
-  function constructor() result(ozone_off)
-    !
-    ! !DESCRIPTION:
-    ! Return an instance of ozone_off_type
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(ozone_off_type) :: ozone_off  ! function result
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'constructor'
-    !-----------------------------------------------------------------------
-
-    ! DO NOTHING (simply return a variable of the appropriate type)
-
-    ! Eventually this should call the Init routine (or replace the Init routine
-    ! entirely). But I think it would be confusing to do that until we switch everything
-    ! to use a constructor rather than the init routine.
-    
-  end function constructor
-
-
-  subroutine Init(this, bounds)
-    class(ozone_off_type) , intent(inout) :: this
-    type(bounds_type)     , intent(in)    :: bounds
-
-    call this%InitAllocateBase(bounds)
-    call this%InitColdBase(bounds)
-  end subroutine Init
-
-  subroutine Restart(this, bounds, ncid, flag)
-    use ncdio_pio , only : file_desc_t       
-
-    class(ozone_off_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    type(file_desc_t) , intent(inout) :: ncid ! netcdf id
-    character(len=*)  , intent(in)    :: flag ! 'read', 'write' or 'define'
-    
-    ! DO NOTHING
-
-  end subroutine Restart
-
-  subroutine CalcOzoneStress(this, bounds, num_exposedvegp, filter_exposedvegp, &
-          forc_pbot, forc_th, rssun, rssha, rb, ram, tlai)
-
-    class(ozone_off_type) , intent(inout) :: this
-    type(bounds_type)      , intent(in)    :: bounds
-    integer  , intent(in) :: num_exposedvegp           ! number of points in filter_exposedvegp
-    integer  , intent(in) :: filter_exposedvegp(:)     ! patch filter for non-snow-covered veg
-    real(r8) , intent(in) :: forc_pbot( bounds%begc: ) ! atmospheric pressure (Pa)
-    real(r8) , intent(in) :: forc_th( bounds%begc: )   ! atmospheric potential temperature (K)
-    real(r8) , intent(in) :: rssun( bounds%begp: )     ! leaf stomatal resistance, sunlit leaves (s/m)
-    real(r8) , intent(in) :: rssha( bounds%begp: )     ! leaf stomatal resistance, shaded leaves (s/m)
-    real(r8) , intent(in) :: rb( bounds%begp: )        ! boundary layer resistance (s/m)
-    real(r8) , intent(in) :: ram( bounds%begp: )       ! aerodynamical resistance (s/m)
-    real(r8) , intent(in) :: tlai( bounds%begp: )      ! one-sided leaf area index, no burying by snow
-
-    ! Enforce expected array sizes (mainly so that a debug-mode threaded test with
-    ! ozone-off can pick up problems with the call to this routine)
-    SHR_ASSERT_ALL((ubound(forc_pbot) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(forc_th) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rssun) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rssha) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(rb) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(ram) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(tlai) == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-
-    ! Explicitly set outputs to 1. This isn't really needed, because they should still be
-    ! at 1 from cold-start initialization, but do this for clarity here.
-
-    this%o3coefvsha_patch(bounds%begp:bounds%endp) = 1._r8
-    this%o3coefvsun_patch(bounds%begp:bounds%endp) = 1._r8
-    this%o3coefgsha_patch(bounds%begp:bounds%endp) = 1._r8
-    this%o3coefgsun_patch(bounds%begp:bounds%endp) = 1._r8
-
-  end subroutine CalcOzoneStress
-
-end module OzoneOffMod
diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90
deleted file mode 100644
index 311780b65a..0000000000
--- a/src/biogeophys/PhotosynthesisMod.F90
+++ /dev/null
@@ -1,612 +0,0 @@
-module  PhotosynthesisMod
-
-#include "shr_assert.h"
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Leaf photosynthesis and stomatal conductance calculation as described by
-  ! Bonan et al (2011) JGR, 116, doi:10.1029/2010JG001593 and extended to
-  ! a multi-layer canopy
-  !
-  ! !USES:
-  use shr_sys_mod         , only : shr_sys_flush
-  use shr_kind_mod        , only : r8 => shr_kind_r8
-  use shr_log_mod         , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod      , only : nan => shr_infnan_nan, assignment(=)
-  use abortutils          , only : endrun
-  use clm_varctl          , only : use_cn, use_cndv, use_fates, use_luna, use_hydrstress
-  use clm_varctl          , only : iulog
-  use clm_varpar          , only : nlevcan, nvegwcs, mxpft
-  use clm_varcon          , only : namep, spval
-  use decompMod           , only : bounds_type
-  use pftconMod           , only : pftcon
-  use atm2lndType         , only : atm2lnd_type
-  use CanopyStateType     , only : canopystate_type
-  use WaterStateType      , only : waterstate_type
-  use WaterfluxType       , only : waterflux_type
-  use SoilStateType       , only : soilstate_type
-  use TemperatureType     , only : temperature_type
-  use SolarAbsorbedType   , only : solarabs_type
-  use SurfaceAlbedoType   , only : surfalb_type
-  use OzoneBaseMod        , only : ozone_base_type
-  use LandunitType        , only : lun
-  use PatchType           , only : patch
-  use GridcellType        , only : grc
-  !
-  implicit none
-  private
-  !
-  ! !PRIVATE DATA:
-  integer, parameter, private :: leafresp_mtd_ryan1991  = 1  ! Ryan 1991 method for lmr25top
-  integer, parameter, private :: leafresp_mtd_atkin2015 = 2  ! Atkin 2015 method for lmr25top
-  integer, parameter, private :: sun=1     ! index for sunlit
-  integer, parameter, private :: sha=2     ! index for shaded
-  integer, parameter, private :: xyl=3     ! index for xylem
-  integer, parameter, private :: root=4    ! index for root
-  integer, parameter, private :: veg=0     ! index for vegetation
-  integer, parameter, private :: soil=1    ! index for soil
-  integer, parameter, private :: stomatalcond_mtd_bb1987     = 1   ! Ball-Berry 1987 method for photosynthesis
-  integer, parameter, private :: stomatalcond_mtd_medlyn2011 = 2   ! Medlyn 2011 method for photosynthesis
-  ! !PUBLIC VARIABLES:
-
-  type :: photo_params_type
-     real(r8), allocatable, public  :: krmax              (:)
-     real(r8), allocatable, private :: kmax               (:,:)
-     real(r8), allocatable, private :: psi50              (:,:)
-     real(r8), allocatable, private :: ck                 (:,:)
-     real(r8), allocatable, public  :: psi_soil_ref       (:)
-     real(r8), allocatable, private :: lmr_intercept_atkin(:)
-  contains
-     procedure, private :: allocParams
-  end type photo_params_type
-  !
-  type(photo_params_type), public, protected :: params_inst  ! params_inst is populated in readParamsMod 
-
-  type, public :: photosyns_type
-
-     logical , pointer, private :: c3flag_patch      (:)   ! patch true if C3 and false if C4
-     ! Plant hydraulic stress specific variables
-     real(r8), pointer, private :: ac_phs_patch      (:,:,:) ! patch Rubisco-limited gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: aj_phs_patch      (:,:,:) ! patch RuBP-limited gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: ap_phs_patch      (:,:,:) ! patch product-limited (C3) or CO2-limited (C4) gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: ag_phs_patch      (:,:,:) ! patch co-limited gross leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: an_sun_patch      (:,:)   ! patch sunlit net leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: an_sha_patch      (:,:)   ! patch shaded net leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: vcmax_z_phs_patch (:,:,:) ! patch maximum rate of carboxylation (umol co2/m**2/s)
-     real(r8), pointer, private :: kp_z_phs_patch    (:,:,:) ! patch initial slope of CO2 response curve (C4 plants)
-     real(r8), pointer, private :: tpu_z_phs_patch   (:,:,:) ! patch triose phosphate utilization rate (umol CO2/m**2/s)
-     real(r8), pointer, private :: gs_mol_sun_patch  (:,:) ! patch sunlit leaf stomatal conductance (umol H2O/m**2/s)
-     real(r8), pointer, private :: gs_mol_sha_patch  (:,:) ! patch shaded leaf stomatal conductance (umol H2O/m**2/s)
-
-     real(r8), pointer, private :: ac_patch          (:,:) ! patch Rubisco-limited gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: aj_patch          (:,:) ! patch RuBP-limited gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: ap_patch          (:,:) ! patch product-limited (C3) or CO2-limited (C4) gross photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: ag_patch          (:,:) ! patch co-limited gross leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: an_patch          (:,:) ! patch net leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: vcmax_z_patch     (:,:) ! patch maximum rate of carboxylation (umol co2/m**2/s)
-     real(r8), pointer, private :: cp_patch          (:)   ! patch CO2 compensation point (Pa)
-     real(r8), pointer, private :: kc_patch          (:)   ! patch Michaelis-Menten constant for CO2 (Pa)
-     real(r8), pointer, private :: ko_patch          (:)   ! patch Michaelis-Menten constant for O2 (Pa)
-     real(r8), pointer, private :: qe_patch          (:)   ! patch quantum efficiency, used only for C4 (mol CO2 / mol photons)
-     real(r8), pointer, private :: tpu_z_patch       (:,:) ! patch triose phosphate utilization rate (umol CO2/m**2/s)
-     real(r8), pointer, private :: kp_z_patch        (:,:) ! patch initial slope of CO2 response curve (C4 plants)
-     real(r8), pointer, private :: theta_cj_patch    (:)   ! patch empirical curvature parameter for ac, aj photosynthesis co-limitation
-     real(r8), pointer, private :: bbb_patch         (:)   ! patch Ball-Berry minimum leaf conductance (umol H2O/m**2/s)
-     real(r8), pointer, private :: mbb_patch         (:)   ! patch Ball-Berry slope of conductance-photosynthesis relationship
-     real(r8), pointer, private :: gs_mol_patch      (:,:) ! patch leaf stomatal conductance       (umol H2O/m**2/s)
-     real(r8), pointer, private :: gb_mol_patch      (:)   ! patch leaf boundary layer conductance (umol H2O/m**2/s)
-     real(r8), pointer, private :: rh_leaf_patch     (:)   ! patch fractional humidity at leaf surface (dimensionless)
-
-     real(r8), pointer, private :: alphapsnsun_patch (:)   ! patch sunlit 13c fractionation ([])
-     real(r8), pointer, private :: alphapsnsha_patch (:)   ! patch shaded 13c fractionation ([])
-
-     real(r8), pointer, public  :: psnsun_patch      (:)   ! patch sunlit leaf photosynthesis     (umol CO2/m**2/s)
-     real(r8), pointer, public  :: psnsha_patch      (:)   ! patch shaded leaf photosynthesis     (umol CO2/m**2/s)
-
-     real(r8), pointer, private :: psnsun_z_patch    (:,:) ! patch canopy layer: sunlit leaf photosynthesis   (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsha_z_patch    (:,:) ! patch canopy layer: shaded leaf photosynthesis   (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsun_wc_patch   (:)   ! patch Rubsico-limited sunlit leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsha_wc_patch   (:)   ! patch Rubsico-limited shaded leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsun_wj_patch   (:)   ! patch RuBP-limited sunlit leaf photosynthesis    (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsha_wj_patch   (:)   ! patch RuBP-limited shaded leaf photosynthesis    (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsun_wp_patch   (:)   ! patch product-limited sunlit leaf photosynthesis (umol CO2/m**2/s)
-     real(r8), pointer, private :: psnsha_wp_patch   (:)   ! patch product-limited shaded leaf photosynthesis (umol CO2/m**2/s)
-
-     real(r8), pointer, public  :: fpsn_patch        (:)   ! patch photosynthesis                 (umol CO2/m**2 ground/s)
-     real(r8), pointer, private :: fpsn_wc_patch     (:)   ! patch Rubisco-limited photosynthesis (umol CO2/m**2 ground/s)
-     real(r8), pointer, private :: fpsn_wj_patch     (:)   ! patch RuBP-limited photosynthesis    (umol CO2/m**2 ground/s)
-     real(r8), pointer, private :: fpsn_wp_patch     (:)   ! patch product-limited photosynthesis (umol CO2/m**2 ground/s)
-
-     real(r8), pointer, public  :: lnca_patch        (:)   ! top leaf layer leaf N concentration (gN leaf/m^2)
-
-     real(r8), pointer, public  :: lmrsun_patch      (:)   ! patch sunlit leaf maintenance respiration rate               (umol CO2/m**2/s)
-     real(r8), pointer, public  :: lmrsha_patch      (:)   ! patch shaded leaf maintenance respiration rate               (umol CO2/m**2/s)
-     real(r8), pointer, private :: lmrsun_z_patch    (:,:) ! patch canopy layer: sunlit leaf maintenance respiration rate (umol CO2/m**2/s)
-     real(r8), pointer, private :: lmrsha_z_patch    (:,:) ! patch canopy layer: shaded leaf maintenance respiration rate (umol CO2/m**2/s)
-
-     real(r8), pointer, public  :: cisun_z_patch     (:,:) ! patch intracellular sunlit leaf CO2 (Pa)
-     real(r8), pointer, public  :: cisha_z_patch     (:,:) ! patch intracellular shaded leaf CO2 (Pa)
-
-     real(r8), pointer, private :: rssun_z_patch     (:,:) ! patch canopy layer: sunlit leaf stomatal resistance (s/m)
-     real(r8), pointer, private :: rssha_z_patch     (:,:) ! patch canopy layer: shaded leaf stomatal resistance (s/m)
-     real(r8), pointer, public  :: rssun_patch       (:)   ! patch sunlit stomatal resistance (s/m)
-     real(r8), pointer, public  :: rssha_patch       (:)   ! patch shaded stomatal resistance (s/m)
-     real(r8), pointer, public  :: luvcmax25top_patch (:)   ! vcmax25 !     (umol/m2/s)
-     real(r8), pointer, public  :: lujmax25top_patch  (:)   ! vcmax25 (umol/m2/s)
-     real(r8), pointer, public  :: lutpu25top_patch   (:)   ! vcmax25 (umol/m2/s)
-!!
-
-
-     ! LUNA specific variables
-     real(r8), pointer, public  :: vcmx25_z_patch    (:,:) ! patch  leaf Vc,max25 (umol CO2/m**2/s) for canopy layer 
-     real(r8), pointer, public  :: jmx25_z_patch     (:,:) ! patch  leaf Jmax25 (umol electron/m**2/s) for canopy layer 
-     real(r8), pointer, public  :: pnlc_z_patch      (:,:) ! patch proportion of leaf nitrogen allocated for light capture for canopy layer
-     real(r8), pointer, public  :: enzs_z_patch      (:,:) ! enzyme decay status 1.0-fully active; 0-all decayed during stress
-     real(r8), pointer, public  :: fpsn24_patch      (:)   ! 24 hour mean patch photosynthesis (umol CO2/m**2 ground/day)
-
-     ! Logical switches for different options
-     logical, public  :: rootstem_acc                      ! Respiratory acclimation for roots and stems
-     logical, private :: light_inhibit                     ! If light should inhibit respiration
-     integer, private :: leafresp_method                   ! leaf maintencence respiration at 25C for canopy top method to use
-     integer, private :: stomatalcond_mtd                  ! Stomatal conduction method type
-     logical, private :: modifyphoto_and_lmr_forcrop       ! Modify photosynthesis and LMR for crop
-   contains
-
-     ! Public procedures
-     procedure, public  :: Init
-     procedure, public  :: Restart
-     procedure, public  :: ReadParams
-
-     ! Private procedures
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-
-  end type photosyns_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(photosyns_type) :: this
-    type(bounds_type), intent(in) :: bounds
-
-    call this%InitAllocate (bounds)
-    call this%InitHistory  (bounds)
-    call this%InitCold     (bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(photosyns_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    allocate(this%c3flag_patch      (begp:endp))             ; this%c3flag_patch      (:)     =.false.
-    allocate(this%ac_phs_patch      (begp:endp,2,1:nlevcan)) ; this%ac_phs_patch      (:,:,:) = nan
-    allocate(this%aj_phs_patch      (begp:endp,2,1:nlevcan)) ; this%aj_phs_patch      (:,:,:) = nan
-    allocate(this%ap_phs_patch      (begp:endp,2,1:nlevcan)) ; this%ap_phs_patch      (:,:,:) = nan
-    allocate(this%ag_phs_patch      (begp:endp,2,1:nlevcan)) ; this%ag_phs_patch      (:,:,:) = nan
-    allocate(this%an_sun_patch      (begp:endp,1:nlevcan))   ; this%an_sun_patch      (:,:)   = nan
-    allocate(this%an_sha_patch      (begp:endp,1:nlevcan))   ; this%an_sha_patch      (:,:)   = nan
-    allocate(this%vcmax_z_phs_patch (begp:endp,2,1:nlevcan)) ; this%vcmax_z_phs_patch (:,:,:) = nan
-    allocate(this%tpu_z_phs_patch   (begp:endp,2,1:nlevcan)) ; this%tpu_z_phs_patch   (:,:,:) = nan
-    allocate(this%kp_z_phs_patch    (begp:endp,2,1:nlevcan)) ; this%kp_z_phs_patch    (:,:,:) = nan
-    allocate(this%gs_mol_sun_patch  (begp:endp,1:nlevcan))   ; this%gs_mol_sun_patch  (:,:)   = nan
-    allocate(this%gs_mol_sha_patch  (begp:endp,1:nlevcan))   ; this%gs_mol_sha_patch  (:,:)   = nan
-    allocate(this%ac_patch          (begp:endp,1:nlevcan)) ; this%ac_patch          (:,:) = nan
-    allocate(this%aj_patch          (begp:endp,1:nlevcan)) ; this%aj_patch          (:,:) = nan
-    allocate(this%ap_patch          (begp:endp,1:nlevcan)) ; this%ap_patch          (:,:) = nan
-    allocate(this%ag_patch          (begp:endp,1:nlevcan)) ; this%ag_patch          (:,:) = nan
-    allocate(this%an_patch          (begp:endp,1:nlevcan)) ; this%an_patch          (:,:) = nan
-    allocate(this%vcmax_z_patch     (begp:endp,1:nlevcan)) ; this%vcmax_z_patch     (:,:) = nan
-    allocate(this%tpu_z_patch       (begp:endp,1:nlevcan)) ; this%tpu_z_patch       (:,:) = nan
-    allocate(this%kp_z_patch        (begp:endp,1:nlevcan)) ; this%kp_z_patch        (:,:) = nan
-    allocate(this%gs_mol_patch      (begp:endp,1:nlevcan)) ; this%gs_mol_patch      (:,:) = nan
-    allocate(this%cp_patch          (begp:endp))           ; this%cp_patch          (:)   = nan
-    allocate(this%kc_patch          (begp:endp))           ; this%kc_patch          (:)   = nan
-    allocate(this%ko_patch          (begp:endp))           ; this%ko_patch          (:)   = nan
-    allocate(this%qe_patch          (begp:endp))           ; this%qe_patch          (:)   = nan
-    allocate(this%theta_cj_patch    (begp:endp))           ; this%theta_cj_patch    (:)   = nan
-    allocate(this%bbb_patch         (begp:endp))           ; this%bbb_patch         (:)   = nan
-    allocate(this%mbb_patch         (begp:endp))           ; this%mbb_patch         (:)   = nan
-    allocate(this%gb_mol_patch      (begp:endp))           ; this%gb_mol_patch      (:)   = nan
-    allocate(this%rh_leaf_patch     (begp:endp))           ; this%rh_leaf_patch     (:)   = nan
-
-    allocate(this%psnsun_patch      (begp:endp))           ; this%psnsun_patch      (:)   = nan
-    allocate(this%psnsha_patch      (begp:endp))           ; this%psnsha_patch      (:)   = nan
-
-    allocate(this%psnsun_z_patch    (begp:endp,1:nlevcan)) ; this%psnsun_z_patch    (:,:) = nan
-    allocate(this%psnsha_z_patch    (begp:endp,1:nlevcan)) ; this%psnsha_z_patch    (:,:) = nan
-    allocate(this%psnsun_wc_patch   (begp:endp))           ; this%psnsun_wc_patch   (:)   = nan
-    allocate(this%psnsha_wc_patch   (begp:endp))           ; this%psnsha_wc_patch   (:)   = nan
-    allocate(this%psnsun_wj_patch   (begp:endp))           ; this%psnsun_wj_patch   (:)   = nan
-    allocate(this%psnsha_wj_patch   (begp:endp))           ; this%psnsha_wj_patch   (:)   = nan
-    allocate(this%psnsun_wp_patch   (begp:endp))           ; this%psnsun_wp_patch   (:)   = nan
-    allocate(this%psnsha_wp_patch   (begp:endp))           ; this%psnsha_wp_patch   (:)   = nan
-    allocate(this%fpsn_patch        (begp:endp))           ; this%fpsn_patch        (:)   = nan
-    allocate(this%fpsn_wc_patch     (begp:endp))           ; this%fpsn_wc_patch     (:)   = nan
-    allocate(this%fpsn_wj_patch     (begp:endp))           ; this%fpsn_wj_patch     (:)   = nan
-    allocate(this%fpsn_wp_patch     (begp:endp))           ; this%fpsn_wp_patch     (:)   = nan
-    
-    allocate(this%lnca_patch        (begp:endp))           ; this%lnca_patch        (:)   = nan
-
-    allocate(this%lmrsun_z_patch    (begp:endp,1:nlevcan)) ; this%lmrsun_z_patch    (:,:) = nan
-    allocate(this%lmrsha_z_patch    (begp:endp,1:nlevcan)) ; this%lmrsha_z_patch    (:,:) = nan
-    allocate(this%lmrsun_patch      (begp:endp))           ; this%lmrsun_patch      (:)   = nan
-    allocate(this%lmrsha_patch      (begp:endp))           ; this%lmrsha_patch      (:)   = nan
-
-    allocate(this%alphapsnsun_patch (begp:endp))           ; this%alphapsnsun_patch (:)   = nan
-    allocate(this%alphapsnsha_patch (begp:endp))           ; this%alphapsnsha_patch (:)   = nan
-
-    allocate(this%cisun_z_patch     (begp:endp,1:nlevcan)) ; this%cisun_z_patch     (:,:) = nan
-    allocate(this%cisha_z_patch     (begp:endp,1:nlevcan)) ; this%cisha_z_patch     (:,:) = nan
-
-    allocate(this%rssun_z_patch     (begp:endp,1:nlevcan)) ; this%rssun_z_patch     (:,:) = nan
-    allocate(this%rssha_z_patch     (begp:endp,1:nlevcan)) ; this%rssha_z_patch     (:,:) = nan
-    allocate(this%rssun_patch       (begp:endp))           ; this%rssun_patch       (:)   = nan
-    allocate(this%rssha_patch       (begp:endp))           ; this%rssha_patch       (:)   = nan
-    allocate(this%luvcmax25top_patch(begp:endp))           ; this%luvcmax25top_patch(:) = nan
-    allocate(this%lujmax25top_patch (begp:endp))           ; this%lujmax25top_patch(:)  = nan
-    allocate(this%lutpu25top_patch  (begp:endp))           ; this%lutpu25top_patch(:)   = nan
-!!
-!    allocate(this%psncanopy_patch   (begp:endp))           ; this%psncanopy_patch   (:)   = nan
-!    allocate(this%lmrcanopy_patch   (begp:endp))           ; this%lmrcanopy_patch   (:)   = nan
-    if(use_luna)then
-      ! NOTE(bja, 2015-09) because these variables are only allocated
-      ! when luna is turned on, they can not be placed into associate
-      ! statements.
-      allocate(this%vcmx25_z_patch  (begp:endp,1:nlevcan)) ; this%vcmx25_z_patch    (:,:) = 30._r8
-      allocate(this%jmx25_z_patch   (begp:endp,1:nlevcan)) ; this%jmx25_z_patch     (:,:) = 60._r8 
-      allocate(this%pnlc_z_patch    (begp:endp,1:nlevcan)) ; this%pnlc_z_patch      (:,:) = 0.01_r8
-      allocate(this%fpsn24_patch    (begp:endp))           ; this%fpsn24_patch      (:)   = nan
-      allocate(this%enzs_z_patch    (begp:endp,1:nlevcan)) ; this%enzs_z_patch      (:,:) = 1._r8
-    endif
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(photosyns_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    real(r8), pointer  :: ptr_1d(:)  ! pointer to 1d patch array
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-
-    this%rh_leaf_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RH_LEAF', units='fraction', &
-         avgflag='A', long_name='fractional humidity at leaf surface', &
-         ptr_patch=this%rh_leaf_patch, set_spec=spval, default='inactive')
-    this%lnca_patch(begp:endp) = spval
-    call hist_addfld1d (fname='LNC', units='gN leaf/m^2', &
-         avgflag='A', long_name='leaf N concentration', &
-         ptr_patch=this%lnca_patch, set_spec=spval, default='inactive')
-
-    ! Don't output photosynthesis variables when FATES is on as they aren't calculated
-    if (.not. use_fates) then
-       this%fpsn_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FPSN', units='umol/m2s',  &
-            avgflag='A', long_name='photosynthesis', &
-            ptr_patch=this%fpsn_patch, set_lake=0._r8, set_urb=0._r8, default='inactive')
-
-       ! Don't by default output this rate limiting step as only makes sense if you are outputing
-       ! the others each time-step
-       this%fpsn_wc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FPSN_WC', units='umol/m2s',  &
-            avgflag='I', long_name='Rubisco-limited photosynthesis', &
-            ptr_patch=this%fpsn_wc_patch, set_lake=0._r8, set_urb=0._r8, &
-            default='inactive')
-
-       ! Don't by default output this rate limiting step as only makes sense if you are outputing
-       ! the others each time-step
-       this%fpsn_wj_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FPSN_WJ', units='umol/m2s',  &
-            avgflag='I', long_name='RuBP-limited photosynthesis', &
-            ptr_patch=this%fpsn_wj_patch, set_lake=0._r8, set_urb=0._r8, &
-            default='inactive')
-
-       ! Don't by default output this rate limiting step as only makes sense if you are outputing
-       ! the others each time-step
-       this%fpsn_wp_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FPSN_WP', units='umol/m2s',  &
-            avgflag='I', long_name='Product-limited photosynthesis', &
-            ptr_patch=this%fpsn_wp_patch, set_lake=0._r8, set_urb=0._r8, &
-            default='inactive')
-    end if
-
-    if (use_cn) then
-       this%psnsun_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PSNSUN', units='umolCO2/m^2/s', &
-            avgflag='A', long_name='sunlit leaf photosynthesis', &
-            ptr_patch=this%psnsun_patch, default='inactive')
-
-       this%psnsha_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PSNSHA', units='umolCO2/m^2/s', &
-            avgflag='A', long_name='shaded leaf photosynthesis', &
-            ptr_patch=this%psnsha_patch, default='inactive')
-    end if
-
-    this%rssun_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RSSUN', units='s/m',  &
-         avgflag='M', long_name='sunlit leaf stomatal resistance', &
-         ptr_patch=this%rssun_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-    this%rssha_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RSSHA', units='s/m',  &
-         avgflag='M', long_name='shaded leaf stomatal resistance', &
-         ptr_patch=this%rssha_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-    this%gs_mol_sun_patch(begp:endp,:) = spval
-    this%gs_mol_sha_patch(begp:endp,:) = spval
-    if (nlevcan>1) then 
-       call hist_addfld2d (fname='GSSUN', units='umol H20/m2/s', type2d='nlevcan', &
-          avgflag='A', long_name='sunlit leaf stomatal conductance', &
-          ptr_patch=this%gs_mol_sun_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-       call hist_addfld2d (fname='GSSHA', units='umol H20/m2/s', type2d='nlevcan', &
-          avgflag='A', long_name='shaded leaf stomatal conductance', &
-          ptr_patch=this%gs_mol_sha_patch, set_lake=spval, set_urb=spval, default='inactive')
-    else
-       ptr_1d => this%gs_mol_sun_patch(begp:endp,1)
-       call hist_addfld1d (fname='GSSUN', units='umol H20/m2/s', &
-          avgflag='A', long_name='sunlit leaf stomatal conductance', &
-          ptr_patch=ptr_1d, default='inactive')
-
-       ptr_1d => this%gs_mol_sha_patch(begp:endp,1)
-       call hist_addfld1d (fname='GSSHA', units='umol H20/m2/s', &
-          avgflag='A', long_name='shaded leaf stomatal conductance', &
-          ptr_patch=ptr_1d, default='inactive')
-
-    endif
-
-    if(use_luna)then  
-       if(nlevcan>1)then
-         call hist_addfld2d (fname='Vcmx25Z', units='umol/m2/s', type2d='nlevcan', &
-            avgflag='A', long_name='canopy profile of vcmax25 predicted by LUNA model', &
-            ptr_patch=this%vcmx25_z_patch, default='inactive')
- 
-         call hist_addfld2d (fname='Jmx25Z', units='umol/m2/s', type2d='nlevcan', &
-            avgflag='A', long_name='canopy profile of  vcmax25 predicted by LUNA model', &
-            ptr_patch=this%jmx25_z_patch, default='inactive')
-
-         call hist_addfld2d (fname='PNLCZ', units='unitless', type2d='nlevcan', &
-            avgflag='A', long_name='Proportion of nitrogen allocated for light capture', &
-            ptr_patch=this%pnlc_z_patch,default='inactive')
-       else
-         ptr_1d => this%vcmx25_z_patch(:,1)
-         call hist_addfld1d (fname='Vcmx25Z', units='umol/m2/s',&
-            avgflag='A', long_name='canopy profile of vcmax25 predicted by LUNA model', &
-            ptr_patch=ptr_1d, default='inactive')
-         ptr_1d => this%jmx25_z_patch(:,1)
-         call hist_addfld1d (fname='Jmx25Z', units='umol/m2/s',&
-            avgflag='A', long_name='canopy profile of  vcmax25 predicted by LUNA model', &
-            ptr_patch=ptr_1d, default='inactive')
-         ptr_1d => this%pnlc_z_patch(:,1)
-         call hist_addfld1d (fname='PNLCZ', units='unitless', &
-            avgflag='A', long_name='Proportion of nitrogen allocated for light capture', &
-            ptr_patch=ptr_1d,default='inactive')
-
-         this%luvcmax25top_patch(begp:endp) = spval
-         call hist_addfld1d (fname='VCMX25T', units='umol/m2/s',  &
-            avgflag='M', long_name='canopy profile of vcmax25', &
-            ptr_patch=this%luvcmax25top_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-         this%lujmax25top_patch(begp:endp) = spval
-         call hist_addfld1d (fname='JMX25T', units='umol/m2/s',  &
-            avgflag='M', long_name='canopy profile of jmax', &
-            ptr_patch=this%lujmax25top_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-            this%lutpu25top_patch(begp:endp) = spval
-            call hist_addfld1d (fname='TPU25T', units='umol/m2/s',  &
-            avgflag='M', long_name='canopy profile of tpu', &
-            ptr_patch=this%lutpu25top_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-       endif
-       this%fpsn24_patch = spval 
-       call hist_addfld1d (fname='FPSN24', units='umol CO2/m**2 ground/day',&
-           avgflag='A', long_name='24 hour accumulative patch photosynthesis starting from mid-night', &
-           ptr_patch=this%fpsn24_patch, default='inactive')
-   
-    endif
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(photosyns_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,l                        ! indices
-    !-----------------------------------------------------------------------
-
-    do p = bounds%begp,bounds%endp
-       l = patch%landunit(p)
-
-       this%alphapsnsun_patch(p) = spval
-       this%alphapsnsha_patch(p) = spval
-
-       if (lun%ifspecial(l)) then
-          this%psnsun_patch(p) = 0._r8
-          this%psnsha_patch(p) = 0._r8
-       end if
-    end do
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine allocParams ( this )
-    !
-    implicit none
-
-    ! !ARGUMENTS:
-    class(photo_params_type) :: this
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'allocParams'
-    !-----------------------------------------------------------------------
-
-    ! allocate parameters
-
-    allocate( this%krmax       (0:mxpft) )          ; this%krmax(:)        = nan
-    allocate( this%kmax        (0:mxpft,nvegwcs) )  ; this%kmax(:,:)       = nan
-    allocate( this%psi50       (0:mxpft,nvegwcs) )  ; this%psi50(:,:)      = nan
-    allocate( this%ck          (0:mxpft,nvegwcs) )  ; this%ck(:,:)         = nan
-    allocate( this%psi_soil_ref(0:mxpft) )          ; this%psi_soil_ref(:) = nan
-
-    if ( use_hydrstress .and. nvegwcs /= 4 )then
-       call endrun(msg='Error:: the Plant Hydraulics Stress methodology is for the spacA function is hardcoded for nvegwcs==4' &
-                   //errMsg(__FILE__, __LINE__))
-    end if
-
-  end subroutine allocParams
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( this, ncid )
-    !
-    ! !USES:
-    use ncdio_pio , only : file_desc_t,ncd_io
-    implicit none
-
-    ! !ARGUMENTS:
-    class(photosyns_type) :: this
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'readParams'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: temp1d(0:mxpft) ! temporary to read in parameter
-    real(r8)           :: temp2d(0:mxpft,nvegwcs) ! temporary to read in parameter
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    ! read in parameters
-
-
-    call params_inst%allocParams()
-
-    tString = "krmax"
-    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%krmax=temp1d
-    tString = "psi_soil_ref"
-    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%psi_soil_ref=temp1d
-    tString = "lmr_intercept_atkin"
-    call ncd_io(varname=trim(tString),data=temp1d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%lmr_intercept_atkin=temp1d
-    tString = "kmax"
-    call ncd_io(varname=trim(tString),data=temp2d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%kmax=temp2d
-    tString = "psi50"
-    call ncd_io(varname=trim(tString),data=temp2d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%psi50=temp2d
-    tString = "ck"
-    call ncd_io(varname=trim(tString),data=temp2d, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%ck=temp2d
-
-  end subroutine readParams
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(photosyns_type) :: this
-    type(bounds_type), intent(in)    :: bounds
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    !-----------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='GSSUN', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='sunlit leaf stomatal conductance', units='umol H20/m2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%gs_mol_sun_patch)
-    
-    call restartvar(ncid=ncid, flag=flag, varname='GSSHA', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='shaded leaf stomatal conductance', units='umol H20/m2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%gs_mol_sha_patch)
-    
-    call restartvar(ncid=ncid, flag=flag, varname='lnca', xtype=ncd_double,  &
-       dim1name='pft', long_name='leaf N concentration', units='gN leaf/m^2', &
-       interpinic_flag='interp', readvar=readvar, data=this%lnca_patch)
-
-    if(use_luna) then
-      call restartvar(ncid=ncid, flag=flag, varname='vcmx25_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Maximum carboxylation rate at 25 celcius for canopy layers', units='umol CO2/m**2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%vcmx25_z_patch)
-      call restartvar(ncid=ncid, flag=flag, varname='jmx25_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Maximum carboxylation rate at 25 celcius for canopy layers', units='umol CO2/m**2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%jmx25_z_patch)
-      call restartvar(ncid=ncid, flag=flag, varname='pnlc_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='proportion of leaf nitrogen allocated for light capture', units='unitless', &
-         interpinic_flag='interp', readvar=readvar, data=this%pnlc_z_patch )
-      call restartvar(ncid=ncid, flag=flag, varname='enzs_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='enzyme decay status during stress: 1.0-fully active; 0.0-all decayed', units='unitless', &
-         interpinic_flag='interp', readvar=readvar, data=this%enzs_z_patch )
-      call restartvar(ncid=ncid, flag=flag, varname='gpp24', xtype=ncd_double,  &
-            dim1name='pft', long_name='accumulative gross primary production', units='umol CO2/m**2 ground/day', &
-            interpinic_flag='interp', readvar=readvar, data=this%fpsn24_patch)    
-   endif
-   call restartvar(ncid=ncid, flag=flag, varname='vcmx25t', xtype=ncd_double,  &
-         dim1name='pft', long_name='canopy profile of vcmax25', &
-         units='umol/m2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%luvcmax25top_patch)    
-
-   call restartvar(ncid=ncid, flag=flag, varname='jmx25t', xtype=ncd_double,  &
-         dim1name='pft', long_name='canopy profile of jmax', &
-         units='umol/m2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%lujmax25top_patch)    
-
-   call restartvar(ncid=ncid, flag=flag, varname='tpu25t', xtype=ncd_double,  &
-         dim1name='pft', long_name='canopy profile of tpu', &
-         units='umol/m2/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%lutpu25top_patch)    
-
-  end subroutine Restart
-
-end module PhotosynthesisMod
diff --git a/src/biogeophys/QSatMod.F90 b/src/biogeophys/QSatMod.F90
index 0b1819e467..76d1a40689 100644
--- a/src/biogeophys/QSatMod.F90
+++ b/src/biogeophys/QSatMod.F90
@@ -12,7 +12,6 @@ module QSatMod
   !
   ! !PUBLIC MEMBER FUNCTIONS:
   public :: QSat
-  public :: rhoSat
   !-----------------------------------------------------------------------
 
     ! For water vapor (temperature range 0C-100C)
@@ -123,45 +122,4 @@ subroutine QSat (T, p, es, esdT, qs, qsdT)
 
   end subroutine QSat
 
-
-  
-!-------------------------------------------------------------------------------
-  subroutine rhoSat(T, rho, rhodT)
-  ! compute the saturated vapor pressure density and its derivative against the temperature
-  ! jyt
-  use clm_varcon,    only: rwat
-  use shr_const_mod, only: SHR_CONST_TKFRZ
-
-  implicit none
-  real(r8), intent(in) :: T
-  real(r8), intent(out) :: rho
-  real(r8), optional, intent(out) :: rhodT
-    
-
-  !------------------
-    
-  real(r8) :: T_limit
-  real(r8) :: td, es, esdT
-  
-  T_limit = T - SHR_CONST_TKFRZ
-  if (T_limit > 100.0_r8) T_limit=100.0_r8
-  if (T_limit < -75.0_r8) T_limit=-75.0_r8
-
-  td       = T_limit
-  if (td >= 0.0_r8) then
-    es   = a0 + td*(a1 + td*(a2 + td*(a3 + td*(a4 &
-            + td*(a5 + td*(a6 + td*(a7 + td*a8)))))))
-    esdT = b0 + td*(b1 + td*(b2 + td*(b3 + td*(b4 &
-            + td*(b5 + td*(b6 + td*(b7 + td*b8)))))))
-  else
-    es   = c0 + td*(c1 + td*(c2 + td*(c3 + td*(c4 &
-            + td*(c5 + td*(c6 + td*(c7 + td*c8)))))))
-    esdT = d0 + td*(d1 + td*(d2 + td*(d3 + td*(d4 &
-            + td*(d5 + td*(d6 + td*(d7 + td*d8)))))))
-  endif
-
-  es    = es    * 100._r8            ! pa
-  rho   = es/(rwat*T)                !kg  m^-3
-  if(present(rhodT))rhodT= esdT/(rwat*T)-rho/T         !kg  m^-3 K^-1
-  end subroutine rhoSat  
 end module QSatMod
diff --git a/src/biogeophys/RootBiophysMod.F90 b/src/biogeophys/RootBiophysMod.F90
deleted file mode 100644
index ba05705614..0000000000
--- a/src/biogeophys/RootBiophysMod.F90
+++ /dev/null
@@ -1,332 +0,0 @@
-module RootBiophysMod
-
-#include "shr_assert.h"
-
-  !-------------------------------------------------------------------------------------- 
-  ! DESCRIPTION:
-  ! module contains subroutine for root biophysics
-  !
-  ! HISTORY
-  ! created by Jinyun Tang, Mar 1st, 2014
-  implicit none
-  private
-  !
-  public  :: init_vegrootfr
-  public  :: init_rootprof
-
-  integer, private, parameter :: zeng_2001_root    = 0 !the zeng 2001 root profile function
-  integer, private, parameter :: jackson_1996_root = 1 !the jackson 1996 root profile function
-  integer, private, parameter :: koven_exp_root    = 2 !the koven exponential root profile function
-
-  integer, public :: rooting_profile_method_water     !select the type of rooting profile parameterization for water  
-  integer, public :: rooting_profile_method_carbon    !select the type of rooting profile parameterization for carbon   
-  integer, public :: rooting_profile_varindex_water   !select the variant number of rooting profile parameterization for water  
-  integer, public :: rooting_profile_varindex_carbon  !select the variant number of rooting profile parameterization for carbon   
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !-------------------------------------------------------------------------------------- 
-
-contains
-
-  !-------------------------------------------------------------------------------------- 
-  subroutine init_rootprof(NLFilename)
-    !
-    !DESCRIPTION
-    ! initialize methods for root profile calculation
-
-    ! !USES:
-    use abortutils      , only : endrun   
-    use fileutils       , only : getavu, relavu
-    use spmdMod         , only : mpicom, masterproc
-    use shr_mpi_mod     , only : shr_mpi_bcast
-    use clm_varctl      , only : iulog
-    use clm_nlUtilsMod  , only : find_nlgroup_name
-
-    ! !ARGUMENTS:
-    !------------------------------------------------------------------------------
-    implicit none
-    character(len=*), intent(in) :: NLFilename
-
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    character(*), parameter    :: subName = "('init_rootprof')"
-
-    !-----------------------------------------------------------------------
-
-! MUST agree with name in namelist and read statement
-    namelist /rooting_profile_inparm/ rooting_profile_method_water, rooting_profile_method_carbon, &
-                                      rooting_profile_varindex_water, rooting_profile_varindex_carbon
-
-    ! Default values for namelist
-
-    rooting_profile_method_water    = zeng_2001_root
-    rooting_profile_method_carbon   = zeng_2001_root
-    rooting_profile_varindex_water  = 1
-    rooting_profile_varindex_carbon = 2
-
-    ! Read rooting_profile namelist
-    if (masterproc) then
-       nu_nml = getavu()
-       open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'rooting_profile_inparm', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=rooting_profile_inparm,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading rooting_profile namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR finding rooting_profile namelist')
-       end if
-       close(nu_nml)
-       call relavu( nu_nml )
-
-    endif
-
-    call shr_mpi_bcast(rooting_profile_method_water,    mpicom)
-    call shr_mpi_bcast(rooting_profile_method_carbon,   mpicom)
-    call shr_mpi_bcast(rooting_profile_varindex_water,  mpicom)
-    call shr_mpi_bcast(rooting_profile_varindex_carbon, mpicom)
-
-    if (masterproc) then
-
-       write(iulog,*) ' '
-       write(iulog,*) 'rooting_profile settings:'
-       write(iulog,*) '  rooting_profile_method_water  = ',rooting_profile_method_water
-       if ( rooting_profile_method_water == jackson_1996_root )then
-          write(iulog,*) '  (rooting_profile_varindex_water  = ',rooting_profile_varindex_water, ')'
-       end if
-       write(iulog,*) '  rooting_profile_method_carbon = ',rooting_profile_method_carbon
-       if ( rooting_profile_method_carbon == jackson_1996_root )then
-          write(iulog,*) '  (rooting_profile_varindex_carbon  = ',rooting_profile_varindex_carbon, ')'
-       end if
-
-    endif
-
-  end subroutine init_rootprof
-
-  !-------------------------------------------------------------------------------------- 
-  subroutine init_vegrootfr(bounds, nlevsoi, nlevgrnd, rootfr, water_carbon)
-    !
-    !DESCRIPTION
-    !initialize plant root profiles
-    !
-    ! USES
-    use shr_kind_mod   , only : r8 => shr_kind_r8   
-    use shr_assert_mod , only : shr_assert
-    use shr_log_mod    , only : errMsg => shr_log_errMsg
-    use decompMod      , only : bounds_type
-    use abortutils     , only : endrun         
-    use ColumnType            , only : col                
-    use PatchType             , only : patch                
-        !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds                     ! bounds
-    integer,           intent(in) :: nlevsoi                    ! number of hydactive layers
-    integer,           intent(in) :: nlevgrnd                   ! number of soil layers
-    real(r8),          intent(out):: rootfr(bounds%begp: , 1: ) ! root fraction by layer
-    character(len=*),  intent(in) :: water_carbon               ! roots for water or carbon
-
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32) :: subname = 'init_vegrootfr'  ! subroutine name
-    integer           :: c,p
-    integer           :: rooting_profile_method      ! Rooting profile method to use
-    integer           :: rooting_profile_varidx      ! Rooting profile variant index to use
-    !------------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(rootfr) == (/bounds%endp, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-
-    if (     water_carbon == 'water' ) then 
-       rooting_profile_method = rooting_profile_method_water
-       rooting_profile_varidx = rooting_profile_varindex_water
-    else if (water_carbon == 'carbon') then
-       rooting_profile_method = rooting_profile_method_carbon
-       rooting_profile_varidx = rooting_profile_varindex_carbon
-    else
-       call endrun(subname // ':: input type can only be water or carbon = '//water_carbon )
-    end if
- 
-    select case( rooting_profile_method )
-
-    case (zeng_2001_root)
-       rootfr(bounds%begp:bounds%endp, 1 : nlevsoi) = zeng2001_rootfr(bounds, nlevsoi)
-    case (jackson_1996_root)
-       rootfr(bounds%begp:bounds%endp, 1 : nlevsoi) = jackson1996_rootfr(bounds, nlevsoi, rooting_profile_varidx, water_carbon)
-    case (koven_exp_root)
-       rootfr(bounds%begp:bounds%endp, 1 : nlevsoi) = exponential_rootfr(bounds, nlevsoi)
-    case default
-       call endrun(subname // ':: a root fraction function must be specified!')   
-    end select
-    rootfr(bounds%begp:bounds%endp,nlevsoi+1:nlevgrnd)=0._r8   
-
-    ! shift roots up above bedrock boundary (distribute equally to each layer)
-    ! may not matter if normalized later
-    do p = bounds%begp,bounds%endp   
-       c = patch%column(p)
-       rootfr(p,1:col%nbedrock(c)) = rootfr(p,1:col%nbedrock(c)) &
-            + sum(rootfr(p,col%nbedrock(c)+1:nlevsoi))/real(col%nbedrock(c))
-       rootfr(p,col%nbedrock(c)+1:nlevsoi) = 0._r8
-    enddo
-  end subroutine init_vegrootfr
-
-  !-------------------------------------------------------------------------   
-  function zeng2001_rootfr(bounds, ubj) result(rootfr)
-    !
-    ! DESCRIPTION
-    ! compute root profile for soil water uptake
-    ! using equation from Zeng 2001, J. Hydrometeorology
-    !
-    ! USES
-    use shr_kind_mod   , only : r8 => shr_kind_r8   
-    use shr_assert_mod , only : shr_assert
-    use shr_log_mod    , only : errMsg => shr_log_errMsg   
-    use decompMod      , only : bounds_type
-    use pftconMod      , only : pftcon
-    use PatchType      , only : patch
-    use ColumnType     , only : col
-    !
-    ! !ARGUMENTS:
-    type(bounds_type) , intent(in)    :: bounds                  ! bounds
-    integer           , intent(in)    :: ubj                     ! ubnd
-    !
-    ! !RESULT
-    real(r8) :: rootfr(bounds%begp:bounds%endp , 1:ubj ) !
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p, lev, c
-    !------------------------------------------------------------------------
-
-    !(computing from surface, d is depth in meter):
-    ! Y = 1 -1/2 (exp(-ad)+exp(-bd) under the constraint that
-    ! Y(d =0.1m) = 1-beta^(10 cm) and Y(d=d_obs)=0.99 with
-    ! beta & d_obs given in Zeng et al. (1998).   
-
-    do p = bounds%begp,bounds%endp   
-
-       if (.not. patch%is_fates(p)) then
-          c = patch%column(p)
-          do lev = 1, ubj-1
-             rootfr(p,lev) = .5_r8*( &
-                    exp(-pftcon%roota_par(patch%itype(p)) * col%zi(c,lev-1))  &
-                  + exp(-pftcon%rootb_par(patch%itype(p)) * col%zi(c,lev-1))  &
-                  - exp(-pftcon%roota_par(patch%itype(p)) * col%zi(c,lev  ))  &
-                  - exp(-pftcon%rootb_par(patch%itype(p)) * col%zi(c,lev  )) )
-          end do
-          rootfr(p,ubj) = .5_r8*( &
-                 exp(-pftcon%roota_par(patch%itype(p)) * col%zi(c,ubj-1))  &
-               + exp(-pftcon%rootb_par(patch%itype(p)) * col%zi(c,ubj-1)) )
-
-       else
-          rootfr(p,1:ubj) = 0._r8
-       endif
-
-    enddo
-    return
-
-  end function zeng2001_rootfr
-
-  !-------------------------------------------------------------------------   
-  function jackson1996_rootfr(bounds, ubj, varindx, water_carbon) result(rootfr)
-    !
-    ! DESCRIPTION
-    ! compute root profile for soil water uptake
-    ! using equation from Jackson et al. 1996, Oec.
-    !
-    ! USES
-    use shr_kind_mod   , only : r8 => shr_kind_r8   
-    use shr_assert_mod , only : shr_assert
-    use shr_log_mod    , only : errMsg => shr_log_errMsg   
-    use decompMod      , only : bounds_type
-    use pftconMod      , only : pftcon
-    use PatchType      , only : patch
-    use ColumnType     , only : col
-    !
-    ! !ARGUMENTS:
-    type(bounds_type) , intent(in)    :: bounds                  ! bounds
-    integer           , intent(in)    :: ubj                     ! ubnd
-    integer           , intent(in)    :: varindx                 ! variant index
-    character(len=*)  , intent(in)    :: water_carbon            ! roots for water or carbon
-    !
-    ! !RESULT
-    real(r8) :: rootfr(bounds%begp:bounds%endp , 1:ubj ) !
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), parameter :: m_to_cm = 1.e2_r8
-    real(r8) :: beta !patch specific shape parameter
-    integer :: p, lev, c
-    !------------------------------------------------------------------------
-
-    !(computing from surface, d is depth in centimeters):
-    ! Y = (1 - beta^d); beta given in Jackson et al. (1996).   
-
-    rootfr(bounds%begp:bounds%endp, :)     = 0._r8
-    do p = bounds%begp,bounds%endp   
-       c = patch%column(p)       
-       if (.not.patch%is_fates(p)) then
-          beta = pftcon%rootprof_beta(patch%itype(p),varindx)
-          do lev = 1, ubj
-             rootfr(p,lev) = ( &
-                  beta ** (col%zi(c,lev-1)*m_to_cm) - &
-                  beta ** (col%zi(c,lev)*m_to_cm) )
-          end do
-       else
-          rootfr(p,:) = 0.
-       endif
-       
-    enddo
-    return
-
-  end function jackson1996_rootfr
-
-  !-------------------------------------------------------------------------   
-  function exponential_rootfr(bounds, ubj) result(rootfr)
-    !
-    ! DESCRIPTION
-    ! compute root profile for soil water uptake
-    ! using equation from Koven
-    !
-    ! USES
-    use shr_kind_mod   , only : r8 => shr_kind_r8   
-    use shr_assert_mod , only : shr_assert
-    use shr_log_mod    , only : errMsg => shr_log_errMsg   
-    use decompMod      , only : bounds_type
-    use pftconMod      , only : pftcon
-    use PatchType      , only : patch
-    use ColumnType     , only : col
-    !
-    ! !ARGUMENTS:
-    type(bounds_type) , intent(in)    :: bounds                  ! bounds
-    integer           , intent(in)    :: ubj                     ! ubnd
-    !
-    ! !RESULT
-    real(r8) :: rootfr(bounds%begp:bounds%endp , 1:ubj ) !
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), parameter :: rootprof_exp  = 3.  ! how steep profile is for root C inputs (1/ e-folding depth) (1/m)      
-    real(r8) :: norm
-    integer :: p, lev, c
-
-    !------------------------------------------------------------------------
-
-    rootfr(bounds%begp:bounds%endp, :)     = 0._r8
-    do p = bounds%begp,bounds%endp   
-       c = patch%column(p)
-       if (.not.patch%is_fates(p)) then
-          do lev = 1, ubj
-             rootfr(p,lev) = exp(-rootprof_exp * col%z(c,lev)) * col%dz(c,lev)
-          end do
-       else
-          rootfr(p,1) = 0.
-       endif
-       norm = -1./rootprof_exp * (exp(-rootprof_exp * col%z(c,ubj)) - 1._r8)
-       rootfr(p,:) = rootfr(p,:) / norm
-
-    enddo
-
-    return
-
-  end function exponential_rootfr
-  
-end module RootBiophysMod
diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90
deleted file mode 100644
index fe731e5195..0000000000
--- a/src/biogeophys/SnowSnicarMod.F90
+++ /dev/null
@@ -1,300 +0,0 @@
-module SnowSnicarMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculate albedo of snow containing impurities 
-  ! and the evolution of snow effective radius
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_sys_mod     , only : shr_sys_flush
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use clm_varctl      , only : iulog
-  use clm_varcon      , only : namec , tfrz
-  use shr_const_mod   , only : SHR_CONST_RHOICE
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type
-  use AerosolMod      , only : snw_rds_min
-  !
-  implicit none
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: SnowAge_init     ! Initial read in of snow-aging file
-  public :: SnowOptics_init  ! Initial read in of snow-optics file
-  !
-  ! !PUBLIC DATA MEMBERS:
-  integer,  public, parameter :: sno_nbr_aer =   8        ! number of aerosol species in snowpack
-                                                          ! (indices described above) [nbr]
-  logical,  public, parameter :: DO_SNO_OC =    .false.   ! parameter to include organic carbon (OC)
-                                                          ! in snowpack radiative calculations
-  logical,  public, parameter :: DO_SNO_AER =   .true.    ! parameter to include aerosols in snowpack radiative calculations
-
-  ! !PRIVATE DATA MEMBERS:
-  integer,  parameter :: numrad_snw  =   5               ! number of spectral bands used in snow model [nbr]
-  integer,  parameter :: nir_bnd_bgn =   2               ! first band index in near-IR spectrum [idx]
-  integer,  parameter :: nir_bnd_end =   5               ! ending near-IR band index [idx]
-
-  integer,  parameter :: idx_Mie_snw_mx = 1471           ! number of effective radius indices used in Mie lookup table [idx]
-  integer,  parameter :: idx_T_max      = 11             ! maxiumum temperature index used in aging lookup table [idx]
-  integer,  parameter :: idx_T_min      = 1              ! minimum temperature index used in aging lookup table [idx]
-  integer,  parameter :: idx_Tgrd_max   = 31             ! maxiumum temperature gradient index used in aging lookup table [idx]
-  integer,  parameter :: idx_Tgrd_min   = 1              ! minimum temperature gradient index used in aging lookup table [idx]
-  integer,  parameter :: idx_rhos_max   = 8              ! maxiumum snow density index used in aging lookup table [idx]
-  integer,  parameter :: idx_rhos_min   = 1              ! minimum snow density index used in aging lookup table [idx]
-
-  integer,  parameter :: snw_rds_max_tbl = 1500          ! maximum effective radius defined in Mie lookup table [microns]
-  integer,  parameter :: snw_rds_min_tbl = 30            ! minimium effective radius defined in Mie lookup table [microns]
-  integer,  parameter :: snw_rds_min_int = nint(snw_rds_min) ! minimum allowed snow effective radius as integer [microns]
-  real(r8), parameter :: snw_rds_max     = 1500._r8      ! maximum allowed snow effective radius [microns]
-  real(r8), parameter :: snw_rds_refrz   = 1000._r8      ! effective radius of re-frozen snow [microns]
-
-  real(r8), parameter :: min_snw = 1.0E-30_r8            ! minimum snow mass required for SNICAR RT calculation [kg m-2]
-
-  !real(r8), parameter :: C1_liq_Brun89 = 1.28E-17_r8    ! constant for liquid water grain growth [m3 s-1],
-                                                         ! from Brun89
-  real(r8), parameter :: C1_liq_Brun89 = 0._r8           ! constant for liquid water grain growth [m3 s-1],
-                                                         ! from Brun89: zeroed to accomodate dry snow aging
-  real(r8), parameter :: C2_liq_Brun89 = 4.22E-13_r8     ! constant for liquid water grain growth [m3 s-1],
-                                                         ! from Brun89: corrected for LWC in units of percent
-
-  real(r8), parameter :: tim_cns_bc_rmv  = 2.2E-8_r8     ! time constant for removal of BC in snow on sea-ice
-                                                         ! [s-1] (50% mass removal/year)
-  real(r8), parameter :: tim_cns_oc_rmv  = 2.2E-8_r8     ! time constant for removal of OC in snow on sea-ice
-                                                         ! [s-1] (50% mass removal/year)
-  real(r8), parameter :: tim_cns_dst_rmv = 2.2E-8_r8     ! time constant for removal of dust in snow on sea-ice
-                                                         ! [s-1] (50% mass removal/year)
-
-  ! scaling of the snow aging rate (tuning option):
-  logical :: flg_snoage_scl    = .false.                 ! flag for scaling the snow aging rate by some arbitrary factor
-  real(r8), parameter :: xdrdt = 1.0_r8                  ! arbitrary factor applied to snow aging rate
-
-  ! snow and aerosol Mie parameters:
-  ! (arrays declared here, but are set in iniTimeConst)
-  ! (idx_Mie_snw_mx is number of snow radii with defined parameters (i.e. from 30um to 1500um))
-  
-  ! direct-beam weighted ice optical properties
-  real(r8) :: ss_alb_snw_drc(idx_Mie_snw_mx,numrad_snw)
-  real(r8) :: asm_prm_snw_drc(idx_Mie_snw_mx,numrad_snw)
-  real(r8) :: ext_cff_mss_snw_drc(idx_Mie_snw_mx,numrad_snw)
-
-  ! diffuse radiation weighted ice optical properties
-  real(r8) :: ss_alb_snw_dfs(idx_Mie_snw_mx,numrad_snw)
-  real(r8) :: asm_prm_snw_dfs(idx_Mie_snw_mx,numrad_snw)
-  real(r8) :: ext_cff_mss_snw_dfs(idx_Mie_snw_mx,numrad_snw)
-
-  ! hydrophiliic BC
-  real(r8) :: ss_alb_bc1(numrad_snw)
-  real(r8) :: asm_prm_bc1(numrad_snw)
-  real(r8) :: ext_cff_mss_bc1(numrad_snw)
-
-  ! hydrophobic BC
-  real(r8) :: ss_alb_bc2(numrad_snw)
-  real(r8) :: asm_prm_bc2(numrad_snw)
-  real(r8) :: ext_cff_mss_bc2(numrad_snw)
-
-  ! hydrophobic OC
-  real(r8) :: ss_alb_oc1(numrad_snw)
-  real(r8) :: asm_prm_oc1(numrad_snw)
-  real(r8) :: ext_cff_mss_oc1(numrad_snw)
-
-  ! hydrophilic OC
-  real(r8) :: ss_alb_oc2(numrad_snw)
-  real(r8) :: asm_prm_oc2(numrad_snw)
-  real(r8) :: ext_cff_mss_oc2(numrad_snw)
-
-  ! dust species 1:
-  real(r8) :: ss_alb_dst1(numrad_snw)
-  real(r8) :: asm_prm_dst1(numrad_snw)
-  real(r8) :: ext_cff_mss_dst1(numrad_snw)
-
-  ! dust species 2:
-  real(r8) :: ss_alb_dst2(numrad_snw)
-  real(r8) :: asm_prm_dst2(numrad_snw)
-  real(r8) :: ext_cff_mss_dst2(numrad_snw)
-
-  ! dust species 3:
-  real(r8) :: ss_alb_dst3(numrad_snw)
-  real(r8) :: asm_prm_dst3(numrad_snw)
-  real(r8) :: ext_cff_mss_dst3(numrad_snw)
-
-  ! dust species 4:
-  real(r8) :: ss_alb_dst4(numrad_snw)
-  real(r8) :: asm_prm_dst4(numrad_snw)
-  real(r8) :: ext_cff_mss_dst4(numrad_snw)
-
-  ! best-fit parameters for snow aging defined over:
-  !  11 temperatures from 225 to 273 K
-  !  31 temperature gradients from 0 to 300 K/m
-  !   8 snow densities from 0 to 350 kg/m3
-  ! (arrays declared here, but are set in iniTimeConst)
-  real(r8), pointer :: snowage_tau(:,:,:) ! (idx_rhos_max,idx_Tgrd_max,idx_T_max)
-  real(r8), pointer :: snowage_kappa(:,:,:) ! (idx_rhos_max,idx_Tgrd_max,idx_T_max)
-  real(r8), pointer :: snowage_drdt0(:,:,:) ! idx_rhos_max,idx_Tgrd_max,idx_T_max)
-  !
-  ! !REVISION HISTORY:
-  ! Created by Mark Flanner
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-   subroutine SnowOptics_init( )
-     
-     use fileutils  , only : getfil
-     use CLM_varctl , only : fsnowoptics
-     use spmdMod    , only : masterproc
-     use ncdio_pio  , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile
-
-     type(file_desc_t)  :: ncid                        ! netCDF file id
-     character(len=256) :: locfn                       ! local filename
-     character(len= 32) :: subname = 'SnowOptics_init' ! subroutine name
-     integer            :: ier                         ! error status
-
-     return    ! return early
-     !
-     ! Open optics file:
-     if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....'
-     call getfil (fsnowoptics, locfn, 0)
-     call ncd_pio_openfile(ncid, locfn, 0)
-     if(masterproc) write(iulog,*) subname,trim(fsnowoptics)
-
-     ! direct-beam snow Mie parameters:
-     call ncd_io('ss_alb_ice_drc', ss_alb_snw_drc,            'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_ice_drc',asm_prm_snw_drc,          'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_ice_drc', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.)
-
-     ! diffuse snow Mie parameters
-     call ncd_io( 'ss_alb_ice_dfs', ss_alb_snw_dfs,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_ice_dfs', asm_prm_snw_dfs,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_ice_dfs', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.)
-
-     ! BC species 1 Mie parameters
-     call ncd_io( 'ss_alb_bcphil', ss_alb_bc1,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_bcphil', asm_prm_bc1,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_bcphil', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.)
-
-     ! BC species 2 Mie parameters
-     call ncd_io( 'ss_alb_bcphob', ss_alb_bc2,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_bcphob', asm_prm_bc2,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.)
-
-     ! OC species 1 Mie parameters
-     call ncd_io( 'ss_alb_ocphil', ss_alb_oc1,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_ocphil', asm_prm_oc1,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_ocphil', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.)
-
-     ! OC species 2 Mie parameters
-     call ncd_io( 'ss_alb_ocphob', ss_alb_oc2,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_ocphob', asm_prm_oc2,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.)
-
-     ! dust species 1 Mie parameters
-     call ncd_io( 'ss_alb_dust01', ss_alb_dst1,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_dust01', asm_prm_dst1,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_dust01', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.)
-
-     ! dust species 2 Mie parameters
-     call ncd_io( 'ss_alb_dust02', ss_alb_dst2,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_dust02', asm_prm_dst2,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_dust02', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.)
-
-     ! dust species 3 Mie parameters
-     call ncd_io( 'ss_alb_dust03', ss_alb_dst3,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_dust03', asm_prm_dst3,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_dust03', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.)
-
-     ! dust species 4 Mie parameters
-     call ncd_io( 'ss_alb_dust04', ss_alb_dst4,           'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'asm_prm_dust04', asm_prm_dst4,         'read', ncid, posNOTonfile=.true.)
-     call ncd_io( 'ext_cff_mss_dust04', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.)
-
-
-     call ncd_pio_closefile(ncid)
-     if (masterproc) then
-
-        write(iulog,*) 'Successfully read snow optical properties'
-        ! print some diagnostics:
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for direct-beam ice, rds=100um: ', &
-             ss_alb_snw_drc(71,1), ss_alb_snw_drc(71,2), ss_alb_snw_drc(71,3),     &
-             ss_alb_snw_drc(71,4), ss_alb_snw_drc(71,5)
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for diffuse ice, rds=100um: ',     &
-             ss_alb_snw_dfs(71,1), ss_alb_snw_dfs(71,2), ss_alb_snw_dfs(71,3),     &
-             ss_alb_snw_dfs(71,4), ss_alb_snw_dfs(71,5)
-        if (DO_SNO_OC) then
-           write (iulog,*) 'SNICAR: Including OC aerosols from snow radiative transfer calculations'
-        else
-           write (iulog,*) 'SNICAR: Excluding OC aerosols from snow radiative transfer calculations'
-        endif
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophillic BC: ', &
-             ss_alb_bc1(1), ss_alb_bc1(2), ss_alb_bc1(3), ss_alb_bc1(4), ss_alb_bc1(5)
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic BC: ', &
-             ss_alb_bc2(1), ss_alb_bc2(2), ss_alb_bc2(3), ss_alb_bc2(4), ss_alb_bc2(5)
-        if (DO_SNO_OC) then
-           write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophillic OC: ', &
-                ss_alb_oc1(1), ss_alb_oc1(2), ss_alb_oc1(3), ss_alb_oc1(4), ss_alb_oc1(5)
-           write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic OC: ', &
-                ss_alb_oc2(1), ss_alb_oc2(2), ss_alb_oc2(3), ss_alb_oc2(4), ss_alb_oc2(5)
-        endif
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for dust species 1: ', &
-             ss_alb_dst1(1), ss_alb_dst1(2), ss_alb_dst1(3), ss_alb_dst1(4), ss_alb_dst1(5)
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for dust species 2: ', &
-             ss_alb_dst2(1), ss_alb_dst2(2), ss_alb_dst2(3), ss_alb_dst2(4), ss_alb_dst2(5)
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for dust species 3: ', &
-             ss_alb_dst3(1), ss_alb_dst3(2), ss_alb_dst3(3), ss_alb_dst3(4), ss_alb_dst3(5)
-        write (iulog,*) 'SNICAR: Mie single scatter albedos for dust species 4: ', &
-             ss_alb_dst4(1), ss_alb_dst4(2), ss_alb_dst4(3), ss_alb_dst4(4), ss_alb_dst4(5)
-        write(iulog,*)
-     end if
-
-   end subroutine SnowOptics_init
-
-   !-----------------------------------------------------------------------
-   subroutine SnowAge_init( )
-     use CLM_varctl      , only : fsnowaging
-     use fileutils       , only : getfil
-     use spmdMod         , only : masterproc
-     use ncdio_pio       , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile
-
-     type(file_desc_t)  :: ncid                        ! netCDF file id
-     character(len=256) :: locfn                       ! local filename
-     character(len= 32) :: subname = 'SnowOptics_init' ! subroutine name
-     integer            :: varid                       ! netCDF id's
-     integer            :: ier                         ! error status
-
-     ! Open snow aging (effective radius evolution) file:
-     allocate(snowage_tau(idx_rhos_max,idx_Tgrd_max,idx_T_max))
-     allocate(snowage_kappa(idx_rhos_max,idx_Tgrd_max,idx_T_max))
-     allocate(snowage_drdt0(idx_rhos_max,idx_Tgrd_max,idx_T_max))
-
-     return    ! return early
-     if(masterproc)  write(iulog,*) 'Attempting to read snow aging parameters .....'
-     call getfil (fsnowaging, locfn, 0)
-     call ncd_pio_openfile(ncid, locfn, 0)
-     if(masterproc) write(iulog,*) subname,trim(fsnowaging)
-
-     ! snow aging parameters
-
-     call ncd_io('tau', snowage_tau,       'read', ncid, posNOTonfile=.true.)
-     call ncd_io('kappa', snowage_kappa,   'read', ncid, posNOTonfile=.true.)
-     call ncd_io('drdsdt0', snowage_drdt0, 'read', ncid, posNOTonfile=.true.)
-
-     call ncd_pio_closefile(ncid)
-     if (masterproc) then
-
-        write(iulog,*) 'Successfully read snow aging properties'
-
-        ! print some diagnostics:
-        write (iulog,*) 'SNICAR: snowage tau for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: ', snowage_tau(3,11,9)
-        write (iulog,*) 'SNICAR: snowage kappa for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: ', snowage_kappa(3,11,9)
-        write (iulog,*) 'SNICAR: snowage dr/dt_0 for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: ', snowage_drdt0(3,11,9)
-     endif
-
-   end subroutine SnowAge_init
-   
- end module SnowSnicarMod
diff --git a/src/biogeophys/SoilHydrologyInitTimeConstMod.F90 b/src/biogeophys/SoilHydrologyInitTimeConstMod.F90
deleted file mode 100644
index b399b1042a..0000000000
--- a/src/biogeophys/SoilHydrologyInitTimeConstMod.F90
+++ /dev/null
@@ -1,565 +0,0 @@
-module SoilHydrologyInitTimeConstMod
-
-  !------------------------------------------------------------------------------
-  ! DESCRIPTION:
-  ! Initialize time constant variables for SoilHydrologyType
-  !
-  ! !USES
-  use shr_kind_mod      , only : r8 => shr_kind_r8
-  use shr_log_mod       , only : errMsg => shr_log_errMsg
-  use decompMod         , only : bounds_type
-  use SoilHydrologyType , only : soilhydrology_type
-  use LandunitType      , only : lun                
-  use ColumnType        , only : col                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: SoilHydrologyInitTimeConst
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: initSoilParVIC    ! Convert default CLM soil properties to VIC parameters
-  private :: initCLMVICMap     ! Initialize map from VIC to CLM layers
-  private :: linear_interp     ! function for linear interperation 
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-  !
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine SoilHydrologyInitTimeConst(bounds, soilhydrology_inst) 
-    !
-    ! !USES:
-    use shr_const_mod   , only : shr_const_pi
-    use shr_spfn_mod    , only : shr_spfn_erf
-    use abortutils      , only : endrun
-    use clm_varctl      , only : fsurdat, paramfile, iulog, use_vichydro, soil_layerstruct
-    use clm_varpar      , only : nlevsoifl, toplev_equalspace 
-    use clm_varpar      , only : nlevsoi, nlevgrnd, nlevsno, nlevlak, nlevurb, nlayer, nlayert 
-    use clm_varcon      , only : zsoi, dzsoi, zisoi, spval, nlvic, dzvic, pc, grlnd
-    use clm_varcon      , only : aquifer_water_baseline
-    use landunit_varcon , only : istwet, istsoil, istdlak, istcrop, istice_mec
-    use column_varcon   , only : icol_shadewall, icol_road_perv, icol_road_imperv, icol_roof, icol_sunwall
-    use fileutils       , only : getfil
-    use organicFileMod  , only : organicrd 
-    use ncdio_pio       , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)        , intent(in)    :: bounds                                    
-    type(soilhydrology_type) , intent(inout) :: soilhydrology_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: p,c,j,l,g,lev,nlevs 
-    integer            :: ivic,ivicstrt,ivicend   
-    real(r8)           :: maxslope, slopemax, minslope
-    real(r8)           :: d, fd, dfdd, slope0,slopebeta
-    real(r8) ,pointer  :: tslope(:)  
-    logical            :: readvar 
-    type(file_desc_t)  :: ncid        
-    character(len=256) :: locfn       
-    real(r8)           :: clay,sand        ! temporaries
-    real(r8)           :: om_frac          ! organic matter fraction
-    real(r8)           :: organic_max      ! organic matter (kg/m3) where soil is assumed to act like peat 
-    real(r8) ,pointer  :: b2d        (:)   ! read in - VIC b  
-    real(r8) ,pointer  :: ds2d       (:)   ! read in - VIC Ds 
-    real(r8) ,pointer  :: dsmax2d    (:)   ! read in - VIC Dsmax 
-    real(r8) ,pointer  :: ws2d       (:)   ! read in - VIC Ws 
-    real(r8), pointer  :: sandcol    (:,:) ! column level sand fraction for calculating VIC parameters
-    real(r8), pointer  :: claycol    (:,:) ! column level clay fraction for calculating VIC parameters
-    real(r8), pointer  :: om_fraccol (:,:) ! column level organic matter fraction for calculating VIC parameters
-    real(r8) ,pointer  :: sand3d     (:,:) ! read in - soil texture: percent sand 
-    real(r8) ,pointer  :: clay3d     (:,:) ! read in - soil texture: percent clay 
-    real(r8) ,pointer  :: organic3d  (:,:) ! read in - organic matter: kg/m3 
-    real(r8) ,pointer  :: zisoifl    (:)   ! original soil interface depth 
-    real(r8) ,pointer  :: zsoifl     (:)   ! original soil midpoint 
-    real(r8) ,pointer  :: dzsoifl    (:)   ! original soil thickness 
-    !-----------------------------------------------------------------------
-    ! -----------------------------------------------------------------
-    ! Initialize frost table
-    ! -----------------------------------------------------------------
-
-    soilhydrology_inst%wa_col(bounds%begc:bounds%endc)  = aquifer_water_baseline
-    soilhydrology_inst%zwt_col(bounds%begc:bounds%endc) = 0._r8
-
-    do c = bounds%begc,bounds%endc
-       l = col%landunit(c)
-       if (.not. lun%lakpoi(l)) then  !not lake
-          if (lun%urbpoi(l)) then
-             if (col%itype(c) == icol_road_perv) then
-                ! Note that the following hard-coded constants (on the next two lines)
-                ! seem implicitly related to aquifer_water_baseline
-                soilhydrology_inst%wa_col(c)  = 4800._r8
-                soilhydrology_inst%zwt_col(c) = (25._r8 + col%zi(c,nlevsoi)) - soilhydrology_inst%wa_col(c)/0.2_r8 /1000._r8  ! One meter below soil column
-             else
-                soilhydrology_inst%wa_col(c)  = spval
-                soilhydrology_inst%zwt_col(c) = spval
-             end if
-             ! initialize frost_table, zwt_perched
-             soilhydrology_inst%zwt_perched_col(c) = spval
-             soilhydrology_inst%frost_table_col(c) = spval
-          else
-             ! Note that the following hard-coded constants (on the next two lines) seem
-             ! implicitly related to aquifer_water_baseline
-             soilhydrology_inst%wa_col(c)  = 4000._r8
-             soilhydrology_inst%zwt_col(c) = (25._r8 + col%zi(c,nlevsoi)) - soilhydrology_inst%wa_col(c)/0.2_r8 /1000._r8  ! One meter below soil column
-             ! initialize frost_table, zwt_perched to bottom of soil column
-             soilhydrology_inst%zwt_perched_col(c) = col%zi(c,nlevsoi)
-             soilhydrology_inst%frost_table_col(c) = col%zi(c,nlevsoi)
-          end if
-       end if
-    end do
-
-    ! Initialize VIC variables
-
-    if (use_vichydro) then
-
-       allocate(b2d        (bounds%begg:bounds%endg))
-       allocate(ds2d       (bounds%begg:bounds%endg))
-       allocate(dsmax2d    (bounds%begg:bounds%endg))
-       allocate(ws2d       (bounds%begg:bounds%endg))
-       allocate(sandcol    (bounds%begc:bounds%endc,1:nlevgrnd ))
-       allocate(claycol    (bounds%begc:bounds%endc,1:nlevgrnd ))
-       allocate(om_fraccol (bounds%begc:bounds%endc,1:nlevgrnd ))
-
-       call getfil (fsurdat, locfn, 0)
-       call ncd_pio_openfile (ncid, locfn, 0)
-       call ncd_io(ncid=ncid, varname='binfl', flag='read', data=b2d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: binfl NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-       end if
-       call ncd_io(ncid=ncid, varname='Ds', flag='read', data=ds2d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: Ds NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-       end if
-       call ncd_io(ncid=ncid, varname='Dsmax', flag='read', data=dsmax2d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: Dsmax NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-       end if
-       call ncd_io(ncid=ncid, varname='Ws', flag='read', data=ws2d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: Ws NOT on surfdata file'//errMsg(sourcefile, __LINE__))
-       end if
-       call ncd_pio_closefile(ncid)
-
-       !define the depth of VIC soil layers here
-       nlvic(1) = 3
-       nlvic(2) = toplev_equalspace - nlvic(1)
-       nlvic(3) = nlevsoi - (nlvic(1) + nlvic(2))
-
-       dzvic(:) = 0._r8
-       ivicstrt = 1
-
-       do ivic = 1,nlayer
-          ivicend = ivicstrt+nlvic(ivic)-1
-          do j = ivicstrt,ivicend
-             dzvic(ivic) = dzvic(ivic)+dzsoi(j)
-          end do
-          ivicstrt = ivicend+1
-       end do
-
-       do c = bounds%begc, bounds%endc
-          g = col%gridcell(c)
-          soilhydrology_inst%b_infil_col(c) = b2d(g)
-          soilhydrology_inst%ds_col(c)      = ds2d(g)
-          soilhydrology_inst%dsmax_col(c)   = dsmax2d(g)
-          soilhydrology_inst%Wsvic_col(c)   = ws2d(g)
-       end do
-
-       do c = bounds%begc, bounds%endc
-          soilhydrology_inst%max_infil_col(c) = spval
-          soilhydrology_inst%i_0_col(c)       = spval
-          do lev = 1, nlayer
-             soilhydrology_inst%ice_col(c,lev)       = spval
-             soilhydrology_inst%moist_col(c,lev)     = spval
-             soilhydrology_inst%moist_vol_col(c,lev) = spval
-             soilhydrology_inst%max_moist_col(c,lev) = spval
-             soilhydrology_inst%porosity_col(c,lev)  = spval
-             soilhydrology_inst%expt_col(c,lev)      = spval
-             soilhydrology_inst%ksat_col(c,lev)      = spval
-             soilhydrology_inst%phi_s_col(c,lev)     = spval
-             soilhydrology_inst%depth_col(c,lev)     = spval
-             sandcol(c,lev)            = spval
-             claycol(c,lev)            = spval
-             om_fraccol(c,lev)         = spval
-          end do
-       end do
-
-       allocate(sand3d(bounds%begg:bounds%endg,nlevsoifl))
-       allocate(clay3d(bounds%begg:bounds%endg,nlevsoifl))
-       allocate(organic3d(bounds%begg:bounds%endg,nlevsoifl))
-
-       call organicrd(organic3d)
-
-       call getfil (fsurdat, locfn, 0)
-       call ncd_pio_openfile (ncid, locfn, 0)
-       call ncd_io(ncid=ncid, varname='PCT_SAND', flag='read', data=sand3d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: PCT_SAND NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-       end if
-       call ncd_io(ncid=ncid, varname='PCT_CLAY', flag='read', data=clay3d, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun(msg=' ERROR: PCT_CLAY NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-       end if
-       call ncd_pio_closefile(ncid)
-
-       ! Determine organic_max
-       call getfil (paramfile, locfn, 0)
-       call ncd_pio_openfile (ncid, trim(locfn), 0)
-       call ncd_io(ncid=ncid, varname='organic_max', flag='read', data=organic_max, readvar=readvar)
-       if ( .not. readvar ) then
-          call endrun(msg=' ERROR: organic_max not on param file'//errMsg(sourcefile, __LINE__))
-       end if
-       call ncd_pio_closefile(ncid)
-
-       ! get original soil depths to be used in interpolation of sand and clay
-       allocate(zsoifl(1:nlevsoifl), zisoifl(0:nlevsoifl), dzsoifl(1:nlevsoifl))
-       do j = 1, nlevsoifl
-          zsoifl(j) = 0.025*(exp(0.5_r8*(j-0.5_r8))-1._r8)    !node depths
-       enddo
-
-       dzsoifl(1) = 0.5_r8*(zsoifl(1)+zsoifl(2))             !thickness b/n two interfaces
-       do j = 2,nlevsoifl-1
-          dzsoifl(j)= 0.5_r8*(zsoifl(j+1)-zsoifl(j-1))
-       enddo
-       dzsoifl(nlevsoifl) = zsoifl(nlevsoifl)-zsoifl(nlevsoifl-1)
-
-       zisoifl(0) = 0._r8
-       do j = 1, nlevsoifl-1
-          zisoifl(j) = 0.5_r8*(zsoifl(j)+zsoifl(j+1))         !interface depths
-       enddo
-       zisoifl(nlevsoifl) = zsoifl(nlevsoifl) + 0.5_r8*dzsoifl(nlevsoifl)
-
-       do c = bounds%begc, bounds%endc
-          g = col%gridcell(c)
-          l = col%landunit(c)
-
-          if (lun%itype(l) /= istdlak) then  ! soil columns of both urban and non-urban types
-             if (lun%itype(l)==istwet .or. lun%itype(l)==istice_mec) then
-                ! do nothing
-             else if (lun%urbpoi(l) .and. (col%itype(c) /= icol_road_perv) .and. (col%itype(c) /= icol_road_imperv) )then
-                ! do nothing
-             else
-                do lev = 1,nlevgrnd
-                   if ( soil_layerstruct /= '10SL_3.5m' )then
-                      write(iulog,*) 'Setting clay, sand, organic, in Soil Hydrology for VIC'
-                      if (lev .eq. 1) then
-                         clay    = clay3d(g,1)
-                         sand    = sand3d(g,1)
-                         om_frac = organic3d(g,1)/organic_max 
-                      else if (lev <= nlevsoi) then
-                         do j = 1,nlevsoifl-1
-                            if (zisoi(lev) >= zisoifl(j) .AND. zisoi(lev) < zisoifl(j+1)) then
-                               clay    = clay3d(g,j+1)
-                               sand    = sand3d(g,j+1)
-                               om_frac = organic3d(g,j+1)/organic_max    
-                            endif
-                         end do
-                      else
-                         clay    = clay3d(g,nlevsoifl)
-                         sand    = sand3d(g,nlevsoifl)
-                         om_frac = 0._r8
-                      endif
-                   else
-                      ! duplicate clay and sand values from 10th soil layer
-                      if (lev <= nlevsoi) then
-                         clay    = clay3d(g,lev)
-                         sand    = sand3d(g,lev)
-                         om_frac = (organic3d(g,lev)/organic_max)**2._r8
-                      else
-                         clay    = clay3d(g,nlevsoi)
-                         sand    = sand3d(g,nlevsoi)
-                         om_frac = 0._r8
-                      endif
-                   end if
-
-                   if (lun%urbpoi(l)) om_frac = 0._r8
-                   claycol(c,lev)    = clay
-                   sandcol(c,lev)    = sand
-                   om_fraccol(c,lev) = om_frac
-                end do
-             end if
-          end if ! end of if not lake
-
-          if (lun%itype(l) /= istdlak) then  ! soil columns of both urban and non-urban types
-             if (lun%urbpoi(l)) then
-                if (col%itype(c)==icol_sunwall .or. col%itype(c)==icol_shadewall .or. col%itype(c)==icol_roof) then
-                   ! do nothing
-                else
-                   soilhydrology_inst%depth_col(c, 1:nlayer)         = dzvic
-                   soilhydrology_inst%depth_col(c, nlayer+1:nlayert) = col%dz(c, nlevsoi+1:nlevgrnd)
-
-                   ! create weights to map soil moisture profiles (10 layer) to 3 layers for VIC hydrology, M.Huang
-                   call initCLMVICMap(c, soilhydrology_inst)
-                   call initSoilParVIC(c, claycol, sandcol, om_fraccol, soilhydrology_inst)
-                end if
-             else 
-                soilhydrology_inst%depth_col(c, 1:nlayer) = dzvic
-                soilhydrology_inst%depth_col(c, nlayer+1:nlayert) = col%dz(c, nlevsoi+1:nlevgrnd)
-
-                ! create weights to map soil moisture profiles (10 layer) to 3 layers for VIC hydrology, M.Huang
-                call initCLMVICMap(c, soilhydrology_inst)
-                call initSoilParVIC(c, claycol, sandcol, om_fraccol, soilhydrology_inst)
-             end if
-          end if ! end of if not lake
-
-       end do ! end of loop over columns
-
-      deallocate(b2d, ds2d, dsmax2d, ws2d)
-      deallocate(sandcol, claycol, om_fraccol)
-      deallocate(sand3d, clay3d, organic3d)
-      deallocate(zisoifl, zsoifl, dzsoifl)
-
-    end if ! end of if use_vichydro
-
-    associate(micro_sigma => col%micro_sigma)
-      do c = bounds%begc, bounds%endc
-         
-         ! determine h2osfc threshold ("fill & spill" concept)
-         ! set to zero for no h2osfc (w/frac_infclust =large)
-         
-         soilhydrology_inst%h2osfc_thresh_col(c) = 0._r8
-         if (micro_sigma(c) > 1.e-6_r8 .and. (soilhydrology_inst%h2osfcflag /= 0)) then
-            d = 0.0
-            do p = 1,4
-               fd   = 0.5*(1.0_r8+shr_spfn_erf(d/(micro_sigma(c)*sqrt(2.0)))) - pc
-               dfdd = exp(-d**2/(2.0*micro_sigma(c)**2))/(micro_sigma(c)*sqrt(2.0*shr_const_pi))
-               d    = d - fd/dfdd
-            enddo
-            soilhydrology_inst%h2osfc_thresh_col(c) = 0.5*d*(1.0_r8+shr_spfn_erf(d/(micro_sigma(c)*sqrt(2.0)))) + &
-                 micro_sigma(c)/sqrt(2.0*shr_const_pi)*exp(-d**2/(2.0*micro_sigma(c)**2))         
-            soilhydrology_inst%h2osfc_thresh_col(c) = 1.e3_r8 * soilhydrology_inst%h2osfc_thresh_col(c) !convert to mm from meters
-         else
-            soilhydrology_inst%h2osfc_thresh_col(c) = 0._r8
-         endif
-
-         if (soilhydrology_inst%h2osfcflag == 0) then 
-            soilhydrology_inst%h2osfc_thresh_col(c) = 0._r8    ! set to zero for no h2osfc (w/frac_infclust =large)
-         endif
-
-         ! set decay factor
-         soilhydrology_inst%hkdepth_col(c) = 1._r8/2.5_r8
-
-      end do
-    end associate
-
-  end subroutine SoilhydrologyInitTimeConst
-
-  !-----------------------------------------------------------------------
-  subroutine initSoilParVIC(c, claycol, sandcol, om_fraccol, soilhydrology_inst)
-    !
-    ! !DESCRIPTION:
-    ! Convert default CLM soil properties to VIC parameters
-    ! to be used for runoff simulations (added by M. Huang)
-    !
-    ! !USES:
-    use clm_varpar, only : nlevsoi, nlayert, nlayer
-    !
-    ! !ARGUMENTS:
-    integer                  , intent(in)    :: c               ! column index
-    real(r8)                 , pointer       :: sandcol(:,:)    ! read in - soil texture: percent sand
-    real(r8)                 , pointer       :: claycol(:,:)    ! read in - soil texture: percent clay
-    real(r8)                 , pointer       :: om_fraccol(:,:) ! read in - organic matter: kg/m3
-    type(soilhydrology_type) , intent(inout) :: soilhydrology_inst
-
-    ! !LOCAL VARIABLES:
-    real(r8) :: om_watsat    = 0.9_r8             ! porosity of organic soil
-    real(r8) :: om_hksat     = 0.1_r8             ! saturated hydraulic conductivity of organic soil [mm/s]
-    real(r8) :: om_tkm       = 0.25_r8            ! thermal conductivity of organic soil (Farouki, 1986) [W/m/K]
-    real(r8) :: om_sucsat    = 10.3_r8            ! saturated suction for organic matter (Letts, 2000)
-    real(r8) :: om_csol      = 2.5_r8             ! heat capacity of peat soil *10^6 (J/K m3) (Farouki, 1986)
-    real(r8) :: om_tkd       = 0.05_r8            ! thermal conductivity of dry organic soil (Farouki, 1981)
-    real(r8) :: om_b         = 2.7_r8             ! Clapp Hornberger paramater for oragnic soil (Letts, 2000)
-    real(r8) :: om_expt      = 3._r8+2._r8*2.7_r8 ! soil expt for VIC        
-    real(r8) :: csol_bedrock = 2.0e6_r8           ! vol. heat capacity of granite/sandstone  J/(m3 K)(Shabbir, 2000)
-    real(r8) :: pc           = 0.5_r8             ! percolation threshold
-    real(r8) :: pcbeta       = 0.139_r8           ! percolation exponent
-    real(r8) :: xksat                             ! maximum hydraulic conductivity of soil [mm/s]
-    real(r8) :: perc_frac                         ! "percolating" fraction of organic soil
-    real(r8) :: perc_norm                         ! normalize to 1 when 100% organic soil
-    real(r8) :: uncon_hksat                       ! series conductivity of mineral/organic soil
-    real(r8) :: uncon_frac                        ! fraction of "unconnected" soil
-    real(r8) :: temp_sum_frac                     ! sum of node fractions in each VIC layer
-    real(r8) :: sandvic(1:nlayert)                ! temporary, weighted averaged sand% for VIC layers
-    real(r8) :: clayvic(1:nlayert)                ! temporary, weighted averaged clay% for VIC layers
-    real(r8) :: om_fracvic(1:nlayert)             ! temporary, weighted averaged organic matter fract for VIC layers
-    integer  :: i, j                              ! indices
-    !-------------------------------------------------------------------------------------------
-
-    ! soilhydrology_inst%depth_col(:,:)           Output: layer depth of upper layer(m) 
-    ! soilhydrology_inst%vic_clm_fract_col(:,:,:) Output: fraction of VIC layers in CLM layers
-    ! soilhydrology_inst%c_param_col(:)           Output: baseflow exponent (Qb)
-    ! soilhydrology_inst%expt_col(:,:)            Output: pore-size distribution related paramter(Q12)
-    ! soilhydrology_inst%ksat_col(:,:)            Output: Saturated hydrologic conductivity (mm/s)
-    ! soilhydrology_inst%phi_s_col(:,:)           Output: soil moisture dissusion parameter
-    ! soilhydrology_inst%porosity_col(:,:)        Output: soil porosity
-    ! soilhydrology_inst%max_moist_col(:,:)       Output: maximum soil moisture (ice + liq)
-
-    !  map parameters between VIC layers and CLM layers
-    soilhydrology_inst%c_param_col(c) = 2._r8
-
-    ! map the CLM layers to VIC layers 
-    do i = 1, nlayer      
-
-       sandvic(i)    = 0._r8
-       clayvic(i)    = 0._r8   
-       om_fracvic(i) = 0._r8  
-       temp_sum_frac = 0._r8     
-       do j = 1, nlevsoi
-          sandvic(i)    = sandvic(i)    + sandcol(c,j)    * soilhydrology_inst%vic_clm_fract_col(c,i,j)
-          clayvic(i)    = clayvic(i)    + claycol(c,j)    * soilhydrology_inst%vic_clm_fract_col(c,i,j)
-          om_fracvic(i) = om_fracvic(i) + om_fraccol(c,j) * soilhydrology_inst%vic_clm_fract_col(c,i,j) 
-          temp_sum_frac = temp_sum_frac +                   soilhydrology_inst%vic_clm_fract_col(c,i,j)
-       end do
-
-       !average soil properties, M.Huang, 08/11/2010
-       sandvic(i) = sandvic(i)/temp_sum_frac
-       clayvic(i) = clayvic(i)/temp_sum_frac
-       om_fracvic(i) = om_fracvic(i)/temp_sum_frac
-
-       !make sure sand, clay and om fractions are between 0 and 100% 
-       sandvic(i)    = min(100._r8 , sandvic(i))
-       clayvic(i)    = min(100._r8 , clayvic(i))
-       om_fracvic(i) = min(100._r8 , om_fracvic(i))
-       sandvic(i)    = max(0._r8   , sandvic(i))
-       clayvic(i)    = max(0._r8   , clayvic(i))
-       om_fracvic(i) = max(0._r8   , om_fracvic(i))
-
-       !calculate other parameters based on teh percentages
-       soilhydrology_inst%porosity_col(c, i) = 0.489_r8 - 0.00126_r8*sandvic(i)
-       soilhydrology_inst%expt_col(c, i)     = 3._r8+ 2._r8*(2.91_r8 + 0.159_r8*clayvic(i))
-       xksat = 0.0070556 *( 10.**(-0.884+0.0153*sandvic(i)) )
-
-       !consider organic matter, M.Huang 
-       soilhydrology_inst%expt_col(c, i)    = &
-            (1._r8 - om_fracvic(i))*soilhydrology_inst%expt_col(c, i)    + om_fracvic(i)*om_expt 
-       soilhydrology_inst%porosity_col(c,i) = &
-            (1._r8 - om_fracvic(i))*soilhydrology_inst%porosity_col(c,i) + om_watsat*om_fracvic(i) 
-
-       ! perc_frac is zero unless perf_frac greater than percolation threshold
-       if (om_fracvic(i) > pc) then
-          perc_norm=(1._r8 - pc)**(-pcbeta)
-          perc_frac=perc_norm*(om_fracvic(i) - pc)**pcbeta
-       else
-          perc_frac=0._r8
-       endif
-       ! uncon_frac is fraction of mineral soil plus fraction of "nonpercolating" organic soil
-       uncon_frac=(1._r8-om_fracvic(i))+(1._r8-perc_frac)*om_fracvic(i)
-
-       ! uncon_hksat is series addition of mineral/organic conductivites
-       if (om_fracvic(i) < 1._r8) then
-          uncon_hksat=uncon_frac/((1._r8-om_fracvic(i))/xksat &
-               +((1._r8-perc_frac)*om_fracvic(i))/om_hksat)
-       else
-          uncon_hksat = 0._r8
-       end if
-
-       soilhydrology_inst%ksat_col(c,i)  = &
-            uncon_frac*uncon_hksat + (perc_frac*om_fracvic(i))*om_hksat
-
-       soilhydrology_inst%max_moist_col(c,i) = &
-            soilhydrology_inst%porosity_col(c,i) * soilhydrology_inst%depth_col(c,i) * 1000._r8 !in mm!
-
-       soilhydrology_inst%phi_s_col(c,i) = &
-            -(exp((1.54_r8 - 0.0095_r8*sandvic(i) + &
-            0.0063_r8*(100.0_r8-sandvic(i)-clayvic(i)))*log(10.0_r8))*9.8e-5_r8)
-
-    end do ! end of loop over layers
-
-  end subroutine initSoilParVIC
-
-   !-----------------------------------------------------------------------
-   subroutine initCLMVICMap(c, soilhydrology_inst)
-     !
-     ! !DESCRIPTION:
-     ! Calculates mapping between CLM and VIC layers
-     ! added by AWang, modified by M.Huang for CLM4 
-     ! NOTE: in CLM h2osoil_liq unit is kg/m2, in VIC moist is mm
-     ! h2osoi_ice is actually water equavlent ice content.
-     !
-     ! !USES:
-     use clm_varpar  , only : nlevsoi, nlayer
-     !
-     ! !ARGUMENTS:
-     integer , intent(in)  :: c
-     type(soilhydrology_type), intent(inout) :: soilhydrology_inst
-     !
-     ! !REVISION HISTORY:
-     ! Created by Maoyi Huang
-     ! 11/13/2012, Maoyi Huang: rewrite the mapping modules in CLM4VIC 
-     !
-     ! !LOCAL VARIABLES
-     real(r8) :: sum_frac(1:nlayer)                  ! sum of fraction for each layer
-     real(r8) :: deltal(1:nlayer+1)                  ! temporary
-     real(r8) :: zsum                                ! temporary
-     real(r8) :: lsum                                ! temporary
-     real(r8) :: temp                                ! temporary
-     integer :: i, j, fc
-     !-----------------------------------------------------------------------
-
-     associate(                                                    & 
-          dz            =>    col%dz    ,                          & ! Input:  [real(r8) (:,:)   ]  layer depth (m)                       
-          zi            =>    col%zi    ,                          & ! Input:  [real(r8) (:,:)   ]  interface level below a "z" level (m) 
-          z             =>    col%z     ,                          & ! Input:  [real(r8) (:,:)   ]  layer thickness (m)                   
-
-          depth         =>    soilhydrology_inst%depth_col ,       & ! Input:  [real(r8) (:,:)   ]  layer depth of VIC (m)                
-          vic_clm_fract =>    soilhydrology_inst%vic_clm_fract_col & ! Output: [real(r8) (:,:,:) ]  fraction of VIC layers in clm layers
-          )
-
-       !  set fraction of VIC layer in each CLM layer
-
-       lsum = 0._r8
-       do i = 1, nlayer
-          deltal(i) = depth(c,i)
-       end do
-       do i = 1, nlayer
-          zsum = 0._r8
-          sum_frac(i) = 0._r8
-          do j = 1, nlevsoi
-             if( (zsum < lsum) .and. (zsum + dz(c,j) >= lsum ))  then
-                call linear_interp(lsum, temp, zsum, zsum + dz(c,j), 0._r8, 1._r8)
-                vic_clm_fract(c,i,j) = 1._r8 - temp
-                if(lsum + deltal(i) < zsum + dz(c,j)) then
-                   call linear_interp(lsum + deltal(i), temp, zsum, zsum + dz(c,j), 1._r8, 0._r8)
-                   vic_clm_fract(c,i,j) = vic_clm_fract(c,i,j) - temp
-                end if
-             else if( (zsum < lsum + deltal(i)) .and. (zsum + dz(c,j) >= lsum + deltal(i)) ) then
-                call linear_interp(lsum + deltal(i), temp, zsum, zsum + dz(c,j), 0._r8, 1._r8)
-                vic_clm_fract(c,i,j) = temp
-                if(zsum<=lsum) then
-                   call linear_interp(lsum, temp, zsum, zsum + dz(c,j), 0._r8, 1._r8)
-                   vic_clm_fract(c,i,j) = vic_clm_fract(c,i,j) - temp
-                end if
-             else if( (zsum >= lsum .and. zsum + dz(c,j) <= lsum + deltal(i)) )  then
-                vic_clm_fract(c,i,j) = 1._r8
-             else
-                vic_clm_fract(c,i,j) = 0._r8
-             end if
-             zsum = zsum + dz(c,j)
-             sum_frac(i) = sum_frac(i) + vic_clm_fract(c,i,j)
-          end do                           ! end CLM layer calculation
-          lsum = lsum + deltal(i)
-       end do                             ! end VIC layer calcultion 
-
-     end associate 
-
-   end subroutine initCLMVICMap
-
-   !-------------------------------------------------------------------
-   subroutine linear_interp(x,y, x0, x1, y0, y1)
-     !
-     ! !DESCRIPTION:
-     ! Provides linear interpolation
-     !
-     ! !ARGUMENTS:
-     real(r8), intent(in)  :: x, x0, y0, x1, y1
-     real(r8), intent(out) :: y
-     !-------------------------------------------------------------------
-
-     y = y0 + (x - x0) * (y1 - y0) / (x1 - x0)
-
-   end subroutine linear_interp
-
-end module SoilHydrologyInitTimeConstMod
diff --git a/src/biogeophys/SoilHydrologyType.F90 b/src/biogeophys/SoilHydrologyType.F90
deleted file mode 100644
index be78df49c0..0000000000
--- a/src/biogeophys/SoilHydrologyType.F90
+++ /dev/null
@@ -1,338 +0,0 @@
-Module SoilHydrologyType
-
-  use shr_kind_mod          , only : r8 => shr_kind_r8
-  use shr_log_mod           , only : errMsg => shr_log_errMsg
-  use abortutils            , only : endrun
-  use decompMod             , only : bounds_type
-  use clm_varpar            , only : nlevgrnd, nlayer, nlayert, nlevsoi 
-  use clm_varcon            , only : spval
-  use clm_varctl            , only : iulog
-  use LandunitType          , only : lun                
-  use ColumnType            , only : col                
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  !
-  type, public :: soilhydrology_type
-
-     integer :: h2osfcflag              ! true => surface water is active (namelist)       
-     integer :: origflag                ! used to control soil hydrology properties (namelist)
-
-     real(r8), pointer :: num_substeps_col   (:)    ! col adaptive timestep counter     
-     ! NON-VIC
-     real(r8), pointer :: frost_table_col   (:)     ! col frost table depth                    
-     real(r8), pointer :: zwt_col           (:)     ! col water table depth
-     real(r8), pointer :: zwts_col          (:)     ! col water table depth, the shallower of the two water depths
-     real(r8), pointer :: zwt_perched_col   (:)     ! col perched water table depth
-     real(r8), pointer :: wa_col            (:)     ! col water in the unconfined aquifer (mm)
-     real(r8), pointer :: qcharge_col       (:)     ! col aquifer recharge rate (mm/s) 
-     real(r8), pointer :: fracice_col       (:,:)   ! col fractional impermeability (-)
-     real(r8), pointer :: icefrac_col       (:,:)   ! col fraction of ice       
-     real(r8), pointer :: fcov_col          (:)     ! col fractional impermeable area
-     real(r8), pointer :: fsat_col          (:)     ! col fractional area with water table at surface
-     real(r8), pointer :: h2osfc_thresh_col (:)     ! col level at which h2osfc "percolates"   (time constant)
-
-     ! VIC 
-     real(r8), pointer :: hkdepth_col       (:)     ! col VIC decay factor (m) (time constant)                    
-     real(r8), pointer :: b_infil_col       (:)     ! col VIC b infiltration parameter (time constant)                    
-     real(r8), pointer :: ds_col            (:)     ! col VIC fracton of Dsmax where non-linear baseflow begins (time constant)                    
-     real(r8), pointer :: dsmax_col         (:)     ! col VIC max. velocity of baseflow (mm/day) (time constant)
-     real(r8), pointer :: Wsvic_col         (:)     ! col VIC fraction of maximum soil moisutre where non-liear base flow occurs (time constant)
-     real(r8), pointer :: porosity_col      (:,:)   ! col VIC porosity (1-bulk_density/soil_density)
-     real(r8), pointer :: vic_clm_fract_col (:,:,:) ! col VIC fraction of VIC layers in CLM layers 
-     real(r8), pointer :: depth_col         (:,:)   ! col VIC layer depth of upper layer  
-     real(r8), pointer :: c_param_col       (:)     ! col VIC baseflow exponent (Qb) 
-     real(r8), pointer :: expt_col          (:,:)   ! col VIC pore-size distribution related paramter(Q12) 
-     real(r8), pointer :: ksat_col          (:,:)   ! col VIC Saturated hydrologic conductivity 
-     real(r8), pointer :: phi_s_col         (:,:)   ! col VIC soil moisture dissusion parameter 
-     real(r8), pointer :: moist_col         (:,:)   ! col VIC soil moisture (kg/m2) for VIC soil layers 
-     real(r8), pointer :: moist_vol_col     (:,:)   ! col VIC volumetric soil moisture for VIC soil layers 
-     real(r8), pointer :: max_moist_col     (:,:)   ! col VIC max layer moist + ice (mm) 
-     real(r8), pointer :: max_infil_col     (:)     ! col VIC maximum infiltration rate calculated in VIC
-     real(r8), pointer :: i_0_col           (:)     ! col VIC average saturation in top soil layers 
-     real(r8), pointer :: ice_col           (:,:)   ! col VIC soil ice (kg/m2) for VIC soil layers
-
-   contains
-
-     ! Public routines
-     procedure, public  :: Init
-     procedure, public  :: Restart
-
-     ! Private routines
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-     procedure, private :: ReadNL
-
-  end type soilhydrology_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-  
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
-
-    class(soilhydrology_type) :: this
-    type(bounds_type), intent(in)    :: bounds  
-    character(len=*), intent(in) :: NLFilename
-
-    call this%ReadNL(NLFilename)
-    call this%InitAllocate(bounds) 
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(soilhydrology_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    integer :: begg, endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate(this%num_substeps_col   (begc:endc))                ; this%num_substeps_col   (:)     = nan
-    allocate(this%frost_table_col   (begc:endc))                 ; this%frost_table_col   (:)     = nan
-    allocate(this%zwt_col           (begc:endc))                 ; this%zwt_col           (:)     = nan
-    allocate(this%zwt_perched_col   (begc:endc))                 ; this%zwt_perched_col   (:)     = nan
-    allocate(this%zwts_col          (begc:endc))                 ; this%zwts_col          (:)     = nan
-
-    allocate(this%wa_col            (begc:endc))                 ; this%wa_col            (:)     = nan
-    allocate(this%qcharge_col       (begc:endc))                 ; this%qcharge_col       (:)     = nan
-    allocate(this%fracice_col       (begc:endc,nlevgrnd))        ; this%fracice_col       (:,:)   = nan
-    allocate(this%icefrac_col       (begc:endc,nlevgrnd))        ; this%icefrac_col       (:,:)   = nan
-    allocate(this%fcov_col          (begc:endc))                 ; this%fcov_col          (:)     = nan   
-    allocate(this%fsat_col          (begc:endc))                 ; this%fsat_col          (:)     = nan
-    allocate(this%h2osfc_thresh_col (begc:endc))                 ; this%h2osfc_thresh_col (:)     = nan
-
-    allocate(this%hkdepth_col       (begc:endc))                 ; this%hkdepth_col       (:)     = nan
-    allocate(this%b_infil_col       (begc:endc))                 ; this%b_infil_col       (:)     = nan
-    allocate(this%ds_col            (begc:endc))                 ; this%ds_col            (:)     = nan
-    allocate(this%dsmax_col         (begc:endc))                 ; this%dsmax_col         (:)     = nan
-    allocate(this%Wsvic_col         (begc:endc))                 ; this%Wsvic_col         (:)     = nan
-    allocate(this%depth_col         (begc:endc,nlayert))         ; this%depth_col         (:,:)   = nan
-    allocate(this%porosity_col      (begc:endc,nlayer))          ; this%porosity_col      (:,:)   = nan
-    allocate(this%vic_clm_fract_col (begc:endc,nlayer, nlevsoi)) ; this%vic_clm_fract_col (:,:,:) = nan
-    allocate(this%c_param_col       (begc:endc))                 ; this%c_param_col       (:)     = nan
-    allocate(this%expt_col          (begc:endc,nlayer))          ; this%expt_col          (:,:)   = nan
-    allocate(this%ksat_col          (begc:endc,nlayer))          ; this%ksat_col          (:,:)   = nan
-    allocate(this%phi_s_col         (begc:endc,nlayer))          ; this%phi_s_col         (:,:)   = nan
-    allocate(this%moist_col         (begc:endc,nlayert))         ; this%moist_col         (:,:)   = nan
-    allocate(this%moist_vol_col     (begc:endc,nlayert))         ; this%moist_vol_col     (:,:)   = nan
-    allocate(this%max_moist_col     (begc:endc,nlayer))          ; this%max_moist_col     (:,:)   = nan
-    allocate(this%max_infil_col     (begc:endc))                 ; this%max_infil_col     (:)     = nan
-    allocate(this%i_0_col           (begc:endc))                 ; this%i_0_col           (:)     = nan
-    allocate(this%ice_col           (begc:endc,nlayert))         ; this%ice_col           (:,:)   = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod    , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(soilhydrology_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begc, endc
-    integer           :: begg, endg
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    this%wa_col(begc:endc) = spval
-    call hist_addfld1d (fname='WA',  units='mm',  &
-         avgflag='A', long_name='water in the unconfined aquifer (vegetated landunits only)', &
-         ptr_col=this%wa_col, l2g_scale_type='veg', default='inactive')
-
-    this%qcharge_col(begc:endc) = spval
-    call hist_addfld1d (fname='QCHARGE',  units='mm/s',  &
-         avgflag='A', long_name='aquifer recharge rate (vegetated landunits only)', &
-         ptr_col=this%qcharge_col, l2g_scale_type='veg', default='inactive')
-
-    this%fcov_col(begc:endc) = spval
-    call hist_addfld1d (fname='FCOV',  units='unitless',  &
-         avgflag='A', long_name='fractional impermeable area', &
-         ptr_col=this%fcov_col, l2g_scale_type='veg', default='inactive')
-
-    this%fsat_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSAT',  units='unitless',  &
-         avgflag='A', long_name='fractional area with water table at surface', &
-         ptr_col=this%fsat_col, l2g_scale_type='veg', default='inactive')
-
-    this%num_substeps_col(begc:endc) = spval
-    call hist_addfld1d (fname='NSUBSTEPS',  units='unitless',  &
-         avgflag='A', long_name='number of adaptive timesteps in CLM timestep', &
-         ptr_col=this%num_substeps_col, l2g_scale_type='veg', &
-         default='inactive')
-
-    this%frost_table_col(begc:endc) = spval
-    call hist_addfld1d (fname='FROST_TABLE',  units='m',  &
-         avgflag='A', long_name='frost table depth (vegetated landunits only)', &
-         ptr_col=this%frost_table_col, l2g_scale_type='veg', default='inactive')
-
-    this%zwt_col(begc:endc) = spval
-    call hist_addfld1d (fname='ZWT',  units='m',  &
-         avgflag='A', long_name='water table depth (vegetated landunits only)', &
-         ptr_col=this%zwt_col, l2g_scale_type='veg', default='inactive')
-
-    this%zwt_perched_col(begc:endc) = spval
-    call hist_addfld1d (fname='ZWT_PERCH',  units='m',  &
-         avgflag='A', long_name='perched water table depth (vegetated landunits only)', &
-         ptr_col=this%zwt_perched_col, l2g_scale_type='veg', default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(soilhydrology_type) :: this
-    type(bounds_type) , intent(in)    :: bounds
-    ! !LOCAL VARIABLES:
-    integer :: c ! indices
-
-    !-----------------------------------------------------------------------
-
-    ! Nothing for now
-
-    ! needs to be initialized to spval to avoid problems when 
-    ! averaging for the accum field
-    do c = bounds%begc, bounds%endc
-       this%num_substeps_col(c) = spval
-    end do
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !USES:
-    use ncdio_pio  , only : file_desc_t, ncd_io, ncd_double
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(soilhydrology_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    !-----------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='FROST_TABLE', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='frost table depth', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%frost_table_col)
-    if (flag == 'read' .and. .not. readvar) then
-       this%frost_table_col(bounds%begc:bounds%endc) = col%zi(bounds%begc:bounds%endc,nlevsoi)
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='WA', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='water in the unconfined aquifer', units='mm', &
-         interpinic_flag='interp', readvar=readvar, data=this%wa_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='ZWT', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='water table depth', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%zwt_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='ZWT_PERCH', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='perched water table depth', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%zwt_perched_col)
-    if (flag == 'read' .and. .not. readvar) then
-       this%zwt_perched_col(bounds%begc:bounds%endc) = col%zi(bounds%begc:bounds%endc,nlevsoi)
-    end if
-
-  end subroutine Restart
-
-   !-----------------------------------------------------------------------
-   subroutine ReadNL( this, NLFilename )
-     !
-     ! !DESCRIPTION:
-     ! Read namelist for SoilHydrology
-     !
-     ! !USES:
-     use shr_mpi_mod    , only : shr_mpi_bcast
-     use shr_log_mod    , only : errMsg => shr_log_errMsg
-     use spmdMod        , only : masterproc, mpicom
-     use fileutils      , only : getavu, relavu, opnfil
-     use clm_nlUtilsMod , only : find_nlgroup_name
-     use clm_varctl     , only : iulog 
-     use abortutils     , only : endrun
-     !
-     ! !ARGUMENTS:
-     class(soilhydrology_type) :: this
-     character(len=*), intent(IN) :: NLFilename ! Namelist filename
-     !
-     ! !LOCAL VARIABLES:
-     integer :: ierr                 ! error code
-     integer :: unitn                ! unit for namelist file
-     integer :: origflag=0            !use to control soil hydraulic properties
-     integer :: h2osfcflag=1          !If surface water is active or not
-     character(len=32) :: subname = 'SoilHydrology_readnl'  ! subroutine name
-     !-----------------------------------------------------------------------
-
-     namelist / clm_soilhydrology_inparm / h2osfcflag, origflag
-
-     ! preset values
-
-     origflag = 0          
-     h2osfcflag = 1        
-
-     if ( masterproc )then
-
-        unitn = getavu()
-        write(iulog,*) 'Read in clm_soilhydrology_inparm  namelist'
-        call opnfil (NLFilename, unitn, 'F')
-        call find_nlgroup_name(unitn, 'clm_soilhydrology_inparm', status=ierr)
-        if (ierr == 0) then
-           read(unitn, clm_soilhydrology_inparm, iostat=ierr)
-           if (ierr /= 0) then
-              call endrun(msg="ERROR reading clm_soilhydrology_inparm namelist"//errmsg(sourcefile, __LINE__))
-           end if
-        else
-           call endrun(msg="ERROR finding clm_soilhydrology_inparm namelist"//errmsg(sourcefile, __LINE__))
-        end if
-        call relavu( unitn )
-
-     end if
-
-     call shr_mpi_bcast(h2osfcflag, mpicom)
-     call shr_mpi_bcast(origflag,   mpicom)
-
-     this%h2osfcflag = h2osfcflag
-     this%origflag   = origflag
-
-   end subroutine ReadNL
-
-end Module SoilHydrologyType
diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90
deleted file mode 100644
index 1c8f13427e..0000000000
--- a/src/biogeophys/SoilStateInitTimeConstMod.F90
+++ /dev/null
@@ -1,630 +0,0 @@
-module SoilStateInitTimeConstMod
-
-  !------------------------------------------------------------------------------
-  ! DESCRIPTION:
-  ! Set hydraulic and thermal properties 
-  !
-  ! !USES
-  use SoilStateType , only : soilstate_type
-  use LandunitType  , only : lun                
-  use ColumnType    , only : col                
-  use PatchType     , only : patch                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public  :: SoilStateInitTimeConst
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: ReadNL
-  !
-  ! !PRIVATE DATA:
-  ! Control variables (from namelist)
-  logical, private :: organic_frac_squared ! If organic fraction should be squared (as in CLM4.5)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-  !
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine ReadNL( nlfilename )
-    !
-    ! !DESCRIPTION:
-    ! Read namelist for SoilStateType
-    !
-    ! !USES:
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    use shr_log_mod    , only : errMsg => shr_log_errMsg
-    use fileutils      , only : getavu, relavu, opnfil
-    use clm_nlUtilsMod , only : find_nlgroup_name
-    use clm_varctl     , only : iulog
-    use spmdMod        , only : mpicom, masterproc
-    use abortUtils     , only : endrun    
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: nlfilename ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    character(len=32) :: subname = 'SoilState_readnl'  ! subroutine name
-    !-----------------------------------------------------------------------
-
-    character(len=*), parameter :: nl_name  = 'clm_soilstate_inparm'  ! Namelist name
-                                                                      ! MUST agree with name in namelist and read
-    namelist / clm_soilstate_inparm / organic_frac_squared
-
-    ! preset values
-
-    organic_frac_squared = .false.
-
-    if ( masterproc )then
-
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nl_name//' namelist'
-       call opnfil (nlfilename, unitn, 'F')
-       call find_nlgroup_name(unitn, nl_name, status=ierr)
-       if (ierr == 0) then
-          read(unit=unitn, nml=clm_soilstate_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading '//nl_name//' namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR finding '//nl_name//' namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-
-    end if
-
-    call shr_mpi_bcast(organic_frac_squared, mpicom)
-
-  end subroutine ReadNL
-
-  !-----------------------------------------------------------------------
-  subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename) 
-    !
-    ! !USES:
-    use shr_kind_mod        , only : r8 => shr_kind_r8
-    use shr_log_mod         , only : errMsg => shr_log_errMsg
-    use shr_infnan_mod      , only : nan => shr_infnan_nan, assignment(=)
-    use decompMod           , only : bounds_type
-    use abortutils          , only : endrun
-    use spmdMod             , only : masterproc
-    use ncdio_pio           , only : file_desc_t, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use ncdio_pio           , only : ncd_pio_openfile, ncd_pio_closefile, ncd_inqdlen
-    use clm_varpar          , only : numpft, numrad
-    use clm_varpar          , only : nlevsoi, nlevgrnd, nlevlak, nlevsoifl, nlayer, nlayert, nlevurb, nlevsno
-    use clm_varcon          , only : zsoi, dzsoi, zisoi, spval
-    use clm_varcon          , only : secspday, pc, mu, denh2o, denice, grlnd
-    use clm_varctl          , only : use_cn, use_fates
-    use clm_varctl          , only : iulog, fsurdat, paramfile, soil_layerstruct
-    use landunit_varcon     , only : istdlak, istwet, istsoil, istcrop, istice_mec
-    use column_varcon       , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv 
-    use fileutils           , only : getfil
-    use organicFileMod      , only : organicrd 
-    use FuncPedotransferMod , only : pedotransf, get_ipedof
-    use RootBiophysMod      , only : init_vegrootfr
-    use GridcellType     , only : grc                
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)    , intent(in)    :: bounds  
-    type(soilstate_type) , intent(inout) :: soilstate_inst
-    character(len=*)     , intent(in)    :: nlfilename ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: p, lev, c, l, g, j            ! indices
-    real(r8)           :: om_frac                       ! organic matter fraction
-    real(r8)           :: om_tkm         = 0.25_r8      ! thermal conductivity of organic soil (Farouki, 1986) [W/m/K]
-    real(r8)           :: om_watsat_lake = 0.9_r8       ! porosity of organic soil
-    real(r8)           :: om_hksat_lake  = 0.1_r8       ! saturated hydraulic conductivity of organic soil [mm/s]
-    real(r8)           :: om_sucsat_lake = 10.3_r8      ! saturated suction for organic matter (Letts, 2000)
-    real(r8)           :: om_b_lake      = 2.7_r8       ! Clapp Hornberger paramater for oragnic soil (Letts, 2000) (lake)
-    real(r8)           :: om_watsat                     ! porosity of organic soil
-    real(r8)           :: om_hksat                      ! saturated hydraulic conductivity of organic soil [mm/s]
-    real(r8)           :: om_sucsat                     ! saturated suction for organic matter (mm)(Letts, 2000)
-    real(r8)           :: om_csol        = 2.5_r8       ! heat capacity of peat soil *10^6 (J/K m3) (Farouki, 1986)
-    real(r8)           :: om_tkd         = 0.05_r8      ! thermal conductivity of dry organic soil (Farouki, 1981)
-    real(r8)           :: om_b                          ! Clapp Hornberger paramater for oragnic soil (Letts, 2000)
-    real(r8)           :: zsapric        = 0.5_r8       ! depth (m) that organic matter takes on characteristics of sapric peat
-    real(r8)           :: pcalpha        = 0.5_r8       ! percolation threshold
-    real(r8)           :: pcbeta         = 0.139_r8     ! percolation exponent
-    real(r8)           :: pc_lake        = 0.5_r8       ! percolation threshold
-    real(r8)           :: perc_frac                     ! "percolating" fraction of organic soil
-    real(r8)           :: perc_norm                     ! normalize to 1 when 100% organic soil
-    real(r8)           :: uncon_hksat                   ! series conductivity of mineral/organic soil
-    real(r8)           :: uncon_frac                    ! fraction of "unconnected" soil
-    real(r8)           :: bd                            ! bulk density of dry soil material [kg/m^3]
-    real(r8)           :: tkm                           ! mineral conductivity
-    real(r8)           :: xksat                         ! maximum hydraulic conductivity of soil [mm/s]
-    real(r8)           :: clay,sand                     ! temporaries
-    real(r8)           :: organic_max                   ! organic matter (kg/m3) where soil is assumed to act like peat
-    integer            :: dimid                         ! dimension id
-    logical            :: readvar 
-    type(file_desc_t)  :: ncid                          ! netcdf id
-    real(r8) ,pointer  :: zsoifl (:)                    ! Output: [real(r8) (:)]  original soil midpoint 
-    real(r8) ,pointer  :: zisoifl (:)                   ! Output: [real(r8) (:)]  original soil interface depth 
-    real(r8) ,pointer  :: dzsoifl (:)                   ! Output: [real(r8) (:)]  original soil thickness 
-    real(r8) ,pointer  :: gti (:)                       ! read in - fmax 
-    real(r8) ,pointer  :: sand3d (:,:)                  ! read in - soil texture: percent sand (needs to be a pointer for use in ncdio)
-    real(r8) ,pointer  :: clay3d (:,:)                  ! read in - soil texture: percent clay (needs to be a pointer for use in ncdio)
-    real(r8) ,pointer  :: organic3d (:,:)               ! read in - organic matter: kg/m3 (needs to be a pointer for use in ncdio)
-    character(len=256) :: locfn                         ! local filename
-    integer            :: ipedof  
-    integer            :: begp, endp
-    integer            :: begc, endc
-    integer            :: begg, endg
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    do c = begc,endc
-       soilstate_inst%smpmin_col(c) = -1.e8_r8
-    end do
-
-    ! --------------------------------------------------------------------
-    ! Read namelist
-    ! --------------------------------------------------------------------
-
-    call ReadNL( nlfilename )
-
-    ! --------------------------------------------------------------------
-    ! Initialize root fraction (computing from surface, d is depth in meter):
-    ! --------------------------------------------------------------------
-
-    ! Currently pervious road has same properties as soil
-    do c = begc,endc
-       l = col%landunit(c)
-
-       if (lun%urbpoi(l) .and. col%itype(c) == icol_road_perv) then 
-          do lev = 1, nlevgrnd
-             soilstate_inst%rootfr_road_perv_col(c,lev) = 0._r8
-          enddo
-          do lev = 1,nlevsoi
-             soilstate_inst%rootfr_road_perv_col(c,lev) = 1.0_r8/real(nlevsoi,r8)
-          end do
-! remove roots below bedrock layer
-          soilstate_inst%rootfr_road_perv_col(c,1:col%nbedrock(c)) = &
-               soilstate_inst%rootfr_road_perv_col(c,1:col%nbedrock(c)) &
-               + sum(soilstate_inst%rootfr_road_perv_col(c,col%nbedrock(c)+1:nlevsoi)) &
-               /real(col%nbedrock(c))
-          soilstate_inst%rootfr_road_perv_col(c,col%nbedrock(c)+1:nlevsoi) = 0._r8
-       end if
-    end do
-
-    do c = bounds%begc,bounds%endc
-       l = col%landunit(c)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          soilstate_inst%rootfr_col (c,nlevsoi+1:nlevgrnd) = 0._r8
-       else
-          ! Inactive CH4 columns 
-          ! (Also includes (lun%itype(l)==istdlak .and.  allowlakeprod), which used to be
-          ! in a separate branch of the conditional)
-          soilstate_inst%rootfr_col (c,:) = spval
-       end if
-    end do
-
-    ! Initialize root fraction 
-    ! Note that fates has its own root fraction root fraction routine and should not
-    ! use the following since it depends on patch%itype - which fates should not use
-
-    if (.not. use_fates) then
-        call init_vegrootfr(bounds, nlevsoi, nlevgrnd, &
-             soilstate_inst%rootfr_patch(begp:endp,1:nlevgrnd),'water')
-        call init_vegrootfr(bounds, nlevsoi, nlevgrnd, &
-             soilstate_inst%crootfr_patch(begp:endp,1:nlevgrnd),'carbon')
-     end if
-
-    ! --------------------------------------------------------------------
-    ! dynamic memory allocation
-    ! --------------------------------------------------------------------
-
-    allocate(sand3d(begg:endg,nlevsoifl))
-    allocate(clay3d(begg:endg,nlevsoifl))
-
-    ! Determine organic_max from parameter file
-
-    call getfil (paramfile, locfn, 0)
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-    call ncd_io(ncid=ncid, varname='organic_max', flag='read', data=organic_max, readvar=readvar)
-    if ( .not. readvar ) call endrun(msg=' ERROR: organic_max not on param file'//errMsg(sourcefile, __LINE__))
-    call ncd_pio_closefile(ncid)
-
-    ! --------------------------------------------------------------------
-    ! Read surface dataset
-    ! --------------------------------------------------------------------
-
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read soil color, sand and clay boundary data .....'
-    end if
-
-    call getfil (fsurdat, locfn, 0)
-    call ncd_pio_openfile (ncid, locfn, 0)
-
-    ! Read in organic matter dataset 
-
-    allocate(organic3d(begg:endg,nlevsoifl))
-    call organicrd(organic3d)
-
-    ! Read in sand and clay data
-
-    call ncd_io(ncid=ncid, varname='PCT_SAND', flag='read', data=sand3d, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: PCT_SAND NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-
-    call ncd_io(ncid=ncid, varname='PCT_CLAY', flag='read', data=clay3d, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: PCT_CLAY NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-
-    do p = begp,endp
-       g = patch%gridcell(p)
-       if ( sand3d(g,1)+clay3d(g,1) == 0.0_r8 )then
-          if ( any( sand3d(g,:)+clay3d(g,:) /= 0.0_r8 ) )then
-             call endrun(msg='found depth points that do NOT sum to zero when surface does'//&
-                  errMsg(sourcefile, __LINE__)) 
-          end if
-          sand3d(g,:) = 1.0_r8
-          clay3d(g,:) = 1.0_r8
-       end if
-       if ( any( sand3d(g,:)+clay3d(g,:) == 0.0_r8 ) )then
-          call endrun(msg='after setting, found points sum to zero'//errMsg(sourcefile, __LINE__)) 
-       end if
-
-       soilstate_inst%sandfrac_patch(p) = sand3d(g,1)/100.0_r8
-       soilstate_inst%clayfrac_patch(p) = clay3d(g,1)/100.0_r8
-    end do
-
-    ! Read fmax
-
-    allocate(gti(begg:endg))
-    call ncd_io(ncid=ncid, varname='FMAX', flag='read', data=gti, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: FMAX NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = begc, endc
-       g = col%gridcell(c)
-       soilstate_inst%wtfact_col(c) = gti(g)
-    end do
-    deallocate(gti)
-
-    ! Close file
-
-    call ncd_pio_closefile(ncid)
-
-    ! --------------------------------------------------------------------
-    ! get original soil depths to be used in interpolation of sand and clay
-    ! --------------------------------------------------------------------
-
-    allocate(zsoifl(1:nlevsoifl), zisoifl(0:nlevsoifl), dzsoifl(1:nlevsoifl))
-    do j = 1, nlevsoifl
-       zsoifl(j) = 0.025*(exp(0.5_r8*(j-0.5_r8))-1._r8)    !node depths
-    enddo
-
-    dzsoifl(1) = 0.5_r8*(zsoifl(1)+zsoifl(2))             !thickness b/n two interfaces
-    do j = 2,nlevsoifl-1
-       dzsoifl(j)= 0.5_r8*(zsoifl(j+1)-zsoifl(j-1))
-    enddo
-    dzsoifl(nlevsoifl) = zsoifl(nlevsoifl)-zsoifl(nlevsoifl-1)
-
-    zisoifl(0) = 0._r8
-    do j = 1, nlevsoifl-1
-       zisoifl(j) = 0.5_r8*(zsoifl(j)+zsoifl(j+1))         !interface depths
-    enddo
-    zisoifl(nlevsoifl) = zsoifl(nlevsoifl) + 0.5_r8*dzsoifl(nlevsoifl)
-
-    ! --------------------------------------------------------------------
-    ! Set soil hydraulic and thermal properties: non-lake
-    ! --------------------------------------------------------------------
-
-    !   urban roof, sunwall and shadewall thermal properties used to 
-    !   derive thermal conductivity and heat capacity are set to special 
-    !   value because thermal conductivity and heat capacity for urban 
-    !   roof, sunwall and shadewall are prescribed in SoilThermProp.F90 
-    !   in SoilPhysicsMod.F90
-
-
-    do c = begc, endc
-       g = col%gridcell(c)
-       l = col%landunit(c)
-
-       if (lun%itype(l)==istwet .or. lun%itype(l)==istice_mec) then
-
-          do lev = 1,nlevgrnd
-             soilstate_inst%bsw_col(c,lev)    = spval
-             soilstate_inst%watsat_col(c,lev) = spval
-             soilstate_inst%watfc_col(c,lev)  = spval
-             soilstate_inst%hksat_col(c,lev)  = spval
-             soilstate_inst%sucsat_col(c,lev) = spval
-             soilstate_inst%watdry_col(c,lev) = spval 
-             soilstate_inst%watopt_col(c,lev) = spval 
-             soilstate_inst%bd_col(c,lev)     = spval 
-             if (lev <= nlevsoi) then
-                soilstate_inst%cellsand_col(c,lev) = spval
-                soilstate_inst%cellclay_col(c,lev) = spval
-                soilstate_inst%cellorg_col(c,lev)  = spval
-             end if
-          end do
-
-          do lev = 1,nlevgrnd
-             soilstate_inst%tkmg_col(c,lev)   = spval
-             soilstate_inst%tksatu_col(c,lev) = spval
-             soilstate_inst%tkdry_col(c,lev)  = spval
-             soilstate_inst%csol_col(c,lev)= spval
-          end do
-
-       else if (lun%urbpoi(l) .and. (col%itype(c) /= icol_road_perv) .and. (col%itype(c) /= icol_road_imperv) )then
-
-          ! Urban Roof, sunwall, shadewall properties set to special value
-          do lev = 1,nlevgrnd
-             soilstate_inst%watsat_col(c,lev) = spval
-             soilstate_inst%watfc_col(c,lev)  = spval
-             soilstate_inst%bsw_col(c,lev)    = spval
-             soilstate_inst%hksat_col(c,lev)  = spval
-             soilstate_inst%sucsat_col(c,lev) = spval
-             soilstate_inst%watdry_col(c,lev) = spval 
-             soilstate_inst%watopt_col(c,lev) = spval 
-             soilstate_inst%bd_col(c,lev) = spval 
-             if (lev <= nlevsoi) then
-                soilstate_inst%cellsand_col(c,lev) = spval
-                soilstate_inst%cellclay_col(c,lev) = spval
-                soilstate_inst%cellorg_col(c,lev)  = spval
-             end if
-          end do
-
-          do lev = 1,nlevgrnd
-             soilstate_inst%tkmg_col(c,lev)   = spval
-             soilstate_inst%tksatu_col(c,lev) = spval
-             soilstate_inst%tkdry_col(c,lev)  = spval
-             soilstate_inst%csol_col(c,lev)   = spval
-          end do
-
-       else
-
-          do lev = 1,nlevgrnd
-             ! DML - this if statement could probably be removed and just the
-             ! top part used for all soil layer structures
-             if ( soil_layerstruct /= '10SL_3.5m' )then ! apply soil texture from 10 layer input dataset 
-                if (lev .eq. 1) then
-                   clay = clay3d(g,1)
-                   sand = sand3d(g,1)
-                   om_frac = organic3d(g,1)/organic_max 
-                else if (lev <= nlevsoi) then
-                   do j = 1,nlevsoifl-1
-                      if (zisoi(lev) >= zisoifl(j) .AND. zisoi(lev) < zisoifl(j+1)) then
-                         clay = clay3d(g,j+1)
-                         sand = sand3d(g,j+1)
-                         om_frac = organic3d(g,j+1)/organic_max    
-                      endif
-                   end do
-                else
-                   clay = clay3d(g,nlevsoifl)
-                   sand = sand3d(g,nlevsoifl)
-                   om_frac = 0._r8
-                endif
-             else
-                if (lev <= nlevsoi) then ! duplicate clay and sand values from 10th soil layer
-                   clay = clay3d(g,lev)
-                   sand = sand3d(g,lev)
-                   if ( organic_frac_squared )then
-                      om_frac = (organic3d(g,lev)/organic_max)**2._r8
-                   else
-                      om_frac = organic3d(g,lev)/organic_max
-                   end if
-                else
-                   clay = clay3d(g,nlevsoi)
-                   sand = sand3d(g,nlevsoi)
-                   om_frac = 0._r8
-                endif
-             end if
-
-             if (lun%itype(l) == istdlak) then
-
-                if (lev <= nlevsoi) then
-                   soilstate_inst%cellsand_col(c,lev) = sand
-                   soilstate_inst%cellclay_col(c,lev) = clay
-                   soilstate_inst%cellorg_col(c,lev)  = om_frac*organic_max
-                end if
-
-             else if (lun%itype(l) /= istdlak) then  ! soil columns of both urban and non-urban types
-
-                if (lun%urbpoi(l)) then
-                   om_frac = 0._r8 ! No organic matter for urban
-                end if
-
-                if (lev <= nlevsoi) then
-                   soilstate_inst%cellsand_col(c,lev) = sand
-                   soilstate_inst%cellclay_col(c,lev) = clay
-                   soilstate_inst%cellorg_col(c,lev)  = om_frac*organic_max
-                end if
-
-                ! Note that the following properties are overwritten for urban impervious road 
-                ! layers that are not soil in SoilThermProp.F90 within SoilTemperatureMod.F90
-
-                !determine the type of pedotransfer function to be used based on soil order
-                !I will use the following implementation to further explore the ET problem, now
-                !I set soil order to 0 for all soils. Jinyun Tang, Mar 20, 2014
-
-                ipedof=get_ipedof(0)
-                call pedotransf(ipedof, sand, clay, &
-                     soilstate_inst%watsat_col(c,lev), soilstate_inst%bsw_col(c,lev), soilstate_inst%sucsat_col(c,lev), xksat)
-
-                om_watsat         = max(0.93_r8 - 0.1_r8   *(zsoi(lev)/zsapric), 0.83_r8)
-                om_b              = min(2.7_r8  + 9.3_r8   *(zsoi(lev)/zsapric), 12.0_r8)
-                om_sucsat         = min(10.3_r8 - 0.2_r8   *(zsoi(lev)/zsapric), 10.1_r8)
-                om_hksat          = max(0.28_r8 - 0.2799_r8*(zsoi(lev)/zsapric), xksat)
-
-                soilstate_inst%bd_col(c,lev)        = (1._r8 - soilstate_inst%watsat_col(c,lev))*2.7e3_r8 
-                soilstate_inst%watsat_col(c,lev)    = (1._r8 - om_frac) * soilstate_inst%watsat_col(c,lev) + om_watsat*om_frac
-                tkm                                 = (1._r8-om_frac) * (8.80_r8*sand+2.92_r8*clay)/(sand+clay)+om_tkm*om_frac ! W/(m K)
-                soilstate_inst%bsw_col(c,lev)       = (1._r8-om_frac) * (2.91_r8 + 0.159_r8*clay) + om_frac*om_b   
-                soilstate_inst%sucsat_col(c,lev)    = (1._r8-om_frac) * soilstate_inst%sucsat_col(c,lev) + om_sucsat*om_frac  
-                soilstate_inst%hksat_min_col(c,lev) = xksat
-
-                ! perc_frac is zero unless perf_frac greater than percolation threshold
-                if (om_frac > pcalpha) then
-                   perc_norm=(1._r8 - pcalpha)**(-pcbeta)
-                   perc_frac=perc_norm*(om_frac - pcalpha)**pcbeta
-                else
-                   perc_frac=0._r8
-                endif
-
-                ! uncon_frac is fraction of mineral soil plus fraction of "nonpercolating" organic soil
-                uncon_frac=(1._r8-om_frac)+(1._r8-perc_frac)*om_frac
-
-                ! uncon_hksat is series addition of mineral/organic conductivites
-                if (om_frac < 1._r8) then
-                   uncon_hksat=uncon_frac/((1._r8-om_frac)/xksat &
-                        +((1._r8-perc_frac)*om_frac)/om_hksat)
-                else
-                   uncon_hksat = 0._r8
-                end if
-                soilstate_inst%hksat_col(c,lev)  = uncon_frac*uncon_hksat + (perc_frac*om_frac)*om_hksat
-
-                soilstate_inst%tkmg_col(c,lev)   = tkm ** (1._r8- soilstate_inst%watsat_col(c,lev))           
-
-                soilstate_inst%tksatu_col(c,lev) = soilstate_inst%tkmg_col(c,lev)*0.57_r8**soilstate_inst%watsat_col(c,lev)
-
-                soilstate_inst%tkdry_col(c,lev)  = ((0.135_r8*soilstate_inst%bd_col(c,lev) + 64.7_r8) / &
-                     (2.7e3_r8 - 0.947_r8*soilstate_inst%bd_col(c,lev)))*(1._r8-om_frac) + om_tkd*om_frac  
-
-                soilstate_inst%csol_col(c,lev)   = ((1._r8-om_frac)*(2.128_r8*sand+2.385_r8*clay) / (sand+clay) + &
-                     om_csol*om_frac)*1.e6_r8  ! J/(m3 K)
-
-                soilstate_inst%watdry_col(c,lev) = soilstate_inst%watsat_col(c,lev) * &
-                     (316230._r8/soilstate_inst%sucsat_col(c,lev)) ** (-1._r8/soilstate_inst%bsw_col(c,lev)) 
-                soilstate_inst%watopt_col(c,lev) = soilstate_inst%watsat_col(c,lev) * &
-                     (158490._r8/soilstate_inst%sucsat_col(c,lev)) ** (-1._r8/soilstate_inst%bsw_col(c,lev)) 
-
-                !! added by K.Sakaguchi for beta from Lee and Pielke, 1992
-                ! water content at field capacity, defined as hk = 0.1 mm/day
-                ! used eqn (7.70) in CLM3 technote with k = 0.1 (mm/day) / secspday (day/sec)
-                soilstate_inst%watfc_col(c,lev) = soilstate_inst%watsat_col(c,lev) * &
-                     (0.1_r8 / (soilstate_inst%hksat_col(c,lev)*secspday))**(1._r8/(2._r8*soilstate_inst%bsw_col(c,lev)+3._r8))
-             end if
-          end do
-
-          ! Urban pervious and impervious road
-          if (col%itype(c) == icol_road_imperv) then
-             ! Impervious road layers -- same as above except set watdry and watopt as missing
-             do lev = 1,nlevgrnd
-                soilstate_inst%watdry_col(c,lev) = spval 
-                soilstate_inst%watopt_col(c,lev) = spval 
-             end do
-          else if (col%itype(c) == icol_road_perv) then 
-             ! pervious road layers  - set in UrbanInitTimeConst
-          end if
-
-       end if
-    end do
-
-    ! --------------------------------------------------------------------
-    ! Set soil hydraulic and thermal properties: lake
-    ! --------------------------------------------------------------------
-
-    do c = begc, endc
-       g = col%gridcell(c)
-       l = col%landunit(c)
-
-       if (lun%itype(l)==istdlak) then
-
-          do lev = 1,nlevgrnd
-             if ( lev <= nlevsoi )then
-                clay    =  soilstate_inst%cellclay_col(c,lev)
-                sand    =  soilstate_inst%cellsand_col(c,lev)
-                if ( organic_frac_squared )then
-                   om_frac = (soilstate_inst%cellorg_col(c,lev)/organic_max)**2._r8
-                else
-                   om_frac = soilstate_inst%cellorg_col(c,lev)/organic_max
-                end if
-             else
-                clay    = soilstate_inst%cellclay_col(c,nlevsoi)
-                sand    = soilstate_inst%cellsand_col(c,nlevsoi)
-                om_frac = 0.0_r8
-             end if
-
-             soilstate_inst%watsat_col(c,lev) = 0.489_r8 - 0.00126_r8*sand
-
-             soilstate_inst%bsw_col(c,lev)    = 2.91 + 0.159*clay
-
-             soilstate_inst%sucsat_col(c,lev) = 10._r8 * ( 10._r8**(1.88_r8-0.0131_r8*sand) )
-
-             bd = (1._r8-soilstate_inst%watsat_col(c,lev))*2.7e3_r8
-
-             soilstate_inst%watsat_col(c,lev) = (1._r8 - om_frac)*soilstate_inst%watsat_col(c,lev) + om_watsat_lake * om_frac
-
-             tkm = (1._r8-om_frac)*(8.80_r8*sand+2.92_r8*clay)/(sand+clay) + om_tkm * om_frac ! W/(m K)
-
-             soilstate_inst%bsw_col(c,lev)    = (1._r8-om_frac)*(2.91_r8 + 0.159_r8*clay) + om_frac * om_b_lake
-
-             soilstate_inst%sucsat_col(c,lev) = (1._r8-om_frac)*soilstate_inst%sucsat_col(c,lev) + om_sucsat_lake * om_frac
-
-             xksat = 0.0070556 *( 10.**(-0.884+0.0153*sand) ) ! mm/s
-
-             ! perc_frac is zero unless perf_frac greater than percolation threshold
-             if (om_frac > pc_lake) then
-                perc_norm = (1._r8 - pc_lake)**(-pcbeta)
-                perc_frac = perc_norm*(om_frac - pc_lake)**pcbeta
-             else
-                perc_frac = 0._r8
-             endif
-
-             ! uncon_frac is fraction of mineral soil plus fraction of "nonpercolating" organic soil
-             uncon_frac = (1._r8-om_frac) + (1._r8-perc_frac)*om_frac
-
-             ! uncon_hksat is series addition of mineral/organic conductivites
-             if (om_frac < 1._r8) then
-                xksat = 0.0070556 *( 10.**(-0.884+0.0153*sand) ) ! mm/s
-                uncon_hksat = uncon_frac/((1._r8-om_frac)/xksat + ((1._r8-perc_frac)*om_frac)/om_hksat_lake)
-             else
-                uncon_hksat = 0._r8
-             end if
-
-             soilstate_inst%hksat_col(c,lev)  = uncon_frac*uncon_hksat + (perc_frac*om_frac)*om_hksat_lake
-             soilstate_inst%tkmg_col(c,lev)   = tkm ** (1._r8- soilstate_inst%watsat_col(c,lev))
-             soilstate_inst%tksatu_col(c,lev) = soilstate_inst%tkmg_col(c,lev)*0.57_r8**soilstate_inst%watsat_col(c,lev)
-             soilstate_inst%tkdry_col(c,lev)  = ((0.135_r8*bd + 64.7_r8) / (2.7e3_r8 - 0.947_r8*bd))*(1._r8-om_frac) + &
-                                       om_tkd * om_frac
-             soilstate_inst%csol_col(c,lev)   = ((1._r8-om_frac)*(2.128_r8*sand+2.385_r8*clay) / (sand+clay) +   &
-                                       om_csol * om_frac)*1.e6_r8  ! J/(m3 K)
-             soilstate_inst%watdry_col(c,lev) = soilstate_inst%watsat_col(c,lev) &
-                  * (316230._r8/soilstate_inst%sucsat_col(c,lev)) ** (-1._r8/soilstate_inst%bsw_col(c,lev))
-             soilstate_inst%watopt_col(c,lev) = soilstate_inst%watsat_col(c,lev) &
-                  * (158490._r8/soilstate_inst%sucsat_col(c,lev)) ** (-1._r8/soilstate_inst%bsw_col(c,lev))
-
-             !! added by K.Sakaguchi for beta from Lee and Pielke, 1992
-             ! water content at field capacity, defined as hk = 0.1 mm/day
-             ! used eqn (7.70) in CLM3 technote with k = 0.1 (mm/day) / (# seconds/day)
-             soilstate_inst%watfc_col(c,lev) = soilstate_inst%watsat_col(c,lev) * (0.1_r8 / &
-                  (soilstate_inst%hksat_col(c,lev)*secspday))**(1._r8/(2._r8*soilstate_inst%bsw_col(c,lev)+3._r8))
-          end do
-       endif
-
-    end do
-
-    ! --------------------------------------------------------------------
-    ! Initialize threshold soil moisture and mass fracion of clay limited to 0.20
-    ! --------------------------------------------------------------------
-
-    do c = begc,endc
-       g = col%gridcell(c)
-
-       soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8
-       soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8)
-    end do
-
-    ! --------------------------------------------------------------------
-    ! Deallocate memory
-    ! --------------------------------------------------------------------
-
-    deallocate(sand3d, clay3d, organic3d)
-    deallocate(zisoifl, zsoifl, dzsoifl)
-
-  end subroutine SoilStateInitTimeConst
-
-end module SoilStateInitTimeConstMod
diff --git a/src/biogeophys/SoilStateType.F90 b/src/biogeophys/SoilStateType.F90
deleted file mode 100644
index 763165a37b..0000000000
--- a/src/biogeophys/SoilStateType.F90
+++ /dev/null
@@ -1,409 +0,0 @@
-module SoilStateType
-
-  !------------------------------------------------------------------------------
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-  use decompMod       , only : bounds_type
-  use abortutils      , only : endrun
-  use clm_varpar      , only : nlevsoi, nlevgrnd, nlevlak, nlayer, nlevsno
-  use clm_varcon      , only : spval
-  use clm_varctl      , only : use_hydrstress, use_cn, use_dynroot
-  use clm_varctl      , only : iulog, hist_wrtch4diag
-  use LandunitType    , only : lun                
-  use ColumnType      , only : col                
-  use PatchType       , only : patch                
-  !
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: soilstate_type
-
-     ! sand/ clay/ organic matter
-     real(r8), pointer :: sandfrac_patch       (:)   ! patch sand fraction
-     real(r8), pointer :: clayfrac_patch       (:)   ! patch clay fraction
-     real(r8), pointer :: mss_frc_cly_vld_col  (:)   ! col mass fraction clay limited to 0.20
-     real(r8), pointer :: cellorg_col          (:,:) ! col organic matter for gridcell containing column (1:nlevsoi)
-     real(r8), pointer :: cellsand_col         (:,:) ! sand value for gridcell containing column (1:nlevsoi)
-     real(r8), pointer :: cellclay_col         (:,:) ! clay value for gridcell containing column (1:nlevsoi)
-     real(r8), pointer :: bd_col               (:,:) ! col bulk density of dry soil material [kg/m^3] (CN)
-
-     ! hydraulic properties
-     real(r8), pointer :: hksat_col            (:,:) ! col hydraulic conductivity at saturation (mm H2O /s) 
-     real(r8), pointer :: hksat_min_col        (:,:) ! col mineral hydraulic conductivity at saturation (hksat) (mm/s)
-     real(r8), pointer :: hk_l_col             (:,:) ! col hydraulic conductivity (mm/s)
-     real(r8), pointer :: smp_l_col            (:,:) ! col soil matric potential (mm)
-     real(r8), pointer :: smpmin_col           (:)   ! col restriction for min of soil potential (mm) 
-     real(r8), pointer :: bsw_col              (:,:) ! col Clapp and Hornberger "b" (nlevgrnd)  
-     real(r8), pointer :: watsat_col           (:,:) ! col volumetric soil water at saturation (porosity) 
-     real(r8), pointer :: watdry_col           (:,:) ! col btran parameter for btran = 0
-     real(r8), pointer :: watopt_col           (:,:) ! col btran parameter for btran = 1
-     real(r8), pointer :: watfc_col            (:,:) ! col volumetric soil water at field capacity (nlevsoi)
-     real(r8), pointer :: sucsat_col           (:,:) ! col minimum soil suction (mm) (nlevgrnd) 
-     real(r8), pointer :: dsl_col              (:)   ! col dry surface layer thickness (mm)
-     real(r8), pointer :: soilresis_col        (:)   ! col soil evaporative resistance S&L14 (s/m)
-     real(r8), pointer :: soilbeta_col         (:)   ! col factor that reduces ground evaporation L&P1992(-)
-     real(r8), pointer :: soilalpha_col        (:)   ! col factor that reduces ground saturated specific humidity (-)
-     real(r8), pointer :: soilalpha_u_col      (:)   ! col urban factor that reduces ground saturated specific humidity (-) 
-     real(r8), pointer :: soilpsi_col          (:,:) ! col soil water potential in each soil layer (MPa) (CN)
-     real(r8), pointer :: wtfact_col           (:)   ! col maximum saturated fraction for a gridcell
-     real(r8), pointer :: porosity_col         (:,:) ! col soil porisity (1-bulk_density/soil_density) (VIC)
-     real(r8), pointer :: eff_porosity_col     (:,:) ! col effective porosity = porosity - vol_ice (nlevgrnd) 
-     real(r8), pointer :: gwc_thr_col          (:)   ! col threshold soil moisture based on clay content
-!scs: vangenuchten
-     real(r8), pointer :: msw_col              (:,:) ! col vanGenuchtenClapp "m"
-     real(r8), pointer :: nsw_col              (:,:) ! col vanGenuchtenClapp "n"
-     real(r8), pointer :: alphasw_col          (:,:) ! col vanGenuchtenClapp "nalpha"
-     real(r8), pointer :: watres_col           (:,:) ! residual soil water content
-     ! thermal conductivity / heat capacity
-     real(r8), pointer :: thk_col              (:,:) ! col thermal conductivity of each layer [W/m-K] 
-     real(r8), pointer :: tkmg_col             (:,:) ! col thermal conductivity, soil minerals  [W/m-K] (new) (nlevgrnd) 
-     real(r8), pointer :: tkdry_col            (:,:) ! col thermal conductivity, dry soil (W/m/Kelvin) (nlevgrnd) 
-     real(r8), pointer :: tksatu_col           (:,:) ! col thermal conductivity, saturated soil [W/m-K] (new) (nlevgrnd) 
-     real(r8), pointer :: csol_col             (:,:) ! col heat capacity, soil solids (J/m**3/Kelvin) (nlevgrnd) 
-
-     ! roots
-     real(r8), pointer :: rootr_patch          (:,:) ! patch effective fraction of roots in each soil layer (nlevgrnd)
-     real(r8), pointer :: rootr_col            (:,:) ! col effective fraction of roots in each soil layer (nlevgrnd)  
-     real(r8), pointer :: rootfr_col           (:,:) ! col fraction of roots in each soil layer (nlevgrnd) 
-     real(r8), pointer :: rootfr_patch         (:,:) ! patch fraction of roots for water in each soil layer (nlevgrnd)
-     real(r8), pointer :: crootfr_patch        (:,:) ! patch fraction of roots for carbon in each soil layer (nlevgrnd)
-     real(r8), pointer :: root_depth_patch     (:)   ! root depth
-     real(r8), pointer :: rootr_road_perv_col  (:,:) ! col effective fraction of roots in each soil layer of urban pervious road
-     real(r8), pointer :: rootfr_road_perv_col (:,:) ! col effective fraction of roots in each soil layer of urban pervious road
-     real(r8), pointer :: k_soil_root_patch    (:,:) ! patch soil-root interface conductance [mm/s]
-     real(r8), pointer :: root_conductance_patch(:,:) ! patch root conductance [mm/s]
-     real(r8), pointer :: soil_conductance_patch(:,:) ! patch soil conductance [mm/s]
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, public  :: Restart
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type soilstate_type
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(soilstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !ARGUMENTS:
-    class(soilstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    integer :: begg, endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate(this%mss_frc_cly_vld_col  (begc:endc))                     ; this%mss_frc_cly_vld_col  (:)   = nan
-    allocate(this%sandfrac_patch       (begp:endp))                     ; this%sandfrac_patch       (:)   = nan
-    allocate(this%clayfrac_patch       (begp:endp))                     ; this%clayfrac_patch       (:)   = nan
-    allocate(this%cellorg_col          (begc:endc,nlevsoi))             ; this%cellorg_col          (:,:) = nan 
-    allocate(this%cellsand_col         (begc:endc,nlevsoi))             ; this%cellsand_col         (:,:) = nan 
-    allocate(this%cellclay_col         (begc:endc,nlevsoi))             ; this%cellclay_col         (:,:) = nan 
-    allocate(this%bd_col               (begc:endc,nlevgrnd))            ; this%bd_col               (:,:) = nan
-
-    allocate(this%hksat_col            (begc:endc,nlevgrnd))            ; this%hksat_col            (:,:) = spval
-    allocate(this%hksat_min_col        (begc:endc,nlevgrnd))            ; this%hksat_min_col        (:,:) = spval
-    allocate(this%hk_l_col             (begc:endc,nlevgrnd))            ; this%hk_l_col             (:,:) = nan   
-    allocate(this%smp_l_col            (begc:endc,nlevgrnd))            ; this%smp_l_col            (:,:) = nan   
-    allocate(this%smpmin_col           (begc:endc))                     ; this%smpmin_col           (:)   = nan
-
-    allocate(this%bsw_col              (begc:endc,nlevgrnd))            ; this%bsw_col              (:,:) = nan
-    allocate(this%watsat_col           (begc:endc,nlevgrnd))            ; this%watsat_col           (:,:) = nan
-    allocate(this%watdry_col           (begc:endc,nlevgrnd))            ; this%watdry_col           (:,:) = spval
-    allocate(this%watopt_col           (begc:endc,nlevgrnd))            ; this%watopt_col           (:,:) = spval
-    allocate(this%watfc_col            (begc:endc,nlevgrnd))            ; this%watfc_col            (:,:) = nan
-    allocate(this%sucsat_col           (begc:endc,nlevgrnd))            ; this%sucsat_col           (:,:) = spval
-    allocate(this%dsl_col              (begc:endc))                     ; this%dsl_col         (:)   = spval!nan   
-    allocate(this%soilresis_col        (begc:endc))                     ; this%soilresis_col         (:)   = spval!nan   
-    allocate(this%soilbeta_col         (begc:endc))                     ; this%soilbeta_col         (:)   = nan   
-    allocate(this%soilalpha_col        (begc:endc))                     ; this%soilalpha_col        (:)   = nan
-    allocate(this%soilalpha_u_col      (begc:endc))                     ; this%soilalpha_u_col      (:)   = nan
-    allocate(this%soilpsi_col          (begc:endc,nlevgrnd))            ; this%soilpsi_col          (:,:) = nan
-    allocate(this%wtfact_col           (begc:endc))                     ; this%wtfact_col           (:)   = nan
-    allocate(this%porosity_col         (begc:endc,nlayer))              ; this%porosity_col         (:,:) = spval
-    allocate(this%eff_porosity_col     (begc:endc,nlevgrnd))            ; this%eff_porosity_col     (:,:) = spval
-    allocate(this%gwc_thr_col          (begc:endc))                     ; this%gwc_thr_col          (:)   = nan
-
-    allocate(this%thk_col              (begc:endc,-nlevsno+1:nlevgrnd)) ; this%thk_col              (:,:) = nan
-    allocate(this%tkmg_col             (begc:endc,nlevgrnd))            ; this%tkmg_col             (:,:) = nan
-    allocate(this%tkdry_col            (begc:endc,nlevgrnd))            ; this%tkdry_col            (:,:) = nan
-    allocate(this%tksatu_col           (begc:endc,nlevgrnd))            ; this%tksatu_col           (:,:) = nan
-    allocate(this%csol_col             (begc:endc,nlevgrnd))            ; this%csol_col             (:,:) = nan
-
-    allocate(this%rootr_patch          (begp:endp,1:nlevgrnd))          ; this%rootr_patch          (:,:) = nan
-    allocate(this%root_depth_patch     (begp:endp))                     ; this%root_depth_patch     (:)   = nan
-    allocate(this%rootr_col            (begc:endc,nlevgrnd))            ; this%rootr_col            (:,:) = nan
-    allocate(this%rootr_road_perv_col  (begc:endc,1:nlevgrnd))          ; this%rootr_road_perv_col  (:,:) = nan
-    allocate(this%rootfr_patch         (begp:endp,1:nlevgrnd))          ; this%rootfr_patch         (:,:) = nan
-    allocate(this%crootfr_patch        (begp:endp,1:nlevgrnd))          ; this%crootfr_patch        (:,:) = nan
-    allocate(this%rootfr_col           (begc:endc,1:nlevgrnd))          ; this%rootfr_col           (:,:) = nan 
-    allocate(this%rootfr_road_perv_col (begc:endc,1:nlevgrnd))          ; this%rootfr_road_perv_col (:,:) = nan
-    allocate(this%k_soil_root_patch    (begp:endp,1:nlevsoi))           ; this%k_soil_root_patch (:,:) = nan
-    allocate(this%root_conductance_patch(begp:endp,1:nlevsoi))          ; this%root_conductance_patch (:,:) = nan
-    allocate(this%soil_conductance_patch(begp:endp,1:nlevsoi))          ; this%soil_conductance_patch (:,:) = nan
-    allocate(this%msw_col              (begc:endc,1:nlevgrnd))          ; this%msw_col              (:,:) = nan
-    allocate(this%nsw_col              (begc:endc,1:nlevgrnd))          ; this%nsw_col              (:,:) = nan
-    allocate(this%alphasw_col          (begc:endc,1:nlevgrnd))          ; this%alphasw_col          (:,:) = nan
-    allocate(this%watres_col           (begc:endc,1:nlevgrnd))          ; this%watres_col           (:,:) = nan
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d, no_snow_normal
-    !
-    ! !ARGUMENTS:
-    class(soilstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begc, endc
-    integer :: begp, endp
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-
-    active = "inactive"
-
-    call hist_addfld2d (fname='SMP',  units='mm', type2d='levgrnd',  &
-         avgflag='A', long_name='soil matric potential (vegetated landunits only)', &
-         ptr_col=this%smp_l_col, set_spec=spval, l2g_scale_type='veg', default='inactive')
-
-       this%root_conductance_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='KROOT', units='1/s', type2d='levsoi', &
-          avgflag='A', long_name='root conductance each soil layer', &
-          ptr_patch=this%root_conductance_patch, default='inactive')
-
-       this%soil_conductance_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='KSOIL', units='1/s', type2d='levsoi', &
-          avgflag='A', long_name='soil conductance in each soil layer', &
-          ptr_patch=this%soil_conductance_patch, default='inactive')
-
-    if (use_cn) then
-       this%bsw_col(begc:endc,:) = spval 
-       call hist_addfld2d (fname='bsw', units='unitless', type2d='levgrnd', &
-            avgflag='A', long_name='clap and hornberger B', &
-            ptr_col=this%bsw_col, default='inactive')
-    end if
-
-    if (use_dynroot) then
-       this%rootfr_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='ROOTFR', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='fraction of roots in each soil layer', &
-            ptr_patch=this%rootfr_patch, default='inactive')
-    end if
-
-    if ( use_dynroot ) then
-       this%root_depth_patch(begp:endp) = spval
-        call hist_addfld1d (fname='ROOT_DEPTH', units="m", &
-             avgflag='A', long_name='rooting depth', &
-             ptr_patch=this%root_depth_patch, default='inactive' )
-     end if
-
-    if (use_cn) then
-       this%rootr_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='ROOTR', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='effective fraction of roots in each soil layer', &
-            ptr_patch=this%rootr_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%rootr_col(begc:endc,:) = spval
-       call hist_addfld2d (fname='ROOTR_COLUMN', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='effective fraction of roots in each soil layer', &
-            ptr_col=this%rootr_col, default='inactive')
-       
-    end if
-
-    if (use_cn) then
-       this%soilpsi_col(begc:endc,:) = spval
-       call hist_addfld2d (fname='SOILPSI', units='MPa', type2d='levgrnd', &
-            avgflag='A', long_name='soil water potential in each soil layer', &
-            ptr_col=this%soilpsi_col, default='inactive')
-    end if
-
-    this%thk_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%thk_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_TK', units='W/m-K', type2d='levsno', &
-         avgflag='A', long_name='Thermal conductivity', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_TK_ICE', units='W/m-K', type2d='levsno', &
-         avgflag='A', long_name='Thermal conductivity (ice landunits only)', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%hk_l_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='HK',  units='mm/s', type2d='levgrnd',  &
-         avgflag='A', long_name='hydraulic conductivity (vegetated landunits only)', &
-         ptr_col=this%hk_l_col, set_spec=spval, l2g_scale_type='veg', default='inactive')
-
-    this%soilalpha_col(begc:endc) = spval
-    call hist_addfld1d (fname='SoilAlpha',  units='unitless',  &
-         avgflag='A', long_name='factor limiting ground evap', &
-         ptr_col=this%soilalpha_col, set_urb=spval, default='inactive' )
-
-    this%soilalpha_u_col(begc:endc) = spval
-    call hist_addfld1d (fname='SoilAlpha_U',  units='unitless',  &
-         avgflag='A', long_name='urban factor limiting ground evap', &
-         ptr_col=this%soilalpha_u_col, set_nourb=spval, default='inactive')
-
-    if (use_cn) then
-       this%watsat_col(begc:endc,:) = spval 
-       call hist_addfld2d (fname='watsat', units='m^3/m^3', type2d='levgrnd', &
-            avgflag='A', long_name='water saturated', &
-            ptr_col=this%watsat_col, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%eff_porosity_col(begc:endc,:) = spval
-       call hist_addfld2d (fname='EFF_POROSITY', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='effective porosity = porosity - vol_ice', &
-            ptr_col=this%eff_porosity_col, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%watfc_col(begc:endc,:) = spval 
-       call hist_addfld2d (fname='watfc', units='m^3/m^3', type2d='levgrnd', &
-            avgflag='A', long_name='water field capacity', &
-            ptr_col=this%watfc_col, default='inactive')
-    end if
-
-    this%soilresis_col(begc:endc) = spval
-    call hist_addfld1d (fname='SOILRESIS',  units='s/m',  &
-         avgflag='A', long_name='soil resistance to evaporation', &
-         ptr_col=this%soilresis_col, default='inactive')
-
-    this%dsl_col(begc:endc) = spval
-    call hist_addfld1d (fname='DSL',  units='mm',  &
-         avgflag='A', long_name='dry surface layer thickness', &
-         ptr_col=this%dsl_col, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! Initialize module soil state variables to reasonable values
-    !
-    ! !USES:
-    use clm_varpar      , only : nlevgrnd
-    !
-    ! !ARGUMENTS:
-    class(soilstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    !-----------------------------------------------------------------------
-
-    this%smp_l_col(bounds%begc:bounds%endc,1:nlevgrnd) = -1000._r8
-    this%hk_l_col(bounds%begc:bounds%endc,1:nlevgrnd) = 0._r8
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !DESCRIPTION:
-    ! Read/Write module information to/from restart file.
-    !
-    ! !USES:
-    use ncdio_pio        , only : file_desc_t, ncd_io, ncd_double
-    use restUtilMod
-    use spmdMod          , only : masterproc
-    use RootBiophysMod   , only : init_vegrootfr
-    !
-    ! !ARGUMENTS:
-    class(soilstate_type) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c
-    logical  :: readvar
-    logical  :: readrootfr = .false.
-    !------------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='DSL', xtype=ncd_double,  &
-         dim1name='column', long_name='dsl thickness', units='mm', &
-         interpinic_flag='interp', readvar=readvar, data=this%dsl_col)
-    
-    call restartvar(ncid=ncid, flag=flag, varname='SOILRESIS', xtype=ncd_double,  &
-         dim1name='column', long_name='soil resistance', units='s/m', &
-         interpinic_flag='interp', readvar=readvar, data=this%soilresis_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='SMP', xtype=ncd_double,  &
-         dim1name='column', dim2name='levgrnd', switchdim=.true., &
-         long_name='soil matric potential', units='mm', &
-         interpinic_flag='interp', readvar=readvar, data=this%smp_l_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='HK', xtype=ncd_double,  &
-         dim1name='column', dim2name='levgrnd', switchdim=.true., &
-         long_name='hydraulic conductivity', units='mm/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%hk_l_col)
-
-     if( use_dynroot ) then
-         call restartvar(ncid=ncid, flag=flag, varname='root_depth', xtype=ncd_double,  &
-              dim1name='pft', &
-              long_name='root depth', units='m', &
-              interpinic_flag='interp', readvar=readvar, data=this%root_depth_patch)
- 
-         call restartvar(ncid=ncid, flag=flag, varname='rootfr', xtype=ncd_double,  &
-              dim1name='pft', dim2name='levgrnd', switchdim=.true., &
-              long_name='root fraction', units='', &
-              interpinic_flag='interp', readvar=readrootfr, data=this%rootfr_patch)
-     else
-         readrootfr = .false.
-     end if
-     if (flag=='read' .and. .not. readrootfr ) then
-            if (masterproc) then
-               write(iulog,*) "can't find rootfr in restart (or initial) file..."
-               write(iulog,*) "Initialize rootfr to default"
-            end if
-            call init_vegrootfr(bounds, nlevsoi, nlevgrnd, &
-            this%rootfr_patch(bounds%begp:bounds%endp,1:nlevgrnd), 'water')
-            call init_vegrootfr(bounds, nlevsoi, nlevgrnd, &
-            this%crootfr_patch(bounds%begp:bounds%endp,1:nlevgrnd), 'carbon')
-         end if
-    
-  end subroutine Restart
-
-end module SoilStateType
diff --git a/src/biogeophys/SoilWaterMovementMod.F90 b/src/biogeophys/SoilWaterMovementMod.F90
deleted file mode 100644
index d458768ed3..0000000000
--- a/src/biogeophys/SoilWaterMovementMod.F90
+++ /dev/null
@@ -1,194 +0,0 @@
-module SoilWaterMovementMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! DESCRIPTION
-  ! module contains different subroutines to couple soil and root water interactions
-  !
-  ! created by Jinyun Tang, Mar 12, 2014
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use shr_kind_mod      , only : r8 => shr_kind_r8
-  use shr_sys_mod         , only : shr_sys_flush
- 
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: init_soilwater_movement
-  !
-  ! !PUBLIC DATA MEMBERS:
-
-  ! !PRIVATE DATA MEMBERS:
-
-  ! Solution method 
-  integer, parameter :: zengdecker_2009 = 0
-  integer, parameter :: moisture_form = 1
-  integer, parameter :: mixed_form = 2
-  integer, parameter :: head_form = 3
-
-  ! Boundary conditions
-  integer, parameter :: bc_head  = 0
-  integer, parameter :: bc_flux  = 1
-  integer, parameter :: bc_zero_flux  = 2
-  integer, parameter :: bc_waterTable = 3
-  integer, parameter :: bc_aquifer    = 4
-
-  ! Soil hydraulic properties
-  integer, parameter :: soil_hp_clapphornberg_1978=0
-  integer, parameter :: soil_hp_vanGenuchten_1980=1
-
-  real(r8),parameter :: m_to_mm = 1.e3_r8 !convert meters to mm
-
-  integer :: soilwater_movement_method    ! method for solving richards equation
-  integer :: upper_boundary_condition     ! named variable for the boundary condition
-  integer :: lower_boundary_condition     ! named variable for the boundary condition
-
-  ! Adaptive time stepping algorithmic control parameters
-  real(r8) :: dtmin             ! minimum time step length (seconds)
-  real(r8) :: verySmall         ! a very small number: used to check for sub step completion
-  real(r8) :: xTolerUpper       ! tolerance to halve length of substep
-  real(r8) :: xTolerLower       ! tolerance to double length of substep
-  integer  :: expensive
-  integer  :: inexpensive
-  integer  :: flux_calculation
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !-----------------------------------------------------------------------
-
-contains
-
-!#1
-  !-----------------------------------------------------------------------
-  subroutine init_soilwater_movement()
-    !
-    !DESCRIPTION
-    !specify method for doing soil&root water interactions
-    !
-    ! !USES:
-    use abortutils      , only : endrun   
-    use fileutils       , only : getavu, relavu
-    use spmdMod         , only : mpicom, masterproc
-    use shr_mpi_mod     , only : shr_mpi_bcast
-    use clm_varctl      , only : iulog, use_bedrock
-    use controlMod      , only : NLFilename
-    use clm_nlUtilsMod  , only : find_nlgroup_name
-
-    ! !ARGUMENTS:
-    !------------------------------------------------------------------------------
-    implicit none
-    integer            :: nu_nml                     ! unit for namelist file
-    integer            :: nml_error                  ! namelist i/o error flag
-    character(*), parameter    :: subName = "('init_soilwater_movement')"
-
-    !-----------------------------------------------------------------------
-
-! MUST agree with name in namelist and read statement
-    namelist /soilwater_movement_inparm/      &
-         soilwater_movement_method,    &
-         upper_boundary_condition,     &
-         lower_boundary_condition,     &
-         dtmin,                        &
-         verySmall,                    &
-         xTolerUpper,                  &
-         xTolerLower,                  &
-         expensive,                    &
-         inexpensive,                  &
-         flux_calculation
-
-    ! Default values for namelist
-
-    soilwater_movement_method = zengdecker_2009
-    upper_boundary_condition = bc_flux
-    lower_boundary_condition = bc_aquifer
-
-    dtmin=60._r8          
-    verySmall=1.e-8_r8    
-    xTolerUpper=1.e-1_r8  
-    xTolerLower=1.e-2_r8  
-    expensive=42
-    inexpensive=1
-    flux_calculation=inexpensive  
-
-    ! Read soilwater_movement namelist
-    if (masterproc) then
-       nu_nml = getavu()
-       open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error )
-       call find_nlgroup_name(nu_nml, 'soilwater_movement_inparm', status=nml_error)
-       if (nml_error == 0) then
-          read(nu_nml, nml=soilwater_movement_inparm,iostat=nml_error)
-          if (nml_error /= 0) then
-             call endrun(subname // ':: ERROR reading soilwater_movement namelist')
-          end if
-       else
-          call endrun(subname // ':: ERROR reading soilwater_movement namelist')
-       end if
-       close(nu_nml)
-       call relavu( nu_nml )
-
-!  test for namelist consistency
-       if((soilwater_movement_method == zengdecker_2009) .and. &
-            (lower_boundary_condition /= bc_aquifer)) then
-          call endrun(subname // ':: ERROR inconsistent soilwater_movement namelist: ZD09 must use bc_aquifer lbc')
-       endif
-       if((use_bedrock) .and. (lower_boundary_condition /= bc_zero_flux)) then
-          call endrun(subname // ':: ERROR inconsistent soilwater_movement namelist: use_bedrock requires bc_zero_flux lbc')
-       endif
-    endif
-
-    call shr_mpi_bcast(soilwater_movement_method, mpicom)
-    call shr_mpi_bcast(upper_boundary_condition, mpicom)
-    call shr_mpi_bcast(lower_boundary_condition, mpicom)
-    call shr_mpi_bcast(dtmin, mpicom)
-    call shr_mpi_bcast(verySmall, mpicom)
-    call shr_mpi_bcast(xTolerUpper, mpicom)
-    call shr_mpi_bcast(xTolerLower, mpicom)
-    call shr_mpi_bcast(expensive, mpicom)
-    call shr_mpi_bcast(inexpensive, mpicom)
-    call shr_mpi_bcast(flux_calculation, mpicom)
-
-
-    if (masterproc) then
-
-       write(iulog,*) ' '
-       write(iulog,*) 'soilwater_movement settings:'
-       write(iulog,*) '  soilwater_movement_method  = ',soilwater_movement_method
-       write(iulog,*) '  upper_boundary_condition   = ',upper_boundary_condition
-       write(iulog,*) '  lower_boundary_condition   = ',lower_boundary_condition
-
-       write(iulog,*) '  use_bedrock                = ',use_bedrock
-       write(iulog,*) '  dtmin                      = ',dtmin
-       write(iulog,*) '  verySmall                  = ',verySmall
-       write(iulog,*) '  xTolerUpper                = ',xTolerUpper
-       write(iulog,*) '  xTolerLower                = ',xTolerLower
-       write(iulog,*) '  expensive                  = ',expensive
-       write(iulog,*) '  inexpensive                = ',inexpensive
-       write(iulog,*) '  flux_calculation           = ',flux_calculation
-    endif
-
-  end subroutine init_soilwater_movement
-  
-
-!#2
-   !------------------------------------------------------------------------------   
-   function use_aquifer_layer() result(lres)
-     !
-     !DESCRIPTION
-     ! return true if an aquifer layer is used 
-     ! otherwise false
-     implicit none
-     logical :: lres
-
-     if(lower_boundary_condition == bc_aquifer .or. lower_boundary_condition == bc_watertable)then
-        lres=.true.
-     else
-        lres=.false.
-     endif
-     return
-
-   end function use_aquifer_layer
-
- end module SoilWaterMovementMod
diff --git a/src/biogeophys/SoilWaterPlantSinkMod.F90 b/src/biogeophys/SoilWaterPlantSinkMod.F90
deleted file mode 100644
index 32854a3b0a..0000000000
--- a/src/biogeophys/SoilWaterPlantSinkMod.F90
+++ /dev/null
@@ -1,444 +0,0 @@
-module SoilWaterPlantSinkMod
-
-   use clm_varctl       , only : use_hydrstress
-   use decompMod        , only : bounds_type
-   use shr_kind_mod          , only : r8 => shr_kind_r8
-   use shr_log_mod           , only : errMsg => shr_log_errMsg
-   use abortutils            , only : endrun
-   use clm_varctl            , only : iulog
-   use landunit_varcon       , only : istsoil,istcrop
-   use column_varcon         , only : icol_road_perv
-   implicit none
-
-   character(len=*), parameter, private :: sourcefile = &
-         __FILE__
-
-contains
-   
-   subroutine Compute_EffecRootFrac_And_VertTranSink(bounds, num_hydrologyc, &
-         filter_hydrologyc, soilstate_inst, canopystate_inst, waterflux_inst, energyflux_inst)
-      
-      ! ---------------------------------------------------------------------------------
-      ! This is a wrapper for calculating the effective root fraction and soil
-      ! water sink due to plant transpiration. 
-      ! Calculate Soil Water Sink to Roots over different types
-      ! of columns and for different process modules
-      ! The super-set of all columns that should have a root water sink
-      ! is filter_hydrologyc
-      ! There are three groups of columns:
-      ! 1) impervious roads, 2) non-natural vegetation and 3) natural vegetation
-      ! There are several methods available.
-      ! 1) the default version, 2) hydstress version and 3) fates boundary conditions
-      !
-      ! There are only two quantities that are the result of this routine, and its
-      ! children:
-      !   waterflux_inst%qflx_rootsoi_col(c,j)
-      !   soilstate_inst%rootr_col(c,j)
-      !
-      !
-      ! ---------------------------------------------------------------------------------
-
-      use SoilStateType       , only : soilstate_type
-      use WaterFluxType       , only : waterflux_type
-      use CanopyStateType     , only : canopystate_type
-      use EnergyFluxType      , only : energyflux_type
-      use ColumnType          , only : col 
-      use LandunitType        , only : lun
-
-      ! Arguments
-      type(bounds_type)       , intent(in)    :: bounds               ! bounds
-      integer                 , intent(in)    :: num_hydrologyc       ! number of column soil points in column filter
-      integer                 , intent(in)    :: filter_hydrologyc(num_hydrologyc) ! column filter for soil points
-      type(soilstate_type)    , intent(inout) :: soilstate_inst
-      type(waterflux_type)    , intent(inout) :: waterflux_inst
-      type(canopystate_type)  , intent(in)    :: canopystate_inst
-      type(energyflux_type)   , intent(in)    :: energyflux_inst
-
-      ! Local Variables
-      integer  :: filterc(bounds%endc-bounds%begc+1)           !column filter
-      integer  :: num_filterc
-      integer  :: num_filterc_tot
-      integer  :: fc
-      integer  :: c
-      integer  :: l
-
-      num_filterc_tot = 0
-
-      ! 1) pervious roads
-      num_filterc = 0
-      do fc = 1, num_hydrologyc
-         c = filter_hydrologyc(fc)
-         if (col%itype(c) == icol_road_perv) then
-            num_filterc = num_filterc + 1
-            filterc(num_filterc) = c
-         end if
-      end do
-      num_filterc_tot = num_filterc_tot+num_filterc
-      if(use_hydrstress) then
-         call Compute_EffecRootFrac_And_VertTranSink_HydStress_Roads(bounds, &
-               num_filterc,filterc, soilstate_inst, waterflux_inst)
-      else
-         call Compute_EffecRootFrac_And_VertTranSink_Default(bounds, &
-               num_filterc,filterc, soilstate_inst, waterflux_inst)
-      end if
-
-
-      ! Note: 2 and 3 really don't need to be split.  But I am leaving
-      ! it split in case someone wants to calculate uptake in a special
-      ! way for a specific LU or coverage type (RGK 04/2017).  Feel
-      ! free to consolidate if there are no plans to do such a thing.
-
-         
-      ! 2) not ( pervious road or natural vegetation) , everything else
-      num_filterc = 0
-      do fc = 1, num_hydrologyc
-         c = filter_hydrologyc(fc)
-         l = col%landunit(c)
-         if ( (col%itype(c) /= icol_road_perv) .and. (lun%itype(l) /= istsoil) ) then
-            num_filterc = num_filterc + 1
-            filterc(num_filterc) = c
-         end if
-      end do
-      num_filterc_tot = num_filterc_tot+num_filterc
-      if(use_hydrstress) then
-         call Compute_EffecRootFrac_And_VertTranSink_HydStress(bounds, &
-               num_filterc, filterc, waterflux_inst, soilstate_inst, &
-               canopystate_inst, energyflux_inst)
-      else
-         call Compute_EffecRootFrac_And_VertTranSink_Default(bounds, &
-               num_filterc,filterc, soilstate_inst, waterflux_inst)
-      end if
-      
-
-      ! 3) Natural vegetation
-      num_filterc = 0
-      do fc = 1, num_hydrologyc
-         c = filter_hydrologyc(fc)
-         l = col%landunit(c)
-         if ( (lun%itype(l) == istsoil) ) then
-            num_filterc = num_filterc + 1
-            filterc(num_filterc) = c
-         end if
-      end do
-      num_filterc_tot = num_filterc_tot+num_filterc
-      if (use_hydrstress) then
-         call Compute_EffecRootFrac_And_VertTranSink_HydStress(bounds, &
-              num_filterc, filterc, waterflux_inst, soilstate_inst, &
-              canopystate_inst,energyflux_inst)
-      else
-         call Compute_EffecRootFrac_And_VertTranSink_Default(bounds, &
-              num_filterc,filterc, soilstate_inst, waterflux_inst)
-      end if
-
-      if (num_hydrologyc /= num_filterc_tot) then
-          write(iulog,*) 'The total number of columns flagged to root water uptake'
-          write(iulog,*) 'did not match the total number calculated'
-          write(iulog,*) 'This is likely a problem with the interpretation of column/lu filters.'
-          call endrun(msg=errMsg(sourcefile, __LINE__))
-      end if
-
-
-      return
-   end subroutine Compute_EffecRootFrac_And_VertTranSink
-
-   ! ====================================================================================
-
-   subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress_Roads(bounds, &
-         num_filterc,filterc, soilstate_inst, waterflux_inst)
-      
-      use SoilStateType    , only : soilstate_type
-      use WaterFluxType    , only : waterflux_type
-      use clm_varpar       , only : nlevsoi
-      use clm_varpar       , only : max_patch_per_col
-      use PatchType        , only : patch
-      use ColumnType       , only : col
-
-      ! Arguments
-      type(bounds_type)       , intent(in)    :: bounds      
-      integer                 , intent(in)    :: num_filterc
-      integer                 , intent(in)    :: filterc(:) 
-      type(soilstate_type)    , intent(inout) :: soilstate_inst
-      type(waterflux_type)    , intent(inout) :: waterflux_inst
-
-      ! Locals
-      integer :: j
-      integer :: c
-      integer :: fc
-      integer :: pi
-      integer :: p
-      real(r8) :: temp(bounds%begc:bounds%endc)                         ! accumulator for rootr weighting
-
-
-      associate(& 
-            qflx_rootsoi_col    => waterflux_inst%qflx_rootsoi_col    , & ! Output: [real(r8) (:,:) ]  
-                                                                          ! vegetation/soil water exchange (mm H2O/s) (+ = to atm)
-            qflx_tran_veg_patch => waterflux_inst%qflx_tran_veg_patch , & ! Input:  [real(r8) (:)   ]  
-                                                                          ! vegetation transpiration (mm H2O/s) (+ = to atm) 
-            qflx_tran_veg_col   => waterflux_inst%qflx_tran_veg_col   , & ! Input:  [real(r8) (:)   ]  
-                                                                          ! vegetation transpiration (mm H2O/s) (+ = to atm)
-            rootr_patch         => soilstate_inst%rootr_patch         , & ! Input:  [real(r8) (:,:) ]  
-                                                                          ! effective fraction of roots in each soil layer  
-            rootr_col           => soilstate_inst%rootr_col             & ! Output: [real(r8) (:,:) ]  
-                                                                          !effective fraction of roots in each soil layer  
-            )
-
-        ! First step is to calculate the column-level effective rooting
-        ! fraction in each soil layer. This is done outside the usual
-        ! PATCH-to-column averaging routines because it is not a simple
-        ! weighted average of the PATCH level rootr arrays. Instead, the
-        ! weighting depends on both the per-unit-area transpiration
-        ! of the PATCH and the PATCHEs area relative to all PATCHES.
-        
-        temp(bounds%begc : bounds%endc) = 0._r8
-    
-
-        do j = 1, nlevsoi
-           do fc = 1, num_filterc
-              c = filterc(fc)
-              rootr_col(c,j) = 0._r8
-           end do
-        end do
-        
-        do pi = 1,max_patch_per_col
-           do j = 1,nlevsoi
-              do fc = 1, num_filterc
-                 c = filterc(fc)
-                 if (pi <= col%npatches(c)) then
-                    p = col%patchi(c) + pi - 1
-                    if (patch%active(p)) then
-                       rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * &
-                             qflx_tran_veg_patch(p) * patch%wtcol(p)
-                    end if
-                 end if
-              end do
-           end do
-           do fc = 1, num_filterc
-              c = filterc(fc)
-              if (pi <= col%npatches(c)) then
-                 p = col%patchi(c) + pi - 1
-                 if (patch%active(p)) then
-                    temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p)
-                 end if
-              end if
-           end do
-        end do
-
-   
-        do j = 1, nlevsoi
-           do fc = 1, num_filterc
-              c = filterc(fc)
-              if (temp(c) /= 0._r8) then
-                 rootr_col(c,j) = rootr_col(c,j)/temp(c)
-              end if
-              qflx_rootsoi_col(c,j) = rootr_col(c,j)*qflx_tran_veg_col(c)
-           end do
-        end do
-      end associate
-      return
-   end subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress_Roads
-   
-   ! ==================================================================================
-   
-   subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress( bounds, &
-           num_filterc, filterc, waterflux_inst, soilstate_inst, &
-           canopystate_inst, energyflux_inst)
-
-
-        !
-        !USES:
-        use decompMod        , only : bounds_type
-        use clm_varpar       , only : nlevsoi
-        use clm_varpar       , only : max_patch_per_col
-        use SoilStateType    , only : soilstate_type
-        use WaterFluxType    , only : waterflux_type
-        use CanopyStateType  , only : canopystate_type
-        use PatchType        , only : patch
-        use ColumnType       , only : col
-        use clm_varctl       , only : iulog
-        use PhotosynthesisMod, only : params_inst
-        use column_varcon    , only : icol_road_perv
-        use shr_infnan_mod   , only : isnan => shr_infnan_isnan
-        use EnergyFluxType   , only : energyflux_type
-        !
-        ! !ARGUMENTS:
-        type(bounds_type)    , intent(in)    :: bounds          ! bounds
-        integer              , intent(in)    :: num_filterc     ! number of column soil points in column filter
-        integer              , intent(in)    :: filterc(:)      ! column filter for soil points
-        type(waterflux_type) , intent(inout) :: waterflux_inst
-        type(soilstate_type) , intent(inout) :: soilstate_inst
-        type(canopystate_type) , intent(in)  :: canopystate_inst
-        type(energyflux_type), intent(in)    :: energyflux_inst
-        !
-        ! !LOCAL VARIABLES:
-        integer  :: p,c,fc,j                                              ! do loop indices
-        integer  :: pi                                                    ! patch index
-        real(r8) :: temp(bounds%begc:bounds%endc)                         ! accumulator for rootr weighting
-        real(r8) :: grav2                 ! soil layer gravitational potential relative to surface (mm H2O)
-        integer , parameter :: soil=1,root=4  ! index values
-        !-----------------------------------------------------------------------   
-        
-        associate(&
-              k_soil_root         => soilstate_inst%k_soil_root_patch   , & ! Input:  [real(r8) (:,:) ]  
-                                                                            ! soil-root interface conductance (mm/s)
-              qflx_phs_neg_col    => waterflux_inst%qflx_phs_neg_col    , & ! Input:  [real(r8) (:)   ]  n
-                                                                            ! net neg hydraulic redistribution flux(mm H2O/s)
-              qflx_tran_veg_col   => waterflux_inst%qflx_tran_veg_col   , & ! Input:  [real(r8) (:)   ]  
-                                                                            ! vegetation transpiration (mm H2O/s) (+ = to atm)
-              qflx_tran_veg_patch => waterflux_inst%qflx_tran_veg_patch , & ! Input:  [real(r8) (:)   ]  
-                                                                            ! vegetation transpiration (mm H2O/s) (+ = to atm)
-              qflx_rootsoi_col    => waterflux_inst%qflx_rootsoi_col    , & ! Output: [real(r8) (:)   ]
-                                                                            ! col root and soil water 
-                                                                            ! exchange [mm H2O/s] [+ into root]
-              rootr_col           => soilstate_inst%rootr_col           , & ! Input:  [real(r8) (:,:) ]
-                                                                            ! effective fraction of roots in each soil layer
-              rootr_patch         => soilstate_inst%rootr_patch         , & ! Input:  [real(r8) (:,:) ]  
-                                                                            ! effective fraction of roots in each soil layer
-              smp                 => soilstate_inst%smp_l_col           , & ! Input:  [real(r8) (:,:) ]  soil matrix pot. [mm]
-              frac_veg_nosno      => canopystate_inst%frac_veg_nosno_patch , & ! Input:  [integer  (:)  ] 
-                                                                            ! fraction of vegetation not 
-                                                                            ! covered by snow (0 OR 1) [-]  
-              z                   => col%z                              , & ! Input: [real(r8) (:,:) ]  layer node depth (m)
-              vegwp               => canopystate_inst%vegwp_patch         & ! Input: [real(r8) (:,:) ]  vegetation water 
-                                                                            ! matric potential (mm)
-              )
-          
-          do fc = 1, num_filterc
-             c = filterc(fc)
-             qflx_phs_neg_col(c) = 0._r8
-             
-             do j = 1, nlevsoi
-                grav2 = z(c,j) * 1000._r8
-                temp(c) = 0._r8
-                do pi = 1,max_patch_per_col
-                   if (pi <= col%npatches(c)) then
-                      p = col%patchi(c) + pi - 1
-                      if (patch%active(p).and.frac_veg_nosno(p)>0) then 
-                         if (patch%wtcol(p) > 0._r8) then
-                            temp(c) = temp(c) + k_soil_root(p,j) &
-                                  * (smp(c,j) - vegwp(p,4) - grav2)* patch%wtcol(p)
-                         endif
-                      end if
-                   end if
-                end do
-                qflx_rootsoi_col(c,j)= temp(c)
-                
-                if (temp(c) < 0._r8) qflx_phs_neg_col(c) = qflx_phs_neg_col(c) + temp(c)
-             end do
-             
-             ! Back out the effective root density
-             if( sum(qflx_rootsoi_col(c,:))>0.0_r8 ) then
-                do j = 1, nlevsoi
-                   rootr_col(c,j) = qflx_rootsoi_col(c,j)/sum( qflx_rootsoi_col(c,:))
-                end do
-             else
-                rootr_col(c,:) = 0.0_r8
-             end if
-          end do
-          
-        end associate
-
-        return
-     end subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress
-     
-     ! ==================================================================================
-
-     subroutine Compute_EffecRootFrac_And_VertTranSink_Default(bounds, num_filterc, &
-           filterc, soilstate_inst, waterflux_inst)
-
-    !
-    ! Generic routine to apply transpiration as a sink condition that
-    ! is vertically distributed over the soil column. Should be
-    ! applicable to any Richards solver that is not coupled to plant
-    ! hydraulics.
-    !
-    !USES:
-    use decompMod        , only : bounds_type
-    use shr_kind_mod     , only : r8 => shr_kind_r8
-    use clm_varpar       , only : nlevsoi, max_patch_per_col
-    use SoilStateType    , only : soilstate_type
-    use WaterFluxType    , only : waterflux_type
-    use PatchType        , only : patch
-    use ColumnType       , only : col
-    use clm_varctl       , only : use_hydrstress
-    use column_varcon    , only : icol_road_perv
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)    , intent(in)    :: bounds                          ! bounds
-    integer              , intent(in)    :: num_filterc                     ! number of column soil points in column filter
-    integer              , intent(in)    :: filterc(num_filterc)            ! column filter for soil points
-    type(waterflux_type) , intent(inout) :: waterflux_inst
-    type(soilstate_type) , intent(inout) :: soilstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: p,c,fc,j                                              ! do loop indices
-    integer  :: pi                                                    ! patch index
-    real(r8) :: temp(bounds%begc:bounds%endc)                         ! accumulator for rootr weighting
-    associate(& 
-          qflx_rootsoi_col    => waterflux_inst%qflx_rootsoi_col    , & ! Output: [real(r8) (:,:) ]  
-                                                                        ! vegetation/soil water exchange (m H2O/s) (+ = to atm)
-          qflx_tran_veg_patch => waterflux_inst%qflx_tran_veg_patch , & ! Input:  [real(r8) (:)   ]  
-                                                                        ! vegetation transpiration (mm H2O/s) (+ = to atm) 
-          qflx_tran_veg_col   => waterflux_inst%qflx_tran_veg_col   , & ! Input:  [real(r8) (:)   ]  
-                                                                        ! vegetation transpiration (mm H2O/s) (+ = to atm)
-          rootr_patch         => soilstate_inst%rootr_patch         , & ! Input: [real(r8) (:,:) ]
-                                                                        ! effective fraction of roots in each soil layer  
-          rootr_col           => soilstate_inst%rootr_col             & ! Output: [real(r8) (:,:) ]  
-                                                                        ! effective fraction of roots in each soil layer  
-          )
-      
-      ! First step is to calculate the column-level effective rooting
-      ! fraction in each soil layer. This is done outside the usual
-      ! PATCH-to-column averaging routines because it is not a simple
-      ! weighted average of the PATCH level rootr arrays. Instead, the
-      ! weighting depends on both the per-unit-area transpiration
-      ! of the PATCH and the PATCHEs area relative to all PATCHES.
-      
-      temp(bounds%begc : bounds%endc) = 0._r8
-      
-      do j = 1, nlevsoi
-         do fc = 1, num_filterc
-            c = filterc(fc)
-            rootr_col(c,j) = 0._r8
-         end do
-      end do
-      
-      do pi = 1,max_patch_per_col
-         do j = 1,nlevsoi
-            do fc = 1, num_filterc
-               c = filterc(fc)
-               if (pi <= col%npatches(c)) then
-                  p = col%patchi(c) + pi - 1
-                  if (patch%active(p)) then
-                     rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * &
-                           qflx_tran_veg_patch(p) * patch%wtcol(p)
-                  end if
-               end if
-            end do
-         end do
-         do fc = 1, num_filterc
-            c = filterc(fc)
-            if (pi <= col%npatches(c)) then
-               p = col%patchi(c) + pi - 1
-               if (patch%active(p)) then
-                  temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p)
-               end if
-            end if
-         end do
-      end do
-      
-      do j = 1, nlevsoi
-         do fc = 1, num_filterc
-            c = filterc(fc)
-            if (temp(c) /= 0._r8) then
-               rootr_col(c,j) = rootr_col(c,j)/temp(c)
-            end if
-            qflx_rootsoi_col(c,j) = rootr_col(c,j)*qflx_tran_veg_col(c)
-
-         end do
-      end do
-    end associate
-    return
- end subroutine Compute_EffecRootFrac_And_VertTranSink_Default
-
-end module SoilWaterPlantSinkMod
-
diff --git a/src/biogeophys/SoilWaterRetentionCurveClappHornberg1978Mod.F90 b/src/biogeophys/SoilWaterRetentionCurveClappHornberg1978Mod.F90
deleted file mode 100644
index c82e27d851..0000000000
--- a/src/biogeophys/SoilWaterRetentionCurveClappHornberg1978Mod.F90
+++ /dev/null
@@ -1,162 +0,0 @@
-module SoilWaterRetentionCurveClappHornberg1978Mod
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Implementation of soil_water_retention_curve_type using the Clapp-Hornberg 1978
-  ! parameterizations.
-  !
-  ! !USES:
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  public :: soil_water_retention_curve_clapp_hornberg_1978_type
-  
-  type, extends(soil_water_retention_curve_type) :: &
-       soil_water_retention_curve_clapp_hornberg_1978_type
-     private
-   contains
-     procedure :: soil_hk              ! compute hydraulic conductivity
-     procedure :: soil_suction         ! compute soil suction potential
-     procedure :: soil_suction_inverse ! compute relative saturation at which soil suction is equal to a target value
-  end type soil_water_retention_curve_clapp_hornberg_1978_type
-
-  interface soil_water_retention_curve_clapp_hornberg_1978_type
-     ! initialize a new soil_water_retention_curve_clapp_hornberg_1978_type object
-     module procedure constructor  
-  end interface soil_water_retention_curve_clapp_hornberg_1978_type
-
-contains
-
-  !-----------------------------------------------------------------------
-  type(soil_water_retention_curve_clapp_hornberg_1978_type) function constructor()
-    !
-    ! !DESCRIPTION:
-    ! Creates an object of type soil_water_retention_curve_clapp_hornberg_1978_type.
-    ! For now, this is simply a place-holder.
-    !-----------------------------------------------------------------------
-
-  end function constructor
-
-  !-----------------------------------------------------------------------
-  subroutine soil_hk(this, c, j, s, imped, soilstate_inst, hk, dhkds)
-    !
-    ! !DESCRIPTION:
-    ! Compute hydraulic conductivity
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_clapp_hornberg_1978_type), intent(in) :: this
-    integer,  intent(in)             :: c        !column index
-    integer,  intent(in)             :: j        !level index
-    real(r8), intent(in)             :: s        !relative saturation, [0, 1]
-    real(r8), intent(in)             :: imped    !ice impedance
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8), intent(out)            :: hk       !hydraulic conductivity [mm/s]
-    real(r8), optional, intent(out)  :: dhkds    !d[hk]/ds   [mm/s]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_hk'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         hksat             =>    soilstate_inst%hksat_col(c,j)          , & ! Input:  [real(r8) (:,:) ]  hydraulic conductivity at saturation (mm H2O /s)
-         bsw               =>    soilstate_inst%bsw_col(c,j)              & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                        
-         )
-
-
-    !compute hydraulic conductivity
-    hk=imped*hksat*s**(2._r8*bsw+3._r8)
-
-    !compute the derivative
-    if(present(dhkds))then
-       dhkds=(2._r8*bsw+3._r8)*hk/s
-    endif
-
-    end associate 
-
-  end subroutine soil_hk
-
-  !-----------------------------------------------------------------------
-  subroutine soil_suction(this, c, j, s, soilstate_inst, smp, dsmpds)
-    !
-    ! !DESCRIPTION:
-    ! Compute soil suction potential
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_clapp_hornberg_1978_type), intent(in) :: this
-    integer,  intent(in)             :: c       !column index
-    integer,  intent(in)             :: j        !level index
-    real(r8), intent(in)             :: s        !relative saturation, [0, 1]
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8), intent(out)            :: smp      !soil suction, negative, [mm]
-    real(r8), optional, intent(out)  :: dsmpds   !d[smp]/ds, [mm]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_suction'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         bsw               =>    soilstate_inst%bsw_col(c,j)            , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                       
-         sucsat            =>    soilstate_inst%sucsat_col(c,j)           & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm)                       
-         )
-
-    !compute soil suction potential, negative
-    smp = -sucsat*s**(-bsw)
-
-    !compute derivative
-    if(present(dsmpds))then
-       dsmpds=-bsw*smp/s
-    endif
-
-    end associate 
-
-  end subroutine soil_suction
-
-  !-----------------------------------------------------------------------
-  subroutine soil_suction_inverse(this, c, j, smp_target, soilstate_inst, &
-       s_target)
-    !
-    ! !DESCRIPTION:
-    ! Compute relative saturation at which soil suction is equal to a target value.
-    ! This is done by inverting the soil_suction equation to solve for s.
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_clapp_hornberg_1978_type), intent(in) :: this
-    integer,  intent(in)             :: c       !column index
-    integer,  intent(in)             :: j        !level index
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8) , intent(in)  :: smp_target ! target soil suction, negative [mm]
-    real(r8) , intent(out) :: s_target   ! relative saturation at which smp = smp_target [0,1]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_suction_inverse'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         bsw               =>    soilstate_inst%bsw_col(c,j)            , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                        
-         sucsat            =>    soilstate_inst%sucsat_col(c,j)           & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm)                       
-         )
-
-    s_target = (-smp_target/sucsat)**(-1._r8/bsw)
-
-    end associate 
-
-  end subroutine soil_suction_inverse
-
-end module SoilWaterRetentionCurveClappHornberg1978Mod
-
diff --git a/src/biogeophys/SoilWaterRetentionCurveFactoryMod.F90 b/src/biogeophys/SoilWaterRetentionCurveFactoryMod.F90
deleted file mode 100644
index 61e579dd43..0000000000
--- a/src/biogeophys/SoilWaterRetentionCurveFactoryMod.F90
+++ /dev/null
@@ -1,71 +0,0 @@
-module SoilWaterRetentionCurveFactoryMod
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Factory to create an instance of soil_water_retention_curve_type. This module figures
-  ! out the particular type to return.
-  !
-  ! !USES:
-  use abortutils          , only : endrun
-  use shr_log_mod         , only : errMsg => shr_log_errMsg
-  use clm_varctl          , only : iulog
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC ROUTINES:
-  public :: create_soil_water_retention_curve  ! create an object of class soil_water_retention_curve_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  function create_soil_water_retention_curve() result(soil_water_retention_curve)
-    !
-    ! !DESCRIPTION:
-    ! Create and return an object of soil_water_retention_curve_type. The particular type
-    ! is determined based on a namelist parameter.
-    !
-    ! !USES:
-    use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
-    use SoilWaterRetentionCurveClappHornberg1978Mod, only : soil_water_retention_curve_clapp_hornberg_1978_type
-    use SoilWaterRetentionCurveVanGenuchten1980Mod, only : soil_water_retention_curve_vangenuchten_1980_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_type), allocatable :: soil_water_retention_curve  ! function result
-    !
-    ! !LOCAL VARIABLES:
-
-    ! For now, hard-code the method. Eventually this will be set from namelist, either by
-    ! this routine (appropriate if the 'method' is in its own namelist group), or do the
-    ! namelist read outside this module and pass the method in as a parameter (appropriate
-    ! if the 'method' is part of a larger namelist group).
-!scs    character(len=*), parameter :: method = "clapphornberg_1978"
-    character(len=256) :: method
-    
-    character(len=*), parameter :: subname = 'create_soil_water_retention_curve'
-    !-----------------------------------------------------------------------
-    
-    method = "clapphornberg_1978" !scs: placeholder until bld scripts changed
-
-    select case (trim(method))
-       
-    case ("clapphornberg_1978")
-       allocate(soil_water_retention_curve, &
-            source=soil_water_retention_curve_clapp_hornberg_1978_type())
-
-    case ("vangenuchten_1980")
-       allocate(soil_water_retention_curve, &
-            source=soil_water_retention_curve_vangenuchten_1980_type())
-
-    case default
-       write(iulog,*) subname//' ERROR: unknown method: ', method
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-
-    end select
-
-  end function create_soil_water_retention_curve
-
-end module SoilWaterRetentionCurveFactoryMod
diff --git a/src/biogeophys/SoilWaterRetentionCurveMod.F90 b/src/biogeophys/SoilWaterRetentionCurveMod.F90
deleted file mode 100644
index 74f8299d54..0000000000
--- a/src/biogeophys/SoilWaterRetentionCurveMod.F90
+++ /dev/null
@@ -1,111 +0,0 @@
-module SoilWaterRetentionCurveMod
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Abstract base class for functions to compute soil water retention curve
-  !
-  ! !USES:
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  public :: soil_water_retention_curve_type
-
-  type, abstract :: soil_water_retention_curve_type
-     private
-   contains
-     ! compute hydraulic conductivity
-     procedure(soil_hk_interface), deferred :: soil_hk
-
-     ! compute soil suction potential
-     procedure(soil_suction_interface), deferred :: soil_suction
-
-     ! compute relative saturation at which soil suction is equal to a target value
-     procedure(soil_suction_inverse_interface), deferred :: soil_suction_inverse
-  end type soil_water_retention_curve_type
-
-  abstract interface
-
-     ! Note: The following interfaces are set up based on the arguments needed for the
-     ! clapphornberg1978 implementations. It's likely that these interfaces are not
-     ! totally general for all desired implementations. In that case, we'll need to think
-     ! about how to support different interfaces. Some possible solutions are:
-     !
-     ! - Make the interfaces contain all possible inputs that are needed by any
-     !   implementation; each implementation will then ignore the inputs it doesn't need.
-     !
-     ! - For inputs that are needed only by particular implementations - and particularly
-     !   for inputs that are constant in time (e.g., this is the case for bsw, I think):
-     !   pass these into the constructor, and save pointers to these inputs as components
-     !   of the child type that needs them. Then they aren't needed as inputs to the
-     !   individual routines, allowing the interfaces for these routines to remain more
-     !   consistent between different implementations.
-
-     subroutine soil_hk_interface(this, c, j, s, imped, soilstate_inst, &
-          hk, dhkds)
-
-       ! !DESCRIPTION:
-       ! Compute hydraulic conductivity
-       !
-       ! !USES:
-       use shr_kind_mod   , only : r8 => shr_kind_r8
-       use SoilStateType  , only : soilstate_type
-       import :: soil_water_retention_curve_type
-       !
-       ! !ARGUMENTS:
-       class(soil_water_retention_curve_type), intent(in) :: this
-       integer,  intent(in) :: c        !column index
-       integer,  intent(in) :: j        !level index
-       real(r8), intent(in) :: s        !relative saturation, [0, 1]
-       real(r8), intent(in) :: imped    !ice impedance
-       type(soilstate_type), intent(in) :: soilstate_inst
-       real(r8), intent(out):: hk       !hydraulic conductivity [mm/s]
-       real(r8), optional, intent(out):: dhkds    !d[hk]/ds   [mm/s]
-     end subroutine soil_hk_interface
-
-
-     subroutine soil_suction_interface(this, c, j, s, soilstate_inst, &
-          smp, dsmpds)
-
-       ! !DESCRIPTION:
-       ! Compute soil suction potential
-       !
-       ! !USES:
-       use shr_kind_mod   , only : r8 => shr_kind_r8
-       use SoilStateType  , only : soilstate_type
-       import :: soil_water_retention_curve_type
-       !
-       ! !ARGUMENTS:
-       class(soil_water_retention_curve_type), intent(in) :: this
-       integer,  intent(in)             :: c       !column index
-       integer,  intent(in)             :: j       !level index
-       real(r8), intent(in)             :: s       !relative saturation, [0, 1]
-       type(soilstate_type), intent(in) :: soilstate_inst
-       real(r8), intent(out)            :: smp     !soil suction, negative, [mm]
-       real(r8), optional, intent(out)  :: dsmpds  !d[smp]/ds, [mm]
-     end subroutine soil_suction_interface
-
-     subroutine soil_suction_inverse_interface(this, c, j, smp_target, &
-          soilstate_inst, s_target)
-       ! !DESCRIPTION:
-       ! Compute relative saturation at which soil suction is equal to a target value.
-       ! This is done by inverting the soil_suction equation to solve for s.
-       !
-       ! !USES:
-       use shr_kind_mod   , only : r8 => shr_kind_r8
-       use SoilStateType  , only : soilstate_type
-       import :: soil_water_retention_curve_type
-       !
-       ! !ARGUMENTS:
-       class(soil_water_retention_curve_type), intent(in) :: this
-       integer,  intent(in)   :: c          !column index
-       integer,  intent(in)   :: j          !level index
-       real(r8), intent(in)   :: smp_target ! target soil suction, negative [mm]
-       type(soilstate_type), intent(in) :: soilstate_inst
-       real(r8) , intent(out) :: s_target   ! relative saturation at which smp = smp_target [0,1]
-     end subroutine soil_suction_inverse_interface
-
-  end interface
-
-end module SoilWaterRetentionCurveMod
diff --git a/src/biogeophys/SoilWaterRetentionCurveVanGenuchten1980Mod.F90 b/src/biogeophys/SoilWaterRetentionCurveVanGenuchten1980Mod.F90
deleted file mode 100644
index c8dacccb81..0000000000
--- a/src/biogeophys/SoilWaterRetentionCurveVanGenuchten1980Mod.F90
+++ /dev/null
@@ -1,162 +0,0 @@
-module SoilWaterRetentionCurveVanGenuchten1980Mod
-
-  !---------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Implementation of soil_water_retention_curve_type using the Clapp-Hornberg 1978
-  ! parameterizations.
-  !
-  ! !USES:
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC TYPES:
-  public :: soil_water_retention_curve_vangenuchten_1980_type
-  
-  type, extends(soil_water_retention_curve_type) :: &
-       soil_water_retention_curve_vangenuchten_1980_type
-     private
-   contains
-     procedure :: soil_hk              ! compute hydraulic conductivity
-     procedure :: soil_suction         ! compute soil suction potential
-     procedure :: soil_suction_inverse ! compute relative saturation at which soil suction is equal to a target value
-  end type soil_water_retention_curve_vangenuchten_1980_type
-
-  interface soil_water_retention_curve_vangenuchten_1980_type
-     ! initialize a new soil_water_retention_curve_vangenuchten_1980_type object
-     module procedure constructor  
-  end interface soil_water_retention_curve_vangenuchten_1980_type
-
-contains
-
-  !-----------------------------------------------------------------------
-  type(soil_water_retention_curve_vangenuchten_1980_type) function constructor()
-    !
-    ! !DESCRIPTION:
-    ! Creates an object of type soil_water_retention_curve_vangenuchten_1980_type.
-    ! For now, this is simply a place-holder.
-    !-----------------------------------------------------------------------
-
-  end function constructor
-
-  !-----------------------------------------------------------------------
-  subroutine soil_hk(this, c, j, s, imped, soilstate_inst, hk, dhkds)
-    !
-    ! !DESCRIPTION:
-    ! Compute hydraulic conductivity
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_vangenuchten_1980_type), intent(in) :: this
-    integer,  intent(in)             :: c        !column index
-    integer,  intent(in)             :: j        !level index
-    real(r8), intent(in)             :: s        !relative saturation, [0, 1]
-    real(r8), intent(in)             :: imped    !ice impedance
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8), intent(out)            :: hk       !hydraulic conductivity [mm/s]
-    real(r8), optional, intent(out)  :: dhkds    !d[hk]/ds   [mm/s]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_hk'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         hksat             =>    soilstate_inst%hksat_col(c,j)          , & ! Input:  [real(r8) (:,:) ]  hydraulic conductivity at saturation (mm H2O /s)
-         bsw               =>    soilstate_inst%bsw_col(c,j)              & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                        
-         )
-
-
-    !compute hydraulic conductivity
-    hk=imped*hksat*s**(2._r8*bsw+3._r8)
-
-    !compute the derivative
-    if(present(dhkds))then
-       dhkds=(2._r8*bsw+3._r8)*hk/s
-    endif
-
-    end associate 
-
-  end subroutine soil_hk
-
-  !-----------------------------------------------------------------------
-  subroutine soil_suction(this, c, j, s, soilstate_inst, smp, dsmpds)
-    !j, 
-    ! !DESCRIPTION:
-    ! Compute soil suction potential
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_vangenuchten_1980_type), intent(in) :: this
-    integer,  intent(in)             :: c       !column index
-    integer,  intent(in)             :: j        !level index
-    real(r8), intent(in)             :: s        !relative saturation, [0, 1]
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8), intent(out)            :: smp      !soil suction, negative, [mm]
-    real(r8), optional, intent(out)  :: dsmpds   !d[smp]/ds, [mm]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_suction'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         bsw               =>    soilstate_inst%bsw_col(c,j)            , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                       
-         sucsat            =>    soilstate_inst%sucsat_col(c,j)           & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm)                       
-         )
-
-    !compute soil suction potential, negative
-    smp = -sucsat*s**(-bsw)
-
-    !compute derivative
-    if(present(dsmpds))then
-       dsmpds=-bsw*smp/s
-    endif
-
-    end associate 
-
-  end subroutine soil_suction
-
-  !-----------------------------------------------------------------------
-  subroutine soil_suction_inverse(this, c, j, smp_target, soilstate_inst, s_target)
-    !
-    ! !DESCRIPTION:
-    ! Compute relative saturation at which soil suction is equal to a target value.
-    ! This is done by inverting the soil_suction equation to solve for s.
-    !
-    ! !USES:
-    use SoilStateType  , only : soilstate_type
-    !
-    ! !ARGUMENTS:
-    class(soil_water_retention_curve_vangenuchten_1980_type), intent(in) :: this
-    integer,  intent(in)             :: c       !column index
-    integer,  intent(in)             :: j        !level index
-    type(soilstate_type), intent(in) :: soilstate_inst
-    real(r8) , intent(in)  :: smp_target ! target soil suction, negative [mm]
-    real(r8) , intent(out) :: s_target   ! relative saturation at which smp = smp_target [0,1]
-    !
-    ! !LOCAL VARIABLES:
-    
-    character(len=*), parameter :: subname = 'soil_suction_inverse'
-    !-----------------------------------------------------------------------
-    
-    associate(& 
-         bsw               =>    soilstate_inst%bsw_col(c,j)            , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                        
-         sucsat            =>    soilstate_inst%sucsat_col(c,j)           & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm)                       
-         )
-
-    s_target = (-smp_target/sucsat)**(-1._r8/bsw)
-
-    end associate 
-
-  end subroutine soil_suction_inverse
-
-end module SoilWaterRetentionCurveVanGenuchten1980Mod
-
-
diff --git a/src/biogeophys/SolarAbsorbedType.F90 b/src/biogeophys/SolarAbsorbedType.F90
deleted file mode 100644
index e167fb3a63..0000000000
--- a/src/biogeophys/SolarAbsorbedType.F90
+++ /dev/null
@@ -1,423 +0,0 @@
-module SolarAbsorbedType
-
-  !------------------------------------------------------------------------------
-  ! !USES:
-  use shr_kind_mod , only: r8 => shr_kind_r8
-  use shr_log_mod  , only: errMsg => shr_log_errMsg
-  use decompMod    , only : bounds_type
-  use clm_varcon   , only : spval
-  use clm_varctl   , only : use_luna
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC DATA MEMBERS:
-  type, public :: solarabs_type
-
-     ! Solar reflected
-     real(r8), pointer :: fsr_patch              (:)   ! patch solar radiation reflected (W/m**2)         
-     
-     ! Solar Absorbed
-     real(r8), pointer :: fsa_patch              (:)   ! patch solar radiation absorbed (total) (W/m**2)  
-     real(r8), pointer :: fsa_u_patch            (:)   ! patch urban solar radiation absorbed (total) (W/m**2)
-     real(r8), pointer :: fsa_r_patch            (:)   ! patch rural solar radiation absorbed (total) (W/m**2)
-     real(r8), pointer :: parsun_z_patch         (:,:) ! patch absorbed PAR for sunlit leaves in canopy layer (W/m**2) 
-     real(r8), pointer :: parsha_z_patch         (:,:) ! patch absorbed PAR for shaded leaves in canopy layer (W/m**2) 
-     real(r8), pointer :: par240d_z_patch        (:,:) ! 10-day running mean of daytime patch absorbed PAR for leaves in canopy layer (W/m**2) 
-     real(r8), pointer :: par240x_z_patch        (:,:) ! 10-day running mean of maximum patch absorbed PAR for leaves in canopy layer (W/m**2)
-     real(r8), pointer :: par24d_z_patch         (:,:) ! daily accumulated  absorbed PAR for leaves in canopy layer from midnight to current step(J/m**2) 
-     real(r8), pointer :: par24x_z_patch         (:,:) ! daily max of patch absorbed PAR for  leaves in canopy layer from midnight to current step(W/m**2)
-     real(r8), pointer :: sabg_soil_patch        (:)   ! patch solar radiation absorbed by soil (W/m**2)       
-     real(r8), pointer :: sabg_snow_patch        (:)   ! patch solar radiation absorbed by snow (W/m**2)       
-     real(r8), pointer :: sabg_patch             (:)   ! patch solar radiation absorbed by ground (W/m**2)     
-     real(r8), pointer :: sabg_chk_patch         (:)   ! patch fsno weighted sum (W/m**2)                                   
-     real(r8), pointer :: sabg_lyr_patch         (:,:) ! patch absorbed radiation in each snow layer and top soil layer (pft,lyr) [W/m2]
-     real(r8), pointer :: sabg_pen_patch         (:)   ! patch (rural) shortwave radiation penetrating top soisno layer [W/m2]
-
-     real(r8), pointer :: sub_surf_abs_SW_patch  (:)   ! patch fraction of solar radiation absorbed below first snow layer
-     real(r8), pointer :: sabv_patch             (:)   ! patch solar radiation absorbed by vegetation (W/m**2) 
-
-     real(r8), pointer :: sabs_roof_dir_lun      (:,:) ! lun direct solar absorbed by roof per unit ground area per unit incident flux
-     real(r8), pointer :: sabs_roof_dif_lun      (:,:) ! lun diffuse solar absorbed by roof per unit ground area per unit incident flux
-     real(r8), pointer :: sabs_sunwall_dir_lun   (:,:) ! lun direct  solar absorbed by sunwall per unit wall area per unit incident flux
-     real(r8), pointer :: sabs_sunwall_dif_lun   (:,:) ! lun diffuse solar absorbed by sunwall per unit wall area per unit incident flux
-     real(r8), pointer :: sabs_shadewall_dir_lun (:,:) ! lun direct  solar absorbed by shadewall per unit wall area per unit incident flux
-     real(r8), pointer :: sabs_shadewall_dif_lun (:,:) ! lun diffuse solar absorbed by shadewall per unit wall area per unit incident flux
-     real(r8), pointer :: sabs_improad_dir_lun   (:,:) ! lun direct  solar absorbed by impervious road per unit ground area per unit incident flux
-     real(r8), pointer :: sabs_improad_dif_lun   (:,:) ! lun diffuse solar absorbed by impervious road per unit ground area per unit incident flux
-     real(r8), pointer :: sabs_perroad_dir_lun   (:,:) ! lun direct  solar absorbed by pervious road per unit ground area per unit incident flux
-     real(r8), pointer :: sabs_perroad_dif_lun   (:,:) ! lun diffuse solar absorbed by pervious road per unit ground area per unit incident flux
-
-     ! Currently needed by lake code 
-     ! TODO (MV 8/20/2014) should be moved in the future
-     real(r8), pointer :: fsds_nir_d_patch       (:)   ! patch incident direct beam nir solar radiation (W/m**2)
-     real(r8), pointer :: fsds_nir_i_patch       (:)   ! patch incident diffuse nir solar radiation (W/m**2)    
-     real(r8), pointer :: fsds_nir_d_ln_patch    (:)   ! patch incident direct beam nir solar radiation at local noon (W/m**2)
-     real(r8), pointer :: fsr_nir_d_patch        (:)   ! patch reflected direct beam nir solar radiation (W/m**2) 
-     real(r8), pointer :: fsr_nir_i_patch        (:)   ! patch reflected diffuse nir solar radiation (W/m**2)     
-     real(r8), pointer :: fsr_nir_d_ln_patch     (:)   ! patch reflected direct beam nir solar radiation at local noon (W/m**2)
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-     procedure, public  :: Restart      
-
-  end type solarabs_type
-  !-----------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(solarabs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar    , only : nlevcan, nlevcan, numrad, nlevsno
-    !
-    ! !ARGUMENTS:
-    class(solarabs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    integer :: begl, endl
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-    begl = bounds%begl; endl = bounds%endl
-
-    allocate(this%fsa_patch              (begp:endp))              ; this%fsa_patch              (:)   = nan
-    allocate(this%fsa_u_patch            (begp:endp))              ; this%fsa_u_patch            (:)   = nan
-    allocate(this%fsa_r_patch            (begp:endp))              ; this%fsa_r_patch            (:)   = nan
-    allocate(this%parsun_z_patch         (begp:endp,1:nlevcan))    ; this%parsun_z_patch         (:,:) = nan
-    allocate(this%parsha_z_patch         (begp:endp,1:nlevcan))    ; this%parsha_z_patch         (:,:) = nan 
-    if(use_luna)then
-        allocate(this%par240d_z_patch    (begp:endp,1:nlevcan))    ; this%par240d_z_patch        (:,:) = spval
-        allocate(this%par240x_z_patch    (begp:endp,1:nlevcan))    ; this%par240x_z_patch        (:,:) = spval 
-        allocate(this%par24d_z_patch     (begp:endp,1:nlevcan))    ; this%par24d_z_patch         (:,:) = spval
-        allocate(this%par24x_z_patch     (begp:endp,1:nlevcan))    ; this%par24x_z_patch         (:,:) = spval
-    endif    
-    allocate(this%sabv_patch             (begp:endp))              ; this%sabv_patch             (:)   = nan
-    allocate(this%sabg_patch             (begp:endp))              ; this%sabg_patch             (:)   = nan
-    allocate(this%sabg_lyr_patch         (begp:endp,-nlevsno+1:1)) ; this%sabg_lyr_patch         (:,:) = nan
-    allocate(this%sabg_pen_patch         (begp:endp))              ; this%sabg_pen_patch         (:)   = nan
-    allocate(this%sabg_soil_patch        (begp:endp))              ; this%sabg_soil_patch        (:)   = nan
-    allocate(this%sabg_snow_patch        (begp:endp))              ; this%sabg_snow_patch        (:)   = nan
-    allocate(this%sabg_chk_patch         (begp:endp))              ; this%sabg_chk_patch         (:)   = nan
-    allocate(this%sabs_roof_dir_lun      (begl:endl,1:numrad))     ; this%sabs_roof_dir_lun      (:,:) = nan
-    allocate(this%sabs_roof_dif_lun      (begl:endl,1:numrad))     ; this%sabs_roof_dif_lun      (:,:) = nan
-    allocate(this%sabs_sunwall_dir_lun   (begl:endl,1:numrad))     ; this%sabs_sunwall_dir_lun   (:,:) = nan
-    allocate(this%sabs_sunwall_dif_lun   (begl:endl,1:numrad))     ; this%sabs_sunwall_dif_lun   (:,:) = nan
-    allocate(this%sabs_shadewall_dir_lun (begl:endl,1:numrad))     ; this%sabs_shadewall_dir_lun (:,:) = nan
-    allocate(this%sabs_shadewall_dif_lun (begl:endl,1:numrad))     ; this%sabs_shadewall_dif_lun (:,:) = nan
-    allocate(this%sabs_improad_dir_lun   (begl:endl,1:numrad))     ; this%sabs_improad_dir_lun   (:,:) = nan
-    allocate(this%sabs_improad_dif_lun   (begl:endl,1:numrad))     ; this%sabs_improad_dif_lun   (:,:) = nan
-    allocate(this%sabs_perroad_dir_lun   (begl:endl,1:numrad))     ; this%sabs_perroad_dir_lun   (:,:) = nan
-    allocate(this%sabs_perroad_dif_lun   (begl:endl,1:numrad))     ; this%sabs_perroad_dif_lun   (:,:) = nan 
-    allocate(this%sub_surf_abs_SW_patch  (begp:endp))              ; this%sub_surf_abs_SW_patch  (:)   = nan
-    allocate(this%fsr_patch              (begp:endp))              ; this%fsr_patch              (:)   = nan
-    allocate(this%fsr_nir_d_patch        (begp:endp))              ; this%fsr_nir_d_patch        (:)   = nan
-    allocate(this%fsr_nir_i_patch        (begp:endp))              ; this%fsr_nir_i_patch        (:)   = nan
-    allocate(this%fsr_nir_d_ln_patch     (begp:endp))              ; this%fsr_nir_d_ln_patch     (:)   = nan
-    allocate(this%fsds_nir_d_patch       (begp:endp))              ; this%fsds_nir_d_patch       (:)   = nan
-    allocate(this%fsds_nir_i_patch       (begp:endp))              ; this%fsds_nir_i_patch       (:)   = nan
-    allocate(this%fsds_nir_d_ln_patch    (begp:endp))              ; this%fsds_nir_d_ln_patch    (:)   = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
-    use clm_varctl    , only : use_snicar_frc 
-    use clm_varpar    , only : nlevsno
-    use histFileMod   , only : hist_addfld1d, hist_addfld2d
-    use histFileMod   , only : no_snow_normal
-    !
-    ! !ARGUMENTS:
-    class(solarabs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr_1d(:)      ! pointer to 1d patch array
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    this%fsa_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSA', units='W/m^2',  &
-         avgflag='A', long_name='absorbed solar radiation', &
-         ptr_patch=this%fsa_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FSA_ICE', units='W/m^2',  &
-         avgflag='A', long_name='absorbed solar radiation (ice landunits only)', &
-         ptr_patch=this%fsa_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%fsa_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSA_R', units='W/m^2',  &
-         avgflag='A', long_name='Rural absorbed solar radiation', &
-         ptr_patch=this%fsa_r_patch, set_spec=spval, default='inactive')
-
-    this%fsa_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSA_U', units='W/m^2',  &
-         avgflag='A', long_name='Urban absorbed solar radiation', &
-         ptr_patch=this%fsa_u_patch, c2l_scale_type='urbanf', set_nourb=spval, default='inactive')
-
-    this%fsr_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSR', units='W/m^2',  &
-         avgflag='A', long_name='reflected solar radiation', &
-         ptr_patch=this%fsr_patch, c2l_scale_type='urbanf', default='inactive')
-    ! Rename of FSR for Urban intercomparision project
-    call hist_addfld1d (fname='SWup', units='W/m^2',  &
-         avgflag='A', long_name='upwelling shortwave radiation', &
-         ptr_patch=this%fsr_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='FSR_ICE', units='W/m^2',  &
-         avgflag='A', long_name='reflected solar radiation (ice landunits only)', &
-         ptr_patch=this%fsr_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%sabg_lyr_patch(begp:endp,-nlevsno+1:0) = spval
-    data2dptr => this%sabg_lyr_patch(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_ABS', units='W/m^2', type2d='levsno',  &
-         avgflag='A', long_name='Absorbed solar radiation in each snow layer', &
-         ptr_patch=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_ABS_ICE', units='W/m^2', type2d='levsno',  &
-         avgflag='A', long_name='Absorbed solar radiation in each snow layer (ice landunits only)', &
-         ptr_patch=data2dptr, no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%sabv_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SABV', units='W/m^2',  &
-         avgflag='A', long_name='solar rad absorbed by veg', &
-         ptr_patch=this%sabv_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%sabg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SABG', units='W/m^2',  &
-         avgflag='A', long_name='solar rad absorbed by ground', &
-         ptr_patch=this%sabg_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%sabg_pen_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SABG_PEN', units='watt/m^2',  &
-         avgflag='A', long_name='Rural solar rad penetrating top soil or snow layer', &
-         ptr_patch=this%sabg_pen_patch, set_spec=spval, default='inactive')
-
-     ! Currently needed by lake code - TODO should not be here
-    this%fsds_nir_d_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSND', units='W/m^2',  &
-         avgflag='A', long_name='direct nir incident solar radiation', &
-         ptr_patch=this%fsds_nir_d_patch, default='inactive')
-
-    this%fsds_nir_i_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSNI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse nir incident solar radiation', &
-         ptr_patch=this%fsds_nir_i_patch, default='inactive')
-
-    this%fsds_nir_d_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSNDLN', units='W/m^2',  &
-         avgflag='A', long_name='direct nir incident solar radiation at local noon', &
-         ptr_patch=this%fsds_nir_d_ln_patch, default='inactive')
-
-    this%fsr_nir_d_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRND', units='W/m^2',  &
-         avgflag='A', long_name='direct nir reflected solar radiation', &
-         ptr_patch=this%fsr_nir_d_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%fsr_nir_i_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRNI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse nir reflected solar radiation', &
-         ptr_patch=this%fsr_nir_i_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%fsr_nir_d_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRNDLN', units='W/m^2',  &
-         avgflag='A', long_name='direct nir reflected solar radiation at local noon', &
-         ptr_patch=this%fsr_nir_d_ln_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%sub_surf_abs_SW_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOINTABS', units='-', &
-         avgflag='A', long_name='Fraction of incoming solar absorbed by lower snow layers', &
-         ptr_patch=this%sub_surf_abs_SW_patch, set_lake=spval, set_urb=spval, default='inactive')
-
-    if(use_luna)then
-       ptr_1d => this%par240d_z_patch(:,1)
-       call hist_addfld1d (fname='PAR240DZ', units='W/m^2', &
-         avgflag='A', long_name='10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer', &
-         ptr_patch=ptr_1d, default='inactive')
-       ptr_1d => this%par240x_z_patch(:,1)
-       call hist_addfld1d (fname='PAR240XZ', units='W/m^2', &
-         avgflag='A', long_name='10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer', &
-         ptr_patch=ptr_1d, default='inactive')
-
-    endif
-
-  end subroutine InitHistory
-
-  !------------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! Initialize module surface albedos to reasonable values
-    !
-    use landunit_varcon, only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    class(solarabs_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begl, endl
-    !-----------------------------------------------------------------------
-
-    begl = bounds%begl; endl = bounds%endl
-
-    this%sabs_roof_dir_lun      (begl:endl, :) = 0._r8    
-    this%sabs_roof_dif_lun      (begl:endl, :) = 0._r8    
-    this%sabs_sunwall_dir_lun   (begl:endl, :) = 0._r8
-    this%sabs_sunwall_dif_lun   (begl:endl, :) = 0._r8
-    this%sabs_shadewall_dir_lun (begl:endl, :) = 0._r8
-    this%sabs_shadewall_dif_lun (begl:endl, :) = 0._r8
-    this%sabs_improad_dir_lun   (begl:endl, :) = 0._r8
-    this%sabs_improad_dif_lun   (begl:endl, :) = 0._r8
-    this%sabs_perroad_dir_lun   (begl:endl, :) = 0._r8
-    this%sabs_perroad_dif_lun   (begl:endl, :) = 0._r8
-
-  end subroutine InitCold
-
-  !---------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !DESCRIPTION:
-    ! Read/Write module information to/from restart file.
-    !
-    ! !USES:
-    use shr_infnan_mod , only : shr_infnan_isnan
-    use clm_varctl     , only : use_snicar_frc, iulog 
-    use spmdMod        , only : masterproc
-    use abortutils     , only : endrun
-    use ncdio_pio      , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(solarabs_type) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    logical :: readvar      ! determine if variable is on initial file
-    integer :: p
-    !---------------------------------------------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_roof_dir', xtype=ncd_double,  dim1name='landunit',            & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='direct solar absorbed by roof per unit ground area per unit incident flux', units='',             &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_roof_dir_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_roof_dif', xtype=ncd_double,  dim1name='landunit',            & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='diffuse solar absorbed by roof per unit ground area per unit incident flux', units='',            &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_roof_dif_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_sunwall_dir', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='direct solar absorbed by sunwall per unit wall area per unit incident flux', units='',            &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_sunwall_dir_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_sunwall_dif', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='diffuse solar absorbed by sunwall per unit wall area per unit incident flux', units='',           &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_sunwall_dif_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_shadewall_dir', xtype=ncd_double,  dim1name='landunit',       & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='direct solar absorbed by shadewall per unit wall area per unit incident flux', units='',          &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_shadewall_dir_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_shadewall_dif', xtype=ncd_double,  dim1name='landunit',       & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='diffuse solar absorbed by shadewall per unit wall area per unit incident flux', units='',         &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_shadewall_dif_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_improad_dir', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='direct solar absorbed by impervious road per unit ground area per unit incident flux', units='',  &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_improad_dir_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_improad_dif', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='diffuse solar absorbed by impervious road per unit ground area per unit incident flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_improad_dif_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_perroad_dir', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='direct solar absorbed by pervious road per unit ground area per unit incident flux', units='',    &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_perroad_dir_lun)
-
-    call restartvar(ncid=ncid, flag=flag, varname='sabs_perroad_dif', xtype=ncd_double,  dim1name='landunit',         & 
-         dim2name='numrad', switchdim=.true.,                                                                         &
-         long_name='diffuse solar absorbed by pervious road per unit ground area per unit incident flux', units='',   &
-         interpinic_flag='interp', readvar=readvar, data=this%sabs_perroad_dif_lun)
-
-   if(use_luna)then
-      call restartvar(ncid=ncid, flag=flag, varname='par240d', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='10-day running mean of daytime absorbed PAR for leaves in canopy layer', units='W/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%par240d_z_patch )
-      call restartvar(ncid=ncid, flag=flag, varname='par24d', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Accumulative daytime absorbed PAR for leaves in canopy layer for 24 hours', units='J/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%par24d_z_patch )
-
-      call restartvar(ncid=ncid, flag=flag, varname='par240x', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='10-day running mean of maximum absorbed PAR for leaves in canopy layers', units='W/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%par240x_z_patch )
-      call restartvar(ncid=ncid, flag=flag, varname='par24x', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Maximum absorbed PAR for leaves in canopy layer in 24 hours', units='J/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%par24x_z_patch )
-
-      call restartvar(ncid=ncid, flag=flag, varname='parsun', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Instaneous absorbed PAR for sunlit leaves in canopy layer', units='W/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%parsun_z_patch )
-      call restartvar(ncid=ncid, flag=flag, varname='parsha', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='Instaneous absorbed PAR for shaded leaves in canopy layer', units='W/m**2 leaf', &
-         interpinic_flag='interp', readvar=readvar, data=this%parsha_z_patch )
-
-   endif
-
-  end subroutine Restart
-
-end module SolarAbsorbedType
diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90
deleted file mode 100644
index 93caf268a8..0000000000
--- a/src/biogeophys/SurfaceAlbedoMod.F90
+++ /dev/null
@@ -1,143 +0,0 @@
-module SurfaceAlbedoMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Performs surface albedo calculations
-  !
-  ! !PUBLIC TYPES:
-  use shr_kind_mod      , only : r8 => shr_kind_r8
-  use shr_log_mod       , only : errMsg => shr_log_errMsg
-  use decompMod         , only : bounds_type
-  use landunit_varcon   , only : istsoil, istcrop
-  use clm_varcon        , only : grlnd, namep
-  use clm_varpar        , only : numrad, nlevcan, nlevsno, nlevcan
-  use clm_varctl        , only : fsurdat, iulog, use_snicar_frc
-  use pftconMod         , only : pftcon
-  use ColumnType        , only : col                
-  !
-  implicit none
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: SurfaceAlbedoInitTimeConst
-  !
-  ! !PUBLIC DATA MEMBERS:
-  ! The CLM default albice values are too high.
-  ! Full-spectral albedo for land ice is ~0.5 (Paterson, Physics of Glaciers, 1994, p. 59)
-  ! This is the value used in CAM3 by Pritchard et al., GRL, 35, 2008.
-
-  ! albedo land ice by waveband (1=vis, 2=nir)
-  real(r8), public  :: albice(numrad) = (/ 0.80_r8, 0.55_r8 /)
-
-  ! namelist default setting for inputting alblakwi
-  real(r8), public  :: lake_melt_icealb(numrad) = (/ 0.10_r8, 0.10_r8/)
-
-  ! Coefficient for calculating ice "fraction" for lake surface albedo
-  ! From D. Mironov (2010) Boreal Env. Research
-  real(r8), parameter :: calb = 95.6_r8   
-
-  !
-  ! !PRIVATE DATA MEMBERS:
-
-  ! !PRIVATE DATA FUNCTIONS:
-  real(r8), allocatable, private :: albsat(:,:) ! wet soil albedo by color class and waveband (1=vis,2=nir)
-  real(r8), allocatable, private :: albdry(:,:) ! dry soil albedo by color class and waveband (1=vis,2=nir)
-  integer , allocatable, private :: isoicol(:)  ! column soil color class
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine SurfaceAlbedoInitTimeConst(bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module time constant variables
-    !
-    ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use fileutils  , only : getfil
-    use abortutils , only : endrun
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_pio_openfile, ncd_pio_closefile
-    use spmdMod    , only : masterproc
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: c,g          ! indices
-    integer            :: mxsoil_color ! maximum number of soil color classes
-    type(file_desc_t)  :: ncid         ! netcdf id
-    character(len=256) :: locfn        ! local filename
-    integer            :: ier          ! error status
-    logical            :: readvar 
-    integer  ,pointer  :: soic2d (:)   ! read in - soil color 
-    !---------------------------------------------------------------------
-
-    ! Allocate module variable for soil color
-
-    allocate(isoicol(bounds%begc:bounds%endc)) 
-
-    ! Determine soil color and number of soil color classes 
-    ! if number of soil color classes is not on input dataset set it to 8
-
-    call getfil (fsurdat, locfn, 0)
-    call ncd_pio_openfile (ncid, locfn, 0)
-
-    call ncd_io(ncid=ncid, varname='mxsoil_color', flag='read', data=mxsoil_color, readvar=readvar)
-    if ( .not. readvar ) mxsoil_color = 8  
-
-    allocate(soic2d(bounds%begg:bounds%endg)) 
-    call ncd_io(ncid=ncid, varname='SOIL_COLOR', flag='read', data=soic2d, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call endrun(msg=' ERROR: SOIL_COLOR NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = bounds%begc, bounds%endc
-       g = col%gridcell(c)
-       isoicol(c) = soic2d(g)
-    end do
-    deallocate(soic2d)
-
-    call ncd_pio_closefile(ncid)
-
-    ! Determine saturated and dry soil albedos for n color classes and 
-    ! numrad wavebands (1=vis, 2=nir)
-
-    allocate(albsat(mxsoil_color,numrad), albdry(mxsoil_color,numrad), stat=ier)
-    if (ier /= 0) then
-       write(iulog,*)'allocation error for albsat, albdry'
-       call endrun(msg=errMsg(sourcefile, __LINE__)) 
-    end if
-
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read soil colo data .....'
-    end if
-    
-    if (mxsoil_color == 8) then
-       albsat(1:8,1) = (/0.12_r8,0.11_r8,0.10_r8,0.09_r8,0.08_r8,0.07_r8,0.06_r8,0.05_r8/)
-       albsat(1:8,2) = (/0.24_r8,0.22_r8,0.20_r8,0.18_r8,0.16_r8,0.14_r8,0.12_r8,0.10_r8/)
-       albdry(1:8,1) = (/0.24_r8,0.22_r8,0.20_r8,0.18_r8,0.16_r8,0.14_r8,0.12_r8,0.10_r8/)
-       albdry(1:8,2) = (/0.48_r8,0.44_r8,0.40_r8,0.36_r8,0.32_r8,0.28_r8,0.24_r8,0.20_r8/)
-    else if (mxsoil_color == 20) then
-       albsat(1:20,1) = (/0.25_r8,0.23_r8,0.21_r8,0.20_r8,0.19_r8,0.18_r8,0.17_r8,0.16_r8,&
-            0.15_r8,0.14_r8,0.13_r8,0.12_r8,0.11_r8,0.10_r8,0.09_r8,0.08_r8,0.07_r8,0.06_r8,0.05_r8,0.04_r8/)
-       albsat(1:20,2) = (/0.50_r8,0.46_r8,0.42_r8,0.40_r8,0.38_r8,0.36_r8,0.34_r8,0.32_r8,&
-            0.30_r8,0.28_r8,0.26_r8,0.24_r8,0.22_r8,0.20_r8,0.18_r8,0.16_r8,0.14_r8,0.12_r8,0.10_r8,0.08_r8/)
-       albdry(1:20,1) = (/0.36_r8,0.34_r8,0.32_r8,0.31_r8,0.30_r8,0.29_r8,0.28_r8,0.27_r8,&
-            0.26_r8,0.25_r8,0.24_r8,0.23_r8,0.22_r8,0.20_r8,0.18_r8,0.16_r8,0.14_r8,0.12_r8,0.10_r8,0.08_r8/)
-       albdry(1:20,2) = (/0.61_r8,0.57_r8,0.53_r8,0.51_r8,0.49_r8,0.48_r8,0.45_r8,0.43_r8,&
-            0.41_r8,0.39_r8,0.37_r8,0.35_r8,0.33_r8,0.31_r8,0.29_r8,0.27_r8,0.25_r8,0.23_r8,0.21_r8,0.16_r8/)
-    else
-       write(iulog,*)'maximum color class = ',mxsoil_color,' is not supported'
-       call endrun(msg=errMsg(sourcefile, __LINE__)) 
-    end if
-
-    ! Set alblakwi
-    !alblakwi(:) = lake_melt_icealb(:)
-
-  end subroutine SurfaceAlbedoInitTimeConst
-
-end module SurfaceAlbedoMod
diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90
index 1540d9f991..3bda969af9 100644
--- a/src/biogeophys/SurfaceAlbedoType.F90
+++ b/src/biogeophys/SurfaceAlbedoType.F90
@@ -4,10 +4,8 @@ module SurfaceAlbedoType
 
   !-----------------------------------------------------------------------
   use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
   use decompMod      , only : bounds_type
-  use clm_varpar     , only : numrad, nlevcan, nlevsno
-  use abortutils     , only : endrun
+  use clm_varpar     , only : numrad
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -16,55 +14,13 @@ module SurfaceAlbedoType
   ! !PUBLIC DATA MEMBERS:
   type, public :: surfalb_type
 
-     real(r8), pointer :: coszen_col           (:)   ! col cosine of solar zenith angle
-     real(r8), pointer :: albd_patch           (:,:) ! patch surface albedo (direct)   (numrad)                    
-     real(r8), pointer :: albi_patch           (:,:) ! patch surface albedo (diffuse)  (numrad)                    
-     real(r8), pointer :: albgrd_pur_col       (:,:) ! col pure snow ground direct albedo     (numrad)             
-     real(r8), pointer :: albgri_pur_col       (:,:) ! col pure snow ground diffuse albedo    (numrad)             
-     real(r8), pointer :: albgrd_bc_col        (:,:) ! col ground direct  albedo without BC   (numrad)             
-     real(r8), pointer :: albgri_bc_col        (:,:) ! col ground diffuse albedo without BC   (numrad)             
-     real(r8), pointer :: albgrd_oc_col        (:,:) ! col ground direct  albedo without OC   (numrad)             
-     real(r8), pointer :: albgri_oc_col        (:,:) ! col ground diffuse albedo without OC   (numrad)             
-     real(r8), pointer :: albgrd_dst_col       (:,:) ! col ground direct  albedo without dust (numrad)             
-     real(r8), pointer :: albgri_dst_col       (:,:) ! col ground diffuse albedo without dust (numrad)             
-     real(r8), pointer :: albgrd_col           (:,:) ! col ground albedo (direct)  (numrad)                        
-     real(r8), pointer :: albgri_col           (:,:) ! col ground albedo (diffuse) (numrad)                        
-     real(r8), pointer :: albsod_col           (:,:) ! col soil albedo: direct  (col,bnd) [frc]                    
-     real(r8), pointer :: albsoi_col           (:,:) ! col soil albedo: diffuse (col,bnd) [frc]                    
-     real(r8), pointer :: albsnd_hst_col       (:,:) ! col snow albedo, direct , for history files (col,bnd) [frc] 
-     real(r8), pointer :: albsni_hst_col       (:,:) ! col snow albedo, diffuse, for history files (col,bnd) [frc] 
-
-     real(r8), pointer :: ftdd_patch           (:,:) ! patch down direct flux below canopy per unit direct flx    (numrad)
-     real(r8), pointer :: ftid_patch           (:,:) ! patch down diffuse flux below canopy per unit direct flx   (numrad)
-     real(r8), pointer :: ftii_patch           (:,:) ! patch down diffuse flux below canopy per unit diffuse flx  (numrad)
-     real(r8), pointer :: fabd_patch           (:,:) ! patch flux absorbed by canopy per unit direct flux         (numrad)
-     real(r8), pointer :: fabd_sun_patch       (:,:) ! patch flux absorbed by sunlit canopy per unit direct flux  (numrad)
-     real(r8), pointer :: fabd_sha_patch       (:,:) ! patch flux absorbed by shaded canopy per unit direct flux  (numrad)
-     real(r8), pointer :: fabi_patch           (:,:) ! patch flux absorbed by canopy per unit diffuse flux        (numrad)
-     real(r8), pointer :: fabi_sun_patch       (:,:) ! patch flux absorbed by sunlit canopy per unit diffuse flux (numrad)
-     real(r8), pointer :: fabi_sha_patch       (:,:) ! patch flux absorbed by shaded canopy per unit diffuse flux (numrad)
-     real(r8), pointer :: fabd_sun_z_patch     (:,:) ! patch absorbed sunlit leaf direct  PAR (per unit lai+sai) for each canopy layer
-     real(r8), pointer :: fabd_sha_z_patch     (:,:) ! patch absorbed shaded leaf direct  PAR (per unit lai+sai) for each canopy layer
-     real(r8), pointer :: fabi_sun_z_patch     (:,:) ! patch absorbed sunlit leaf diffuse PAR (per unit lai+sai) for each canopy layer
-     real(r8), pointer :: fabi_sha_z_patch     (:,:) ! patch absorbed shaded leaf diffuse PAR (per unit lai+sai) for each canopy layer
-     real(r8), pointer :: flx_absdv_col        (:,:) ! col absorbed flux per unit incident direct flux:  VIS (col,lyr) [frc]
-     real(r8), pointer :: flx_absdn_col        (:,:) ! col absorbed flux per unit incident direct flux:  NIR (col,lyr) [frc]
-     real(r8), pointer :: flx_absiv_col        (:,:) ! col absorbed flux per unit incident diffuse flux: VIS (col,lyr) [frc]
-     real(r8), pointer :: flx_absin_col        (:,:) ! col absorbed flux per unit incident diffuse flux: NIR (col,lyr) [frc]
-
-     real(r8) , pointer :: fsun_z_patch        (:,:) ! patch patch sunlit fraction of canopy layer
-     real(r8) , pointer :: tlai_z_patch        (:,:) ! patch tlai increment for canopy layer                         
-     real(r8) , pointer :: tsai_z_patch        (:,:) ! patch tsai increment for canopy layer                         
-     integer  , pointer :: ncan_patch          (:)   ! patch number of canopy layers
-     integer  , pointer :: nrad_patch          (:)   ! patch number of canopy layers, above snow for radiative transfer
-     real(r8) , pointer :: vcmaxcintsun_patch  (:)   ! patch leaf to canopy scaling coefficient, sunlit leaf vcmax   
-     real(r8) , pointer :: vcmaxcintsha_patch  (:)   ! patch leaf to canopy scaling coefficient, shaded leaf vcmax   
+     real(r8), pointer :: albd_patch(:,:)  ! patch surface albedo (direct)   (numrad)
+     real(r8), pointer :: albi_patch(:,:)  ! patch surface albedo (diffuse)  (numrad)
 
    contains
 
      procedure, public  :: Init         
      procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
      procedure, private :: InitCold     
      procedure, public  :: Restart      
 
@@ -83,7 +39,6 @@ subroutine Init(this, bounds)
     type(bounds_type), intent(in) :: bounds  
 
     call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
     call this%InitCold(bounds)
 
   end subroutine Init
@@ -95,7 +50,6 @@ subroutine InitAllocate(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use clm_varcon    , only: spval, ispval
     !
     ! !ARGUMENTS:
     class(surfalb_type) :: this
@@ -103,107 +57,15 @@ subroutine InitAllocate(this, bounds)
     !
     ! !LOCAL VARIABLES:
     integer :: begp, endp
-    integer :: begc, endc
     !---------------------------------------------------------------------
 
     begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    allocate(this%coszen_col         (begc:endc))              ; this%coszen_col         (:)   = nan
-    allocate(this%albgrd_col         (begc:endc,numrad))       ; this%albgrd_col         (:,:) = nan
-    allocate(this%albgri_col         (begc:endc,numrad))       ; this%albgri_col         (:,:) = nan
-    allocate(this%albsnd_hst_col     (begc:endc,numrad))       ; this%albsnd_hst_col     (:,:) = spval
-    allocate(this%albsni_hst_col     (begc:endc,numrad))       ; this%albsni_hst_col     (:,:) = spval
-    allocate(this%albsod_col         (begc:endc,numrad))       ; this%albsod_col         (:,:) = spval
-    allocate(this%albsoi_col         (begc:endc,numrad))       ; this%albsoi_col         (:,:) = spval
-    allocate(this%albgrd_pur_col     (begc:endc,numrad))       ; this%albgrd_pur_col     (:,:) = nan
-    allocate(this%albgri_pur_col     (begc:endc,numrad))       ; this%albgri_pur_col     (:,:) = nan
-    allocate(this%albgrd_bc_col      (begc:endc,numrad))       ; this%albgrd_bc_col      (:,:) = nan
-    allocate(this%albgri_bc_col      (begc:endc,numrad))       ; this%albgri_bc_col      (:,:) = nan
-    allocate(this%albgrd_oc_col      (begc:endc,numrad))       ; this%albgrd_oc_col      (:,:) = nan
-    allocate(this%albgri_oc_col      (begc:endc,numrad))       ; this%albgri_oc_col      (:,:) = nan
-    allocate(this%albgrd_dst_col     (begc:endc,numrad))       ; this%albgrd_dst_col     (:,:) = nan
-    allocate(this%albgri_dst_col     (begc:endc,numrad))       ; this%albgri_dst_col     (:,:) = nan
-    allocate(this%albd_patch         (begp:endp,numrad))       ; this%albd_patch         (:,:) = nan
-    allocate(this%albi_patch         (begp:endp,numrad))       ; this%albi_patch         (:,:) = nan
 
-    allocate(this%ftdd_patch         (begp:endp,numrad))       ; this%ftdd_patch         (:,:) = nan
-    allocate(this%ftid_patch         (begp:endp,numrad))       ; this%ftid_patch         (:,:) = nan
-    allocate(this%ftii_patch         (begp:endp,numrad))       ; this%ftii_patch         (:,:) = nan
-    allocate(this%fabd_patch         (begp:endp,numrad))       ; this%fabd_patch         (:,:) = nan
-    allocate(this%fabd_sun_patch     (begp:endp,numrad))       ; this%fabd_sun_patch     (:,:) = nan
-    allocate(this%fabd_sha_patch     (begp:endp,numrad))       ; this%fabd_sha_patch     (:,:) = nan
-    allocate(this%fabi_patch         (begp:endp,numrad))       ; this%fabi_patch         (:,:) = nan
-    allocate(this%fabi_sun_patch     (begp:endp,numrad))       ; this%fabi_sun_patch     (:,:) = nan
-    allocate(this%fabi_sha_patch     (begp:endp,numrad))       ; this%fabi_sha_patch     (:,:) = nan
-    allocate(this%fabd_sun_z_patch   (begp:endp,nlevcan))      ; this%fabd_sun_z_patch   (:,:) = 0._r8
-    allocate(this%fabd_sha_z_patch   (begp:endp,nlevcan))      ; this%fabd_sha_z_patch   (:,:) = 0._r8
-    allocate(this%fabi_sun_z_patch   (begp:endp,nlevcan))      ; this%fabi_sun_z_patch   (:,:) = 0._r8
-    allocate(this%fabi_sha_z_patch   (begp:endp,nlevcan))      ; this%fabi_sha_z_patch   (:,:) = 0._r8
-    allocate(this%flx_absdv_col      (begc:endc,-nlevsno+1:1)) ; this%flx_absdv_col      (:,:) = spval
-    allocate(this%flx_absdn_col      (begc:endc,-nlevsno+1:1)) ; this%flx_absdn_col      (:,:) = spval
-    allocate(this%flx_absiv_col      (begc:endc,-nlevsno+1:1)) ; this%flx_absiv_col      (:,:) = spval
-    allocate(this%flx_absin_col      (begc:endc,-nlevsno+1:1)) ; this%flx_absin_col      (:,:) = spval
-
-    allocate(this%fsun_z_patch       (begp:endp,nlevcan))      ; this%fsun_z_patch       (:,:) = 0._r8
-    allocate(this%tlai_z_patch       (begp:endp,nlevcan))      ; this%tlai_z_patch       (:,:) = 0._r8
-    allocate(this%tsai_z_patch       (begp:endp,nlevcan))      ; this%tsai_z_patch       (:,:) = 0._r8
-    allocate(this%ncan_patch         (begp:endp))              ; this%ncan_patch         (:)   = 0
-    allocate(this%nrad_patch         (begp:endp))              ; this%nrad_patch         (:)   = 0
-    allocate(this%vcmaxcintsun_patch (begp:endp))              ; this%vcmaxcintsun_patch (:)   = nan
-    allocate(this%vcmaxcintsha_patch (begp:endp))              ; this%vcmaxcintsha_patch (:)   = nan
+    allocate(this%albd_patch(begp:endp,numrad)); this%albd_patch(:,:) = nan
+    allocate(this%albi_patch(begp:endp,numrad)); this%albi_patch(:,:) = nan
 
   end subroutine InitAllocate
 
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=)
-    use clm_varcon    , only: spval
-    use histFileMod   , only: hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(surfalb_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    this%coszen_col(begc:endc) = spval
-    call hist_addfld1d (fname='COSZEN', units='none', &
-         avgflag='A', long_name='cosine of solar zenith angle', &
-         ptr_col=this%coszen_col, default='inactive')
-
-    this%albgri_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='ALBGRD', units='proportion', type2d='numrad', &
-         avgflag='A', long_name='ground albedo (direct)', &
-         ptr_col=this%albgrd_col, default='inactive')
-
-    this%albgri_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='ALBGRI', units='proportion', type2d='numrad', &
-         avgflag='A', long_name='ground albedo (indirect)', &
-         ptr_col=this%albgri_col, default='inactive')
-
-    this%albd_patch(begp:endp,:) = spval
-    call hist_addfld2d (fname='ALBD', units='proportion', type2d='numrad', &
-         avgflag='A', long_name='surface albedo (direct)', &
-         ptr_patch=this%albd_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%albi_patch(begp:endp,:) = spval
-    call hist_addfld2d (fname='ALBI', units='proportion', type2d='numrad', &
-         avgflag='A', long_name='surface albedo (indirect)', &
-         ptr_patch=this%albi_patch, default='inactive', c2l_scale_type='urbanf')
-
-  end subroutine InitHistory
-
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds)
     !
@@ -214,56 +76,25 @@ subroutine InitCold(this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer :: begc, endc
     integer :: begp, endp
     !-----------------------------------------------------------------------
 
     begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
 
-    this%albgrd_col     (begc:endc, :) = 0.2_r8
-    this%albgri_col     (begc:endc, :) = 0.2_r8
-    this%albsod_col     (begc:endc, :) = 0.2_r8
-    this%albsoi_col     (begc:endc, :) = 0.2_r8
-    this%albsnd_hst_col (begc:endc, :) = 0.6_r8
-    this%albsni_hst_col (begc:endc, :) = 0.6_r8
     this%albd_patch     (begp:endp, :) = 0.2_r8
     this%albi_patch     (begp:endp, :) = 0.2_r8
 
-    this%albgrd_pur_col (begc:endc, :) = 0.2_r8
-    this%albgri_pur_col (begc:endc, :) = 0.2_r8
-    this%albgrd_bc_col  (begc:endc, :) = 0.2_r8
-    this%albgri_bc_col  (begc:endc, :) = 0.2_r8
-    this%albgrd_oc_col  (begc:endc, :) = 0.2_r8
-    this%albgri_oc_col  (begc:endc, :) = 0.2_r8
-    this%albgrd_dst_col (begc:endc, :) = 0.2_r8
-    this%albgri_dst_col (begc:endc, :) = 0.2_r8
- 
-    this%fabi_patch     (begp:endp, :) = 0.0_r8
-    this%fabd_patch     (begp:endp, :) = 0.0_r8
-    this%fabi_sun_patch (begp:endp, :) = 0.0_r8
-    this%fabd_sun_patch (begp:endp, :) = 0.0_r8
-    this%fabd_sha_patch (begp:endp, :) = 0.0_r8
-    this%fabi_sha_patch (begp:endp, :) = 0.0_r8
-    this%ftdd_patch     (begp:endp, :) = 1.0_r8
-    this%ftid_patch     (begp:endp, :) = 0.0_r8
-    this%ftii_patch     (begp:endp, :) = 1.0_r8
- 
   end subroutine InitCold
    
   !---------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, &
-       tlai_patch, tsai_patch)
+  subroutine Restart(this, bounds, ncid, flag)
     ! 
     ! !DESCRIPTION:
     ! Read/Write module information to/from restart file.
     !
     ! !USES:
-    use clm_varctl , only : use_snicar_frc, iulog 
-    use spmdMod    , only : masterproc
     use decompMod  , only : bounds_type
-    use abortutils , only : endrun
-    use ncdio_pio  , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen
+    use ncdio_pio  , only : file_desc_t, ncd_double
     use restUtilMod
     !
     ! !ARGUMENTS:
@@ -271,366 +102,21 @@ subroutine Restart(this, bounds, ncid, flag, &
     type(bounds_type) , intent(in)    :: bounds 
     type(file_desc_t) , intent(inout) :: ncid ! netcdf id
     character(len=*)  , intent(in)    :: flag ! 'read' or 'write'
-    real(r8)          , intent(in)    :: tlai_patch(bounds%begp:)
-    real(r8)          , intent(in)    :: tsai_patch(bounds%begp:)
     !
     ! !LOCAL VARIABLES:
     logical :: readvar      ! determine if variable is on initial file
-    integer :: iv
-    integer :: begp, endp
-    integer :: begc, endc
     !---------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(tlai_patch)  == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(tsai_patch)  == (/bounds%endp/)), errMsg(sourcefile, __LINE__))
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    call restartvar(ncid=ncid, flag=flag, varname='coszen', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='cosine of solar zenith angle', units='unitless', &
-         interpinic_flag='interp', readvar=readvar, data=this%coszen_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='albd', xtype=ncd_double,  & 
+    call restartvar(ncid=ncid, flag=flag, varname='albd', xtype=ncd_double,  &
          dim1name='pft', dim2name='numrad', switchdim=.true., &
          long_name='surface albedo (direct) (0 to 1)', units='', &
          interpinic_flag='interp', readvar=readvar, data=this%albd_patch)
 
-    call restartvar(ncid=ncid, flag=flag, varname='albi', xtype=ncd_double,  & 
+    call restartvar(ncid=ncid, flag=flag, varname='albi', xtype=ncd_double,  &
          dim1name='pft', dim2name='numrad', switchdim=.true., &
          long_name='surface albedo (diffuse) (0 to 1)', units='', &
          interpinic_flag='interp', readvar=readvar, data=this%albi_patch)
 
-    call restartvar(ncid=ncid, flag=flag, varname='albgrd', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='ground albedo (direct) (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%albgrd_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='albgri', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='ground albedo (indirect) (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%albgri_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='albsod', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='soil albedo (direct) (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%albsod_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='albsoi', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='soil albedo (indirect) (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%albsoi_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='albsnd_hst', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='snow albedo (direct) (0 to 1)', units='proportion', &
-         interpinic_flag='interp', readvar=readvar, data=this%albsnd_hst_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='albsni_hst', xtype=ncd_double,  &
-         dim1name='column', dim2name='numrad', switchdim=.true., &
-         long_name='snow albedo (diffuse) (0 to 1)', units='proportion', &
-         interpinic_flag='interp', readvar=readvar, data=this%albsni_hst_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='tlai_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='tlai increment for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tlai_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) then
-          write(iulog,*) "can't find tlai_z in restart (or initial) file..."
-          write(iulog,*) "Initialize tlai_z to tlai/nlevcan" 
-       end if
-       do iv=1,nlevcan
-          this%tlai_z_patch(begp:endp,iv) =  tlai_patch(begp:endp) / nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='tsai_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='tsai increment for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%tsai_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) then
-          write(iulog,*) "can't find tsai_z in restart (or initial) file..."
-          write(iulog,*) "Initialize tsai_z to tsai/nlevcan" 
-       end if
-       do iv=1,nlevcan
-          this%tsai_z_patch(begp:endp,iv) = tsai_patch(begp:endp) / nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='ncan', xtype=ncd_int,  &
-         dim1name='pft', long_name='number of canopy layers', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%ncan_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find ncan in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize ncan to nlevcan" 
-       this%ncan_patch(begp:endp) = nlevcan
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='nrad', xtype=ncd_int,  &
-         dim1name='pft', long_name='number of canopy layers, above snow for radiative transfer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%nrad_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find nrad in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize nrad to nlevcan" 
-       this%nrad_patch(begp:endp) = nlevcan
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fsun_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='sunlit fraction for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fsun_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fsun_z in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fsun_z to 0"
-       do iv=1,nlevcan
-          this%fsun_z_patch(begp:endp,iv) = 0._r8
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='vcmaxcintsun', xtype=ncd_double, &
-         dim1name='pft', long_name='sunlit canopy scaling coefficient', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%vcmaxcintsun_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find vcmaxcintsun in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize vcmaxcintsun to 1"
-       this%vcmaxcintsun_patch(begp:endp) = 1._r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='vcmaxcintsha', xtype=ncd_double,  &
-         dim1name='pft', long_name='shaded canopy scaling coefficient', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%vcmaxcintsha_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find vcmaxcintsha in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize vcmaxcintsha to 1"
-       this%vcmaxcintsha_patch(begp:endp) = 1._r8
-    end if
-
-    if (use_snicar_frc) then
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgrd_bc', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without BC (direct) (0 to 1)', units='', &
-            interpinic_flag='interp',readvar=readvar, data=this%albgrd_bc_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgrd_bc in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgrd_bc to albgrd"
-          this%albgrd_bc_col(begc:endc,:) = this%albgrd_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgri_bc', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without BC (diffuse) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgri_bc_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgri_bc in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgri_bc to albgri"
-          this%albgri_bc_col(begc:endc,:) = this%albgri_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgrd_pur', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='pure snow ground albedo (direct) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgrd_pur_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgrd_pur in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgrd_pur to albgrd"
-          this%albgrd_pur_col(begc:endc,:) = this%albgrd_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgri_pur', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='pure snow ground albedo (diffuse) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgri_pur_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgri_pur in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgri_pur to albgri"
-          this%albgri_pur_col(begc:endc,:) = this%albgri_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgrd_oc', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without OC (direct) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgrd_oc_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgrd_oc in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgrd_oc to albgrd"
-          this%albgrd_oc_col(begc:endc,:) = this%albgrd_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgri_oc', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without OC (diffuse) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgri_oc_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgri_oc in restart (or initial) file..."
-          if (masterproc) write(iulog,*) "Initialize albgri_oc to albgri"
-          this%albgri_oc_col(begc:endc,:) = this%albgri_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgrd_dst', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without dust (direct) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgrd_dst_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgrd_dst in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgrd_dst to albgrd"
-          this%albgrd_dst_col(begc:endc,:) = this%albgrd_col(begc:endc,:)
-       end if
-
-       call restartvar(ncid=ncid, flag=flag, varname='albgri_dst', xtype=ncd_double,  &
-            dim1name='column', dim2name='numrad', switchdim=.true., &
-            long_name='ground albedo without dust (diffuse) (0 to 1)', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%albgri_dst_col)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "SNICAR: can't find albgri_dst in initial file..."
-          if (masterproc) write(iulog,*) "Initialize albgri_dst to albgri"
-          this%albgri_dst_col(begc:endc,:) = this%albgri_col(begc:endc,:)
-       end if
-
-    end if  ! end of if-use_snicar_frc 
-
-    ! patch type physical state variable - fabd
-    call restartvar(ncid=ncid, flag=flag, varname='fabd', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by veg per unit direct flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabd_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabi', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by veg per unit diffuse flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabi_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabd_sun', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by sunlit leaf per unit direct flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabd_sun_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabd_sun in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabd_sun to fabd/2"
-       this%fabd_sun_patch(begp:endp,:) = this%fabd_patch(begp:endp,:)/2._r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabd_sha', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by shaded leaf per unit direct flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabd_sha_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabd_sha in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabd_sha to fabd/2"
-       this%fabd_sha_patch(begp:endp,:) = this%fabd_patch(begp:endp,:)/2._r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabi_sun', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by sunlit leaf per unit diffuse flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabi_sun_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabi_sun in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabi_sun to fabi/2"
-       this%fabi_sun_patch(begp:endp,:) = this%fabi_patch(begp:endp,:)/2._r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabi_sha', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='flux absorbed by shaded leaf per unit diffuse flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabi_sha_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabi_sha in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabi_sha to fabi/2"
-       this%fabi_sha_patch(begp:endp,:) = this%fabi_patch(begp:endp,:)/2._r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabd_sun_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='absorbed sunlit leaf direct PAR (per unit lai+sai) for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabd_sun_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabd_sun_z in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabd_sun_z to (fabd/2)/nlevcan" 
-       do iv=1,nlevcan
-          this%fabd_sun_z_patch(begp:endp,iv) = (this%fabd_patch(begp:endp,1)/2._r8)/nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabd_sha_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='absorbed shaded leaf direct PAR (per unit lai+sai) for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabd_sha_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabd_sha_z in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabd_sha_z to (fabd/2)/nlevcan" 
-       do iv=1,nlevcan
-          this%fabd_sha_z_patch(begp:endp,iv) = (this%fabd_patch(begp:endp,1)/2._r8)/nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabi_sun_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='absorbed sunlit leaf diffuse PAR (per unit lai+sai) for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabi_sun_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabi_sun_z in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabi_sun_z to (fabi/2)/nlevcan"
-       do iv=1,nlevcan
-          this%fabi_sun_z_patch(begp:endp,iv) = (this%fabi_patch(begp:endp,1)/2._r8)/nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fabi_sha_z', xtype=ncd_double,  &
-         dim1name='pft', dim2name='levcan', switchdim=.true., &
-         long_name='absorbed shaded leaf diffuse PAR (per unit lai+sai) for canopy layer', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fabi_sha_z_patch)
-    if (flag=='read' .and. .not. readvar) then
-       if (masterproc) write(iulog,*) "can't find fabi_sha_z in restart (or initial) file..."
-       if (masterproc) write(iulog,*) "Initialize fabi_sha_z to (fabi/2)/nlevcan"
-       do iv=1,nlevcan
-          this%fabi_sha_z_patch(begp:endp,iv) = &
-               (this%fabi_patch(begp:endp,1)/2._r8)/nlevcan
-       end do
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='ftdd', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='down direct flux below veg per unit direct flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%ftdd_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='ftid', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='down diffuse flux below veg per unit direct flux', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%ftid_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='ftii', xtype=ncd_double,  &
-         dim1name='pft', dim2name='numrad', switchdim=.true., &
-         long_name='down diffuse flux below veg per unit diffuse flux', units='', &      
-         interpinic_flag='interp', readvar=readvar, data=this%ftii_patch)
-
-    !--------------------------------
-    ! variables needed for SNICAR
-    !--------------------------------
-
-    call restartvar(ncid=ncid, flag=flag, varname='flx_absdv', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno1', switchdim=.true., lowerb2=-nlevsno+1, upperb2=1, &
-         long_name='snow layer flux absorption factors (direct, VIS)', units='fraction', &
-         interpinic_flag='interp', readvar=readvar, data=this%flx_absdv_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='flx_absdn', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno1', switchdim=.true., lowerb2=-nlevsno+1, upperb2=1, &
-         long_name='snow layer flux absorption factors (direct, NIR)', units='fraction', &
-         interpinic_flag='interp', readvar=readvar, data=this%flx_absdn_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='flx_absiv', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno1', switchdim=.true., lowerb2=-nlevsno+1, upperb2=1, &
-         long_name='snow layer flux absorption factors (diffuse, VIS)', units='fraction', &
-         interpinic_flag='interp', readvar=readvar, data=this%flx_absiv_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='flx_absin', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno1', switchdim=.true., lowerb2=-nlevsno+1, upperb2=1, &
-         long_name='snow layer flux absorption factors (diffuse, NIR)', units='fraction', &
-         interpinic_flag='interp', readvar=readvar, data=this%flx_absin_col)
-
   end subroutine Restart
 
 end module SurfaceAlbedoType
diff --git a/src/biogeophys/SurfaceRadiationMod.F90 b/src/biogeophys/SurfaceRadiationMod.F90
deleted file mode 100644
index f021c6fdbf..0000000000
--- a/src/biogeophys/SurfaceRadiationMod.F90
+++ /dev/null
@@ -1,304 +0,0 @@
-module SurfaceRadiationMod
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculate solar fluxes absorbed by vegetation and ground surface
-  !
-  ! !USES:
-  use shr_kind_mod      , only : r8 => shr_kind_r8
-  use shr_log_mod       , only : errMsg => shr_log_errMsg
-  use clm_varctl        , only : use_snicar_frc, use_fates
-  use decompMod         , only : bounds_type
-  use clm_varcon        , only : namec
-  use atm2lndType       , only : atm2lnd_type
-  use WaterstateType    , only : waterstate_type
-  use CanopyStateType   , only : canopystate_type
-  use SurfaceAlbedoType , only : surfalb_type
-  use SolarAbsorbedType , only : solarabs_type
-  use GridcellType      , only : grc                
-  use LandunitType      , only : lun                
-  use ColumnType        , only : col                
-  use PatchType         , only : patch
-
-  !
-  ! !PRIVATE TYPES:
-  implicit none
-  private
-
-  logical :: DEBUG = .false.  ! for debugging this module
-
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-
-  !
-  ! !PRIVATE DATA:
-  type, public :: surfrad_type
-     real(r8), pointer, private  :: sfc_frc_aer_patch     (:) ! patch surface forcing of snow with all aerosols (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_bc_patch      (:) ! patch surface forcing of snow with BC (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_oc_patch      (:) ! patch surface forcing of snow with OC (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_dst_patch     (:) ! patch surface forcing of snow with dust (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_aer_sno_patch (:) ! patch surface forcing of snow with all aerosols, averaged only when snow is present (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_bc_sno_patch  (:) ! patch surface forcing of snow with BC, averaged only when snow is present (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_oc_sno_patch  (:) ! patch surface forcing of snow with OC, averaged only when snow is present (patch) [W/m2]
-     real(r8), pointer, private  :: sfc_frc_dst_sno_patch (:) ! patch surface forcing of snow with dust, averaged only when snow is present (patch) [W/m2]
-
-     real(r8), pointer, private  :: parveg_ln_patch       (:) ! patch  absorbed par by vegetation at local noon (W/m**2)
-
-     real(r8), pointer, private  :: fsr_sno_vd_patch      (:) ! patch reflected direct beam vis solar radiation from snow (W/m**2)
-     real(r8), pointer, private  :: fsr_sno_nd_patch      (:) ! patch reflected direct beam NIR solar radiation from snow (W/m**2)
-     real(r8), pointer, private  :: fsr_sno_vi_patch      (:) ! patch reflected diffuse vis solar radiation from snow (W/m**2)
-     real(r8), pointer, private  :: fsr_sno_ni_patch      (:) ! patch reflected diffuse NIR solar radiation from snow (W/m**2)
-
-     real(r8), pointer, private  :: fsr_vis_d_patch       (:) ! patch reflected direct beam vis solar radiation (W/m**2)
-     real(r8), pointer, private  :: fsr_vis_i_patch       (:) ! patch reflected diffuse vis solar radiation (W/m**2)
-     real(r8), pointer, private  :: fsr_vis_d_ln_patch    (:) ! patch reflected direct beam vis solar radiation at local noon (W/m**2)
-
-     real(r8), pointer, private  :: fsds_sno_vd_patch     (:) ! patch incident visible, direct radiation on snow  (for history files)  [W/m2]
-     real(r8), pointer, private  :: fsds_sno_nd_patch     (:) ! patch incident near-IR, direct radiation on snow  (for history files)  [W/m2]
-     real(r8), pointer, private  :: fsds_sno_vi_patch     (:) ! patch incident visible, diffuse radiation on snow (for history files) [W/m2]
-     real(r8), pointer, private  :: fsds_sno_ni_patch     (:) ! patch incident near-IR, diffuse radiation on snow (for history files) [W/m2]
-
-     real(r8), pointer, private  :: fsds_vis_d_patch      (:) ! patch incident direct beam vis solar radiation (W/m**2)
-     real(r8), pointer, private  :: fsds_vis_i_patch      (:) ! patch incident diffuse vis solar radiation (W/m**2)
-     real(r8), pointer, private  :: fsds_vis_d_ln_patch   (:) ! patch incident direct beam vis solar radiation at local noon (W/m**2)
-     real(r8), pointer, private  :: fsds_vis_i_ln_patch   (:) ! patch incident diffuse beam vis solar radiation at local noon (W/m**2)
-
-   contains
-
-     procedure, public  :: Init
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type surfrad_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(surfrad_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !USES:
-    use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(surfrad_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    allocate(this%sfc_frc_aer_patch     (begp:endp))              ; this%sfc_frc_aer_patch     (:)   = nan
-    allocate(this%sfc_frc_bc_patch      (begp:endp))              ; this%sfc_frc_bc_patch      (:)   = nan
-    allocate(this%sfc_frc_oc_patch      (begp:endp))              ; this%sfc_frc_oc_patch      (:)   = nan
-    allocate(this%sfc_frc_dst_patch     (begp:endp))              ; this%sfc_frc_dst_patch     (:)   = nan
-    allocate(this%sfc_frc_aer_sno_patch (begp:endp))              ; this%sfc_frc_aer_sno_patch (:)   = nan
-    allocate(this%sfc_frc_bc_sno_patch  (begp:endp))              ; this%sfc_frc_bc_sno_patch  (:)   = nan
-    allocate(this%sfc_frc_oc_sno_patch  (begp:endp))              ; this%sfc_frc_oc_sno_patch  (:)   = nan
-    allocate(this%sfc_frc_dst_sno_patch (begp:endp))              ; this%sfc_frc_dst_sno_patch (:)   = nan
-
-    allocate(this%parveg_ln_patch       (begp:endp))              ; this%parveg_ln_patch       (:)   = nan
-
-    allocate(this%fsr_vis_d_patch       (begp:endp))              ; this%fsr_vis_d_patch       (:)   = nan
-    allocate(this%fsr_vis_d_ln_patch    (begp:endp))              ; this%fsr_vis_d_ln_patch    (:)   = nan
-    allocate(this%fsr_vis_i_patch       (begp:endp))              ; this%fsr_vis_i_patch       (:)   = nan
-    allocate(this%fsr_sno_vd_patch      (begp:endp))              ; this%fsr_sno_vd_patch      (:)   = nan
-    allocate(this%fsr_sno_nd_patch      (begp:endp))              ; this%fsr_sno_nd_patch      (:)   = nan
-    allocate(this%fsr_sno_vi_patch      (begp:endp))              ; this%fsr_sno_vi_patch      (:)   = nan
-    allocate(this%fsr_sno_ni_patch      (begp:endp))              ; this%fsr_sno_ni_patch      (:)   = nan
-
-    allocate(this%fsds_vis_d_patch      (begp:endp))              ; this%fsds_vis_d_patch      (:)   = nan
-    allocate(this%fsds_vis_i_patch      (begp:endp))              ; this%fsds_vis_i_patch      (:)   = nan
-    allocate(this%fsds_vis_d_ln_patch   (begp:endp))              ; this%fsds_vis_d_ln_patch   (:)   = nan
-    allocate(this%fsds_vis_i_ln_patch   (begp:endp))              ; this%fsds_vis_i_ln_patch   (:)   = nan
-    allocate(this%fsds_sno_vd_patch     (begp:endp))              ; this%fsds_sno_vd_patch     (:)   = nan
-    allocate(this%fsds_sno_nd_patch     (begp:endp))              ; this%fsds_sno_nd_patch     (:)   = nan
-    allocate(this%fsds_sno_vi_patch     (begp:endp))              ; this%fsds_sno_vi_patch     (:)   = nan
-    allocate(this%fsds_sno_ni_patch     (begp:endp))              ; this%fsds_sno_ni_patch     (:)   = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! History fields initialization
-    !
-    ! !USES:
-    use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=)
-    use clm_varcon    , only : spval
-    use histFileMod   , only : hist_addfld1d, hist_addfld2d
-    !
-    ! !ARGUMENTS:
-    class(surfrad_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointers for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
-
-    if (use_snicar_frc) then
-       this%sfc_frc_aer_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOAERFRCL', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of all aerosols in snow (land) ', &
-            ptr_patch=this%sfc_frc_aer_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_aer_sno_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOAERFRC2L', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of all aerosols in snow, averaged only when snow is present (land)', &
-            ptr_patch=this%sfc_frc_aer_sno_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_bc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOBCFRCL', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of BC in snow (land) ', &
-            ptr_patch=this%sfc_frc_bc_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_bc_sno_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOBCFRC2L', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of BC in snow, averaged only when snow is present (land)', &
-            ptr_patch=this%sfc_frc_bc_sno_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_oc_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOOCFRCL', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of OC in snow (land) ', &
-            ptr_patch=this%sfc_frc_oc_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_oc_sno_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNOOCFRC2L', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of OC in snow, averaged only when snow is present (land)', &
-            ptr_patch=this%sfc_frc_oc_sno_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_dst_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNODSTFRCL', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of dust in snow (land) ', &
-            ptr_patch=this%sfc_frc_dst_patch, set_urb=spval, default='inactive')
-
-       this%sfc_frc_dst_sno_patch(begp:endp) = spval
-       call hist_addfld1d (fname='SNODSTFRC2L', units='W/m^2', &
-            avgflag='A', long_name='surface forcing of dust in snow, averaged only when snow is present (land)', &
-            ptr_patch=this%sfc_frc_dst_sno_patch, set_urb=spval, default='inactive')
-    end if
-
-    this%fsds_vis_d_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSVD', units='W/m^2',  &
-         avgflag='A', long_name='direct vis incident solar radiation', &
-         ptr_patch=this%fsds_vis_d_patch, default='inactive')
-
-    this%fsds_vis_i_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSVI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse vis incident solar radiation', &
-         ptr_patch=this%fsds_vis_i_patch, default='inactive')
-
-    this%fsr_vis_d_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRVD', units='W/m^2',  &
-         avgflag='A', long_name='direct vis reflected solar radiation', &
-         ptr_patch=this%fsr_vis_d_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%fsr_vis_i_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRVI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse vis reflected solar radiation', &
-         ptr_patch=this%fsr_vis_i_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%fsds_vis_d_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSVDLN', units='W/m^2',  &
-         avgflag='A', long_name='direct vis incident solar radiation at local noon', &
-         ptr_patch=this%fsds_vis_d_ln_patch, default='inactive')
-
-    this%fsds_vis_i_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSDSVILN', units='W/m^2',  &
-         avgflag='A', long_name='diffuse vis incident solar radiation at local noon', &
-         ptr_patch=this%fsds_vis_i_ln_patch, default='inactive')
-
-    this%parveg_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='PARVEGLN', units='W/m^2',  &
-         avgflag='A', long_name='absorbed par by vegetation at local noon', &
-         ptr_patch=this%parveg_ln_patch, default='inactive')
-
-    this%fsr_vis_d_ln_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSRVDLN', units='W/m^2',  &
-         avgflag='A', long_name='direct vis reflected solar radiation at local noon', &
-         ptr_patch=this%fsr_vis_d_ln_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%fsds_sno_vd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSDSVD', units='W/m^2',  &
-         avgflag='A', long_name='direct vis incident solar radiation on snow', &
-         ptr_patch=this%fsds_sno_vd_patch, default='inactive')
-
-    this%fsds_sno_nd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSDSND', units='W/m^2',  &
-         avgflag='A', long_name='direct nir incident solar radiation on snow', &
-         ptr_patch=this%fsds_sno_nd_patch, default='inactive')
-
-    this%fsds_sno_vi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSDSVI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse vis incident solar radiation on snow', &
-         ptr_patch=this%fsds_sno_vi_patch, default='inactive')
-
-    this%fsds_sno_ni_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSDSNI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse nir incident solar radiation on snow', &
-         ptr_patch=this%fsds_sno_ni_patch, default='inactive')
-
-    this%fsr_sno_vd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSRVD', units='W/m^2',  &
-         avgflag='A', long_name='direct vis reflected solar radiation from snow', &
-         ptr_patch=this%fsr_sno_vd_patch, default='inactive')
-
-    this%fsr_sno_nd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSRND', units='W/m^2',  &
-         avgflag='A', long_name='direct nir reflected solar radiation from snow', &
-         ptr_patch=this%fsr_sno_nd_patch, default='inactive')
-
-    this%fsr_sno_vi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSRVI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse vis reflected solar radiation from snow', &
-         ptr_patch=this%fsr_sno_vi_patch, default='inactive')
-
-    this%fsr_sno_ni_patch(begp:endp) = spval
-    call hist_addfld1d (fname='SNOFSRNI', units='W/m^2',  &
-         avgflag='A', long_name='diffuse nir reflected solar radiation from snow', &
-         ptr_patch=this%fsr_sno_ni_patch, default='inactive')
-
-
-  end subroutine InitHistory
-
-  !------------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(surfrad_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,l
-    !-----------------------------------------------------------------------
-
-    ! nothing for now
-    
-  end subroutine InitCold
-  
-end module SurfaceRadiationMod
diff --git a/src/biogeophys/SurfaceResistanceMod.F90 b/src/biogeophys/SurfaceResistanceMod.F90
deleted file mode 100644
index 76813b71c5..0000000000
--- a/src/biogeophys/SurfaceResistanceMod.F90
+++ /dev/null
@@ -1,294 +0,0 @@
-module SurfaceResistanceMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding routines for calculation of surface resistances of the different tracers
-  ! transported with BeTR. The surface here refers to water and soil, not including canopy
-  !
-  ! !USES:
-  use shr_kind_mod  , only: r8 => shr_kind_r8
-  use shr_const_mod , only: SHR_CONST_TKFRZ
-  use clm_varctl    , only: iulog
-  use SoilStateType , only: soilstate_type
-  use WaterStateType, only: waterstate_type 
-   use TemperatureType   , only : temperature_type
-  implicit none
-  save
-  private
-  integer :: soil_resis_method   !choose the method for soil resistance calculation
-  
-  integer, parameter :: leepielke_1992 = 0 !
-  integer, parameter :: sl_14 = 1 
-  
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: calc_soilevap_resis
-  public :: do_soilevap_beta, do_soil_resistance_sl14
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !
-  ! !REVISION HISTORY:
-  ! 6/25/2013 Created by Jinyun Tang
-  !-----------------------------------------------------------------------
-  
-contains
-
-   !------------------------------------------------------------------------------   
-   subroutine calc_soilevap_resis(bounds, num_nolakec, filter_nolakec, &
-        soilstate_inst, waterstate_inst, temperature_inst)
-     !
-     ! DESCRIPTIONS
-     ! compute the resis factor for soil evaporation calculation
-     !
-     use shr_kind_mod  , only : r8 => shr_kind_r8     
-     use shr_const_mod , only : SHR_CONST_PI  
-     use decompMod     , only : bounds_type
-     use ColumnType    , only : col
-     use LandunitType  , only : lun
-     use abortutils    , only : endrun      
-     !
-     ! !ARGUMENTS:
-     implicit none
-     type(bounds_type)     , intent(in)    :: bounds    ! bounds   
-     integer               , intent(in)    :: num_nolakec
-     integer               , intent(in)    :: filter_nolakec(:)
-     type(soilstate_type)  , intent(inout) :: soilstate_inst
-     type(waterstate_type) , intent(in)    :: waterstate_inst
-     type(temperature_type), intent(in)    :: temperature_inst
-     character(len=32) :: subname = 'calc_soilevap_resis'  ! subroutine name
-     associate(                &
-          soilbeta =>  soilstate_inst%soilbeta_col  , & ! Output: [real(r8) (:)] factor that reduces ground evaporation
-          dsl       =>  soilstate_inst%dsl_col      , & ! Output: [real(r8) (:)] soil dry surface layer thickness
-          soilresis =>  soilstate_inst%soilresis_col  & ! Output: [real(r8) (:)] soil evaporative resistance
-          )
-   
-       !select the right method and do the calculation
-       select case (soil_resis_method)
-
-       case (leepielke_1992)
-          call calc_beta_leepielke1992(bounds, num_nolakec, filter_nolakec, &
-               soilstate_inst, waterstate_inst, soilbeta(bounds%begc:bounds%endc))
-
-               case (sl_14)
-          call calc_soil_resistance_sl14(bounds, num_nolakec, filter_nolakec, &
-               soilstate_inst, waterstate_inst,temperature_inst, &
-               dsl(bounds%begc:bounds%endc), soilresis(bounds%begc:bounds%endc))
-               case default
-          call endrun(subname // ':: a soilevap resis function must be specified!')     
-       end select
-
-     end associate
-
-   end subroutine calc_soilevap_resis
-   
-   !------------------------------------------------------------------------------   
-   subroutine calc_beta_leepielke1992(bounds, num_nolakec, filter_nolakec, &
-        soilstate_inst, waterstate_inst, soilbeta)
-     !
-     ! DESCRIPTION
-     ! compute the lee-pielke beta factor to scal actual soil evaporation from potential evaporation
-     !
-     ! USES
-     use shr_kind_mod    , only : r8 => shr_kind_r8     
-     use shr_const_mod   , only : SHR_CONST_PI
-     use shr_log_mod     , only : errMsg => shr_log_errMsg   
-     use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-     use decompMod       , only : bounds_type
-     use clm_varcon      , only : denh2o, denice
-     use landunit_varcon , only : istice_mec, istwet, istsoil, istcrop
-     use column_varcon   , only : icol_roof, icol_sunwall, icol_shadewall
-     use column_varcon   , only : icol_road_imperv, icol_road_perv
-     use ColumnType      , only : col
-     use LandunitType    , only : lun
-     !
-     implicit none
-     type(bounds_type)     , intent(in)    :: bounds    ! bounds   
-     integer               , intent(in)    :: num_nolakec
-     integer               , intent(in)    :: filter_nolakec(:)
-     type(soilstate_type)  , intent(in)    :: soilstate_inst
-     type(waterstate_type) , intent(in)    :: waterstate_inst
-     real(r8)              , intent(inout) :: soilbeta(bounds%begc:bounds%endc)
-
-     !local variables
-     real(r8) :: fac, fac_fc, wx      !temporary variables
-     integer  :: c, l, fc     !indices
-
-     SHR_ASSERT_ALL((ubound(soilbeta)    == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-     associate(                                              &
-          watsat      =>    soilstate_inst%watsat_col      , & ! Input:  [real(r8) (:,:)] volumetric soil water at saturation (porosity)
-          watfc       =>    soilstate_inst%watfc_col       , & ! Input:  [real(r8) (:,:)] volumetric soil water at field capacity
-          
-          h2osoi_ice  =>    waterstate_inst%h2osoi_ice_col , & ! Input:  [real(r8) (:,:)] ice lens (kg/m2)                       
-          h2osoi_liq  =>    waterstate_inst%h2osoi_liq_col , & ! Input:  [real(r8) (:,:)] liquid water (kg/m2)                   
-          frac_sno    =>    waterstate_inst%frac_sno_col   , & ! Input:  [real(r8) (:)] fraction of ground covered by snow (0 to 1)
-          frac_h2osfc =>    waterstate_inst%frac_h2osfc_col  & ! Input:  [real(r8) (:)]  fraction of ground covered by surface water (0 to 1)
-          )
-
-       do fc = 1,num_nolakec
-          c = filter_nolakec(fc)
-          l = col%landunit(c)   
-          if (lun%itype(l)/=istwet .AND. lun%itype(l)/=istice_mec) then
-             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-                wx   = (h2osoi_liq(c,1)/denh2o+h2osoi_ice(c,1)/denice)/col%dz(c,1)
-                fac  = min(1._r8, wx/watsat(c,1))
-                fac  = max( fac, 0.01_r8 )
-                !! Lee and Pielke 1992 beta, added by K.Sakaguchi
-                if (wx < watfc(c,1) ) then  !when water content of ths top layer is less than that at F.C.
-                   fac_fc  = min(1._r8, wx/watfc(c,1))  !eqn5.66 but divided by theta at field capacity
-                   fac_fc  = max( fac_fc, 0.01_r8 )
-                   ! modify soil beta by snow cover. soilbeta for snow surface is one
-                   soilbeta(c) = (1._r8-frac_sno(c)-frac_h2osfc(c)) &
-                        *0.25_r8*(1._r8 - cos(SHR_CONST_PI*fac_fc))**2._r8 &
-                        + frac_sno(c)+ frac_h2osfc(c)
-                else   !when water content of ths top layer is more than that at F.C.
-                   soilbeta(c) = 1._r8
-                end if
-             else if (col%itype(c) == icol_road_perv) then
-                soilbeta(c) = 0._r8
-             else if (col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall) then
-                soilbeta(c) = 0._r8          
-             else if (col%itype(c) == icol_roof .or. col%itype(c) == icol_road_imperv) then
-                soilbeta(c) = 0._r8
-             endif
-          else
-             soilbeta(c) =   1._r8
-          endif
-       enddo
-
-     end associate
-
-   end subroutine calc_beta_leepielke1992
-   
-   !------------------------------------------------------------------------------   
-   function do_soilevap_beta()result(lres)
-     !
-     !DESCRIPTION
-     ! return true if the moisture stress for soil evaporation is computed as beta factor
-     ! otherwise false
-     implicit none
-     logical :: lres
-
-     if(soil_resis_method==leepielke_1992)then
-        lres=.true.
-     else
-        lres=.false.
-     endif
-     return
-
-   end function do_soilevap_beta
-
-  !------------------------------------------------------------------------------   
-   subroutine calc_soil_resistance_sl14(bounds, num_nolakec, filter_nolakec, &
-        soilstate_inst, waterstate_inst, temperature_inst, dsl, soilresis)
-     !
-     ! DESCRIPTION
-     ! compute the lee-pielke beta factor to scal actual soil evaporation from potential evaporation
-     !
-     ! USES
-     use shr_kind_mod    , only : r8 => shr_kind_r8     
-     use shr_const_mod   , only : SHR_CONST_PI
-     use shr_log_mod     , only : errMsg => shr_log_errMsg   
-     use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-     use decompMod       , only : bounds_type
-     use clm_varcon      , only : denh2o, denice
-     use landunit_varcon , only : istice_mec, istwet, istsoil, istcrop
-     use column_varcon   , only : icol_roof, icol_sunwall, icol_shadewall
-     use column_varcon   , only : icol_road_imperv, icol_road_perv
-     use ColumnType      , only : col
-     use LandunitType    , only : lun
-     !
-     implicit none
-     type(bounds_type)     , intent(in)    :: bounds    ! bounds   
-     integer               , intent(in)    :: num_nolakec
-     integer               , intent(in)    :: filter_nolakec(:)
-     type(soilstate_type)  , intent(in)    :: soilstate_inst
-     type(waterstate_type) , intent(in)    :: waterstate_inst
-     type(temperature_type), intent(in)    :: temperature_inst
-     real(r8)              , intent(inout) :: dsl(bounds%begc:bounds%endc)
-     real(r8)              , intent(inout) :: soilresis(bounds%begc:bounds%endc)
-
-   !local variables
-     real(r8) :: aird, eps, dg, d0, vwc_liq
-     real(r8) :: eff_por_top
-     integer  :: c, l, fc     !indices
-     
-     SHR_ASSERT_ALL((ubound(dsl)    == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-     SHR_ASSERT_ALL((ubound(soilresis)    == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-     associate(                                              &
-          dz                =>    col%dz                             , & ! Input:  [real(r8) (:,:) ]  layer thickness (m)                             
-          watsat            =>    soilstate_inst%watsat_col      , & ! Input:  [real(r8) (:,:)] volumetric soil water at saturation (porosity)
-          bsw               =>    soilstate_inst%bsw_col             , & ! Input:  [real(r8) (:,:) ]  Clapp and Hornberger "b"                        
-          sucsat            =>    soilstate_inst%sucsat_col          , & ! Input:  [real(r8) (:,:) ]  minimum soil suction (mm)                       
-!          eff_porosity      =>    soilstate_inst%eff_porosity_col    , & ! Input:  [real(r8) (:,:) ]  effective porosity = porosity - vol_ice         
-          t_soisno          =>    temperature_inst%t_soisno_col      ,  & ! Input:  [real(r8) (:,:) ]  soil temperature (Kelvin)                       
-         
-          h2osoi_ice        =>    waterstate_inst%h2osoi_ice_col , & ! Input:  [real(r8) (:,:)] ice lens (kg/m2)                       
-          h2osoi_liq        =>    waterstate_inst%h2osoi_liq_col  & ! Input:  [real(r8) (:,:)] liquid water (kg/m2)                   
-          )
-
-   do fc = 1,num_nolakec
-      c = filter_nolakec(fc)
-      l = col%landunit(c)  
-      if (lun%itype(l)/=istwet .AND. lun%itype(l)/=istice_mec) then
-         if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-            vwc_liq = max(h2osoi_liq(c,1),1.0e-6_r8)/(dz(c,1)*denh2o)
-! eff_porosity not calculated til SoilHydrology
-             eff_por_top = max(0.01_r8,watsat(c,1)-min(watsat(c,1), h2osoi_ice(c,1)/(dz(c,1)*denice)))
-
-! calculate diffusivity and air free pore space
-            aird = watsat(c,1)*(sucsat(c,1)/1.e7_r8)**(1./bsw(c,1))
-            d0 = 2.12e-5*(t_soisno(c,1)/273.15)**1.75 ![Bitelli et al., JH, 08]
-            eps = watsat(c,1) - aird
-            dg = eps*d0*(eps/watsat(c,1))**(3._r8/max(3._r8,bsw(c,1)))
-            
-!      dsl(c) = dzmm(c,1)*max(0.001_r8,(0.8*eff_porosity(c,1) - vwc_liq)) &
-! try arbitrary scaling (not top layer thickness)
-!            dsl(c) = 15._r8*max(0.001_r8,(0.8*eff_porosity(c,1) - vwc_liq)) &
-            dsl(c) = 15._r8*max(0.001_r8,(0.8*eff_por_top - vwc_liq)) &
-                 !           /max(0.001_r8,(watsat(c,1)- aird))
-                 /max(0.001_r8,(0.8*watsat(c,1)- aird))
-            
-            dsl(c)=max(dsl(c),0._r8)
-            dsl(c)=min(dsl(c),200._r8)
-            
-            soilresis(c) = dsl(c)/(dg*eps*1.e3) + 20._r8
-            soilresis(c) = min(1.e6_r8,soilresis(c))
-
-         else if (col%itype(c) == icol_road_perv) then
-            soilresis(c) = 1.e6_r8
-         else if (col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall) then
-            soilresis(c) = 1.e6_r8          
-         else if (col%itype(c) == icol_roof .or. col%itype(c) == icol_road_imperv) then
-            soilresis(c) = 1.e6_r8
-         endif   
-      else
-         soilresis(c) =   0._r8
-      endif
-   enddo   
-   end associate
-   end subroutine calc_soil_resistance_sl14
-
-   !------------------------------------------------------------------------------   
-   function do_soil_resistance_sl14()result(lres)
-     !
-     !DESCRIPTION
-     ! return true if the soil evaporative resistance is computed using a DSL
-     ! otherwise false
-     implicit none
-     logical :: lres
-
-     if(soil_resis_method==sl_14)then
-        lres=.true.
-     else
-        lres=.false.
-     endif
-     return
-
-   end function do_soil_resistance_sl14
-
-end module SurfaceResistanceMod
diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90
index a98c143023..5506f56af9 100644
--- a/src/biogeophys/TemperatureType.F90
+++ b/src/biogeophys/TemperatureType.F90
@@ -6,11 +6,8 @@ module TemperatureType
   use shr_kind_mod    , only : r8 => shr_kind_r8
   use shr_log_mod     , only : errMsg => shr_log_errMsg
   use decompMod       , only : bounds_type
-  use abortutils      , only : endrun
-  use clm_varctl      , only : use_cndv, iulog, use_luna, use_crop
-  use clm_varpar      , only : nlevsno, nlevgrnd, nlevlak, nlevlak, nlevurb
-  use clm_varcon      , only : spval, ispval
-  use GridcellType    , only : grc
+  use clm_varpar      , only : nlevsno, nlevgrnd, nlevurb
+  use clm_varcon      , only : spval
   use LandunitType    , only : lun                
   use ColumnType      , only : col                
   use PatchType       , only : patch                
@@ -22,104 +19,15 @@ module TemperatureType
   type, public :: temperature_type
 
      ! Temperatures
-     real(r8), pointer :: t_veg_patch              (:)   ! patch vegetation temperature (Kelvin)
-     real(r8), pointer :: t_veg_day_patch          (:)   ! patch daytime  accumulative vegetation temperature (Kelvinx*nsteps), LUNA specific, from midnight to current step
-     real(r8), pointer :: t_veg_night_patch        (:)   ! patch night-time accumulative vegetation temperature (Kelvin*nsteps), LUNA specific, from midnight to current step
-     real(r8), pointer :: t_veg10_day_patch        (:)   ! 10 day running mean of patch daytime time vegetation temperature (Kelvin), LUNA specific, but can be reused
-     real(r8), pointer :: t_veg10_night_patch      (:)   ! 10 day running mean of patch night time vegetation temperature (Kelvin), LUNA specific, but can be reused
-     integer,  pointer :: ndaysteps_patch          (:)   ! number of daytime steps accumulated from mid-night, LUNA specific
-     integer,  pointer :: nnightsteps_patch        (:)   ! number of nighttime steps accumulated from mid-night, LUNA specific
-     real(r8), pointer :: t_h2osfc_col             (:)   ! col surface water temperature
-     real(r8), pointer :: t_h2osfc_bef_col         (:)   ! col surface water temperature from time-step before  
-     real(r8), pointer :: t_ssbef_col              (:,:) ! col soil/snow temperature before update (-nlevsno+1:nlevgrnd) 
-     real(r8), pointer :: t_soisno_col             (:,:) ! col soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd) 
-     real(r8), pointer :: t_soi10cm_col            (:)   ! col soil temperature in top 10cm of soil (Kelvin)
-     real(r8), pointer :: t_soi17cm_col            (:)   ! col soil temperature in top 17cm of soil (Kelvin)
-     real(r8), pointer :: t_lake_col               (:,:) ! col lake temperature (Kelvin)  (1:nlevlak)          
-     real(r8), pointer :: t_grnd_col               (:)   ! col ground temperature (Kelvin)
-     real(r8), pointer :: t_grnd_r_col             (:)   ! col rural ground temperature (Kelvin)
-     real(r8), pointer :: t_grnd_u_col             (:)   ! col urban ground temperature (Kelvin) (needed by Hydrology2Mod)
-     real(r8), pointer :: t_building_lun           (:)   ! lun internal building air temperature (K)
-     real(r8), pointer :: t_roof_inner_lun         (:)   ! lun roof inside surface temperature (K)
-     real(r8), pointer :: t_sunw_inner_lun         (:)   ! lun sunwall inside surface temperature (K)
-     real(r8), pointer :: t_shdw_inner_lun         (:)   ! lun shadewall inside surface temperature (K)
-     real(r8), pointer :: t_floor_lun              (:)   ! lun floor temperature (K)
-     real(r8), pointer :: snot_top_col             (:)   ! col temperature of top snow layer [K]
-     real(r8), pointer :: dTdz_top_col             (:)   ! col temperature gradient in top layer  [K m-1]
-     real(r8), pointer :: dt_veg_patch             (:)   ! patch change in t_veg, last iteration (Kelvin)
-
-     real(r8), pointer :: dt_grnd_col              (:)   ! col change in t_grnd, last iteration (Kelvin)
-     real(r8), pointer :: thv_col                  (:)   ! col virtual potential temperature (kelvin)
-     real(r8), pointer :: thm_patch                (:)   ! patch intermediate variable (forc_t+0.0098*forc_hgt_t_patch)
-     real(r8), pointer :: t_a10_patch              (:)   ! patch 10-day running mean of the 2 m temperature (K)
-     real(r8), pointer :: t_a10min_patch           (:)   ! patch 10-day running mean of min 2-m temperature
-     real(r8), pointer :: t_a5min_patch            (:)   ! patch 5-day running mean of min 2-m temperature
-
-     real(r8), pointer :: taf_lun                  (:)   ! lun urban canopy air temperature (K)
-
-     real(r8), pointer :: t_ref2m_patch            (:)   ! patch 2 m height surface air temperature (Kelvin)
-     real(r8), pointer :: t_ref2m_r_patch          (:)   ! patch rural 2 m height surface air temperature (Kelvin)
-     real(r8), pointer :: t_ref2m_u_patch          (:)   ! patch urban 2 m height surface air temperature (Kelvin)
-     real(r8), pointer :: t_ref2m_min_patch        (:)   ! patch daily minimum of average 2 m height surface air temperature (K)
-     real(r8), pointer :: t_ref2m_min_r_patch      (:)   ! patch daily minimum of average 2 m height surface air temperature - rural(K)
-     real(r8), pointer :: t_ref2m_min_u_patch      (:)   ! patch daily minimum of average 2 m height surface air temperature - urban (K)
-     real(r8), pointer :: t_ref2m_max_patch        (:)   ! patch daily maximum of average 2 m height surface air temperature (K)
-     real(r8), pointer :: t_ref2m_max_r_patch      (:)   ! patch daily maximum of average 2 m height surface air temperature - rural(K)
-     real(r8), pointer :: t_ref2m_max_u_patch      (:)   ! patch daily maximum of average 2 m height surface air temperature - urban (K)
-     real(r8), pointer :: t_ref2m_min_inst_patch   (:)   ! patch instantaneous daily min of average 2 m height surface air temp (K)
-     real(r8), pointer :: t_ref2m_min_inst_r_patch (:)   ! patch instantaneous daily min of average 2 m height surface air temp - rural (K)
-     real(r8), pointer :: t_ref2m_min_inst_u_patch (:)   ! patch instantaneous daily min of average 2 m height surface air temp - urban (K)
-     real(r8), pointer :: t_ref2m_max_inst_patch   (:)   ! patch instantaneous daily max of average 2 m height surface air temp (K)
-     real(r8), pointer :: t_ref2m_max_inst_r_patch (:)   ! patch instantaneous daily max of average 2 m height surface air temp - rural (K)
-     real(r8), pointer :: t_ref2m_max_inst_u_patch (:)   ! patch instantaneous daily max of average 2 m height surface air temp - urban (K)
-
-     ! Accumulated quantities
-     !
-     ! TODO(wjs, 2014-08-05) Move these to the module(s) where they are used, to improve
-     ! modularity. In cases where they are used by two completely different modules,
-     ! which only use the same variable out of convenience, introduce a duplicate (point
-     ! being: that way one parameterization is free to change the exact meaning of its
-     ! accumulator without affecting the other).
-     !
-     real(r8), pointer :: t_veg24_patch           (:)   ! patch 24hr average vegetation temperature (K)
-     real(r8), pointer :: t_veg240_patch          (:)   ! patch 240hr average vegetation temperature (Kelvin)
-     real(r8), pointer :: gdd0_patch              (:)   ! patch growing degree-days base  0C from planting  (ddays)
-     real(r8), pointer :: gdd8_patch              (:)   ! patch growing degree-days base  8C from planting  (ddays)
-     real(r8), pointer :: gdd10_patch             (:)   ! patch growing degree-days base 10C from planting  (ddays)
-     real(r8), pointer :: gdd020_patch            (:)   ! patch 20-year average of gdd0                     (ddays)
-     real(r8), pointer :: gdd820_patch            (:)   ! patch 20-year average of gdd8                     (ddays)
-     real(r8), pointer :: gdd1020_patch           (:)   ! patch 20-year average of gdd10                    (ddays)
-
-     ! Heat content
-     real(r8), pointer :: beta_col                 (:)   ! coefficient of convective velocity [-]
-     real(r8), pointer :: heat1_grc                (:)   ! grc initial gridcell total heat content
-     real(r8), pointer :: heat2_grc                (:)   ! grc post land cover change total heat content
-     real(r8), pointer :: liquid_water_temp1_grc   (:)   ! grc initial weighted average liquid water temperature (K)
-     real(r8), pointer :: liquid_water_temp2_grc   (:)   ! grc post land cover change weighted average liquid water temperature (K)
-
-     ! Flags
-     integer , pointer :: imelt_col                (:,:) ! flag for melting (=1), freezing (=2), Not=0 (-nlevsno+1:nlevgrnd) 
-
-     ! Emissivities
-     real(r8), pointer :: emv_patch                (:)   ! patch vegetation emissivity 
-     real(r8), pointer :: emg_col                  (:)   ! col ground emissivity
-
-     ! Misc
-     real(r8), pointer    :: xmf_col               (:)   ! total latent heat of phase change of ground water
-     real(r8), pointer    :: xmf_h2osfc_col        (:)   ! latent heat of phase change of surface water
-     real(r8), pointer    :: fact_col              (:,:) ! used in computing tridiagonal matrix
-     real(r8), pointer    :: c_h2osfc_col          (:)   ! heat capacity of surface water
+     real(r8), pointer :: t_soisno_col (:,:) ! col soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd) 
+     real(r8), pointer :: t_grnd_col   (:)   ! col ground temperature (Kelvin)
 
    contains
 
      procedure, public  :: Init
      procedure, public  :: Restart      
      procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
      procedure, private :: InitCold     
-     procedure, public  :: InitAccBuffer
-     procedure, public  :: InitAccVars
-     procedure, public  :: UpdateAccVars
 
   end type temperature_type
 
@@ -130,9 +38,7 @@ module TemperatureType
 contains
 
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, &
-       em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp)
+  subroutine Init(this, bounds)
     !
     ! !DESCRIPTION:
     !
@@ -141,21 +47,9 @@ subroutine Init(this, bounds, &
     !
     class(temperature_type)        :: this
     type(bounds_type) , intent(in) :: bounds  
-    real(r8)          , intent(in) :: em_roof_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_wall_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_improad_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
-    logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
-    logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
 
     call this%InitAllocate ( bounds )
-    call this%InitHistory ( bounds, is_simple_buildtemp, is_prog_buildtemp )
-    call this%InitCold ( bounds,                  &
-         em_roof_lun(bounds%begl:bounds%endl),    &
-         em_wall_lun(bounds%begl:bounds%endl),    &
-         em_improad_lun(bounds%begl:bounds%endl), &
-         em_perroad_lun(bounds%begl:bounds%endl), &
-         is_simple_buildtemp, is_prog_buildtemp)
+    call this%InitCold ( bounds)
 
   end subroutine Init
 
@@ -173,466 +67,40 @@ subroutine InitAllocate(this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer :: begp, endp
     integer :: begc, endc
-    integer :: begl, endl
-    integer :: begg, endg
     !------------------------------------------------------------------------
 
-    begp = bounds%begp; endp= bounds%endp
     begc = bounds%begc; endc= bounds%endc
-    begl = bounds%begl; endl= bounds%endl
-    begg = bounds%begg; endg= bounds%endg
 
     ! Temperatures
-    allocate(this%t_veg_patch              (begp:endp))                      ; this%t_veg_patch              (:)   = nan
-    if(use_luna) then
-     allocate(this%t_veg_day_patch         (begp:endp))                      ; this%t_veg_day_patch          (:)   = spval
-     allocate(this%t_veg_night_patch       (begp:endp))                      ; this%t_veg_night_patch        (:)   = spval
-     allocate(this%t_veg10_day_patch       (begp:endp))                      ; this%t_veg10_day_patch        (:)   = spval
-     allocate(this%t_veg10_night_patch     (begp:endp))                      ; this%t_veg10_night_patch      (:)   = spval
-     allocate(this%ndaysteps_patch         (begp:endp))                      ; this%ndaysteps_patch          (:)   = ispval
-     allocate(this%nnightsteps_patch       (begp:endp))                      ; this%nnightsteps_patch        (:)   = ispval
-    endif
-    allocate(this%t_h2osfc_col             (begc:endc))                      ; this%t_h2osfc_col             (:)   = nan
-    allocate(this%t_h2osfc_bef_col         (begc:endc))                      ; this%t_h2osfc_bef_col         (:)   = nan
-    allocate(this%t_ssbef_col              (begc:endc,-nlevsno+1:nlevgrnd))  ; this%t_ssbef_col              (:,:) = nan
-    allocate(this%t_soisno_col             (begc:endc,-nlevsno+1:nlevgrnd))  ; this%t_soisno_col             (:,:) = nan
-    allocate(this%t_lake_col               (begc:endc,1:nlevlak))            ; this%t_lake_col               (:,:) = nan
-    allocate(this%t_grnd_col               (begc:endc))                      ; this%t_grnd_col               (:)   = nan
-    allocate(this%t_grnd_r_col             (begc:endc))                      ; this%t_grnd_r_col             (:)   = nan
-    allocate(this%t_grnd_u_col             (begc:endc))                      ; this%t_grnd_u_col             (:)   = nan
-    allocate(this%t_building_lun           (begl:endl))                      ; this%t_building_lun           (:)   = nan
-    allocate(this%t_roof_inner_lun         (begl:endl))                      ; this%t_roof_inner_lun         (:)   = nan
-    allocate(this%t_sunw_inner_lun         (begl:endl))                      ; this%t_sunw_inner_lun         (:)   = nan
-    allocate(this%t_shdw_inner_lun         (begl:endl))                      ; this%t_shdw_inner_lun         (:)   = nan
-    allocate(this%t_floor_lun              (begl:endl))                      ; this%t_floor_lun              (:)   = nan
-    allocate(this%snot_top_col             (begc:endc))                      ; this%snot_top_col             (:)   = nan
-    allocate(this%dTdz_top_col             (begc:endc))                      ; this%dTdz_top_col             (:)   = nan
-    allocate(this%dt_veg_patch             (begp:endp))                      ; this%dt_veg_patch             (:)   = nan
-
-    allocate(this%t_soi10cm_col            (begc:endc))                      ; this%t_soi10cm_col            (:)   = nan
-    allocate(this%t_soi17cm_col            (begc:endc))                      ; this%t_soi17cm_col            (:)   = spval
-    allocate(this%dt_grnd_col              (begc:endc))                      ; this%dt_grnd_col              (:)   = nan
-    allocate(this%thv_col                  (begc:endc))                      ; this%thv_col                  (:)   = nan
-    allocate(this%thm_patch                (begp:endp))                      ; this%thm_patch                (:)   = nan
-    allocate(this%t_a10_patch              (begp:endp))                      ; this%t_a10_patch              (:)   = nan
-    allocate(this%t_a10min_patch           (begp:endp))                      ; this%t_a10min_patch           (:)   = nan
-    allocate(this%t_a5min_patch            (begp:endp))                      ; this%t_a5min_patch            (:)   = nan
-
-    allocate(this%taf_lun                  (begl:endl))                      ; this%taf_lun                  (:)   = nan
-
-    allocate(this%t_ref2m_patch            (begp:endp))                      ; this%t_ref2m_patch            (:)   = nan
-    allocate(this%t_ref2m_r_patch          (begp:endp))                      ; this%t_ref2m_r_patch          (:)   = nan
-    allocate(this%t_ref2m_u_patch          (begp:endp))                      ; this%t_ref2m_u_patch          (:)   = nan
-    allocate(this%t_ref2m_min_patch        (begp:endp))                      ; this%t_ref2m_min_patch        (:)   = nan
-    allocate(this%t_ref2m_min_r_patch      (begp:endp))                      ; this%t_ref2m_min_r_patch      (:)   = nan
-    allocate(this%t_ref2m_min_u_patch      (begp:endp))                      ; this%t_ref2m_min_u_patch      (:)   = nan
-    allocate(this%t_ref2m_max_patch        (begp:endp))                      ; this%t_ref2m_max_patch        (:)   = nan
-    allocate(this%t_ref2m_max_r_patch      (begp:endp))                      ; this%t_ref2m_max_r_patch      (:)   = nan
-    allocate(this%t_ref2m_max_u_patch      (begp:endp))                      ; this%t_ref2m_max_u_patch      (:)   = nan
-    allocate(this%t_ref2m_max_inst_patch   (begp:endp))                      ; this%t_ref2m_max_inst_patch   (:)   = nan
-    allocate(this%t_ref2m_max_inst_r_patch (begp:endp))                      ; this%t_ref2m_max_inst_r_patch (:)   = nan
-    allocate(this%t_ref2m_max_inst_u_patch (begp:endp))                      ; this%t_ref2m_max_inst_u_patch (:)   = nan
-    allocate(this%t_ref2m_min_inst_patch   (begp:endp))                      ; this%t_ref2m_min_inst_patch   (:)   = nan
-    allocate(this%t_ref2m_min_inst_r_patch (begp:endp))                      ; this%t_ref2m_min_inst_r_patch (:)   = nan
-    allocate(this%t_ref2m_min_inst_u_patch (begp:endp))                      ; this%t_ref2m_min_inst_u_patch (:)   = nan
-
-    ! Accumulated fields
-    allocate(this%t_veg24_patch            (begp:endp))                      ; this%t_veg24_patch            (:)   = nan
-    allocate(this%t_veg240_patch           (begp:endp))                      ; this%t_veg240_patch           (:)   = nan
-    allocate(this%gdd0_patch               (begp:endp))                      ; this%gdd0_patch               (:)   = spval
-    allocate(this%gdd8_patch               (begp:endp))                      ; this%gdd8_patch               (:)   = spval
-    allocate(this%gdd10_patch              (begp:endp))                      ; this%gdd10_patch              (:)   = spval
-    allocate(this%gdd020_patch             (begp:endp))                      ; this%gdd020_patch             (:)   = spval
-    allocate(this%gdd820_patch             (begp:endp))                      ; this%gdd820_patch             (:)   = spval
-    allocate(this%gdd1020_patch            (begp:endp))                      ; this%gdd1020_patch            (:)   = spval
-
-    ! Heat content
-    allocate(this%beta_col                 (begc:endc))                      ; this%beta_col                 (:)   = nan
-    allocate(this%heat1_grc                (begg:endg))                      ; this%heat1_grc                (:)   = nan
-    allocate(this%heat2_grc                (begg:endg))                      ; this%heat2_grc                (:)   = nan
-    allocate(this%liquid_water_temp1_grc   (begg:endg))                      ; this%liquid_water_temp1_grc   (:)   = nan
-    allocate(this%liquid_water_temp2_grc   (begg:endg))                      ; this%liquid_water_temp2_grc   (:)   = nan
-
-    ! flags
-    allocate(this%imelt_col                (begc:endc,-nlevsno+1:nlevgrnd))  ; this%imelt_col                (:,:) = huge(1)
-
-    ! emissivities
-    allocate(this%emv_patch                (begp:endp))                      ; this%emv_patch                (:)   = nan
-    allocate(this%emg_col                  (begc:endc))                      ; this%emg_col                  (:)   = nan
-
-    allocate(this%xmf_col                  (begc:endc))                      ; this%xmf_col                  (:)   = nan
-    allocate(this%xmf_h2osfc_col           (begc:endc))                      ; this%xmf_h2osfc_col           (:)   = nan
-    allocate(this%fact_col                 (begc:endc, -nlevsno+1:nlevgrnd)) ; this%fact_col                 (:,:) = nan
-    allocate(this%c_h2osfc_col             (begc:endc))                      ; this%c_h2osfc_col             (:)   = nan
+    allocate(this%t_soisno_col (begc:endc,-nlevsno+1:nlevgrnd))  ; this%t_soisno_col             (:,:) = nan
+    allocate(this%t_grnd_col   (begc:endc))                      ; this%t_grnd_col               (:)   = nan
 
   end subroutine InitAllocate
 
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp )
-    !
-    ! !DESCRIPTION:
-    ! Setup the fields that can be output on history files.
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varctl     , only : use_cn, use_cndv
-    use histFileMod    , only : hist_addfld1d, hist_addfld2d, no_snow_normal
-    !
-    ! !ARGUMENTS:
-    class(temperature_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    logical          , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
-    logical          , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    integer           :: begl, endl
-    integer           :: begg, endg
-    character(10)     :: active
-    character(100)    :: lname
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begl = bounds%begl; endl= bounds%endl
-    begg = bounds%begg; endg= bounds%endg
-
-    this%t_h2osfc_col(begc:endc) = spval
-    call hist_addfld1d (fname='TH2OSFC',  units='K',  &
-         avgflag='A', long_name='surface water temperature', &
-         ptr_col=this%t_h2osfc_col, default='inactive')
-
-    this%t_grnd_u_col(begc:endc) = spval
-    call hist_addfld1d (fname='TG_U', units='K',  &
-         avgflag='A', long_name='Urban ground temperature', &
-         ptr_col=this%t_grnd_u_col, set_nourb=spval, c2l_scale_type='urbans', default='inactive')
-
-    this%t_lake_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='TLAKE',  units='K', type2d='levlak', &
-         avgflag='A', long_name='lake temperature', &
-         ptr_col=this%t_lake_col, default='inactive')
-
-    this%t_soisno_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%t_soisno_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_T', units='K', type2d='levsno',  &
-         avgflag='A', long_name='Snow temperatures', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_T_ICE', units='K', type2d='levsno',  &
-         avgflag='A', long_name='Snow temperatures (ice landunits only)', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%t_ref2m_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TSA', units='K',  &
-         avgflag='A', long_name='2m air temperature', &
-         ptr_patch=this%t_ref2m_patch, default='inactive')
-
-    call hist_addfld1d (fname='TSA_ICE', units='K',  &
-         avgflag='A', long_name='2m air temperature (ice landunits only)', &
-         ptr_patch=this%t_ref2m_patch, l2g_scale_type='ice', default='inactive')
-
-    this%t_ref2m_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TSA_R', units='K',  &
-         avgflag='A', long_name='Rural 2m air temperature', &
-         ptr_patch=this%t_ref2m_r_patch, set_spec=spval, default='inactive')
-
-    this%t_ref2m_min_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMNAV', units='K',  &
-         avgflag='A', long_name='daily minimum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_min_patch, default='inactive')
-
-    this%t_ref2m_max_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMXAV', units='K',  &
-         avgflag='A', long_name='daily maximum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_max_patch, default='inactive')
-
-    this%t_ref2m_min_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMNAV_R', units='K',  &
-         avgflag='A', long_name='Rural daily minimum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_min_r_patch, set_spec=spval, default='inactive')
-
-    this%t_ref2m_max_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMXAV_R', units='K',  &
-         avgflag='A', long_name='Rural daily maximum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_max_r_patch, set_spec=spval, default='inactive')
-
-    this%t_ref2m_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TSA_U', units='K',  &
-         avgflag='A', long_name='Urban 2m air temperature', &
-         ptr_patch=this%t_ref2m_u_patch, set_nourb=spval, default='inactive')
-
-    this%t_ref2m_min_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMNAV_U', units='K',  &
-         avgflag='A', long_name='Urban daily minimum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_min_u_patch, set_nourb=spval, default='inactive')
-
-    this%t_ref2m_max_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TREFMXAV_U', units='K',  &
-         avgflag='A', long_name='Urban daily maximum of average 2-m temperature', &
-         ptr_patch=this%t_ref2m_max_u_patch, set_nourb=spval, default='inactive')
-
-    this%t_veg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TV', units='K',  &
-         avgflag='A', long_name='vegetation temperature', &
-         ptr_patch=this%t_veg_patch, default='inactive')
-
-    this%t_grnd_col(begc:endc) = spval
-    call hist_addfld1d (fname='TG',  units='K',  &
-         avgflag='A', long_name='ground temperature', &
-         ptr_col=this%t_grnd_col, c2l_scale_type='urbans', default='inactive')
-
-    call hist_addfld1d (fname='TG_ICE', units='K',  &
-         avgflag='A', long_name='ground temperature (ice landunits only)', &
-         ptr_col=this%t_grnd_col, c2l_scale_type='urbans', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%t_grnd_r_col(begc:endc) = spval
-    call hist_addfld1d (fname='TG_R', units='K',  &
-         avgflag='A', long_name='Rural ground temperature', &
-         ptr_col=this%t_grnd_r_col, set_spec=spval, default='inactive')
-
-    this%t_soisno_col(begc:endc,:) = spval
-    call hist_addfld2d (fname='TSOI',  units='K', type2d='levgrnd', &
-         avgflag='A', long_name='soil temperature (vegetated landunits only)', &
-         ptr_col=this%t_soisno_col, l2g_scale_type='veg', default='inactive')
-
-    call hist_addfld2d (fname='TSOI_ICE',  units='K', type2d='levgrnd', &
-         avgflag='A', long_name='soil temperature (ice landunits only)', &
-         ptr_col=this%t_soisno_col, l2g_scale_type='ice', default='inactive')
-
-    this%t_soi10cm_col(begc:endc) = spval
-    call hist_addfld1d (fname='TSOI_10CM',  units='K', &
-         avgflag='A', long_name='soil temperature in top 10cm of soil', &
-         ptr_col=this%t_soi10cm_col, set_urb=spval, default='inactive')
-
-    if (use_cndv .or. use_crop) then
-       active = "active"
-    else
-       active = "active"
-    end if
-    this%t_a10_patch(begp:endp) = spval
-    call hist_addfld1d (fname='T10', units='K',  &
-         avgflag='A', long_name='10-day running mean of 2-m temperature', &
-         ptr_patch=this%t_a10_patch, default='inactive')
-
-    if (use_cn .and.  use_crop )then
-       this%t_a5min_patch(begp:endp) = spval
-       call hist_addfld1d (fname='A5TMIN', units='K',  &
-            avgflag='A', long_name='5-day running mean of min 2-m temperature', &
-            ptr_patch=this%t_a5min_patch, default='inactive')
-    end if
-
-    if (use_cn .and. use_crop )then
-       this%t_a10min_patch(begp:endp) = spval
-       call hist_addfld1d (fname='A10TMIN', units='K',  &
-            avgflag='A', long_name='10-day running mean of min 2-m temperature', &
-            ptr_patch=this%t_a10min_patch, default='inactive')
-    end if
-
-    this%t_building_lun(begl:endl) = spval
-    if (      is_simple_buildtemp )then
-       lname = 'internal urban building temperature'
-    else if ( is_prog_buildtemp   )then
-       lname = 'internal urban building air temperature'
-    end if
-    call hist_addfld1d(fname='TBUILD', units='K',  &
-         avgflag='A', long_name=lname, &
-         ptr_lunit=this%t_building_lun, set_nourb=spval, l2g_scale_type='unity', default='inactive')
-
-    if ( is_prog_buildtemp )then
-       this%t_roof_inner_lun(begl:endl) = spval
-       call hist_addfld1d(fname='TROOF_INNER', units='K',  &
-            avgflag='A', long_name='roof inside surface temperature', &
-            ptr_lunit=this%t_roof_inner_lun, set_nourb=spval, l2g_scale_type='unity', &
-            default='inactive')
-
-       this%t_sunw_inner_lun(begl:endl) = spval
-       call hist_addfld1d(fname='TSUNW_INNER', units='K',  &
-            avgflag='A', long_name='sunwall inside surface temperature', &
-            ptr_lunit=this%t_sunw_inner_lun, set_nourb=spval, l2g_scale_type='unity', &
-            default='inactive')
-
-       this%t_shdw_inner_lun(begl:endl) = spval
-       call hist_addfld1d(fname='TSHDW_INNER', units='K',  &
-            avgflag='A', long_name='shadewall inside surface temperature', &
-            ptr_lunit=this%t_shdw_inner_lun, set_nourb=spval, l2g_scale_type='unity', &
-            default='inactive')
-
-       this%t_floor_lun(begl:endl) = spval
-       call hist_addfld1d(fname='TFLOOR', units='K',  &
-            avgflag='A', long_name='floor temperature', &
-            ptr_lunit=this%t_floor_lun, set_nourb=spval, l2g_scale_type='unity', &
-            default='inactive')
-    end if
-
-    this%heat1_grc(begg:endg) = spval
-    call hist_addfld1d (fname='HEAT_CONTENT1',  units='J/m^2',  &
-         avgflag='A', long_name='initial gridcell total heat content', &
-         ptr_lnd=this%heat1_grc, default='inactive')
-    call hist_addfld1d (fname='HEAT_CONTENT1_VEG',  units='J/m^2',  &
-         avgflag='A', long_name='initial gridcell total heat content - vegetated landunits only', &
-         ptr_lnd=this%heat1_grc, l2g_scale_type='veg', default='inactive')
-
-    this%heat2_grc(begg:endg) = spval
-    call hist_addfld1d (fname='HEAT_CONTENT2',  units='J/m^2',  &
-         avgflag='A', long_name='post land cover change total heat content', &
-         ptr_lnd=this%heat2_grc, default='inactive')  
-
-    this%liquid_water_temp1_grc(begg:endg) = spval
-    call hist_addfld1d (fname='LIQUID_WATER_TEMP1', units='K', &
-         avgflag='A', long_name='initial gridcell weighted average liquid water temperature', &
-         ptr_lnd=this%liquid_water_temp1_grc, default='inactive')
-
-    this%snot_top_col(begc:endc) = spval 
-    call hist_addfld1d (fname='SNOTTOPL', units='K', &
-         avgflag='A', long_name='snow temperature (top layer)', &
-         ptr_col=this%snot_top_col, set_urb=spval, default='inactive')
-
-    call hist_addfld1d (fname='SNOTTOPL_ICE', units='K',  &
-         avgflag='A', long_name='snow temperature (top layer, ice landunits only)', &
-         ptr_col=this%snot_top_col, set_urb=spval, l2g_scale_type='ice', default='inactive')
-
-    this%dTdz_top_col(begc:endc) = spval 
-    call hist_addfld1d (fname='SNOdTdzL', units='K/m', &
-         avgflag='A', long_name='top snow layer temperature gradient (land)', &
-         ptr_col=this%dTdz_top_col, set_urb=spval, default='inactive')
-
-    if (use_cn) then
-       this%dt_veg_patch(begp:endp) = spval
-       call hist_addfld1d (fname='DT_VEG', units='K', &
-            avgflag='A', long_name='change in t_veg, last iteration', &
-            ptr_patch=this%dt_veg_patch, default='inactive')
-    end if
-
-    if (use_cn ) then
-       this%emv_patch(begp:endp) = spval
-       call hist_addfld1d (fname='EMV', units='proportion', &
-            avgflag='A', long_name='vegetation emissivity', &
-            ptr_patch=this%emv_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%emg_col(begc:endc) = spval
-       call hist_addfld1d (fname='EMG', units='proportion', &
-            avgflag='A', long_name='ground emissivity', &
-            ptr_col=this%emg_col, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%beta_col(begc:endc) = spval
-       call hist_addfld1d (fname='BETA', units='none', &
-            avgflag='A', long_name='coefficient of convective velocity', &
-            ptr_col=this%beta_col, default='inactive')
-    end if
-
-    ! Accumulated quantities
-
-    this%t_veg24_patch(begp:endp) = spval
-    call hist_addfld1d (fname='TV24', units='K',  &
-         avgflag='A', long_name='vegetation temperature (last 24hrs)', &
-         ptr_patch=this%t_veg24_patch, default='inactive')
-
-    this%t_veg240_patch(begp:endp)  = spval
-    call hist_addfld1d (fname='TV240', units='K',  &
-         avgflag='A', long_name='vegetation temperature (last 240hrs)', &
-         ptr_patch=this%t_veg240_patch, default='inactive')
-
-    if (use_crop) then
-       this%gdd0_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD0', units='ddays', &
-            avgflag='A', long_name='Growing degree days base  0C from planting', &
-            ptr_patch=this%gdd0_patch, default='inactive')
-    end if
-
-    if (use_crop) then
-       this%gdd8_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD8', units='ddays', &
-            avgflag='A', long_name='Growing degree days base  8C from planting', &
-            ptr_patch=this%gdd8_patch, default='inactive')
-
-       this%gdd10_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD10', units='ddays', &
-            avgflag='A', long_name='Growing degree days base 10C from planting', &
-            ptr_patch=this%gdd10_patch, default='inactive')
-
-       this%gdd020_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD020', units='ddays', &
-            avgflag='A', long_name='Twenty year average of growing degree days base  0C from planting', &
-            ptr_patch=this%gdd020_patch, default='inactive')
-
-       this%gdd820_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD820', units='ddays', &
-            avgflag='A', long_name='Twenty year average of growing degree days base  8C from planting', &
-            ptr_patch=this%gdd820_patch, default='inactive')
-
-       this%gdd1020_patch(begp:endp) = spval
-       call hist_addfld1d (fname='GDD1020', units='ddays', &
-            avgflag='A', long_name='Twenty year average of growing degree days base 10C from planting', &
-            ptr_patch=this%gdd1020_patch, default='inactive')
-
-    end if
-    if(use_luna)then
-         call hist_addfld1d (fname='TVEGD10', units='Kelvin', &
-            avgflag='A', long_name='10 day running mean of patch daytime vegetation temperature', &
-            ptr_patch=this%t_veg10_day_patch, default='inactive')
-         call hist_addfld1d (fname='TVEGN10', units='Kelvin', &
-            avgflag='A', long_name='10 day running mean of patch night-time vegetation temperature', &
-            ptr_patch=this%t_veg10_night_patch, default='inactive')
-    endif
-
-
-  end subroutine InitHistory
-
   !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, &
-       em_roof_lun,  em_wall_lun, em_improad_lun, em_perroad_lun, &
-       is_simple_buildtemp, is_prog_buildtemp)
+  subroutine InitCold(this, bounds)
     !
     ! !DESCRIPTION:
     ! Initialize cold start conditions for module variables
     !
     ! !USES:
     use shr_kind_mod   , only : r8 => shr_kind_r8
-    use shr_const_mod  , only : SHR_CONST_TKFRZ
-    use clm_varcon     , only : denice, denh2o, sb
-    use landunit_varcon, only : istwet, istsoil, istdlak, istice_mec
+    use landunit_varcon, only : istwet, istice_mec
     use column_varcon  , only : icol_road_imperv, icol_roof, icol_sunwall
     use column_varcon  , only : icol_shadewall, icol_road_perv
-    use clm_varctl     , only : iulog, use_vancouver, use_mexicocity
     !
     ! !ARGUMENTS:
     class(temperature_type)        :: this
     type(bounds_type) , intent(in) :: bounds  
-    real(r8)          , intent(in) :: em_roof_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_wall_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_improad_lun(bounds%begl:)
-    real(r8)          , intent(in) :: em_perroad_lun(bounds%begl:)
-    logical           , intent(in) :: is_simple_buildtemp  ! Simple building temp is being used
-    logical           , intent(in) :: is_prog_buildtemp    ! Prognostic building temp is being used
     !
     ! !LOCAL VARIABLES:
     integer  :: j,l,c,p ! indices
-    integer  :: nlevs   ! number of levels
-    real(r8) :: snowbd  ! temporary calculation of snow bulk density (kg/m3)
-    real(r8) :: fmelt   ! snowbd/100
-    integer  :: lev
     !-----------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(em_roof_lun)    == (/bounds%endl/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(em_wall_lun)    == (/bounds%endl/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(em_improad_lun) == (/bounds%endl/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(em_perroad_lun) == (/bounds%endl/)), errMsg(sourcefile, __LINE__))
-
     associate(snl => col%snl) ! Output: [integer (:)    ]  number of snow layers   
-
       ! Set snow/soil temperature
-      ! t_lake only has valid values over non-lake   
-      ! t_soisno, t_grnd and t_veg have valid values over all land 
+      ! t_soisno, t_grnd have valid values over all land 
 
       do c = bounds%begc,bounds%endc
          l = col%landunit(c)
@@ -656,33 +124,6 @@ subroutine InitCold(this, bounds, &
                this%t_soisno_col(c,1:nlevgrnd) = 277._r8
 
             else if (lun%urbpoi(l)) then
-               if (use_vancouver) then
-                  if (col%itype(c) == icol_road_perv .or. col%itype(c) == icol_road_imperv) then 
-                     ! Set road top layer to initial air temperature and interpolate other
-                     ! layers down to 20C in bottom layer
-                     do j = 1, nlevgrnd
-                        this%t_soisno_col(c,j) = 297.56 - (j-1) * ((297.56-293.16)/(nlevgrnd-1)) 
-                     end do
-                     ! Set wall and roof layers to initial air temperature
-                  else if (col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall .or. col%itype(c) == icol_roof) then
-                     this%t_soisno_col(c,1:nlevurb) = 297.56
-                  else
-                     this%t_soisno_col(c,1:nlevgrnd) = 283._r8
-                  end if
-               else if (use_mexicocity) then
-                  if (col%itype(c) == icol_road_perv .or. col%itype(c) == icol_road_imperv) then 
-                     ! Set road top layer to initial air temperature and interpolate other
-                     ! layers down to 22C in bottom layer
-                     do j = 1, nlevgrnd
-                        this%t_soisno_col(c,j) = 289.46 - (j-1) * ((289.46-295.16)/(nlevgrnd-1)) 
-                     end do
-                  else if (col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall .or. col%itype(c) == icol_roof) then
-                     ! Set wall and roof layers to initial air temperature
-                     this%t_soisno_col(c,1:nlevurb) = 289.46
-                  else
-                     this%t_soisno_col(c,1:nlevgrnd) = 283._r8
-                  end if
-               else
                   if (col%itype(c) == icol_road_perv .or. col%itype(c) == icol_road_imperv) then 
                      this%t_soisno_col(c,1:nlevgrnd) = 274._r8
                   else if (col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall &
@@ -691,7 +132,6 @@ subroutine InitCold(this, bounds, &
                      ! shock from large heating/air conditioning flux
                      this%t_soisno_col(c,1:nlevurb) = 292._r8
                   end if
-               end if
             else
                this%t_soisno_col(c,1:nlevgrnd) = 274._r8
 
@@ -699,130 +139,36 @@ subroutine InitCold(this, bounds, &
          endif
       end do
 
-      ! Initialize internal building temperature, inner temperatures of building
-      ! surfaces, and floor temperature
-      if ( is_prog_buildtemp )then
-         do l = bounds%begl, bounds%endl
-           do  c = lun%coli(l),lun%colf(l)
-             if (col%itype(c) == icol_roof)  then
-               this%t_roof_inner_lun(l) = this%t_soisno_col(c,nlevurb)
-               this%t_building_lun(l)   = this%t_soisno_col(c,nlevurb)        ! arbitrarily set to roof temperature
-               this%t_floor_lun(l)      = this%t_soisno_col(c,nlevurb)        ! arbitrarily set to roof temperature
-             else if (col%itype(c) == icol_sunwall) then
-               this%t_sunw_inner_lun(l) = this%t_soisno_col(c,nlevurb)
-             else if (col%itype(c) == icol_shadewall) then
-               this%t_shdw_inner_lun(l) = this%t_soisno_col(c,nlevurb)
-             end if
-           end do
-         end do
-      end if
-
       ! Set Ground temperatures
 
       do c = bounds%begc,bounds%endc
          l = col%landunit(c)
-
          if (lun%lakpoi(l)) then 
             this%t_grnd_col(c) = 277._r8
          else
             this%t_grnd_col(c) = this%t_soisno_col(c,snl(c)+1)
          end if
-         this%t_soi17cm_col(c) = this%t_grnd_col(c)
       end do
 
       do c = bounds%begc,bounds%endc
          l = col%landunit(c)
          if (lun%lakpoi(l)) then ! lake
-            this%t_lake_col(c,1:nlevlak) = this%t_grnd_col(c)
             this%t_soisno_col(c,1:nlevgrnd) = this%t_grnd_col(c)
          end if
       end do
 
-      ! Set t_h2osfc_col
-
-      this%t_h2osfc_col(bounds%begc:bounds%endc)  = 274._r8
-
-      ! Set t_veg, t_ref2m, t_ref2m_u and tref2m_r 
-
-      do p = bounds%begp, bounds%endp
-         c = patch%column(p)
-         l = patch%landunit(p)
-
-         if (use_vancouver) then
-            this%t_veg_patch(p)   = 297.56
-         else if (use_mexicocity) then
-            this%t_veg_patch(p)   = 289.46
-         else
-            this%t_veg_patch(p)   = 283._r8
-         end if
-
-         if (use_vancouver) then
-            this%t_ref2m_patch(p) = 297.56
-         else if (use_mexicocity) then
-            this%t_ref2m_patch(p) = 289.46
-         else
-            this%t_ref2m_patch(p) = 283._r8
-         end if
-
-         if (lun%urbpoi(l)) then
-            if (use_vancouver) then
-               this%t_ref2m_u_patch(p) = 297.56
-            else if (use_mexicocity) then
-               this%t_ref2m_u_patch(p) = 289.46
-            else
-               this%t_ref2m_u_patch(p) = 283._r8
-            end if
-         else 
-            if (.not. lun%ifspecial(l)) then 
-               if (use_vancouver) then
-                  this%t_ref2m_r_patch(p) = 297.56
-               else if (use_mexicocity) then
-                  this%t_ref2m_r_patch(p) = 289.46
-               else
-                  this%t_ref2m_r_patch(p) = 283._r8
-               end if
-            else 
-               this%t_ref2m_r_patch(p) = spval
-            end if
-         end if
-
-      end do
-
     end associate
 
-    do l = bounds%begl, bounds%endl 
-       if (lun%urbpoi(l)) then
-          if (use_vancouver) then
-             this%taf_lun(l) = 297.56_r8
-          else if (use_mexicocity) then
-             this%taf_lun(l) = 289.46_r8
-          else
-             this%taf_lun(l) = 283._r8
-          end if
-       end if
-    end do
-
-    do c = bounds%begc,bounds%endc
-       l = col%landunit(c)
-
-       if (col%itype(c) == icol_roof       ) this%emg_col(c) = em_roof_lun(l)
-       if (col%itype(c) == icol_sunwall    ) this%emg_col(c) = em_wall_lun(l)
-       if (col%itype(c) == icol_shadewall  ) this%emg_col(c) = em_wall_lun(l)
-       if (col%itype(c) == icol_road_imperv) this%emg_col(c) = em_improad_lun(l)
-       if (col%itype(c) == icol_road_perv  ) this%emg_col(c) = em_perroad_lun(l)
-    end do
-
   end subroutine InitCold
 
   !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildtemp)
+  subroutine Restart(this, bounds, ncid, flag)
     ! 
     ! !DESCRIPTION:
     ! Read/Write module information to/from restart file.
     !
     ! !USES:
     use shr_log_mod     , only : errMsg => shr_log_errMsg
-    use spmdMod         , only : masterproc
     use abortutils      , only : endrun
     use ncdio_pio       , only : file_desc_t, ncd_double
     use restUtilMod
@@ -832,8 +178,6 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
     type(bounds_type), intent(in)    :: bounds 
     type(file_desc_t), intent(inout) :: ncid   
     character(len=*) , intent(in)    :: flag   
-    logical          , intent(in)    :: is_simple_buildtemp  ! Simple building temp is being used
-    logical          , intent(in)    :: is_prog_buildtemp    ! Prognostic building temp is being used
     !
     ! !LOCAL VARIABLES:
     integer :: j,c       ! indices
@@ -845,630 +189,11 @@ subroutine Restart(this, bounds, ncid, flag, is_simple_buildtemp, is_prog_buildt
          long_name='soil-snow temperature', units='K', &
          interpinic_flag='interp', readvar=readvar, data=this%t_soisno_col)
 
-    call restartvar(ncid=ncid, flag=flag, varname='T_VEG', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='vegetation temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_veg_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='TH2OSFC', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='surface water temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_h2osfc_col)
-    if (flag=='read' .and. .not. readvar) then
-       this%t_h2osfc_col(bounds%begc:bounds%endc) = 274.0_r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_LAKE', xtype=ncd_double,  &
-         dim1name='column', dim2name='levlak', switchdim=.true., &
-         long_name='lake temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_lake_col)
-
     call restartvar(ncid=ncid, flag=flag, varname='T_GRND', xtype=ncd_double,  &
          dim1name='column', &
          long_name='ground temperature', units='K', &
          interpinic_flag='interp', readvar=readvar, data=this%t_grnd_col)
 
-    call restartvar(ncid=ncid, flag=flag, varname='T_GRND_R', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='rural ground temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_grnd_r_col)
-         
-    call restartvar(ncid=ncid, flag=flag, varname='T_GRND_U', xtype=ncd_double, &
-         dim1name='column',                    &
-         long_name='urban ground temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_grnd_u_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='2m height surface air temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_patch)
-    if (flag=='read' .and. .not. readvar) call endrun(msg=errMsg(sourcefile, __LINE__))
-
-    call restartvar(ncid=ncid, flag=flag, varname="T_REF2M_R", xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='Rural 2m height surface air temperature', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_r_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname="T_REF2M_U", xtype=ncd_double, dim1name='pft',                      &
-         long_name='Urban 2m height surface air temperature', units='K',                                              &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_u_patch)
-
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='daily minimum of average 2 m height surface air temperature (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN_R', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='rural daily minimum of average 2 m height surface air temperature (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_r_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN_U', xtype=ncd_double, dim1name='pft',                  &
-         long_name='urban daily minimum of average 2 m height surface air temperature (K)', units='K',                &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_u_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='daily maximum of average 2 m height surface air temperature (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX_R', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='rural daily maximum of average 2 m height surface air temperature (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_r_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX_U', xtype=ncd_double, dim1name='pft',                  &
-         long_name='urban daily maximum of average 2 m height surface air temperature (K)', units='K',                &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_u_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN_INST', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='instantaneous daily min of average 2 m height surface air temp (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_inst_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN_INST_R', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='rural instantaneous daily min of average 2 m height surface air temp (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_inst_r_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MIN_INST_U', xtype=ncd_double, dim1name='pft',             &
-         long_name='urban instantaneous daily min of average 2 m height surface air temp (K)', units='K',             &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_min_inst_u_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX_INST', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='instantaneous daily max of average 2 m height surface air temp (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_inst_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX_INST_R', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='rural instantaneous daily max of average 2 m height surface air temp (K)', units='K', &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_inst_r_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='T_REF2M_MAX_INST_U', xtype=ncd_double,  dim1name='pft',            &
-         long_name='urban instantaneous daily max of average 2 m height surface air temp (K)', units='K',             &
-         interpinic_flag='interp', readvar=readvar, data=this%t_ref2m_max_inst_u_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='taf', xtype=ncd_double, dim1name='landunit',                       &
-         long_name='urban canopy air temperature', units='K',                                                         &
-         interpinic_flag='interp', readvar=readvar, data=this%taf_lun)
-
-    if (use_crop) then
-       call restartvar(ncid=ncid, flag=flag,  varname='gdd1020', xtype=ncd_double,  &
-            dim1name='pft', long_name='20 year average of growing degree-days base 10C from planting', units='ddays', &
-            interpinic_flag='interp', readvar=readvar, data=this%gdd1020_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='gdd820', xtype=ncd_double,  &
-            dim1name='pft', long_name='20 year average of growing degree-days base 8C from planting', units='ddays', &
-            interpinic_flag='interp', readvar=readvar, data=this%gdd820_patch)
-
-       call restartvar(ncid=ncid, flag=flag,  varname='gdd020', xtype=ncd_double,  &
-            dim1name='pft', long_name='20 year average of growing degree-days base 0C from planting', units='ddays', &
-            interpinic_flag='interp', readvar=readvar, data=this%gdd020_patch)
-    end if
-
-    if(use_luna)then
-       call restartvar(ncid=ncid, flag=flag, varname='tvegd10', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean daytime vegetation temperature', units='Kelvin', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_veg10_day_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='tvegd', xtype=ncd_double,  &
-            dim1name='pft', long_name='accumulative daytime vegetation temperature', units='Kelvin*steps', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_veg_day_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='tvegn10', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean nighttime vegetation temperature', units='Kelvin', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_veg10_night_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='tvegn', xtype=ncd_double,  &
-            dim1name='pft', long_name='accumulative nighttime vegetation temperature', units='Kelvin*steps', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_veg_night_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='tair10', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean air temperature', units='Kelvin', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_a10_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='ndaysteps', xtype=ncd_double,  &
-            dim1name='pft', long_name='accumulative daytime steps', units='steps', &
-            interpinic_flag='interp', readvar=readvar, data=this%ndaysteps_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='nnightsteps', xtype=ncd_double,  &
-            dim1name='pft', long_name='accumulative nighttime steps', units='steps', &
-            interpinic_flag='interp', readvar=readvar, data=this%nnightsteps_patch )
-    endif
-
-    if ( is_prog_buildtemp )then
-       ! landunit type physical state variable - t_building
-       call restartvar(ncid=ncid, flag=flag, varname='t_building', xtype=ncd_double,  & 
-            dim1name='landunit', &
-            long_name='internal building air temperature', units='K', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_building_lun)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "can't find t_building in initial file..."
-          if (masterproc) write(iulog,*) "Initialize t_building to taf"
-          this%t_building_lun(bounds%begl:bounds%endl) = this%taf_lun(bounds%begl:bounds%endl)
-       end if
-
-       ! landunit type physical state variable - t_roof_inner
-       call restartvar(ncid=ncid, flag=flag, varname='t_roof_inner', xtype=ncd_double,  & 
-            dim1name='landunit', &
-            long_name='roof inside surface temperature', units='K', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_roof_inner_lun)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "can't find t_roof_inner in initial file..."
-          if (masterproc) write(iulog,*) "Initialize t_roof_inner to taf"
-          this%t_roof_inner_lun(bounds%begl:bounds%endl) = this%taf_lun(bounds%begl:bounds%endl)
-       end if
-
-       ! landunit type physical state variable - t_sunw_inner
-       call restartvar(ncid=ncid, flag=flag, varname='t_sunw_inner', xtype=ncd_double,  & 
-            dim1name='landunit', &
-            long_name='sunwall inside surface temperature', units='K', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_sunw_inner_lun)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "can't find t_sunw_inner in initial file..."
-          if (masterproc) write(iulog,*) "Initialize t_sunw_inner to taf"
-          this%t_sunw_inner_lun(bounds%begl:bounds%endl) = this%taf_lun(bounds%begl:bounds%endl)
-       end if
-
-       ! landunit type physical state variable - t_shdw_inner
-       call restartvar(ncid=ncid, flag=flag, varname='t_shdw_inner', xtype=ncd_double,  & 
-            dim1name='landunit', &
-            long_name='shadewall inside surface temperature', units='K', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_shdw_inner_lun)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "can't find t_shdw_inner in initial file..."
-          if (masterproc) write(iulog,*) "Initialize t_shdw_inner to taf"
-          this%t_shdw_inner_lun(bounds%begl:bounds%endl) = this%taf_lun(bounds%begl:bounds%endl)
-       end if
-
-       ! landunit type physical state variable - t_floor
-       call restartvar(ncid=ncid, flag=flag, varname='t_floor', xtype=ncd_double,  & 
-            dim1name='landunit', &
-            long_name='floor temperature', units='K', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_floor_lun)
-       if (flag=='read' .and. .not. readvar) then
-          if (masterproc) write(iulog,*) "can't find t_floor in initial file..."
-          if (masterproc) write(iulog,*) "Initialize t_floor to taf"
-          this%t_floor_lun(bounds%begl:bounds%endl) = this%taf_lun(bounds%begl:bounds%endl)
-       end if
-    end if
-   
-
   end subroutine Restart
 
-  !-----------------------------------------------------------------------
-  subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    ! Each interval and accumulation type is unique to each field processed.
-    ! Routine [initAccBuffer] defines the fields to be processed
-    ! and the type of accumulation. 
-    ! Routine [updateAccVars] does the actual accumulation for a given field.
-    ! Fields are accumulated by calls to subroutine [update_accum_field]. 
-    ! To accumulate a field, it must first be defined in subroutine [initAccVars] 
-    ! and then accumulated by calls to [updateAccVars].
-    ! Four types of accumulations are possible:
-    !   o average over time interval
-    !   o running mean over time interval
-    !   o running accumulation over time interval
-    ! Time average fields are only valid at the end of the averaging interval.
-    ! Running means are valid once the length of the simulation exceeds the
-    ! averaging interval. Accumulated fields are continuously accumulated.
-    ! The trigger value "-99999." resets the accumulation to zero.
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field
-    use clm_time_manager , only : get_step_size
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    !
-    ! !ARGUMENTS:
-    class(temperature_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES: 
-    real(r8) :: dtime
-    integer, parameter :: not_used = huge(1)
-    !---------------------------------------------------------------------
-
-    dtime = get_step_size()
-
-    this%t_veg24_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='T_VEG24', units='K',                                              &
-         desc='24hr average of vegetation temperature',  accum_type='runmean', accum_period=-1,    &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    this%t_veg240_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='T_VEG240', units='K',                                             &
-         desc='240hr average of vegetation temperature',  accum_type='runmean', accum_period=-10,  &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    call init_accum_field(name='TREFAV', units='K', &
-         desc='average over an hour of 2-m temperature', accum_type='timeavg', accum_period=nint(3600._r8/dtime), &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    call init_accum_field(name='TREFAV_U', units='K', &
-         desc='average over an hour of urban 2-m temperature', accum_type='timeavg', accum_period=nint(3600._r8/dtime), &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    call init_accum_field(name='TREFAV_R', units='K', &
-         desc='average over an hour of rural 2-m temperature', accum_type='timeavg', accum_period=nint(3600._r8/dtime), &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    ! The following is a running mean. The accumulation period is set to -10 for a 10-day running mean.
-    call init_accum_field (name='T10', units='K', &
-         desc='10-day running mean of 2-m temperature', accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1,init_value=SHR_CONST_TKFRZ+20._r8)
-
-    if ( use_crop )then
-       call init_accum_field (name='TDM10', units='K', &
-            desc='10-day running mean of min 2-m temperature', accum_type='runmean', accum_period=-10, &
-            subgrid_type='pft', numlev=1, init_value=SHR_CONST_TKFRZ)
-
-       call init_accum_field (name='TDM5', units='K', &
-            desc='5-day running mean of min 2-m temperature', accum_type='runmean', accum_period=-5, &
-            subgrid_type='pft', numlev=1, init_value=SHR_CONST_TKFRZ)
-    end if
-
-    if ( use_crop )then
-
-       ! All GDD summations are relative to the planting date (Kucharik & Brye 2003)
-       call init_accum_field (name='GDD0', units='K', &
-            desc='growing degree-days base 0C from planting', accum_type='runaccum', accum_period=not_used, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-       call init_accum_field (name='GDD8', units='K', &
-            desc='growing degree-days base 8C from planting', accum_type='runaccum', accum_period=not_used, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-       call init_accum_field (name='GDD10', units='K', &
-            desc='growing degree-days base 10C from planting', accum_type='runaccum', accum_period=not_used,  &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    end if
-
-    if (use_cndv) then
-       ! 30-day average of 2m temperature.
-       call init_accum_field (name='TDA', units='K', &
-            desc='30-day average of 2-m temperature', accum_type='timeavg', accum_period=-30, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    end if
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-  subroutine InitAccVars(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! !USES 
-    use accumulMod       , only : init_accum_field, extract_accum_field
-    use clm_time_manager , only : get_nstep
-    use clm_varctl       , only : nsrest, nsrStartup
-    use abortutils       , only : endrun
-    !
-    ! !ARGUMENTS:
-    class(temperature_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begp, endp
-    integer  :: nstep
-    integer  :: ier
-    real(r8), pointer :: rbufslp(:)  ! temporary
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    ! Allocate needed dynamic memory for single level pft field
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)' in '
-       call endrun(msg="extract_accum_hist allocation error for rbufslp"//&
-            errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Determine time step
-    nstep = get_nstep()
-
-    call extract_accum_field ('T_VEG24', rbufslp, nstep)
-    this%t_veg24_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('T_VEG240', rbufslp, nstep)
-    this%t_veg240_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('T10', rbufslp, nstep)
-    this%t_a10_patch(begp:endp) = rbufslp(begp:endp)
-
-    if (use_crop) then
-       call extract_accum_field ('TDM10', rbufslp, nstep) 
-       this%t_a10min_patch(begp:endp)= rbufslp(begp:endp)
-
-       call extract_accum_field ('TDM5', rbufslp, nstep) 
-       this%t_a5min_patch(begp:endp) = rbufslp(begp:endp)
-    end if
-
-    ! Initialize variables that are to be time accumulated
-    ! Initialize 2m ref temperature max and min values
-
-    if (nsrest == nsrStartup) then 
-       this%t_ref2m_max_patch(begp:endp)        =  spval
-       this%t_ref2m_max_r_patch(begp:endp)      =  spval
-       this%t_ref2m_max_u_patch(begp:endp)      =  spval
-
-       this%t_ref2m_min_patch(begp:endp)        =  spval
-       this%t_ref2m_min_r_patch(begp:endp)      =  spval
-       this%t_ref2m_min_u_patch(begp:endp)      =  spval
-
-       this%t_ref2m_max_inst_patch(begp:endp)   = -spval
-       this%t_ref2m_max_inst_r_patch(begp:endp) = -spval
-       this%t_ref2m_max_inst_u_patch(begp:endp) = -spval
-
-       this%t_ref2m_min_inst_patch(begp:endp)   =  spval
-       this%t_ref2m_min_inst_r_patch(begp:endp) =  spval
-       this%t_ref2m_min_inst_u_patch(begp:endp) =  spval
-    end if
-
-    if ( use_crop ) then
-
-       call extract_accum_field ('GDD0', rbufslp, nstep)
-       this%gdd0_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('GDD8', rbufslp, nstep) ;
-       this%gdd8_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('GDD10', rbufslp, nstep) 
-       this%gdd10_patch(begp:endp) = rbufslp(begp:endp)
-
-    end if
-
-    deallocate(rbufslp)
-
-  end subroutine InitAccVars
-
-  !-----------------------------------------------------------------------
-  subroutine UpdateAccVars (this, bounds)
-    !
-    ! USES
-    use shr_const_mod    , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ
-    use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date
-    use accumulMod       , only : update_accum_field, extract_accum_field, accumResetVal
-    !
-    ! !ARGUMENTS:
-    class(temperature_type)                :: this
-    type(bounds_type)      , intent(in)    :: bounds
-
-    !
-    ! !LOCAL VARIABLES:
-    integer :: m,g,l,c,p                 ! indices
-    integer :: ier                       ! error status
-    integer :: dtime                     ! timestep size [seconds]
-    integer :: nstep                     ! timestep number
-    integer :: year                      ! year (0, ...) for nstep
-    integer :: month                     ! month (1, ..., 12) for nstep
-    integer :: day                       ! day of month (1, ..., 31) for nstep
-    integer :: secs                      ! seconds into current date for nstep
-    logical :: end_cd                    ! temporary for is_end_curr_day() value
-    integer :: begp, endp
-    real(r8), pointer :: rbufslp(:)      ! temporary single level - pft level
-    !---------------------------------------------------------------------
-
-    begp = bounds%begp; endp = bounds%endp
-
-    dtime = get_step_size()
-    nstep = get_nstep()
-    call get_curr_date (year, month, day, secs)
-
-    ! Allocate needed dynamic memory for single level pft field
-
-    allocate(rbufslp(begp:endp), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'update_accum_hist allocation error for rbuf1dp'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-
-    ! Accumulate and extract T_VEG24 & T_VEG240 
-    do p = begp,endp
-       rbufslp(p) = this%t_veg_patch(p)
-    end do
-    call update_accum_field  ('T_VEG24' , rbufslp             , nstep)
-    call extract_accum_field ('T_VEG24' , this%t_veg24_patch  , nstep)
-    call update_accum_field  ('T_VEG240', rbufslp             , nstep)
-    call extract_accum_field ('T_VEG240', this%t_veg240_patch , nstep)
-
-    ! Accumulate and extract TREFAV - hourly average 2m air temperature
-    ! Used to compute maximum and minimum of hourly averaged 2m reference
-    ! temperature over a day. Note that "spval" is returned by the call to
-    ! accext if the time step does not correspond to the end of an
-    ! accumulation interval. First, initialize the necessary values for
-    ! an initial run at the first time step the accumulator is called
-
-    call update_accum_field  ('TREFAV', this%t_ref2m_patch, nstep)
-    call extract_accum_field ('TREFAV', rbufslp, nstep)
-    end_cd = is_end_curr_day()
-    do p = begp,endp
-       if (rbufslp(p) /= spval) then
-          this%t_ref2m_max_inst_patch(p) = max(rbufslp(p), this%t_ref2m_max_inst_patch(p))
-          this%t_ref2m_min_inst_patch(p) = min(rbufslp(p), this%t_ref2m_min_inst_patch(p))
-       endif
-       if (end_cd) then
-          this%t_ref2m_max_patch(p) = this%t_ref2m_max_inst_patch(p)
-          this%t_ref2m_min_patch(p) = this%t_ref2m_min_inst_patch(p)
-          this%t_ref2m_max_inst_patch(p) = -spval
-          this%t_ref2m_min_inst_patch(p) =  spval
-       else if (secs == dtime) then
-          this%t_ref2m_max_patch(p) = spval
-          this%t_ref2m_min_patch(p) = spval
-       endif
-    end do
-
-    ! Accumulate and extract TREFAV_U - hourly average urban 2m air temperature
-    ! Used to compute maximum and minimum of hourly averaged 2m reference
-    ! temperature over a day. Note that "spval" is returned by the call to
-    ! accext if the time step does not correspond to the end of an
-    ! accumulation interval. First, initialize the necessary values for
-    ! an initial run at the first time step the accumulator is called
-
-    call update_accum_field  ('TREFAV_U', this%t_ref2m_u_patch, nstep)
-    call extract_accum_field ('TREFAV_U', rbufslp, nstep)
-    do p = begp,endp
-       l = patch%landunit(p)
-       if (rbufslp(p) /= spval) then
-          this%t_ref2m_max_inst_u_patch(p) = max(rbufslp(p), this%t_ref2m_max_inst_u_patch(p))
-          this%t_ref2m_min_inst_u_patch(p) = min(rbufslp(p), this%t_ref2m_min_inst_u_patch(p))
-       endif
-       if (end_cd) then
-         if (lun%urbpoi(l)) then
-          this%t_ref2m_max_u_patch(p) = this%t_ref2m_max_inst_u_patch(p)
-          this%t_ref2m_min_u_patch(p) = this%t_ref2m_min_inst_u_patch(p)
-          this%t_ref2m_max_inst_u_patch(p) = -spval
-          this%t_ref2m_min_inst_u_patch(p) =  spval
-         end if
-       else if (secs == dtime) then
-          this%t_ref2m_max_u_patch(p) = spval
-          this%t_ref2m_min_u_patch(p) = spval
-       endif
-    end do
-
-    ! Accumulate and extract TREFAV_R - hourly average rural 2m air temperature
-    ! Used to compute maximum and minimum of hourly averaged 2m reference
-    ! temperature over a day. Note that "spval" is returned by the call to
-    ! accext if the time step does not correspond to the end of an
-    ! accumulation interval. First, initialize the necessary values for
-    ! an initial run at the first time step the accumulator is called
-
-    call update_accum_field  ('TREFAV_R', this%t_ref2m_r_patch, nstep)
-    call extract_accum_field ('TREFAV_R', rbufslp, nstep)
-    do p = begp,endp
-       l = patch%landunit(p)
-       if (rbufslp(p) /= spval) then
-          this%t_ref2m_max_inst_r_patch(p) = max(rbufslp(p), this%t_ref2m_max_inst_r_patch(p))
-          this%t_ref2m_min_inst_r_patch(p) = min(rbufslp(p), this%t_ref2m_min_inst_r_patch(p))
-       endif
-       if (end_cd) then
-         if (.not.(lun%ifspecial(l))) then
-          this%t_ref2m_max_r_patch(p) = this%t_ref2m_max_inst_r_patch(p)
-          this%t_ref2m_min_r_patch(p) = this%t_ref2m_min_inst_r_patch(p)
-          this%t_ref2m_max_inst_r_patch(p) = -spval
-          this%t_ref2m_min_inst_r_patch(p) =  spval
-         end if
-       else if (secs == dtime) then
-          this%t_ref2m_max_r_patch(p) = spval
-          this%t_ref2m_min_r_patch(p) = spval
-       endif
-    end do
-
-    ! Accumulate and extract T10
-    !(acumulates TSA as 10-day running mean)
-
-    call update_accum_field  ('T10', this%t_ref2m_patch, nstep)
-    call extract_accum_field ('T10', this%t_a10_patch, nstep)
-
-    if ( use_crop )then
-       ! Accumulate and extract TDM10
-
-       do p = begp,endp
-          rbufslp(p) = min(this%t_ref2m_min_patch(p),this%t_ref2m_min_inst_patch(p)) !slevis: ok choice?
-          if (rbufslp(p) > 1.e30_r8) rbufslp(p) = SHR_CONST_TKFRZ !and were 'min'&
-       end do                                                     !'min_inst' not initialized?
-       call update_accum_field  ('TDM10', rbufslp, nstep)
-       call extract_accum_field ('TDM10', this%t_a10min_patch, nstep)
-
-       ! Accumulate and extract TDM5
-
-       do p = begp,endp
-          rbufslp(p) = min(this%t_ref2m_min_patch(p),this%t_ref2m_min_inst_patch(p)) !slevis: ok choice?
-          if (rbufslp(p) > 1.e30_r8) rbufslp(p) = SHR_CONST_TKFRZ !and were 'min'&
-       end do                                         !'min_inst' not initialized?
-       call update_accum_field  ('TDM5', rbufslp, nstep)
-       call extract_accum_field ('TDM5', this%t_a5min_patch, nstep)
-
-       ! Accumulate and extract GDD0
-
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(26._r8, this%t_ref2m_patch(p)-SHR_CONST_TKFRZ)) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD0', rbufslp, nstep)
-       call extract_accum_field ('GDD0', this%gdd0_patch, nstep)
-
-       ! Accumulate and extract GDD8
-
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(30._r8, &
-                     this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + 8._r8))) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD8', rbufslp, nstep)
-       call extract_accum_field ('GDD8', this%gdd8_patch, nstep)
-
-       ! Accumulate and extract GDD10
-
-       do p = begp,endp
-          ! Avoid unnecessary calculations over inactive points
-          if (patch%active(p)) then
-             g = patch%gridcell(p)
-             if (month==1 .and. day==1 .and. secs==dtime) then
-                rbufslp(p) = accumResetVal ! reset gdd
-             else if (( month > 3 .and. month < 10 .and. grc%latdeg(g) >= 0._r8) .or. &
-                  ((month > 9 .or.  month < 4) .and. grc%latdeg(g) <  0._r8)     ) then
-                rbufslp(p) = max(0._r8, min(30._r8, &
-                     this%t_ref2m_patch(p)-(SHR_CONST_TKFRZ + 10._r8))) * dtime/SHR_CONST_CDAY
-             else
-                rbufslp(p) = 0._r8      ! keeps gdd unchanged at other times (eg, through Dec in NH)
-             end if
-          end if
-       end do
-       call update_accum_field  ('GDD10', rbufslp, nstep)
-       call extract_accum_field ('GDD10', this%gdd10_patch, nstep)
-
-    end if
-
-    deallocate(rbufslp)
-
-  end subroutine UpdateAccVars
-
 end module TemperatureType
diff --git a/src/biogeophys/TridiagonalMod.F90 b/src/biogeophys/TridiagonalMod.F90
deleted file mode 100644
index 68dbd71cce..0000000000
--- a/src/biogeophys/TridiagonalMod.F90
+++ /dev/null
@@ -1,118 +0,0 @@
-module TridiagonalMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Tridiagonal matrix solution
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: Tridiagonal
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Tridiagonal (bounds, lbj, ubj, jtop, numf, filter, a, b, c, r, u)
-    !
-    ! !DESCRIPTION:
-    ! Tridiagonal matrix solution
-    !
-    ! !USES:
-    use shr_kind_mod   , only : r8 => shr_kind_r8
-    use shr_log_mod    , only : errMsg => shr_log_errMsg
-    use clm_varpar     , only : nlevurb
-    use column_varcon  , only : icol_roof, icol_sunwall, icol_shadewall
-    use clm_varctl     , only : iulog
-    use decompMod      , only : bounds_type
-    use ColumnType     , only : col                
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds             
-    integer , intent(in)    :: lbj, ubj                 ! lbinning and ubing level indices
-    integer , intent(in)    :: jtop( bounds%begc: )     ! top level for each column [col]
-    integer , intent(in)    :: numf                     ! filter dimension
-    integer , intent(in)    :: filter(:)                ! filter
-    real(r8), intent(in)    :: a( bounds%begc: , lbj: ) ! "a" left off diagonal of tridiagonal matrix [col, j]
-    real(r8), intent(in)    :: b( bounds%begc: , lbj: ) ! "b" diagonal column for tridiagonal matrix [col, j]
-    real(r8), intent(in)    :: c( bounds%begc: , lbj: ) ! "c" right off diagonal tridiagonal matrix [col, j]
-    real(r8), intent(in)    :: r( bounds%begc: , lbj: ) ! "r" forcing term of tridiagonal matrix [col, j]
-    real(r8), intent(inout) :: u( bounds%begc: , lbj: ) ! solution [col, j]
-    !
-    integer  :: j,ci,fc                   !indices
-    real(r8) :: gam(bounds%begc:bounds%endc,lbj:ubj)      !temporary
-    real(r8) :: bet(bounds%begc:bounds%endc)              !temporary
-    !-----------------------------------------------------------------------
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(jtop) == (/bounds%endc/)),      errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(a)    == (/bounds%endc, ubj/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(b)    == (/bounds%endc, ubj/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(c)    == (/bounds%endc, ubj/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(r)    == (/bounds%endc, ubj/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(u)    == (/bounds%endc, ubj/)), errMsg(sourcefile, __LINE__))
-
-    ! Solve the matrix
-
-    do fc = 1,numf
-       ci = filter(fc)
-       bet(ci) = b(ci,jtop(ci))
-    end do
-
-    do j = lbj, ubj
-       do fc = 1,numf
-          ci = filter(fc)
-          if ((col%itype(ci) == icol_sunwall .or. col%itype(ci) == icol_shadewall &
-              .or. col%itype(ci) == icol_roof) .and. j <= nlevurb) then
-             if (j >= jtop(ci)) then
-                if (j == jtop(ci)) then
-                   u(ci,j) = r(ci,j) / bet(ci)
-                else
-                   gam(ci,j) = c(ci,j-1) / bet(ci)
-                   bet(ci) = b(ci,j) - a(ci,j) * gam(ci,j)
-                   u(ci,j) = (r(ci,j) - a(ci,j)*u(ci,j-1)) / bet(ci)
-                end if
-             end if
-          else if (col%itype(ci) /= icol_sunwall .and. col%itype(ci) /= icol_shadewall &
-                   .and. col%itype(ci) /= icol_roof) then
-             if (j >= jtop(ci)) then
-                if (j == jtop(ci)) then
-                   u(ci,j) = r(ci,j) / bet(ci)
-                else
-                   gam(ci,j) = c(ci,j-1) / bet(ci)
-                   bet(ci) = b(ci,j) - a(ci,j) * gam(ci,j)
-                   u(ci,j) = (r(ci,j) - a(ci,j)*u(ci,j-1)) / bet(ci)
-                end if
-             end if
-          end if
-       end do
-    end do
-
-    do j = ubj-1,lbj,-1
-       do fc = 1,numf
-          ci = filter(fc)
-          if ((col%itype(ci) == icol_sunwall .or. col%itype(ci) == icol_shadewall &
-              .or. col%itype(ci) == icol_roof) .and. j <= nlevurb-1) then
-             if (j >= jtop(ci)) then
-                u(ci,j) = u(ci,j) - gam(ci,j+1) * u(ci,j+1)
-             end if
-          else if (col%itype(ci) /= icol_sunwall .and. col%itype(ci) /= icol_shadewall &
-                   .and. col%itype(ci) /= icol_roof) then
-             if (j >= jtop(ci)) then
-                u(ci,j) = u(ci,j) - gam(ci,j+1) * u(ci,j+1)
-             end if
-          end if
-       end do
-    end do
-
-  end subroutine Tridiagonal
-
-end module TridiagonalMod
diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90
deleted file mode 100644
index eaf1c14c36..0000000000
--- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90
+++ /dev/null
@@ -1,938 +0,0 @@
-module UrbBuildTempOleson2015Mod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculates internal building air temperature
-  !
-  ! !USES:
-  use shr_kind_mod      , only : r8 => shr_kind_r8
-  use shr_log_mod       , only : errMsg => shr_log_errMsg
-  use decompMod         , only : bounds_type
-  use abortutils        , only : endrun
-  use perf_mod          , only : t_startf, t_stopf
-  use clm_varctl        , only : iulog
-  use UrbanParamsType   , only : urbanparams_type
-  use UrbanTimeVarType  , only : urbantv_type  
-  use EnergyFluxType    , only : energyflux_type
-  use TemperatureType   , only : temperature_type
-  use LandunitType      , only : lun                
-  use ColumnType        , only : col                
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  save
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public  :: BuildingTemperature ! Calculation of interior building air temperature, inner 
-                                 ! surface temperatures of walls and roof, and floor temperature
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: BuildingTemperature
-!
-! !INTERFACE:
-  subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, &
-                                  filter_nolakec, tk, urbanparams_inst, temperature_inst, &
-                                  energyflux_inst, urbantv_inst)
-!
-! !DESCRIPTION:
-! Solve for t_building, inner surface temperatures of roof, sunw, shdw, and floor temperature
-! Five equations, five unknowns (t_roof_inner,t_sunw_inner,t_shdw_inner,t_floor,t_building at n+1)
-! Derived from energy balance equations at each surface and building air
-! rd (radiation), cd (conduction), cv (convection)
-! qrd_roof + qcd_roof + qcv_roof = 0
-! qrd_sunw + qcd_sunw + qcv_sunw = 0
-! qrd_shdw + qcd_shdw + qcv_shdw = 0
-! qrd_floor + qcd_floor + qcv_floor = 0
-! Vbld*rho_dair*cpair*(dt_building/dt) = sum(Asfc*hcv_sfc*(t_sfc - t_building) 
-!                                        + Vvent*rho_dair*cpair*(taf - t_building)
-!   where Vlbd is volume of building air,
-!         rho_dair is density of dry air at t_building (kg m-3),
-!         cpair is specific heat of dry air (J kg-1 K-1),
-!         dt_building is change in interior building temperature (K),
-!         dt is timestep (s),
-!         Asfc is surface area of roof, sunw, shdw, floor (m2)
-!         hcv_sfc is convective heat transfer coefficient for roof, sunw, shdw, floor (W m-2 K-1)
-!         t_sfc is inner surface temperature of roof, sunw, shdw, floor (K)
-!         t_building is interior building temperature (K)
-!         Vvent is ventilation airflow rate (m3 s-1)
-!         taf is urban canyon air temperature (K)
-!
-! This methodology was introduced as part of CLM5.0. 
-!
-! Conduction fluxes are obtained from terms of soil temperature equations
-! Radiation fluxes are obtained from linearizing the longwave radiation equations taking into
-! account view factors for each surface.
-
-! qrd is positive away from the surface toward room air, so qrd = emitted - absorbed,
-!   so positive qrd will result in a decrease in temperature
-! qcd_floor is positive away from surface toward room air, so positive
-!   qcd will result in a decrease in temperature 
-! qcv is positive toward room air, so positive qcv (t_surface > t_room) will 
-!   result in a decrease in temperature
-
-! The LAPACK routine DGESV is used to compute the solution to the real system of linear equations
-!     a * x = b,
-!  where a is an n-by-n matrix and x and b are n-by-nrhs matrices.
-! 
-!  The LU decomposition with partial pivoting and row interchanges is
-!  used to factor a as
-!     a = P * L * U,
-!  where P is a permutation matrix, L is unit lower triangular, and U is
-!  upper triangular.  The factored form of a is then used to solve the
-!  system of equations a * x = b.
-
-! The following is from LAPACK documentation
-! DGESV computes the solution to system of linear equations A * X = B for GE matrices
-!
-!  =========== DOCUMENTATION ===========
-!
-! Online html documentation available at 
-!            http://www.netlib.org/lapack/explore-html/ 
-!
-!  Download DGESV + dependencies 
-!  <a href="http://www.netlib.org/cgi-bin/netlibfiles.tgz?format=tgz&filename=/lapack/lapack_routine/dgesv.f"> 
-!  [TGZ]</a> 
-!  <a href="http://www.netlib.org/cgi-bin/netlibfiles.zip?format=zip&filename=/lapack/lapack_routine/dgesv.f"> 
-!  [ZIP]</a> 
-!  <a href="http://www.netlib.org/cgi-bin/netlibfiles.txt?format=txt&filename=/lapack/lapack_routine/dgesv.f"> 
-!  [TXT]</a>
-!
-!  Definition:
-!  ===========
-!
-!       SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO )
-! 
-!       .. Scalar Arguments ..
-!       INTEGER            INFO, LDA, LDB, N, NRHS
-!       ..
-!       .. Array Arguments ..
-!       INTEGER            IPIV( * )
-!       DOUBLE PRECISION   A( LDA, * ), B( LDB, * )
-!       ..
-!  
-!
-!  =============
-! 
-! 
-!  DGESV computes the solution to a real system of linear equations
-!     A * X = B,
-!  where A is an N-by-N matrix and X and B are N-by-NRHS matrices.
-! 
-!  The LU decomposition with partial pivoting and row interchanges is
-!  used to factor A as
-!     A = P * L * U,
-!  where P is a permutation matrix, L is unit lower triangular, and U is
-!  upper triangular.  The factored form of A is then used to solve the
-!  system of equations A * X = B.
-!
-!  Arguments:
-!  ==========
-!
-!  \param[in] N
-!           N is INTEGER
-!           The number of linear equations, i.e., the order of the
-!           matrix A.  N >= 0.
-! 
-!  \param[in] NRHS
-!           NRHS is INTEGER
-!           The number of right hand sides, i.e., the number of columns
-!           of the matrix B.  NRHS >= 0.
-! 
-!  \param[in,out] A
-!           A is DOUBLE PRECISION array, dimension (LDA,N)
-!           On entry, the N-by-N coefficient matrix A.
-!           On exit, the factors L and U from the factorization
-!           A = P*L*U; the unit diagonal elements of L are not stored.
-! 
-!  \param[in] LDA
-!           LDA is INTEGER
-!           The leading dimension of the array A.  LDA >= max(1,N).
-! 
-!  \param[out] IPIV
-!           IPIV is INTEGER array, dimension (N)
-!           The pivot indices that define the permutation matrix P;
-!           row i of the matrix was interchanged with row IPIV(i).
-! 
-!  \param[in,out] B
-!           B is DOUBLE PRECISION array, dimension (LDB,NRHS)
-!           On entry, the N-by-NRHS matrix of right hand side matrix B.
-!           On exit, if INFO = 0, the N-by-NRHS solution matrix X.
-! 
-!  \param[in] LDB
-!           LDB is INTEGER
-!           The leading dimension of the array B.  LDB >= max(1,N).
-! 
-!  \param[out] INFO
-!           INFO is INTEGER
-!           = 0:  successful exit
-!           < 0:  if INFO = -i, the i-th argument had an illegal value
-!           > 0:  if INFO = i, U(i,i) is exactly zero.  The factorization
-!                 has been completed, but the factor U is exactly
-!                 singular, so the solution could not be computed.
-!
-!  Authors:
-!  ========
-!
-!  \author Univ. of Tennessee 
-!  \author Univ. of California Berkeley 
-!  \author Univ. of Colorado Denver 
-!  \author NAG Ltd. 
-!
-!  \date November 2011
-!
-!  \ingroup doubleGEsolve
-
-! !CALLED FROM:
-! subroutine SoilTemperature in this module
-!
-! !REVISION HISTORY:
-! 08/17/12 Keith Oleson: Initial code
-
-!
-! !USES:
-    use shr_kind_mod    , only : r8 => shr_kind_r8
-    use clm_time_manager, only : get_step_size
-    use clm_varcon      , only : rair, pstd, cpair, sb, hcv_roof, hcv_roof_enhanced, &
-                                 hcv_floor, hcv_floor_enhanced, hcv_sunw, hcv_shdw, &
-                                 em_roof_int, em_floor_int, em_sunw_int, em_shdw_int, &
-                                 dz_floor, dens_floor, cp_floor, vent_ach
-    use column_varcon   , only : icol_roof, icol_sunwall, icol_shadewall
-    use clm_varctl      , only : iulog
-    use abortutils      , only : endrun
-    use clm_varpar      , only : nlevurb, nlevsno, nlevgrnd
-    use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on
-!
-! !ARGUMENTS:
-    implicit none
-    type(bounds_type), intent(in) :: bounds                   ! bounds
-    integer , intent(in)  :: num_nolakec                      ! number of column non-lake points in column filter
-    integer , intent(in)  :: filter_nolakec(:)                ! column filter for non-lake points
-    integer , intent(in)  :: num_urbanl                       ! number of urban landunits in clump
-    integer , intent(in)  :: filter_urbanl(:)                 ! urban landunit filter
-    real(r8), intent(in)  :: tk(bounds%begc: , -nlevsno+1: )  ! thermal conductivity (W m-1 K-1) [col, j]
-    type(urbanparams_type), intent(in)    :: urbanparams_inst ! urban parameters
-    type(temperature_type), intent(inout) :: temperature_inst ! temperature variables
-    type(energyflux_type) , intent(inout) :: energyflux_inst  ! energy flux variables
-    type(urbantv_type)    , intent(in)    :: urbantv_inst     ! urban time varying variables
-!
-! !LOCAL VARIABLES:
-    integer, parameter :: neq = 5          ! number of equation/unknowns
-    integer  :: fc,fl,c,l                  ! indices
-    real(r8) :: dtime                      ! land model time step (s)
-    real(r8) :: t_roof_inner_bef(bounds%begl:bounds%endl)  ! roof inside surface temperature at previous time step (K)              
-    real(r8) :: t_sunw_inner_bef(bounds%begl:bounds%endl)  ! sunwall inside surface temperature at previous time step (K)              
-    real(r8) :: t_shdw_inner_bef(bounds%begl:bounds%endl)  ! shadewall inside surface temperature at previous time step (K)              
-    real(r8) :: t_floor_bef(bounds%begl:bounds%endl)       ! floor temperature at previous time step (K)              
-    real(r8) :: t_building_bef(bounds%begl:bounds%endl)    ! internal building air temperature at previous time step [K]
-    real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K]
-    real(r8) :: hcv_roofi(bounds%begl:bounds%endl)         ! roof convective heat transfer coefficient (W m-2 K-1)
-    real(r8) :: hcv_sunwi(bounds%begl:bounds%endl)         ! sunwall convective heat transfer coefficient (W m-2 K-1)
-    real(r8) :: hcv_shdwi(bounds%begl:bounds%endl)         ! shadewall convective heat transfer coefficient (W m-2 K-1)
-    real(r8) :: hcv_floori(bounds%begl:bounds%endl)        ! floor convective heat transfer coefficient (W m-2 K-1)
-    real(r8) :: em_roofi(bounds%begl:bounds%endl)          ! roof inside surface emissivity (-)
-    real(r8) :: em_sunwi(bounds%begl:bounds%endl)          ! sunwall inside surface emissivity (-)
-    real(r8) :: em_shdwi(bounds%begl:bounds%endl)          ! shadewall inside surface emissivity (-)
-    real(r8) :: em_floori(bounds%begl:bounds%endl)         ! floor inside surface emissivity (-)
-    real(r8) :: dz_floori(bounds%begl:bounds%endl)         ! concrete floor thickness (m)
-    real(r8) :: cp_floori(bounds%begl:bounds%endl)         ! concrete floor volumetric heat capacity (J m-3 K-1)
-    real(r8) :: cv_floori(bounds%begl:bounds%endl)         ! intermediate calculation for concrete floor (W m-2 K-1)
-    real(r8) :: rho_dair(bounds%begl:bounds%endl)          ! density of dry air at standard pressure and t_building (kg m-3)
-    real(r8) :: vf_rf(bounds%begl:bounds%endl)             ! view factor of roof for floor (-)
-    real(r8) :: vf_fr(bounds%begl:bounds%endl)             ! view factor of floor for roof (-)
-    real(r8) :: vf_wf(bounds%begl:bounds%endl)             ! view factor of wall for floor (-)
-    real(r8) :: vf_fw(bounds%begl:bounds%endl)             ! view factor of floor for wall (-)
-    real(r8) :: vf_rw(bounds%begl:bounds%endl)             ! view factor of roof for wall (-)
-    real(r8) :: vf_wr(bounds%begl:bounds%endl)             ! view factor of wall for roof (-)
-    real(r8) :: vf_ww(bounds%begl:bounds%endl)             ! view factor of wall for wall (-)
-    real(r8) :: zi_roof_innerl(bounds%begl:bounds%endl)    ! interface depth of nlevurb roof (m)
-    real(r8) :: z_roof_innerl(bounds%begl:bounds%endl)     ! node depth of nlevurb roof (m)
-    real(r8) :: zi_sunw_innerl(bounds%begl:bounds%endl)    ! interface depth of nlevurb sunwall (m)
-    real(r8) :: z_sunw_innerl(bounds%begl:bounds%endl)     ! node depth of nlevurb sunwall (m)
-    real(r8) :: zi_shdw_innerl(bounds%begl:bounds%endl)    ! interface depth of nlevurb shadewall (m)
-    real(r8) :: z_shdw_innerl(bounds%begl:bounds%endl)     ! node depth of nlevurb shadewall (m)
-    real(r8) :: t_roof_innerl_bef(bounds%begl:bounds%endl) ! roof temperature at nlevurb node depth at previous time step (K)
-    real(r8) :: t_sunw_innerl_bef(bounds%begl:bounds%endl) ! sunwall temperature at nlevurb node depth at previous time step (K)
-    real(r8) :: t_shdw_innerl_bef(bounds%begl:bounds%endl) ! shadewall temperature at nlevurb node depth at previous time step (K)
-    real(r8) :: t_roof_innerl(bounds%begl:bounds%endl)     ! roof temperature at nlevurb node depth (K)
-    real(r8) :: t_sunw_innerl(bounds%begl:bounds%endl)     ! sunwall temperature at nlevurb node depth (K)
-    real(r8) :: t_shdw_innerl(bounds%begl:bounds%endl)     ! shadewall temperature at nlevurb node depth (K)
-    real(r8) :: tk_roof_innerl(bounds%begl:bounds%endl)    ! roof thermal conductivity at nlevurb interface depth (W m-1 K-1)
-    real(r8) :: tk_sunw_innerl(bounds%begl:bounds%endl)    ! sunwall thermal conductivity at nlevurb interface depth (W m-1 K-1)
-    real(r8) :: tk_shdw_innerl(bounds%begl:bounds%endl)    ! shadewall thermal conductivity at nlevurb interface depth (W m-1 K-1)
-    real(r8) :: qrd_roof(bounds%begl:bounds%endl)          ! roof inside net longwave for energy balance check (W m-2)
-    real(r8) :: qrd_sunw(bounds%begl:bounds%endl)          ! sunwall inside net longwave for energy balance check (W m-2)
-    real(r8) :: qrd_shdw(bounds%begl:bounds%endl)          ! shadewall inside net longwave for energy balance check (W m-2)
-    real(r8) :: qrd_floor(bounds%begl:bounds%endl)         ! floor inside net longwave for energy balance check (W m-2)
-    real(r8) :: qrd_building(bounds%begl:bounds%endl)      ! building inside net longwave for energy balance check (W m-2)
-    real(r8) :: qcv_roof(bounds%begl:bounds%endl)          ! roof inside convection flux for energy balance check (W m-2)
-    real(r8) :: qcv_sunw(bounds%begl:bounds%endl)          ! sunwall inside convection flux for energy balance check (W m-2)
-    real(r8) :: qcv_shdw(bounds%begl:bounds%endl)          ! shadewall inside convection flux for energy balance check (W m-2)
-    real(r8) :: qcv_floor(bounds%begl:bounds%endl)         ! floor inside convection flux for energy balance check (W m-2)
-    real(r8) :: qcd_roof(bounds%begl:bounds%endl)          ! roof inside conduction flux for energy balance check (W m-2)
-    real(r8) :: qcd_sunw(bounds%begl:bounds%endl)          ! sunwall inside conduction flux for energy balance check (W m-2)
-    real(r8) :: qcd_shdw(bounds%begl:bounds%endl)          ! shadewall inside conduction flux for energy balance check (W m-2)
-    real(r8) :: qcd_floor(bounds%begl:bounds%endl)         ! floor inside conduction flux for energy balance check (W m-2)
-    real(r8) :: enrgy_bal_roof(bounds%begl:bounds%endl)    ! roof inside energy balance (W m-2)
-    real(r8) :: enrgy_bal_sunw(bounds%begl:bounds%endl)    ! sunwall inside energy balance (W m-2)
-    real(r8) :: enrgy_bal_shdw(bounds%begl:bounds%endl)    ! shadewall inside energy balance (W m-2)
-    real(r8) :: enrgy_bal_floor(bounds%begl:bounds%endl)   ! floor inside energy balance (W m-2)
-    real(r8) :: enrgy_bal_buildair(bounds%begl:bounds%endl)! building air energy balance (W m-2)
-    real(r8) :: sum                        ! sum of view factors for floor, wall, roof
-    integer  :: n                          ! number of linear equations (= neq)
-    integer  :: nrhs                       ! number of right hand sides (= 1) 
-    real(r8) :: a(neq,neq)                 ! n-by-n coefficient matrix a
-    integer  :: lda                        ! leading dimension of the matrix a
-    integer  :: ldb                        ! leading dimension of the matrix b
-    real(r8) :: result(neq)                ! on entry, the right hand side of matrix b
-                                           ! on exit, if info = 0, the n-by-nrhs solution matrix x
-    integer  :: info                       ! exit information for LAPACK routine dgesv
-    integer  :: ipiv(neq)                  ! the pivot indices that define the permutation matrix P
-!EOP
-!-----------------------------------------------------------------------
-
-    ! Enforce expected array sizes
-    SHR_ASSERT_ALL((ubound(tk)  == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-
-    associate(&
-    clandunit         => col%landunit                      , & ! Input:  [integer (:)]  column's landunit
-    ctype             => col%itype                         , & ! Input:  [integer (:)]  column type
-    zi                => col%zi                            , & ! Input:  [real(r8) (:,:)]  interface level below a "z" level (m)
-    z                 => col%z                             , & ! Input:  [real(r8) (:,:)]  layer thickness (m)
-
-    ht_roof           => lun%ht_roof                       , & ! Input:  [real(r8) (:)]  height of urban roof (m) 
-    canyon_hwr        => lun%canyon_hwr                    , & ! Input:  [real(r8) (:)]  ratio of building height to street hwidth (-)
-    wtlunit_roof      => lun%wtlunit_roof                  , & ! Input:  [real(r8) (:)]  weight of roof with respect to landunit
-    urbpoi            => lun%urbpoi                        , & ! Input:  [logical (:)]  true => landunit is an urban point
-
-    taf               => temperature_inst%taf_lun          , & ! Input:  [real(r8) (:)]  urban canopy air temperature (K)
-    tssbef            => temperature_inst%t_ssbef_col      , & ! Input:  [real(r8) (:,:)]  temperature at previous time step (K)
-    t_soisno          => temperature_inst%t_soisno_col     , & ! Input:  [real(r8) (:,:)]  soil temperature (K)
-    t_roof_inner      => temperature_inst%t_roof_inner_lun , & ! InOut:  [real(r8) (:)]  roof inside surface temperature (K)
-    t_sunw_inner      => temperature_inst%t_sunw_inner_lun , & ! InOut:  [real(r8) (:)]  sunwall inside surface temperature (K)
-    t_shdw_inner      => temperature_inst%t_shdw_inner_lun , & ! InOut:  [real(r8) (:)]  shadewall inside surface temperature (K)
-    t_floor           => temperature_inst%t_floor_lun      , & ! InOut:  [real(r8) (:)]  floor temperature (K)
-    t_building        => temperature_inst%t_building_lun   , & ! InOut:  [real(r8) (:)]  internal building air temperature (K)
-
-    t_building_max    => urbantv_inst%t_building_max       , & ! Input:  [real(r8) (:)]  maximum internal building air temperature (K)
-    t_building_min    => urbanparams_inst%t_building_min   , & ! Input:  [real(r8) (:)]  minimum internal building air temperature (K)
-
-    eflx_building     => energyflux_inst%eflx_building_lun , & ! Output:  [real(r8) (:)]  building heat flux from change in interior building air temperature (W/m**2)
-    eflx_urban_ac     => energyflux_inst%eflx_urban_ac_lun , & ! Output:  [real(r8) (:)]  urban air conditioning flux (W/m**2)
-    eflx_urban_heat   => energyflux_inst%eflx_urban_heat_lun & ! Output:  [real(r8) (:)]  urban heating flux (W/m**2)
-    )
-
-    ! Get step size
-
-    dtime = get_step_size()
-
-    ! 1. Save t_* at previous time step
-    ! 2. Set convective heat transfer coefficients (Bueno et al. 2012, GMD).
-    !    An alternative is Salamanca et al. 2010, TAC, where they are all set to 8 W m-2 K-1.
-    !    See clm_varcon.F90
-    ! 3. Set inner surface emissivities (Bueno et al. 2012, GMD).
-    ! 4. Set concrete floor properties (Salamanca et al. 2010, TAC).
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-         t_roof_inner_bef(l)  = t_roof_inner(l)
-         t_sunw_inner_bef(l)  = t_sunw_inner(l)
-         t_shdw_inner_bef(l)  = t_shdw_inner(l)
-         t_floor_bef(l)       = t_floor(l)
-         t_building_bef(l)    = t_building(l)
-         if (t_roof_inner_bef(l) .le. t_building_bef(l)) then
-           hcv_roofi(l) = hcv_roof_enhanced
-         else
-           hcv_roofi(l) = hcv_roof
-         end if
-         if (t_floor_bef(l) .ge. t_building_bef(l)) then
-           hcv_floori(l) = hcv_floor_enhanced
-         else
-           hcv_floori(l) = hcv_floor
-         end if
-         hcv_sunwi(l) = hcv_sunw
-         hcv_shdwi(l) = hcv_shdw
-         em_roofi(l)  = em_roof_int
-         em_sunwi(l)  = em_sunw_int
-         em_shdwi(l)  = em_shdw_int
-         em_floori(l) = em_floor_int
-         ! Concrete floor thickness (m)
-         dz_floori(l) = dz_floor
-         ! Concrete floor volumetric heat capacity (J m-3 K-1)
-         cp_floori(l) = cp_floor
-         ! Intermediate calculation for concrete floor (W m-2 K-1)
-         cv_floori(l) = (dz_floori(l) * cp_floori(l)) / dtime
-         ! Density of dry air at standard pressure and t_building (kg m-3)
-         rho_dair(l) = pstd / (rair*t_building_bef(l))
-       end if
-    end do
-
-    ! Get terms from soil temperature equations to compute conduction flux
-    ! Negative is toward surface - heat added
-    ! Note that the conduction flux here is in W m-2 wall area but for purposes of solving the set of
-    ! simultaneous equations this must be converted to W m-2 ground area. This is done below when 
-    ! setting up the equation coefficients.
-
-    do fc = 1,num_nolakec
-       c = filter_nolakec(fc)
-       l = clandunit(c)
-       if (urbpoi(l)) then
-         if (ctype(c) == icol_roof) then
-           zi_roof_innerl(l) = zi(c,nlevurb)
-           z_roof_innerl(l) = z(c,nlevurb)
-           t_roof_innerl_bef(l) = tssbef(c,nlevurb)
-           t_roof_innerl(l) = t_soisno(c,nlevurb)
-           tk_roof_innerl(l) = tk(c,nlevurb)
-         else if (ctype(c) == icol_sunwall) then
-           zi_sunw_innerl(l) = zi(c,nlevurb)
-           z_sunw_innerl(l) = z(c,nlevurb)
-           t_sunw_innerl_bef(l) = tssbef(c,nlevurb)
-           t_sunw_innerl(l) = t_soisno(c,nlevurb)
-           tk_sunw_innerl(l) = tk(c,nlevurb)
-         else if (ctype(c) == icol_shadewall) then
-           zi_shdw_innerl(l) = zi(c,nlevurb)
-           z_shdw_innerl(l) = z(c,nlevurb)
-           t_shdw_innerl_bef(l) = tssbef(c,nlevurb)
-           t_shdw_innerl(l) = t_soisno(c,nlevurb)
-           tk_shdw_innerl(l) = tk(c,nlevurb)
-         end if
-       end if
-    end do
-
-    ! Calculate view factors
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-
-         vf_rf(l) = sqrt(1._r8 + canyon_hwr(l)**2._r8) - canyon_hwr(l)
-         vf_fr(l) = vf_rf(l)
-
-         ! This view factor implicitly converts from per unit wall area to per unit floor area
-         vf_wf(l)  = 0.5_r8*(1._r8 - vf_rf(l))
-
-         ! This view factor implicitly converts from per unit floor area to per unit wall area
-         vf_fw(l) = vf_wf(l) / canyon_hwr(l)
-
-         ! This view factor implicitly converts from per unit roof area to per unit wall area
-         vf_rw(l)  = vf_fw(l)
-
-         ! This view factor implicitly converts from per unit wall area to per unit roof area
-         vf_wr(l)  = vf_wf(l)
-
-         vf_ww(l)  = 1._r8 - vf_rw(l) - vf_fw(l)
-
-      end if
-    end do
-
-    ! error check -- make sure view factor sums to one for floor, wall, and roof
-
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-
-         sum = vf_rf(l) + 2._r8*vf_wf(l)
-         if (abs(sum-1._r8) > 1.e-06_r8 ) then
-            write (iulog,*) 'urban floor view factor error',sum
-            write (iulog,*) 'clm model is stopping'
-            call endrun()
-         endif
-         sum = vf_rw(l) + vf_fw(l) + vf_ww(l)
-         if (abs(sum-1._r8) > 1.e-06_r8 ) then
-            write (iulog,*) 'urban wall view factor error',sum
-            write (iulog,*) 'clm model is stopping'
-            call endrun()
-         endif
-         sum = vf_fr(l) + vf_wr(l) + vf_wr(l)
-         if (abs(sum-1._r8) > 1.e-06_r8 ) then
-            write (iulog,*) 'urban roof view factor error',sum
-            write (iulog,*) 'clm model is stopping'
-            call endrun()
-         endif
-
-       endif
-    end do
-
-    n = neq
-    nrhs = 1
-    lda = neq
-    ldb = neq
-
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-
-         ! ROOF
-         a(1,1) =   0.5_r8*hcv_roofi(l) &
-                  + 0.5_r8*tk_roof_innerl(l)/(zi_roof_innerl(l) - z_roof_innerl(l)) &
-                  + 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8 &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fr(l)
-
-         a(1,2) = - 4._r8*em_roofi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wr(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l)
-
-         a(1,3) = - 4._r8*em_roofi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wr(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l)
-
-         a(1,4) = - 4._r8*em_roofi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fr(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wr(l)
-
-         a(1,5) = - 0.5_r8*hcv_roofi(l)
-
-         result(1) =   0.5_r8*tk_roof_innerl(l)*t_roof_innerl(l)/(zi_roof_innerl(l) - z_roof_innerl(l)) &
-                     - 0.5_r8*tk_roof_innerl(l)*(t_roof_inner_bef(l)-t_roof_innerl_bef(l))/(zi_roof_innerl(l) &
-                     - z_roof_innerl(l)) &
-                     - 3._r8*em_roofi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wr(l) &
-                     - 3._r8*em_roofi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wr(l) &
-                     - 3._r8*em_roofi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fr(l) &
-                     + 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8 &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                     - 0.5_r8*hcv_roofi(l)*(t_roof_inner_bef(l) - t_building_bef(l))
-
-         ! SUNWALL
-         a(2,1) = - 4._r8*em_sunwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l)
-
-         a(2,2) =   0.5_r8*hcv_sunwi(l)*canyon_hwr(l) &
-                  + 0.5_r8*tk_sunw_innerl(l)/(zi_sunw_innerl(l) - z_sunw_innerl(l))*canyon_hwr(l) &
-                  + 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8 &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)
-
-         a(2,3) = - 4._r8*em_sunwi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)
-
-         a(2,4) = - 4._r8*em_sunwi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_ww(l)
-         a(2,5) = - 0.5_r8*hcv_sunwi(l)*canyon_hwr(l)
-
-         result(2) =   0.5_r8*tk_sunw_innerl(l)*t_sunw_innerl(l)/(zi_sunw_innerl(l) - z_sunw_innerl(l))*canyon_hwr(l) &
-                     - 0.5_r8*tk_sunw_innerl(l)*(t_sunw_inner_bef(l)-t_sunw_innerl_bef(l))/(zi_sunw_innerl(l) &
-                     - z_sunw_innerl(l))*canyon_hwr(l) &
-                     - 3._r8*em_sunwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l) &
-                     - 3._r8*em_sunwi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_ww(l) &
-                     - 3._r8*em_sunwi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l) &
-                     + 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8 &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                     - 0.5_r8*hcv_sunwi(l)*(t_sunw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l)
-
-         ! SHADEWALL
-         a(3,1) = - 4._r8*em_shdwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l)
-
-         a(3,2) = - 4._r8*em_shdwi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)
-
-         a(3,3) =   0.5_r8*hcv_shdwi(l)*canyon_hwr(l) &
-                  + 0.5_r8*tk_shdw_innerl(l)/(zi_shdw_innerl(l) - z_shdw_innerl(l))*canyon_hwr(l) &
-                  + 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8 &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)
-
-         a(3,4) = - 4._r8*em_shdwi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_ww(l)
-
-         a(3,5) = - 0.5_r8*hcv_shdwi(l)*canyon_hwr(l)
-
-         result(3) =   0.5_r8*tk_shdw_innerl(l)*t_shdw_innerl(l)/(zi_shdw_innerl(l) - z_shdw_innerl(l))*canyon_hwr(l) &
-                     - 0.5_r8*tk_shdw_innerl(l)*(t_shdw_inner_bef(l)-t_shdw_innerl_bef(l))/(zi_shdw_innerl(l) &
-                     - z_shdw_innerl(l))*canyon_hwr(l) &
-                     - 3._r8*em_shdwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l) &
-                     - 3._r8*em_shdwi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_ww(l) &
-                     - 3._r8*em_shdwi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l) &
-                     + 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8 &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                     - 0.5_r8*hcv_shdwi(l)*(t_shdw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l)
-
-         ! FLOOR
-         a(4,1) = - 4._r8*em_floori(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                  - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wf(l)
-
-         a(4,2) = - 4._r8*em_floori(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                  - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l)
-
-         a(4,3) = - 4._r8*em_floori(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                  - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wf(l)
-
-         a(4,4) =   (cv_floori(l) + 0.5_r8*hcv_floori(l)) &
-                  + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8 &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                  - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wf(l)
-
-         a(4,5) = - 0.5_r8*hcv_floori(l)
-
-         result(4) =   cv_floori(l)*t_floor_bef(l) &
-                     - 3._r8*em_floori(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rf(l) &
-                     - 3._r8*em_floori(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wf(l) &
-                     - 3._r8*em_floori(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wf(l) &
-                     + 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8 &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                     - 3._r8*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                     - 3._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                     - 3._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                     - 3._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                     - 0.5_r8*hcv_floori(l)*(t_floor_bef(l) - t_building_bef(l))
-
-         ! Building air temperature
-         a(5,1) = - 0.5_r8*hcv_roofi(l)
-         a(5,2) = - 0.5_r8*hcv_sunwi(l)*canyon_hwr(l)
-
-         a(5,3) = - 0.5_r8*hcv_shdwi(l)*canyon_hwr(l)
-
-         a(5,4) = - 0.5_r8*hcv_floori(l)
-
-         a(5,5) =  ((ht_roof(l)*rho_dair(l)*cpair)/dtime) + &
-                   ((ht_roof(l)*vent_ach)/3600._r8)*rho_dair(l)*cpair + &
-                   0.5_r8*hcv_roofi(l) + &
-                   0.5_r8*hcv_sunwi(l)*canyon_hwr(l) + &
-                   0.5_r8*hcv_shdwi(l)*canyon_hwr(l) + &
-                   0.5_r8*hcv_floori(l)
-
-         result(5) = (ht_roof(l)*rho_dair(l)*cpair/dtime)*t_building_bef(l) &
-                      + ((ht_roof(l)*vent_ach)/3600._r8)*rho_dair(l)*cpair*taf(l) &
-                      + 0.5_r8*hcv_roofi(l)*(t_roof_inner_bef(l) - t_building_bef(l)) &
-                      + 0.5_r8*hcv_sunwi(l)*(t_sunw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l) &
-                      + 0.5_r8*hcv_shdwi(l)*(t_shdw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l) &
-                      + 0.5_r8*hcv_floori(l)*(t_floor_bef(l) - t_building_bef(l))
-
-         ! Solve equations
-         call dgesv(n, nrhs, a, lda, ipiv, result, ldb, info)
-
-         ! If dgesv fails, abort 
-         if (info /= 0) then
-           write(iulog,*)'fl: ',fl
-           write(iulog,*)'l: ',l
-           write(iulog,*)'dgesv info: ',info
-           write (iulog,*) 'dgesv error'
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-         ! Assign new temperatures
-         t_roof_inner(l)  = result(1)
-         t_sunw_inner(l)  = result(2)
-         t_shdw_inner(l)  = result(3)
-         t_floor(l) = result(4)
-         t_building(l)    = result(5)
-       end if
-    end do
-
-    ! Energy balance checks
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-         qrd_roof(l) = - em_roofi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wr(l) &
-                       - 4._r8*em_roofi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wr(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - em_roofi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wr(l) &
-                       - 4._r8*em_roofi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wr(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - em_roofi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fr(l) &
-                       - 4._r8*em_roofi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fr(l)*(t_floor(l) - t_floor_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wr(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wr(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l)*(1._r8-em_floori(l))*vf_fr(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wr(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wr(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l)*(1._r8-em_floori(l))*vf_fr(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wr(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wr(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wr(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wr(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       + em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8 &
-                       + 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*(t_roof_inner(l) - t_roof_inner_bef(l)) 
-
-         qrd_sunw(l) = - em_sunwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l) &
-                       - 4._r8*em_sunwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - em_sunwi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_ww(l)  &
-                       - 4._r8*em_sunwi(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_ww(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - em_sunwi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l) &
-                       - 4._r8*em_sunwi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(t_floor(l) - t_floor_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_ww(l)*(1._r8-em_shdwi(l))*vf_ww(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rw(l)*(1._r8-em_shdwi(l))*vf_ww(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_shdwi(l))*vf_ww(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fw(l)*(1._r8-em_shdwi(l))*vf_ww(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       + em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8 &
-                       + 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*(t_sunw_inner(l) - t_sunw_inner_bef(l))
-
-         qrd_shdw(l) = - em_shdwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rw(l) &
-                       - 4._r8*em_shdwi(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rw(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - em_shdwi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_ww(l) &
-                       - 4._r8*em_shdwi(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_ww(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - em_shdwi(l)*em_floori(l)*sb*t_floor_bef(l)**4._r8*vf_fw(l) &
-                       - 4._r8*em_shdwi(l)*em_floori(l)*sb*t_floor_bef(l)**3._r8*vf_fw(l)*(t_floor(l) - t_floor_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_ww(l)*(1._r8-em_sunwi(l))*vf_ww(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_shdw_inner(l) &
-                       - t_shdw_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_wf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_sunw_inner(l) &
-                       - t_sunw_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rw(l)*(1._r8-em_sunwi(l))*vf_ww(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l) &
-                       - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rf(l)*(1._r8-em_floori(l))*vf_fw(l)*(t_roof_inner(l) &
-                       - t_roof_inner_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fr(l)*(1._r8-em_roofi(l))*vf_rw(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_sunwi(l))*vf_ww(l) &
-                       - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fw(l)*(1._r8-em_sunwi(l))*vf_ww(l)*(t_floor(l) &
-                       - t_floor_bef(l)) &
-                       + em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8 &
-                       + 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*(t_shdw_inner(l) - t_shdw_inner_bef(l))
-
-         qrd_floor(l) = - em_floori(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8*vf_rf(l) &
-                        - 4._r8*em_floori(l)*em_roofi(l)*sb*t_roof_inner_bef(l)**3._r8*vf_rf(l)*(t_roof_inner(l) &
-                        - t_roof_inner_bef(l)) &
-                        - em_floori(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8*vf_wf(l) &
-                        - 4._r8*em_floori(l)*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3._r8*vf_wf(l)*(t_sunw_inner(l) &
-                        - t_sunw_inner_bef(l)) &
-                        - em_floori(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8*vf_wf(l) &
-                        - 4._r8*em_floori(l)*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3._r8*vf_wf(l)*(t_shdw_inner(l) &
-                        - t_shdw_inner_bef(l)) &
-                        - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                        - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fr(l)*(1._r8-em_roofi(l))*vf_rf(l)*(t_floor(l) &
-                        - t_floor_bef(l)) &
-                        - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                        - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fw(l)*(1._r8-em_sunwi(l))*vf_wf(l)*(t_floor(l) &
-                        - t_floor_bef(l)) &
-                        - (em_floori(l)*sb*t_floor_bef(l)**4._r8)*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                        - 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*vf_fw(l)*(1._r8-em_shdwi(l))*vf_wf(l)*(t_floor(l) &
-                        - t_floor_bef(l)) &
-                        - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                        - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_ww(l)*(1._r8-em_shdwi(l))*vf_wf(l)*(t_sunw_inner(l) &
-                        - t_sunw_inner_bef(l)) &
-                        - (em_sunwi(l)*sb*t_sunw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                        - 4._r8*em_sunwi(l)*sb*t_sunw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l)*(t_sunw_inner(l) &
-                        - t_sunw_inner_bef(l)) &
-                        - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l) &
-                        - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_wr(l)*(1._r8-em_roofi(l))*vf_rf(l)*(t_shdw_inner(l) &
-                        - t_shdw_inner_bef(l)) &
-                        - (em_shdwi(l)*sb*t_shdw_inner_bef(l)**4._r8)*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                        - 4._r8*em_shdwi(l)*sb*t_shdw_inner_bef(l)**3.*vf_ww(l)*(1._r8-em_sunwi(l))*vf_wf(l)*(t_shdw_inner(l) &
-                        - t_shdw_inner_bef(l)) &
-                        - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wf(l) &
-                        - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rw(l)*(1._r8-em_sunwi(l))*vf_wf(l)*(t_roof_inner(l) &
-                        - t_roof_inner_bef(l)) &
-                        - (em_roofi(l)*sb*t_roof_inner_bef(l)**4._r8)*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wf(l) &
-                        - 4._r8*em_roofi(l)*sb*t_roof_inner_bef(l)**3.*vf_rw(l)*(1._r8-em_shdwi(l))*vf_wf(l)*(t_roof_inner(l) &
-                        - t_roof_inner_bef(l)) &
-                        + em_floori(l)*sb*t_floor_bef(l)**4._r8 &
-                        + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l))
-
-         qrd_building(l) = qrd_roof(l) + canyon_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l)
-
-         if (abs(qrd_building(l)) > .10_r8 ) then
-           write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-
-         qcv_roof(l) = 0.5_r8*hcv_roofi(l)*(t_roof_inner(l) - t_building(l)) + 0.5_r8*hcv_roofi(l)*(t_roof_inner_bef(l) &
-                       - t_building_bef(l))
-         qcd_roof(l) = 0.5_r8*tk_roof_innerl(l)*(t_roof_inner(l) - t_roof_innerl(l))/(zi_roof_innerl(l) - z_roof_innerl(l))  &
-                       + 0.5_r8*tk_roof_innerl(l)*(t_roof_inner_bef(l) - t_roof_innerl_bef(l))/(zi_roof_innerl(l) &
-                       - z_roof_innerl(l))
-         enrgy_bal_roof(l) = qrd_roof(l) + qcv_roof(l) + qcd_roof(l)
-         if (abs(enrgy_bal_roof(l)) > .10_r8 ) then
-           write (iulog,*) 'urban inside roof energy balance error ',enrgy_bal_roof(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-
-         qcv_sunw(l) = 0.5_r8*hcv_sunwi(l)*(t_sunw_inner(l) - t_building(l)) + 0.5_r8*hcv_sunwi(l)*(t_sunw_inner_bef(l) &
-                       - t_building_bef(l))
-         qcd_sunw(l) = 0.5_r8*tk_sunw_innerl(l)*(t_sunw_inner(l) - t_sunw_innerl(l))/(zi_sunw_innerl(l) - z_sunw_innerl(l))  &
-                       + 0.5_r8*tk_sunw_innerl(l)*(t_sunw_inner_bef(l) - t_sunw_innerl_bef(l))/(zi_sunw_innerl(l) &
-                       - z_sunw_innerl(l))
-         enrgy_bal_sunw(l) = qrd_sunw(l) + qcv_sunw(l)*canyon_hwr(l) + qcd_sunw(l)*canyon_hwr(l)
-         if (abs(enrgy_bal_sunw(l)) > .10_r8 ) then
-           write (iulog,*) 'urban inside sunwall energy balance error ',enrgy_bal_sunw(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-
-         qcv_shdw(l) = 0.5_r8*hcv_shdwi(l)*(t_shdw_inner(l) - t_building(l)) + 0.5_r8*hcv_shdwi(l)*(t_shdw_inner_bef(l) &
-                       - t_building_bef(l))
-         qcd_shdw(l) = 0.5_r8*tk_shdw_innerl(l)*(t_shdw_inner(l) - t_shdw_innerl(l))/(zi_shdw_innerl(l) - z_shdw_innerl(l))  &
-                       + 0.5_r8*tk_shdw_innerl(l)*(t_shdw_inner_bef(l) - t_shdw_innerl_bef(l))/(zi_shdw_innerl(l) &
-                       - z_shdw_innerl(l))
-         enrgy_bal_shdw(l) = qrd_shdw(l) + qcv_shdw(l)*canyon_hwr(l) + qcd_shdw(l)*canyon_hwr(l)
-         if (abs(enrgy_bal_shdw(l)) > .10_r8 ) then
-           write (iulog,*) 'urban inside shadewall energy balance error ',enrgy_bal_shdw(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-
-         qcv_floor(l) = 0.5_r8*hcv_floori(l)*(t_floor(l) - t_building(l)) + 0.5_r8*hcv_floori(l)*(t_floor_bef(l) &
-                        - t_building_bef(l))
-         qcd_floor(l) = cv_floori(l)*(t_floor(l) - t_floor_bef(l))
-         enrgy_bal_floor(l) = qrd_floor(l) + qcv_floor(l) + qcd_floor(l)
-         if (abs(enrgy_bal_floor(l)) > .10_r8 ) then
-           write (iulog,*) 'urban inside floor energy balance error ',enrgy_bal_floor(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-
-         enrgy_bal_buildair(l) = (ht_roof(l)*rho_dair(l)*cpair/dtime)*(t_building(l) - t_building_bef(l)) &
-                                 - ht_roof(l)*(vent_ach/3600._r8)*rho_dair(l)*cpair*(taf(l) - t_building(l)) &
-                                 - 0.5_r8*hcv_roofi(l)*(t_roof_inner(l) - t_building(l)) &
-                                 - 0.5_r8*hcv_roofi(l)*(t_roof_inner_bef(l) - t_building_bef(l)) &
-                                 - 0.5_r8*hcv_sunwi(l)*(t_sunw_inner(l) - t_building(l))*canyon_hwr(l) &
-                                 - 0.5_r8*hcv_sunwi(l)*(t_sunw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l) &
-                                 - 0.5_r8*hcv_shdwi(l)*(t_shdw_inner(l) - t_building(l))*canyon_hwr(l) &
-                                 - 0.5_r8*hcv_shdwi(l)*(t_shdw_inner_bef(l) - t_building_bef(l))*canyon_hwr(l) &
-                                 - 0.5_r8*hcv_floori(l)*(t_floor(l) - t_building(l)) &
-                                 - 0.5_r8*hcv_floori(l)*(t_floor_bef(l) - t_building_bef(l))
-         if (abs(enrgy_bal_buildair(l)) > .10_r8 ) then
-           write (iulog,*) 'urban building air energy balance error ',enrgy_bal_buildair(l)
-           write (iulog,*) 'clm model is stopping'
-           call endrun()
-         end if
-       end if
-    end do
-
-    ! Restrict internal building air temperature to between min and max
-    ! Calculate heating or air conditioning flux from energy required to change
-    ! internal building air temperature to t_building_min or t_building_max. 
-
-    do fl = 1,num_urbanl
-       l = filter_urbanl(fl)
-       if (urbpoi(l)) then
-          if (trim(urban_hac) == urban_hac_on .or. trim(urban_hac) == urban_wasteheat_on) then
-            t_building_bef_hac(l) = t_building(l)
-!           rho_dair(l) = pstd / (rair*t_building(l))
-
-            if (t_building_bef_hac(l) > t_building_max(l)) then
-              t_building(l) = t_building_max(l)
-              eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-                                 - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-            else if (t_building_bef_hac(l) < t_building_min(l)) then
-              t_building(l) = t_building_min(l)
-              eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) &
-                                   - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) )
-            else
-              eflx_urban_ac(l) = 0._r8
-              eflx_urban_heat(l) = 0._r8
-            end if
-          else
-            eflx_urban_ac(l) = 0._r8
-            eflx_urban_heat(l) = 0._r8
-          end if
-          eflx_building(l) = wtlunit_roof(l) * (ht_roof(l) * rho_dair(l)*cpair/dtime) * (t_building(l) - t_building_bef(l))
-       end if
-    end do
-
-    end associate 
-  end subroutine BuildingTemperature
-
-  !-----------------------------------------------------------------------
-
-end module UrbBuildTempOleson2015Mod
diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90
index 4b4187c3af..858becc368 100644
--- a/src/biogeophys/UrbanParamsType.F90
+++ b/src/biogeophys/UrbanParamsType.F90
@@ -10,7 +10,7 @@ module UrbanParamsType
   use abortutils   , only : endrun
   use decompMod    , only : bounds_type
   use clm_varctl   , only : iulog, fsurdat
-  use clm_varcon   , only : namel, grlnd, spval
+  use clm_varcon   , only : grlnd
   use LandunitType , only : lun                
   !
   implicit none
@@ -18,78 +18,24 @@ module UrbanParamsType
   private
   !
   ! !PUBLIC MEMBER FUNCTIONS:
-  public  :: UrbanReadNML      ! Read in the urban namelist items
   public  :: UrbanInput        ! Read in urban input data
-  public  :: CheckUrban        ! Check validity of urban points
-  public  :: IsSimpleBuildTemp ! If using the simple building temperature method
-  public  :: IsProgBuildTemp   ! If using the prognostic building temperature method
   !
   ! !PRIVATE TYPE
   type urbinp_type
      real(r8), pointer :: canyon_hwr      (:,:)  
      real(r8), pointer :: wtlunit_roof    (:,:)  
      real(r8), pointer :: wtroad_perv     (:,:)  
-     real(r8), pointer :: em_roof         (:,:)   
-     real(r8), pointer :: em_improad      (:,:)  
-     real(r8), pointer :: em_perroad      (:,:)  
-     real(r8), pointer :: em_wall         (:,:)  
-     real(r8), pointer :: alb_roof_dir    (:,:,:)  
-     real(r8), pointer :: alb_roof_dif    (:,:,:)  
-     real(r8), pointer :: alb_improad_dir (:,:,:)  
-     real(r8), pointer :: alb_improad_dif (:,:,:)  
-     real(r8), pointer :: alb_perroad_dir (:,:,:)  
-     real(r8), pointer :: alb_perroad_dif (:,:,:)  
-     real(r8), pointer :: alb_wall_dir    (:,:,:)  
-     real(r8), pointer :: alb_wall_dif    (:,:,:)  
-     real(r8), pointer :: ht_roof         (:,:)
-     real(r8), pointer :: wind_hgt_canyon (:,:)
-     real(r8), pointer :: tk_wall         (:,:,:)
-     real(r8), pointer :: tk_roof         (:,:,:)
-     real(r8), pointer :: tk_improad      (:,:,:)
-     real(r8), pointer :: cv_wall         (:,:,:)
-     real(r8), pointer :: cv_roof         (:,:,:)
-     real(r8), pointer :: cv_improad      (:,:,:)
      real(r8), pointer :: thick_wall      (:,:)
      real(r8), pointer :: thick_roof      (:,:)
-     integer,  pointer :: nlev_improad    (:,:)
-     real(r8), pointer :: t_building_min  (:,:)
   end type urbinp_type
   type (urbinp_type), public :: urbinp   ! urban input derived type
 
   ! !PUBLIC TYPE
   type, public :: urbanparams_type
-     real(r8), allocatable :: wind_hgt_canyon     (:)   ! lun height above road at which wind in canyon is to be computed (m)
-     real(r8), allocatable :: em_roof             (:)   ! lun roof emissivity
-     real(r8), allocatable :: em_improad          (:)   ! lun impervious road emissivity
-     real(r8), allocatable :: em_perroad          (:)   ! lun pervious road emissivity
-     real(r8), allocatable :: em_wall             (:)   ! lun wall emissivity
-     real(r8), allocatable :: alb_roof_dir        (:,:) ! lun direct  roof albedo
-     real(r8), allocatable :: alb_roof_dif        (:,:) ! lun diffuse roof albedo
-     real(r8), allocatable :: alb_improad_dir     (:,:) ! lun direct  impervious road albedo
-     real(r8), allocatable :: alb_improad_dif     (:,:) ! lun diffuse impervious road albedo
-     real(r8), allocatable :: alb_perroad_dir     (:,:) ! lun direct  pervious road albedo
-     real(r8), allocatable :: alb_perroad_dif     (:,:) ! lun diffuse pervious road albedo
-     real(r8), allocatable :: alb_wall_dir        (:,:) ! lun direct  wall albedo
-     real(r8), allocatable :: alb_wall_dif        (:,:) ! lun diffuse wall albedo
-
-     integer , pointer     :: nlev_improad        (:)   ! lun number of impervious road layers (-)
-     real(r8), pointer     :: tk_wall             (:,:) ! lun thermal conductivity of urban wall (W/m/K)
-     real(r8), pointer     :: tk_roof             (:,:) ! lun thermal conductivity of urban roof (W/m/K)
-     real(r8), pointer     :: tk_improad          (:,:) ! lun thermal conductivity of urban impervious road (W/m/K)
-     real(r8), pointer     :: cv_wall             (:,:) ! lun heat capacity of urban wall (J/m^3/K)
-     real(r8), pointer     :: cv_roof             (:,:) ! lun heat capacity of urban roof (J/m^3/K)
-     real(r8), pointer     :: cv_improad          (:,:) ! lun heat capacity of urban impervious road (J/m^3/K)
+
      real(r8), pointer     :: thick_wall          (:)   ! lun total thickness of urban wall (m)
      real(r8), pointer     :: thick_roof          (:)   ! lun total thickness of urban roof (m)
 
-     real(r8), pointer     :: vf_sr               (:)   ! lun view factor of sky for road
-     real(r8), pointer     :: vf_wr               (:)   ! lun view factor of one wall for road
-     real(r8), pointer     :: vf_sw               (:)   ! lun view factor of sky for one wall
-     real(r8), pointer     :: vf_rw               (:)   ! lun view factor of road for one wall
-     real(r8), pointer     :: vf_ww               (:)   ! lun view factor of opposing wall for one wall
-
-     real(r8), pointer     :: t_building_min      (:)   ! lun minimum internal building air temperature (K)
-     real(r8), pointer     :: eflx_traffic_factor (:)   ! lun multiplicative traffic factor for sensible heat flux from urban traffic (-)
    contains
 
      procedure, public :: Init 
@@ -97,17 +43,9 @@ module UrbanParamsType
   end type urbanparams_type
   !
   ! !Urban control variables
-  character(len= *), parameter, public :: urban_hac_off = 'OFF'                
-  character(len= *), parameter, public :: urban_hac_on =  'ON'                 
   character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'  
-  character(len= 16), public           :: urban_hac = urban_hac_off
-  logical, public                      :: urban_traffic = .false.     ! urban traffic fluxes
 
   ! !PRIVATE MEMBER DATA:
-  logical, private    :: ReadNamelist = .false.     ! If namelist was read yet or not
-  integer, parameter, private :: BUILDING_TEMP_METHOD_SIMPLE = 0       ! Simple method introduced in CLM4.5
-  integer, parameter, private :: BUILDING_TEMP_METHOD_PROG   = 1       ! Prognostic method introduced in CLM5.0
-  integer, private :: building_temp_method = BUILDING_TEMP_METHOD_PROG ! Method to calculate the building temperature
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -122,12 +60,6 @@ subroutine Init(this, bounds)
     !
     ! !USES:
     use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varpar      , only : nlevcan, nlevcan, numrad, nlevgrnd, nlevurb
-    use clm_varpar      , only : nlevsoi, nlevgrnd
-    use clm_varctl      , only : use_vancouver, use_mexicocity
-    use clm_varcon      , only : vkc
-    use column_varcon   , only : icol_roof, icol_sunwall, icol_shadewall
-    use column_varcon   , only : icol_road_perv, icol_road_imperv, icol_road_perv
     use landunit_varcon , only : isturb_MIN
     !
     ! !ARGUMENTS:
@@ -135,65 +67,22 @@ subroutine Init(this, bounds)
     type(bounds_type)      , intent(in)    :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer             :: j,l,c,p,g       ! indices
-    integer             :: nc,fl,ib        ! indices 
-    integer             :: dindx           ! urban density type index
-    integer             :: ier             ! error status
-    real(r8)            :: sumvf           ! sum of view factors for wall or road
-    real(r8), parameter :: alpha = 4.43_r8 ! coefficient used to calculate z_d_town
-    real(r8), parameter :: beta = 1.0_r8   ! coefficient used to calculate z_d_town
-    real(r8), parameter :: C_d = 1.2_r8    ! drag coefficient as used in Grimmond and Oke (1999)
-    real(r8)            :: plan_ai         ! plan area index - ratio building area to plan area (-)
-    real(r8)            :: frontal_ai      ! frontal area index of buildings (-)
-    real(r8)            :: build_lw_ratio  ! building short/long side ratio (-)
-    integer		:: begl, endl
-    integer		:: begc, endc
-    integer		:: begp, endp
-    integer             :: begg, endg
+    integer :: l,c,g  ! indices
+    integer :: dindx  ! urban density type index
+    integer :: begl, endl
+    integer :: begg, endg
     !---------------------------------------------------------------------
 
-    begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
     begl = bounds%begl; endl = bounds%endl
     begg = bounds%begg; endg = bounds%endg
 
     ! Allocate urbanparams data structure
-
-    if ( nlevurb > 0 )then
-       allocate(this%tk_wall          (begl:endl,nlevurb))  ; this%tk_wall             (:,:) = nan
-       allocate(this%tk_roof          (begl:endl,nlevurb))  ; this%tk_roof             (:,:) = nan
-       allocate(this%cv_wall          (begl:endl,nlevurb))  ; this%cv_wall             (:,:) = nan
-       allocate(this%cv_roof          (begl:endl,nlevurb))  ; this%cv_roof             (:,:) = nan
-    end if
-    allocate(this%t_building_min      (begl:endl))          ; this%t_building_min      (:)   = nan
-    allocate(this%tk_improad          (begl:endl,nlevurb))  ; this%tk_improad          (:,:) = nan
-    allocate(this%cv_improad          (begl:endl,nlevurb))  ; this%cv_improad          (:,:) = nan
     allocate(this%thick_wall          (begl:endl))          ; this%thick_wall          (:)   = nan
     allocate(this%thick_roof          (begl:endl))          ; this%thick_roof          (:)   = nan
-    allocate(this%nlev_improad        (begl:endl))          ; this%nlev_improad        (:)   = huge(1)
-    allocate(this%vf_sr               (begl:endl))          ; this%vf_sr               (:)   = nan
-    allocate(this%vf_wr               (begl:endl))          ; this%vf_wr               (:)   = nan
-    allocate(this%vf_sw               (begl:endl))          ; this%vf_sw               (:)   = nan
-    allocate(this%vf_rw               (begl:endl))          ; this%vf_rw               (:)   = nan
-    allocate(this%vf_ww               (begl:endl))          ; this%vf_ww               (:)   = nan
-    allocate(this%wind_hgt_canyon     (begl:endl))          ; this%wind_hgt_canyon     (:)   = nan
-    allocate(this%em_roof             (begl:endl))          ; this%em_roof             (:)   = nan
-    allocate(this%em_improad          (begl:endl))          ; this%em_improad          (:)   = nan
-    allocate(this%em_perroad          (begl:endl))          ; this%em_perroad          (:)   = nan
-    allocate(this%em_wall             (begl:endl))          ; this%em_wall             (:)   = nan
-    allocate(this%alb_roof_dir        (begl:endl,numrad))   ; this%alb_roof_dir        (:,:) = nan
-    allocate(this%alb_roof_dif        (begl:endl,numrad))   ; this%alb_roof_dif        (:,:) = nan    
-    allocate(this%alb_improad_dir     (begl:endl,numrad))   ; this%alb_improad_dir     (:,:) = nan       
-    allocate(this%alb_perroad_dir     (begl:endl,numrad))   ; this%alb_perroad_dir     (:,:) = nan       
-    allocate(this%alb_improad_dif     (begl:endl,numrad))   ; this%alb_improad_dif     (:,:) = nan       
-    allocate(this%alb_perroad_dif     (begl:endl,numrad))   ; this%alb_perroad_dif     (:,:) = nan       
-    allocate(this%alb_wall_dir        (begl:endl,numrad))   ; this%alb_wall_dir        (:,:) = nan    
-    allocate(this%alb_wall_dif        (begl:endl,numrad))   ; this%alb_wall_dif        (:,:) = nan
-    allocate(this%eflx_traffic_factor (begl:endl))          ; this%eflx_traffic_factor (:)   = nan
 
     ! Initialize time constant urban variables
 
-    do l = bounds%begl,bounds%endl
+    do l = begl,endl
 
        ! "0" refers to urban wall/roof surface and "nlevsoi" refers to urban wall/roof bottom
        if (lun%urbpoi(l)) then
@@ -201,166 +90,18 @@ subroutine Init(this, bounds)
           g = lun%gridcell(l)
           dindx = lun%itype(l) - isturb_MIN + 1
 
-          this%wind_hgt_canyon(l) = urbinp%wind_hgt_canyon(g,dindx)
-          do ib = 1,numrad
-             this%alb_roof_dir   (l,ib) = urbinp%alb_roof_dir   (g,dindx,ib)
-             this%alb_roof_dif   (l,ib) = urbinp%alb_roof_dif   (g,dindx,ib)
-             this%alb_improad_dir(l,ib) = urbinp%alb_improad_dir(g,dindx,ib)
-             this%alb_perroad_dir(l,ib) = urbinp%alb_perroad_dir(g,dindx,ib)
-             this%alb_improad_dif(l,ib) = urbinp%alb_improad_dif(g,dindx,ib)
-             this%alb_perroad_dif(l,ib) = urbinp%alb_perroad_dif(g,dindx,ib)
-             this%alb_wall_dir   (l,ib) = urbinp%alb_wall_dir   (g,dindx,ib)
-             this%alb_wall_dif   (l,ib) = urbinp%alb_wall_dif   (g,dindx,ib)
-          end do
-          this%em_roof   (l) = urbinp%em_roof   (g,dindx)
-          this%em_improad(l) = urbinp%em_improad(g,dindx)
-          this%em_perroad(l) = urbinp%em_perroad(g,dindx)
-          this%em_wall   (l) = urbinp%em_wall   (g,dindx)
-
           ! Landunit level initialization for urban wall and roof layers and interfaces
 
           lun%canyon_hwr(l)   = urbinp%canyon_hwr(g,dindx)
           lun%wtroad_perv(l)  = urbinp%wtroad_perv(g,dindx)
-          lun%ht_roof(l)      = urbinp%ht_roof(g,dindx)
           lun%wtlunit_roof(l) = urbinp%wtlunit_roof(g,dindx)
 
-          this%tk_wall(l,:)      = urbinp%tk_wall(g,dindx,:)
-          this%tk_roof(l,:)      = urbinp%tk_roof(g,dindx,:)
-          this%tk_improad(l,:)   = urbinp%tk_improad(g,dindx,:)
-          this%cv_wall(l,:)      = urbinp%cv_wall(g,dindx,:)
-          this%cv_roof(l,:)      = urbinp%cv_roof(g,dindx,:)
-          this%cv_improad(l,:)   = urbinp%cv_improad(g,dindx,:)
           this%thick_wall(l)     = urbinp%thick_wall(g,dindx)
           this%thick_roof(l)     = urbinp%thick_roof(g,dindx)
-          this%nlev_improad(l)   = urbinp%nlev_improad(g,dindx)
-          this%t_building_min(l) = urbinp%t_building_min(g,dindx)
-
-          ! Inferred from Sailor and Lu 2004
-          if (urban_traffic) then
-             this%eflx_traffic_factor(l) = 3.6_r8 * (lun%canyon_hwr(l)-0.5_r8) + 1.0_r8
-          else
-             this%eflx_traffic_factor(l) = 0.0_r8
-          end if
-
-          if (use_vancouver .or. use_mexicocity) then
-             ! Freely evolving
-             this%t_building_min(l) = 200.00_r8
-          else
-             if (urban_hac == urban_hac_off) then
-                ! Overwrite values read in from urbinp by freely evolving values
-                this%t_building_min(l) = 200.00_r8
-             end if
-          end if
-
-          !----------------------------------------------------------------------------------
-          ! View factors for road and one wall in urban canyon (depends only on canyon_hwr)
-          ! ---------------------------------------------------------------------------------------
-          !                                                        WALL    |
-          !                  ROAD                                          |
-          !                                                         wall   |
-          !          -----\          /-----   -             -  |\----------/
-          !              | \  vsr   / |       |         r   |  | \  vww   /   s
-          !              |  \      /  |       h         o   w  |  \      /    k
-          !        wall  |   \    /   | wall  |         a   |  |   \    /     y
-          !              |vwr \  / vwr|       |         d   |  |vrw \  / vsw 
-          !              ------\/------       -             -  |-----\/-----
-          !                   road                                  wall   |
-          !              <----- w ---->                                    |
-          !                                                    <---- h --->|
-          !
-          !    vsr = view factor of sky for road          vrw = view factor of road for wall
-          !    vwr = view factor of one wall for road     vww = view factor of opposing wall for wall
-          !                                               vsw = view factor of sky for wall
-          !    vsr + vwr + vwr = 1                        vrw + vww + vsw = 1
-          !
-          ! Source: Masson, V. (2000) A physically-based scheme for the urban energy budget in 
-          ! atmospheric models. Boundary-Layer Meteorology 94:357-397
-          !
-          ! - Calculate urban land unit aerodynamic constants using Macdonald (1998) as used in
-          ! Grimmond and Oke (1999)
-          ! ---------------------------------------------------------------------------------------
-          
-          ! road -- sky view factor -> 1 as building height -> 0 
-          ! and -> 0 as building height -> infinity
-
-          this%vf_sr(l) = sqrt(lun%canyon_hwr(l)**2 + 1._r8) - lun%canyon_hwr(l)
-          this%vf_wr(l) = 0.5_r8 * (1._r8 - this%vf_sr(l))
-
-          ! one wall -- sky view factor -> 0.5 as building height -> 0 
-          ! and -> 0 as building height -> infinity
-
-          this%vf_sw(l) = 0.5_r8 * (lun%canyon_hwr(l) + 1._r8 - sqrt(lun%canyon_hwr(l)**2+1._r8)) / lun%canyon_hwr(l)
-          this%vf_rw(l) = this%vf_sw(l)
-          this%vf_ww(l) = 1._r8 - this%vf_sw(l) - this%vf_rw(l)
-
-          ! error check -- make sure view factor sums to one for road and wall
-          sumvf = this%vf_sr(l) + 2._r8*this%vf_wr(l)
-          if (abs(sumvf-1._r8) > 1.e-06_r8 ) then
-             write (iulog,*) 'urban road view factor error',sumvf
-             write (iulog,*) 'clm model is stopping'
-             call endrun(decomp_index=l, clmlevel=namel, msg=errmsg(sourcefile, __LINE__))
-          endif
-          sumvf = this%vf_sw(l) + this%vf_rw(l) + this%vf_ww(l)
-          if (abs(sumvf-1._r8) > 1.e-06_r8 ) then
-             write (iulog,*) 'urban wall view factor error',sumvf
-             write (iulog,*) 'clm model is stopping'
-             call endrun(decomp_index=l, clmlevel=namel, msg=errmsg(sourcefile, __LINE__))
-          endif
-
-          !----------------------------------------------------------------------------------
-          ! Calculate urban land unit aerodynamic constants using Macdonald (1998) as used in
-          ! Grimmond and Oke (1999)
-          !----------------------------------------------------------------------------------
-
-          ! Calculate plan area index 
-          plan_ai = lun%canyon_hwr(l)/(lun%canyon_hwr(l) + 1._r8)
-
-          ! Building shape shortside/longside ratio (e.g. 1 = square )
-          ! This assumes the building occupies the entire canyon length
-          build_lw_ratio = plan_ai
-
-          ! Calculate frontal area index
-          frontal_ai = (1._r8 - plan_ai) * lun%canyon_hwr(l)
-
-          ! Adjust frontal area index for different building configuration
-          frontal_ai = frontal_ai * sqrt(1/build_lw_ratio) * sqrt(plan_ai)
-
-          ! Calculate displacement height
-          if (use_vancouver) then
-             lun%z_d_town(l) = 3.5_r8
-          else if (use_mexicocity) then
-             lun%z_d_town(l) = 10.9_r8
-          else
-             lun%z_d_town(l) = (1._r8 + alpha**(-plan_ai) * (plan_ai - 1._r8)) * lun%ht_roof(l)
-          end if
-
-          ! Calculate the roughness length
-          if (use_vancouver) then
-             lun%z_0_town(l) = 0.35_r8
-          else if (use_mexicocity) then
-             lun%z_0_town(l) = 2.2_r8
-          else
-             lun%z_0_town(l) = lun%ht_roof(l) * (1._r8 - lun%z_d_town(l) / lun%ht_roof(l)) * &
-                  exp(-1.0_r8 * (0.5_r8 * beta * C_d / vkc**2 * &
-                  (1 - lun%z_d_town(l) / lun%ht_roof(l)) * frontal_ai)**(-0.5_r8))
-          end if
-
-       else ! Not urban point 
-
-          this%eflx_traffic_factor(l) = spval
-          this%t_building_min(l) = spval
-
-          this%vf_sr(l) = spval
-          this%vf_wr(l) = spval
-          this%vf_sw(l) = spval
-          this%vf_rw(l) = spval
-          this%vf_ww(l) = spval
 
        end if
     end do
 
-    ! Deallocate memory for urbinp datatype
-    
     call UrbanInput(bounds%begg, bounds%endg, mode='finalize')
 
   end subroutine Init
@@ -433,30 +174,8 @@ subroutine UrbanInput(begg, endg, mode)
        allocate(urbinp%canyon_hwr(begg:endg, numurbl), &  
                 urbinp%wtlunit_roof(begg:endg, numurbl), &  
                 urbinp%wtroad_perv(begg:endg, numurbl), &
-                urbinp%em_roof(begg:endg, numurbl), &     
-                urbinp%em_improad(begg:endg, numurbl), &    
-                urbinp%em_perroad(begg:endg, numurbl), &    
-                urbinp%em_wall(begg:endg, numurbl), &    
-                urbinp%alb_roof_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_roof_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_improad_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_perroad_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_improad_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_perroad_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_wall_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_wall_dif(begg:endg, numurbl, numrad), &
-                urbinp%ht_roof(begg:endg, numurbl), &
-                urbinp%wind_hgt_canyon(begg:endg, numurbl), &
-                urbinp%tk_wall(begg:endg, numurbl,nlevurb), &
-                urbinp%tk_roof(begg:endg, numurbl,nlevurb), &
-                urbinp%tk_improad(begg:endg, numurbl,nlevurb), &
-                urbinp%cv_wall(begg:endg, numurbl,nlevurb), &
-                urbinp%cv_roof(begg:endg, numurbl,nlevurb), &
-                urbinp%cv_improad(begg:endg, numurbl,nlevurb), &
                 urbinp%thick_wall(begg:endg, numurbl), &
                 urbinp%thick_roof(begg:endg, numurbl), &
-                urbinp%nlev_improad(begg:endg, numurbl), &
-                urbinp%t_building_min(begg:endg, numurbl), &
                 stat=ier)
        if (ier /= 0) then
           call endrun(msg="Allocation error "//errmsg(sourcefile, __LINE__))
@@ -511,42 +230,6 @@ subroutine UrbanInput(begg, endg, mode)
           call endrun( msg=' ERROR: WTROAD_PERV NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
        end if
 
-       call ncd_io(ncid=ncid, varname='EM_ROOF', flag='read', data=urbinp%em_roof, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: EM_ROOF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='EM_IMPROAD', flag='read', data=urbinp%em_improad, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: EM_IMPROAD NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='EM_PERROAD', flag='read', data=urbinp%em_perroad, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: EM_PERROAD NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='EM_WALL', flag='read', data=urbinp%em_wall, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: EM_WALL NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='HT_ROOF', flag='read', data=urbinp%ht_roof, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: HT_ROOF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='WIND_HGT_CANYON', flag='read', data=urbinp%wind_hgt_canyon, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: WIND_HGT_CANYON NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
        call ncd_io(ncid=ncid, varname='THICK_WALL', flag='read', data=urbinp%thick_wall, &
             dim1name=grlnd, readvar=readvar)
        if (.not. readvar) then
@@ -559,102 +242,6 @@ subroutine UrbanInput(begg, endg, mode)
           call endrun( msg=' ERROR: THICK_ROOF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
        end if
 
-       call ncd_io(ncid=ncid, varname='NLEV_IMPROAD', flag='read', data=urbinp%nlev_improad, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: NLEV_IMPROAD NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='T_BUILDING_MIN', flag='read', data=urbinp%t_building_min, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: T_BUILDING_MIN NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_IMPROAD_DIR', flag='read', data=urbinp%alb_improad_dir, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not.readvar) then
-          call endrun( msg=' ERROR: ALB_IMPROAD_DIR NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_IMPROAD_DIF', flag='read', data=urbinp%alb_improad_dif, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not.readvar) then
-          call endrun( msg=' ERROR: ALB_IMPROAD_DIF NOT on fsurdat file'//errmsg(sourcefile, __LINE__) )
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_PERROAD_DIR', flag='read',data=urbinp%alb_perroad_dir, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_PERROAD_DIR NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_PERROAD_DIF', flag='read',data=urbinp%alb_perroad_dif, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_PERROAD_DIF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_ROOF_DIR', flag='read', data=urbinp%alb_roof_dir,  &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_ROOF_DIR NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_ROOF_DIF', flag='read', data=urbinp%alb_roof_dif,  &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_ROOF_DIF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_WALL_DIR', flag='read', data=urbinp%alb_wall_dir, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_WALL_DIR NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='ALB_WALL_DIF', flag='read', data=urbinp%alb_wall_dif, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: ALB_WALL_DIF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='TK_IMPROAD', flag='read', data=urbinp%tk_improad, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: TK_IMPROAD NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='TK_ROOF', flag='read', data=urbinp%tk_roof, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: TK_ROOF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='TK_WALL', flag='read', data=urbinp%tk_wall, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: TK_WALL NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='CV_IMPROAD', flag='read', data=urbinp%cv_improad, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: CV_IMPROAD NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='CV_ROOF', flag='read', data=urbinp%cv_roof, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: CV_ROOF NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
-       call ncd_io(ncid=ncid, varname='CV_WALL', flag='read', data=urbinp%cv_wall, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          call endrun( msg=' ERROR: CV_WALL NOT on fsurdat file'//errmsg(sourcefile, __LINE__))
-       end if
-
        call ncd_pio_closefile(ncid)
        if (masterproc) then
           write(iulog,*)' Sucessfully read urban input data' 
@@ -668,30 +255,8 @@ subroutine UrbanInput(begg, endg, mode)
        deallocate(urbinp%canyon_hwr, &
                   urbinp%wtlunit_roof, &
                   urbinp%wtroad_perv, &
-                  urbinp%em_roof, &
-                  urbinp%em_improad, &
-                  urbinp%em_perroad, &
-                  urbinp%em_wall, &
-                  urbinp%alb_roof_dir, &
-                  urbinp%alb_roof_dif, &
-                  urbinp%alb_improad_dir, &
-                  urbinp%alb_perroad_dir, &
-                  urbinp%alb_improad_dif, &
-                  urbinp%alb_perroad_dif, &
-                  urbinp%alb_wall_dir, &
-                  urbinp%alb_wall_dif, &
-                  urbinp%ht_roof, &
-                  urbinp%wind_hgt_canyon, &
-                  urbinp%tk_wall, &
-                  urbinp%tk_roof, &
-                  urbinp%tk_improad, &
-                  urbinp%cv_wall, &
-                  urbinp%cv_roof, &
-                  urbinp%cv_improad, &
                   urbinp%thick_wall, &
                   urbinp%thick_roof, &
-                  urbinp%nlev_improad, &
-                  urbinp%t_building_min, &
                   stat=ier)
        if (ier /= 0) then
           call endrun(msg='initUrbanInput: deallocation error '//errmsg(sourcefile, __LINE__))
@@ -703,257 +268,6 @@ subroutine UrbanInput(begg, endg, mode)
 
   end subroutine UrbanInput
 
-  !-----------------------------------------------------------------------
-  subroutine CheckUrban(begg, endg, pcturb, caller)
-
-    !-----------------------------------------------------------------------
-    ! !DESCRIPTION:
-    ! Confirm that we have valid urban data for all points with pct urban > 0. If this isn't
-    ! true, abort with a message.
-    !
-    ! !USES:
-    use clm_instur      , only : urban_valid
-    use landunit_varcon , only : numurbl
-    !
-    ! !ARGUMENTS:
-    implicit none
-    integer         , intent(in) :: begg, endg           ! beg & end grid cell indices
-    real(r8)        , intent(in) :: pcturb(begg:,:)      ! % urban
-    character(len=*), intent(in) :: caller               ! identifier of caller, for more meaningful error messages
-    !
-    ! !REVISION HISTORY:
-    ! Created by Bill Sacks 7/2013, mostly by moving code from surfrd_special
-    !
-    ! !LOCAL VARIABLES:
-    logical :: found
-    integer :: nl, n
-    integer :: nindx, dindx
-    integer :: nlev
-    !-----------------------------------------------------------------------
-
-    found = .false.
-    do nl = begg,endg
-       do n = 1, numurbl
-          if ( pcturb(nl,n) > 0.0_r8 ) then
-             if ( .not. urban_valid(nl) .or. &
-                  urbinp%canyon_hwr(nl,n)            <= 0._r8 .or. &
-                  urbinp%em_improad(nl,n)            <= 0._r8 .or. &
-                  urbinp%em_perroad(nl,n)            <= 0._r8 .or. &
-                  urbinp%em_roof(nl,n)               <= 0._r8 .or. &
-                  urbinp%em_wall(nl,n)               <= 0._r8 .or. &
-                  urbinp%ht_roof(nl,n)               <= 0._r8 .or. &
-                  urbinp%thick_roof(nl,n)            <= 0._r8 .or. &
-                  urbinp%thick_wall(nl,n)            <= 0._r8 .or. &
-                  urbinp%t_building_min(nl,n)        <= 0._r8 .or. &
-                  urbinp%wind_hgt_canyon(nl,n)       <= 0._r8 .or. &
-                  urbinp%wtlunit_roof(nl,n)          <= 0._r8 .or. &
-                  urbinp%wtroad_perv(nl,n)           <= 0._r8 .or. &
-                  any(urbinp%alb_improad_dir(nl,n,:) <= 0._r8) .or. &
-                  any(urbinp%alb_improad_dif(nl,n,:) <= 0._r8) .or. &
-                  any(urbinp%alb_perroad_dir(nl,n,:) <= 0._r8) .or. &
-                  any(urbinp%alb_perroad_dif(nl,n,:) <= 0._r8) .or. &
-                  any(urbinp%alb_roof_dir(nl,n,:)    <= 0._r8) .or. &
-                  any(urbinp%alb_roof_dif(nl,n,:)    <= 0._r8) .or. &
-                  any(urbinp%alb_wall_dir(nl,n,:)    <= 0._r8) .or. &
-                  any(urbinp%alb_wall_dif(nl,n,:)    <= 0._r8) .or. &
-                  any(urbinp%tk_roof(nl,n,:)         <= 0._r8) .or. &
-                  any(urbinp%tk_wall(nl,n,:)         <= 0._r8) .or. &
-                  any(urbinp%cv_roof(nl,n,:)         <= 0._r8) .or. &
-                  any(urbinp%cv_wall(nl,n,:)         <= 0._r8)) then
-                found = .true.
-                nindx = nl
-                dindx = n
-                exit
-             else
-                if (urbinp%nlev_improad(nl,n) > 0) then
-                   nlev = urbinp%nlev_improad(nl,n)
-                   if ( any(urbinp%tk_improad(nl,n,1:nlev) <= 0._r8) .or. &
-                        any(urbinp%cv_improad(nl,n,1:nlev) <= 0._r8)) then
-                      found = .true.
-                      nindx = nl
-                      dindx = n
-                      exit
-                   end if
-                end if
-             end if
-             if (found) exit
-          end if
-       end do
-    end do
-    if ( found ) then
-       write(iulog,*) trim(caller), ' ERROR: no valid urban data for nl=',nindx
-       write(iulog,*)'density type:    ',dindx
-       write(iulog,*)'urban_valid:     ',urban_valid(nindx)
-       write(iulog,*)'canyon_hwr:      ',urbinp%canyon_hwr(nindx,dindx)
-       write(iulog,*)'em_improad:      ',urbinp%em_improad(nindx,dindx)
-       write(iulog,*)'em_perroad:      ',urbinp%em_perroad(nindx,dindx)
-       write(iulog,*)'em_roof:         ',urbinp%em_roof(nindx,dindx)
-       write(iulog,*)'em_wall:         ',urbinp%em_wall(nindx,dindx)
-       write(iulog,*)'ht_roof:         ',urbinp%ht_roof(nindx,dindx)
-       write(iulog,*)'thick_roof:      ',urbinp%thick_roof(nindx,dindx)
-       write(iulog,*)'thick_wall:      ',urbinp%thick_wall(nindx,dindx)
-       write(iulog,*)'t_building_min:  ',urbinp%t_building_min(nindx,dindx)
-       write(iulog,*)'wind_hgt_canyon: ',urbinp%wind_hgt_canyon(nindx,dindx)
-       write(iulog,*)'wtlunit_roof:    ',urbinp%wtlunit_roof(nindx,dindx)
-       write(iulog,*)'wtroad_perv:     ',urbinp%wtroad_perv(nindx,dindx)
-       write(iulog,*)'alb_improad_dir: ',urbinp%alb_improad_dir(nindx,dindx,:)
-       write(iulog,*)'alb_improad_dif: ',urbinp%alb_improad_dif(nindx,dindx,:)
-       write(iulog,*)'alb_perroad_dir: ',urbinp%alb_perroad_dir(nindx,dindx,:)
-       write(iulog,*)'alb_perroad_dif: ',urbinp%alb_perroad_dif(nindx,dindx,:)
-       write(iulog,*)'alb_roof_dir:    ',urbinp%alb_roof_dir(nindx,dindx,:)
-       write(iulog,*)'alb_roof_dif:    ',urbinp%alb_roof_dif(nindx,dindx,:)
-       write(iulog,*)'alb_wall_dir:    ',urbinp%alb_wall_dir(nindx,dindx,:)
-       write(iulog,*)'alb_wall_dif:    ',urbinp%alb_wall_dif(nindx,dindx,:)
-       write(iulog,*)'tk_roof:         ',urbinp%tk_roof(nindx,dindx,:)
-       write(iulog,*)'tk_wall:         ',urbinp%tk_wall(nindx,dindx,:)
-       write(iulog,*)'cv_roof:         ',urbinp%cv_roof(nindx,dindx,:)
-       write(iulog,*)'cv_wall:         ',urbinp%cv_wall(nindx,dindx,:)
-       if (urbinp%nlev_improad(nindx,dindx) > 0) then
-          nlev = urbinp%nlev_improad(nindx,dindx)
-          write(iulog,*)'tk_improad: ',urbinp%tk_improad(nindx,dindx,1:nlev)
-          write(iulog,*)'cv_improad: ',urbinp%cv_improad(nindx,dindx,1:nlev)
-       end if
-       call endrun(msg=errmsg(sourcefile, __LINE__))
-    end if
-
-  end subroutine CheckUrban
-
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !BOP
-  !
-  ! !IROUTINE: UrbanReadNML
-  !
-  ! !INTERFACE:
-  !
-  subroutine UrbanReadNML ( NLFilename )
-    !
-    ! !DESCRIPTION:
-    !
-    ! Read in the urban namelist
-    !
-    ! !USES:
-    use shr_mpi_mod   , only : shr_mpi_bcast
-    use abortutils    , only : endrun
-    use spmdMod       , only : masterproc, mpicom
-    use fileutils     , only : getavu, relavu, opnfil
-    use shr_nl_mod    , only : shr_nl_find_group_name
-    use shr_mpi_mod   , only : shr_mpi_bcast
-    implicit none
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(IN) :: NLFilename ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    character(len=32) :: subname = 'UrbanReadNML'  ! subroutine name
-
-    namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method
-    !EOP
-    !-----------------------------------------------------------------------
-
-    ! ----------------------------------------------------------------------
-    ! Read namelist from input namelist filename
-    ! ----------------------------------------------------------------------
-
-    if ( masterproc )then
-
-       unitn = getavu()
-       write(iulog,*) 'Read in clmu_inparm  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, 'clmu_inparm', status=ierr)
-       if (ierr == 0) then
-          read(unitn, clmu_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading clmu_inparm namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR finding clmu_inparm namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-
-    end if
-
-    ! Broadcast namelist variables read in
-    call shr_mpi_bcast(urban_hac,             mpicom)
-    call shr_mpi_bcast(urban_traffic,         mpicom)
-    call shr_mpi_bcast(building_temp_method,  mpicom)
-
-    !
-    if (urban_traffic) then
-       write(iulog,*)'Urban traffic fluxes are not implemented currently'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-    !
-    if ( masterproc )then
-       write(iulog,*) '   urban air conditioning/heating and wasteheat   = ', urban_hac
-       write(iulog,*) '   urban traffic flux   = ', urban_traffic
-    end if
-
-    ReadNamelist = .true.
-
-  end subroutine UrbanReadNML
-
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !BOP
-  !
-  ! !IROUTINE: IsSimpleBuildTemp
-  !
-  ! !INTERFACE:
-  !
-  logical function IsSimpleBuildTemp( )
-    !
-    ! !DESCRIPTION:
-    !
-    ! If the simple building temperature method is being used
-    !
-    ! !USES:
-    implicit none
-    !EOP
-    !-----------------------------------------------------------------------
-
-    if ( .not. ReadNamelist )then
-       write(iulog,*)'Testing on building_temp_method before urban namelist was read in'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-    IsSimpleBuildTemp = building_temp_method == BUILDING_TEMP_METHOD_SIMPLE
-
-  end function IsSimpleBuildTemp
-
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !BOP
-  !
-  ! !IROUTINE: IsProgBuildTemp
-  !
-  ! !INTERFACE:
-  !
-  logical function IsProgBuildTemp( )
-    !
-    ! !DESCRIPTION:
-    !
-    ! If the prognostic building temperature method is being used
-    !
-    ! !USES:
-    implicit none
-    !EOP
-    !-----------------------------------------------------------------------
-
-    if ( .not. ReadNamelist )then
-       write(iulog,*)'Testing on building_temp_method before urban namelist was read in'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    end if
-    IsProgBuildTemp = building_temp_method == BUILDING_TEMP_METHOD_PROG
-
-  end function IsProgBuildTemp
-
-  !-----------------------------------------------------------------------
-
 end module UrbanParamsType
 
 
diff --git a/src/biogeophys/UrbanTimeVarType.F90 b/src/biogeophys/UrbanTimeVarType.F90
deleted file mode 100644
index 600f506f26..0000000000
--- a/src/biogeophys/UrbanTimeVarType.F90
+++ /dev/null
@@ -1,168 +0,0 @@
-module UrbanTimeVarType
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Urban Time Varying Data
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8, CL => shr_kind_CL
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use abortutils      , only : endrun
-  use decompMod       , only : bounds_type
-  use clm_varctl      , only : iulog
-  use landunit_varcon , only : isturb_MIN, isturb_MAX
-  use clm_varcon      , only : spval
-  use LandunitType    , only : lun                
-  use GridcellType    , only : grc
-  use mct_mod
-  use shr_strdata_mod , only : shr_strdata_type
-  !
-  implicit none
-  save
-  private
-  !
-  !
-
-  ! !PUBLIC TYPE
-  type, public :: urbantv_type
-
-     real(r8), public, pointer     :: t_building_max(:)    ! lun maximum internal building air temperature (K)
-     type(shr_strdata_type)        :: sdat_urbantv         ! urban time varying input data stream
-   contains
-
-     ! !PUBLIC MEMBER FUNCTIONS:
-     procedure, public :: Init              ! Allocate and initialize urbantv
-     procedure, public :: urbantv_interp    ! Interpolate urban time varying stream
-     
-  end type urbantv_type
-
-  !----------------------------------------------------------------------- 
-  character(15), private :: stream_var_name(isturb_MIN:isturb_MAX)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
-    !
-    ! Allocate module variables and data structures
-    !
-    ! !USES:
-    use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-    use histFileMod     , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(urbantv_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    character(len=*)  , intent(in) :: NLFilename   ! Namelist filename
-    !
-    ! !LOCAL VARIABLES:
-    integer		:: begl, endl
-    !---------------------------------------------------------------------
-
-    begl = bounds%begl; endl = bounds%endl
-
-    ! Allocate urbantv data structure
-
-    allocate(this%t_building_max      (begl:endl))          ; this%t_building_max      (:)   = nan
-
-    call this%urbantv_interp(bounds)
-
-    ! Add history fields
-    call hist_addfld1d (fname='TBUILD_MAX', units='K',      &
-          avgflag='A', long_name='prescribed maximum interior building temperature',   &
-          ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, &
-          l2g_scale_type='unity')
-
-
-  end subroutine Init
-
-  !-----------------------------------------------------------------------
-  subroutine urbantv_interp(this, bounds)
-  !
-  ! !DESCRIPTION:
-  ! Interpolate data stream information for urban time varying data.
-  !
-  ! !USES:
-  use clm_time_manager, only : get_curr_date
-  use spmdMod         , only : mpicom
-  use shr_strdata_mod , only : shr_strdata_advance
-  use clm_instur      , only : urban_valid
-  !
-  ! !ARGUMENTS:
-  class(urbantv_type)           :: this
-  type(bounds_type), intent(in) :: bounds
-  !
-  ! !LOCAL VARIABLES:
-  logical :: found
-  integer :: l, glun, ig, g, ip
-  integer :: year    ! year (0, ...) for nstep+1
-  integer :: mon     ! month (1, ..., 12) for nstep+1
-  integer :: day     ! day of month (1, ..., 31) for nstep+1
-  integer :: sec     ! seconds into current date for nstep+1
-  integer :: mcdate  ! Current model date (yyyymmdd)
-  integer :: lindx   ! landunit index
-  integer :: gindx   ! gridcell index
-  !-----------------------------------------------------------------------
-
-   call get_curr_date(year, mon, day, sec)
-   mcdate = year*10000 + mon*100 + day
-
-   call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn')
-
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l))))
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig)
-      else
-         this%t_building_max(l) = spval
-      end if
-   end do
-
-   found = .false.
-   do l = bounds%begl,bounds%endl
-      if (lun%urbpoi(l)) then
-         glun  = lun%gridcell(l)
-         !
-         ! Determine vector index corresponding to glun
-         !
-         ig = 0
-         do g = bounds%begg,bounds%endg
-            ig = ig+1
-            if (g == glun) exit
-         end do
-
-         if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then
-            found = .true.
-            gindx = g
-            lindx = l
-            exit
-         end if
-      end if
-   end do
-   if ( found ) then
-      write(iulog,*)'ERROR: no valid urban data for g= ',gindx
-      write(iulog,*)'landunit type:   ',lun%itype(l)
-      write(iulog,*)'urban_valid:     ',urban_valid(gindx)
-      write(iulog,*)'t_building_max:  ',this%t_building_max(lindx)
-      call endrun(msg=errmsg(sourcefile, __LINE__))
-   end if
-
-
-  end subroutine urbantv_interp
-
-  !-----------------------------------------------------------------------
-
-end module UrbanTimeVarType
diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90
index 4615e22f4d..bb2b0ea7b1 100644
--- a/src/biogeophys/WaterStateType.F90
+++ b/src/biogeophys/WaterStateType.F90
@@ -8,13 +8,7 @@ module WaterstateType
   !
   ! !USES:
   use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
   use decompMod      , only : bounds_type
-  use clm_varctl     , only : use_vancouver, use_mexicocity, use_cn, iulog, use_luna
-  use clm_varpar     , only : nlevgrnd, nlevurb, nlevsno   
-  use clm_varcon     , only : spval
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col                
   !
   implicit none
   save
@@ -22,96 +16,17 @@ module WaterstateType
   !
   ! !PUBLIC TYPES:
   type, public :: waterstate_type
-
-     real(r8), pointer :: snow_depth_col         (:)   ! col snow height of snow covered area (m)
-     real(r8), pointer :: snow_persistence_col   (:)   ! col length of time that ground has had non-zero snow thickness (sec)
-     real(r8), pointer :: snowdp_col             (:)   ! col area-averaged snow height (m)
-     real(r8), pointer :: snowice_col            (:)   ! col average snow ice lens
-     real(r8), pointer :: snowliq_col            (:)   ! col average snow liquid water
-     real(r8), pointer :: int_snow_col           (:)   ! col integrated snowfall (mm H2O)
-     real(r8), pointer :: snow_layer_unity_col   (:,:) ! value 1 for each snow layer, used for history diagnostics
-     real(r8), pointer :: bw_col                 (:,:) ! col partial density of water in the snow pack (ice + liquid) [kg/m3] 
-
      real(r8), pointer :: h2osno_col             (:)   ! col snow water (mm H2O)
-     real(r8), pointer :: h2osno_old_col         (:)   ! col snow mass for previous time step (kg/m2) (new)
-     real(r8), pointer :: h2osoi_liq_col         (:,:) ! col liquid water (kg/m2) (new) (-nlevsno+1:nlevgrnd)    
-     real(r8), pointer :: h2osoi_ice_col         (:,:) ! col ice lens (kg/m2) (new) (-nlevsno+1:nlevgrnd)    
-     real(r8), pointer :: h2osoi_liq_tot_col     (:)   ! vertically summed col liquid water (kg/m2) (new) (-nlevsno+1:nlevgrnd)    
-     real(r8), pointer :: h2osoi_ice_tot_col     (:)   ! vertically summed col ice lens (kg/m2) (new) (-nlevsno+1:nlevgrnd)    
-     real(r8), pointer :: h2osoi_liqice_10cm_col (:)   ! col liquid water + ice lens in top 10cm of soil (kg/m2)
-     real(r8), pointer :: h2osoi_vol_col         (:,:) ! col volumetric soil water (0<=h2osoi_vol<=watsat) [m3/m3]  (nlevgrnd)
-     real(r8), pointer :: air_vol_col            (:,:) ! col air filled porosity
-     real(r8), pointer :: h2osoi_liqvol_col      (:,:) ! col volumetric liquid water content (v/v)
-     real(r8), pointer :: h2ocan_patch           (:)   ! patch canopy water (mm H2O)
-     real(r8), pointer :: h2osfc_col             (:)   ! col surface water (mm H2O)
-     real(r8), pointer :: snocan_patch           (:)   ! patch canopy snow water (mm H2O)
-     real(r8), pointer :: liqcan_patch           (:)   ! patch canopy liquid water (mm H2O)
-     real(r8), pointer :: snounload_patch        (:)   ! Canopy snow unloading (mm H2O)
-     real(r8), pointer :: swe_old_col            (:,:) ! col initial snow water
-     real(r8), pointer :: liq1_grc               (:)   ! grc initial gridcell total h2o liq content
-     real(r8), pointer :: liq2_grc               (:)   ! grc post land cover change total liq content
-     real(r8), pointer :: ice1_grc               (:)   ! grc initial gridcell total h2o ice content
-     real(r8), pointer :: ice2_grc               (:)   ! grc post land cover change total ice content
-     real(r8), pointer :: tws_grc                (:)   ! grc total water storage (mm H2O)
-
-     real(r8), pointer :: total_plant_stored_h2o_col(:) ! col water that is bound in plants, including roots, sapwood, leaves, etc
-                                                        ! in most cases, the vegetation scheme does not have a dynamic
-                                                        ! water storage in plants, and thus 0.0 is a suitable for the trivial case.
-                                                        ! When FATES is coupled in with plant hydraulics turned on, this storage
-                                                        ! term is set to non-zero. (kg/m2 H2O)
-
-     real(r8), pointer :: snw_rds_col            (:,:) ! col snow grain radius (col,lyr)    [m^-6, microns]
-     real(r8), pointer :: snw_rds_top_col        (:)   ! col snow grain radius (top layer)  [m^-6, microns]
-     real(r8), pointer :: h2osno_top_col         (:)   ! col top-layer mass of snow  [kg]
-     real(r8), pointer :: sno_liq_top_col        (:)   ! col snow liquid water fraction (mass), top layer  [fraction]
-
-     real(r8), pointer :: q_ref2m_patch          (:)   ! patch 2 m height surface specific humidity (kg/kg)
-     real(r8), pointer :: rh_ref2m_patch         (:)   ! patch 2 m height surface relative humidity (%)
-     real(r8), pointer :: rh_ref2m_r_patch       (:)   ! patch 2 m height surface relative humidity - rural (%)
-     real(r8), pointer :: rh_ref2m_u_patch       (:)   ! patch 2 m height surface relative humidity - urban (%)
-     real(r8), pointer :: rh_af_patch            (:)   ! patch fractional humidity of canopy air (dimensionless) ! private
-     real(r8), pointer :: rh10_af_patch          (:)   ! 10-day mean patch fractional humidity of canopy air (dimensionless)
-     real(r8), pointer :: qg_snow_col            (:)   ! col ground specific humidity [kg/kg]
-     real(r8), pointer :: qg_soil_col            (:)   ! col ground specific humidity [kg/kg]
-     real(r8), pointer :: qg_h2osfc_col          (:)   ! col ground specific humidity [kg/kg]
-     real(r8), pointer :: qg_col                 (:)   ! col ground specific humidity [kg/kg]
-     real(r8), pointer :: dqgdT_col              (:)   ! col d(qg)/dT
-     real(r8), pointer :: qaf_lun                (:)   ! lun urban canopy air specific humidity (kg/kg)
-
-     ! Fractions
-     real(r8), pointer :: frac_sno_col           (:)   ! col fraction of ground covered by snow (0 to 1)
-     real(r8), pointer :: frac_sno_eff_col       (:)   ! col fraction of ground covered by snow (0 to 1)
-     real(r8), pointer :: frac_iceold_col        (:,:) ! col fraction of ice relative to the tot water (new) (-nlevsno+1:nlevgrnd) 
-     real(r8), pointer :: frac_h2osfc_col        (:)   ! col fractional area with surface water greater than zero
-     real(r8), pointer :: frac_h2osfc_nosnow_col (:)   ! col fractional area with surface water greater than zero (if no snow present)
-     real(r8), pointer :: wf_col                 (:)   ! col soil water as frac. of whc for top 0.05 m (0-1) 
-     real(r8), pointer :: wf2_col                (:)   ! col soil water as frac. of whc for top 0.17 m (0-1) 
-     real(r8), pointer :: fwet_patch             (:)   ! patch canopy fraction that is wet (0 to 1)
-     real(r8), pointer :: fcansno_patch          (:)   ! patch canopy fraction that is snow covered (0 to 1)
-     real(r8), pointer :: fdry_patch             (:)   ! patch canopy fraction of foliage that is green and dry [-] (new)
-
-     ! Balance Checks
-
-     real(r8), pointer :: begwb_col              (:)   ! water mass begining of the time step
-     real(r8), pointer :: endwb_col              (:)   ! water mass end of the time step
-     real(r8), pointer :: errh2o_patch           (:)   ! water conservation error (mm H2O)
-     real(r8), pointer :: errh2o_col             (:)   ! water conservation error (mm H2O)
-     real(r8), pointer :: errh2osno_col          (:)   ! snow water conservation error(mm H2O)
 
    contains
 
      procedure          :: Init         
      procedure          :: Restart      
-     procedure, public  :: Reset 
      procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
+     procedure, private :: InitCold
 
   end type waterstate_type
 
-  ! minimum allowed snow effective radius (also "fresh snow" value) [microns]
-  real(r8), public, parameter :: snw_rds_min = 54.526_r8    
-
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
  !------------------------------------------------------------------------
@@ -119,31 +34,14 @@ module WaterstateType
 contains
 
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, &
-       h2osno_input_col, snow_depth_input_col, watsat_col, t_soisno_col)
+  subroutine Init(this, bounds, h2osno_input_col)
 
     class(waterstate_type)            :: this
     type(bounds_type) , intent(in)    :: bounds  
     real(r8)          , intent(inout) :: h2osno_input_col(bounds%begc:)
-    real(r8)          , intent(inout) :: snow_depth_input_col(bounds%begc:)
-    real(r8)          , intent(inout) :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
-    real(r8)          , intent(inout) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
-
-#ifdef __PGI
-# if __PGIC__ == 14 && __PGIC_MINOR__ == 7
-    ! COMPILER_BUG(bja, 2015-04, pgi 14.7-?) occurs at: call this%InitCold(...)
-    ! PGF90-F-0000-Internal compiler error. normalize_forall_array: non-conformable
-    ! not sure why this fixes things....
-    real(r8), allocatable :: workaround_for_pgi_internal_compiler_error(:)
-# endif
-#endif
 
     call this%InitAllocate(bounds) 
-
-    call this%InitHistory(bounds)
-
-    call this%InitCold(bounds, &
-       h2osno_input_col, snow_depth_input_col, watsat_col, t_soisno_col)
+    call this%InitCold(bounds, h2osno_input_col)
 
   end subroutine Init
 
@@ -161,708 +59,50 @@ subroutine InitAllocate(this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer :: begp, endp
     integer :: begc, endc
-    integer :: begl, endl
-    integer :: begg, endg
     !------------------------------------------------------------------------
 
-    begp = bounds%begp; endp= bounds%endp
     begc = bounds%begc; endc= bounds%endc
-    begl = bounds%begl; endl= bounds%endl
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate(this%snow_depth_col         (begc:endc))                     ; this%snow_depth_col         (:)   = nan
-    allocate(this%snow_persistence_col   (begc:endc))                     ; this%snow_persistence_col   (:)   = nan
-    allocate(this%snowdp_col             (begc:endc))                     ; this%snowdp_col             (:)   = nan
-    allocate(this%snowice_col            (begc:endc))                     ; this%snowice_col            (:)   = nan   
-    allocate(this%snowliq_col            (begc:endc))                     ; this%snowliq_col            (:)   = nan   
-    allocate(this%int_snow_col           (begc:endc))                     ; this%int_snow_col           (:)   = nan   
-    allocate(this%snow_layer_unity_col   (begc:endc,-nlevsno+1:0))        ; this%snow_layer_unity_col   (:,:) = nan
-    allocate(this%bw_col                 (begc:endc,-nlevsno+1:0))        ; this%bw_col                 (:,:) = nan   
-    allocate(this%h2osno_col             (begc:endc))                     ; this%h2osno_col             (:)   = nan   
-    allocate(this%h2osno_old_col         (begc:endc))                     ; this%h2osno_old_col         (:)   = nan   
-    allocate(this%h2osoi_liqice_10cm_col (begc:endc))                     ; this%h2osoi_liqice_10cm_col (:)   = nan   
-    allocate(this%h2osoi_vol_col         (begc:endc, 1:nlevgrnd))         ; this%h2osoi_vol_col         (:,:) = nan
-    allocate(this%air_vol_col            (begc:endc, 1:nlevgrnd))         ; this%air_vol_col            (:,:) = nan
-    allocate(this%h2osoi_liqvol_col      (begc:endc,-nlevsno+1:nlevgrnd)) ; this%h2osoi_liqvol_col      (:,:) = nan
-    allocate(this%h2osoi_ice_col         (begc:endc,-nlevsno+1:nlevgrnd)) ; this%h2osoi_ice_col         (:,:) = nan
-    allocate(this%h2osoi_liq_col         (begc:endc,-nlevsno+1:nlevgrnd)) ; this%h2osoi_liq_col         (:,:) = nan
-    allocate(this%h2osoi_ice_tot_col     (begc:endc))                     ; this%h2osoi_ice_tot_col     (:)   = nan
-    allocate(this%h2osoi_liq_tot_col     (begc:endc))                     ; this%h2osoi_liq_tot_col     (:)   = nan
-    allocate(this%h2ocan_patch           (begp:endp))                     ; this%h2ocan_patch           (:)   = nan  
-    allocate(this%snocan_patch           (begp:endp))                     ; this%snocan_patch           (:)   = nan  
-    allocate(this%liqcan_patch           (begp:endp))                     ; this%liqcan_patch           (:)   = nan  
-    allocate(this%snounload_patch        (begp:endp))                     ; this%snounload_patch        (:)   = nan  
-    allocate(this%h2osfc_col             (begc:endc))                     ; this%h2osfc_col             (:)   = nan   
-    allocate(this%swe_old_col            (begc:endc,-nlevsno+1:0))        ; this%swe_old_col            (:,:) = nan   
-    allocate(this%liq1_grc               (begg:endg))                     ; this%liq1_grc               (:)   = nan
-    allocate(this%liq2_grc               (begg:endg))                     ; this%liq2_grc               (:)   = nan
-    allocate(this%ice1_grc               (begg:endg))                     ; this%ice1_grc               (:)   = nan
-    allocate(this%ice2_grc               (begg:endg))                     ; this%ice2_grc               (:)   = nan
-    allocate(this%tws_grc                (begg:endg))                     ; this%tws_grc                (:)   = nan
-
-    allocate(this%total_plant_stored_h2o_col(begc:endc))                  ; this%total_plant_stored_h2o_col(:) = nan
-
-    allocate(this%snw_rds_col            (begc:endc,-nlevsno+1:0))        ; this%snw_rds_col            (:,:) = nan
-    allocate(this%snw_rds_top_col        (begc:endc))                     ; this%snw_rds_top_col        (:)   = nan
-    allocate(this%h2osno_top_col         (begc:endc))                     ; this%h2osno_top_col         (:)   = nan
-    allocate(this%sno_liq_top_col        (begc:endc))                     ; this%sno_liq_top_col        (:)   = nan
-
-    allocate(this%qg_snow_col            (begc:endc))                     ; this%qg_snow_col            (:)   = nan   
-    allocate(this%qg_soil_col            (begc:endc))                     ; this%qg_soil_col            (:)   = nan   
-    allocate(this%qg_h2osfc_col          (begc:endc))                     ; this%qg_h2osfc_col          (:)   = nan   
-    allocate(this%qg_col                 (begc:endc))                     ; this%qg_col                 (:)   = nan   
-    allocate(this%dqgdT_col              (begc:endc))                     ; this%dqgdT_col              (:)   = nan   
-    allocate(this%qaf_lun                (begl:endl))                     ; this%qaf_lun                (:)   = nan
-    allocate(this%q_ref2m_patch          (begp:endp))                     ; this%q_ref2m_patch          (:)   = nan
-    allocate(this%rh_ref2m_patch         (begp:endp))                     ; this%rh_ref2m_patch         (:)   = nan
-    allocate(this%rh_ref2m_u_patch       (begp:endp))                     ; this%rh_ref2m_u_patch       (:)   = nan
-    allocate(this%rh_ref2m_r_patch       (begp:endp))                     ; this%rh_ref2m_r_patch       (:)   = nan
-    allocate(this%rh_af_patch            (begp:endp))                     ; this%rh_af_patch            (:)   = nan
-    allocate(this%rh10_af_patch          (begp:endp))                     ; this%rh10_af_patch          (:)   = spval
+    allocate(this%h2osno_col(begc:endc)); this%h2osno_col(:) = nan   
 
-    allocate(this%frac_sno_col           (begc:endc))                     ; this%frac_sno_col           (:)   = nan
-    allocate(this%frac_sno_eff_col       (begc:endc))                     ; this%frac_sno_eff_col       (:)   = nan
-    allocate(this%frac_iceold_col        (begc:endc,-nlevsno+1:nlevgrnd)) ; this%frac_iceold_col        (:,:) = nan
-    allocate(this%frac_h2osfc_col        (begc:endc))                     ; this%frac_h2osfc_col        (:)   = nan 
-    allocate(this%frac_h2osfc_nosnow_col (begc:endc))                     ; this%frac_h2osfc_nosnow_col        (:)   = nan 
-    allocate(this%wf_col                 (begc:endc))                     ; this%wf_col                 (:)   = nan
-    allocate(this%wf2_col                (begc:endc))                     ; 
-    allocate(this%fwet_patch             (begp:endp))                     ; this%fwet_patch             (:)   = nan
-    allocate(this%fcansno_patch          (begp:endp))                     ; this%fcansno_patch          (:)   = nan
-    allocate(this%fdry_patch             (begp:endp))                     ; this%fdry_patch             (:)   = nan
-
-    allocate(this%begwb_col              (begc:endc))                     ; this%begwb_col              (:)   = nan
-    allocate(this%endwb_col              (begc:endc))                     ; this%endwb_col              (:)   = nan
-    allocate(this%errh2o_patch           (begp:endp))                     ; this%errh2o_patch           (:)   = nan
-    allocate(this%errh2o_col             (begc:endc))                     ; this%errh2o_col             (:)   = nan
-    allocate(this%errh2osno_col          (begc:endc))                     ; this%errh2osno_col          (:)   = nan
   end subroutine InitAllocate
 
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    use clm_varctl     , only : use_cn
-    use clm_varctl     , only : hist_wrtch4diag
-    use clm_varpar     , only : nlevsno, nlevsoi
-    use histFileMod    , only : hist_addfld1d, hist_addfld2d, no_snow_normal, no_snow_zero
-    !
-    ! !ARGUMENTS:
-    class(waterstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    integer           :: begg, endg
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    ! h2osno also includes snow that is part of the soil column (an 
-    ! initial snow layer is only created if h2osno > 10mm). 
-
-    data2dptr => this%h2osoi_liq_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_LIQH2O', units='kg/m2', type2d='levsno',  &
-         avgflag='A', long_name='Snow liquid water content', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    data2dptr => this%h2osoi_ice_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_ICE', units='kg/m2', type2d='levsno',  &
-         avgflag='A', long_name='Snow ice content', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    data2dptr => this%h2osoi_vol_col(begc:endc,1:nlevsoi)
-    call hist_addfld2d (fname='H2OSOI',  units='mm3/mm3', type2d='levsoi', &
-         avgflag='A', long_name='volumetric soil water (vegetated landunits only)', &
-         ptr_col=this%h2osoi_vol_col, l2g_scale_type='veg', default='inactive')
-
-!    this%h2osoi_liq_col(begc:endc,:) = spval
-!    call hist_addfld2d (fname='SOILLIQ',  units='kg/m2', type2d='levgrnd', &
-!         avgflag='A', long_name='soil liquid water (vegetated landunits only)', &
-!         ptr_col=this%h2osoi_liq_col, l2g_scale_type='veg')
-
-    data2dptr => this%h2osoi_liq_col(begc:endc,1:nlevsoi) 
-    call hist_addfld2d (fname='SOILLIQ',  units='kg/m2', type2d='levsoi', &
-         avgflag='A', long_name='soil liquid water (vegetated landunits only)', &
-         ptr_col=data2dptr, l2g_scale_type='veg', default='inactive')
-
-    data2dptr => this%h2osoi_ice_col(begc:endc,1:nlevsoi)
-    call hist_addfld2d (fname='SOILICE',  units='kg/m2', type2d='levsoi', &
-         avgflag='A', long_name='soil ice (vegetated landunits only)', &
-         ptr_col=data2dptr, l2g_scale_type='veg', default='inactive')
-
-    this%h2osoi_liqice_10cm_col(begc:endc) = spval
-    call hist_addfld1d (fname='SOILWATER_10CM',  units='kg/m2', &
-         avgflag='A', long_name='soil liquid water + ice in top 10cm of soil (veg landunits only)', &
-         ptr_col=this%h2osoi_liqice_10cm_col, set_urb=spval, set_lake=spval, l2g_scale_type='veg', default='inactive')
-
-    this%h2osoi_liq_tot_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTSOILLIQ',  units='kg/m2', &
-         avgflag='A', long_name='vertically summed soil liquid water (veg landunits only)', &
-         ptr_col=this%h2osoi_liq_tot_col, set_urb=spval, set_lake=spval, l2g_scale_type='veg', default='inactive')
-
-    this%h2osoi_ice_tot_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTSOILICE',  units='kg/m2', &
-         avgflag='A', long_name='vertically summed soil cie (veg landunits only)', &
-         ptr_col=this%h2osoi_ice_tot_col, set_urb=spval, set_lake=spval, l2g_scale_type='veg', default='inactive')
-
-    this%h2ocan_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='H2OCAN', units='mm',  &
-         avgflag='A', long_name='intercepted water', &
-         ptr_patch=this%h2ocan_patch, set_lake=0._r8, default='inactive')
-
-    this%snocan_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='SNOCAN', units='mm',  &
-         avgflag='A', long_name='intercepted snow', &
-         ptr_patch=this%snocan_patch, set_lake=0._r8, default='inactive')
-
-    this%liqcan_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='LIQCAN', units='mm',  &
-         avgflag='A', long_name='intercepted liquid water', &
-         ptr_patch=this%liqcan_patch, set_lake=0._r8, default='inactive')
-
-    this%snounload_patch(begp:endp) = spval 
-    call hist_addfld1d (fname='SNOUNLOAD', units='mm',  &
-         avgflag='A', long_name='Canopy snow unloading', &
-         ptr_patch=this%snounload_patch, set_lake=0._r8, default='inactive')
-
-    call hist_addfld1d (fname='H2OSNO',  units='mm',  &
-         avgflag='A', long_name='snow depth (liquid water)', &
-         ptr_col=this%h2osno_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='H2OSNO_ICE', units='mm',  &
-         avgflag='A', long_name='snow depth (liquid water, ice landunits only)', &
-         ptr_col=this%h2osno_col, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%liq1_grc(begg:endg) = spval
-    call hist_addfld1d (fname='LIQUID_CONTENT1',  units='mm',  &
-         avgflag='A', long_name='initial gridcell total liq content', &
-         ptr_lnd=this%liq1_grc, default='inactive')
-
-    this%liq2_grc(begg:endg) = spval
-    call hist_addfld1d (fname='LIQUID_CONTENT2',  units='mm',  &  
-         avgflag='A', long_name='post landuse change gridcell total liq content', &              
-         ptr_lnd=this%liq2_grc, default='inactive')     
-
-    this%ice1_grc(begg:endg) = spval
-    call hist_addfld1d (fname='ICE_CONTENT1',  units='mm',  &  
-         avgflag='A', long_name='initial gridcell total ice content', &              
-         ptr_lnd=this%ice1_grc, default='inactive')     
-
-    this%ice2_grc(begg:endg) = spval
-    call hist_addfld1d (fname='ICE_CONTENT2',  units='mm',  &  
-         avgflag='A', long_name='post land cover change total ice content', &              
-         ptr_lnd=this%ice2_grc, default='inactive')
-
-    this%h2osfc_col(begc:endc) = spval
-    call hist_addfld1d (fname='H2OSFC',  units='mm',  &
-         avgflag='A', long_name='surface water depth', &
-         ptr_col=this%h2osfc_col, default='inactive')
-
-    this%tws_grc(begg:endg) = spval
-    call hist_addfld1d (fname='TWS',  units='mm',  &
-         avgflag='A', long_name='total water storage', &
-         ptr_lnd=this%tws_grc, default='inactive')
-
-    ! (rgk 02-02-2017) There is intentionally no entry  here for stored plant water
-    !                  I think that since the value is zero in all cases except
-    !                  for FATES plant hydraulics, it will be confusing for users
-    !                  when they see their plants have no water in output files.
-    !                  So it is not useful diagnostic information. The information
-    !                  can be provided through FATES specific history diagnostics
-    !                  if need be.
-
-    ! Humidity
-
-    this%q_ref2m_patch(begp:endp) = spval
-    call hist_addfld1d (fname='Q2M', units='kg/kg',  &
-         avgflag='A', long_name='2m specific humidity', &
-         ptr_patch=this%q_ref2m_patch, default='inactive')
-
-    this%rh_ref2m_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RH2M', units='%',  &
-         avgflag='A', long_name='2m relative humidity', &
-         ptr_patch=this%rh_ref2m_patch, default='inactive')
-
-    this%rh_ref2m_r_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RH2M_R', units='%',  &
-         avgflag='A', long_name='Rural 2m specific humidity', &
-         ptr_patch=this%rh_ref2m_r_patch, set_spec=spval, default='inactive')
-
-    this%rh_ref2m_u_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RH2M_U', units='%',  &
-         avgflag='A', long_name='Urban 2m relative humidity', &
-         ptr_patch=this%rh_ref2m_u_patch, set_nourb=spval, default='inactive')
-
-    this%rh_af_patch(begp:endp) = spval
-    call hist_addfld1d (fname='RHAF', units='fraction', &
-         avgflag='A', long_name='fractional humidity of canopy air', &
-         ptr_patch=this%rh_af_patch, set_spec=spval, default='inactive')
-
-    if(use_luna)then
-       call hist_addfld1d (fname='RHAF10', units='fraction', &
-        avgflag='A', long_name='10 day running mean of fractional humidity of canopy air', &
-        ptr_patch=this%rh10_af_patch, set_spec=spval, default='inactive')
-    endif
-
-    ! Fractions
-
-    this%frac_h2osfc_col(begc:endc) = spval
-    call hist_addfld1d (fname='FH2OSFC',  units='unitless',  &
-         avgflag='A', long_name='fraction of ground covered by surface water', &
-         ptr_col=this%frac_h2osfc_col, default='inactive')
-
-    this%frac_h2osfc_nosnow_col(begc:endc) = spval
-    call hist_addfld1d (fname='FH2OSFC_NOSNOW',  units='unitless',  &
-         avgflag='A', &
-         long_name='fraction of ground covered by surface water (if no snow present)', &
-         ptr_col=this%frac_h2osfc_nosnow_col, default='inactive')
-
-    this%frac_sno_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSNO',  units='unitless',  &
-         avgflag='A', long_name='fraction of ground covered by snow', &
-         ptr_col=this%frac_sno_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%frac_sno_eff_col(begc:endc) = spval
-    call hist_addfld1d (fname='FSNO_EFF',  units='unitless',  &
-         avgflag='A', long_name='effective fraction of ground covered by snow', &
-         ptr_col=this%frac_sno_eff_col, c2l_scale_type='urbanf', default='inactive')
-
-    if (use_cn) then
-       this%fwet_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FWET', units='proportion', &
-            avgflag='A', long_name='fraction of canopy that is wet', &
-            ptr_patch=this%fwet_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%fcansno_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FCANSNO', units='proportion', &
-            avgflag='A', long_name='fraction of canopy that is wet', &
-            ptr_patch=this%fcansno_patch, default='inactive')
-    end if
-
-    if (use_cn) then
-       this%fdry_patch(begp:endp) = spval
-       call hist_addfld1d (fname='FDRY', units='proportion', &
-            avgflag='A', long_name='fraction of foliage that is green and dry', &
-            ptr_patch=this%fdry_patch, default='inactive')
-    end if
-
-    if (use_cn)then
-       this%frac_iceold_col(begc:endc,:) = spval
-       call hist_addfld2d (fname='FRAC_ICEOLD', units='proportion', type2d='levgrnd', &
-            avgflag='A', long_name='fraction of ice relative to the tot water', &
-            ptr_col=this%frac_iceold_col, default='inactive')
-    end if
-
-    ! Snow properties - these will be vertically averaged over the snow profile
-
-    this%snow_depth_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOW_DEPTH',  units='m',  &
-         avgflag='A', long_name='snow height of snow covered area', &
-         ptr_col=this%snow_depth_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='SNOW_DEPTH_ICE', units='m',  &
-         avgflag='A', long_name='snow height of snow covered area (ice landunits only)', &
-         ptr_col=this%snow_depth_col, c2l_scale_type='urbanf', l2g_scale_type='ice', &
-         default='inactive')
-
-    this%snowdp_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOWDP',  units='m',  &
-         avgflag='A', long_name='gridcell mean snow height', &
-         ptr_col=this%snowdp_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%snowliq_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOWLIQ',  units='kg/m2',  &
-         avgflag='A', long_name='snow liquid water', &
-         ptr_col=this%snowliq_col, default='inactive')
-
-    this%snowice_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOWICE',  units='kg/m2', &
-         avgflag='A', long_name='snow ice', &
-         ptr_col=this%snowice_col, default='inactive')
-
-    this%int_snow_col(begc:endc) = spval
-    call hist_addfld1d (fname='INT_SNOW',  units='mm',  &
-         avgflag='A', long_name='accumulated swe (vegetated landunits only)', &
-         ptr_col=this%int_snow_col, l2g_scale_type='veg', &
-         default='inactive')
-
-    call hist_addfld1d (fname='INT_SNOW_ICE',  units='mm',  &
-         avgflag='A', long_name='accumulated swe (ice landunits only)', &
-         ptr_col=this%int_snow_col, l2g_scale_type='ice', &
-         default='inactive')
-
-    this%snow_persistence_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOW_PERSISTENCE',  units='seconds',  &
-         avgflag='I', long_name='Length of time of continuous snow cover (nat. veg. landunits only)', &
-         ptr_col=this%snow_persistence_col, l2g_scale_type='natveg', default='inactive') 
-
-    if (use_cn) then
-       this%wf_col(begc:endc) = spval
-       call hist_addfld1d (fname='WF', units='proportion', &
-            avgflag='A', long_name='soil water as frac. of whc for top 0.05 m', &
-            ptr_col=this%wf_col, default='inactive')
-    end if
-
-    this%h2osno_top_col(begc:endc) = spval
-    call hist_addfld1d (fname='H2OSNO_TOP', units='kg/m2', &
-         avgflag='A', long_name='mass of snow in top snow layer', &
-         ptr_col=this%h2osno_top_col, set_urb=spval, default='inactive')
-
-    this%snw_rds_top_col(begc:endc) = spval 
-    call hist_addfld1d (fname='SNORDSL', units='m^-6', &
-         avgflag='A', long_name='top snow layer effective grain radius', &
-         ptr_col=this%snw_rds_top_col, set_urb=spval, default='inactive')
-
-    this%sno_liq_top_col(begc:endc) = spval 
-    call hist_addfld1d (fname='SNOLIQFL', units='fraction', &
-         avgflag='A', long_name='top snow layer liquid water fraction (land)', &
-         ptr_col=this%sno_liq_top_col, set_urb=spval, default='inactive')
-
-    ! We determine the fractional time (and fraction of the grid cell) over which each
-    ! snow layer existed by running the snow averaging routine on a field whose value is 1
-    ! everywhere
-    data2dptr => this%snow_layer_unity_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_EXISTENCE', units='unitless', type2d='levsno', &
-         avgflag='A', long_name='Fraction of averaging period for which each snow layer existed', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_zero, default='inactive')
-
-    this%bw_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%bw_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_BW', units='kg/m3', type2d='levsno', &
-         avgflag='A', long_name='Partial density of water in the snow pack (ice + liquid)', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_BW_ICE', units='kg/m3', type2d='levsno', &
-         avgflag='A', long_name='Partial density of water in the snow pack (ice + liquid, ice landunits only)', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%snw_rds_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%snw_rds_col(:,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_GS', units='Microns', type2d='levsno',  &
-         avgflag='A', long_name='Mean snow grain size', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_GS_ICE', units='Microns', type2d='levsno',  &
-         avgflag='A', long_name='Mean snow grain size (ice landunits only)', &
-         ptr_col=data2dptr, no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%errh2o_col(begc:endc) = spval
-    call hist_addfld1d (fname='ERRH2O', units='mm',  &
-         avgflag='A', long_name='total water conservation error', &
-         ptr_col=this%errh2o_col, default='inactive')
-
-    this%errh2osno_col(begc:endc) = spval
-    call hist_addfld1d (fname='ERRH2OSNO',  units='mm',  &
-         avgflag='A', long_name='imbalance in snow depth (liquid water)', &
-         ptr_col=this%errh2osno_col, c2l_scale_type='urbanf', default='inactive')
-
-  end subroutine InitHistory
-
   !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, &
-       h2osno_input_col, snow_depth_input_col, watsat_col, t_soisno_col)
+  subroutine InitCold(this, bounds, h2osno_input_col)
     !
     ! !DESCRIPTION:
-    ! Initialize time constant variables and cold start conditions 
+    ! Initialize time constant variables and cold start conditions
     !
     ! !USES:
-    use shr_const_mod   , only : shr_const_pi
     use shr_log_mod     , only : errMsg => shr_log_errMsg
-    use shr_spfn_mod    , only : shr_spfn_erf
     use shr_kind_mod    , only : r8 => shr_kind_r8
-    use shr_const_mod   , only : SHR_CONST_TKFRZ
-    use clm_varpar      , only : nlevsoi, nlevgrnd, nlevsno, nlevlak, nlevurb
-    use landunit_varcon , only : istwet, istsoil, istdlak, istcrop, istice_mec  
-    use column_varcon   , only : icol_shadewall, icol_road_perv
-    use column_varcon   , only : icol_road_imperv, icol_roof, icol_sunwall
-    use clm_varcon      , only : denice, denh2o, spval, sb, bdsno 
-    use clm_varcon      , only : zlnd, tfrz, spval, pc
-    use clm_varctl      , only : fsurdat, iulog
-    use clm_varctl        , only : use_bedrock
-    use spmdMod         , only : masterproc
-    use abortutils      , only : endrun
-    use fileutils       , only : getfil
-    use ncdio_pio       , only : file_desc_t, ncd_io
     !
     ! !ARGUMENTS:
     class(waterstate_type)                :: this
     type(bounds_type)     , intent(in)    :: bounds
     real(r8)              , intent(in)    :: h2osno_input_col(bounds%begc:)
-    real(r8)              , intent(in)    :: snow_depth_input_col(bounds%begc:)
-    real(r8)              , intent(in)    :: watsat_col(bounds%begc:, 1:)          ! volumetric soil water at saturation (porosity)
-    real(r8)              , intent(in)    :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin)
     !
     ! !LOCAL VARIABLES:
-    integer            :: p,c,j,l,g,lev,nlevs 
-    real(r8)           :: maxslope, slopemax, minslope
-    real(r8)           :: d, fd, dfdd, slope0,slopebeta
-    real(r8) ,pointer  :: std (:)     
-    logical            :: readvar 
-    type(file_desc_t)  :: ncid        
-    character(len=256) :: locfn       
-    real(r8)           :: snowbd      ! temporary calculation of snow bulk density (kg/m3)
-    real(r8)           :: fmelt       ! snowbd/100
-    integer            :: nbedrock
+    integer :: c
     !-----------------------------------------------------------------------
 
     SHR_ASSERT_ALL((ubound(h2osno_input_col)     == (/bounds%endc/))          , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(snow_depth_input_col) == (/bounds%endc/))          , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(watsat_col)           == (/bounds%endc,nlevgrnd/)) , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(t_soisno_col)         == (/bounds%endc,nlevgrnd/)) , errMsg(sourcefile, __LINE__))
 
     ! The first three arrays are initialized from the input argument
     do c = bounds%begc,bounds%endc
-       this%h2osno_col(c)             = h2osno_input_col(c) 
-       this%int_snow_col(c)           = h2osno_input_col(c) 
-       this%snow_depth_col(c)         = snow_depth_input_col(c)
-       this%snow_persistence_col(c)   = 0._r8
-       this%snow_layer_unity_col(c,:) = 1._r8
-    end do
-
-    do c = bounds%begc,bounds%endc
-       this%wf_col(c) = spval
-       this%wf2_col(c) = spval
-    end do
-
-    do l = bounds%begl, bounds%endl 
-       if (lun%urbpoi(l)) then
-          if (use_vancouver) then
-             this%qaf_lun(l) = 0.0111_r8
-          else if (use_mexicocity) then
-             this%qaf_lun(l) = 0.00248_r8
-          else
-             this%qaf_lun(l) = 1.e-4_r8 ! Arbitrary set since forc_q is not yet available
-          end if
-       end if
+       this%h2osno_col(c)             = h2osno_input_col(c)
     end do
 
-    ! Water Stored in plants is almost always a static entity, with the exception
-    ! of when FATES-hydraulics is used. As such, this is trivially set to 0.0 (rgk 03-2017)
-    this%total_plant_stored_h2o_col(bounds%begc:bounds%endc) = 0.0_r8
-
-
-    associate(snl => col%snl) 
-
-      this%h2osfc_col(bounds%begc:bounds%endc) = 0._r8
-      this%h2ocan_patch(bounds%begp:bounds%endp) = 0._r8
-      this%snocan_patch(bounds%begp:bounds%endp) = 0._r8
-      this%liqcan_patch(bounds%begp:bounds%endp) = 0._r8
-      this%snounload_patch(bounds%begp:bounds%endp) = 0._r8
-      this%frac_h2osfc_col(bounds%begc:bounds%endc) = 0._r8
-
-      this%fwet_patch(bounds%begp:bounds%endp) = 0._r8
-      this%fdry_patch(bounds%begp:bounds%endp) = 0._r8
-      this%fcansno_patch(bounds%begp:bounds%endp) = 0._r8
-      !--------------------------------------------
-      ! Set snow water
-      !--------------------------------------------
-
-      ! Note: Glacier_mec columns are initialized with half the maximum snow cover.
-      ! This gives more realistic values of qflx_glcice sooner in the simulation
-      ! for columns with net ablation, at the cost of delaying ice formation
-      ! in columns with net accumulation.
-
-      do c = bounds%begc, bounds%endc
-         l = col%landunit(c)
-         if (lun%urbpoi(l)) then
-            ! From Bonan 1996 (LSM technical note)
-            this%frac_sno_col(c) = min( this%snow_depth_col(c)/0.05_r8, 1._r8)
-         else
-            this%frac_sno_col(c) = 0._r8
-            ! snow cover fraction as in Niu and Yang 2007
-            if(this%snow_depth_col(c) > 0.0)  then
-               snowbd   = min(400._r8, this%h2osno_col(c)/this%snow_depth_col(c)) !bulk density of snow (kg/m3)
-               fmelt    = (snowbd/100.)**1.
-               ! 100 is the assumed fresh snow density; 1 is a melting factor that could be
-               ! reconsidered, optimal value of 1.5 in Niu et al., 2007
-               this%frac_sno_col(c) = tanh( this%snow_depth_col(c) /(2.5 * zlnd * fmelt) )
-            endif
-         end if
-      end do
-
-      do c = bounds%begc,bounds%endc
-         if (snl(c) < 0) then
-            this%snw_rds_col(c,snl(c)+1:0)        = snw_rds_min
-            this%snw_rds_col(c,-nlevsno+1:snl(c)) = 0._r8
-            this%snw_rds_top_col(c)               = snw_rds_min
-         elseif (this%h2osno_col(c) > 0._r8) then
-            this%snw_rds_col(c,0)                 = snw_rds_min
-            this%snw_rds_col(c,-nlevsno+1:-1)     = 0._r8
-            this%snw_rds_top_col(c)               = spval
-            this%sno_liq_top_col(c)               = spval
-         else
-            this%snw_rds_col(c,:)                 = 0._r8
-            this%snw_rds_top_col(c)               = spval
-            this%sno_liq_top_col(c)               = spval
-         endif
-      end do
-
-      !--------------------------------------------
-      ! Set soil water
-      !--------------------------------------------
-
-      ! volumetric water is set first and liquid content and ice lens are obtained
-      ! NOTE: h2osoi_vol, h2osoi_liq and h2osoi_ice only have valid values over soil
-      ! and urban pervious road (other urban columns have zero soil water)
-
-      this%h2osoi_vol_col(bounds%begc:bounds%endc,         1:) = spval
-      this%h2osoi_liq_col(bounds%begc:bounds%endc,-nlevsno+1:) = spval
-      this%h2osoi_ice_col(bounds%begc:bounds%endc,-nlevsno+1:) = spval
-      do c = bounds%begc,bounds%endc
-         l = col%landunit(c)
-         if (.not. lun%lakpoi(l)) then  !not lake
-
-            ! volumetric water
-            if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-               nlevs = nlevgrnd
-               do j = 1, nlevs
-                  if (use_bedrock) then
-                     nbedrock = col%nbedrock(c)
-                  else
-                     nbedrock = nlevsoi
-                  endif
-                  if (j > nbedrock) then
-                     this%h2osoi_vol_col(c,j) = 0.0_r8
-                  else
-                     this%h2osoi_vol_col(c,j) = 0.15_r8
-                  endif
-               end do
-            else if (lun%urbpoi(l)) then
-               if (col%itype(c) == icol_road_perv) then
-                  nlevs = nlevgrnd
-                  do j = 1, nlevs
-                     if (j <= nlevsoi) then
-                        this%h2osoi_vol_col(c,j) = 0.3_r8
-                     else
-                        this%h2osoi_vol_col(c,j) = 0.0_r8
-                     end if
-                  end do
-               else if (col%itype(c) == icol_road_imperv) then
-                  nlevs = nlevgrnd
-                  do j = 1, nlevs
-                     this%h2osoi_vol_col(c,j) = 0.0_r8
-                  end do
-               else
-                  nlevs = nlevurb
-                  do j = 1, nlevs
-                     this%h2osoi_vol_col(c,j) = 0.0_r8
-                  end do
-               end if
-            else if (lun%itype(l) == istwet) then
-               nlevs = nlevgrnd
-               do j = 1, nlevs
-                  if (j > nlevsoi) then
-                     this%h2osoi_vol_col(c,j) = 0.0_r8
-                  else
-                     this%h2osoi_vol_col(c,j) = 1.0_r8
-                  endif
-               end do
-            else if (lun%itype(l) == istice_mec) then
-               nlevs = nlevgrnd 
-               do j = 1, nlevs
-                  this%h2osoi_vol_col(c,j) = 1.0_r8
-               end do
-            endif
-            do j = 1, nlevs
-               this%h2osoi_vol_col(c,j) = min(this%h2osoi_vol_col(c,j), watsat_col(c,j))
-               if (t_soisno_col(c,j) <= SHR_CONST_TKFRZ) then
-                  this%h2osoi_ice_col(c,j) = col%dz(c,j)*denice*this%h2osoi_vol_col(c,j)
-                  this%h2osoi_liq_col(c,j) = 0._r8
-               else
-                  this%h2osoi_ice_col(c,j) = 0._r8
-                  this%h2osoi_liq_col(c,j) = col%dz(c,j)*denh2o*this%h2osoi_vol_col(c,j)
-               endif
-            end do
-            do j = -nlevsno+1, 0
-               if (j > snl(c)) then
-                  this%h2osoi_ice_col(c,j) = col%dz(c,j)*250._r8
-                  this%h2osoi_liq_col(c,j) = 0._r8
-               end if
-            end do
-         end if
-      end do
-
-
-      !--------------------------------------------
-      ! Set Lake water
-      !--------------------------------------------
-
-      do c = bounds%begc, bounds%endc
-         l = col%landunit(c)
-
-         if (lun%lakpoi(l)) then
-            do j = -nlevsno+1, 0
-               if (j > snl(c)) then
-                  this%h2osoi_ice_col(c,j) = col%dz(c,j)*bdsno
-                  this%h2osoi_liq_col(c,j) = 0._r8
-               end if
-            end do
-            do j = 1,nlevgrnd
-               if (j <= nlevsoi) then ! soil
-                  this%h2osoi_vol_col(c,j) = watsat_col(c,j)
-                  this%h2osoi_liq_col(c,j) = spval
-                  this%h2osoi_ice_col(c,j) = spval
-               else                  ! bedrock
-                  this%h2osoi_vol_col(c,j) = 0._r8
-               end if
-            end do
-         end if
-      end do
-
-      !--------------------------------------------
-      ! For frozen layers !TODO - does the following make sense ???? it seems to overwrite everything
-      !--------------------------------------------
-
-      do c = bounds%begc, bounds%endc
-         do j = 1,nlevgrnd
-            if (this%h2osoi_vol_col(c,j) /= spval) then
-               if (t_soisno_col(c,j) <= tfrz) then
-                  this%h2osoi_ice_col(c,j) = col%dz(c,j)*denice*this%h2osoi_vol_col(c,j)
-                  this%h2osoi_liq_col(c,j) = 0._r8
-               else
-                  this%h2osoi_ice_col(c,j) = 0._r8
-                  this%h2osoi_liq_col(c,j) = col%dz(c,j)*denh2o*this%h2osoi_vol_col(c,j)
-               endif
-            end if
-         end do
-      end do
-
-    end associate
-
   end subroutine InitCold
 
   !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag, &
-       watsat_col)
+  subroutine Restart(this, bounds, ncid, flag)
     ! 
     ! !DESCRIPTION:
     ! Read/Write module information to/from restart file.
     !
     ! !USES:
-    use spmdMod          , only : masterproc
-    use clm_varcon       , only : denice, denh2o, pondmx, watmin, spval, nameg
-    use landunit_varcon  , only : istcrop, istdlak, istsoil  
-    use column_varcon    , only : icol_roof, icol_sunwall, icol_shadewall
-    use clm_time_manager , only : is_first_step
-    use clm_varctl       , only : bound_h2osoi
-    use ncdio_pio        , only : file_desc_t, ncd_io, ncd_double
+    use ncdio_pio        , only : file_desc_t, ncd_double
     use restUtilMod
     !
     ! !ARGUMENTS:
@@ -870,253 +110,16 @@ subroutine Restart(this, bounds, ncid, flag, &
     type(bounds_type), intent(in)    :: bounds 
     type(file_desc_t), intent(inout) :: ncid   ! netcdf id
     character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    real(r8)         , intent(in)    :: watsat_col (bounds%begc:, 1:)  ! volumetric soil water at saturation (porosity)
     !
     ! !LOCAL VARIABLES:
-    integer  :: c,l,j,nlevs
     logical  :: readvar
-    real(r8) :: maxwatsat    ! maximum porosity    
-    real(r8) :: excess       ! excess volumetric soil water
-    real(r8) :: totwat       ! total soil water (mm)
     !------------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(watsat_col) == (/bounds%endc,nlevgrnd/)) , errMsg(sourcefile, __LINE__))
-
-    call restartvar(ncid=ncid, flag=flag, varname='INT_SNOW', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='accuumulated snow', units='mm', &
-         interpinic_flag='interp', readvar=readvar, data=this%int_snow_col)
-    if (flag=='read' .and. .not. readvar) then
-       this%int_snow_col(:) = 0.0_r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='H2OSFC', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='surface water', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%h2osfc_col)
-    if (flag=='read' .and. .not. readvar) then
-       this%h2osfc_col(bounds%begc:bounds%endc) = 0.0_r8
-    end if
-
     call restartvar(ncid=ncid, flag=flag, varname='H2OSNO', xtype=ncd_double,  &
          dim1name='column', &
          long_name='snow water', units='kg/m2', &
          interpinic_flag='interp', readvar=readvar, data=this%h2osno_col)
 
-    call restartvar(ncid=ncid, flag=flag, varname='H2OSOI_LIQ', xtype=ncd_double,  &
-         dim1name='column', dim2name='levtot', switchdim=.true., &
-         long_name='liquid water', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%h2osoi_liq_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='H2OSOI_ICE', xtype=ncd_double,   &
-         dim1name='column', dim2name='levtot', switchdim=.true., &
-         long_name='ice lens', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%h2osoi_ice_col)
-         
-    call restartvar(ncid=ncid, flag=flag, varname='H2OCAN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='canopy water', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%h2ocan_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='SNOCAN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='canopy snow water', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%snocan_patch)
-
-    ! NOTE(wjs, 2015-07-01) In old restart files, there was no LIQCAN variable. However,
-    ! H2OCAN had similar meaning. So if we can't find LIQCAN, use H2OCAN to initialize
-    ! liqcan_patch.
-    call restartvar(ncid=ncid, flag=flag, varname='LIQCAN:H2OCAN', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='canopy liquid water', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%liqcan_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='SNOUNLOAD', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='Canopy snow unloading', units='kg/m2', &
-         interpinic_flag='interp', readvar=readvar, data=this%snounload_patch)
-
-    ! TWS is needed when methane is on and the TWS_inversion is used to get exact
-    ! restart.
-    call restartvar(ncid=ncid, flag=flag, varname='TWS', xtype=ncd_double,  &
-         dim1name=nameg, &
-         long_name='Total Water Storage', units='mm', &
-         interpinic_flag='interp', readvar=readvar, data=this%tws_grc)
-
-    if(use_luna)then
-       call restartvar(ncid=ncid, flag=flag, varname='rh10', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean boundary layer relatie humidity', units='unitless', &
-            interpinic_flag='interp', readvar=readvar, data=this%rh10_af_patch)
-    endif
-
-    ! Determine volumetric soil water (for read only)
-    if (flag == 'read' ) then
-       do c = bounds%begc, bounds%endc
-          l = col%landunit(c)
-          if ( col%itype(c) == icol_sunwall   .or. &
-               col%itype(c) == icol_shadewall .or. &
-               col%itype(c) == icol_roof )then
-             nlevs = nlevurb
-          else
-             nlevs = nlevgrnd
-          end if
-          if ( lun%itype(l) /= istdlak ) then ! This calculation is now done for lakes in initLake.
-             do j = 1,nlevs
-                this%h2osoi_vol_col(c,j) = this%h2osoi_liq_col(c,j)/(col%dz(c,j)*denh2o) &
-                                         + this%h2osoi_ice_col(c,j)/(col%dz(c,j)*denice)
-             end do
-          end if
-       end do
-    end if
-
-    ! If initial run -- ensure that water is properly bounded (read only)
-    if (flag == 'read' ) then
-       if ( is_first_step() .and. bound_h2osoi) then
-          do c = bounds%begc, bounds%endc
-             l = col%landunit(c)
-             if ( col%itype(c) == icol_sunwall .or. col%itype(c) == icol_shadewall .or. &
-                  col%itype(c) == icol_roof )then
-                nlevs = nlevurb
-             else
-                nlevs = nlevgrnd
-             end if
-             do j = 1,nlevs
-                l = col%landunit(c)
-                if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-                   this%h2osoi_liq_col(c,j) = max(0._r8,this%h2osoi_liq_col(c,j))
-                   this%h2osoi_ice_col(c,j) = max(0._r8,this%h2osoi_ice_col(c,j))
-                   this%h2osoi_vol_col(c,j) = this%h2osoi_liq_col(c,j)/(col%dz(c,j)*denh2o) &
-                                       + this%h2osoi_ice_col(c,j)/(col%dz(c,j)*denice)
-                   if (j == 1) then
-                      maxwatsat = (watsat_col(c,j)*col%dz(c,j)*1000.0_r8 + pondmx) / (col%dz(c,j)*1000.0_r8)
-                   else
-                      maxwatsat =  watsat_col(c,j)
-                   end if
-                   if (this%h2osoi_vol_col(c,j) > maxwatsat) then 
-                      excess = (this%h2osoi_vol_col(c,j) - maxwatsat)*col%dz(c,j)*1000.0_r8
-                      totwat = this%h2osoi_liq_col(c,j) + this%h2osoi_ice_col(c,j)
-                      this%h2osoi_liq_col(c,j) = this%h2osoi_liq_col(c,j) - &
-                                           (this%h2osoi_liq_col(c,j)/totwat) * excess
-                      this%h2osoi_ice_col(c,j) = this%h2osoi_ice_col(c,j) - &
-                                           (this%h2osoi_ice_col(c,j)/totwat) * excess
-                   end if
-                   this%h2osoi_liq_col(c,j) = max(watmin,this%h2osoi_liq_col(c,j))
-                   this%h2osoi_ice_col(c,j) = max(watmin,this%h2osoi_ice_col(c,j))
-                   this%h2osoi_vol_col(c,j) = this%h2osoi_liq_col(c,j)/(col%dz(c,j)*denh2o) &
-                                             + this%h2osoi_ice_col(c,j)/(col%dz(c,j)*denice)
-                end if
-             end do
-          end do
-       end if
-
-    endif   ! end if if-read flag
-
-    call restartvar(ncid=ncid, flag=flag, varname='FH2OSFC', xtype=ncd_double,  &
-         dim1name='column',&
-         long_name='fraction of ground covered by h2osfc (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%frac_h2osfc_col)
-    if (flag == 'read' .and. .not. readvar) then
-       this%frac_h2osfc_col(bounds%begc:bounds%endc) = 0.0_r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='SNOW_DEPTH', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='snow depth', units='m', &
-         interpinic_flag='interp', readvar=readvar, data=this%snow_depth_col) 
-
-    call restartvar(ncid=ncid, flag=flag, varname='SNOW_PERS', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='continuous snow cover time', units='sec', &
-         interpinic_flag='interp', readvar=readvar, data=this%snow_persistence_col)    
-    if (flag=='read' .and. .not. readvar) then
-         this%snow_persistence_col(:) = 0.0_r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='frac_sno_eff', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='fraction of ground covered by snow (0 to 1)',units='unitless', &
-         interpinic_flag='interp', readvar=readvar, data=this%frac_sno_eff_col)
-    if (flag == 'read' .and. .not. readvar) then
-       this%frac_sno_eff_col(bounds%begc:bounds%endc) = 0.0_r8
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='frac_sno', xtype=ncd_double,  & 
-         dim1name='column', &
-         long_name='fraction of ground covered by snow (0 to 1)',units='unitless',&
-         interpinic_flag='interp', readvar=readvar, data=this%frac_sno_col)
-
-    call restartvar(ncid=ncid, flag=flag, varname='FWET', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='fraction of canopy that is wet (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fwet_patch)
-
-    call restartvar(ncid=ncid, flag=flag, varname='FCANSNO', xtype=ncd_double,  &
-         dim1name='pft', &
-         long_name='fraction of canopy that is snow covered (0 to 1)', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fcansno_patch)
-
-    ! column type physical state variable - snw_rds
-    call restartvar(ncid=ncid, flag=flag, varname='snw_rds', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno', switchdim=.true., lowerb2=-nlevsno+1, upperb2=0, &
-         long_name='snow layer effective radius', units='um', &
-         interpinic_flag='interp', readvar=readvar, data=this%snw_rds_col)
-    if (flag == 'read' .and. .not. readvar) then
-
-       ! initial run, not restart: initialize snw_rds
-       if (masterproc) then
-          write(iulog,*) "SNICAR: This is an initial run (not a restart), and grain size/aerosol " // &
-               "mass data are not defined in initial condition file. Initialize snow " // &
-               "effective radius to fresh snow value, and snow/aerosol masses to zero."
-       endif
-
-       do c= bounds%begc, bounds%endc
-          if (col%snl(c) < 0) then
-             this%snw_rds_col(c,col%snl(c)+1:0) = snw_rds_min
-             this%snw_rds_col(c,-nlevsno+1:col%snl(c)) = 0._r8
-             this%snw_rds_top_col(c) = snw_rds_min
-             this%sno_liq_top_col(c) = this%h2osoi_liq_col(c,col%snl(c)+1) / &
-                                      (this%h2osoi_liq_col(c,col%snl(c)+1)+this%h2osoi_ice_col(c,col%snl(c)+1))
-          elseif (this%h2osno_col(c) > 0._r8) then
-             this%snw_rds_col(c,0) = snw_rds_min
-             this%snw_rds_col(c,-nlevsno+1:-1) = 0._r8
-             this%snw_rds_top_col(c) = spval
-             this%sno_liq_top_col(c) = spval
-          else
-             this%snw_rds_col(c,:) = 0._r8
-             this%snw_rds_top_col(c) = spval
-             this%sno_liq_top_col(c) = spval
-          endif
-       enddo
-    endif
-
-    call restartvar(ncid=ncid, flag=flag, varname='qaf', xtype=ncd_double, dim1name='landunit',                       &
-         long_name='urban canopy specific humidity', units='kg/kg',                                                   &
-         interpinic_flag='interp', readvar=readvar, data=this%qaf_lun)
-
-    if (use_cn) then
-       call restartvar(ncid=ncid, flag=flag, varname='wf', xtype=ncd_double,  &
-            dim1name='column', &
-            long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%wf_col) 
-    end if
-
-
-
   end subroutine Restart
 
-  !-----------------------------------------------------------------------
-  subroutine Reset(this, column)
-    !
-    ! !DESCRIPTION:
-    ! Intitialize SNICAR variables for fresh snow column
-    !
-    ! !ARGUMENTS:
-    class(waterstate_type) :: this
-    integer , intent(in)   :: column     ! column index
-    !-----------------------------------------------------------------------
-
-    this%snw_rds_col(column,0)  = snw_rds_min
-
-  end subroutine Reset
-
 end module WaterstateType
diff --git a/src/biogeophys/WaterfluxType.F90 b/src/biogeophys/WaterfluxType.F90
deleted file mode 100644
index 5541ab39ad..0000000000
--- a/src/biogeophys/WaterfluxType.F90
+++ /dev/null
@@ -1,721 +0,0 @@
-module WaterfluxType
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !
-  ! !USES:
-  use shr_kind_mod   , only: r8 => shr_kind_r8
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar     , only : nlevsno, nlevsoi
-  use clm_varcon     , only : spval
-  use decompMod      , only : bounds_type
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col                
-  use PatchType      , only : patch   
-  use CNSharedParamsMod           , only : use_fun             
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC TYPES:
-  type, public :: waterflux_type
-
-     ! water fluxes are in units or mm/s
-
-     real(r8), pointer :: qflx_prec_grnd_patch     (:)   ! patch water onto ground including canopy runoff [kg/(m2 s)]
-     real(r8), pointer :: qflx_prec_grnd_col       (:)   ! col water onto ground including canopy runoff [kg/(m2 s)]
-     real(r8), pointer :: qflx_rain_grnd_patch     (:)   ! patch rain on ground after interception (mm H2O/s) [+]
-     real(r8), pointer :: qflx_rain_grnd_col       (:)   ! col rain on ground after interception (mm H2O/s) [+]
-     real(r8), pointer :: qflx_snow_grnd_patch     (:)   ! patch snow on ground after interception (mm H2O/s) [+]
-     real(r8), pointer :: qflx_snow_grnd_col       (:)   ! col snow on ground after interception (mm H2O/s) [+]
-     real(r8), pointer :: qflx_sub_snow_patch      (:)   ! patch sublimation rate from snow pack (mm H2O /s) [+]
-     real(r8), pointer :: qflx_sub_snow_col        (:)   ! col sublimation rate from snow pack (mm H2O /s) [+]
-     real(r8), pointer :: qflx_evap_soi_patch      (:)   ! patch soil evaporation (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_soi_col        (:)   ! col soil evaporation (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_veg_patch      (:)   ! patch vegetation evaporation (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_veg_col        (:)   ! col vegetation evaporation (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_can_patch      (:)   ! patch evaporation from leaves and stems (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_can_col        (:)   ! col evaporation from leaves and stems (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_evap_tot_patch      (:)   ! patch pft_qflx_evap_soi + pft_qflx_evap_veg + qflx_tran_veg
-     real(r8), pointer :: qflx_evap_tot_col        (:)   ! col col_qflx_evap_soi + col_qflx_evap_veg + qflx_tran_veg
-     real(r8), pointer :: qflx_evap_grnd_patch     (:)   ! patch ground surface evaporation rate (mm H2O/s) [+]
-     real(r8), pointer :: qflx_evap_grnd_col       (:)   ! col ground surface evaporation rate (mm H2O/s) [+]
-     real(r8), pointer :: qflx_phs_neg_col         (:)   ! col sum of negative hydraulic redistribution fluxes (mm H2O/s) [+]
-
-     ! In the snow capping parametrization excess mass above h2osno_max is removed.  A breakdown of mass into liquid 
-     ! and solid fluxes is done, these are represented by qflx_snwcp_liq_col and qflx_snwcp_ice_col. 
-     real(r8), pointer :: qflx_snwcp_liq_col       (:)   ! col excess liquid h2o due to snow capping (outgoing) (mm H2O /s)
-     real(r8), pointer :: qflx_snwcp_ice_col       (:)   ! col excess solid h2o due to snow capping (outgoing) (mm H2O /s)
-     real(r8), pointer :: qflx_snwcp_discarded_liq_col(:) ! col excess liquid h2o due to snow capping, which we simply discard in order to reset the snow pack (mm H2O /s)
-     real(r8), pointer :: qflx_snwcp_discarded_ice_col(:) ! col excess solid h2o due to snow capping, which we simply discard in order to reset the snow pack (mm H2O /s)
-
-     real(r8), pointer :: qflx_tran_veg_patch      (:)   ! patch vegetation transpiration (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_tran_veg_col        (:)   ! col vegetation transpiration (mm H2O/s) (+ = to atm)
-     real(r8), pointer :: qflx_dew_snow_patch      (:)   ! patch surface dew added to snow pack (mm H2O /s) [+]
-     real(r8), pointer :: qflx_dew_snow_col        (:)   ! col surface dew added to snow pack (mm H2O /s) [+]
-     real(r8), pointer :: qflx_dew_grnd_patch      (:)   ! patch ground surface dew formation (mm H2O /s) [+]
-     real(r8), pointer :: qflx_dew_grnd_col        (:)   ! col ground surface dew formation (mm H2O /s) [+] (+ = to atm); usually eflx_bot >= 0)
-     real(r8), pointer :: qflx_prec_intr_patch     (:)   ! patch interception of precipitation [mm/s]
-     real(r8), pointer :: qflx_prec_intr_col       (:)   ! col interception of precipitation [mm/s]
-     real(r8), pointer :: qflx_snowindunload_patch (:)   ! patch canopy snow wind unloading (mm H2O /s)
-     real(r8), pointer :: qflx_snowindunload_col   (:)   ! col canopy snow wind unloading (mm H2O /s)
-     real(r8), pointer :: qflx_snotempunload_patch (:)   ! patch canopy snow temp unloading (mm H2O /s) 
-     real(r8), pointer :: qflx_snotempunload_col   (:)   ! col canopy snow temp unloading (mm H2O /s) 
-
-     real(r8), pointer :: qflx_ev_snow_patch       (:)   ! patch evaporation heat flux from snow       (mm H2O/s) [+ to atm]
-     real(r8), pointer :: qflx_ev_snow_col         (:)   ! col evaporation heat flux from snow         (mm H2O/s) [+ to atm]
-     real(r8), pointer :: qflx_ev_soil_patch       (:)   ! patch evaporation heat flux from soil       (mm H2O/s) [+ to atm]
-     real(r8), pointer :: qflx_ev_soil_col         (:)   ! col evaporation heat flux from soil         (mm H2O/s) [+ to atm]
-     real(r8), pointer :: qflx_ev_h2osfc_patch     (:)   ! patch evaporation heat flux from soil       (mm H2O/s) [+ to atm]
-     real(r8), pointer :: qflx_ev_h2osfc_col       (:)   ! col evaporation heat flux from soil         (mm H2O/s) [+ to atm]
-
-     real(r8), pointer :: qflx_adv_col             (:,:) ! col advective flux across different soil layer interfaces [mm H2O/s] [+ downward]
-     real(r8), pointer :: qflx_rootsoi_col         (:,:) ! col root and soil water exchange [mm H2O/s] [+ into root]
-     real(r8), pointer :: qflx_infl_col            (:)   ! col infiltration (mm H2O /s)
-     real(r8), pointer :: qflx_surf_col            (:)   ! col surface runoff (mm H2O /s)
-     real(r8), pointer :: qflx_drain_col           (:)   ! col sub-surface runoff (mm H2O /s)
-     real(r8), pointer :: qflx_top_soil_col        (:)   ! col net water input into soil from top (mm/s)
-     real(r8), pointer :: qflx_h2osfc_to_ice_col   (:)   ! col conversion of h2osfc to ice
-     real(r8), pointer :: qflx_h2osfc_surf_col     (:)   ! col surface water runoff
-     real(r8), pointer :: qflx_snow_h2osfc_col     (:)   ! col snow falling on surface water
-     real(r8), pointer :: qflx_drain_perched_col   (:)   ! col sub-surface runoff from perched wt (mm H2O /s)
-     real(r8), pointer :: qflx_deficit_col         (:)   ! col water deficit to keep non-negative liquid water content (mm H2O)   
-     real(r8), pointer :: qflx_floodc_col          (:)   ! col flood water flux at column level
-     real(r8), pointer :: qflx_sl_top_soil_col     (:)   ! col liquid water + ice from layer above soil to top soil layer or sent to qflx_qrgwl (mm H2O/s)
-     real(r8), pointer :: qflx_snomelt_col         (:)   ! col snow melt (mm H2O /s)
-     real(r8), pointer :: qflx_snomelt_lyr_col     (:,:) ! col snow melt in each layer (mm H2O /s)
-     real(r8), pointer :: qflx_snow_drain_col      (:)   ! col drainage from snow pack
-     real(r8), pointer :: qflx_qrgwl_col           (:)   ! col qflx_surf at glaciers, wetlands, lakes
-     real(r8), pointer :: qflx_runoff_col          (:)   ! col total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s)
-     real(r8), pointer :: qflx_runoff_r_col        (:)   ! col Rural total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s)
-     real(r8), pointer :: qflx_runoff_u_col        (:)   ! col urban total runoff (qflx_drain+qflx_surf) (mm H2O /s) 
-     real(r8), pointer :: qflx_ice_runoff_snwcp_col(:)   ! col solid runoff from snow capping (mm H2O /s)
-     real(r8), pointer :: qflx_ice_runoff_xs_col   (:)   ! col solid runoff from excess ice in soil (mm H2O /s)
-     real(r8), pointer :: qflx_rsub_sat_col        (:)   ! col soil saturation excess [mm/s]
-     real(r8), pointer :: qflx_snofrz_lyr_col      (:,:) ! col snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1]
-     real(r8), pointer :: qflx_snofrz_col          (:)   ! col column-integrated snow freezing rate (positive definite) (col) [kg m-2 s-1]
-     real(r8), pointer :: qflx_drain_vr_col        (:,:) ! col liquid water losted as drainage (m /time step)
-     real(r8), pointer :: snow_sources_col         (:)   ! col snow sources (mm H2O/s)
-     real(r8), pointer :: snow_sinks_col           (:)   ! col snow sinks (mm H2O/s)
-
-     ! Dynamic land cover change
-     real(r8), pointer :: qflx_liq_dynbal_grc      (:)   ! grc liq dynamic land cover change conversion runoff flux
-     real(r8), pointer :: qflx_ice_dynbal_grc      (:)   ! grc ice dynamic land cover change conversion runoff flux
-
-     ! ET accumulation
-     real(r8), pointer :: AnnEt                    (:)   ! Annual average ET flux mmH20/s
-
-
-   contains
- 
-     
-     
-     procedure, public  :: Init
-     procedure, public  :: Restart      
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-     procedure, public  :: InitAccBuffer
-     procedure, public  :: InitAccVars
-     procedure, public  :: UpdateAccVars
-
-  end type waterflux_type
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(waterflux_type) :: this
-    type(bounds_type), intent(in)    :: bounds  
-
-    call this%InitAllocate(bounds) ! same as "call initAllocate_type(hydro, bounds)"
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    integer :: begg, endg
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    allocate(this%qflx_prec_intr_patch     (begp:endp))              ; this%qflx_prec_intr_patch     (:)   = nan
-    allocate(this%qflx_prec_grnd_patch     (begp:endp))              ; this%qflx_prec_grnd_patch     (:)   = nan
-    allocate(this%qflx_rain_grnd_patch     (begp:endp))              ; this%qflx_rain_grnd_patch     (:)   = nan
-    allocate(this%qflx_snow_grnd_patch     (begp:endp))              ; this%qflx_snow_grnd_patch     (:)   = nan
-    allocate(this%qflx_sub_snow_patch      (begp:endp))              ; this%qflx_sub_snow_patch      (:)   = 0.0_r8
-    allocate(this%qflx_tran_veg_patch      (begp:endp))              ; this%qflx_tran_veg_patch      (:)   = nan
-
-    allocate(this%qflx_snowindunload_patch (begp:endp))              ; this%qflx_snowindunload_patch (:)   = nan
-    allocate(this%qflx_snowindunload_col   (begp:endp))              ; this%qflx_snowindunload_col   (:)   = nan
-    allocate(this%qflx_snotempunload_patch (begp:endp))              ; this%qflx_snotempunload_patch (:)   = nan
-    allocate(this%qflx_snotempunload_col   (begp:endp))              ; this%qflx_snotempunload_col   (:)   = nan
-	
-    allocate(this%qflx_dew_grnd_patch      (begp:endp))              ; this%qflx_dew_grnd_patch      (:)   = nan
-    allocate(this%qflx_dew_snow_patch      (begp:endp))              ; this%qflx_dew_snow_patch      (:)   = nan
-
-    allocate(this%qflx_prec_intr_col       (begc:endc))              ; this%qflx_prec_intr_col       (:)   = nan
-    allocate(this%qflx_prec_grnd_col       (begc:endc))              ; this%qflx_prec_grnd_col       (:)   = nan
-    allocate(this%qflx_rain_grnd_col       (begc:endc))              ; this%qflx_rain_grnd_col       (:)   = nan
-    allocate(this%qflx_snow_grnd_col       (begc:endc))              ; this%qflx_snow_grnd_col       (:)   = nan
-    allocate(this%qflx_sub_snow_col        (begc:endc))              ; this%qflx_sub_snow_col        (:)   = 0.0_r8
-    allocate(this%qflx_snwcp_liq_col       (begc:endc))              ; this%qflx_snwcp_liq_col       (:)   = nan
-    allocate(this%qflx_snwcp_ice_col       (begc:endc))              ; this%qflx_snwcp_ice_col       (:)   = nan
-    allocate(this%qflx_snwcp_discarded_liq_col(begc:endc))           ; this%qflx_snwcp_discarded_liq_col(:) = nan
-    allocate(this%qflx_snwcp_discarded_ice_col(begc:endc))           ; this%qflx_snwcp_discarded_ice_col(:) = nan
-    allocate(this%qflx_tran_veg_col        (begc:endc))              ; this%qflx_tran_veg_col        (:)   = nan
-    allocate(this%qflx_evap_veg_col        (begc:endc))              ; this%qflx_evap_veg_col        (:)   = nan
-    allocate(this%qflx_evap_can_col        (begc:endc))              ; this%qflx_evap_can_col        (:)   = nan
-    allocate(this%qflx_evap_soi_col        (begc:endc))              ; this%qflx_evap_soi_col        (:)   = nan
-    allocate(this%qflx_evap_tot_col        (begc:endc))              ; this%qflx_evap_tot_col        (:)   = nan
-    allocate(this%qflx_evap_grnd_col       (begc:endc))              ; this%qflx_evap_grnd_col       (:)   = nan
-    allocate(this%qflx_dew_grnd_col        (begc:endc))              ; this%qflx_dew_grnd_col        (:)   = nan
-    allocate(this%qflx_dew_snow_col        (begc:endc))              ; this%qflx_dew_snow_col        (:)   = nan
-    allocate(this%qflx_evap_veg_patch      (begp:endp))              ; this%qflx_evap_veg_patch      (:)   = nan
-    allocate(this%qflx_evap_can_patch      (begp:endp))              ; this%qflx_evap_can_patch      (:)   = nan
-    allocate(this%qflx_evap_soi_patch      (begp:endp))              ; this%qflx_evap_soi_patch      (:)   = nan
-    allocate(this%qflx_evap_tot_patch      (begp:endp))              ; this%qflx_evap_tot_patch      (:)   = nan
-    allocate(this%qflx_evap_grnd_patch     (begp:endp))              ; this%qflx_evap_grnd_patch     (:)   = nan
-    allocate(this%qflx_phs_neg_col         (begc:endc))              ; this%qflx_phs_neg_col       (:)   = nan
-
-    allocate( this%qflx_ev_snow_patch      (begp:endp))              ; this%qflx_ev_snow_patch       (:)   = nan
-    allocate( this%qflx_ev_snow_col        (begc:endc))              ; this%qflx_ev_snow_col         (:)   = nan
-    allocate( this%qflx_ev_soil_patch      (begp:endp))              ; this%qflx_ev_soil_patch       (:)   = nan
-    allocate( this%qflx_ev_soil_col        (begc:endc))              ; this%qflx_ev_soil_col         (:)   = nan
-    allocate( this%qflx_ev_h2osfc_patch    (begp:endp))              ; this%qflx_ev_h2osfc_patch     (:)   = nan
-    allocate( this%qflx_ev_h2osfc_col      (begc:endc))              ; this%qflx_ev_h2osfc_col       (:)   = nan
-
-    allocate(this%qflx_drain_vr_col      (begc:endc,1:nlevsoi))      ; this%qflx_drain_vr_col        (:,:) = nan
-    allocate(this%qflx_adv_col             (begc:endc,0:nlevsoi))    ; this%qflx_adv_col             (:,:) = nan
-    allocate(this%qflx_rootsoi_col         (begc:endc,1:nlevsoi))    ; this%qflx_rootsoi_col         (:,:) = nan
-    allocate(this%qflx_infl_col            (begc:endc))              ; this%qflx_infl_col            (:)   = nan
-    allocate(this%qflx_surf_col            (begc:endc))              ; this%qflx_surf_col            (:)   = nan
-    allocate(this%qflx_drain_col           (begc:endc))              ; this%qflx_drain_col           (:)   = nan
-    allocate(this%qflx_top_soil_col        (begc:endc))              ; this%qflx_top_soil_col        (:)   = nan
-    allocate(this%qflx_h2osfc_to_ice_col   (begc:endc))              ; this%qflx_h2osfc_to_ice_col   (:)   = nan
-    allocate(this%qflx_h2osfc_surf_col     (begc:endc))              ; this%qflx_h2osfc_surf_col     (:)   = nan
-    allocate(this%qflx_snow_h2osfc_col     (begc:endc))              ; this%qflx_snow_h2osfc_col     (:)   = nan
-    allocate(this%qflx_snomelt_col         (begc:endc))              ; this%qflx_snomelt_col         (:)   = nan
-    allocate(this%qflx_snomelt_lyr_col     (begc:endc,-nlevsno+1:0)) ; this%qflx_snomelt_lyr_col     (:,:) = nan
-    allocate(this%qflx_snow_drain_col      (begc:endc))              ; this%qflx_snow_drain_col      (:)   = nan
-    allocate(this%qflx_snofrz_col          (begc:endc))              ; this%qflx_snofrz_col          (:)   = nan
-    allocate(this%qflx_snofrz_lyr_col      (begc:endc,-nlevsno+1:0)) ; this%qflx_snofrz_lyr_col      (:,:) = nan
-    allocate(this%qflx_qrgwl_col           (begc:endc))              ; this%qflx_qrgwl_col           (:)   = nan
-    allocate(this%qflx_drain_perched_col   (begc:endc))              ; this%qflx_drain_perched_col   (:)   = nan
-    allocate(this%qflx_deficit_col         (begc:endc))              ; this%qflx_deficit_col         (:)   = nan
-    allocate(this%qflx_floodc_col          (begc:endc))              ; this%qflx_floodc_col          (:)   = nan
-    allocate(this%qflx_sl_top_soil_col     (begc:endc))              ; this%qflx_sl_top_soil_col     (:)   = nan
-    allocate(this%qflx_runoff_col          (begc:endc))              ; this%qflx_runoff_col          (:)   = nan
-    allocate(this%qflx_runoff_r_col        (begc:endc))              ; this%qflx_runoff_r_col        (:)   = nan
-    allocate(this%qflx_runoff_u_col        (begc:endc))              ; this%qflx_runoff_u_col        (:)   = nan
-    allocate(this%qflx_ice_runoff_snwcp_col(begc:endc))              ; this%qflx_ice_runoff_snwcp_col(:)   = nan
-    allocate(this%qflx_ice_runoff_xs_col   (begc:endc))              ; this%qflx_ice_runoff_xs_col   (:)   = nan
-    allocate(this%qflx_rsub_sat_col        (begc:endc))              ; this%qflx_rsub_sat_col        (:)   = nan
-    allocate(this%snow_sources_col         (begc:endc))              ; this%snow_sources_col         (:)   = nan   
-    allocate(this%snow_sinks_col           (begc:endc))              ; this%snow_sinks_col           (:)   = nan   
-
-    allocate(this%qflx_liq_dynbal_grc      (begg:endg))              ; this%qflx_liq_dynbal_grc      (:)   = nan
-    allocate(this%qflx_ice_dynbal_grc      (begg:endg))              ; this%qflx_ice_dynbal_grc      (:)   = nan
-    allocate(this%AnnET                    (begc:endc))              ; this%AnnET                    (:)   = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use clm_varctl  , only : use_cn
-    use histFileMod , only : hist_addfld1d, hist_addfld2d, no_snow_normal
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    integer           :: begg, endg
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-    begg = bounds%begg; endg= bounds%endg
-
-    this%qflx_top_soil_col(begc:endc) = spval
-    call hist_addfld1d (fname='QTOPSOIL',  units='mm/s',  &
-         avgflag='A', long_name='water input to surface', &
-         ptr_col=this%qflx_top_soil_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_infl_col(begc:endc) = spval
-    call hist_addfld1d (fname='QINFL',  units='mm/s',  &
-         avgflag='A', long_name='infiltration', &
-         ptr_col=this%qflx_infl_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_surf_col(begc:endc) = spval
-    call hist_addfld1d (fname='QOVER',  units='mm/s',  &
-         avgflag='A', long_name='surface runoff', &
-         ptr_col=this%qflx_surf_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_qrgwl_col(begc:endc) = spval
-    call hist_addfld1d (fname='QRGWL',  units='mm/s',  &
-         avgflag='A', &
-         long_name='surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff from QSNWCPICE', &
-         ptr_col=this%qflx_qrgwl_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_drain_col(begc:endc) = spval
-    call hist_addfld1d (fname='QDRAI',  units='mm/s',  &
-         avgflag='A', long_name='sub-surface drainage', &
-         ptr_col=this%qflx_drain_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_liq_dynbal_grc(begg:endg) = spval
-    call hist_addfld1d (fname='QFLX_LIQ_DYNBAL',  units='mm/s',  &  
-         avgflag='A', long_name='liq dynamic land cover change conversion runoff flux', &              
-         ptr_lnd=this%qflx_liq_dynbal_grc, default='inactive')     
-
-    this%qflx_ice_dynbal_grc(begg:endg) = spval
-    call hist_addfld1d (fname='QFLX_ICE_DYNBAL',  units='mm/s',  &
-         avgflag='A', long_name='ice dynamic land cover change conversion runoff flux', &                                   
-         ptr_lnd=this%qflx_ice_dynbal_grc, default='inactive')
-
-    this%qflx_runoff_col(begc:endc) = spval
-    call hist_addfld1d (fname='QRUNOFF',  units='mm/s',  &
-         avgflag='A', &
-         long_name='total liquid runoff not including correction for land use change', &
-         ptr_col=this%qflx_runoff_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='QRUNOFF_ICE', units='mm/s', avgflag='A', &
-         long_name='total liquid runoff not incl corret for LULCC (ice landunits only)', &
-         ptr_col=this%qflx_runoff_col, c2l_scale_type='urbanf', l2g_scale_type='ice', default='inactive')
-
-    this%qflx_runoff_u_col(begc:endc) = spval
-    call hist_addfld1d (fname='QRUNOFF_U', units='mm/s',  &
-         avgflag='A', long_name='Urban total runoff', &
-         ptr_col=this%qflx_runoff_u_col, set_nourb=spval, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_runoff_r_col(begc:endc) = spval
-    call hist_addfld1d (fname='QRUNOFF_R', units='mm/s',  &
-         avgflag='A', long_name='Rural total runoff', &
-         ptr_col=this%qflx_runoff_r_col, set_spec=spval, default='inactive')
-
-    this%qflx_snow_drain_col(begc:endc) = spval
-    call hist_addfld1d (fname='QFLX_SNOW_DRAIN',  units='mm/s',  &
-         avgflag='A', long_name='drainage from snow pack', &
-         ptr_col=this%qflx_snow_drain_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='QFLX_SNOW_DRAIN_ICE', units='mm/s',  &
-         avgflag='A', long_name='drainage from snow pack melt (ice landunits only)', &
-         ptr_col=this%qflx_snow_drain_col, c2l_scale_type='urbanf', l2g_scale_type='ice', default='inactive')
-
-    this%qflx_snomelt_col(begc:endc) = spval
-    call hist_addfld1d (fname='QSNOMELT',  units='mm/s',  &
-         avgflag='A', long_name='snow melt rate', &
-         ptr_col=this%qflx_snomelt_col, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='QSNOMELT_ICE', units='mm/s',  &
-         avgflag='A', long_name='snow melt (ice landunits only)', &
-         ptr_col=this%qflx_snomelt_col, c2l_scale_type='urbanf', l2g_scale_type='ice', default='inactive')
-
-    this%qflx_snomelt_lyr_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%qflx_snomelt_lyr_col(begc:endc,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_MELT',  units='mm/s', type2d='levsno', &
-         avgflag='A', long_name='snow melt rate in each snow layer', &
-         ptr_col=data2dptr, c2l_scale_type='urbanf',no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_MELT_ICE',  units='mm/s', type2d='levsno', &
-         avgflag='A', long_name='snow melt rate in each snow layer (ice landunits only)', &
-         ptr_col=data2dptr, c2l_scale_type='urbanf',no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%qflx_snofrz_col(begc:endc) = spval
-    call hist_addfld1d (fname='QSNOFRZ', units='kg/m2/s', &
-         avgflag='A', long_name='column-integrated snow freezing rate', &
-         ptr_col=this%qflx_snofrz_col, set_lake=spval, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='QSNOFRZ_ICE', units='mm/s',  &
-         avgflag='A', long_name='column-integrated snow freezing rate (ice landunits only)', &
-         ptr_col=this%qflx_snofrz_col, c2l_scale_type='urbanf', l2g_scale_type='ice', default='inactive')
-
-    this%qflx_snofrz_lyr_col(begc:endc,-nlevsno+1:0) = spval
-    data2dptr => this%qflx_snofrz_lyr_col(begc:endc,-nlevsno+1:0)
-    call hist_addfld2d (fname='SNO_FRZ',  units='kg/m2/s', type2d='levsno', &
-         avgflag='A', long_name='snow freezing rate in each snow layer', &
-         ptr_col=data2dptr, c2l_scale_type='urbanf',no_snow_behavior=no_snow_normal, default='inactive')
-
-    call hist_addfld2d (fname='SNO_FRZ_ICE',  units='mm/s', type2d='levsno', &
-         avgflag='A', long_name='snow freezing rate in each snow layer (ice landunits only)', &
-         ptr_col=data2dptr, c2l_scale_type='urbanf',no_snow_behavior=no_snow_normal, &
-         l2g_scale_type='ice', default='inactive')
-
-    this%qflx_h2osfc_to_ice_col(begc:endc) = spval
-    call hist_addfld1d (fname='QH2OSFC_TO_ICE',  units='mm/s',  &
-         avgflag='A', long_name='surface water converted to ice', &
-         ptr_col=this%qflx_h2osfc_to_ice_col, default='inactive')
-
-    this%qflx_prec_intr_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QINTR', units='mm/s',  &
-         avgflag='A', long_name='interception', &
-         ptr_patch=this%qflx_prec_intr_patch, set_lake=0._r8, default='inactive')
-
-    this%qflx_prec_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QDRIP', units='mm/s',  &
-         avgflag='A', long_name='throughfall', &
-         ptr_patch=this%qflx_prec_grnd_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_evap_soi_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QSOIL', units='mm/s',  &
-         avgflag='A', long_name= 'Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew)', &
-         ptr_patch=this%qflx_evap_soi_patch, c2l_scale_type='urbanf', default='inactive')
-
-    call hist_addfld1d (fname='QSOIL_ICE', units='mm/s',  &
-         avgflag='A', long_name='Ground evaporation (ice landunits only)', &
-         ptr_patch=this%qflx_evap_soi_patch, c2l_scale_type='urbanf', l2g_scale_type='ice', default='inactive')
-
-    call hist_addfld2d (fname='QROOTSINK',  units='mm/s', type2d='levsoi', &
-         avgflag='A', long_name='water flux from soil to root in each soil-layer', &
-         ptr_col=this%qflx_rootsoi_col, set_spec=spval, l2g_scale_type='veg', default='inactive')
-
-    this%qflx_evap_can_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QVEGE', units='mm/s',  &
-         avgflag='A', long_name='canopy evaporation', &
-         ptr_patch=this%qflx_evap_can_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_tran_veg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QVEGT', units='mm/s',  &
-         avgflag='A', long_name='canopy transpiration', &
-         ptr_patch=this%qflx_tran_veg_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_ev_snow_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QSNOEVAP', units='mm/s',  &
-         avgflag='A', long_name='evaporation from snow', &
-         ptr_patch=this%qflx_tran_veg_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_snowindunload_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QSNO_WINDUNLOAD', units='mm/s',  &
-         avgflag='A', long_name='canopy snow wind unloading', &
-         ptr_patch=this%qflx_snowindunload_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_snotempunload_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QSNO_TEMPUNLOAD', units='mm/s',  &
-         avgflag='A', long_name='canopy snow temp unloading', &
-         ptr_patch=this%qflx_snotempunload_patch, set_lake=0._r8, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_snwcp_liq_col(begc:endc) = spval
-    call hist_addfld1d (fname='QSNOCPLIQ', units='mm H2O/s', &
-         avgflag='A', long_name='excess liquid h2o due to snow capping not including correction for land use change', &
-         ptr_col=this%qflx_snwcp_liq_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_snwcp_ice_col(begc:endc) = spval
-    call hist_addfld1d (fname='QSNWCPICE', units='mm H2O/s', &
-         avgflag='A', long_name='excess solid h2o due to snow capping not including correction for land use change', &
-         ptr_col=this%qflx_snwcp_ice_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_rain_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_RAIN_GRND', units='mm H2O/s', &
-         avgflag='A', long_name='rain on ground after interception', &
-         ptr_patch=this%qflx_rain_grnd_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%qflx_snow_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_SNOW_GRND', units='mm H2O/s', &
-         avgflag='A', long_name='snow on ground after interception', &
-         ptr_patch=this%qflx_snow_grnd_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%qflx_evap_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_EVAP_GRND', units='mm H2O/s', &
-         avgflag='A', long_name='ground surface evaporation', &
-         ptr_patch=this%qflx_evap_grnd_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%qflx_evap_veg_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_EVAP_VEG', units='mm H2O/s', &
-         avgflag='A', long_name='vegetation evaporation', &
-         ptr_patch=this%qflx_evap_veg_patch, default='inactive', c2l_scale_type='urbanf')
-
-    this%qflx_evap_tot_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_EVAP_TOT', units='mm H2O/s', &
-         avgflag='A', long_name='qflx_evap_soi + qflx_evap_can + qflx_tran_veg', &
-         ptr_patch=this%qflx_evap_tot_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_dew_grnd_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_DEW_GRND', units='mm H2O/s', &
-         avgflag='A', long_name='ground surface dew formation', &
-         ptr_patch=this%qflx_dew_grnd_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_sub_snow_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_SUB_SNOW', units='mm H2O/s', &
-         avgflag='A', long_name='sublimation rate from snow pack', &
-         ptr_patch=this%qflx_sub_snow_patch,  c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_dew_snow_patch(begp:endp) = spval
-    call hist_addfld1d (fname='QFLX_DEW_SNOW', units='mm H2O/s', &
-         avgflag='A', long_name='surface dew added to snow pacK', &
-         ptr_patch=this%qflx_dew_snow_patch, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_h2osfc_surf_col(begc:endc) = spval
-    call hist_addfld1d (fname='QH2OSFC',  units='mm/s',  &
-         avgflag='A', long_name='surface water runoff', &
-         ptr_col=this%qflx_h2osfc_surf_col, default='inactive')
-
-    this%qflx_drain_perched_col(begc:endc) = spval
-    call hist_addfld1d (fname='QDRAI_PERCH',  units='mm/s',  &
-         avgflag='A', long_name='perched wt drainage', &
-         ptr_col=this%qflx_drain_perched_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_rsub_sat_col(begc:endc) = spval
-    call hist_addfld1d (fname='QDRAI_XS',  units='mm/s',  &
-         avgflag='A', long_name='saturation excess drainage', &
-         ptr_col=this%qflx_rsub_sat_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%qflx_phs_neg_col(begc:endc) = spval
-    call hist_addfld1d (fname='QPHSNEG',  units='mm/s',  &
-         avgflag='A', long_name='net negative hydraulic redistribution flux', &
-         ptr_col=this%qflx_phs_neg_col, default='inactive')
-
-    ! As defined here, snow_sources - snow_sinks will equal the change in h2osno at any
-    ! given time step but only if there is at least one snow layer (for all landunits 
-    ! except lakes).  Also note that monthly average files of snow_sources and snow_sinks
-    ! sinks must be weighted by number of days in the month to diagnose, for example, an 
-    ! annual value of the change in h2osno. 
-
-    this%snow_sources_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOW_SOURCES',  units='mm/s',  &
-         avgflag='A', long_name='snow sources (liquid water)', &
-         ptr_col=this%snow_sources_col, c2l_scale_type='urbanf', default='inactive')
-
-    this%snow_sinks_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOW_SINKS',  units='mm/s',  &
-         avgflag='A', long_name='snow sinks (liquid water)', &
-         ptr_col=this%snow_sinks_col, c2l_scale_type='urbanf', default='inactive')
-         
-    this%AnnET(begc:endc) = spval
-    call hist_addfld1d (fname='AnnET',  units='mm/s',  &
-         avgflag='A', long_name='Annual ET', &
-         ptr_col=this%AnnET, c2l_scale_type='urbanf', default='inactive')
-
-  end subroutine InitHistory
-  
-  
-  
-   !-----------------------------------------------------------------------
-    subroutine InitAccBuffer (this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize accumulation buffer for all required module accumulated fields
-    ! This routine set defaults values that are then overwritten by the
-    ! restart file for restart or branch runs
-    !
-    ! !USES 
-    use clm_varcon  , only : spval
-    use accumulMod  , only : init_accum_field
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !---------------------------------------------------------------------
-
-    if (use_fun) then
-   
-       call init_accum_field (name='AnnET', units='MM H2O/S', &
-            desc='365-day running mean of total ET', accum_type='runmean', accum_period=-365, &
-            subgrid_type='column', numlev=1, init_value=0._r8)
-
-    end if
-
-  end subroutine InitAccBuffer
-
-  !-----------------------------------------------------------------------
-    !
-     subroutine InitAccVars (this, bounds)
-    ! !DESCRIPTION:
-    ! Initialize module variables that are associated with
-    ! time accumulated fields. This routine is called for both an initial run
-    ! and a restart run (and must therefore must be called after the restart file 
-    ! is read in and the accumulation buffer is obtained)
-    !
-    ! !USES 
-    use accumulMod       , only : extract_accum_field
-    use clm_time_manager , only : get_nstep
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begc, endc
-    integer  :: nstep
-    integer  :: ier
-    real(r8), pointer :: rbufslp(:)  ! temporary
-    !---------------------------------------------------------------------
-    begc = bounds%begc; endc = bounds%endc
-
-    ! Allocate needed dynamic memory for single level patch field
-    allocate(rbufslp(begc:endc), stat=ier)
-
-    ! Determine time step
-    nstep = get_nstep()
-
-    if (use_fun) then
-       call extract_accum_field ('AnnET', rbufslp, nstep)
-       this%qflx_evap_tot_col(begc:endc) = rbufslp(begc:endc)
-    end if
-
-    deallocate(rbufslp)
-
-  end subroutine InitAccVars
-  
-  
-  !-----------------------------------------------------------------------
-  subroutine UpdateAccVars (this, bounds)
-    !
-    ! USES
-    use clm_time_manager, only : get_nstep
-    use accumulMod      , only : update_accum_field, extract_accum_field
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type)                 :: this
-    type(bounds_type)      , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g,c,p                     ! indices
-    integer :: dtime                     ! timestep size [seconds]
-    integer :: nstep                     ! timestep number
-    integer :: ier                       ! error status
-    integer :: begc, endc
-    real(r8), pointer :: rbufslp(:)      ! temporary single level - patch level
-    !---------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    nstep = get_nstep()
-
-    ! Allocate needed dynamic memory for single level patch field
-
-    allocate(rbufslp(begc:endc), stat=ier)
-    
-    do c = begc,endc
-       rbufslp(c) = this%qflx_evap_tot_col(c)
-    end do
-    if (use_fun) then
-       ! Accumulate and extract AnnET (accumulates total ET as 365-day running mean)
-       call update_accum_field  ('AnnET', rbufslp, nstep)
-       call extract_accum_field ('AnnET', this%AnnET, nstep)
-    
-    end if
-
-    deallocate(rbufslp)
-    
-  end subroutine UpdateAccVars
-
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !USES:
-    use landunit_varcon, only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type) :: this
-    type(bounds_type) , intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,c,l
-    !-----------------------------------------------------------------------
-
-    this%qflx_evap_grnd_patch(bounds%begp:bounds%endp) = 0.0_r8
-    this%qflx_dew_grnd_patch (bounds%begp:bounds%endp) = 0.0_r8
-    this%qflx_dew_snow_patch (bounds%begp:bounds%endp) = 0.0_r8
-
-    this%qflx_evap_grnd_col(bounds%begc:bounds%endc) = 0.0_r8
-    this%qflx_dew_grnd_col (bounds%begc:bounds%endc) = 0.0_r8
-    this%qflx_dew_snow_col (bounds%begc:bounds%endc) = 0.0_r8
-
-    this%qflx_phs_neg_col(bounds%begc:bounds%endc)   = 0.0_r8
-
-    this%qflx_h2osfc_surf_col(bounds%begc:bounds%endc) = 0._r8
-    this%qflx_snow_drain_col(bounds%begc:bounds%endc)  = 0._r8
-
-    ! This variable only gets set in the hydrology filter; need to initialize it to 0 for
-    ! the sake of columns outside this filter
-    this%qflx_ice_runoff_xs_col(bounds%begc:bounds%endc) = 0._r8
-
-    this%AnnEt(bounds%begc:bounds%endc)                 = 0._r8
-  
-    ! needed for CNNLeaching 
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%qflx_drain_col(c) = 0._r8
-          this%qflx_surf_col(c)  = 0._r8
-       end if
-    end do
-
-  end subroutine InitCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    ! 
-    ! !USES:
-    use ncdio_pio, only : file_desc_t, ncd_double
-    use restUtilMod
-    !
-    ! !ARGUMENTS:
-    class(waterflux_type)            :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   ! netcdf id
-    character(len=*) , intent(in)    :: flag   ! 'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    logical :: readvar      ! determine if variable is on initial file
-    !-----------------------------------------------------------------------
-
-    ! needed for SNICAR
-    call restartvar(ncid=ncid, flag=flag, varname='qflx_snofrz_lyr', xtype=ncd_double,  &
-         dim1name='column', dim2name='levsno', switchdim=.true., lowerb2=-nlevsno+1, upperb2=0, &
-         long_name='snow layer ice freezing rate', units='kg m-2 s-1', &
-         interpinic_flag='interp', readvar=readvar, data=this%qflx_snofrz_lyr_col)
-    if (flag == 'read' .and. .not. readvar) then
-       ! initial run, not restart: initialize qflx_snofrz_lyr to zero
-       this%qflx_snofrz_lyr_col(bounds%begc:bounds%endc,-nlevsno+1:0) = 0._r8
-    endif
-
-    call restartvar(ncid=ncid, flag=flag, varname='qflx_snow_drain:qflx_snow_melt', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='drainage from snow column', units='mm/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%qflx_snow_drain_col)
-    if (flag == 'read' .and. .not. readvar) then
-       ! initial run, not restart: initialize qflx_snow_drain to zero
-       this%qflx_snow_drain_col(bounds%begc:bounds%endc) = 0._r8
-    endif
-    
-    
-    call restartvar(ncid=ncid, flag=flag, varname='AnnET', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='Annual ET ', units='mm/s', &
-         interpinic_flag='interp', readvar=readvar, data=this%AnnET)
-    if (flag == 'read' .and. .not. readvar) then
-       ! initial run, not restart: initialize qflx_snow_drain to zero
-       this%AnnET(bounds%begc:bounds%endc) = 0._r8
-    endif
-   
-  end subroutine Restart
-
-end module WaterfluxType
diff --git a/src/cpl/clm_cpl_indices.F90 b/src/cpl/clm_cpl_indices.F90
index 525b709cc6..89283ee26d 100644
--- a/src/cpl/clm_cpl_indices.F90
+++ b/src/cpl/clm_cpl_indices.F90
@@ -18,16 +18,12 @@ module clm_cpl_indices
   !
   ! !PUBLIC DATA MEMBERS:
   !
-  integer , public :: glc_nec     ! number of elevation classes for glacier_mec landunits 
-                                  ! (from coupler) - must equal maxpatch_glcmec from namelist
-
   ! lnd -> drv (required)
 
   integer, public ::index_l2x_Flrl_rofsur     ! lnd->rtm input liquid surface fluxes
   integer, public ::index_l2x_Flrl_rofgwl     ! lnd->rtm input liquid gwl fluxes
   integer, public ::index_l2x_Flrl_rofsub     ! lnd->rtm input liquid subsurface fluxes
   integer, public ::index_l2x_Flrl_rofi       ! lnd->rtm input frozen fluxes
-  integer, public ::index_l2x_Flrl_irrig      ! irrigation withdrawal
 
   integer, public ::index_l2x_Sl_t            ! temperature
   integer, public ::index_l2x_Sl_tref         ! 2m reference temperature
@@ -54,16 +50,7 @@ module clm_cpl_indices
   integer, public ::index_l2x_Fall_flxdst2    ! dust flux size bin 2    
   integer, public ::index_l2x_Fall_flxdst3    ! dust flux size bin 3    
   integer, public ::index_l2x_Fall_flxdst4    ! dust flux size bin 4
-  integer, public ::index_l2x_Fall_flxvoc     ! MEGAN fluxes
-  integer, public ::index_l2x_Fall_flxfire    ! Fire fluxes
-  integer, public ::index_l2x_Sl_ztopfire     ! Top of fire emissions (m)
-
-  ! In the following, index 0 is bare land, other indices are glc elevation classes
-  integer, allocatable, public ::index_l2x_Sl_tsrf(:)   ! glc MEC temperature
-  integer, allocatable, public ::index_l2x_Sl_topo(:)   ! glc MEC topo height
-  integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux
 
-  integer, public ::index_x2l_Sa_methane
   integer, public ::index_l2x_Fall_methane
 
   integer, public :: nflds_l2x = 0
@@ -104,9 +91,6 @@ module clm_cpl_indices
   integer, public ::index_x2l_Faxa_dstdry3    ! flux: Size 3 dust -- dry deposition
   integer, public ::index_x2l_Faxa_dstdry4    ! flux: Size 4 dust -- dry deposition
  
-  integer, public ::index_x2l_Faxa_nhx        ! flux nhx from atm
-  integer, public ::index_x2l_Faxa_noy        ! flux noy from atm
-
   integer, public ::index_x2l_Flrr_flood      ! rtm->lnd rof flood flux
   integer, public ::index_x2l_Flrr_volr       ! rtm->lnd rof volr total volume
   integer, public ::index_x2l_Flrr_volrmch    ! rtm->lnd rof volr main channel volume
@@ -136,10 +120,6 @@ subroutine clm_cpl_indices_set( )
     use seq_flds_mod   , only: seq_flds_x2l_fields, seq_flds_l2x_fields
     use mct_mod        , only: mct_aVect, mct_aVect_init, mct_avect_indexra
     use mct_mod        , only: mct_aVect_clean, mct_avect_nRattr
-    use seq_drydep_mod , only: drydep_fields_token, lnd_drydep
-    use shr_megan_mod  , only: shr_megan_fields_token, shr_megan_mechcomps_n
-    use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n
-    use clm_varctl     , only:  ndep_from_cpl
     use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string
     !
     ! !ARGUMENTS:
@@ -175,7 +155,6 @@ subroutine clm_cpl_indices_set( )
     index_l2x_Flrl_rofgwl   = mct_avect_indexra(l2x,'Flrl_rofgwl')
     index_l2x_Flrl_rofsub   = mct_avect_indexra(l2x,'Flrl_rofsub')
     index_l2x_Flrl_rofi     = mct_avect_indexra(l2x,'Flrl_rofi')
-    index_l2x_Flrl_irrig    = mct_avect_indexra(l2x,'Flrl_irrig')
 
     index_l2x_Sl_t          = mct_avect_indexra(l2x,'Sl_t')
     index_l2x_Sl_snowh      = mct_avect_indexra(l2x,'Sl_snowh')
@@ -190,12 +169,6 @@ subroutine clm_cpl_indices_set( )
     index_l2x_Sl_fv         = mct_avect_indexra(l2x,'Sl_fv')
     index_l2x_Sl_soilw      = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet')
 
-    if ( lnd_drydep )then
-       index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token))
-    else
-       index_l2x_Sl_ddvel = 0
-    end if
-
     index_l2x_Fall_taux     = mct_avect_indexra(l2x,'Fall_taux')
     index_l2x_Fall_tauy     = mct_avect_indexra(l2x,'Fall_tauy')
     index_l2x_Fall_lat      = mct_avect_indexra(l2x,'Fall_lat')
@@ -212,22 +185,6 @@ subroutine clm_cpl_indices_set( )
 
     index_l2x_Fall_methane  = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet')
 
-    ! MEGAN fluxes
-    if (shr_megan_mechcomps_n>0) then
-       index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token))
-    else
-       index_l2x_Fall_flxvoc = 0
-    endif
-
-    ! Fire fluxes
-    if (shr_fire_emis_mechcomps_n>0) then
-       index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token))
-       index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token))
-    else
-       index_l2x_Fall_flxfire = 0
-       index_l2x_Sl_ztopfire = 0
-    endif
-
     !-------------------------------------------------------------
     ! drv -> clm
     !-------------------------------------------------------------
@@ -243,8 +200,6 @@ subroutine clm_cpl_indices_set( )
     index_x2l_Sa_co2prog    = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet')
     index_x2l_Sa_co2diag    = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet')
 
-    index_x2l_Sa_methane    = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet')
-
     index_x2l_Flrr_volr     = mct_avect_indexra(x2l,'Flrr_volr')
     index_x2l_Flrr_volrmch  = mct_avect_indexra(x2l,'Flrr_volrmch')
 
@@ -272,13 +227,6 @@ subroutine clm_cpl_indices_set( )
     index_x2l_Faxa_dstwet3  = mct_avect_indexra(x2l,'Faxa_dstwet3')
     index_x2l_Faxa_dstwet4  = mct_avect_indexra(x2l,'Faxa_dstwet4')
 
-    index_x2l_Faxa_nhx      = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet')
-    index_x2l_Faxa_noy      = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet')
-
-    if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then
-       ndep_from_cpl = .true.
-    end if
-
     index_x2l_Flrr_flood    = mct_avect_indexra(x2l,'Flrr_flood')
 
     !-------------------------------------------------------------
@@ -288,21 +236,13 @@ subroutine clm_cpl_indices_set( )
     index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask')
     index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes')
 
-    glc_nec = glc_get_num_elevation_classes()
-    if (glc_nec < 1) then
-       call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.')
-    end if
-
     ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land
     ! (index 0).
-    allocate(index_l2x_Sl_tsrf(0:glc_nec))
-    allocate(index_l2x_Sl_topo(0:glc_nec))
-    allocate(index_l2x_Flgl_qice(0:glc_nec))
-    allocate(index_x2l_Sg_ice_covered(0:glc_nec))
-    allocate(index_x2l_Sg_topo(0:glc_nec))
-    allocate(index_x2l_Flgg_hflx(0:glc_nec))
-
-    do num = 0,glc_nec
+    allocate(index_x2l_Sg_ice_covered(0:10))
+    allocate(index_x2l_Sg_topo(0:10))
+    allocate(index_x2l_Flgg_hflx(0:10))
+
+    do num = 0,10
        nec_str = glc_elevclass_as_string(num)
 
        name = 'Sg_ice_covered' // nec_str
@@ -311,13 +251,6 @@ subroutine clm_cpl_indices_set( )
        index_x2l_Sg_topo(num)   = mct_avect_indexra(x2l,trim(name))
        name = 'Flgg_hflx' // nec_str
        index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name))
-
-       name = 'Sl_tsrf' // nec_str
-       index_l2x_Sl_tsrf(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Sl_topo' // nec_str
-       index_l2x_Sl_topo(num)   = mct_avect_indexra(l2x,trim(name))
-       name = 'Flgl_qice' // nec_str
-       index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name))
     end do
 
     call mct_aVect_clean(x2l)
diff --git a/src/cpl/lnd_comp_mct.F90 b/src/cpl/lnd_comp_mct.F90
index 394ea63e56..577d0f274b 100644
--- a/src/cpl/lnd_comp_mct.F90
+++ b/src/cpl/lnd_comp_mct.F90
@@ -42,10 +42,9 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
     use shr_kind_mod     , only : shr_kind_cl
     use abortutils       , only : endrun
     use clm_time_manager , only : get_nstep, get_step_size, set_timemgr_init, set_nextsw_cday
-    use clm_initializeMod, only : initialize1, initialize2, lnd2atm_inst, lnd2glc_inst
+    use clm_initializeMod, only : initialize1, initialize2, lnd2atm_inst
     use clm_varctl       , only : finidat,single_column, clm_varctl_set, iulog, noland
     use clm_varctl       , only : inst_index, inst_suffix, inst_name
-    use clm_varorb       , only : eccen, obliqr, lambm0, mvelpp
     use controlMod       , only : control_setNL
     use decompMod        , only : get_proc_bounds
     use domainMod        , only : ldomain
@@ -151,11 +150,6 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
     call shr_file_getLogLevel(shrloglev)
     call shr_file_setLogUnit (iulog)
     
-    ! Use infodata to set orbital values
-
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-
     ! Consistency check on namelist filename	
 
     call control_setNL("lnd_in"//trim(inst_suffix))
@@ -252,7 +246,7 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
 
     ! Create land export state 
 
-    call lnd_export(bounds, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
+    call lnd_export(bounds, lnd2atm_inst, l2x_l%rattr)
     !write(iulog,*)'MML back from lnd_export'
 
     ! Fill in infodata settings
@@ -295,14 +289,13 @@ subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
     !
     ! !USES:
     use shr_kind_mod    ,  only : r8 => shr_kind_r8
-    use clm_initializeMod, only : lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst
+    use clm_initializeMod, only : lnd2atm_inst, atm2lnd_inst
     use clm_driver      ,  only : clm_drv
     use clm_time_manager,  only : get_curr_date, get_nstep, get_curr_calday, get_step_size
     use clm_time_manager,  only : advance_timestep, set_nextsw_cday,update_rad_dtime
     use decompMod       ,  only : get_proc_bounds
     use abortutils      ,  only : endrun
     use clm_varctl      ,  only : iulog
-    use clm_varorb      ,  only : eccen, obliqr, lambm0, mvelpp
     use shr_file_mod    ,  only : shr_file_setLogUnit, shr_file_setLogLevel
     use shr_file_mod    ,  only : shr_file_getLogUnit, shr_file_getLogLevel
     use seq_cdata_mod   ,  only : seq_cdata, seq_cdata_setptrs
@@ -340,16 +333,13 @@ subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
     logical      :: dosend               ! true => send data back to driver
     logical      :: doalb                ! .true. ==> do albedo calculation on this time step
     logical      :: rof_prognostic       ! .true. => running with a prognostic ROF model
-    logical      :: glc_present          ! .true. => running with a non-stub GLC model
     real(r8)     :: nextsw_cday          ! calday from clock of next radiation computation
     real(r8)     :: caldayp1             ! clm calday plus dtime offset
     integer      :: shrlogunit,shrloglev ! old values for share log unit and log level
     integer      :: lbnum                ! input to memory diagnostic
     integer      :: g,i,lsize            ! counters
-    real(r8)     :: calday               ! calendar day for nstep
     real(r8)     :: declin               ! solar declination angle in radians for nstep
     real(r8)     :: declinp1             ! solar declination angle in radians for nstep+1
-    real(r8)     :: eccf                 ! earth orbit eccentricity factor
     real(r8)     :: recip                ! reciprical
     logical,save :: first_call = .true.  ! first call work
     type(seq_infodata_type),pointer :: infodata             ! CESM information from the driver
@@ -398,8 +388,7 @@ subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
     ! their being set in initialization, so need to get them in the run method.
 
     call seq_infodata_GetData( infodata, &
-         rof_prognostic=rof_prognostic, &
-         glc_present=glc_present)
+         rof_prognostic=rof_prognostic)
 
     ! Map MCT to land data type
     ! Perform downscaling if appropriate
@@ -411,18 +400,9 @@ subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
     call t_startf ('lc_lnd_import')
     call lnd_import( bounds, &
          x2l = x2l_l%rattr, &
-         glc_present = glc_present, &
-         atm2lnd_inst = atm2lnd_inst, &
-         glc2lnd_inst = glc2lnd_inst)
+         atm2lnd_inst = atm2lnd_inst)
     call t_stopf ('lc_lnd_import')
 
-    !write(*,*)'MML just after lc_lnd_impoft'
-	
-    ! Use infodata to set orbital values if updated mid-run
-
-    call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, &
-         orb_lambm0=lambm0, orb_obliqr=obliqr )
-    !write(*,*)'MML just after se_infodata_GetData'
     ! Loop over time steps in coupling interval
 
     dosend = .false.
@@ -468,18 +448,13 @@ subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l)
 
        call t_barrierf('sync_clm_run1', mpicom)
        call t_startf ('clm_run')
-       call t_startf ('shr_orb_decl')
-       calday = get_curr_calday()
-       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
-       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
-       call t_stopf ('shr_orb_decl')
        call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
        call t_stopf ('clm_run')
 
        ! Create l2x_l export state - add river runoff input to l2x_l if appropriate
        !write(*,*)'MML export l2x_l'
        call t_startf ('lc_lnd_export')
-       call lnd_export(bounds, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr)
+       call lnd_export(bounds, lnd2atm_inst, l2x_l%rattr)
        call t_stopf ('lc_lnd_export')
 
        ! Advance clm time step
diff --git a/src/cpl/lnd_import_export.F90 b/src/cpl/lnd_import_export.F90
index 0232c0aa61..2e8662c4ed 100644
--- a/src/cpl/lnd_import_export.F90
+++ b/src/cpl/lnd_import_export.F90
@@ -4,9 +4,7 @@ module lnd_import_export
   use abortutils   , only: endrun
   use decompmod    , only: bounds_type
   use lnd2atmType  , only: lnd2atm_type
-  use lnd2glcMod   , only: lnd2glc_type
   use atm2lndType  , only: atm2lnd_type
-  use glc2lndMod   , only: glc2lnd_type 
   use clm_cpl_indices
   !
   implicit none
@@ -15,7 +13,7 @@ module lnd_import_export
 contains
 
   !===============================================================================
-  subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst)
+  subroutine lnd_import( bounds, x2l, atm2lnd_inst)
 
     !---------------------------------------------------------------------------
     ! !DESCRIPTION:
@@ -24,8 +22,7 @@ subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst)
     ! !USES:
     use seq_flds_mod    , only: seq_flds_x2l_fields
     use clm_varctl      , only: co2_type, co2_ppmv, iulog
-    use clm_varctl      , only: ndep_from_cpl 
-    use clm_varcon      , only: rair, o2_molar_const, c13ratio
+    use clm_varcon      , only: rair, o2_molar_const
     use shr_const_mod   , only: SHR_CONST_TKFRZ
     use shr_string_mod  , only: shr_string_listGetName
     use domainMod       , only: ldomain
@@ -34,9 +31,7 @@ subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst)
     ! !ARGUMENTS:
     type(bounds_type)  , intent(in)    :: bounds   ! bounds
     real(r8)           , intent(in)    :: x2l(:,:) ! driver import state to land model
-    logical            , intent(in)    :: glc_present       ! .true. => running with a non-stub GLC model
     type(atm2lnd_type) , intent(inout) :: atm2lnd_inst      ! clm internal input data type
-    type(glc2lnd_type) , intent(inout) :: glc2lnd_inst      ! clm internal input data type
     !
     ! !LOCAL VARIABLES:
     integer  :: g,i,k,nstep,ier      ! indices, number of steps, and error code
@@ -162,10 +157,6 @@ subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst)
           co2_ppmv_diag = co2_ppmv
        end if
 
-       if (index_x2l_Sa_methane /= 0) then
-          atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i)
-       endif
-
        ! Determine derived quantities for required fields
 
        forc_t = atm2lnd_inst%forc_t_not_downscaled_grc(g)
@@ -249,33 +240,13 @@ subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst)
        end if
        atm2lnd_inst%forc_pco2_grc(g)   = co2_ppmv_val * 1.e-6_r8 * forc_pbot 
 
-       if (ndep_from_cpl) then
-          ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the
-          ! following conversion needs to happen
-          atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8
-       end if
-
     end do
 
-    call glc2lnd_inst%set_glc2lnd_fields( &
-         bounds = bounds, &
-         glc_present = glc_present, &
-         ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds
-         ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in
-         ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is
-         ! outside a clump loop.
-         x2l = x2l, &
-         index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, &
-         index_x2l_Sg_topo = index_x2l_Sg_topo, &
-         index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, &
-         index_x2l_Sg_icemask = index_x2l_Sg_icemask, &
-         index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes)
-
   end subroutine lnd_import
 
   !===============================================================================
 
-  subroutine lnd_export( bounds, lnd2atm_inst, lnd2glc_inst, l2x)
+  subroutine lnd_export( bounds, lnd2atm_inst, l2x)
 
     !---------------------------------------------------------------------------
     ! !DESCRIPTION:
@@ -286,9 +257,6 @@ subroutine lnd_export( bounds, lnd2atm_inst, lnd2glc_inst, l2x)
     use seq_flds_mod       , only : seq_flds_l2x_fields
     use clm_varctl         , only : iulog
     use clm_time_manager   , only : get_nstep, get_step_size  
-    use seq_drydep_mod     , only : n_drydep
-    use shr_megan_mod      , only : shr_megan_mechcomps_n
-    use shr_fire_emis_mod  , only : shr_fire_emis_mechcomps_n
     use domainMod          , only : ldomain
     use shr_string_mod     , only : shr_string_listGetName
     use shr_infnan_mod     , only : isnan => shr_infnan_isnan
@@ -297,7 +265,6 @@ subroutine lnd_export( bounds, lnd2atm_inst, lnd2glc_inst, l2x)
     implicit none
     type(bounds_type) , intent(in)    :: bounds  ! bounds
     type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type
-    type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type
     real(r8)          , intent(out)   :: l2x(:,:)! land to coupler export state on land grid
     !
     ! !LOCAL VARIABLES:
@@ -336,41 +303,16 @@ subroutine lnd_export( bounds, lnd2atm_inst, lnd2glc_inst, l2x)
           l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g)  
        end if
 
-       ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC
+       ! Additional fields for DUST, PROGSSLT, dry-deposition
        ! These are now standard fields, but the check on the index makes sure the driver handles them
        if (index_l2x_Sl_ram1      /= 0 )  l2x(index_l2x_Sl_ram1,i)     =  lnd2atm_inst%ram1_grc(g)
        if (index_l2x_Sl_fv        /= 0 )  l2x(index_l2x_Sl_fv,i)       =  lnd2atm_inst%fv_grc(g)
-       if (index_l2x_Sl_soilw     /= 0 )  l2x(index_l2x_Sl_soilw,i)    =  lnd2atm_inst%h2osoi_vol_grc(g,1)
+       if (index_l2x_Sl_soilw     /= 0 )  l2x(index_l2x_Sl_soilw,i)    =  0.5_r8
        if (index_l2x_Fall_flxdst1 /= 0 )  l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1)
        if (index_l2x_Fall_flxdst2 /= 0 )  l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2)
        if (index_l2x_Fall_flxdst3 /= 0 )  l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3)
        if (index_l2x_Fall_flxdst4 /= 0 )  l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4)
 
-
-       ! for dry dep velocities
-       if (index_l2x_Sl_ddvel     /= 0 )  then
-          l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = &
-               lnd2atm_inst%ddvel_grc(g,:n_drydep)
-       end if
-
-       ! for MEGAN VOC emis fluxes
-       if (index_l2x_Fall_flxvoc  /= 0 ) then
-          l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = &
-               -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n)
-       end if
-
-
-       ! for fire emis fluxes
-       if (index_l2x_Fall_flxfire  /= 0 ) then
-          l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = &
-               -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n)
-          l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g)
-       end if
-
-       if (index_l2x_Fall_methane /= 0) then
-          l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%flux_ch4_grc(g) 
-       endif
-
        ! sign convention is positive downward with 
        ! hierarchy of atm/glc/lnd/rof/ice/ocn.  
        ! I.e. water sent from land to rof is positive
@@ -389,19 +331,6 @@ subroutine lnd_export( bounds, lnd2atm_inst, lnd2glc_inst, l2x)
        ! ice  sent individually to coupler
        l2x(index_l2x_Flrl_rofi,i) = lnd2atm_inst%qflx_rofice_grc(g)
 
-       ! irrigation flux to be removed from main channel storage (negative)
-       l2x(index_l2x_Flrl_irrig,i) = - lnd2atm_inst%qirrig_grc(g)
-
-       ! glc coupling
-       ! We could avoid setting these fields if glc_present is .false., if that would
-       ! help with performance. (The downside would be that we wouldn't have these fields
-       ! available for diagnostic purposes or to force a later T compset with dlnd.)
-       do num = 0,glc_nec
-          l2x(index_l2x_Sl_tsrf(num),i)   = lnd2glc_inst%tsrf_grc(g,num)
-          l2x(index_l2x_Sl_topo(num),i)   = lnd2glc_inst%topo_grc(g,num)
-          l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num)
-       end do
-
        ! Check if any output sent to the coupler is NaN
        if ( any(isnan(l2x(:,i))) )then
           write(iulog,*) '# of NaNs = ', count(isnan(l2x(:,i)))
diff --git a/src/init_interp/initInterp.F90 b/src/init_interp/initInterp.F90
index 07d93178cd..b2c6bcbafc 100644
--- a/src/init_interp/initInterp.F90
+++ b/src/init_interp/initInterp.F90
@@ -208,7 +208,6 @@ subroutine initInterp (filei, fileo, bounds)
     ! maintenance problem - or maybe even remove check_dim_level entirely.
     call check_dim_level(ncidi, ncido, dimname='levsno' , must_be_same=.false.)
     call check_dim_level(ncidi, ncido, dimname='levsno1', must_be_same=.false.)
-    call check_dim_level(ncidi, ncido, dimname='levcan' , must_be_same=.true.)
     call check_dim_level(ncidi, ncido, dimname='levlak' , must_be_same=.true.)
     call check_dim_level(ncidi, ncido, dimname='levtot' , must_be_same=.false.)
     call check_dim_level(ncidi, ncido, dimname='levgrnd', must_be_same=.false.)
diff --git a/src/main/ColumnType.F90 b/src/main/ColumnType.F90
index 7043bfa159..eacab7335c 100644
--- a/src/main/ColumnType.F90
+++ b/src/main/ColumnType.F90
@@ -47,13 +47,6 @@ module ColumnType
      logical , pointer :: active               (:)   ! true=>do computations on this column 
      logical , pointer :: type_is_dynamic      (:)   ! true=>itype can change throughout the run
 
-     ! topography
-     ! TODO(wjs, 2016-04-05) Probably move these things into topoMod
-     real(r8), pointer :: micro_sigma          (:)   ! microtopography pdf sigma (m)
-     real(r8), pointer :: n_melt               (:)   ! SCA shape parameter
-     real(r8), pointer :: topo_slope           (:)   ! gridcell topographic slope
-     real(r8), pointer :: topo_std             (:)   ! gridcell elevation standard deviation
-
      ! vertical levels
      integer , pointer :: snl                  (:)   ! number of snow layers
      real(r8), pointer :: dz                   (:,:) ! layer thickness (m)  (-nlevsno+1:nlevgrnd) 
@@ -63,20 +56,9 @@ module ColumnType
      real(r8), pointer :: dz_lake              (:,:) ! lake layer thickness (m)  (1:nlevlak)
      real(r8), pointer :: z_lake               (:,:) ! layer depth for lake (m)
      real(r8), pointer :: lakedepth            (:)   ! variable lake depth (m)                             
-     integer , pointer :: nbedrock             (:)   ! variable depth to bedrock index
-
      ! other column characteristics
      logical , pointer :: hydrologically_active(:)   ! true if this column is a hydrologically active type
 
-     ! levgrnd_class gives the class in which each layer falls. This is relevant for
-     ! columns where there are 2 or more fundamentally different layer types. For
-     ! example, this distinguishes between soil and bedrock layers. The particular value
-     ! assigned to each class is irrelevant; the important thing is that different
-     ! classes (e.g., soil vs. bedrock) have different values of levgrnd_class.
-     !
-     ! levgrnd_class = ispval indicates that the given layer is completely unused for
-     ! this column (i.e., this column doesn't use the full nlevgrnd layers).
-     integer , pointer :: levgrnd_class        (:,:) ! class in which each layer falls (1:nlevgrnd)
    contains
 
      procedure, public :: Init
@@ -124,13 +106,6 @@ subroutine Init(this, begc, endc)
     allocate(this%dz_lake     (begc:endc,nlevlak))             ; this%dz_lake     (:,:) = nan
     allocate(this%z_lake      (begc:endc,nlevlak))             ; this%z_lake      (:,:) = nan
 
-    allocate(this%nbedrock   (begc:endc))                     ; this%nbedrock   (:)   = ispval  
-    allocate(this%levgrnd_class(begc:endc,nlevgrnd))           ; this%levgrnd_class(:,:) = ispval
-    allocate(this%micro_sigma (begc:endc))                     ; this%micro_sigma (:)   = nan
-    allocate(this%n_melt      (begc:endc))                     ; this%n_melt      (:)   = nan 
-    allocate(this%topo_slope  (begc:endc))                     ; this%topo_slope  (:)   = nan
-    allocate(this%topo_std    (begc:endc))                     ; this%topo_std    (:)   = nan
-
     allocate(this%hydrologically_active(begc:endc))            ; this%hydrologically_active(:) = .false.
 
   end subroutine Init
@@ -160,12 +135,6 @@ subroutine Clean(this)
     deallocate(this%lakedepth  )
     deallocate(this%dz_lake    )
     deallocate(this%z_lake     )
-    deallocate(this%micro_sigma)
-    deallocate(this%n_melt     )
-    deallocate(this%topo_slope )
-    deallocate(this%topo_std   )
-    deallocate(this%nbedrock   )
-    deallocate(this%levgrnd_class)
     deallocate(this%hydrologically_active)
 
   end subroutine Clean
diff --git a/src/main/FuncPedotransferMod.F90 b/src/main/FuncPedotransferMod.F90
deleted file mode 100644
index 41e751344e..0000000000
--- a/src/main/FuncPedotransferMod.F90
+++ /dev/null
@@ -1,141 +0,0 @@
-module FuncPedotransferMod
-!
-!DESCRIPTIONS:
-!module contains different pedotransfer functions to
-!compute the mineral soil hydraulic properties.
-!currenty, only the Clapp-Hornberg formulation is used.
-!HISTORY:
-!created by Jinyun Tang, Mar.1st, 2014
-implicit none
-  private
-  public :: pedotransf
-  public :: get_ipedof
-  public :: init_pedof
-
-  integer, parameter :: cosby_1984_table5 = 0    !by default uses this form
-  integer, parameter :: cosby_1984_table4 = 1
-  integer, parameter :: noilhan_lacarrere_1995 = 2
-  integer :: ipedof0
-contains
-
-   subroutine init_pedof()
-   !
-   !DESCRIPTIONS
-   !initialize the default pedotransfer function
-   implicit none
-   
-   
-   ipedof0 = cosby_1984_table5         !the default pedotransfer function
-   end subroutine init_pedof
-   
-   subroutine pedotransf(ipedof, sand, clay, watsat, bsw, sucsat, xksat)
-   !pedotransfer function to compute hydraulic properties of mineral soil
-   !based on input soil texture
-   
-   use shr_kind_mod         , only : r8 => shr_kind_r8
-   use abortutils    , only : endrun         
-   implicit none
-   integer,  intent(in) :: ipedof !type of pedotransfer function, use the default pedotransfer function  
-   real(r8), intent(in) :: sand   !% sand
-   real(r8), intent(in) :: clay   !% clay
-   real(r8), intent(out):: watsat !v/v saturate moisture
-   real(r8), intent(out):: bsw    !b shape parameter
-   real(r8), intent(out):: sucsat !mm, soil matric potential
-   real(r8), intent(out):: xksat  !mm/s, saturated hydraulic conductivity
-   
-   character(len=32) :: subname = 'pedotransf'  ! subroutine name 
-   select case (ipedof)
-   case (cosby_1984_table4)
-      call pedotransf_cosby1984_table4(sand, clay, watsat, bsw, sucsat, xksat)
-   case (noilhan_lacarrere_1995)
-      call pedotransf_noilhan_lacarrere1995(sand, clay, watsat, bsw, sucsat, xksat) 
-   case (cosby_1984_table5)  
-      call pedotransf_cosby1984_table5(sand, clay, watsat, bsw, sucsat, xksat)
-   case default
-      call endrun(subname // ':: a pedotransfer function must be specified!')  
-   end select
-
-   end subroutine pedotransf
-   
-!------------------------------------------------------------------------------------------
-   subroutine pedotransf_cosby1984_table4(sand, clay, watsat, bsw, sucsat, xksat)
-   !
-   !DESCRIPTIONS
-   !compute hydraulic properties based on functions derived from Table 4 in cosby et al, 1984
-   use shr_kind_mod         , only : r8 => shr_kind_r8   
-   implicit none
-   real(r8), intent(in) :: sand   !% sand
-   real(r8), intent(in) :: clay   !% clay
-   real(r8), intent(out):: watsat !v/v saturate moisture
-   real(r8), intent(out):: bsw    !b shape parameter
-   real(r8), intent(out):: sucsat !mm, soil matric potential
-   real(r8), intent(out):: xksat  !mm/s, saturated hydraulic conductivity
-   
-   !Cosby et al. Table 4
-   watsat = 0.505_r8-0.00142_r8*sand-0.00037*clay
-   bsw = 3.10+0.157*clay-0.003*sand            
-   sucsat  = 10._r8 * ( 10._r8**(1.54_r8-0.0095_r8*sand+0.0063*(100._r8-sand-clay)))            
-   xksat         = 0.0070556 *(10.**(-0.60+0.0126*sand-0.0064*clay) )     !mm/s now use table 4.
-      
-   end subroutine pedotransf_cosby1984_table4
-   
-!------------------------------------------------------------------------------------------
-   subroutine pedotransf_cosby1984_table5(sand, clay, watsat, bsw, sucsat, xksat)
-   !
-   !DESCRIPTIONS
-   !compute hydraulic properties based on functions derived from Table 5 in cosby et al, 1984
-   
-   use shr_kind_mod         , only : r8 => shr_kind_r8   
-   implicit none
-   real(r8), intent(in) :: sand   !% sand
-   real(r8), intent(in) :: clay   !% clay
-   real(r8), intent(out):: watsat !v/v saturate moisture
-   real(r8), intent(out):: bsw    !b shape parameter
-   real(r8), intent(out):: sucsat !mm, soil matric potential
-   real(r8), intent(out):: xksat  !mm/s, saturated hydraulic conductivity
-   
-   !Cosby et al. Table 5     
-   watsat = 0.489_r8 - 0.00126_r8*sand
-   bsw    = 2.91 + 0.159*clay
-   sucsat = 10._r8 * ( 10._r8**(1.88_r8-0.0131_r8*sand) )            
-   xksat         = 0.0070556 *( 10.**(-0.884+0.0153*sand) ) ! mm/s, from table 5 
-      
-   end subroutine pedotransf_cosby1984_table5
-   
-!------------------------------------------------------------------------------------------
-   subroutine pedotransf_noilhan_lacarrere1995(sand, clay, watsat, bsw, sucsat, xksat)
-   !
-   !DESCRIPTIONS
-   !compute hydraulic properties based on functions derived from Noilhan and Lacarrere, 1995
-   
-   use shr_kind_mod         , only : r8 => shr_kind_r8   
-   implicit none
-   real(r8), intent(in) :: sand   !% sand
-   real(r8), intent(in) :: clay   !% clay
-   real(r8), intent(out):: watsat !v/v saturate moisture
-   real(r8), intent(out):: bsw    !b shape parameter
-   real(r8), intent(out):: sucsat !mm, soil matric potential
-   real(r8), intent(out):: xksat  !mm/s, saturated hydraulic conductivity
-   
-   !Noilhan and Lacarrere, 1995
-   watsat = -0.00108*sand+0.494305
-   bsw = 0.137*clay + 3.501
-   sucsat = 10._r8**(-0.0088*sand+2.85)
-   xksat = 10._r8**(-0.0582*clay-0.00091*sand+0.000529*clay**2._r8-0.0001203*sand**2._r8-1.38)
-   end subroutine pedotransf_noilhan_lacarrere1995
-!------------------------------------------------------------------------------------------
-   function get_ipedof(soil_order)result(ipedof)
-   !
-   ! DESCRIPTION
-   ! select the pedotransfer function to be used
-   implicit none
-   integer, intent(in) :: soil_order
-   
-   integer :: ipedof
-   
-   if(soil_order==0)then
-      ipedof=ipedof0
-   endif
-   
-   end function get_ipedof   
-end module FuncpedotransferMod
diff --git a/src/main/GridcellType.F90 b/src/main/GridcellType.F90
index 30fe988eff..209d59a5e6 100644
--- a/src/main/GridcellType.F90
+++ b/src/main/GridcellType.F90
@@ -29,8 +29,6 @@ module GridcellType
      real(r8), pointer :: londeg           (:) ! longitude (degrees)
      logical , pointer :: active           (:) ! just needed for symmetry with other subgrid types
 
-     integer,  pointer :: nbedrock         (:) ! index of uppermost bedrock layer
-
      ! Daylength
      real(r8) , pointer :: max_dayl        (:) ! maximum daylength for this grid cell (s)
      real(r8) , pointer :: dayl            (:) ! daylength (seconds)
@@ -70,7 +68,6 @@ subroutine Init(this, begg, endg)
     allocate(this%latdeg    (begg:endg)) ; this%latdeg    (:) = nan
     allocate(this%londeg    (begg:endg)) ; this%londeg    (:) = nan
     allocate(this%active    (begg:endg)) ; this%active    (:) = .true.
-    allocate(this%nbedrock  (begg:endg)) ; this%nbedrock  (:) = ispval
 
     ! This is initiailized in module DayLength
     allocate(this%max_dayl  (begg:endg)) ; this%max_dayl  (:) = nan
@@ -95,7 +92,6 @@ subroutine Clean(this)
     deallocate(this%latdeg           )
     deallocate(this%londeg           )
     deallocate(this%active           )
-    deallocate(this%nbedrock         )
     deallocate(this%max_dayl         )
     deallocate(this%dayl             )
     deallocate(this%prev_dayl        )
diff --git a/src/main/LandunitType.F90 b/src/main/LandunitType.F90
index 2236ca2780..a9ca17ce53 100644
--- a/src/main/LandunitType.F90
+++ b/src/main/LandunitType.F90
@@ -48,9 +48,6 @@ module LandunitType
      real(r8), pointer :: canyon_hwr   (:) ! urban landunit canyon height to width ratio (-)   
      real(r8), pointer :: wtroad_perv  (:) ! urban landunit weight of pervious road column to total road (-)
      real(r8), pointer :: wtlunit_roof (:) ! weight of roof with respect to urban landunit (-)
-     real(r8), pointer :: ht_roof      (:) ! height of urban roof (m)
-     real(r8), pointer :: z_0_town     (:) ! urban landunit momentum roughness length (m)
-     real(r8), pointer :: z_d_town     (:) ! urban landunit displacement height (m)
 
    contains
 
@@ -97,10 +94,7 @@ subroutine Init(this, begl, endl)
     ! The following is set in routine urbanparams_inst%Init in module UrbanParamsType
     allocate(this%canyon_hwr   (begl:endl)); this%canyon_hwr   (:) = nan
     allocate(this%wtroad_perv  (begl:endl)); this%wtroad_perv  (:) = nan
-    allocate(this%ht_roof      (begl:endl)); this%ht_roof      (:) = nan
     allocate(this%wtlunit_roof (begl:endl)); this%wtlunit_roof (:) = nan
-    allocate(this%z_0_town     (begl:endl)); this%z_0_town     (:) = nan
-    allocate(this%z_d_town     (begl:endl)); this%z_d_town     (:) = nan
 
   end subroutine Init
 
@@ -130,10 +124,7 @@ subroutine Clean(this)
     deallocate(this%active       )
     deallocate(this%canyon_hwr   )
     deallocate(this%wtroad_perv  )
-    deallocate(this%ht_roof      )
     deallocate(this%wtlunit_roof )
-    deallocate(this%z_0_town     )
-    deallocate(this%z_d_town     )
 
   end subroutine Clean
 
diff --git a/src/main/PatchType.F90 b/src/main/PatchType.F90
index d00f5588b0..9d99ea83f6 100644
--- a/src/main/PatchType.F90
+++ b/src/main/PatchType.F90
@@ -23,74 +23,11 @@ module PatchType
   !   14 => c4_grass
   !   15 => c3_crop
   !   16 => c3_irrigated
-  !   17 => temperate_corn
-  !   18 => irrigated_temperate_corn
-  !   19 => spring_wheat
-  !   20 => irrigated_spring_wheat
-  !   21 => winter_wheat
-  !   22 => irrigated_winter_wheat
-  !   23 => temperate_soybean
-  !   24 => irrigated_temperate_soybean
-  !   25 => barley
-  !   26 => irrigated_barley
-  !   27 => winter_barley
-  !   28 => irrigated_winter_barley
-  !   29 => rye
-  !   30 => irrigated_rye
-  !   31 => winter_rye
-  !   32 => irrigated_winter_rye
-  !   33 => cassava
-  !   34 => irrigated_cassava
-  !   35 => citrus
-  !   36 => irrigated_citrus
-  !   37 => cocoa
-  !   38 => irrigated_cocoa
-  !   39 => coffee
-  !   40 => irrigated_coffee
-  !   41 => cotton
-  !   42 => irrigated_cotton
-  !   43 => datepalm
-  !   44 => irrigated_datepalm
-  !   45 => foddergrass
-  !   46 => irrigated_foddergrass
-  !   47 => grapes
-  !   48 => irrigated_grapes
-  !   49 => groundnuts
-  !   50 => irrigated_groundnuts
-  !   51 => millet
-  !   52 => irrigated_millet
-  !   53 => oilpalm
-  !   54 => irrigated_oilpalm
-  !   55 => potatoes
-  !   56 => irrigated_potatoes
-  !   57 => pulses
-  !   58 => irrigated_pulses
-  !   59 => rapeseed
-  !   60 => irrigated_rapeseed
-  !   61 => rice
-  !   62 => irrigated_rice
-  !   63 => sorghum
-  !   64 => irrigated_sorghum
-  !   65 => sugarbeet
-  !   66 => irrigated_sugarbeet
-  !   67 => sugarcane
-  !   68 => irrigated_sugarcane
-  !   69 => sunflower
-  !   70 => irrigated_sunflower
-  !   71 => miscanthus
-  !   72 => irrigated_miscanthus
-  !   73 => switchgrass
-  !   74 => irrigated_switchgrass
-  !   75 => tropical_corn
-  !   76 => irrigated_tropical_corn
-  !   77 => tropical_soybean
-  !   78 => irrigated_tropical_soybean
   ! -------------------------------------------------------- 
   !
   use shr_kind_mod   , only : r8 => shr_kind_r8
   use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
   use clm_varcon     , only : ispval
-  use clm_varctl     , only : use_fates 
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -112,20 +49,6 @@ module PatchType
      integer , pointer :: mxy      (:) ! m index for laixy(i,j,m),etc. (undefined for special landunits)
      logical , pointer :: active   (:) ! true=>do computations on this patch
 
-     ! fates only
-     logical , pointer :: is_veg   (:) ! This is an ACTIVE fates patch
-     logical , pointer :: is_bareground  (:)
-     real(r8), pointer :: wt_ed       (:) !TODO mv ? can this be removed
-
-     
-     logical, pointer  :: is_fates (:) ! true for patch vector space reserved
-                                       ! for FATES.
-                                       ! this is static and is true for all 
-                                       ! patches within fates jurisdiction
-                                       ! including patches which are not currently
-                                       ! associated with a FATES linked-list patch
-
-
    contains
 
      procedure, public :: Init
@@ -168,14 +91,6 @@ subroutine Init(this, begp, endp)
 
     allocate(this%itype      (begp:endp)); this%itype      (:) = ispval
 
-    allocate(this%is_fates   (begp:endp)); this%is_fates   (:) = .false.
-
-    if (use_fates) then
-       allocate(this%is_veg  (begp:endp)); this%is_veg  (:) = .false.
-       allocate(this%is_bareground (begp:endp)); this%is_bareground (:) = .false.
-       allocate(this%wt_ed      (begp:endp)); this%wt_ed      (:) = nan 
-    end if
-
   end subroutine Init
 
   !------------------------------------------------------------------------
@@ -194,13 +109,6 @@ subroutine Clean(this)
     deallocate(this%itype   )
     deallocate(this%mxy     )
     deallocate(this%active  )
-    deallocate(this%is_fates)
-
-    if (use_fates) then
-       deallocate(this%is_veg)
-       deallocate(this%is_bareground)
-       deallocate(this%wt_ed)
-    end if
 
   end subroutine Clean
 
diff --git a/src/main/TopoMod.F90 b/src/main/TopoMod.F90
index 9841f59b92..6420adcae9 100644
--- a/src/main/TopoMod.F90
+++ b/src/main/TopoMod.F90
@@ -11,7 +11,6 @@ module TopoMod
   use PatchType      , only : patch
   use ColumnType     , only : col
   use LandunitType   , only : lun
-  use glc2lndMod     , only : glc2lnd_type
   use glcBehaviorMod , only : glc_behavior_type
   use landunit_varcon, only : istice_mec
   use filterColMod   , only : filter_col_type, col_filter_from_logical_array_active_only
@@ -31,15 +30,13 @@ module TopoMod
      ! Private member data
 
      logical, pointer :: needs_downscaling_col(:)  ! whether a column needs to be downscaled
+
    contains
      procedure, public :: Init
      procedure, public :: Restart
      procedure, public :: Clean
-     procedure, public :: UpdateTopo  ! Update topographic height each time step
-     procedure, public :: DownscaleFilterc  ! Returns column-level filter: which columns need downscaling
 
      procedure, private :: InitAllocate
-     procedure, private :: InitHistory
      procedure, private :: InitCold
   end type topo_type
 
@@ -57,7 +54,6 @@ subroutine Init(this, bounds)
     !-----------------------------------------------------------------------
 
     call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
     call this%InitCold(bounds)
 
   end subroutine Init
@@ -85,26 +81,6 @@ subroutine InitAllocate(this, bounds)
 
   end subroutine InitAllocate
 
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    ! !USES:
-    use histFileMod  , only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(topo_type), intent(inout) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-
-    call hist_addfld1d(fname='TOPO_COL', units='m', &
-         avgflag='A', long_name='column-level topographic height', &
-         ptr_col=this%topo_col, default='inactive')
-
-  end subroutine InitHistory
-
   !-----------------------------------------------------------------------
   subroutine InitCold(this, bounds)
     ! !USES:
@@ -164,9 +140,6 @@ subroutine Restart(this, bounds, ncid, flag)
 
     allocate(rparr(bounds%begp:bounds%endp))
 
-    ! TODO(wjs, 2016-04-05) Rename these restart variables to get rid of 'glc' in their
-    ! names. However, this will require some changes to init_interp, too.
-
     call restartvar(ncid=ncid, flag=flag, varname='cols1d_topoglc', xtype=ncd_double,   &
          dim1name='column',                                                             &
          long_name='mean elevation on glacier elevation classes', units='m',            &
@@ -187,115 +160,6 @@ subroutine Restart(this, bounds, ncid, flag)
 
   end subroutine Restart
 
-
-  !-----------------------------------------------------------------------
-  subroutine UpdateTopo(this, bounds, num_icemecc, filter_icemecc, &
-       glc2lnd_inst, glc_behavior, atm_topo)
-    !
-    ! !DESCRIPTION:
-    ! Update topographic heights
-    !
-    ! Should be called each time step.
-    !
-    ! Should be called after glc2lndMod:update_glc2lnd_fracs, and before
-    ! atm2lndMod:downscale_forcings
-    !
-    ! !ARGUMENTS:
-    class(topo_type)        , intent(inout) :: this
-    type(bounds_type)       , intent(in)    :: bounds
-    integer                 , intent(in)    :: num_icemecc       ! number of points in filter_icemecc
-    integer                 , intent(in)    :: filter_icemecc(:) ! col filter for ice_mec
-    type(glc2lnd_type)      , intent(in)    :: glc2lnd_inst
-    type(glc_behavior_type) , intent(in)    :: glc_behavior
-    real(r8)                , intent(in)    :: atm_topo( bounds%begg: ) ! atmosphere topographic height [m]
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begc, endc
-    integer :: c, g
-
-    character(len=*), parameter :: subname = 'UpdateTopo'
-    !-----------------------------------------------------------------------
-
-    begc = bounds%begc
-    endc = bounds%endc
-
-    ! Reset needs_downscaling_col each time step, because this is potentially
-    ! time-varying for some columns. It's simplest just to reset it everywhere, rather
-    ! than trying to figure out where it does and does not need to be reset.
-    this%needs_downscaling_col(begc:endc) = .false.
-
-    call glc_behavior%icemec_cols_need_downscaling(bounds, num_icemecc, filter_icemecc, &
-         this%needs_downscaling_col(begc:endc))
-
-    ! In addition to updating topo_col, this also sets some additional elements of
-    ! needs_downscaling_col to .true. (but leaves the already-.true. values as is.)
-    call glc2lnd_inst%update_glc2lnd_topo(bounds, &
-         this%topo_col(begc:endc), &
-         this%needs_downscaling_col(begc:endc))
-
-    ! For any point that isn't downscaled, set its topo value to the atmosphere's
-    ! topographic height. This shouldn't matter, but is useful if topo_col is written to
-    ! the history file.
-    !
-    ! This could operate over a filter like 'allc' in order to just operate over active
-    ! points, but I'm not sure that would speed things up much, and would require passing
-    ! in this additional filter.
-    do c = bounds%begc, bounds%endc
-       if (.not. this%needs_downscaling_col(c)) then
-          g = col%gridcell(c)
-          this%topo_col(c) = atm_topo(g)
-       end if
-    end do
-
-    call glc_behavior%update_glc_classes(bounds, this%topo_col(begc:endc))
-
-  end subroutine UpdateTopo
-
-  !-----------------------------------------------------------------------
-  function DownscaleFilterc(this, bounds) result(filter)
-    !
-    ! !DESCRIPTION:
-    ! Returns a column-level filter: which columns need downscaling.
-    !
-    ! This filter only contains active points.
-    !
-    ! The main reason it's important to have this filter (as opposed to just doing the
-    ! downscaling for all columns) is because of downscaled fields that are normalized
-    ! (like longwave radiation): Consider a gridcell with a glc_mec column and a
-    ! vegetated column (outside of the icemask, so the vegetated column doesn't have its
-    ! topographic height explicitly set). If we called the downscaling code for all
-    ! columns, the longwave radiation would get adjusted over the vegetated column. This
-    ! is undesirable, because it means that adding a downscaled column in a gridcell can
-    ! change answers for all other columns in that gridcell.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(filter_col_type) :: filter  ! function result
-    class(topo_type), intent(in) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'DownscaleFilterc'
-    !-----------------------------------------------------------------------
-
-    ! Currently this creates the filter on the fly, recreating it every time this function
-    ! is called. In principle, we should be able to compute and save this filter when
-    ! UpdateTopo is called, returning the already-computed filter when this function is
-    ! called. However, the problem with that is the need to have a different filter for
-    ! each clump (and potentially another filter for calls from outside a clump
-    ! loop). This will become easier to handle if we rework CLM's threading so that there
-    ! is a separate instance of each object for each clump: in that case, we'll have
-    ! multiple instances of topo_type, each corresponding to one clump, each with its own
-    ! filter.
-
-    filter = col_filter_from_logical_array_active_only(bounds, &
-         this%needs_downscaling_col(bounds%begc:bounds%endc))
-
-  end function DownscaleFilterc
-
-
   !-----------------------------------------------------------------------
   subroutine Clean(this)
     ! !ARGUMENTS:
diff --git a/src/main/atm2lndMod.F90 b/src/main/atm2lndMod.F90
deleted file mode 100644
index bfa868b2f2..0000000000
--- a/src/main/atm2lndMod.F90
+++ /dev/null
@@ -1,682 +0,0 @@
-module atm2lndMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Handle atm2lnd forcing
-  !
-  ! !USES:
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use clm_varpar     , only : numrad, ndst, nlevgrnd !ndst = number of dust bins.
-  use clm_varcon     , only : rair, grav, cpair, hfus, tfrz, denh2o, spval
-  use clm_varcon     , only : wv_to_dair_weight_ratio
-  use clm_varctl     , only : iulog, use_cn, iulog
-  use abortutils     , only : endrun
-  use decompMod      , only : bounds_type
-  use atm2lndType    , only : atm2lnd_type
-  use TopoMod        , only : topo_type
-  use filterColMod   , only : filter_col_type
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col
-  use landunit_varcon, only : istice_mec
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: downscale_forcings           ! Downscale atm forcing fields from gridcell to column
-
-  ! The following routines are public for the sake of unit testing; they should not be
-  ! called by production code outside this module
-  public :: partition_precip              ! Partition precipitation into rain/snow
-  public :: sens_heat_from_precip_conversion  ! Compute sensible heat flux needed to compensate for rain-snow conversion
-  !
-  ! !PRIVATE MEMBER FUNCTIONS:
-  private :: rhos  ! calculate atmospheric density
-  private :: repartition_rain_snow_one_col ! Re-partition precipitation for a single column
-  private :: downscale_longwave          ! Downscale longwave radiation from gridcell to column
-  private :: build_normalization         ! Compute normalization factors so that downscaled fields are conservative
-  private :: check_downscale_consistency ! Check consistency of downscaling
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine downscale_forcings(bounds, &
-       topo_inst, atm2lnd_inst, eflx_sh_precip_conversion)
-    !
-    ! !DESCRIPTION:
-    ! Downscale atmospheric forcing fields from gridcell to column.
-    !
-    ! Downscaling is done based on the difference between each CLM column's elevation and
-    ! the atmosphere's surface elevation (which is the elevation at which the atmospheric
-    ! forcings are valid).
-    !
-    ! Note that the downscaling procedure can result in changes in grid cell mean values
-    ! compared to what was provided by the atmosphere. We conserve fluxes of mass and
-    ! energy, but allow states such as temperature to differ.
-    !
-    ! For most variables, downscaling is done over columns defined by
-    ! topo_inst%DownscaleFilterc. But we also do direct copies of gridcell-level forcings
-    ! into column-level forcings over all other active columns. In addition, precipitation
-    ! (rain vs. snow partitioning) is adjusted everywhere.
-    !
-    ! !USES:
-    use clm_varcon      , only : rair, cpair, grav
-    use QsatMod         , only : Qsat
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)  , intent(in)    :: bounds  
-    class(topo_type)   , intent(in)    :: topo_inst
-    type(atm2lnd_type) , intent(inout) :: atm2lnd_inst
-    real(r8)           , intent(out)   :: eflx_sh_precip_conversion(bounds%begc:) ! sensible heat flux from precipitation conversion (W/m**2) [+ to atm]
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g, l, c, fc         ! indices
-    integer :: clo, cc
-    type(filter_col_type) :: downscale_filter_c
-
-    ! temporaries for topo downscaling
-    real(r8) :: hsurf_g,hsurf_c
-    real(r8) :: Hbot, zbot
-    real(r8) :: tbot_g, pbot_g, thbot_g, qbot_g, qs_g, es_g, rhos_g
-    real(r8) :: tbot_c, pbot_c, thbot_c, qbot_c, qs_c, es_c, rhos_c
-    real(r8) :: rhos_c_estimate, rhos_g_estimate
-    real(r8) :: dum1,   dum2
-
-    character(len=*), parameter :: subname = 'downscale_forcings'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(eflx_sh_precip_conversion) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-    associate(&
-         ! Parameters:
-         lapse_rate => atm2lnd_inst%params%lapse_rate              , & ! Input:  [real(r8)] Surface temperature lapse rate (K m-1)
-
-         ! Gridcell-level metadata:
-         forc_topo_g  => atm2lnd_inst%forc_topo_grc                , & ! Input:  [real(r8) (:)]  atmospheric surface height (m)
-
-         ! Column-level metadata:
-         topo_c       => topo_inst%topo_col                        , & ! Input:  [real(r8) (:)] column surface height (m)
-
-         ! Gridcell-level non-downscaled fields:
-         forc_t_g     => atm2lnd_inst%forc_t_not_downscaled_grc    , & ! Input:  [real(r8) (:)]  atmospheric temperature (Kelvin)        
-         forc_th_g    => atm2lnd_inst%forc_th_not_downscaled_grc   , & ! Input:  [real(r8) (:)]  atmospheric potential temperature (Kelvin)
-         forc_q_g     => atm2lnd_inst%forc_q_not_downscaled_grc    , & ! Input:  [real(r8) (:)]  atmospheric specific humidity (kg/kg)   
-         forc_pbot_g  => atm2lnd_inst%forc_pbot_not_downscaled_grc , & ! Input:  [real(r8) (:)]  atmospheric pressure (Pa)               
-         forc_rho_g   => atm2lnd_inst%forc_rho_not_downscaled_grc  , & ! Input:  [real(r8) (:)]  atmospheric density (kg/m**3)           
-         
-         ! Column-level downscaled fields:
-         forc_t_c     => atm2lnd_inst%forc_t_downscaled_col        , & ! Output: [real(r8) (:)]  atmospheric temperature (Kelvin)        
-         forc_th_c    => atm2lnd_inst%forc_th_downscaled_col       , & ! Output: [real(r8) (:)]  atmospheric potential temperature (Kelvin)
-         forc_q_c     => atm2lnd_inst%forc_q_downscaled_col        , & ! Output: [real(r8) (:)]  atmospheric specific humidity (kg/kg)   
-         forc_pbot_c  => atm2lnd_inst%forc_pbot_downscaled_col     , & ! Output: [real(r8) (:)]  atmospheric pressure (Pa)               
-         forc_rho_c   => atm2lnd_inst%forc_rho_downscaled_col        & ! Output: [real(r8) (:)]  atmospheric density (kg/m**3)           
-         )
-      
-      ! Initialize column forcing (needs to be done for ALL active columns)
-      do c = bounds%begc,bounds%endc
-         if (col%active(c)) then
-            g = col%gridcell(c)
-
-            forc_t_c(c)     = forc_t_g(g)
-            forc_th_c(c)    = forc_th_g(g)
-            forc_q_c(c)     = forc_q_g(g)
-            forc_pbot_c(c)  = forc_pbot_g(g)
-            forc_rho_c(c)   = forc_rho_g(g)
-         end if
-      end do
-
-      downscale_filter_c = topo_inst%DownscaleFilterc(bounds)
-
-      ! Downscale forc_t, forc_th, forc_q, forc_pbot, and forc_rho to columns.
-      ! For glacier_mec columns the downscaling is based on surface elevation.
-      ! For other columns the downscaling is a simple copy (above).
-      do fc = 1, downscale_filter_c%num
-         c = downscale_filter_c%indices(fc)
-         l = col%landunit(c)
-         g = col%gridcell(c)
-
-         ! This is a simple downscaling procedure 
-         ! Note that forc_hgt, forc_u, and forc_v are not downscaled.
-
-         hsurf_g = forc_topo_g(g)                        ! gridcell sfc elevation
-         hsurf_c = topo_c(c)                             ! column sfc elevation
-         tbot_g  = forc_t_g(g)                           ! atm sfc temp
-         thbot_g = forc_th_g(g)                          ! atm sfc pot temp
-         qbot_g  = forc_q_g(g)                           ! atm sfc spec humid
-         pbot_g  = forc_pbot_g(g)                        ! atm sfc pressure
-         rhos_g  = forc_rho_g(g)                         ! atm density
-         zbot    = atm2lnd_inst%forc_hgt_grc(g)          ! atm ref height
-         tbot_c  = tbot_g-lapse_rate*(hsurf_c-hsurf_g)   ! sfc temp for column
-         Hbot    = rair*0.5_r8*(tbot_g+tbot_c)/grav      ! scale ht at avg temp
-         pbot_c  = pbot_g*exp(-(hsurf_c-hsurf_g)/Hbot)   ! column sfc press
-
-         ! Derivation of potential temperature calculation:
-         ! 
-         ! The textbook definition would be:
-         ! thbot_c = tbot_c * (p0/pbot_c)^(rair/cpair)
-         ! 
-         ! Note that pressure is related to scale height as:
-         ! pbot_c = p0 * exp(-zbot/H)
-         !
-         ! Using Hbot in place of H, we get:
-         ! pbot_c = p0 * exp(-zbot/Hbot)
-         !
-         ! Plugging this in to the textbook definition, then manipulating, we get:
-         ! thbot_c = tbot_c * (p0/(p0*exp(-zbot/Hbot)))^(rair/cpair)
-         !         = tbot_c * (1/exp(-zbot/Hbot))^(rair/cpair)
-         !         = tbot_c * (exp(zbot/Hbot))^(rair/cpair)
-         !         = tbot_c * exp((zbot/Hbot) * (rair/cpair))
-         !
-         ! But we want everything expressed in delta form, resulting in:
-         ! thbot_c = thbot_g + (tbot_c - tbot_g)*exp((zbot/Hbot)*(rair/cpair))
-
-         thbot_c= thbot_g + (tbot_c - tbot_g)*exp((zbot/Hbot)*(rair/cpair))  ! pot temp calc
-
-         call Qsat(tbot_g,pbot_g,es_g,dum1,qs_g,dum2)
-         call Qsat(tbot_c,pbot_c,es_c,dum1,qs_c,dum2)
-
-         qbot_c = qbot_g*(qs_c/qs_g)
-
-         ! For forc_rho_c: We could simply set:
-         !
-         !    rhos_c = rhos(pbot_c, egcm_c, tbot_c)
-         !
-         ! However, we want forc_rho_c to be identical to forc_rho_g when topo_c equals
-         ! forc_topo_g. So we compute our own version of forc_rho_g using the rhos
-         ! function, and then multiply forc_rho_g by the ratio of (computed column-level
-         ! rho) to (computed gridcell-level rho).
-         rhos_c_estimate = rhos(qbot=qbot_c, pbot=pbot_c, tbot=tbot_c)
-         rhos_g_estimate = rhos(qbot=qbot_g, pbot=pbot_g, tbot=tbot_g)
-         rhos_c = rhos_g * (rhos_c_estimate / rhos_g_estimate)
-
-         forc_t_c(c)    = tbot_c
-         forc_th_c(c)   = thbot_c
-         forc_q_c(c)    = qbot_c
-         forc_pbot_c(c) = pbot_c
-         forc_rho_c(c)  = rhos_c
-
-      end do
-
-      call partition_precip(bounds, atm2lnd_inst, &
-           eflx_sh_precip_conversion(bounds%begc:bounds%endc))
-
-      call downscale_longwave(bounds, downscale_filter_c, topo_inst, atm2lnd_inst)
-
-      call check_downscale_consistency(bounds, atm2lnd_inst)
-
-    end associate
-
-  end subroutine downscale_forcings
-
-  !-----------------------------------------------------------------------
-  pure function rhos(qbot, pbot, tbot)
-    !
-    ! !DESCRIPTION:
-    ! Compute atmospheric density (kg/m**3)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    real(r8) :: rhos  ! function result: atmospheric density (kg/m**3)
-    real(r8), intent(in) :: qbot  ! atmospheric specific humidity (kg/kg)
-    real(r8), intent(in) :: pbot  ! atmospheric pressure (Pa)
-    real(r8), intent(in) :: tbot  ! atmospheric temperature (K)
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: egcm
-
-    character(len=*), parameter :: subname = 'rhos'
-    !-----------------------------------------------------------------------
-
-    egcm = qbot*pbot / &
-         (wv_to_dair_weight_ratio + (1._r8 - wv_to_dair_weight_ratio)*qbot)
-    rhos = (pbot - (1._r8 - wv_to_dair_weight_ratio)*egcm) / (rair*tbot)
-    
-  end function rhos
-
-  !-----------------------------------------------------------------------
-  subroutine partition_precip(bounds, atm2lnd_inst, eflx_sh_precip_conversion)
-    !
-    ! !DESCRIPTION:
-    ! Partition precipitation into rain/snow based on temperature.
-    !
-    ! Note that, unlike the other downscalings done here, this is currently applied over
-    ! all points - not just those within the downscale filter.
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)  , intent(in)    :: bounds  
-    type(atm2lnd_type) , intent(inout) :: atm2lnd_inst
-    real(r8), intent(inout) :: eflx_sh_precip_conversion(bounds%begc:) ! sensible heat flux from precipitation conversion (W/m**2) [+ to atm]
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,l,g      ! indices
-    real(r8) :: rain_old   ! rain before conversion
-    real(r8) :: snow_old   ! snow before conversion
-    real(r8) :: all_snow_t ! temperature at which all precip falls as snow (K)
-    real(r8) :: frac_rain_slope ! slope of the frac_rain vs. temperature relationship
-
-    character(len=*), parameter :: subname = 'partition_precip'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(eflx_sh_precip_conversion) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-    associate(&
-         ! Gridcell-level non-downscaled fields:
-         forc_rain_g  => atm2lnd_inst%forc_rain_not_downscaled_grc , & ! Input:  [real(r8) (:)]  rain rate [mm/s]
-         forc_snow_g  => atm2lnd_inst%forc_snow_not_downscaled_grc , & ! Input:  [real(r8) (:)]  snow rate [mm/s]
-         
-         ! Column-level downscaled fields:
-         forc_t_c     => atm2lnd_inst%forc_t_downscaled_col        , & ! Input:  [real(r8) (:)]  atmospheric temperature (Kelvin)        
-         forc_rain_c  => atm2lnd_inst%forc_rain_downscaled_col     , & ! Output: [real(r8) (:)]  rain rate [mm/s]
-         forc_snow_c  => atm2lnd_inst%forc_snow_downscaled_col       & ! Output: [real(r8) (:)]  snow rate [mm/s]
-         )
-
-    ! Initialize column forcing
-    do c = bounds%begc,bounds%endc
-       if (col%active(c)) then
-          g = col%gridcell(c)
-          forc_rain_c(c)  = forc_rain_g(g)
-          forc_snow_c(c)  = forc_snow_g(g)
-          eflx_sh_precip_conversion(c) = 0._r8
-       end if
-    end do
-
-    ! Optionally, convert rain to snow or vice versa based on forc_t_c
-    if (atm2lnd_inst%params%repartition_rain_snow) then
-       do c = bounds%begc, bounds%endc
-          if (col%active(c)) then
-             l = col%landunit(c)
-             rain_old = forc_rain_c(c)
-             snow_old = forc_snow_c(c)
-             if (lun%itype(l) == istice_mec) then
-                all_snow_t = atm2lnd_inst%params%precip_repartition_glc_all_snow_t
-                frac_rain_slope = atm2lnd_inst%params%precip_repartition_glc_frac_rain_slope
-             else
-                all_snow_t = atm2lnd_inst%params%precip_repartition_nonglc_all_snow_t
-                frac_rain_slope = atm2lnd_inst%params%precip_repartition_nonglc_frac_rain_slope
-             end if
-             call repartition_rain_snow_one_col(&
-                  temperature = forc_t_c(c), &
-                  all_snow_t = all_snow_t, &
-                  frac_rain_slope = frac_rain_slope, &
-                  rain = forc_rain_c(c), &
-                  snow = forc_snow_c(c))
-             call sens_heat_from_precip_conversion(&
-                  rain_old = rain_old, &
-                  snow_old = snow_old, &
-                  rain_new = forc_rain_c(c), &
-                  snow_new = forc_snow_c(c), &
-                  sens_heat_flux = eflx_sh_precip_conversion(c))
-          end if
-       end do
-    end if
-
-    end associate
-
-  end subroutine partition_precip
-
-  !-----------------------------------------------------------------------
-  subroutine repartition_rain_snow_one_col(temperature, all_snow_t, frac_rain_slope, &
-       rain, snow)
-    !
-    ! !DESCRIPTION:
-    ! Re-partition precipitation into rain/snow for a single column.
-    !
-    ! Rain and snow variables should be set initially, and are updated here
-    !
-    ! !ARGUMENTS:
-    real(r8) , intent(in)    :: temperature ! near-surface temperature (K)
-    real(r8) , intent(in)    :: all_snow_t  ! temperature at which precip falls entirely as snow (K)
-    real(r8) , intent(in)    :: frac_rain_slope ! slope of the frac_rain vs. T relationship
-    real(r8) , intent(inout) :: rain        ! atm rain rate [mm/s]
-    real(r8) , intent(inout) :: snow        ! atm snow rate [(mm water equivalent)/s]
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: frac_rain     ! fraction of precipitation that should become rain
-    real(r8) :: total_precip
-
-    character(len=*), parameter :: subname = 'repartition_rain_snow_one_col'
-    !-----------------------------------------------------------------------
-
-    frac_rain = (temperature - all_snow_t) * frac_rain_slope
-
-    ! bound in [0,1]
-    frac_rain = min(1.0_r8,max(0.0_r8,frac_rain))
-
-    total_precip = rain + snow
-    rain = total_precip * frac_rain
-    snow = total_precip - rain
-
-  end subroutine repartition_rain_snow_one_col
-
-  !-----------------------------------------------------------------------
-  subroutine sens_heat_from_precip_conversion(rain_old, snow_old, rain_new, snow_new, &
-       sens_heat_flux)
-    !
-    ! !DESCRIPTION:
-    ! Given old and new rain and snow amounts, compute the sensible heat flux needed to
-    ! compensate for the rain-snow conversion.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    real(r8), intent(in)  :: rain_old        ! [mm/s]
-    real(r8), intent(in)  :: snow_old        ! [(mm water equivalent)/s]
-    real(r8), intent(in)  :: rain_new        ! [mm/s]
-    real(r8), intent(in)  :: snow_new        ! [(mm water equivalent)/s]
-    real(r8), intent(out) :: sens_heat_flux  ! [W/m^2]
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: total_old
-    real(r8) :: total_new
-    real(r8) :: rain_to_snow  ! net conversion of rain to snow
-
-    real(r8), parameter :: mm_to_m = 1.e-3_r8  ! multiply by this to convert from mm to m
-    real(r8), parameter :: tol = 1.e-13_r8     ! relative tolerance for error checks
-
-    character(len=*), parameter :: subname = 'sens_heat_from_precip_conversion'
-    !-----------------------------------------------------------------------
-
-    total_old = rain_old + snow_old
-    total_new = rain_new + snow_new
-    SHR_ASSERT(abs(total_new - total_old) <= (tol * total_old), subname//' ERROR: mismatch between old and new totals')
-
-    ! rain to snow releases energy, so results in a positive heat flux to atm
-    rain_to_snow = snow_new - snow_old
-    sens_heat_flux = rain_to_snow * mm_to_m * denh2o * hfus
-
-  end subroutine sens_heat_from_precip_conversion
-
-
-  !-----------------------------------------------------------------------
-  subroutine downscale_longwave(bounds, downscale_filter_c, &
-       topo_inst, atm2lnd_inst)
-    !
-    ! !DESCRIPTION:
-    ! Downscale longwave radiation from gridcell to column
-    ! Must be done AFTER temperature downscaling
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)     , intent(in)    :: bounds
-    type(filter_col_type) , intent(in)    :: downscale_filter_c
-    class(topo_type)      , intent(in)    :: topo_inst
-    type(atm2lnd_type)    , intent(inout) :: atm2lnd_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,l,g,fc     ! indices
-    real(r8) :: hsurf_c      ! column-level elevation (m)
-    real(r8) :: hsurf_g      ! gridcell-level elevation (m)
-
-    real(r8), dimension(bounds%begg : bounds%endg) :: sum_lwrad_g    ! weighted sum of column-level lwrad
-    real(r8), dimension(bounds%begg : bounds%endg) :: sum_wts_g      ! sum of weights that contribute to sum_lwrad_g
-    real(r8), dimension(bounds%begg : bounds%endg) :: lwrad_norm_g   ! normalization factors
-    real(r8), dimension(bounds%begg : bounds%endg) :: newsum_lwrad_g ! weighted sum of column-level lwrad after normalization
-
-    character(len=*), parameter :: subname = 'downscale_longwave'
-    !-----------------------------------------------------------------------
-
-    associate(&
-         ! Parameters:
-         lapse_rate_longwave => atm2lnd_inst%params%lapse_rate_longwave  , & ! Input:  [real(r8)] longwave radiation lapse rate (W m-2 m-1)
-         longwave_downscaling_limit => atm2lnd_inst%params%longwave_downscaling_limit, & ! Input:  [real(r8)] Relative limit for how much longwave downscaling can be done (unitless)
-
-         ! Gridcell-level metadata:
-         forc_topo_g  => atm2lnd_inst%forc_topo_grc                , & ! Input:  [real(r8) (:)]  atmospheric surface height (m)
-
-         ! Column-level metadata:
-         topo_c       => topo_inst%topo_col                        , & ! Input:  [real(r8) (:)] column surface height (m)
-
-         ! Gridcell-level fields:
-         forc_lwrad_g => atm2lnd_inst%forc_lwrad_not_downscaled_grc, & ! Input:  [real(r8) (:)]  downward longwave (W/m**2)
-         
-         ! Column-level (downscaled) fields:
-         forc_lwrad_c => atm2lnd_inst%forc_lwrad_downscaled_col      & ! Output: [real(r8) (:)]  downward longwave (W/m**2)
-         )
-    
-      ! Initialize column forcing (needs to be done for ALL active columns)
-      do c = bounds%begc, bounds%endc
-         if (col%active(c)) then
-            g = col%gridcell(c)
-            forc_lwrad_c(c) = forc_lwrad_g(g)
-         end if
-      end do
-
-      ! Optionally, downscale the longwave radiation, conserving energy
-      if (atm2lnd_inst%params%glcmec_downscale_longwave) then
-
-         ! Initialize variables related to normalization
-         do g = bounds%begg, bounds%endg
-            sum_lwrad_g(g) = 0._r8
-            sum_wts_g(g) = 0._r8
-            newsum_lwrad_g(g) = 0._r8
-         end do
-
-         ! Do the downscaling
-         do fc = 1, downscale_filter_c%num
-            c = downscale_filter_c%indices(fc)
-            l = col%landunit(c)
-            g = col%gridcell(c)
-
-            hsurf_g = forc_topo_g(g)
-            hsurf_c = topo_c(c)
-
-            ! Assume a linear decrease in downwelling longwave radiation with increasing
-            ! elevation, based on Van Tricht et al. (2016, TC) Figure 6,
-            ! doi:10.5194/tc-10-2379-2016
-            forc_lwrad_c(c) = forc_lwrad_g(g) - lapse_rate_longwave * (hsurf_c-hsurf_g)
-            ! But ensure that we don't depart too far from the atmospheric forcing value:
-            ! negative values of lwrad are certainly bad, but small positive values might
-            ! also be bad. We can especially run into trouble due to the normalization: a
-            ! small lwrad value in one column can lead to a big normalization factor,
-            ! leading to huge lwrad values in other columns.
-            forc_lwrad_c(c) = min(forc_lwrad_c(c), &
-                 forc_lwrad_g(g) * (1._r8 + longwave_downscaling_limit))
-            forc_lwrad_c(c) = max(forc_lwrad_c(c), &
-                 forc_lwrad_g(g) * (1._r8 - longwave_downscaling_limit))
-
-            ! Keep track of the gridcell-level weighted sum for later normalization.
-            !
-            ! This gridcell-level weighted sum just includes points for which we do the
-            ! downscaling (e.g., glc_mec points). Thus the contributing weights
-            ! generally do not add to 1. So to do the normalization properly, we also
-            ! need to keep track of the weights that have contributed to this sum.
-            sum_lwrad_g(g) = sum_lwrad_g(g) + col%wtgcell(c)*forc_lwrad_c(c)
-            sum_wts_g(g) = sum_wts_g(g) + col%wtgcell(c)
-         end do
-
-
-         ! Normalize forc_lwrad_c(c) to conserve energy
-
-         call build_normalization(orig_field=forc_lwrad_g(bounds%begg:bounds%endg), &
-              sum_field=sum_lwrad_g(bounds%begg:bounds%endg), &
-              sum_wts=sum_wts_g(bounds%begg:bounds%endg), &
-              norms=lwrad_norm_g(bounds%begg:bounds%endg))
-
-         do fc = 1, downscale_filter_c%num
-            c = downscale_filter_c%indices(fc)
-            l = col%landunit(c)
-            g = col%gridcell(c)
-
-            forc_lwrad_c(c) = forc_lwrad_c(c) * lwrad_norm_g(g)
-            newsum_lwrad_g(g) = newsum_lwrad_g(g) + col%wtgcell(c)*forc_lwrad_c(c)
-         end do
-
-
-         ! Make sure that, after normalization, the grid cell mean is conserved
-
-         do g = bounds%begg, bounds%endg
-            if (sum_wts_g(g) > 0._r8) then
-               if (abs((newsum_lwrad_g(g) / sum_wts_g(g)) - forc_lwrad_g(g)) > 1.e-8_r8) then
-                  write(iulog,*) 'g, newsum_lwrad_g, sum_wts_g, forc_lwrad_g: ', &
-                       g, newsum_lwrad_g(g), sum_wts_g(g), forc_lwrad_g(g)
-                  call endrun(msg=' ERROR: Energy conservation error downscaling longwave'//&
-                       errMsg(sourcefile, __LINE__))
-               end if
-            end if
-         end do
-
-      end if    ! glcmec_downscale_longwave
-
-    end associate
-
-  end subroutine downscale_longwave
-
-  !-----------------------------------------------------------------------
-  subroutine build_normalization(orig_field, sum_field, sum_wts, norms)
-    !
-    ! !DESCRIPTION:
-    ! Build an array of normalization factors that can be applied to a downscaled forcing
-    ! field, in order to force the mean of the new field to be the same as the mean of
-    ! the old field (for conservation).
-    !
-    ! This allows for the possibility that only a subset of columns are downscaled. Only
-    ! the columns that are adjusted should be included in the weighted sum, sum_field;
-    ! sum_wts gives the sum of contributing weights on the grid cell level. 
-
-    ! For example, if a grid cell has an original forcing value of 1.0, and contains 4
-    ! columns with the following weights on the gridcell, and the following values after
-    ! normalization:
-    !
-    !       col #:    1     2     3     4
-    !      weight:  0.1   0.2   0.3   0.4
-    ! downscaled?:  yes   yes    no    no
-    !       value:  0.9   1.1   1.0   1.0
-    !
-    ! Then we would have:
-    ! orig_field(g) = 1.0
-    ! sum_field(g) = 0.1*0.9 + 0.2*1.1 = 0.31
-    ! sum_wts(g) = 0.1 + 0.2 = 0.3
-    ! norms(g) = 1.0 / (0.31 / 0.3) = 0.9677
-    !
-    ! The field can then be normalized as:
-    !              forc_lwrad_c(c) = forc_lwrad_c(c) * lwrad_norm_g(g)
-    !   where lwrad_norm_g is the array of norms computed by this routine
-
-    !
-    ! !ARGUMENTS:
-    real(r8), intent(in)  :: orig_field(:)  ! the original field, at the grid cell level
-    real(r8), intent(in)  :: sum_field(:)   ! the new weighted sum across columns (dimensioned by grid cell)
-    real(r8), intent(in)  :: sum_wts(:)     ! sum of the weights used to create sum_field (dimensioned by grid cell)
-    real(r8), intent(out) :: norms(:)       ! computed normalization factors
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT((size(orig_field) == size(norms)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT((size(sum_field) == size(norms)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT((size(sum_wts) == size(norms)), errMsg(sourcefile, __LINE__))
-
-    where (sum_wts == 0._r8)
-       ! Avoid divide by zero; if sum_wts is 0, then the normalization doesn't matter,
-       ! because the adjusted values won't affect the grid cell mean.
-       norms = 1.0_r8
-
-    elsewhere (sum_field == 0._r8)
-       ! Avoid divide by zero. If this is because both sum_field and orig_field are 0,
-       ! then the normalization doesn't matter. If sum_field == 0 while orig_field /= 0,
-       ! then we have a problem: no normalization will allow us to recover the original
-       ! gridcell mean. We should probably catch this and abort, but for now we're
-       ! relying on error checking in the caller (checking for conservation) to catch
-       ! this potential problem.
-       norms = 1.0_r8
-
-    elsewhere
-       ! The standard case
-       norms = orig_field / (sum_field / sum_wts)
-
-    end where
-
-  end subroutine build_normalization
-
-
-  !-----------------------------------------------------------------------
-  subroutine check_downscale_consistency(bounds, atm2lnd_inst)
-    !
-    ! !DESCRIPTION:
-    ! Check consistency of downscaling
-    !
-    ! Note that this operates over more than just the filter used for the downscaling,
-    ! because it checks some things outside that filter.
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(bounds_type) , intent(in) :: bounds  
-    type(atm2lnd_type), intent(in) :: atm2lnd_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g, l, c    ! indices
-    character(len=*), parameter :: subname = 'check_downscale_consistency'
-    !-----------------------------------------------------------------------
-
-    associate(&
-         ! Gridcell-level fields:
-         forc_t_g     => atm2lnd_inst%forc_t_not_downscaled_grc     , & ! Input:  [real(r8) (:)]  atmospheric temperature (Kelvin)        
-         forc_th_g    => atm2lnd_inst%forc_th_not_downscaled_grc    , & ! Input:  [real(r8) (:)]  atmospheric potential temperature (Kelvin)
-         forc_q_g     => atm2lnd_inst%forc_q_not_downscaled_grc     , & ! Input:  [real(r8) (:)]  atmospheric specific humidity (kg/kg)   
-         forc_pbot_g  => atm2lnd_inst%forc_pbot_not_downscaled_grc  , & ! Input:  [real(r8) (:)]  atmospheric pressure (Pa)               
-         forc_rho_g   => atm2lnd_inst%forc_rho_not_downscaled_grc   , & ! Input:  [real(r8) (:)]  atmospheric density (kg/m**3)           
-         forc_rain_g  => atm2lnd_inst%forc_rain_not_downscaled_grc  , & ! Input:  [real(r8) (:)]  rain rate [mm/s]
-         forc_snow_g  => atm2lnd_inst%forc_snow_not_downscaled_grc  , & ! Input:  [real(r8) (:)]  snow rate [mm/s]
-         forc_lwrad_g => atm2lnd_inst%forc_lwrad_not_downscaled_grc , & ! Input:  [real(r8) (:)]  downward longwave (W/m**2)
-         
-         ! Column-level (downscaled) fields:
-         forc_t_c     => atm2lnd_inst%forc_t_downscaled_col         , & ! Input:  [real(r8) (:)]  atmospheric temperature (Kelvin)        
-         forc_th_c    => atm2lnd_inst%forc_th_downscaled_col        , & ! Input:  [real(r8) (:)]  atmospheric potential temperature (Kelvin)
-         forc_q_c     => atm2lnd_inst%forc_q_downscaled_col         , & ! Input:  [real(r8) (:)]  atmospheric specific humidity (kg/kg)   
-         forc_pbot_c  => atm2lnd_inst%forc_pbot_downscaled_col      , & ! Input:  [real(r8) (:)]  atmospheric pressure (Pa)               
-         forc_rho_c   => atm2lnd_inst%forc_rho_downscaled_col       , & ! Input:  [real(r8) (:)]  atmospheric density (kg/m**3)           
-         forc_rain_c  => atm2lnd_inst%forc_rain_downscaled_col      , & ! Input:  [real(r8) (:)]  rain rate [mm/s]
-         forc_snow_c  => atm2lnd_inst%forc_snow_downscaled_col      , & ! Input:  [real(r8) (:)]  snow rate [mm/s]
-         forc_lwrad_c => atm2lnd_inst%forc_lwrad_downscaled_col       & ! Input:  [real(r8) (:)]  downward longwave (W/m**2)
-         )
-
-    ! BUG(wjs, 2016-11-15, bugz 2377)
-    !
-    ! Make sure that, for urban points, the column-level forcing fields are identical to
-    ! the gridcell-level forcing fields. This is needed because the urban-specific code
-    ! sometimes uses the gridcell-level forcing fields (and it would take a large
-    ! refactor to change this to use column-level fields).
-    !
-    ! However, do NOT check rain & snow: these ARE downscaled for urban points (as for
-    ! all other points), and the urban code does not refer to the gridcell-level versions
-    ! of these fields.
-    
-    do c = bounds%begc, bounds%endc
-       if (col%active(c)) then
-          l = col%landunit(c)
-          g = col%gridcell(c)
-
-          if (lun%urbpoi(l)) then
-             if (forc_t_c(c)     /= forc_t_g(g)    .or. &
-                  forc_th_c(c)    /= forc_th_g(g)   .or. &
-                  forc_q_c(c)     /= forc_q_g(g)    .or. &
-                  forc_pbot_c(c)  /= forc_pbot_g(g) .or. &
-                  forc_rho_c(c)   /= forc_rho_g(g)  .or. &
-                  forc_lwrad_c(c) /= forc_lwrad_g(g)) then
-                write(iulog,*) subname//' ERROR: column-level forcing differs from gridcell-level forcing for urban point'
-                write(iulog,*) 'c, g = ', c, g
-                write(iulog,*) 'forc_t_c, forc_t_g = ', forc_t_c(c), forc_t_g(g)
-                write(iulog,*) 'forc_th_c, forc_th_g = ', forc_th_c(c), forc_th_g(g)
-                write(iulog,*) 'forc_q_c, forc_q_g = ', forc_q_c(c), forc_q_g(g)
-                write(iulog,*) 'forc_pbot_c, forc_pbot_g = ', forc_pbot_c(c), forc_pbot_g(g)
-                write(iulog,*) 'forc_rho_c, forc_rho_g = ', forc_rho_c(c), forc_rho_g(g)
-                write(iulog,*) 'forc_lwrad_c, forc_lwrad_g = ', forc_lwrad_c(c), forc_lwrad_g(g)
-                call endrun(msg=errMsg(sourcefile, __LINE__))
-             end if  ! inequal
-          end if  ! urbpoi
-       end if  ! active
-    end do
-
-    end associate
-
-  end subroutine check_downscale_consistency
-
-end module atm2lndMod
diff --git a/src/main/atm2lndType.F90 b/src/main/atm2lndType.F90
index f0d58fe158..80e3dd93cd 100644
--- a/src/main/atm2lndType.F90
+++ b/src/main/atm2lndType.F90
@@ -10,7 +10,7 @@ module atm2lndType
   use shr_log_mod   , only : errMsg => shr_log_errMsg
   use clm_varpar    , only : numrad, ndst, nlevgrnd !ndst = number of dust bins.  ! MML: numrad = 2, 1=vis, 2=nir
   use clm_varcon    , only : rair, grav, cpair, hfus, tfrz, spval
-  use clm_varctl    , only : iulog, use_cn, use_cndv, use_fates, use_luna
+  use clm_varctl    , only : iulog
   use decompMod     , only : bounds_type
   use abortutils    , only : endrun
   use PatchType     , only : patch
@@ -21,38 +21,6 @@ module atm2lndType
   save
   !
   ! !PUBLIC DATA TYPES:
-
-  type, public :: atm2lnd_params_type
-     ! true => repartition rain/snow from atm based on temperature
-     logical :: repartition_rain_snow
-
-     ! true => downscale longwave radiation
-     logical :: glcmec_downscale_longwave
-
-     ! Surface temperature lapse rate (K m-1)
-     real(r8) :: lapse_rate
-
-     ! longwave radiation lapse rate (W m-2 m-1)
-     real(r8) :: lapse_rate_longwave
-
-     ! Relative limit for how much longwave downscaling can be done (unitless)
-     ! The pre-normalized, downscaled longwave is restricted to be in the range
-     ! [lwrad*(1-longwave_downscaling_limit), lwrad*(1+longwave_downscaling_limit)]
-     real(r8) :: longwave_downscaling_limit
-
-     ! Rain-snow ramp for glacier landunits
-     ! frac_rain = (temp - all_snow_t) * frac_rain_slope
-     ! (all_snow_t is in K)
-     real(r8) :: precip_repartition_glc_all_snow_t
-     real(r8) :: precip_repartition_glc_frac_rain_slope
-
-     ! Rain-snow ramp for non-glacier landunits
-     ! frac_rain = (temp - all_snow_t) * frac_rain_slope
-     ! (all_snow_t is in K)
-     real(r8) :: precip_repartition_nonglc_all_snow_t
-     real(r8) :: precip_repartition_nonglc_frac_rain_slope
-  end type atm2lnd_params_type
-
   !----------------------------------------------------
   ! atmosphere -> land variables structure
   !
@@ -68,7 +36,6 @@ module atm2lndType
   ! MML: I don't think this applies to me... I'm working at the grc level, not the col level...
   !----------------------------------------------------
   type, public :: atm2lnd_type
-     type(atm2lnd_params_type) :: params
 
      ! atm->lnd not downscaled
      real(r8), pointer :: forc_u_grc                    (:)   => null() ! atm wind speed, east direction (m/s)
@@ -84,23 +51,17 @@ module atm2lndType
      real(r8), pointer :: forc_rh_grc                   (:)   => null() ! atmospheric relative humidity (%)
      real(r8), pointer :: forc_psrf_grc                 (:)   => null() ! surface pressure (Pa)
      real(r8), pointer :: forc_pco2_grc                 (:)   => null() ! CO2 partial pressure (Pa)
-     real(r8), pointer :: forc_pco2_240_patch           (:)   => null() ! 10-day mean CO2 partial pressure (Pa)
      real(r8), pointer :: forc_solad_grc                (:,:) => null() ! direct beam radiation (numrad) (vis=forc_sols , nir=forc_soll )
      real(r8), pointer :: forc_solai_grc                (:,:) => null() ! diffuse radiation (numrad) (vis=forc_solsd, nir=forc_solld)
      real(r8), pointer :: forc_solar_grc                (:)   => null() ! incident solar radiation
-     real(r8), pointer :: forc_ndep_grc                 (:)   => null() ! nitrogen deposition rate (gN/m2/s)
-     real(r8), pointer :: forc_pc13o2_grc               (:)   => null() ! C13O2 partial pressure (Pa)
      real(r8), pointer :: forc_po2_grc                  (:)   => null() ! O2 partial pressure (Pa)
-     real(r8), pointer :: forc_po2_240_patch            (:)   => null() ! 10-day mean O2 partial pressure (Pa)
      real(r8), pointer :: forc_aer_grc                  (:,:) => null() ! aerosol deposition array
-     real(r8), pointer :: forc_pch4_grc                 (:)   => null() ! CH4 partial pressure (Pa)
 
      real(r8), pointer :: forc_t_not_downscaled_grc     (:)   => null() ! not downscaled atm temperature (Kelvin)       
      real(r8), pointer :: forc_th_not_downscaled_grc    (:)   => null() ! not downscaled atm potential temperature (Kelvin)    
      real(r8), pointer :: forc_q_not_downscaled_grc     (:)   => null() ! not downscaled atm specific humidity (kg/kg)  
      			! MML: I think this is the q I need to check if the negative LH is too big. 
      real(r8), pointer :: forc_pbot_not_downscaled_grc  (:)   => null() ! not downscaled atm pressure (Pa)   
-     real(r8), pointer :: forc_pbot240_downscaled_patch (:)   => null() ! 10-day mean downscaled atm pressure (Pa)           
      real(r8), pointer :: forc_rho_not_downscaled_grc   (:)   => null() ! not downscaled atm density (kg/m**3)                      
      real(r8), pointer :: forc_rain_not_downscaled_grc  (:)   => null() ! not downscaled atm rain rate [mm/s]                       
      real(r8), pointer :: forc_snow_not_downscaled_grc  (:)   => null() ! not downscaled atm snow rate [mm/s]                       
@@ -276,54 +237,18 @@ module atm2lndType
 	
 	 
 	! ------------------------------------------------------------------------------------
-	
-	 	 
-     ! atm->lnd downscaled
-     real(r8), pointer :: forc_t_downscaled_col         (:)   => null() ! downscaled atm temperature (Kelvin)
-     real(r8), pointer :: forc_th_downscaled_col        (:)   => null() ! downscaled atm potential temperature (Kelvin)
-     real(r8), pointer :: forc_q_downscaled_col         (:)   => null() ! downscaled atm specific humidity (kg/kg)
-     real(r8), pointer :: forc_pbot_downscaled_col      (:)   => null() ! downscaled atm pressure (Pa)
-     real(r8), pointer :: forc_rho_downscaled_col       (:)   => null() ! downscaled atm density (kg/m**3)
-     real(r8), pointer :: forc_rain_downscaled_col      (:)   => null() ! downscaled atm rain rate [mm/s]
-     real(r8), pointer :: forc_snow_downscaled_col      (:)   => null() ! downscaled atm snow rate [mm/s]
-     real(r8), pointer :: forc_lwrad_downscaled_col     (:)   => null() ! downscaled atm downwrd IR longwave radiation (W/m**2)
 
      !  rof->lnd
      real(r8), pointer :: forc_flood_grc                (:)   => null() ! rof flood (mm/s)
      real(r8), pointer :: volr_grc                      (:)   => null() ! rof volr total volume (m3)
      real(r8), pointer :: volrmch_grc                   (:)   => null() ! rof volr main channel (m3)
 
-     ! anomaly forcing
-     real(r8), pointer :: af_precip_grc                 (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_uwind_grc                  (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_vwind_grc                  (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_tbot_grc                   (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_pbot_grc                   (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_shum_grc                   (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_swdn_grc                   (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: af_lwdn_grc                   (:)   => null() ! anomaly forcing 
-     real(r8), pointer :: bc_precip_grc                 (:)   => null() ! anomaly forcing - add bias correction
-
      ! time averaged quantities
-     real(r8) , pointer :: fsd24_patch                  (:)   => null() ! patch 24hr average of direct beam radiation 
      real(r8) , pointer :: fsd240_patch                 (:)   => null() ! patch 240hr average of direct beam radiation 
-     real(r8) , pointer :: fsi24_patch                  (:)   => null() ! patch 24hr average of diffuse beam radiation 
-     real(r8) , pointer :: fsi240_patch                 (:)   => null() ! patch 240hr average of diffuse beam radiation 
-     real(r8) , pointer :: prec365_col                  (:)   => null() ! col 365-day running mean of tot. precipitation (see comment in UpdateAccVars regarding why this is col-level despite other prec accumulators being patch-level)
-     real(r8) , pointer :: prec60_patch                 (:)   => null() ! patch 60-day running mean of tot. precipitation (mm/s) 
-     real(r8) , pointer :: prec10_patch                 (:)   => null() ! patch 10-day running mean of tot. precipitation (mm/s) 
-     real(r8) , pointer :: rh30_patch                   (:)   => null() ! patch 30-day running mean of relative humidity 
-     real(r8) , pointer :: prec24_patch                 (:)   => null() ! patch 24-hour running mean of tot. precipitation (mm/s) 
-     real(r8) , pointer :: rh24_patch                   (:)   => null() ! patch 24-hour running mean of relative humidity
-     real(r8) , pointer :: wind24_patch                 (:)   => null() ! patch 24-hour running mean of wind
-     real(r8) , pointer :: t_mo_patch                   (:)   => null() ! patch 30-day average temperature (Kelvin)
-     real(r8) , pointer :: t_mo_min_patch               (:)   => null() ! patch annual min of t_mo (Kelvin)
 
    contains
 
      procedure, public  :: Init
-     procedure, public  :: InitForTesting  ! version of Init meant for unit testing
-     procedure, private :: ReadNamelist
      procedure, private :: InitAllocate
      procedure, private :: InitHistory  
      procedure, private :: InitCold    		! MML 2016.01.15 adding InitCold to give accumulating variables a starting point 
@@ -335,165 +260,19 @@ module atm2lndType
 
   end type atm2lnd_type
 
-  interface atm2lnd_params_type
-     module procedure atm2lnd_params_constructor
-  end interface atm2lnd_params_type
-
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
   !----------------------------------------------------
 
 contains
 
-  !-----------------------------------------------------------------------
-  function atm2lnd_params_constructor(repartition_rain_snow, glcmec_downscale_longwave, &
-       lapse_rate, lapse_rate_longwave, longwave_downscaling_limit, &
-       precip_repartition_glc_all_snow_t, precip_repartition_glc_all_rain_t, &
-       precip_repartition_nonglc_all_snow_t, precip_repartition_nonglc_all_rain_t) &
-       result(params)
-    !
-    ! !DESCRIPTION:
-    ! Creates a new instance of atm2lnd_params_type
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(atm2lnd_params_type) :: params  ! function result
-    logical, intent(in) :: repartition_rain_snow
-    logical, intent(in) :: glcmec_downscale_longwave
-
-    ! Surface temperature lapse rate (K m-1)
-    real(r8), intent(in) :: lapse_rate
-
-    ! Longwave radiation lapse rate (W m-2 m-1)
-    ! Must be present if glcmec_downscale_longwave is true; ignored otherwise
-    real(r8), intent(in), optional :: lapse_rate_longwave
-
-    ! Relative limit for how much longwave downscaling can be done (unitless)
-    ! Must be present if glcmec_downscale_longwave is true; ignored otherwise
-    real(r8), intent(in), optional :: longwave_downscaling_limit
-
-    ! End-points of the rain-snow ramp for glacier landunits (degrees C)
-    ! Must be present if repartition_rain_snow is true; ignored otherwise
-    real(r8), intent(in), optional :: precip_repartition_glc_all_snow_t
-    real(r8), intent(in), optional :: precip_repartition_glc_all_rain_t
-
-    ! End-points of the rain-snow ramp for non-glacier landunits (degrees C)
-    ! Must be present if repartition_rain_snow is true; ignored otherwise
-    real(r8), intent(in), optional :: precip_repartition_nonglc_all_snow_t
-    real(r8), intent(in), optional :: precip_repartition_nonglc_all_rain_t
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'atm2lnd_params_constructor'
-    !-----------------------------------------------------------------------
-
-    params%repartition_rain_snow = repartition_rain_snow
-    params%glcmec_downscale_longwave = glcmec_downscale_longwave
-
-    params%lapse_rate = lapse_rate
-
-    if (glcmec_downscale_longwave) then
-       if (.not. present(lapse_rate_longwave)) then
-          call endrun(subname // &
-               ' ERROR: For glcmec_downscale_longwave true, lapse_rate_longwave must be provided')
-       end if
-       if (.not. present(longwave_downscaling_limit)) then
-          call endrun(subname // &
-               ' ERROR: For glcmec_downscale_longwave true, longwave_downscaling_limit must be provided')
-       end if
-
-       if (longwave_downscaling_limit < 0._r8 .or. &
-            longwave_downscaling_limit > 1._r8) then
-          call endrun(subname // &
-               ' ERROR: longwave_downscaling_limit must be between 0 and 1')
-       end if
-
-       params%lapse_rate_longwave = lapse_rate_longwave
-       params%longwave_downscaling_limit = longwave_downscaling_limit
-    else
-       params%lapse_rate_longwave = nan
-       params%longwave_downscaling_limit = nan
-    end if
-
-    if (repartition_rain_snow) then
-
-       ! Make sure all of the repartitioning-related parameters are present
-
-       if (.not. present(precip_repartition_glc_all_snow_t)) then
-          call endrun(subname // &
-               ' ERROR: For repartition_rain_snow true, precip_repartition_glc_all_snow_t must be provided')
-       end if
-       if (.not. present(precip_repartition_glc_all_rain_t)) then
-          call endrun(subname // &
-               ' ERROR: For repartition_rain_snow true, precip_repartition_glc_all_rain_t must be provided')
-       end if
-       if (.not. present(precip_repartition_nonglc_all_snow_t)) then
-          call endrun(subname // &
-               ' ERROR: For repartition_rain_snow true, precip_repartition_nonglc_all_snow_t must be provided')
-       end if
-       if (.not. present(precip_repartition_nonglc_all_rain_t)) then
-          call endrun(subname // &
-               ' ERROR: For repartition_rain_snow true, precip_repartition_nonglc_all_rain_t must be provided')
-       end if
-
-       ! Do some other error checking
-
-       if (precip_repartition_glc_all_rain_t <= precip_repartition_glc_all_snow_t) then
-          call endrun(subname // &
-               ' ERROR: Must have precip_repartition_glc_all_snow_t < precip_repartition_glc_all_rain_t')
-       end if
-
-       if (precip_repartition_nonglc_all_rain_t <= precip_repartition_nonglc_all_snow_t) then
-          call endrun(subname // &
-               ' ERROR: Must have precip_repartition_nonglc_all_snow_t < precip_repartition_nonglc_all_rain_t')
-       end if
-
-       ! Convert to the form of the parameters we want for the main code
-
-       call compute_ramp_params( &
-            all_snow_t_c = precip_repartition_glc_all_snow_t, &
-            all_rain_t_c = precip_repartition_glc_all_rain_t, &
-            all_snow_t_k = params%precip_repartition_glc_all_snow_t, &
-            frac_rain_slope = params%precip_repartition_glc_frac_rain_slope)
-
-       call compute_ramp_params( &
-            all_snow_t_c = precip_repartition_nonglc_all_snow_t, &
-            all_rain_t_c = precip_repartition_nonglc_all_rain_t, &
-            all_snow_t_k = params%precip_repartition_nonglc_all_snow_t, &
-            frac_rain_slope = params%precip_repartition_nonglc_frac_rain_slope)
-
-    else  ! .not. repartition_rain_snow
-       params%precip_repartition_glc_all_snow_t = nan
-       params%precip_repartition_glc_frac_rain_slope = nan
-       params%precip_repartition_nonglc_all_snow_t = nan
-       params%precip_repartition_nonglc_frac_rain_slope = nan
-    end if
-
-  contains
-    subroutine compute_ramp_params(all_snow_t_c, all_rain_t_c, &
-         all_snow_t_k, frac_rain_slope)
-      real(r8), intent(in)  :: all_snow_t_c  ! Temperature at which precip falls entirely as rain (deg C)
-      real(r8), intent(in)  :: all_rain_t_c  ! Temperature at which precip falls entirely as snow (deg C)
-      real(r8), intent(out) :: all_snow_t_k  ! Temperature at which precip falls entirely as snow (K)
-      real(r8), intent(out) :: frac_rain_slope ! Slope of the frac_rain vs. T relationship
-
-      frac_rain_slope = 1._r8 / (all_rain_t_c - all_snow_t_c)
-      all_snow_t_k = all_snow_t_c + tfrz
-    end subroutine compute_ramp_params
-
-  end function atm2lnd_params_constructor
-
-
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
+  subroutine Init(this, bounds)
 
     class(atm2lnd_type) :: this
     type(bounds_type), intent(in) :: bounds
-    character(len=*), intent(in) :: NLFilename ! namelist filename
 
     call this%InitAllocate(bounds)
-    call this%ReadNamelist(NLFilename)
     call this%InitHistory(bounds)
     
     ! MML 2016.01.15 adding call to InitCold (make sure it doesn't keep using the 
@@ -502,156 +281,6 @@ subroutine Init(this, bounds, NLFilename)
     
   end subroutine Init
 
-  !-----------------------------------------------------------------------
-  subroutine InitForTesting(this, bounds, params)
-    !
-    ! !DESCRIPTION:
-    ! Does initialization needed for unit testing. Allows caller to prescribe parameter
-    ! values (bypassing the namelist read)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(atm2lnd_type) :: this
-    type(bounds_type), intent(in) :: bounds
-
-    ! If params isn't provided, we use default values
-    type(atm2lnd_params_type), intent(in), optional :: params
-    !
-    ! !LOCAL VARIABLES:
-    type(atm2lnd_params_type) :: l_params
-
-    character(len=*), parameter :: subname = 'InitForTesting'
-    !-----------------------------------------------------------------------
-
-    if (present(params)) then
-       l_params = params
-    else
-       ! Use arbitrary values
-       l_params = atm2lnd_params_type( &
-            repartition_rain_snow = .false., &
-            glcmec_downscale_longwave = .false., &
-            lapse_rate = 0.01_r8)
-    end if
-
-    call this%InitAllocate(bounds)
-    this%params = l_params
-
-  end subroutine InitForTesting
-
-
-  !-----------------------------------------------------------------------
-  subroutine ReadNamelist(this, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Read the atm2lnd namelist
-    !
-    ! !USES:
-    use fileutils      , only : getavu, relavu, opnfil
-    use shr_nl_mod     , only : shr_nl_find_group_name
-    use spmdMod        , only : masterproc, mpicom
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
-    class(atm2lnd_type), intent(inout) :: this
-    !
-    ! !LOCAL VARIABLES:
-
-    ! temporary variables corresponding to the components of atm2lnd_params_type
-    logical :: repartition_rain_snow
-    logical :: glcmec_downscale_longwave
-    real(r8) :: lapse_rate
-    real(r8) :: lapse_rate_longwave
-    real(r8) :: longwave_downscaling_limit
-    real(r8) :: precip_repartition_glc_all_snow_t
-    real(r8) :: precip_repartition_glc_all_rain_t
-    real(r8) :: precip_repartition_nonglc_all_snow_t
-    real(r8) :: precip_repartition_nonglc_all_rain_t
-
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    character(len=*), parameter :: nmlname = 'atm2lnd_inparm'
-
-    character(len=*), parameter :: subname = 'ReadNamelist'
-    !-----------------------------------------------------------------------
-
-    namelist /atm2lnd_inparm/ repartition_rain_snow, glcmec_downscale_longwave, &
-         lapse_rate, lapse_rate_longwave, longwave_downscaling_limit, &
-         precip_repartition_glc_all_snow_t, precip_repartition_glc_all_rain_t, &
-         precip_repartition_nonglc_all_snow_t, precip_repartition_nonglc_all_rain_t
-
-    ! Initialize namelist variables to defaults
-    repartition_rain_snow = .false.
-    glcmec_downscale_longwave = .false.
-    lapse_rate = nan
-    lapse_rate_longwave = nan
-    longwave_downscaling_limit = nan
-    precip_repartition_glc_all_snow_t = nan
-    precip_repartition_glc_all_rain_t = nan
-    precip_repartition_nonglc_all_snow_t = nan
-    precip_repartition_nonglc_all_rain_t = nan
-
-    if (masterproc) then
-       unitn = getavu()
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
-       if (ierr == 0) then
-          read(unitn, nml=atm2lnd_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-    end if
-
-    call shr_mpi_bcast(repartition_rain_snow, mpicom)
-    call shr_mpi_bcast(glcmec_downscale_longwave, mpicom)
-    call shr_mpi_bcast(lapse_rate, mpicom)
-    call shr_mpi_bcast(lapse_rate_longwave, mpicom)
-    call shr_mpi_bcast(longwave_downscaling_limit, mpicom)
-    call shr_mpi_bcast(precip_repartition_glc_all_snow_t, mpicom)
-    call shr_mpi_bcast(precip_repartition_glc_all_rain_t, mpicom)
-    call shr_mpi_bcast(precip_repartition_nonglc_all_snow_t, mpicom)
-    call shr_mpi_bcast(precip_repartition_nonglc_all_rain_t, mpicom)
-
-    if (masterproc) then
-       write(iulog,*) ' '
-       write(iulog,*) nmlname//' settings:'
-       ! Write settings one-by-one rather than with a nml write because some settings may
-       ! be NaN if certain options are turned off.
-       write(iulog,*) 'repartition_rain_snow = ', repartition_rain_snow
-       write(iulog,*) 'glcmec_downscale_longwave = ', glcmec_downscale_longwave
-       write(iulog,*) 'lapse_rate = ', lapse_rate
-       if (glcmec_downscale_longwave) then
-          write(iulog,*) 'lapse_rate_longwave = ', lapse_rate_longwave
-          write(iulog,*) 'longwave_downscaling_limit = ', longwave_downscaling_limit
-       end if
-       if (repartition_rain_snow) then
-          write(iulog,*) 'precip_repartition_glc_all_snow_t = ', precip_repartition_glc_all_snow_t
-          write(iulog,*) 'precip_repartition_glc_all_rain_t = ', precip_repartition_glc_all_rain_t
-          write(iulog,*) 'precip_repartition_nonglc_all_snow_t = ', precip_repartition_nonglc_all_snow_t
-          write(iulog,*) 'precip_repartition_nonglc_all_rain_t = ', precip_repartition_nonglc_all_rain_t
-       end if
-       write(iulog,*) ' '
-    end if
-
-    this%params = atm2lnd_params_type( &
-         repartition_rain_snow = repartition_rain_snow, &
-         glcmec_downscale_longwave = glcmec_downscale_longwave, &
-         lapse_rate = lapse_rate, &
-         lapse_rate_longwave = lapse_rate_longwave, &
-         longwave_downscaling_limit = longwave_downscaling_limit, &
-         precip_repartition_glc_all_snow_t = precip_repartition_glc_all_snow_t, &
-         precip_repartition_glc_all_rain_t = precip_repartition_glc_all_rain_t, &
-         precip_repartition_nonglc_all_snow_t = precip_repartition_nonglc_all_snow_t, &
-         precip_repartition_nonglc_all_rain_t = precip_repartition_nonglc_all_rain_t)
-
-  end subroutine ReadNamelist
-
-
   !------------------------------------------------------------------------
   subroutine InitAllocate(this, bounds)
     !
@@ -689,16 +318,8 @@ subroutine InitAllocate(this, bounds)
     allocate(this%forc_solad_grc                (begg:endg,numrad)) ; this%forc_solad_grc                (:,:) = ival
     allocate(this%forc_solai_grc                (begg:endg,numrad)) ; this%forc_solai_grc                (:,:) = ival
     allocate(this%forc_solar_grc                (begg:endg))        ; this%forc_solar_grc                (:)   = ival
-    allocate(this%forc_ndep_grc                 (begg:endg))        ; this%forc_ndep_grc                 (:)   = ival
-    allocate(this%forc_pc13o2_grc               (begg:endg))        ; this%forc_pc13o2_grc               (:)   = ival
     allocate(this%forc_po2_grc                  (begg:endg))        ; this%forc_po2_grc                  (:)   = ival
     allocate(this%forc_aer_grc                  (begg:endg,14))     ; this%forc_aer_grc                  (:,:) = ival
-    allocate(this%forc_pch4_grc                 (begg:endg))        ; this%forc_pch4_grc                 (:)   = ival
-    if(use_luna)then
-     allocate(this%forc_pco2_240_patch          (begp:endp))        ; this%forc_pco2_240_patch           (:)   = ival
-     allocate(this%forc_po2_240_patch           (begp:endp))        ; this%forc_po2_240_patch            (:)   = ival
-     allocate(this%forc_pbot240_downscaled_patch(begp:endp))        ; this%forc_pbot240_downscaled_patch (:)   = ival
-    endif
 
     ! atm->lnd not downscaled
     allocate(this%forc_t_not_downscaled_grc     (begg:endg))        ; this%forc_t_not_downscaled_grc     (:)   = ival
@@ -847,48 +468,12 @@ subroutine InitAllocate(this, bounds)
 	
 	! ---------------------------------------
 
-    
-    ! atm->lnd downscaled
-    allocate(this%forc_t_downscaled_col         (begc:endc))        ; this%forc_t_downscaled_col         (:)   = ival
-    allocate(this%forc_q_downscaled_col         (begc:endc))        ; this%forc_q_downscaled_col         (:)   = ival
-    allocate(this%forc_pbot_downscaled_col      (begc:endc))        ; this%forc_pbot_downscaled_col      (:)   = ival
-    allocate(this%forc_th_downscaled_col        (begc:endc))        ; this%forc_th_downscaled_col        (:)   = ival
-    allocate(this%forc_rho_downscaled_col       (begc:endc))        ; this%forc_rho_downscaled_col       (:)   = ival
-    allocate(this%forc_lwrad_downscaled_col     (begc:endc))        ; this%forc_lwrad_downscaled_col     (:)   = ival
-    allocate(this%forc_rain_downscaled_col      (begc:endc))        ; this%forc_rain_downscaled_col      (:)   = ival
-    allocate(this%forc_snow_downscaled_col      (begc:endc))        ; this%forc_snow_downscaled_col      (:)   = ival
-
     ! rof->lnd
     allocate(this%forc_flood_grc                (begg:endg))        ; this%forc_flood_grc                (:)   = ival
     allocate(this%volr_grc                      (begg:endg))        ; this%volr_grc                      (:)   = ival
     allocate(this%volrmch_grc                   (begg:endg))        ; this%volrmch_grc                   (:)   = ival
 
-    ! anomaly forcing
-    allocate(this%bc_precip_grc                 (begg:endg))        ; this%bc_precip_grc                 (:)   = ival
-    allocate(this%af_precip_grc                 (begg:endg))        ; this%af_precip_grc                 (:)   = ival
-    allocate(this%af_uwind_grc                  (begg:endg))        ; this%af_uwind_grc                  (:)   = ival
-    allocate(this%af_vwind_grc                  (begg:endg))        ; this%af_vwind_grc                  (:)   = ival
-    allocate(this%af_tbot_grc                   (begg:endg))        ; this%af_tbot_grc                   (:)   = ival
-    allocate(this%af_pbot_grc                   (begg:endg))        ; this%af_pbot_grc                   (:)   = ival
-    allocate(this%af_shum_grc                   (begg:endg))        ; this%af_shum_grc                   (:)   = ival
-    allocate(this%af_swdn_grc                   (begg:endg))        ; this%af_swdn_grc                   (:)   = ival
-    allocate(this%af_lwdn_grc                   (begg:endg))        ; this%af_lwdn_grc                   (:)   = ival
-
-    allocate(this%fsd24_patch                   (begp:endp))        ; this%fsd24_patch                   (:)   = nan
     allocate(this%fsd240_patch                  (begp:endp))        ; this%fsd240_patch                  (:)   = nan
-    allocate(this%fsi24_patch                   (begp:endp))        ; this%fsi24_patch                   (:)   = nan
-    allocate(this%fsi240_patch                  (begp:endp))        ; this%fsi240_patch                  (:)   = nan
-    allocate(this%prec10_patch                  (begp:endp))        ; this%prec10_patch                  (:)   = nan
-    allocate(this%prec60_patch                  (begp:endp))        ; this%prec60_patch                  (:)   = nan
-    allocate(this%rh30_patch                    (begp:endp))        ; this%rh30_patch                    (:)   = nan 
-    allocate(this%prec365_col                   (begc:endc))        ; this%prec365_col                   (:)   = nan
-    if (use_fates) then
-       allocate(this%prec24_patch               (begp:endp))        ; this%prec24_patch                  (:)   = nan
-       allocate(this%rh24_patch                 (begp:endp))        ; this%rh24_patch                    (:)   = nan
-       allocate(this%wind24_patch               (begp:endp))        ; this%wind24_patch                  (:)   = nan
-    end if
-    allocate(this%t_mo_patch                    (begp:endp))        ; this%t_mo_patch               (:)   = nan
-    allocate(this%t_mo_min_patch                (begp:endp))        ; this%t_mo_min_patch           (:)   = spval ! TODO - initialize this elsewhere
 
   end subroutine InitAllocate
 
@@ -898,7 +483,7 @@ subroutine InitHistory(this, bounds)
     ! !USES:
     ! use histFileMod, only : hist_addfld1d 
     ! MML:
-    use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp
+    use histFileMod, only : hist_addfld1d, hist_addfld2d
     !
     ! !ARGUMENTS:
     class(atm2lnd_type) :: this
@@ -920,29 +505,10 @@ subroutine InitHistory(this, bounds)
 	
 	!write(iulog,*)  'MML trying write h0 - start'
 	
-    this%forc_flood_grc(begg:endg) = spval
-    call hist_addfld1d (fname='QFLOOD',  units='mm/s',  &
-         avgflag='A', long_name='runoff from river flooding', &
-         ptr_lnd=this%forc_flood_grc)
-
-    this%volr_grc(begg:endg) = spval
-    call hist_addfld1d (fname='VOLR',  units='m3',  &
-         avgflag='A', long_name='river channel total water storage', &
-         ptr_lnd=this%volr_grc)
-
-    this%volrmch_grc(begg:endg) = spval
-    call hist_addfld1d (fname='VOLRMCH',  units='m3',  &
-         avgflag='A', long_name='river channel main channel water storage', &
-         ptr_lnd=this%volrmch_grc)
-
     this%forc_wind_grc(begg:endg) = spval
     call hist_addfld1d (fname='WIND', units='m/s',  &
          avgflag='A', long_name='atmospheric wind velocity magnitude', &
          ptr_lnd=this%forc_wind_grc)
-    ! Rename of WIND for Urban intercomparision project
-    call hist_addfld1d (fname='Wind', units='m/s',  &
-         avgflag='A', long_name='atmospheric wind velocity magnitude', &
-         ptr_gcell=this%forc_wind_grc, default = 'inactive')
 
     this%forc_hgt_grc(begg:endg) = spval
     call hist_addfld1d (fname='ZBOT', units='m',  &
@@ -979,30 +545,6 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='atmospheric air temperature received from atmosphere (pre-downscaling)', &
          ptr_gcell=this%forc_t_not_downscaled_grc, default='inactive')
 
-    this%forc_t_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='TBOT', units='K',  &
-         avgflag='A', long_name='atmospheric air temperature (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_t_downscaled_col)
-    call hist_addfld1d (fname='Tair', units='K', &
-         avgflag='A', long_name='atmospheric air temperature (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_t_downscaled_col, default='inactive')
-
-    this%forc_pbot_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='PBOT', units='Pa',  &
-         avgflag='A', long_name='atmospheric pressure at surface (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_pbot_downscaled_col)
-    call hist_addfld1d (fname='PSurf', units='Pa',  &
-         avgflag='A', long_name='atmospheric pressure at surface (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_pbot_downscaled_col, default='inactive')
-
-    this%forc_lwrad_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='FLDS', units='W/m^2',  &
-         avgflag='A', long_name='atmospheric longwave radiation (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_lwrad_downscaled_col)
-    call hist_addfld1d (fname='LWdown', units='W/m^2',  &
-         avgflag='A', long_name='atmospheric longwave radiation (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_lwrad_downscaled_col, default='inactive')
-
     this%forc_rain_not_downscaled_grc(begg:endg) = spval
     call hist_addfld1d (fname='RAIN_FROM_ATM', units='mm/s',  &
          avgflag='A', long_name='atmospheric rain received from atmosphere (pre-repartitioning)', &
@@ -1013,41 +555,6 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='atmospheric snow received from atmosphere (pre-repartitioning)', &
          ptr_lnd=this%forc_snow_not_downscaled_grc)
 
-    this%forc_rain_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='RAIN', units='mm/s',  &
-         avgflag='A', long_name='atmospheric rain, after rain/snow repartitioning based on temperature', &
-         ptr_col=this%forc_rain_downscaled_col)
-    call hist_addfld1d (fname='Rainf', units='mm/s',  &
-         avgflag='A', long_name='atmospheric rain, after rain/snow repartitioning based on temperature', &
-         ptr_col=this%forc_rain_downscaled_col, default='inactive')
-
-    this%forc_snow_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='SNOW', units='mm/s',  &
-         avgflag='A', long_name='atmospheric snow, after rain/snow repartitioning based on temperature', &
-         ptr_col=this%forc_snow_downscaled_col)
-
-    this%forc_th_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='THBOT', units='K',  &
-         avgflag='A', long_name='atmospheric air potential temperature (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_th_downscaled_col)
-         
-!	! MML: 2016.01.14 Try and add a new history field variable equal to 2TBOT
-!	! (just to see if it will print)
-!	this%forc_2t_not_downscaled_grc(begg:endg) = spval
-!    call hist_addfld1d (fname='T2BOT', units='K',  &
-!         avgflag='A', long_name='2x atmospheric air temperature MML Test', &
-!         ptr_lnd=this%forc_2t_not_downscaled_grc)
-	
-    this%forc_q_downscaled_col(begc:endc) = spval
-    call hist_addfld1d (fname='QBOT', units='kg/kg',  &
-         avgflag='A', long_name='atmospheric specific humidity (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_q_downscaled_col)
-    ! Rename of QBOT for Urban intercomparison project
-    call hist_addfld1d (fname='Qair', units='kg/kg',  &
-         avgflag='A', long_name='atmospheric specific humidity (downscaled to columns in glacier regions)', &
-         ptr_col=this%forc_q_downscaled_col, default='inactive')
-
-        
     !-----------------------------------------------------------------------
     ! MML: 2016.01.14 Simple Land Energy and Hydrology variables (gridscale)
     
@@ -1376,11 +883,6 @@ subroutine InitHistory(this, bounds)
     ! Soil variables
 ! start 2d
   
-    ! 2d example from SoilBiogeochemCarbonStateType.F90
-    !call hist_addfld2d (fname=fieldname, units='gC/m^3',  type2d='levdcmp', &
-    !              avgflag='A', long_name=longname, &
-    !              ptr_col=data2dptr)
-    
     ! I wanted to add an mml case to the type2d, but for now change it back, since its crashing
  
  	!write(iulog,*)  'MML write to h0: 2d soil vars '
@@ -1601,66 +1103,6 @@ subroutine InitHistory(this, bounds)
 	! End MML simple land model added variables
 	!-----------------------------------------------------------------------
 
-
-    ! Time averaged quantities
-    this%fsi24_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSI24', units='K',  &
-         avgflag='A', long_name='indirect radiation (last 24hrs)', &
-         ptr_patch=this%fsi24_patch, default='inactive')
-
-    this%fsi240_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSI240', units='K',  &
-         avgflag='A', long_name='indirect radiation (last 240hrs)', &
-         ptr_patch=this%fsi240_patch, default='inactive')
-
-    this%fsd24_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSD24', units='K',  &
-         avgflag='A', long_name='direct radiation (last 24hrs)', &
-         ptr_patch=this%fsd24_patch, default='inactive')
-
-    this%fsd240_patch(begp:endp) = spval
-    call hist_addfld1d (fname='FSD240', units='K',  &
-         avgflag='A', long_name='direct radiation (last 240hrs)', &
-         ptr_patch=this%fsd240_patch, default='inactive')
-
-    if (use_cn) then
-       this%rh30_patch(begp:endp) = spval
-       call hist_addfld1d (fname='RH30', units='%',  &
-            avgflag='A', long_name='30-day running mean of relative humidity', &
-            ptr_patch=this%rh30_patch, default='inactive')
-
-       this%prec10_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PREC10', units='MM H2O/S',  &
-            avgflag='A', long_name='10-day running mean of PREC', &
-            ptr_patch=this%prec10_patch, default='inactive')
-
-       this%prec60_patch(begp:endp) = spval
-       call hist_addfld1d (fname='PREC60', units='MM H2O/S',  &
-            avgflag='A', long_name='60-day running mean of PREC', &
-            ptr_patch=this%prec60_patch, default='inactive')
-    end if
-
-    if (use_cndv) then
-       call hist_addfld1d (fname='TDA', units='K',  &
-            avgflag='A', long_name='daily average 2-m temperature', &
-            ptr_patch=this%t_mo_patch)
-    end if
-
-    if(use_luna)then
-       this%forc_pco2_240_patch = spval
-       call hist_addfld1d (fname='PCO2_240', units='Pa',  &
-            avgflag='A', long_name='10 day running mean of CO2 pressure', &
-            ptr_patch=this%forc_pco2_240_patch, default='inactive')
-       this%forc_po2_240_patch = spval
-      call hist_addfld1d (fname='PO2_240', units='Pa',  &
-            avgflag='A', long_name='10 day running mean of O2 pressure', &
-            ptr_patch=this%forc_po2_240_patch, default='inactive')
-       this%forc_pbot240_downscaled_patch = spval
-       call hist_addfld1d (fname='PBOT_240', units='Pa',  &
-            avgflag='A', long_name='10 day running mean of air pressure', &
-            ptr_patch=this%forc_pbot240_downscaled_patch, default='inactive')
-    endif
-
   end subroutine InitHistory
 
 !-----------------------------------------------------------------------
@@ -1869,80 +1311,11 @@ subroutine InitAccBuffer (this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !---------------------------------------------------------------------
 
-    this%fsd24_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='FSD24', units='W/m2',                                             &
-         desc='24hr average of direct solar radiation',  accum_type='runmean', accum_period=-1,    &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
     this%fsd240_patch(bounds%begp:bounds%endp) = spval
     call init_accum_field (name='FSD240', units='W/m2',                                            &
          desc='240hr average of direct solar radiation',  accum_type='runmean', accum_period=-10,  &
          subgrid_type='pft', numlev=1, init_value=0._r8)
 
-    this%fsi24_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='FSI24', units='W/m2',                                             &
-         desc='24hr average of diffuse solar radiation',  accum_type='runmean', accum_period=-1,   &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    this%fsi240_patch(bounds%begp:bounds%endp) = spval
-    call init_accum_field (name='FSI240', units='W/m2',                                            &
-         desc='240hr average of diffuse solar radiation',  accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1, init_value=0._r8)
-
-    if (use_cn) then
-       call init_accum_field (name='PREC10', units='MM H2O/S', &
-            desc='10-day running mean of total precipitation', accum_type='runmean', accum_period=-10, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-       call init_accum_field (name='PREC60', units='MM H2O/S', &
-            desc='60-day running mean of total precipitation', accum_type='runmean', accum_period=-60, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-    
-       call init_accum_field (name='RH30', units='%', &
-            desc='30-day running mean of relative humidity', accum_type='runmean', accum_period=-30, &
-            subgrid_type='pft', numlev=1, init_value=100._r8)
-    end if
-
-    if (use_cndv) then
-       ! The following is a running mean with the accumulation period is set to -365 for a 365-day running mean.
-       call init_accum_field (name='PREC365', units='MM H2O/S', &
-            desc='365-day running mean of total precipitation', accum_type='runmean', accum_period=-365, &
-            subgrid_type='column', numlev=1, init_value=0._r8)
-    end if
-
-    if ( use_fates ) then
-       call init_accum_field (name='PREC24', units='m', &
-            desc='24hr sum of precipitation', accum_type='runmean', accum_period=-1, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-
-       ! Fudge - this neds to be initialized from the restat file eventually. 
-       call init_accum_field (name='RH24', units='m', &
-            desc='24hr average of RH', accum_type='runmean', accum_period=-1, &
-            subgrid_type='pft', numlev=1, init_value=100._r8) 
-
-       call init_accum_field (name='WIND24', units='m', &
-            desc='24hr average of wind', accum_type='runmean', accum_period=-1, &
-            subgrid_type='pft', numlev=1, init_value=0._r8)
-    end if
-
-    if(use_luna) then
-      this%forc_po2_240_patch(bounds%begp:bounds%endp) = spval
-      call init_accum_field (name='po2_240', units='Pa',                                            &
-         desc='10-day running mean of parial O2 pressure',  accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1, init_value=21223._r8)
-
-      this%forc_pco2_240_patch(bounds%begp:bounds%endp) = spval
-      call init_accum_field (name='pco2_240', units='Pa',                                            &
-         desc='10-day running mean of parial CO2 pressure',  accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1, init_value=28._r8)
-
-      this%forc_pbot240_downscaled_patch(bounds%begp:bounds%endp) = spval
-      call init_accum_field (name='pbot240', units='Pa',                                            &
-         desc='10-day running mean of air pressure',  accum_type='runmean', accum_period=-10, &
-         subgrid_type='pft', numlev=1, init_value=101325._r8)
-
-    endif
-
   end subroutine InitAccBuffer
 
   !-----------------------------------------------------------------------
@@ -1964,15 +1337,12 @@ subroutine InitAccVars(this, bounds)
     !
     ! !LOCAL VARIABLES:
     integer  :: begp, endp
-    integer  :: begc, endc
     integer  :: nstep
     integer  :: ier
     real(r8), pointer :: rbufslp(:)  ! temporary
-    real(r8), pointer :: rbufslc(:)  ! temporary
     !---------------------------------------------------------------------
 
     begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
 
     ! Allocate needed dynamic memory for single level patch field
     allocate(rbufslp(begp:endp), stat=ier)
@@ -1981,73 +1351,14 @@ subroutine InitAccVars(this, bounds)
        call endrun(msg="InitAccVars allocation error for rbufslp"//&
             errMsg(sourcefile, __LINE__))
     endif
-    ! Allocate needed dynamic memory for single level col field
-    allocate(rbufslc(begc:endc), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)' in '
-       call endrun(msg="InitAccVars allocation error for rbufslc"//&
-            errMsg(sourcefile, __LINE__))
-    endif
 
     ! Determine time step
     nstep = get_nstep()
 
-    call extract_accum_field ('FSD24', rbufslp, nstep)
-    this%fsd24_patch(begp:endp) = rbufslp(begp:endp)
-
     call extract_accum_field ('FSD240', rbufslp, nstep)
     this%fsd240_patch(begp:endp) = rbufslp(begp:endp)
 
-    call extract_accum_field ('FSI24', rbufslp, nstep)
-    this%fsi24_patch(begp:endp) = rbufslp(begp:endp)
-
-    call extract_accum_field ('FSI240', rbufslp, nstep)
-    this%fsi240_patch(begp:endp) = rbufslp(begp:endp)
-
-    if (use_cn) then
-       call extract_accum_field ('PREC10', rbufslp, nstep)
-       this%prec10_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('PREC60', rbufslp, nstep)
-       this%prec60_patch(begp:endp) = rbufslp(begp:endp)
-   
-       call extract_accum_field ('RH30', rbufslp, nstep)
-       this%rh30_patch(begp:endp) = rbufslp(begp:endp)
-    end if
-
-    if (use_cndv) then
-       call extract_accum_field ('PREC365' , rbufslc, nstep) 
-       this%prec365_col(begc:endc) = rbufslc(begc:endc)
-
-       call extract_accum_field ('TDA', rbufslp, nstep) 
-       this%t_mo_patch(begp:endp) = rbufslp(begp:endp)
-    end if
-
-    if (use_fates) then
-       call extract_accum_field ('PREC24', rbufslp, nstep)
-       this%prec24_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('RH24', rbufslp, nstep)
-       this%rh24_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('WIND24', rbufslp, nstep)
-       this%wind24_patch(begp:endp) = rbufslp(begp:endp)
-    end if
-
-    if(use_luna) then
-       call extract_accum_field ('po2_240', rbufslp, nstep)
-       this%forc_po2_240_patch(begp:endp) = rbufslp(begp:endp)
-
-       call extract_accum_field ('pco2_240', rbufslp, nstep)
-       this%forc_pco2_240_patch(begp:endp) = rbufslp(begp:endp)   
-
-       call extract_accum_field ('pbot240', rbufslp, nstep)
-       this%forc_pbot240_downscaled_patch(begp:endp) = rbufslp(begp:endp)  
- 
-    endif
-
     deallocate(rbufslp)
-    deallocate(rbufslc)
 
   end subroutine InitAccVars
 
@@ -2064,17 +1375,13 @@ subroutine UpdateAccVars (this, bounds)
     !
     ! !LOCAL VARIABLES:
     integer :: g,c,p                     ! indices
-    integer :: dtime                     ! timestep size [seconds]
     integer :: nstep                     ! timestep number
     integer :: ier                       ! error status
     integer :: begp, endp
-    integer :: begc, endc
     real(r8), pointer :: rbufslp(:)      ! temporary single level - patch level
-    real(r8), pointer :: rbufslc(:)      ! temporary single level - column level
     !---------------------------------------------------------------------
 
     begp = bounds%begp; endp = bounds%endp
-    begc = bounds%begc; endc = bounds%endc
 
     nstep = get_nstep()
 
@@ -2084,12 +1391,6 @@ subroutine UpdateAccVars (this, bounds)
        write(iulog,*)'UpdateAccVars allocation error for rbufslp'
        call endrun(msg=errMsg(sourcefile, __LINE__))
     endif
-    ! Allocate needed dynamic memory for single level col field
-    allocate(rbufslc(begc:endc), stat=ier)
-    if (ier/=0) then
-       write(iulog,*)'UpdateAccVars allocation error for rbufslc'
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
 
     ! Accumulate and extract forc_solad24 & forc_solad240 
     do p = begp,endp
@@ -2098,121 +1399,8 @@ subroutine UpdateAccVars (this, bounds)
     end do
     call update_accum_field  ('FSD240', rbufslp               , nstep)
     call extract_accum_field ('FSD240', this%fsd240_patch     , nstep)
-    call update_accum_field  ('FSD24' , rbufslp               , nstep)
-    call extract_accum_field ('FSD24' , this%fsd24_patch      , nstep)
-
-    ! Accumulate and extract forc_solai24 & forc_solai240 
-    do p = begp,endp
-       g = patch%gridcell(p)
-       rbufslp(p) = this%forc_solai_grc(g,1)
-    end do
-    call update_accum_field  ('FSI24' , rbufslp               , nstep)
-    call extract_accum_field ('FSI24' , this%fsi24_patch      , nstep)
-    call update_accum_field  ('FSI240', rbufslp               , nstep)
-    call extract_accum_field ('FSI240', this%fsi240_patch     , nstep)
-
-    ! Precipitation accumulators
-    !
-    ! For CNDV, we use a column-level accumulator. We cannot use a patch-level
-    ! accumulator for CNDV because this is used for establishment, so must be available
-    ! for inactive patches. In principle, we could/should switch to column-level for the
-    ! other precip accumulators, too; we'd just need to be careful about backwards
-    ! compatibility with old restart files.
-
-    do p = begp,endp
-       c = patch%column(p)
-       rbufslp(p) = this%forc_rain_downscaled_col(c) + this%forc_snow_downscaled_col(c)
-       rbufslc(c) = this%forc_rain_downscaled_col(c) + this%forc_snow_downscaled_col(c)
-    end do
-
-    if (use_cn) then
-       ! Accumulate and extract PREC60 (accumulates total precipitation as 60-day running mean)
-       call update_accum_field  ('PREC60', rbufslp, nstep)
-       call extract_accum_field ('PREC60', this%prec60_patch, nstep)
-
-       ! Accumulate and extract PREC10 (accumulates total precipitation as 10-day running mean)
-       call update_accum_field  ('PREC10', rbufslp, nstep)
-       call extract_accum_field ('PREC10', this%prec10_patch, nstep)
-    end if
-
-    if (use_cndv) then
-       ! Accumulate and extract PREC365 (accumulates total precipitation as 365-day running mean)
-       ! See above comment regarding why this is at the column-level despite other prec
-       ! accumulators being at the patch level.
-       call update_accum_field  ('PREC365', rbufslc, nstep)
-       call extract_accum_field ('PREC365', this%prec365_col, nstep)
-
-       ! Accumulate and extract TDA (accumulates TBOT as 30-day average) and 
-       ! also determines t_mo_min
-       
-       do p = begp,endp
-          c = patch%column(p)
-          rbufslp(p) = this%forc_t_downscaled_col(c)
-       end do
-       call update_accum_field  ('TDA', rbufslp, nstep)
-       call extract_accum_field ('TDA', rbufslp, nstep)
-       do p = begp,endp
-          this%t_mo_patch(p) = rbufslp(p)
-          this%t_mo_min_patch(p) = min(this%t_mo_min_patch(p), rbufslp(p))
-       end do
-
-    end if
-
-    if (use_fates) then
-       call update_accum_field  ('PREC24', rbufslp, nstep)
-       call extract_accum_field ('PREC24', this%prec24_patch, nstep)
-
-       do p = bounds%begp,bounds%endp
-          g = patch%gridcell(p) 
-          rbufslp(p) = this%forc_wind_grc(g) 
-       end do
-       call update_accum_field  ('WIND24', rbufslp, nstep)
-       call extract_accum_field ('WIND24', this%wind24_patch, nstep)
-
-       do p = bounds%begp,bounds%endp
-          g = patch%gridcell(p) 
-          rbufslp(p) = this%forc_rh_grc(g) 
-       end do
-       call update_accum_field  ('RH24', rbufslp, nstep)
-       call extract_accum_field ('RH24', this%rh24_patch, nstep)
-    end if
-
-    if(use_luna) then
-     do p = bounds%begp,bounds%endp
-       g = patch%gridcell(p)
-       rbufslp(p) = this%forc_pco2_grc(g) 
-     enddo
-     call update_accum_field  ('pco2_240', rbufslp, nstep)
-     call extract_accum_field ('pco2_240', this%forc_pco2_240_patch, nstep)
-
-     do p = bounds%begp,bounds%endp
-       g = patch%gridcell(p)
-       rbufslp(p) = this%forc_po2_grc(g) 
-     enddo
-     call update_accum_field  ('po2_240', rbufslp, nstep)
-     call extract_accum_field ('po2_240', this%forc_po2_240_patch, nstep)
-
-     do p = bounds%begp,bounds%endp
-       c = patch%column(p)
-       rbufslp(p) = this%forc_pbot_downscaled_col(c) 
-     enddo
-     call update_accum_field  ('pbot240', rbufslp, nstep)
-     call extract_accum_field ('pbot240', this%forc_pbot240_downscaled_patch, nstep)
-
-    endif
-
-    if (use_cn) then
-       do p = begp,endp
-          g = patch%gridcell(p) 
-          rbufslp(p) = this%forc_rh_grc(g)
-       end do
-       ! Accumulate and extract RH30 (accumulates RH as 30-day running mean)
-       call update_accum_field  ('RH30', rbufslp, nstep)
-       call extract_accum_field ('RH30', this%rh30_patch, nstep)
-    endif
 
     deallocate(rbufslp)
-    deallocate(rbufslc)
 
   end subroutine UpdateAccVars
 
@@ -2242,24 +1430,6 @@ subroutine Restart(this, bounds, ncid, flag)
        this%forc_flood_grc = 0._r8
     endif
 
-    if (use_cndv) then
-       call restartvar(ncid=ncid, flag=flag, varname='T_MO_MIN', xtype=ncd_double,  &
-            dim1name='pft', long_name='', units='', &
-            interpinic_flag='interp', readvar=readvar, data=this%t_mo_min_patch)
-    end if
-
-    if(use_luna)then
-       call restartvar(ncid=ncid, flag=flag, varname='pco2_240', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean CO2 partial pressure', units='Pa', &
-            interpinic_flag='interp', readvar=readvar, data=this%forc_pco2_240_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='po2_240', xtype=ncd_double,  &
-            dim1name='pft', long_name='10-day mean O2 partial pressure', units='Pa', &
-            interpinic_flag='interp', readvar=readvar, data=this%forc_po2_240_patch )
-       call restartvar(ncid=ncid, flag=flag, varname='pbot240', xtype=ncd_double,  &
-            dim1name='pft', long_name='10 day mean atmospheric pressure(Pa)', units='Pa', &
-            interpinic_flag='interp', readvar=readvar, data=this%forc_pbot240_downscaled_patch )
-    endif
-    
     ! -----------------------------------------------------------------------
     ! Start MML simple land model restart variables section		! MML 2016.01.15
     
@@ -2437,11 +1607,8 @@ subroutine Clean(this)
     deallocate(this%forc_solad_grc)
     deallocate(this%forc_solai_grc)
     deallocate(this%forc_solar_grc)
-    deallocate(this%forc_ndep_grc)
-    deallocate(this%forc_pc13o2_grc)
     deallocate(this%forc_po2_grc)
     deallocate(this%forc_aer_grc)
-    deallocate(this%forc_pch4_grc)
 
     ! atm->lnd not downscaled
     deallocate(this%forc_t_not_downscaled_grc)
@@ -2453,46 +1620,12 @@ subroutine Clean(this)
     deallocate(this%forc_rain_not_downscaled_grc)
     deallocate(this%forc_snow_not_downscaled_grc)
     
-    ! atm->lnd downscaled
-    deallocate(this%forc_t_downscaled_col)
-    deallocate(this%forc_q_downscaled_col)
-    deallocate(this%forc_pbot_downscaled_col)
-    deallocate(this%forc_th_downscaled_col)
-    deallocate(this%forc_rho_downscaled_col)
-    deallocate(this%forc_lwrad_downscaled_col)
-    deallocate(this%forc_rain_downscaled_col)
-    deallocate(this%forc_snow_downscaled_col)
-
     ! rof->lnd
     deallocate(this%forc_flood_grc)
     deallocate(this%volr_grc)
     deallocate(this%volrmch_grc)
 
-    ! anomaly forcing
-    deallocate(this%bc_precip_grc)
-    deallocate(this%af_precip_grc)
-    deallocate(this%af_uwind_grc)
-    deallocate(this%af_vwind_grc)
-    deallocate(this%af_tbot_grc)
-    deallocate(this%af_pbot_grc)
-    deallocate(this%af_shum_grc)
-    deallocate(this%af_swdn_grc)
-    deallocate(this%af_lwdn_grc)
-
-    deallocate(this%fsd24_patch)
     deallocate(this%fsd240_patch)
-    deallocate(this%fsi24_patch)
-    deallocate(this%fsi240_patch)
-    deallocate(this%prec10_patch)
-    deallocate(this%prec60_patch)
-    deallocate(this%prec365_col)
-    if (use_fates) then
-       deallocate(this%prec24_patch)
-       deallocate(this%rh24_patch)
-       deallocate(this%wind24_patch)
-    end if
-    deallocate(this%t_mo_patch)
-    deallocate(this%t_mo_min_patch)
     
     ! MML: deallocate mml vars:
     
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 5a36c237a8..432a09085f 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -10,25 +10,17 @@ module clm_driver
   ! !USES:
   use shr_kind_mod           , only : r8 => shr_kind_r8
   use clm_varctl             , only : wrtdia, iulog
-  use clm_varctl             , only : use_cn, use_noio
+  use clm_varctl             , only : use_noio
   use clm_time_manager       , only : get_nstep
   use spmdMod                , only : masterproc, mpicom
   use decompMod              , only : get_proc_clumps, get_clump_bounds, get_proc_bounds, bounds_type
-  use filterMod              , only : filter_inactive_and_active
   use histFileMod            , only : hist_update_hbuf, hist_htapes_wrapup
   use restFileMod            , only : restFile_write, restFile_filename
   use abortutils             , only : endrun
   !
-  use SoilBiogeochemVerticalProfileMod   , only : SoilBiogeochemVerticalProfile
-  use ActiveLayerMod         , only : alt_calc
-  !
   use perf_mod				! MML: this is where t_startf and t_stopf are 
   !
-  use clm_instMod            , only : temperature_inst, canopystate_inst
-  use clm_instMod            , only : soilstate_inst, soilbiogeochem_state_inst
-  use clm_instMod            , only : bgc_vegetation_inst
   use clm_instMod            , only : atm2lnd_inst, lnd2atm_inst
-  use clm_instMod            , only : soilstate_inst
 
   ! MML: add use simple land model module
   use mml_mainMod			 , only : mml_main	! MML if I don't say "only", it'll be fine, yes?
@@ -98,32 +90,9 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
     call get_proc_bounds(bounds_proc)
     nclumps = get_proc_clumps()
 
-! MML: I think I need this bit
     !$OMP PARALLEL DO PRIVATE (nc,bounds_clump)
     do nc = 1,nclumps
        call get_clump_bounds(nc, bounds_clump)
-
-       ! BUG(wjs, 2014-12-15, bugz 2107) Because of the placement of the following
-       ! routines (alt_calc and SoilBiogeochemVerticalProfile) in the driver sequence -
-       ! they are called very early in each timestep, before weights are adjusted and
-       ! filters are updated - it may be necessary for these routines to compute values
-       ! over inactive as well as active points (since some inactive points may soon
-       ! become active) - so that's what is done now. Currently, it seems to be okay to do
-       ! this, because the variables computed here seem to only depend on quantities that
-       ! are valid over inactive as well as active points.
-
-       call t_startf("decomp_vert")
-       call alt_calc(filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc, &
-            temperature_inst, canopystate_inst) 
-
-       if (use_cn) then
-          call SoilBiogeochemVerticalProfile(bounds_clump                                       , &
-               filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc   , &
-               filter_inactive_and_active(nc)%num_soilp, filter_inactive_and_active(nc)%soilp   , &
-               canopystate_inst, soilstate_inst, soilbiogeochem_state_inst)
-       end if
-
-       call t_stopf("decomp_vert")
     end do
     !$OMP END PARALLEL DO
 
@@ -177,56 +146,22 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
        ! Create history and write history tapes if appropriate
        call t_startf('clm_drv_io_htapes')
 
-       !write(iulog,*)'MML: about to call htapes_wrapup, prepare to die, my name is inigio montoya... also wtf does it want the soilstate for? '
-
-       ! MML workaround to try and avoid the soilstate leading to crashing - this is CLM's soil state, not SLIM's, so the values shouldn't be meaningful anyhow
-       !soilstate_inst%watsat_col(bounds_proc%begc:bounds_proc%endc, :) = 0.0_r8
-       !soilstate_inst%sucsat_col(bounds_proc%begc:bounds_proc%endc, :) = 0.0_r8
-       !soilstate_inst%bsw_col(bounds_proc%begc:bounds_proc%endc, :) = 0.0_r8
-       !soilstate_inst%hksat_col(bounds_proc%begc:bounds_proc%endc, :) = 0.0_r8
-
-       !write(iulog,*)'MML: clobbered the soilstate_inst values, call hist_htapes_wrapup now'
-
-       !write(iulog,*)'MML: rstwr = ',rstwr,', nlend = ',nlend
-
-       call hist_htapes_wrapup( rstwr, nlend, bounds_proc,                    &
-            soilstate_inst%watsat_col(bounds_proc%begc:bounds_proc%endc, 1:), &
-            soilstate_inst%sucsat_col(bounds_proc%begc:bounds_proc%endc, 1:), &
-            soilstate_inst%bsw_col(bounds_proc%begc:bounds_proc%endc, 1:),    &
-            soilstate_inst%hksat_col(bounds_proc%begc:bounds_proc%endc, 1:))
-
-       !write(iulog,*)'MML: back from wrapup, yet we are still running'
+       call hist_htapes_wrapup( rstwr, nlend, bounds_proc )
 
        call t_stopf('clm_drv_io_htapes')
 
-       if (use_cn) then
-          call bgc_vegetation_inst%WriteHistory(bounds_proc)
-       end if
-
        ! Write restart/initial files if appropriate
        if (rstwr) then
-          !write(iulog,*)'MML: write restart file'
           call t_startf('clm_drv_io_wrest')
           filer = restFile_filename(rdate=rdate)
 
           call restFile_write( bounds_proc, filer, rdate=rdate )
 
           call t_stopf('clm_drv_io_wrest')
-          
-          ! MML:
-         ! write(iulog,*)  'MML: end of restart if statment '
-          
        end if
        call t_stopf('clm_drv_io')
-
-	   ! MML:
-       !write(iulog,*)  'MML: after restart call '
-	    
     end if
     
-    ! MML:
-    !write(iulog,*)  'MML: end clm_drv routine '
-
   end subroutine clm_drv
 
   !------------------------------------------------------------------------
diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index 57a915042b..75682fbc89 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -12,10 +12,8 @@ module clm_initializeMod
   use clm_varctl      , only : nsrest, nsrStartup, nsrContinue, nsrBranch
   use clm_varctl      , only : is_cold_start, is_interpolated_start
   use clm_varctl      , only : iulog
-  use clm_varctl      , only : use_cn, use_cndv
-  use clm_instur      , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, fert_cft, wt_glc_mec, topo_glc_mec
+  use clm_instur      , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, wt_glc_mec, topo_glc_mec
   use perf_mod        , only : t_startf, t_stopf
-  use readParamsMod   , only : readParameters
   use ncdio_pio       , only : file_desc_t
   use GridcellType    , only : grc           ! instance     
   use LandunitType    , only : lun           ! instance          
@@ -42,18 +40,17 @@ subroutine initialize1( )
     ! CLM initialization first phase 
     !
     ! !USES:
-    use clm_varpar       , only: clm_varpar_init, natpft_lb, natpft_ub, cft_lb, cft_ub, maxpatch_glcmec
+    use clm_varpar       , only: clm_varpar_init, natpft_lb, natpft_ub, cft_lb, cft_ub
     use clm_varcon       , only: clm_varcon_init
     use landunit_varcon  , only: landunit_varcon_init, max_lunit
     use clm_varctl       , only: fsurdat, fatmlndfrc, noland, version, mml_surdat  
-    use pftconMod        , only: pftcon       
     use decompInitMod    , only: decompInit_lnd, decompInit_clumps, decompInit_glcp
     use domainMod        , only: domain_check, ldomain, domain_init
     use surfrdMod        , only: surfrd_get_globmask, surfrd_get_grid, surfrd_get_data 
     use controlMod       , only: control_init, control_print, NLFilename
     use ncdio_pio        , only: ncd_pio_init
     use initGridCellsMod , only: initGridCells
-    use UrbanParamsType  , only: UrbanInput, IsSimpleBuildTemp
+    use UrbanParamsType  , only: UrbanInput
     !
     ! !LOCAL VARIABLES:
     integer           :: ier                     ! error status
@@ -85,7 +82,7 @@ subroutine initialize1( )
 
     call control_init()
     call clm_varpar_init()
-    call clm_varcon_init( IsSimpleBuildTemp() )
+    call clm_varcon_init()
     call landunit_varcon_init()
     call ncd_pio_init()
 
@@ -153,14 +150,8 @@ subroutine initialize1( )
     allocate (urban_valid  (begg:endg                      ))
     allocate (wt_nat_patch (begg:endg, natpft_lb:natpft_ub ))
     allocate (wt_cft       (begg:endg, cft_lb:cft_ub       ))
-    allocate (fert_cft     (begg:endg, cft_lb:cft_ub       ))
-    allocate (wt_glc_mec  (begg:endg, maxpatch_glcmec))
-    allocate (topo_glc_mec(begg:endg, maxpatch_glcmec))
-
-    ! Read list of Patches and their corresponding parameter values
-    ! Independent of model resolution, Needs to stay before surfrd_get_data
-
-    call pftcon%Init()
+    allocate (wt_glc_mec  (begg:endg, 10))
+    allocate (topo_glc_mec(begg:endg, 10))
 
     ! Read surface dataset and set up subgrid weight arrays
     
@@ -203,7 +194,7 @@ subroutine initialize1( )
     !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
     do nc = 1, nclumps
        call get_clump_bounds(nc, bounds_clump)
-       call reweight_wrapup(bounds_clump, glc_behavior)
+       call reweight_wrapup(bounds_clump)
     end do
     !$OMP END PARALLEL DO
 
@@ -225,20 +216,13 @@ subroutine initialize2( )
     ! CLM initialization - second phase
     !
     ! !USES:
-    use shr_orb_mod           , only : shr_orb_decl
     use shr_scam_mod          , only : shr_scam_getCloseLatLon
-    use seq_drydep_mod        , only : n_drydep, drydep_method, DD_XLND
-    use accumulMod            , only : print_accum_fields 
     use clm_varpar            , only : nlevsno
     use clm_varcon            , only : spval
     use clm_varctl            , only : finidat, finidat_interp_source, finidat_interp_dest, fsurdat, mml_surdat
-    use clm_varctl            , only : use_century_decomp, single_column, scmlat, scmlon, use_cn
-    use clm_varorb            , only : eccen, mvelpp, lambm0, obliqr
-    use clm_time_manager      , only : get_step_size, get_curr_calday
+    use clm_varctl            , only : single_column, scmlat, scmlon
     use clm_time_manager      , only : get_curr_date, get_nstep, advance_timestep 
     use clm_time_manager      , only : timemgr_init, timemgr_restart_io, timemgr_restart
-    !use DaylengthMod          , only : InitDaylength, daylength
-!    use dynSubgridDriverMod   , only : dynSubgrid_init
     use fileutils             , only : getfil
     use initInterpMod         , only : initInterp
     use subgridWeightsMod     , only : init_subgrid_weights_mod
@@ -246,10 +230,6 @@ subroutine initialize2( )
     use histFileMod           , only : hist_addfld1d, hist_addfld2d, no_snow_normal
     use restFileMod           , only : restFile_getfile, restFile_open, restFile_close
     use restFileMod           , only : restFile_read, restFile_write 
-    !use ndepStreamMod         , only : ndep_init, ndep_interp
-    use LakeCon               , only : LakeConInit 
-    use SatellitePhenologyMod , only : SatellitePhenologyInit, readAnnualVegetation, interpMonthlyVeg
-    use SnowSnicarMod         , only : SnowAge_init, SnowOptics_init
     use lnd2atmMod            , only : lnd2atm_minimal
     use controlMod            , only : NLFilename
     !
@@ -267,19 +247,12 @@ subroutine initialize2( )
     character(len=256)    :: pnamer       ! full pathname of netcdf restart file
     character(len=256)    :: locfn        ! local file name
     type(file_desc_t)     :: ncid         ! netcdf id
-    real(r8)              :: dtime        ! time step increment (sec)
     integer               :: nstep        ! model time step
-    real(r8)              :: calday       ! calendar day for nstep
-    real(r8)              :: caldaym1     ! calendar day for nstep-1
-    real(r8)              :: declin       ! solar declination angle in radians for nstep
-    real(r8)              :: declinm1     ! solar declination angle in radians for nstep-1
-    real(r8)              :: eccf         ! earth orbit eccentricity factor
     type(bounds_type)     :: bounds_proc  ! processor bounds
     type(bounds_type)     :: bounds_clump ! clump bounds
     logical               :: lexist
     integer               :: closelatidx,closelonidx
     real(r8)              :: closelat,closelon
-    real(r8)              :: max_decl      ! temporary, for calculation of max_dayl
     integer               :: begp, endp
     integer               :: begc, endc
     integer               :: begl, endl
@@ -296,13 +269,6 @@ subroutine initialize2( )
     call get_proc_bounds(bounds_proc)
     nclumps = get_proc_clumps()
 
-    ! ------------------------------------------------------------------------
-    ! Read in parameters files
-    ! ------------------------------------------------------------------------
-
-    call clm_instReadNML( NLFilename )
-    call readParameters(photosyns_inst)
-
     ! ------------------------------------------------------------------------
     ! Initialize time manager
     ! ------------------------------------------------------------------------
@@ -317,44 +283,6 @@ subroutine initialize2( )
        call timemgr_restart()
     end if
 
-    ! ------------------------------------------------------------------------
-    ! Initialize daylength from the previous time step (needed so prev_dayl can be set correctly)
-    ! ------------------------------------------------------------------------
-
-    call t_startf('init_orbd')
-
-    calday = get_curr_calday()
-    call shr_orb_decl( calday, eccen, mvelpp, lambm0, obliqr, declin, eccf )
-
-    dtime = get_step_size()
-    caldaym1 = get_curr_calday(offset=-int(dtime))
-    call shr_orb_decl( caldaym1, eccen, mvelpp, lambm0, obliqr, declinm1, eccf )
-
-    call t_stopf('init_orbd')
-    
-    !call InitDaylength(bounds_proc, declin=declin, declinm1=declinm1)
-             
-    ! Initialize maximum daylength, based on latitude and maximum declination
-    ! given by the obliquity use negative value for S. Hem
-
-    do g = bounds_proc%begg,bounds_proc%endg
-       max_decl = obliqr
-       if (grc%lat(g) < 0._r8) max_decl = -max_decl
-       !grc%max_dayl(g) = daylength(grc%lat(g), max_decl)
-    end do
-
-    ! History file variables
-
-    if (use_cn) then
-       !call hist_addfld1d (fname='DAYL',  units='s', &
-            !avgflag='A', long_name='daylength', &
-            !ptr_gcell=grc%dayl, default='inactive')
-
-       !call hist_addfld1d (fname='PREV_DAYL', units='s', &
-            !avgflag='A', long_name='daylength from previous timestep', &
-            !ptr_gcell=grc%prev_dayl, default='inactive')
-    end if
-
     ! ------------------------------------------------------------------------
     ! Initialize component data structures 
     ! ------------------------------------------------------------------------
@@ -393,15 +321,10 @@ subroutine initialize2( )
 
     call clm_instInit(bounds_proc)
 
-    ! Initialize SNICAR optical and aging parameters
-
-    call SnowOptics_init( ) ! SNICAR optical parameters:
-    call SnowAge_init( )    ! SNICAR aging   parameters:
-
     call hist_printflds()
 
     ! ------------------------------------------------------------------------
-    ! Initializate dynamic subgrid weights (for prescribed transient Patches, CNDV
+    ! Initializate dynamic subgrid weights (for prescribed transient Patches
     ! and/or dynamic landunits); note that these will be overwritten in a
     ! restart run
     ! ------------------------------------------------------------------------
@@ -414,25 +337,6 @@ subroutine initialize2( )
     ! Initialize modules (after time-manager initialization in most cases)
     ! ------------------------------------------------------------------------
 
-    if (use_cn) then
-       call bgc_vegetation_inst%Init2(bounds_proc, NLFilename)
-
-       ! NOTE(wjs, 2016-02-23) Maybe the rest of the body of this conditional should also
-       ! be moved into bgc_vegetation_inst%Init2
-
-       if (n_drydep > 0 .and. drydep_method == DD_XLND) then
-          ! Must do this also when drydeposition is used so that estimates of monthly 
-          ! differences in LAI can be computed
-          call SatellitePhenologyInit(bounds_proc)
-       end if
-
-    else
-       call SatellitePhenologyInit(bounds_proc)
-    end if
-
-
-    
-
     ! ------------------------------------------------------------------------
     ! On restart only - process the history namelist. 
     ! ------------------------------------------------------------------------
@@ -531,30 +435,7 @@ subroutine initialize2( )
 
     ! The following is called for both initial and restart runs and must
     ! must be called after the restart file is read 
-
     call atm2lnd_inst%initAccVars(bounds_proc)
-    call temperature_inst%initAccVars(bounds_proc)
-    call waterflux_inst%initAccVars(bounds_proc)
-    call energyflux_inst%initAccVars(bounds_proc)
-    call canopystate_inst%initAccVars(bounds_proc)
-
-    call bgc_vegetation_inst%initAccVars(bounds_proc)
-
-    !------------------------------------------------------------       
-    ! Read monthly vegetation
-    !------------------------------------------------------------       
-
-    ! Even if CN is on, and dry-deposition is active, read CLMSP annual vegetation 
-    ! to get estimates of monthly LAI
-
-    if ( n_drydep > 0 .and. drydep_method == DD_XLND )then
-       call readAnnualVegetation(bounds_proc, canopystate_inst)
-       if (nsrest == nsrStartup .and. finidat /= ' ') then
-          ! Call interpMonthlyVeg for dry-deposition so that mlaidiff will be calculated
-          ! This needs to be done even if CN or CNDV is on!
-          call interpMonthlyVeg(bounds_proc, canopystate_inst)
-       end if
-    end if
 
     !------------------------------------------------------------       
     ! Determine gridcell averaged properties to send to atm
@@ -567,23 +448,6 @@ subroutine initialize2( )
        call t_stopf('init_map2gc')
     end if
 
-    !------------------------------------------------------------       
-    ! Initialize sno export state to send to glc
-    !------------------------------------------------------------       
-
-    !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
-    do nc = 1,nclumps
-       call get_clump_bounds(nc, bounds_clump)
-
-       call t_startf('init_lnd2glc')
-       call lnd2glc_inst%update_lnd2glc(bounds_clump,       &
-            filter(nc)%num_do_smb_c, filter(nc)%do_smb_c,   &
-            temperature_inst, glacier_smb_inst, topo_inst, &
-            init=.true.)
-       call t_stopf('init_lnd2glc')
-    end do
-    !$OMP END PARALLEL DO
-
     !------------------------------------------------------------       
     ! Deallocate wt_nat_patch
     !------------------------------------------------------------       
@@ -597,7 +461,7 @@ subroutine initialize2( )
     ! initialize2 because it is used to initialize other variables; now it can be
     ! deallocated
 
-    deallocate(topo_glc_mec, fert_cft)
+    deallocate(topo_glc_mec)
 
     !------------------------------------------------------------       
     ! Write log output for end of initialization
diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90
index 6be25eb402..35eba2a879 100644
--- a/src/main/clm_instMod.F90
+++ b/src/main/clm_instMod.F90
@@ -7,73 +7,33 @@ module clm_instMod
   ! !USES:
   use shr_kind_mod    , only : r8 => shr_kind_r8
   use decompMod       , only : bounds_type
-  use clm_varpar      , only : ndecomp_pools, nlevdecomp_full
-  use clm_varctl      , only : use_cn, use_cndv
-  use clm_varctl      , only : use_century_decomp, use_crop
-  use clm_varcon      , only : bdsno, c13ratio, c14ratio
+  use clm_varcon      , only : bdsno
+  use clm_varctl      , only : iulog
   use landunit_varcon , only : istice_mec, istsoil
   use perf_mod        , only : t_startf, t_stopf
-  use controlMod      , only : NLFilename
 
   !-----------------------------------------
   ! Constants
   !-----------------------------------------
 
   use UrbanParamsType                    , only : urbanparams_type   ! Constants 
-  use UrbanParamsType                    , only : IsSimpleBuildTemp, IsProgBuildTemp
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  !use CNDVType                           , only : dgv_ecophyscon     ! Constants 
-
   !-----------------------------------------
   ! Definition of component types 
   !-----------------------------------------
 
-  use AerosolMod                      , only : aerosol_type
-  use CanopyStateType                 , only : canopystate_type
-  use ch4Mod                          , only : ch4_type
-  use CNVegetationFacade              , only : cn_vegetation_type
-  use SoilBiogeochemStateType         , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonFluxType    , only : soilbiogeochem_carbonflux_type
-  use SoilBiogeochemCarbonStateType   , only : soilbiogeochem_carbonstate_type
-  use SoilBiogeochemNitrogenFluxType  , only : soilbiogeochem_nitrogenflux_type
-  use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-  use CropType                        , only : crop_type
-  use DryDepVelocity                  , only : drydepvel_type
-  use DUSTMod                         , only : dust_type
   use EnergyFluxType                  , only : energyflux_type
-  use FrictionVelocityMod             , only : frictionvel_type
-  use GlacierSurfaceMassBalanceMod    , only : glacier_smb_type
-  use LakeStateType                   , only : lakestate_type
-  use OzoneBaseMod                    , only : ozone_base_type
-  use OzoneFactoryMod                 , only : create_and_init_ozone_type
-  use PhotosynthesisMod               , only : photosyns_type
-  use SoilHydrologyType               , only : soilhydrology_type  
-  use SoilStateType                   , only : soilstate_type
-  use SolarAbsorbedType               , only : solarabs_type
-  use SurfaceRadiationMod             , only : surfrad_type
   use SurfaceAlbedoType               , only : surfalb_type
   use TemperatureType                 , only : temperature_type
-  use WaterFluxType                   , only : waterflux_type
   use WaterStateType                  , only : waterstate_type
   use UrbanParamsType                 , only : urbanparams_type
-  use VOCEmissionMod                  , only : vocemis_type
   use atm2lndType                     , only : atm2lnd_type
   use lnd2atmType                     , only : lnd2atm_type
-  use lnd2glcMod                      , only : lnd2glc_type 
-  use glc2lndMod                      , only : glc2lnd_type
   use glcBehaviorMod                  , only : glc_behavior_type
   use TopoMod                         , only : topo_type
   use GridcellType                    , only : grc
   use LandunitType                    , only : lun                
   use ColumnType                      , only : col                
   use PatchType                       , only : patch                
-  use SoilWaterRetentionCurveMod      , only : soil_water_retention_curve_type
-  !
-  use SoilStateInitTimeConstMod       , only : SoilStateInitTimeConst
-  use SoilHydrologyInitTimeConstMod   , only : SoilHydrologyInitTimeConst
-  use SurfaceAlbedoMod                , only : SurfaceAlbedoInitTimeConst 
-  use LakeCon                         , only : LakeConInit 
-  use SoilBiogeochemPrecisionControlMod, only: SoilBiogeochemPrecisionControlInit
   !
   implicit none
   public   ! By default everything is public 
@@ -83,119 +43,48 @@ module clm_instMod
   !-----------------------------------------
 
   ! Physics types 
-  type(aerosol_type)                      :: aerosol_inst
-  type(canopystate_type)                  :: canopystate_inst
   type(energyflux_type)                   :: energyflux_inst
-  type(frictionvel_type)                  :: frictionvel_inst
-  type(glacier_smb_type)                  :: glacier_smb_inst
-  type(lakestate_type)                    :: lakestate_inst
-  class(ozone_base_type), allocatable     :: ozone_inst
-  type(photosyns_type)                    :: photosyns_inst
-  type(soilstate_type)                    :: soilstate_inst
-  type(soilhydrology_type)                :: soilhydrology_inst
-  type(solarabs_type)                     :: solarabs_inst
   type(surfalb_type)                      :: surfalb_inst
-  type(surfrad_type)                      :: surfrad_inst
   type(temperature_type)                  :: temperature_inst
   type(urbanparams_type)                  :: urbanparams_inst
-  type(waterflux_type)                    :: waterflux_inst
   type(waterstate_type)                   :: waterstate_inst
   type(atm2lnd_type)                      :: atm2lnd_inst
-  type(glc2lnd_type)                      :: glc2lnd_inst
   type(lnd2atm_type)                      :: lnd2atm_inst
-  type(lnd2glc_type)                      :: lnd2glc_inst
   type(glc_behavior_type), target         :: glc_behavior
   type(topo_type)                         :: topo_inst
-  class(soil_water_retention_curve_type) , allocatable :: soil_water_retention_curve
-
-  ! CN vegetation types
-  ! Eventually bgc_vegetation_inst will be an allocatable instance of an abstract
-  ! interface
-  type(cn_vegetation_type)                :: bgc_vegetation_inst
-
-  ! Soil biogeochem types 
-  type(soilbiogeochem_state_type)         :: soilbiogeochem_state_inst
-  type(soilbiogeochem_carbonstate_type)   :: soilbiogeochem_carbonstate_inst
-  type(soilbiogeochem_carbonstate_type)   :: c13_soilbiogeochem_carbonstate_inst
-  type(soilbiogeochem_carbonstate_type)   :: c14_soilbiogeochem_carbonstate_inst
-  type(soilbiogeochem_carbonflux_type)    :: soilbiogeochem_carbonflux_inst
-  type(soilbiogeochem_carbonflux_type)    :: c13_soilbiogeochem_carbonflux_inst
-  type(soilbiogeochem_carbonflux_type)    :: c14_soilbiogeochem_carbonflux_inst
-  type(soilbiogeochem_nitrogenstate_type) :: soilbiogeochem_nitrogenstate_inst
-  type(soilbiogeochem_nitrogenflux_type)  :: soilbiogeochem_nitrogenflux_inst
-
-  ! General biogeochem types
-  type(ch4_type)                          :: ch4_inst
-  type(crop_type)                         :: crop_inst
-  type(dust_type)                         :: dust_inst
-  !type(vocemis_type)                      :: vocemis_inst
-  type(drydepvel_type)                    :: drydepvel_inst
-
-  ! FATES
 
-  !
   public :: clm_instInit       ! Initialize
-  public :: clm_instReadNML    ! Read in namelist
   public :: clm_instRest       ! Setup restart
   !-----------------------------------------------------------------------
 
 contains
 
-  !-----------------------------------------------------------------------
-  subroutine clm_instReadNML( NLFilename )
-    !
-    ! !ARGUMENTS    
-    implicit none
-    character(len=*), intent(IN) :: NLFilename ! Namelist filename
-    ! Read in any namelists that must be read for any clm object instances that need it
-    call canopystate_inst%ReadNML( NLFilename )
-    !call photosyns_inst%ReadNML(   NLFilename )
-    !if (use_cn) then
-       !call crop_inst%ReadNML(     NLFilename )
-    !end if
-
-  end subroutine clm_instReadNML
-
   !-----------------------------------------------------------------------
   subroutine clm_instInit(bounds)
     !
     ! !USES: 
-    use clm_varpar                         , only : nlevsno, numpft
-    use controlMod                         , only : nlfilename, fsurdat
-    use domainMod                          , only : ldomain
-    use SoilBiogeochemDecompCascadeBGCMod  , only : init_decompcascade_bgc
-    use SoilBiogeochemDecompCascadeCNMod   , only : init_decompcascade_cn
-    use SoilBiogeochemDecompCascadeContype , only : init_decomp_cascade_constants
+    use clm_varpar                         , only : nlevsno
     use initVerticalMod                    , only : initVertical
-    use accumulMod                         , only : print_accum_fields 
-    use SoilWaterRetentionCurveFactoryMod  , only : create_soil_water_retention_curve
-    use decompMod                          , only : get_proc_bounds
     !
     ! !ARGUMENTS    
     type(bounds_type), intent(in) :: bounds  ! processor bounds
     !
     ! !LOCAL VARIABLES:
     integer               :: c,l,g
-    integer               :: nclumps,nc
     integer               :: begp, endp
     integer               :: begc, endc
     integer               :: begl, endl
-    type(bounds_type)     :: bounds_clump
     real(r8), allocatable :: h2osno_col(:)
-    real(r8), allocatable :: snow_depth_col(:)
-
-    integer :: dummy_to_make_pgi_happy
     !----------------------------------------------------------------------
 
-    ! Note: h2osno_col and snow_depth_col are initialized as local variable 
-    ! since they are needed to initialize vertical data structures  
+    ! Note: h2osno_col initialized as local variable 
+    ! since needed to initialize vertical data structures  
 
     begp = bounds%begp; endp = bounds%endp 
     begc = bounds%begc; endc = bounds%endc 
     begl = bounds%begl; endl = bounds%endl
 
     allocate (h2osno_col(begc:endc))
-    allocate (snow_depth_col(begc:endc))
 
     ! snow water
     do c = begc,endc
@@ -216,7 +105,6 @@ subroutine clm_instInit(bounds)
        else
           h2osno_col(c) = 0._r8
        endif
-       snow_depth_col(c)  = h2osno_col(c) / bdsno
     end do
 
     ! Initialize urban constants
@@ -227,132 +115,27 @@ subroutine clm_instInit(bounds)
 
     call initVertical(bounds,               &
          glc_behavior, &
-         snow_depth_col(begc:endc),              &
          urbanparams_inst%thick_wall(begl:endl), &
          urbanparams_inst%thick_roof(begl:endl))
 
     ! Initialize clm->drv and drv->clm data structures
 
-    call atm2lnd_inst%Init( bounds, NLFilename )
-    call lnd2atm_inst%Init( bounds, NLFilename )
-
-    call glc2lnd_inst%Init( bounds, glc_behavior )
-    call lnd2glc_inst%Init( bounds )
+    call atm2lnd_inst%Init(bounds)
+    call lnd2atm_inst%Init(bounds)
 
     ! Initialization of public data types
 
-    call temperature_inst%Init(bounds,           &
-         urbanparams_inst%em_roof(begl:endl),    &
-         urbanparams_inst%em_wall(begl:endl),    &
-         urbanparams_inst%em_improad(begl:endl), &
-         urbanparams_inst%em_perroad(begl:endl), &
-         IsSimpleBuildTemp(), IsProgBuildTemp() )
-
-    call canopystate_inst%Init(bounds)
-
-    call soilstate_inst%Init(bounds)
-    call SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename) ! sets hydraulic and thermal soil properties
-
-    call waterstate_inst%Init(bounds,         &
-         h2osno_col(begc:endc),                    &
-         snow_depth_col(begc:endc),                &
-         soilstate_inst%watsat_col(begc:endc, 1:), &
-         temperature_inst%t_soisno_col(begc:endc, -nlevsno+1:) )
-
-    call waterflux_inst%Init(bounds)
-
-    call glacier_smb_inst%Init(bounds)
-
-    ! COMPILER_BUG(wjs, 2014-11-29, pgi 14.7) Without the following assignment, the
-    ! assertion in energyflux_inst%Init fails with pgi 14.7 on yellowstone, presumably due
-    ! to a compiler bug.
-    dummy_to_make_pgi_happy = ubound(temperature_inst%t_grnd_col, 1)
-    call energyflux_inst%Init(bounds, temperature_inst%t_grnd_col(begc:endc), &
-         IsSimpleBuildTemp(), IsProgBuildTemp() )
-
-    !call aerosol_inst%Init(bounds, NLFilename)
-
-    call frictionvel_inst%Init(bounds)
+    call temperature_inst%Init(bounds)
 
-    call lakestate_inst%Init(bounds)
-    call LakeConInit()
+    call waterstate_inst%Init(bounds, h2osno_col(begc:endc))
 
-    allocate(ozone_inst, source = create_and_init_ozone_type(bounds))
-
-    call photosyns_inst%Init(bounds)
-
-    call soilhydrology_inst%Init(bounds, nlfilename)
-    call SoilHydrologyInitTimeConst(bounds, soilhydrology_inst) ! sets time constant properties
-
-    call solarabs_inst%Init(bounds)
+    call energyflux_inst%Init(bounds, temperature_inst%t_grnd_col(begc:endc))
 
     call surfalb_inst%Init(bounds)
-    call SurfaceAlbedoInitTimeConst(bounds)
-
-    call surfrad_inst%Init(bounds)
-
-    call dust_inst%Init(bounds)
 
     call topo_inst%Init(bounds)
 
-    ! Note - always initialize the memory for ch4_inst
-    !call ch4_inst%Init(bounds, soilstate_inst%cellorg_col(begc:endc, 1:), fsurdat, nlfilename)
-
-    !call vocemis_inst%Init(bounds)
-
-    !call drydepvel_inst%Init(bounds)
-
-    if (use_cn ) then
-
-       ! Initialize soilbiogeochem_state_inst
-
-       call soilbiogeochem_state_inst%Init(bounds)
-
-       ! Initialize decompcascade constants
-       ! Note that init_decompcascade_bgc and init_decompcascade_cn need 
-       ! soilbiogeochem_state_inst to be initialized
-
-       call init_decomp_cascade_constants()
-       if (use_century_decomp) then
-          call init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, &
-                                      soilstate_inst )
-       else 
-          call init_decompcascade_cn(bounds, soilbiogeochem_state_inst)
-       end if
-
-       ! Initalize soilbiogeochem carbon types
-
-       call soilbiogeochem_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8)
-
-    end if
-
-    if ( use_cn ) then
-
-       ! Initalize soilbiogeochem nitrogen types
-
-       call soilbiogeochem_nitrogenstate_inst%Init(bounds, &
-            soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), &
-            soilbiogeochem_carbonstate_inst%decomp_cpools_col(begc:endc,1:ndecomp_pools),  &
-            soilbiogeochem_carbonstate_inst%decomp_cpools_1m_col(begc:endc, 1:ndecomp_pools))
-
-       call soilbiogeochem_nitrogenflux_inst%Init(bounds) 
-
-       ! Initialize precision control for soil biogeochemistry
-       call SoilBiogeochemPrecisionControlInit( soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, &
-                                                c14_soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst)
-
-    end if ! end of if use_cn 
-
-    ! Note - always call Init for bgc_vegetation_inst: some pieces need to be initialized always
-    call bgc_vegetation_inst%Init(bounds, nlfilename)
-
-    if (use_cn ) then
-       call crop_inst%Init(bounds)
-    end if
-
-    
     deallocate (h2osno_col)
-    deallocate (snow_depth_col)
 
     ! ------------------------------------------------------------------------
     ! Initialize accumulated fields
@@ -362,25 +145,7 @@ subroutine clm_instInit(bounds)
     ! the step size is needed. 
 
     call t_startf('init_accflds')
-
     call atm2lnd_inst%InitAccBuffer(bounds)
-
-    call temperature_inst%InitAccBuffer(bounds)
-    
-    call waterflux_inst%InitAccBuffer(bounds)
-
-    call energyflux_inst%InitAccBuffer(bounds)
-
-    call canopystate_inst%InitAccBuffer(bounds)
-
-    call bgc_vegetation_inst%InitAccBuffer(bounds)
-
-    if (use_crop) then
-       call crop_inst%InitAccBuffer(bounds)
-    end if
-
-    call print_accum_fields()
-
     call t_stopf('init_accflds')
 
   end subroutine clm_instInit
@@ -390,85 +155,28 @@ subroutine clm_instRest(bounds, ncid, flag)
     !
     ! !USES:
     use ncdio_pio       , only : file_desc_t
-    use UrbanParamsType , only : IsSimpleBuildTemp, IsProgBuildTemp
-    use decompMod       , only : get_proc_bounds, get_proc_clumps, get_clump_bounds
-
     !
     ! !DESCRIPTION:
     ! Define/write/read CLM restart file.
     !
     ! !ARGUMENTS:
     type(bounds_type) , intent(in)    :: bounds          
-    
     type(file_desc_t) , intent(inout) :: ncid ! netcdf id
     character(len=*)  , intent(in)    :: flag ! 'define', 'write', 'read' 
-
-    ! Local variables
-    integer                           :: nc, nclumps
-    type(bounds_type)                 :: bounds_clump
-
     !-----------------------------------------------------------------------
 
     call atm2lnd_inst%restart (bounds, ncid, flag=flag)
 
-    call canopystate_inst%restart (bounds, ncid, flag=flag)
-
-    call energyflux_inst%restart (bounds, ncid, flag=flag, &
-         is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp())
-
-    call frictionvel_inst% restart (bounds, ncid, flag=flag)
-
-    call lakestate_inst%restart (bounds, ncid, flag=flag)
-
-    call ozone_inst%restart (bounds, ncid, flag=flag)
-
-    call photosyns_inst%restart (bounds, ncid, flag=flag)
-
-    call soilhydrology_inst%restart (bounds, ncid, flag=flag)
-
-    call solarabs_inst%restart (bounds, ncid, flag=flag)
-
-    call temperature_inst%restart (bounds, ncid, flag=flag, &
-         is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp())
+    call energyflux_inst%restart (bounds, ncid, flag=flag)
 
-    call soilstate_inst%restart (bounds, ncid, flag=flag)
+    call temperature_inst%restart (bounds, ncid, flag=flag)
 
-    call waterflux_inst%restart (bounds, ncid, flag=flag)
+    call waterstate_inst%restart (bounds, ncid, flag=flag)
 
-    call waterstate_inst%restart (bounds, ncid, flag=flag, &
-         watsat_col=soilstate_inst%watsat_col(bounds%begc:bounds%endc,:)) 
-
-    !call aerosol_inst%restart (bounds, ncid,  flag=flag, &
-         !h2osoi_ice_col=waterstate_inst%h2osoi_ice_col(bounds%begc:bounds%endc,:), &
-         !h2osoi_liq_col=waterstate_inst%h2osoi_liq_col(bounds%begc:bounds%endc,:))
-
-    call surfalb_inst%restart (bounds, ncid, flag=flag, &
-         tlai_patch=canopystate_inst%tlai_patch(bounds%begp:bounds%endp), &
-         tsai_patch=canopystate_inst%tsai_patch(bounds%begp:bounds%endp))
+    call surfalb_inst%restart (bounds, ncid, flag=flag)
 
     call topo_inst%restart (bounds, ncid, flag=flag)
 
-    if ( use_cn ) then
-       ! Need to do vegetation restart before soil bgc restart to get totvegc_col for purpose
-       ! of resetting soil carbon at exit spinup when no vegetation is growing.
-       call bgc_vegetation_inst%restart(bounds, ncid, flag=flag)
-
-       call soilbiogeochem_nitrogenstate_inst%restart(bounds, ncid, flag=flag, &
-            totvegc_col=bgc_vegetation_inst%get_totvegc_col(bounds))
-       call soilbiogeochem_nitrogenflux_inst%restart(bounds, ncid, flag=flag)
-
-       call crop_inst%restart(bounds, ncid, flag=flag)
-    end if
-
-    if (use_cn ) then
-
-       call soilbiogeochem_state_inst%restart(bounds, ncid, flag=flag)
-       call soilbiogeochem_carbonstate_inst%restart(bounds, ncid, flag=flag, carbon_type='c12', &
-            totvegc_col=bgc_vegetation_inst%get_totvegc_col(bounds))
-
-       call soilbiogeochem_carbonflux_inst%restart(bounds, ncid, flag=flag)
-    endif
-
  end subroutine clm_instRest
 
 end module clm_instMod
diff --git a/src/main/clm_varcon.F90 b/src/main/clm_varcon.F90
index d0a2053568..1559100d26 100644
--- a/src/main/clm_varcon.F90
+++ b/src/main/clm_varcon.F90
@@ -14,10 +14,6 @@ module clm_varcon
                            SHR_CONST_PDB, SHR_CONST_PI, SHR_CONST_CDAY,       &
                            SHR_CONST_RGAS, SHR_CONST_PSTD,                    &
                            SHR_CONST_MWDAIR, SHR_CONST_MWWV
-  use clm_varpar   , only: numrad, nlevgrnd, nlevlak, nlevdecomp_full
-  use clm_varpar   , only: ngases
-  use clm_varpar   , only: nlayer
-  
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -42,10 +38,7 @@ module clm_varcon
   ! Initialize physical constants
   !------------------------------------------------------------------
 
-  real(r8), parameter :: n_melt=0.7                         ! fsca shape parameter
-  real(r8), parameter :: e_ice=6.0                          ! soil ice impedance factor
   real(r8), parameter :: pc = 0.4                           ! threshold probability
-  real(r8), parameter :: mu = 0.13889                       ! connectivity exponent 
   real(r8), parameter :: secsphr = 3600._r8                 ! Seconds in an hour
   integer,  parameter :: isecsphr = int(secsphr)            ! Integer seconds in an hour
   integer,  parameter :: isecspmin= 60                      ! Integer seconds in a minute
@@ -88,9 +81,6 @@ module clm_varcon
   real(r8), public, parameter :: secspday= SHR_CONST_CDAY   ! Seconds per day
   integer,  public, parameter :: isecspday= secspday        ! Integer seconds per day
 
-  integer, public, parameter  :: fun_period  = 1            ! A FUN parameter, and probably needs to be changed for testing
-  real(r8),public, parameter  :: smallValue  = 1.e-12_r8    ! A small values used by FUN
-
   ! ------------------------------------------------------------------------
   ! Special value flags
   ! ------------------------------------------------------------------------
@@ -106,111 +96,17 @@ module clm_varcon
   ! Keep this negative to avoid conflicts with possible valid values
   integer , public, parameter :: ispval = -9999             ! special value for int data
 
-  ! ------------------------------------------------------------------------
-  ! These are tunable constants from clm2_3
-  ! ------------------------------------------------------------------------
-
-  real(r8) :: zlnd = 0.01_r8        ! Roughness length for soil [m]
-  real(r8) :: zsno = 0.0024_r8      ! Roughness length for snow [m]
-  real(r8) :: csoilc = 0.004_r8     ! Drag coefficient for soil under canopy [-]
-  real(r8) :: capr   = 0.34_r8      ! Tuning factor to turn first layer T into surface T
-  real(r8) :: cnfac  = 0.5_r8       ! Crank Nicholson factor between 0 and 1
-  real(r8) :: ssi    = 0.033_r8     ! Irreducible water saturation of snow
-  real(r8) :: wimp   = 0.05_r8      ! Water impremeable if porosity less than wimp
-  real(r8) :: pondmx = 0.0_r8       ! Ponding depth (mm)
-  real(r8) :: pondmx_urban = 1.0_r8 ! Ponding depth for urban roof and impervious road (mm)
-
-  real(r8) :: thk_bedrock = 3.0_r8  ! thermal conductivity of 'typical' saturated granitic rock 
-                                    ! (Clauser and Huenges, 1995)(W/m/K)
-  real(r8) :: csol_bedrock = 2.0e6_r8 ! vol. heat capacity of granite/sandstone  J/(m3 K)(Shabbir, 2000) !scs
-  real(r8), parameter :: zmin_bedrock = 0.4_r8 ! minimum soil depth [m]
-
-  real(r8), parameter :: aquifer_water_baseline = 5000._r8 ! baseline value for water in the unconfined aquifer [mm]
-
-  !!! C13
-  real(r8), parameter :: preind_atm_del13c = -6.0   ! preindustrial value for atmospheric del13C
-  real(r8), parameter :: preind_atm_ratio = SHR_CONST_PDB + (preind_atm_del13c * SHR_CONST_PDB)/1000.0  ! 13C/12C
-  real(r8) :: c13ratio = preind_atm_ratio/(1.0+preind_atm_ratio) ! 13C/(12+13)C preind atmosphere
-
-   ! typical del13C for C3 photosynthesis (permil, relative to PDB)
-  real(r8), parameter :: c3_del13c = -28._r8
-
-  ! typical del13C for C4 photosynthesis (permil, relative to PDB)
-  real(r8), parameter :: c4_del13c = -13._r8
-
-  ! isotope ratio (13c/12c) for C3 photosynthesis
-  real(r8), parameter :: c3_r1 = SHR_CONST_PDB + ((c3_del13c*SHR_CONST_PDB)/1000._r8)
-
-  ! isotope ratio (13c/[12c+13c]) for C3 photosynthesis
-  real(r8), parameter :: c3_r2 = c3_r1/(1._r8 + c3_r1)
-
-  ! isotope ratio (13c/12c) for C4 photosynthesis  
-  real(r8), parameter :: c4_r1 = SHR_CONST_PDB + ((c4_del13c*SHR_CONST_PDB)/1000._r8)
-
-  ! isotope ratio (13c/[12c+13c]) for C4 photosynthesis
-  real(r8), parameter :: c4_r2 = c4_r1/(1._r8 + c4_r1)
-
-  !!! C14
-  real(r8) :: c14ratio = 1.e-12_r8
-  ! real(r8) :: c14ratio = 1._r8  ! debug lets set to 1 to try to avoid numerical errors
-
-  !------------------------------------------------------------------
-  ! Urban building temperature constants
-  !------------------------------------------------------------------
-  real(r8) :: ht_wasteheat_factor = 0.2_r8   ! wasteheat factor for urban heating (-)
-  real(r8) :: ac_wasteheat_factor = 0.6_r8   ! wasteheat factor for urban air conditioning (-)
-  real(r8) :: em_roof_int  = 0.9_r8          ! emissivity of interior surface of roof (Bueno et al. 2012, GMD)
-  real(r8) :: em_sunw_int  = 0.9_r8          ! emissivity of interior surface of sunwall (Bueno et al. 2012, GMD)
-  real(r8) :: em_shdw_int  = 0.9_r8          ! emissivity of interior surface of shadewall Bueno et al. 2012, GMD)
-  real(r8) :: em_floor_int = 0.9_r8          ! emissivity of interior surface of floor (Bueno et al. 2012, GMD)
-  real(r8) :: hcv_roof = 0.948_r8            ! interior convective heat transfer coefficient for roof (Bueno et al. 2012, GMD) (W m-2 K-1)
-  real(r8) :: hcv_roof_enhanced  = 4.040_r8  ! enhanced (t_roof_int <= t_room) interior convective heat transfer coefficient for roof (Bueno et al. 2012, GMD) !(W m-2 K-1)
-  real(r8) :: hcv_floor = 0.948_r8           ! interior convective heat transfer coefficient for floor (Bueno et al. 2012, GMD) (W m-2 K-1)
-  real(r8) :: hcv_floor_enhanced  = 4.040_r8 ! enhanced (t_floor_int >= t_room) interior convective heat transfer coefficient for floor (Bueno et al.  !2012, GMD) (W m-2 K-1)
-  real(r8) :: hcv_sunw  = 3.076_r8           ! interior convective heat transfer coefficient for sunwall (Bueno et al. 2012, GMD) (W m-2 K-1)
-  real(r8) :: hcv_shdw  = 3.076_r8           ! interior convective heat transfer coefficient for shadewall (Bueno et al. 2012, GMD) (W m-2 K-1)
-  real(r8) :: dz_floor = 0.1_r8                 ! floor thickness - concrete (Salmanca et al. 2010, TAC) (m)
-  real(r8), parameter :: dens_floor = 2.35e3_r8 ! density of floor - concrete (Salmanca et al. 2010, TAC) (kg m-3)
-  real(r8), parameter :: sh_floor = 880._r8     ! specific heat of floor - concrete (Salmanca et al. 2010, TAC) (J kg-1 K-1)
-  real(r8) :: cp_floor = dens_floor*sh_floor    ! volumetric heat capacity of floor - concrete (Salmanca et al. 2010, TAC) (J m-3 K-1)
-  real(r8) :: vent_ach = 0.3                    ! ventilation rate (air exchanges per hour)
-
-  real(r8) :: wasteheat_limit = 100._r8         ! limit on wasteheat (W/m2)
-
-  !------------------------------------------------------------------
-
-  real(r8) :: h2osno_max   = -999.0_r8            ! max allowed snow thickness (mm H2O)
-  real(r8) :: int_snow_max = -999.0_r8            ! limit applied to integrated snowfall when determining changes in snow-covered fraction during melt (mm H2O)
-  real(r8) :: n_melt_glcmec = -999.0_r8           ! SCA shape parameter for glc_mec columns
-
   integer, private :: i  ! loop index
 
- !real(r8), parameter :: nitrif_n2o_loss_frac = 0.02_r8  ! fraction of N lost as N2O in nitrification (Parton et al., 2001)
-  real(r8), parameter :: nitrif_n2o_loss_frac = 6.e-4_r8 ! fraction of N lost as N2O in nitrification (Li et al., 2000)
-  real(r8), parameter :: frac_minrlztn_to_no3 = 0.2_r8   ! fraction of N mineralized that is dieverted to the nitrification stream (Parton et al., 2001)
-
   !------------------------------------------------------------------
   ! Set subgrid names
   !------------------------------------------------------------------
 
   character(len=16), parameter :: grlnd  = 'lndgrid'      ! name of lndgrid
-  character(len=16), parameter :: namea  = 'gridcellatm'  ! name of atmgrid
   character(len=16), parameter :: nameg  = 'gridcell'     ! name of gridcells
   character(len=16), parameter :: namel  = 'landunit'     ! name of landunits
   character(len=16), parameter :: namec  = 'column'       ! name of columns
   character(len=16), parameter :: namep  = 'pft'          ! name of patches
-  character(len=16), parameter :: nameCohort = 'cohort'   ! name of cohorts (ED specific)
-
-  !------------------------------------------------------------------
-  ! Initialize miscellaneous radiation constants
-  !------------------------------------------------------------------
-
-  real(r8) :: betads  = 0.5_r8            ! two-stream parameter betad for snow
-  real(r8) :: betais  = 0.5_r8            ! two-stream parameter betai for snow
-  real(r8) :: omegas(numrad)           ! two-stream parameter omega for snow by band
-  data (omegas(i),i=1,numrad) /0.8_r8, 0.4_r8/
-
-  ! Lake Model Constants will be defined in LakeCon.
 
   !------------------------------------------------------------------
   ! Soil depths are constants for now; lake depths can vary by gridcell
@@ -223,59 +119,24 @@ module clm_varcon
   real(r8), allocatable :: zsoi(:)         !soil z  (layers)
   real(r8), allocatable :: dzsoi(:)        !soil dz (thickness)
   real(r8), allocatable :: zisoi(:)        !soil zi (interfaces)
-  real(r8), allocatable :: dzsoi_decomp(:) !soil dz (thickness)
-  integer , allocatable :: nlvic(:)        !number of CLM layers in each VIC layer (#)
-  real(r8), allocatable :: dzvic(:)        !soil dz (thickness) of each VIC layer
   real(r8) ,allocatable :: zsoifl(:)       !original soil midpoint (used in interpolation of sand and clay)
   real(r8) ,allocatable :: zisoifl(:)      !original soil interface depth (used in interpolation of sand and clay)
   real(r8) ,allocatable :: dzsoifl(:)      !original soil thickness  (used in interpolation of sand and clay)
 
-  !------------------------------------------------------------------
-  ! (Non-tunable) Constants for the CH4 submodel (Tuneable constants in ch4varcon)
-  !------------------------------------------------------------------
-  ! Note some of these constants are also used in CNNitrifDenitrifMod
-
-  real(r8), parameter :: catomw = 12.011_r8 ! molar mass of C atoms (g/mol)
-
-  real(r8) :: s_con(ngases,4)    ! Schmidt # calculation constants (spp, #)
-  data (s_con(1,i),i=1,4) /1898_r8, -110.1_r8, 2.834_r8, -0.02791_r8/ ! CH4
-  data (s_con(2,i),i=1,4) /1801_r8, -120.1_r8, 3.7818_r8, -0.047608_r8/ ! O2
-  data (s_con(3,i),i=1,4) /1911_r8, -113.7_r8, 2.967_r8, -0.02943_r8/ ! CO2
-
-  real(r8) :: d_con_w(ngases,3)    ! water diffusivity constants (spp, #)  (mult. by 10^-4)
-  data (d_con_w(1,i),i=1,3) /0.9798_r8, 0.02986_r8, 0.0004381_r8/ ! CH4
-  data (d_con_w(2,i),i=1,3) /1.172_r8, 0.03443_r8, 0.0005048_r8/ ! O2
-  data (d_con_w(3,i),i=1,3) /0.939_r8, 0.02671_r8, 0.0004095_r8/ ! CO2
-
-  real(r8) :: d_con_g(ngases,2)    ! gas diffusivity constants (spp, #) (cm^2/s) (mult. by 10^-9)
-  data (d_con_g(1,i),i=1,2) /0.1875_r8, 0.0013_r8/ ! CH4
-  data (d_con_g(2,i),i=1,2) /0.1759_r8, 0.00117_r8/ ! O2
-  data (d_con_g(3,i),i=1,2) /0.1325_r8, 0.0009_r8/ ! CO2
-
-  real(r8) :: c_h_inv(ngases)    ! constant (K) for Henry's law (4.12, Wania)
-  data c_h_inv(1:3) /1600._r8, 1500._r8, 2400._r8/ ! CH4, O2, CO2
-
-  real(r8) :: kh_theta(ngases)    ! Henry's constant (L.atm/mol) at standard temperature (298K)
-  data kh_theta(1:3) /714.29_r8, 769.23_r8, 29.4_r8/ ! CH4, O2, CO2
-
-  real(r8) :: kh_tbase = 298._r8 ! base temperature for calculation of Henry's constant (K)
-  !-----------------------------------------------------------------------
-
 contains
 
   !------------------------------------------------------------------------------
-  subroutine clm_varcon_init( is_simple_buildtemp )
+  subroutine clm_varcon_init()
     !
     ! !DESCRIPTION:
     ! This subroutine initializes constant arrays in clm_varcon. 
     ! MUST be called  after clm_varpar_init.
     !
     ! !USES:
-    use clm_varpar, only: nlevgrnd, nlevlak, nlevdecomp_full, nlevsoifl, nlayer
+    use clm_varpar, only: nlevgrnd, nlevlak, nlevsoifl
     !
     ! !ARGUMENTS:
     implicit none
-    logical, intent(in) :: is_simple_buildtemp   ! If simple building temp method is being used
     !
     ! !REVISION HISTORY:
     !   Created by E. Kluzek
@@ -286,19 +147,10 @@ subroutine clm_varcon_init( is_simple_buildtemp )
     allocate( zsoi(1:nlevgrnd                ))
     allocate( dzsoi(1:nlevgrnd               ))
     allocate( zisoi(0:nlevgrnd               ))
-    allocate( dzsoi_decomp(1:nlevdecomp_full ))
-    allocate( nlvic(1:nlayer                 ))
-    allocate( dzvic(1:nlayer                 ))
     allocate( zsoifl(1:nlevsoifl             ))
     allocate( zisoifl(0:nlevsoifl            ))
     allocate( dzsoifl(1:nlevsoifl            ))
 
-    ! Zero out wastheat factors for simpler building temperature method (introduced in CLM4.5)
-    if ( is_simple_buildtemp )then
-        ht_wasteheat_factor = 0.0_r8
-        ac_wasteheat_factor = 0.0_r8
-    end if
-
   end subroutine clm_varcon_init
 
 end module clm_varcon
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
index a60aa1f68a..b19b981337 100644
--- a/src/main/clm_varctl.F90
+++ b/src/main/clm_varctl.F90
@@ -11,8 +11,6 @@ module clm_varctl
   ! !PUBLIC MEMBER FUNCTIONS:
   implicit none
   public :: clm_varctl_set    ! Set variables
-  public :: cnallocate_carbon_only_set
-  public :: cnallocate_carbon_only
   !
   private
   save
@@ -88,28 +86,18 @@ module clm_varctl
   character(len=fname_len), public :: fsurdat    = ' '        ! surface data file name
   character(len=fname_len), public :: fatmgrid   = ' '        ! atm grid file name
   character(len=fname_len), public :: fatmlndfrc = ' '        ! lnd frac file on atm grid
-  character(len=fname_len), public :: paramfile  = ' '        ! ASCII data file with PFT physiological constants
   character(len=fname_len), public :: nrevsn     = ' '        ! restart data file name for branch run
-  character(len=fname_len), public :: fsnowoptics  = ' '      ! snow optical properties file name
-  character(len=fname_len), public :: fsnowaging   = ' '      ! snow aging parameters file name
 
   !----------------------------------------------------------
   ! MML input files
   !----------------------------------------------------------
   character(len=fname_len), public :: mml_surdat   = ' '      ! MML surface data file for simple model
   	
-  !----------------------------------------------------------
-  ! Flag to read ndep rather than obtain it from coupler
-  !----------------------------------------------------------
-  
-  logical, public :: ndep_from_cpl = .false.
 
   !----------------------------------------------------------
   ! Interpolation of finidat if requested
   !----------------------------------------------------------
 
-  logical, public :: bound_h2osoi = .true. ! for debugging 
-
   ! If finidat_interp_source is non-blank and finidat is blank then interpolation will be
   ! done from finidat_interp_source to finidat_interp_dest. Note that
   ! finidat_interp_source is not read in directly from the namelist - rather, it is set
@@ -118,26 +106,6 @@ module clm_varctl
   character(len=fname_len), public :: finidat_interp_source = ' '
   character(len=fname_len), public :: finidat_interp_dest   = 'finidat_interp_dest.nc'     
 
-  !----------------------------------------------------------
-  ! Crop & Irrigation logic
-  !----------------------------------------------------------
-
-  ! If prognostic crops are turned on
-  logical, public :: use_crop = .false.
-
-  ! true => separate crop landunit is not created by default
-  logical, public :: create_crop_landunit = .false.     
-  
-  ! do not irrigate by default
-  logical, public :: irrigate = .false.            
-
-  !----------------------------------------------------------
-  ! Other subgrid logic
-  !----------------------------------------------------------
-
-  ! true => make ALL patches, cols & landunits active (even if weight is 0)
-  logical, public :: all_active = .false.          
-
   !----------------------------------------------------------
   ! BGC logic and datasets
   !----------------------------------------------------------
@@ -145,130 +113,16 @@ module clm_varctl
   ! values of 'prognostic','diagnostic','constant'
   character(len=16), public :: co2_type = 'constant'    
 
-  ! State of the model for the accelerated decomposition (AD) spinup. 
-  ! 0 (default) = normal model; 1 = AD SPINUP
-  integer, public :: spinup_state = 0 
-
-  ! true => anoxia is applied to heterotrophic respiration also considered in CH4 model
-  ! default value reset in controlMod
-  logical, public :: anoxia  = .true. 
-
-  ! used to override an error check on reading in restart files
-  logical, public :: override_bgc_restart_mismatch_dump = .false. 
-
-  ! Set in CNAllocationInit (TODO - had to move it here to avoid circular dependency)
-  logical, private:: carbon_only      
-
-  ! Set in CNNDynamicsInit 
-  ! NOTE (mvertens, 2014-9 had to move it here to avoid confusion when carbon data types
-  ! wehre split - TODO - should move it our of this module) 
-  ! NOTE(bandre, 2013-10) according to Charlie Koven, nfix_timeconst
-  ! is currently used as a flag and rate constant. 
-  ! Rate constant: time over which to exponentially relax the npp flux for N fixation term
-  ! (days) time over which to exponentially relax the npp flux for N fixation term
-  ! flag: (if  <=  0. or  >=  365; use old annual method). 
-  ! Default value is junk that should always be overwritten by the namelist or init function!
-  !
-  real(r8), public :: nfix_timeconst = -1.2345_r8 
-
   !----------------------------------------------------------
   ! Physics
   !----------------------------------------------------------
 
-  ! use subgrid fluxes
-  integer,  public :: subgridflag = 1                   
-
   ! true => write global average diagnostics to std out
   logical,  public :: wrtdia       = .false.            
 
   ! atmospheric CO2 molar ratio (by volume) (umol/mol)
   real(r8), public :: co2_ppmv     = 355._r8            !
 
-  !----------------------------------------------------------
-  ! C isotopes
-  !----------------------------------------------------------
-
-  logical, public :: use_c13 = .false.                  ! true => use C-13 model
-  logical, public :: use_c14 = .false.                  ! true => use C-14 model
-
-  !----------------------------------------------------------
-  !  FATES switches
-  !----------------------------------------------------------
-
-  logical, public :: use_fates = .false.            ! true => use fates
-
-  ! These are INTERNAL to the FATES module
-  logical, public            :: use_fates_spitfire = .false.           ! true => use spitfire model
-  logical, public            :: use_fates_logging = .false.            ! true => turn on logging module
-  logical, public            :: use_fates_planthydro = .false.         ! true => turn on fates hydro
-  logical, public            :: use_fates_ed_st3   = .false.           ! true => static stand structure
-  logical, public            :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology
-  logical, public            :: use_fates_inventory_init = .false.     ! true => initialize fates from inventory
-  character(len=256), public :: fates_inventory_ctrl_filename = ''     ! filename for inventory control
-
-  !----------------------------------------------------------
-  !  LUNA switches		
-  !----------------------------------------------------------
-
-  logical, public :: use_luna = .false.            ! true => use  LUNA
-
-  !----------------------------------------------------------
-  !  flexibleCN
-  !----------------------------------------------------------
-  !  TODO(bja, 2015-08) some of these need to be moved into the
-  !  appropriate module.
-  logical, public :: use_flexibleCN = .false.
-  logical, public :: MM_Nuptake_opt = .false.
-  logical, public :: downreg_opt = .true.
-  integer, public :: plant_ndemand_opt = 0
-  logical, public :: substrate_term_opt = .true.
-  logical, public :: nscalar_opt = .true.
-  logical, public :: temp_scalar_opt = .true.
-  logical, public :: CNratio_floating = .false.
-  logical, public :: lnc_opt = .false.
-  logical, public :: reduce_dayl_factor = .false.
-  integer, public :: vcmax_opt = 0
-  integer, public :: CN_residual_opt = 0
-  integer, public :: CN_partition_opt = 0
-  integer, public :: CN_evergreen_phenology_opt = 0
-  integer, public :: carbon_resp_opt = 0
-
-  !----------------------------------------------------------
-  ! lai streams switch for Sat. Phenology
-  !----------------------------------------------------------
-
-  logical, public :: use_lai_streams = .false. ! true => use lai streams in SatellitePhenologyMod.F90
-
-  !----------------------------------------------------------
-  ! bedrock / soil depth switch
-  !----------------------------------------------------------
-
-  logical,           public :: use_bedrock = .false. ! true => use spatially variable soil depth
-  character(len=16), public :: soil_layerstruct = '10SL_3.5m'
-
-  !----------------------------------------------------------
-  ! plant hydraulic stress switch
-  !----------------------------------------------------------
-
-  logical, public :: use_hydrstress = .false. ! true => use plant hydraulic stress calculation
-
-  !----------------------------------------------------------
-  ! dynamic root switch
-  !----------------------------------------------------------
-
-  logical, public :: use_dynroot = .false. ! true => use dynamic root module
-
-  !----------------------------------------------------------
-  ! glacier_mec control variables: default values (may be overwritten by namelist)
-  !----------------------------------------------------------
-
-  ! true => CLM glacier area & topography changes dynamically 
-  logical , public :: glc_do_dynglacier = .false.           
-
-  ! number of days before one considers the perennially snow-covered point 'land ice'
-  integer , public :: glc_snow_persistence_max_days = 7300  
-
-  !
   !----------------------------------------------------------
   ! single column control variables
   !----------------------------------------------------------
@@ -302,37 +156,11 @@ module clm_varctl
   ! file name for local restart pointer file
   character(len=256), public :: rpntfil = 'rpointer.lnd' 
 
-  ! moved hist_wrtch4diag from histFileMod.F90 to here - caused compiler error with intel
-  ! namelist: write CH4 extra diagnostic output
-  logical, public :: hist_wrtch4diag = .false.         
-
-  !----------------------------------------------------------
-  ! FATES
-  !----------------------------------------------------------
-  character(len=fname_len), public :: fates_paramfile  = ' '
-
   !----------------------------------------------------------
   ! Migration of CPP variables
   !----------------------------------------------------------
-
-  logical, public :: use_lch4            = .false.
-  logical, public :: use_nitrif_denitrif = .false.
-  logical, public :: use_vertsoilc       = .false.
-  logical, public :: use_extralakelayers = .false.
-  logical, public :: use_vichydro        = .false.
-  logical, public :: use_century_decomp  = .false.
-  logical, public :: use_cn              = .false.
-  logical, public :: use_cndv            = .false.
-  logical, public :: use_grainproduct    = .false.
-  logical, public :: use_fertilizer      = .false.
-  logical, public :: use_ozone           = .false.
-  logical, public :: use_snicar_frc      = .false.
-  logical, public :: use_vancouver       = .false.
-  logical, public :: use_mexicocity      = .false.
   logical, public :: use_noio            = .false.
 
-  logical, public :: use_nguardrail      = .false.
-
   !----------------------------------------------------------
   ! To retrieve namelist
   !----------------------------------------------------------
@@ -382,15 +210,4 @@ subroutine clm_varctl_set( caseid_in, ctitle_in, brnch_retain_casename_in,    &
 
   end subroutine clm_varctl_set
 
-  ! Set module carbon_only flag
-  subroutine cnallocate_carbon_only_set(carbon_only_in)
-    logical, intent(in) :: carbon_only_in
-    carbon_only = carbon_only_in
-  end subroutine cnallocate_carbon_only_set
-
-  ! Get module carbon_only flag
-  logical function CNAllocate_Carbon_only()
-    cnallocate_carbon_only = carbon_only
-  end function CNAllocate_Carbon_only
-
 end module clm_varctl
diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90
index d2011dcae4..da5ca3c59a 100644
--- a/src/main/clm_varpar.F90
+++ b/src/main/clm_varpar.F90
@@ -7,66 +7,33 @@ module clm_varpar
   ! !USES:
   use shr_kind_mod , only: r8 => shr_kind_r8
   use spmdMod      , only: masterproc
-  use clm_varctl   , only: use_extralakelayers, use_vertsoilc
-  use clm_varctl   , only: use_century_decomp, use_c13, use_c14
-  use clm_varctl   , only: iulog, use_crop, create_crop_landunit, irrigate
-  use clm_varctl   , only: use_vichydro, soil_layerstruct
-  use clm_varctl   , only: use_fates
+  use clm_varctl   , only: iulog
 
-  !
   ! !PUBLIC TYPES:
   implicit none
   save
 
   ! Note - model resolution is read in from the surface dataset
 
-  integer, parameter :: nlev_equalspace   = 15
-  integer, parameter :: toplev_equalspace =  6
   integer            :: nlevsoi               ! number of hydrologically active soil layers
   integer            :: nlevsoifl             ! number of soil layers on input file
   integer            :: nlevgrnd              ! number of ground layers 
                                               ! (includes lower layers that are hydrologically inactive)
   integer            :: nlevurb               ! number of urban layers
   integer            :: nlevlak               ! number of lake layers
-  integer            :: nlevdecomp            ! number of biogeochemically active soil layers
-  integer            :: nlevdecomp_full       ! number of biogeochemical layers 
                                               ! (includes lower layers that are biogeochemically inactive)
   integer            :: nlevsno     =  -1     ! maximum number of snow layers
-  integer, parameter :: ngases      =   3     ! CH4, O2, & CO2
-  integer, parameter :: nlevcan     =   1     ! number of leaf layers in canopy layer
-  integer, parameter :: nvegwcs     =   4     ! number of vegetation water conductance segments
   !ED variables
-  integer, parameter :: numwat      =   5     ! number of water types (soil, ice, 2 lakes, wetland)
   integer, parameter :: numrad      =   2     ! number of solar radiation bands: vis, nir
-  integer, parameter :: ivis        =   1     ! index for visible band
-  integer, parameter :: inir        =   2     ! index for near-infrared band
-  integer, parameter :: numsolar    =   2     ! number of solar type bands: direct, diffuse
   integer, parameter :: ndst        =   4     ! number of dust size classes (BGC only)
-  integer, parameter :: dst_src_nbr =   3     ! number of size distns in src soil (BGC only)
-  integer, parameter :: sz_nbr      = 200     ! number of sub-grid bins in large bin of dust size distribution (BGC only)
   integer, parameter :: mxpft       =  78     ! maximum number of PFT's for any mode;
   ! FIX(RF,032414) might we set some of these automatically from reading pft-physiology?
   integer, parameter :: numveg      =  16     ! number of veg types (without specific crop)
-  integer, parameter :: nlayer      =   3     ! number of VIC soil layer --Added by AWang
-  integer            :: nlayert               ! number of VIC soil layer + 3 lower thermal layers
-  integer, parameter :: nvariants   =   2     ! number of variants of PFT constants
 
   integer :: numpft      = mxpft   ! actual # of pfts (without bare)
   integer :: numcft      =  64     ! actual # of crops (includes unused CFTs that are merged into other CFTs)
   integer :: maxpatch_urb= 5       ! max number of urban patches (columns) in urban landunit
 
-  integer :: maxpatch_pft        ! max number of plant functional types in naturally vegetated landunit (namelist setting)
-
-  ! constants for decomposition cascade
-
-  integer, parameter :: i_met_lit  = 1
-  integer, parameter :: i_cel_lit  = i_met_lit + 1
-  integer, parameter :: i_lig_lit  = i_cel_lit + 1
-  integer            :: i_cwd
-
-  integer :: ndecomp_pools
-  integer :: ndecomp_cascade_transitions
-
   ! Indices used in surface file read and set in clm_varpar_init
 
   integer :: natpft_lb          ! In PATCH arrays, lower bound of Patches on the natural veg landunit (i.e., bare ground index)
@@ -82,7 +49,6 @@ module clm_varpar
   integer :: cft_ub             ! In arrays of PFTs, upper bound of PFTs on the crop landunit
   integer :: cft_size           ! Number of PFTs on crop landunit in arrays of PFTs
 
-  integer :: maxpatch_glcmec    ! max number of elevation classes
   integer :: max_patch_per_col
   !
   ! !PUBLIC MEMBER FUNCTIONS:
@@ -108,108 +74,39 @@ subroutine clm_varpar_init()
 
     ! Crop settings and consistency checks
 
-    if (use_crop) then
-       numpft      = mxpft   ! actual # of patches (without bare)
-       numcft      =  64     ! actual # of crops
-    else
-       numpft      = numveg  ! actual # of patches (without bare)
-       numcft      =   2     ! actual # of crops
-    end if
+    numpft      = numveg  ! actual # of patches (without bare)
+    numcft      =   2     ! actual # of crops
 
     ! For arrays containing all Patches (natural veg & crop), determine lower and upper bounds
     ! for (1) Patches on the natural vegetation landunit (includes bare ground, and includes
     ! crops if create_crop_landunit=false), and (2) CFTs on the crop landunit (no elements
     ! if create_crop_landunit=false)
 
-    if (create_crop_landunit) then
-       natpft_size = (numpft + 1) - numcft    ! note that numpft doesn't include bare ground -- thus we add 1
-       cft_size    = numcft
-    else
-       natpft_size = numpft + 1               ! note that numpft doesn't include bare ground -- thus we add 1
-       cft_size    = 0
-    end if
+    natpft_size = (numpft + 1) - numcft    ! note that numpft doesn't include bare ground -- thus we add 1
+    cft_size    = numcft
 
     natpft_lb = 0
     natpft_ub = natpft_lb + natpft_size - 1
     cft_lb = natpft_ub + 1
     cft_ub = cft_lb + cft_size - 1
 
-    ! TODO(wjs, 2015-10-04, bugz 2227) Using numcft in this 'max' gives a significant
-    ! overestimate of max_patch_per_col when use_crop is true. This should be reworked -
-    ! or, better, removed from the code entirely (because it is a maintenance problem, and
-    ! I can't imagine that looping idioms that use it help performance that much, and
-    ! likely they hurt performance.)
     max_patch_per_col= max(numpft+1, numcft, maxpatch_urb)
 
     nlevsoifl   =  10
     nlevurb     =  5
-    if ( masterproc ) write(iulog, *) 'soil_layerstruct varpar ',soil_layerstruct
-    if ( soil_layerstruct == '10SL_3.5m' ) then
-       nlevsoi     =  nlevsoifl
-       nlevgrnd    =  15
-    else if ( soil_layerstruct == '23SL_3.5m' ) then 
-       nlevsoi     =  8  + nlev_equalspace
-       nlevgrnd    =  15 + nlev_equalspace
-    else if ( soil_layerstruct == '49SL_10m' ) then
-      nlevsoi     =  49 ! 10x10 + 9x100 + 30x300 = 1e4mm = 10m
-!       nlevsoi     =  29 ! 10x10 + 9x100 + 10x300 = 4e3mm = 4m
-       nlevgrnd    =  nlevsoi+5
-    else if ( soil_layerstruct == '20SL_8.5m' ) then
-      nlevsoi     =  20 
-      nlevgrnd    =  nlevsoi+5
-    endif
-    if ( masterproc ) write(iulog, *) 'soil_layerstruct varpar ',soil_layerstruct,nlevsoi,nlevgrnd
-
-    if (use_vichydro) then
-       nlayert     =  nlayer + (nlevgrnd -nlevsoi)
-    endif
-
-    ! here is a switch to set the number of soil levels for the biogeochemistry calculations.
-    ! currently it works on either a single level or on nlevsoi and nlevgrnd levels
-    if (use_vertsoilc) then
-       nlevdecomp      = nlevsoi
-       nlevdecomp_full = nlevgrnd
-    else
-       nlevdecomp      = 1
-       nlevdecomp_full = 1
-    end if
+    nlevsoi     =  nlevsoifl
+    nlevgrnd    =  15
 
-    if (.not. use_extralakelayers) then
-       nlevlak     =  10     ! number of lake layers
-    else
-       nlevlak     =  25     ! number of lake layers (Yields better results for site simulations)
-    end if
+    nlevlak     =  10     ! number of lake layers
 
     if ( masterproc )then
        write(iulog, *) 'CLM varpar subsurface discretization levels '
        write(iulog, '(a, i3)') '    nlevsoi = ', nlevsoi
        write(iulog, '(a, i3)') '    nlevgrnd = ', nlevgrnd
-       write(iulog, '(a, i3)') '    nlevdecomp = ', nlevdecomp
-       write(iulog, '(a, i3)') '    nlevdecomp_full = ', nlevdecomp_full
        write(iulog, '(a, i3)') '    nlevlak = ', nlevlak
        write(iulog, *)
     end if
 
-    if ( use_fates ) then
-       i_cwd = 0
-       if (use_century_decomp) then
-          ndecomp_pools = 6
-          ndecomp_cascade_transitions = 8
-       else
-          ndecomp_pools = 7
-          ndecomp_cascade_transitions = 7
-       end if
-    else
-       i_cwd = 4
-       if (use_century_decomp) then
-          ndecomp_pools = 7
-          ndecomp_cascade_transitions = 10
-       else
-          ndecomp_pools = 8
-          ndecomp_cascade_transitions = 9
-       end if
-    endif
-
   end subroutine clm_varpar_init
 
 end module clm_varpar
diff --git a/src/main/clm_varsur.F90 b/src/main/clm_varsur.F90
index a86fe08c64..41e2618576 100644
--- a/src/main/clm_varsur.F90
+++ b/src/main/clm_varsur.F90
@@ -29,11 +29,6 @@ module clm_instur
   ! (second dimension goes cft_lb:cft_ub)
   real(r8), pointer :: wt_cft(:,:)       
 
-  ! for each cft on the crop landunit prescribe annual fertilizer
-  ! landunit for all all grid cells, even  those without any crop)
-  ! (second dimension goes cft_lb:cft_ub)
-  real(r8), pointer :: fert_cft(:,:)       
-
   ! for glc_mec landunits, weight of glacier in each elevation class (adds to 1.0 on the
   ! landunit for all grid cells, even those without any glacier)
   real(r8), pointer :: wt_glc_mec(:,:)   
diff --git a/src/main/column_varcon.F90 b/src/main/column_varcon.F90
index 287df93b72..073e1bf79b 100644
--- a/src/main/column_varcon.F90
+++ b/src/main/column_varcon.F90
@@ -84,7 +84,6 @@ function icemec_class_to_col_itype(icemec_class) result(col_itype)
     ! Convert an icemec class (1..maxpatch_glcmec) into col%itype
     !
     ! !USES:
-    use clm_varpar, only : maxpatch_glcmec
     use landunit_varcon, only : istice_mec
     !
     ! !ARGUMENTS:
@@ -96,8 +95,6 @@ function icemec_class_to_col_itype(icemec_class) result(col_itype)
     character(len=*), parameter :: subname = 'icemec_class_to_col_itype'
     !-----------------------------------------------------------------------
     
-    SHR_ASSERT((1 <= icemec_class .and. icemec_class <= maxpatch_glcmec), errMsg(sourcefile, __LINE__))
-
     col_itype = istice_mec*100 + icemec_class
 
   end function icemec_class_to_col_itype
@@ -109,7 +106,6 @@ function col_itype_to_icemec_class(col_itype) result(icemec_class)
     ! Convert a col%itype value (for an icemec landunit) into an icemec class (1..maxpatch_glcmec)
     !
     ! !USES:
-    use clm_varpar, only : maxpatch_glcmec
     use landunit_varcon, only : istice_mec
     !
     ! !ARGUMENTS:
@@ -123,10 +119,6 @@ function col_itype_to_icemec_class(col_itype) result(icemec_class)
     
     icemec_class = col_itype - istice_mec*100
 
-    ! The following assertion is here to ensure that col_itype is really from an
-    ! istice_mec landunit
-    SHR_ASSERT((1 <= icemec_class .and. icemec_class <= maxpatch_glcmec), errMsg(sourcefile, __LINE__))
-
   end function col_itype_to_icemec_class
 
   !-----------------------------------------------------------------------
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index aef6715a1e..6eba5e4090 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -17,28 +17,20 @@ module controlMod
   use abortutils                       , only: endrun
   use spmdMod                          , only: masterproc
   use decompMod                        , only: clump_pproc
-  use clm_varcon                       , only: h2osno_max, int_snow_max, n_melt_glcmec
-  use clm_varpar                       , only: maxpatch_pft, maxpatch_glcmec, numrad, nlevsno
+  use clm_varpar                       , only: numrad, nlevsno
   use histFileMod                      , only: max_tapes, max_namlen 
   use histFileMod                      , only: hist_empty_htapes, hist_dov2xy, hist_avgflag_pertape, hist_type1d_pertape 
   use histFileMod                      , only: hist_nhtfrq, hist_ndens, hist_mfilt, hist_fincl1, hist_fincl2, hist_fincl3
   use histFileMod                      , only: hist_fincl4, hist_fincl5, hist_fincl6, hist_fexcl1, hist_fexcl2, hist_fexcl3
   use histFileMod                      , only: hist_fexcl4, hist_fexcl5, hist_fexcl6
   use initInterpMod                    , only: initInterp_readnl
-  use UrbanParamsType                  , only: UrbanReadNML
-  use SurfaceAlbedoMod                 , only: albice
-  use CNSharedParamsMod                , only: use_fun
   use clm_varctl                       , only: iundef, rundef, nsrest, caseid, ctitle, nsrStartup, nsrContinue
   use clm_varctl                       , only: nsrBranch, brnch_retain_casename, hostname, username, source, version, conventions
-  use clm_varctl                       , only: iulog, outnc_large_files, finidat, fsurdat, fatmgrid, fatmlndfrc, paramfile, nrevsn
-  use clm_varctl                       , only: mml_surdat, finidat_interp_source, finidat_interp_dest, all_active, co2_type
-  use clm_varctl                       , only: wrtdia, co2_ppmv, use_bedrock, soil_layerstruct, nsegspc, rpntdir, rpntfil
-  use clm_varctl                       , only: use_cn, use_noio, NLFilename_in, use_century_decomp
-  use clm_varctl                       , only: use_nitrif_denitrif, create_crop_landunit, glc_snow_persistence_max_days
-  use clm_varctl                       , only: subgridflag, use_nguardrail, nfix_timeconst, use_vertsoilc
+  use clm_varctl                       , only: iulog, outnc_large_files, finidat, fsurdat, fatmgrid, fatmlndfrc, nrevsn
+  use clm_varctl                       , only: mml_surdat, finidat_interp_source, finidat_interp_dest, co2_type
+  use clm_varctl                       , only: wrtdia, co2_ppmv, nsegspc, rpntdir, rpntfil
+  use clm_varctl                       , only: use_noio, NLFilename_in
   use clm_varctl                       , only: clm_varctl_set
-  use clm_varctl                       , only: use_lch4, irrigate, create_crop_landunit, use_crop, use_dynroot
-  use clm_varctl                       , only: use_fates, use_flexiblecn, use_hydrstress, use_luna, spinup_state
   use clm_varctl                       , only: single_column
   !
   ! !PUBLIC TYPES:
@@ -134,9 +126,7 @@ subroutine control_init( )
 
     ! Input datasets
 
-    namelist /clm_inparm/  &
-         fsurdat, &
-         paramfile
+    namelist /clm_inparm/ fsurdat
 
 	! MML Input datasets for simple model
     namelist /clm_inparm/ &
@@ -162,55 +152,20 @@ subroutine control_init( )
     namelist /clm_inparm / &
          co2_type
 
-    namelist /clm_inparm / use_fun
-
     ! Glacier_mec info
-    namelist /clm_inparm/ &    
-         maxpatch_glcmec, &
-         glc_snow_persistence_max_days, &
-         nlevsno, h2osno_max, int_snow_max, n_melt_glcmec
+    namelist /clm_inparm/ nlevsno
 
     ! Other options
 
     namelist /clm_inparm/  &
          clump_pproc, wrtdia, &
-         create_crop_landunit, nsegspc, co2_ppmv, override_nsrest, &
-         albice, soil_layerstruct, subgridflag, &
-         all_active
-
-    namelist /clm_inparm/ use_bedrock
+         nsegspc, co2_ppmv, override_nsrest
 
     ! All old cpp-ifdefs are below and have been converted to namelist variables 
-
-    ! max number of plant functional types in naturally vegetated landunit
-    namelist /clm_inparm/ maxpatch_pft
-
-    namelist /clm_inparm/ &
-         use_vertsoilc, &
-         use_century_decomp, use_cn, use_noio, &
-         use_nguardrail, use_nitrif_denitrif
+    namelist /clm_inparm/ use_noio
 
     ! Items not really needed, but do need to be properly set as they are used
-    namelist / clm_inparm/ &
-               use_lch4,   &
-               irrigate,   &
-               create_crop_landunit,   &
-               use_crop,   &
-               use_dynroot,   &
-               use_fates,   &
-               use_flexiblecn,   &
-               use_hydrstress,   &
-               use_luna,   &
-               spinup_state, &
-               single_column
-
-    logical :: use_fertilizer = .false.
-    logical :: use_grainproduct = .false.
-    logical :: use_lai_streams = .false.
-    character(len=256) :: fsnowaging, fsnowoptics
-    namelist /clm_inparm/ use_fertilizer, use_grainproduct, use_lai_streams, &
-            fsnowaging, fsnowoptics
-
+    namelist / clm_inparm/ single_column
 
     ! ----------------------------------------------------------------------
     ! Default values
@@ -271,15 +226,6 @@ subroutine control_init( )
        call set_timemgr_init( dtime_in=dtime )
 
        ! Check for namelist variables that SLIM can NOT use
-       if ( use_fates )then
-          call endrun(msg='ERROR SLIM can NOT run with use_fates on'//errMsg(sourcefile, __LINE__))
-       end if
-       if ( use_lai_streams )then
-          call endrun(msg='ERROR SLIM can NOT run with use_lai_streams on'//errMsg(sourcefile, __LINE__))
-       end if
-       if ( use_dynroot )then
-          call endrun(msg='ERROR SLIM can NOT run with use_dynroot on'//errMsg(sourcefile, __LINE__))
-       end if
        if ( single_column )then
           call endrun(msg='ERROR SLIM can NOT run with single_column on'//errMsg(sourcefile, __LINE__))
        end if
@@ -309,24 +255,7 @@ subroutine control_init( )
            call clm_varctl_set( nsrest_in=override_nsrest )
        end if
 
-       if (maxpatch_glcmec <= 0) then
-          call endrun(msg=' ERROR: maxpatch_glcmec must be at least 1 ' // &
-               errMsg(sourcefile, __LINE__))
-       end if
-
-       ! If nfix_timeconst is equal to the junk default value, then it was not specified
-       ! by the user namelist and we need to assign it the correct default value. If the 
-       ! user specified it in the namelist, we leave it alone.
-
-       if (nfix_timeconst == -1.2345_r8) then
-          if (use_nitrif_denitrif) then
-             nfix_timeconst = 10._r8
-          else
-             nfix_timeconst = 0._r8
-          end if
-       end if
-
-       ! If nlevsno, h2osno_max, int_snow_max or n_melt_glcmec are equal to their junk
+       ! If nlevsno are equal to their junk
        ! default value, then they were not specified by the user namelist and we generate
        ! an error message. Also check nlevsno for bounds.
        if (nlevsno < 3 .or. nlevsno > 12)  then
@@ -334,22 +263,6 @@ subroutine control_init( )
           call endrun(msg=' ERROR: invalid value for nlevsno in CLM namelist. '//&
                errMsg(sourcefile, __LINE__))
        endif
-       if (h2osno_max <= 0.0_r8) then
-          write(iulog,*)'ERROR: h2osno_max = ',h2osno_max,' is not supported, must be greater than 0.0.'
-          call endrun(msg=' ERROR: invalid value for h2osno_max in CLM namelist. '//&
-               errMsg(sourcefile, __LINE__))
-       endif
-       if (int_snow_max <= 0.0_r8) then
-          write(iulog,*)'ERROR: int_snow_max = ',int_snow_max,' is not supported, must be greater than 0.0.'
-          call endrun(msg=' ERROR: invalid value for int_snow_max in CLM namelist. '//&
-               errMsg(sourcefile, __LINE__))
-       endif
-       if (n_melt_glcmec <= 0.0_r8) then
-          write(iulog,*)'ERROR: n_melt_glcmec = ',n_melt_glcmec,' is not supported, must be greater than 0.0.'
-          call endrun(msg=' ERROR: invalid value for n_melt_glcmec in CLM namelist. '//&
-               errMsg(sourcefile, __LINE__))
-       endif
-
     endif   ! end of if-masterproc if-block
 
     ! ----------------------------------------------------------------------
@@ -357,7 +270,6 @@ subroutine control_init( )
     ! ----------------------------------------------------------------------
 
     call initInterp_readnl( NLFilename )
-    call UrbanReadNML           ( NLFilename )
 
     ! ----------------------------------------------------------------------
     ! Broadcast all control information if appropriate
@@ -435,13 +347,6 @@ subroutine control_spmd()
     call mpi_bcast (username, len(username), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (nsrest, 1, MPI_INTEGER, 0, mpicom, ier)
 
-    call mpi_bcast (use_lch4, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_nitrif_denitrif, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_vertsoilc, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_century_decomp, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_cn, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_nguardrail, 1, MPI_LOGICAL, 0, mpicom, ier)
-    call mpi_bcast (use_crop, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_noio, 1, MPI_LOGICAL, 0, mpicom, ier)
 
     ! initial file variables
@@ -451,64 +356,20 @@ subroutine control_spmd()
     call mpi_bcast (finidat_interp_dest, len(finidat_interp_dest), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fsurdat, len(fsurdat), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fatmlndfrc,len(fatmlndfrc),MPI_CHARACTER, 0, mpicom, ier)
-    call mpi_bcast (paramfile, len(paramfile) , MPI_CHARACTER, 0, mpicom, ier)
 
 	! mml input file vars for simple model
 	call mpi_bcast (mml_surdat,  len(mml_surdat),   MPI_CHARACTER, 0, mpicom, ier)
 	
-    ! Irrigation
-    call mpi_bcast(irrigate, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    ! Landunit generation
-    call mpi_bcast(create_crop_landunit, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    ! Other subgrid logic
-    call mpi_bcast(all_active, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    ! max number of plant functional types in naturally vegetated landunit
-    call mpi_bcast(maxpatch_pft, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    ! BGC
     call mpi_bcast (co2_type, len(co2_type), MPI_CHARACTER, 0, mpicom, ier)
-    if (use_cn) then
-       call mpi_bcast (nfix_timeconst, 1, MPI_REAL8, 0, mpicom, ier)
-       call mpi_bcast (spinup_state, 1, MPI_INTEGER, 0, mpicom, ier)
-    end if
-
-    call mpi_bcast (use_fates, 1, MPI_LOGICAL, 0, mpicom, ier)
-    ! flexibleCN nitrogen model
-    call mpi_bcast (use_flexibleCN, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    call mpi_bcast (use_luna, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    call mpi_bcast (use_bedrock, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier)
-
-    if (use_cn) then
-       call mpi_bcast (use_fun,            1, MPI_LOGICAL, 0, mpicom, ier)
-    end if
 
     ! physics variables
     call mpi_bcast (nsegspc, 1, MPI_INTEGER, 0, mpicom, ier)
-    call mpi_bcast (subgridflag , 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (wrtdia, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (single_column,1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (co2_ppmv, 1, MPI_REAL8,0, mpicom, ier)
-    call mpi_bcast (albice, 2, MPI_REAL8,0, mpicom, ier)
-    call mpi_bcast (soil_layerstruct,len(soil_layerstruct), MPI_CHARACTER, 0, mpicom, ier)
 
     ! snow pack variables
     call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier)
-    call mpi_bcast (h2osno_max, 1, MPI_REAL8, 0, mpicom, ier)
-    call mpi_bcast (int_snow_max, 1, MPI_REAL8, 0, mpicom, ier)
-    call mpi_bcast (n_melt_glcmec, 1, MPI_REAL8, 0, mpicom, ier)
-
-    ! glacier_mec variables
-    call mpi_bcast (maxpatch_glcmec, 1, MPI_INTEGER, 0, mpicom, ier)
-    call mpi_bcast (glc_snow_persistence_max_days, 1, MPI_INTEGER, 0, mpicom, ier)
 
     ! history file variables
     call mpi_bcast (hist_empty_htapes, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -563,14 +424,9 @@ subroutine control_print ()
     write(iulog,*) '   username              = ',trim(username)
     write(iulog,*) '   hostname              = ',trim(hostname)
     write(iulog,*) 'process control parameters:'
-    write(iulog,*) '    use_nitrif_denitrif = ', use_nitrif_denitrif
-    write(iulog,*) '    use_vertsoilc = ', use_vertsoilc
-    write(iulog,*) '    use_century_decomp = ', use_century_decomp
-    write(iulog,*) '    use_cn = ', use_cn
     write(iulog,*) '    use_noio = ', use_noio
 
     write(iulog,*) 'input data files:'
-    write(iulog,*) '   PFT physiology and parameters file = ',trim(paramfile)
     if (fsurdat == ' ') then
        write(iulog,*) '   fsurdat, surface dataset not set'
     else
@@ -586,23 +442,7 @@ subroutine control_print ()
     else
        write(iulog,*) '   mml_surdat IS set, and = ',trim(mml_surdat)
     end if
-    if (use_cn) then
-       if (nfix_timeconst /= 0._r8) then
-          write(iulog,*) '   nfix_timeconst, timescale for smoothing npp in N fixation term: ', nfix_timeconst
-       else
-          write(iulog,*) '   nfix_timeconst == zero, use standard N fixation scheme. '
-       end if
-       
-    end if
-
     write(iulog,*) '   Number of snow layers =', nlevsno
-    write(iulog,*) '   Max snow depth (mm) =', h2osno_max
-    write(iulog,*) '   Limit applied to integrated snowfall when determining changes in'
-    write(iulog,*) '       snow-covered fraction during melt (mm) =', int_snow_max
-    write(iulog,*) '   SCA shape parameter for glc_mec columns (n_melt_glcmec) =', n_melt_glcmec
-
-    write(iulog,*) '   glc number of elevation classes =', maxpatch_glcmec
-    write(iulog,*) '   glc snow persistence max days = ', glc_snow_persistence_max_days
 
     if (nsrest == nsrStartup) then
        if (finidat /= ' ') then
@@ -628,8 +468,6 @@ subroutine control_print ()
        write(iulog,*) '   CO2 volume mixing ratio                = ', co2_type
     end if
 
-    write(iulog,*) '   land-ice albedos      (unitless 0-1)   = ', albice
-    write(iulog,*) '   soil layer structure = ', soil_layerstruct
     if (nsrest == nsrContinue) then
        write(iulog,*) 'restart warning:'
        write(iulog,*) '   Namelist not checked for agreement with initial run.'
@@ -640,7 +478,6 @@ subroutine control_print ()
        write(iulog,*) '   Namelist not checked for agreement with initial run.'
        write(iulog,*) '   Surface data set and reference date should not differ from initial run'
     end if
-    write(iulog,*) '   maxpatch_pft         = ',maxpatch_pft
     write(iulog,*) '   nsegspc              = ',nsegspc
 
   end subroutine control_print
diff --git a/src/main/decompMod.F90 b/src/main/decompMod.F90
index 13204fabca..90b4028fe0 100644
--- a/src/main/decompMod.F90
+++ b/src/main/decompMod.F90
@@ -10,7 +10,7 @@ module decompMod
   ! Must use shr_sys_abort rather than endrun here to avoid circular dependency
   use shr_sys_mod , only : shr_sys_abort 
   use clm_varctl  , only : iulog
-  use clm_varcon  , only : grlnd, nameg, namel, namec, namep, nameCohort
+  use clm_varcon  , only : grlnd, nameg, namel, namec, namep
   use mct_mod     , only : mct_gsMap
   !
   ! !PUBLIC TYPES:
@@ -231,10 +231,6 @@ subroutine get_clump_bounds_new (n, bounds)
      !------------------------------------------------------------------------------
      !    Make sure this IS being called from a threaded region
 #ifdef _OPENMP
-     ! FIX(SPM, 090314) - for debugging fates and openMP
-     !write(iulog,*) 'SPM omp debug decompMod 1 ', &
-          !OMP_GET_NUM_THREADS(),OMP_GET_MAX_THREADS(),OMP_GET_THREAD_NUM()
-
      if ( OMP_GET_NUM_THREADS() == 1 .and. OMP_GET_MAX_THREADS() > 1 )then
         call shr_sys_abort( trim(subname)//' ERROR: Calling from inside a non-threaded region)')
      end if
@@ -301,10 +297,6 @@ subroutine get_proc_bounds_new (bounds)
      !------------------------------------------------------------------------------
      !    Make sure this is NOT being called from a threaded region
 #ifdef _OPENMP
-     ! FIX(SPM, 090314) - for debugging fates and openMP
-     !write(*,*) 'SPM omp debug decompMod 2 ', &
-          !OMP_GET_NUM_THREADS(),OMP_GET_MAX_THREADS(),OMP_GET_THREAD_NUM()
-
      if ( OMP_GET_NUM_THREADS() > 1 )then
         call shr_sys_abort( trim(subname)//' ERROR: Calling from inside  a threaded region')
      end if
@@ -440,8 +432,6 @@ integer function get_clmlevel_gsize (clmlevel)
         get_clmlevel_gsize = numc
      case(namep)
         get_clmlevel_gsize = nump
-     case(nameCohort)
-        get_clmlevel_gsize = numCohort
      case default
         write(iulog,*) 'get_clmlevel_gsize does not match clmlevel type: ', trim(clmlevel)
         call shr_sys_abort()
@@ -471,8 +461,6 @@ subroutine get_clmlevel_gsmap (clmlevel, gsmap)
        gsmap => gsmap_col_gdc2glo
     case(namep)
        gsmap => gsmap_patch_gdc2glo
-    case(nameCohort)
-       gsmap => gsMap_cohort_gdc2glo
     case default
        write(iulog,*) 'get_clmlevel_gsmap: Invalid expansion character: ',trim(clmlevel)
        call shr_sys_abort()
diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90
index 1201582af7..4e58bb707c 100644
--- a/src/main/filterMod.F90
+++ b/src/main/filterMod.F90
@@ -18,7 +18,6 @@ module filterMod
   use LandunitType   , only : lun                
   use ColumnType     , only : col                
   use PatchType      , only : patch
-  use glcBehaviorMod , only : glc_behavior_type
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -90,9 +89,6 @@ module filterMod
      integer, pointer :: icemecc(:)      ! glacier mec filter (cols)
      integer :: num_icemecc              ! number of columns in glacier mec filter
      
-     integer, pointer :: do_smb_c(:)     ! glacier+bareland SMB calculations-on filter (cols)
-     integer :: num_do_smb_c             ! number of columns in glacier+bareland SMB mec filter         
-
   end type clumpfilter
   public clumpfilter
 
@@ -228,7 +224,6 @@ subroutine allocFiltersOneGroup(this_filter)
        allocate(this_filter(nc)%soilnopcropp(bounds%endp-bounds%begp+1))
 
        allocate(this_filter(nc)%icemecc(bounds%endc-bounds%begc+1))      
-       allocate(this_filter(nc)%do_smb_c(bounds%endc-bounds%begc+1))       
        
     end do
 !$OMP END PARALLEL DO
@@ -236,7 +231,7 @@ subroutine allocFiltersOneGroup(this_filter)
   end subroutine allocFiltersOneGroup
 
   !------------------------------------------------------------------------
-  subroutine setFilters(bounds, glc_behavior)
+  subroutine setFilters(bounds)
     !
     ! !DESCRIPTION:
     ! Set CLM filters.
@@ -244,14 +239,11 @@ subroutine setFilters(bounds, glc_behavior)
     !
     ! !ARGUMENTS:
     type(bounds_type)       , intent(in) :: bounds
-    type(glc_behavior_type) , intent(in) :: glc_behavior
     !------------------------------------------------------------------------
 
     SHR_ASSERT(bounds%level == BOUNDS_LEVEL_CLUMP, errMsg(sourcefile, __LINE__))
 
-    call setFiltersOneGroup(bounds, &
-         filter, include_inactive = .false., &
-         glc_behavior = glc_behavior)
+    call setFiltersOneGroup(bounds, filter, include_inactive = .false.)
 
     ! At least as of June, 2013, the 'inactive_and_active' version of the filters is
     ! static in time. Thus, we could have some logic saying whether we're in
@@ -265,14 +257,13 @@ subroutine setFilters(bounds, glc_behavior)
     ! call.
     
     call setFiltersOneGroup(bounds, &
-         filter_inactive_and_active, include_inactive = .true., &
-         glc_behavior = glc_behavior)
+         filter_inactive_and_active, include_inactive = .true.)
     
   end subroutine setFilters
 
 
   !------------------------------------------------------------------------
-  subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavior)
+  subroutine setFiltersOneGroup(bounds, this_filter, include_inactive)
     !
     ! !DESCRIPTION:
     ! Set CLM filters for one group of filters.
@@ -288,14 +279,12 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio
     !
     ! !USES:
     use decompMod       , only : BOUNDS_LEVEL_CLUMP
-    use pftconMod       , only : npcropmin
     use landunit_varcon , only : istsoil, istcrop, istice_mec
     !
     ! !ARGUMENTS:
     type(bounds_type)       , intent(in)    :: bounds  
     type(clumpfilter)       , intent(inout) :: this_filter(:)   ! the group of filters to set
     logical                 , intent(in)    :: include_inactive ! whether inactive points should be included in the filters
-    type(glc_behavior_type) , intent(in)    :: glc_behavior
     !
     ! LOCAL VARAIBLES:
     integer :: nc          ! clump index
@@ -413,15 +402,10 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio
     fnl = 0
     do p = bounds%begp,bounds%endp
        if (patch%active(p) .or. include_inactive) then
-          if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types
-             fl = fl + 1
-             this_filter(nc)%pcropp(fl) = p
-          else
-             l =patch%landunit(p)
-             if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-                fnl = fnl + 1
-                this_filter(nc)%soilnopcropp(fnl) = p
-             end if
+          l =patch%landunit(p)
+          if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
+             fnl = fnl + 1
+             this_filter(nc)%soilnopcropp(fnl) = p
           end if
        end if
     end do
@@ -496,28 +480,6 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio
     end do
     this_filter(nc)%num_icemecc = f
 
-    f = 0
-    do c = bounds%begc,bounds%endc
-       if (col%active(c) .or. include_inactive) then
-          l = col%landunit(c)
-          g = col%gridcell(c)
-
-          ! Only compute SMB in regions where we replace ice melt with new ice:
-          ! Elsewhere (where ice melt remains in place), we cannot compute a sensible
-          ! negative SMB.
-          !
-          ! In addition to istice_mec columns, we also compute SMB for any soil column in
-          ! this region, in order to provide SMB forcing for the bare ground elevation
-          ! class (elevation class 0).
-          if ( glc_behavior%melt_replaced_by_ice_grc(g) .and. &
-               (lun%itype(l) == istice_mec .or. lun%itype(l) == istsoil)) then
-             f = f + 1
-             this_filter(nc)%do_smb_c(f) = c
-          end if
-       end if
-    end do
-    this_filter(nc)%num_do_smb_c = f    
-
     ! Note: snow filters are reconstructed each time step in
     ! LakeHydrology and SnowHydrology
     ! Note: CNDV "pft present" filter is reconstructed each time CNDV is run
diff --git a/src/main/glc2lndMod.F90 b/src/main/glc2lndMod.F90
deleted file mode 100644
index d27d2e53af..0000000000
--- a/src/main/glc2lndMod.F90
+++ /dev/null
@@ -1,579 +0,0 @@
-module glc2lndMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Handle arrays used for exchanging data from glc to clm.
-  !
-  ! !USES:
-#include "shr_assert.h"
-  use decompMod      , only : bounds_type
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar     , only : maxpatch_glcmec
-  use clm_varctl     , only : iulog, glc_do_dynglacier
-  use clm_varcon     , only : nameg, spval, ispval
-  use abortutils     , only : endrun
-  use GridcellType   , only : grc 
-  use LandunitType   , only : lun
-  use ColumnType     , only : col
-  use landunit_varcon, only : istice_mec
-  use glcBehaviorMod , only : glc_behavior_type
-  !
-  ! !REVISION HISTORY:
-  ! Created by William Lipscomb, Dec. 2007, based on clm_atmlnd.F90.
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  ! glc -> land variables structure
-  type, public :: glc2lnd_type
-
-     ! ------------------------------------------------------------------------
-     ! Public data
-     ! ------------------------------------------------------------------------
-
-     ! Where we should do runoff routing that is appropriate for having a dynamic icesheet underneath.
-     real(r8), pointer :: glc_dyn_runoff_routing_grc (:) => null()
-
-     ! ------------------------------------------------------------------------
-     ! Private data
-     ! ------------------------------------------------------------------------
-
-     type(glc_behavior_type), pointer, private :: glc_behavior  ! reference to the glc_behavior instance
-
-     real(r8), pointer, private :: frac_grc    (:,:) => null()
-     real(r8), pointer, private :: topo_grc    (:,:) => null()
-     real(r8), pointer, private :: hflx_grc    (:,:) => null()
-
-     ! Area in which GLC model can accept surface mass balance, received from glc (0-1)
-     real(r8), pointer, private :: icemask_grc (:)   => null()
-
-     ! icemask_coupled_fluxes_grc is like icemask_grc, but the mask only contains icesheet
-     ! points that potentially send non-zero fluxes to the coupler. i.e., it does not
-     ! contain icesheets that are diagnostic only, because for those diagnostic ice sheets
-     ! (which do not send calving fluxes to the coupler), we need to use the non-dynamic
-     ! form of runoff routing in CLM in order to conserve water properly.
-     !
-     ! (However, note that this measure of "diagnostic-only" does not necessarily
-     ! correspond to whether CLM is updating its glacier areas there - for example, we
-     ! could theoretically have an icesheet whose areas are evolving, and CLM is updating
-     ! its glacier areas to match, but where we're zeroing out the fluxes sent to the
-     ! coupler, and so we're using the non-dynamic form of runoff routing in CLM.)
-     real(r8), pointer, private :: icemask_coupled_fluxes_grc (:)  => null()
-
-   contains
-
-     ! ------------------------------------------------------------------------
-     ! Public routines
-     ! ------------------------------------------------------------------------
-
-     procedure, public  :: Init
-     procedure, public  :: Clean
-
-     ! In each timestep, these routines should be called in order (though they don't need
-     ! to be called all at once):
-     ! - set_glc2lnd_fields
-     ! - update_glc2lnd_topo
-     procedure, public  :: set_glc2lnd_fields       ! set coupling fields sent from glc to lnd
-     procedure, public  :: update_glc2lnd_topo      ! update topographic heights
-
-     ! For unit testing only:
-     procedure, public  :: for_test_set_glc2lnd_fields_directly  ! set glc2lnd fields directly in a unit testing context
-
-     ! ------------------------------------------------------------------------
-     ! Private routines
-     ! ------------------------------------------------------------------------
-
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-     procedure, private :: InitCold
-
-     ! sanity-check icemask from GLC
-     procedure, private :: check_glc2lnd_icemask
-
-     ! sanity-check icemask_coupled_fluxes from GLC
-     procedure, private :: check_glc2lnd_icemask_coupled_fluxes
-
-     ! update glc_dyn_runoff_routing field based on input from GLC
-     procedure, private :: update_glc2lnd_dyn_runoff_routing
-
-  end type glc2lnd_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, glc_behavior)
-
-    class(glc2lnd_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    type(glc_behavior_type), intent(in), target :: glc_behavior
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    call this%InitCold(bounds, glc_behavior)
-    
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize glc variables required by the land
-    !
-    ! !ARGUMENTS:
-    class (glc2lnd_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begg,endg
-    !------------------------------------------------------------------------
-
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%frac_grc    (begg:endg,0:maxpatch_glcmec)) ;   this%frac_grc    (:,:) = nan
-    allocate(this%topo_grc    (begg:endg,0:maxpatch_glcmec)) ;   this%topo_grc    (:,:) = nan
-    allocate(this%hflx_grc    (begg:endg,0:maxpatch_glcmec)) ;   this%hflx_grc    (:,:) = nan
-    allocate(this%icemask_grc (begg:endg))                   ;   this%icemask_grc (:)   = nan
-    allocate(this%icemask_coupled_fluxes_grc (begg:endg))    ;   this%icemask_coupled_fluxes_grc (:)   = nan
-    allocate(this%glc_dyn_runoff_routing_grc (begg:endg))    ;   this%glc_dyn_runoff_routing_grc (:)   = nan
-
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: begg, endg
-    
-    character(len=*), parameter :: subname = 'InitHistory'
-    !-----------------------------------------------------------------------
-
-    begg = bounds%begg
-    endg = bounds%endg
-
-    this%icemask_grc(begg:endg) = spval
-    call hist_addfld1d (fname='ICE_MODEL_FRACTION',  units='unitless',  &
-         avgflag='I', long_name='Ice sheet model fractional coverage', &
-         ptr_gcell=this%icemask_grc, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, glc_behavior)
-    !
-    ! !USES:
-    use domainMod      , only : ldomain
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type) :: this
-    type(bounds_type), intent(in) :: bounds
-    type(glc_behavior_type), intent(in), target :: glc_behavior
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begg, endg
-
-    character(len=*), parameter :: subname = 'InitCold'
-    !-----------------------------------------------------------------------
-
-    begg = bounds%begg
-    endg = bounds%endg
-
-    this%glc_behavior => glc_behavior
-
-    this%frac_grc(begg:endg, :) = 0.0_r8
-    this%topo_grc(begg:endg, :) = 0.0_r8
-    this%hflx_grc(begg:endg, :) = 0.0_r8
-
-    ! When running with a stub glc model, it's important that icemask_grc be initialized
-    ! to 0 everywhere. With an active glc model, icemask_grc will be updated in the first
-    ! time step, and it isn't needed before then, so it's safe to initialize it to 0.
-    ! Since icemask is 0, icemask_coupled_fluxes needs to be 0, too (and the latter is
-    ! safest in case we aren't coupled to CISM, to ensure that we use the uncoupled form
-    ! of runoff routing).
-    this%icemask_grc(begg:endg) = 0.0_r8
-    this%icemask_coupled_fluxes_grc(begg:endg) = 0.0_r8
-    
-    call this%update_glc2lnd_dyn_runoff_routing(bounds)
-
-  end subroutine InitCold
-
-
-  !-----------------------------------------------------------------------
-  subroutine Clean(this)
-    !
-    ! !DESCRIPTION:
-    ! Deallocate memory in this object
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(inout) :: this
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'Clean'
-    !-----------------------------------------------------------------------
-
-    deallocate(this%frac_grc)
-    deallocate(this%topo_grc)
-    deallocate(this%hflx_grc)
-    deallocate(this%icemask_grc)
-    deallocate(this%icemask_coupled_fluxes_grc)
-    deallocate(this%glc_dyn_runoff_routing_grc)
-
-  end subroutine Clean
-
-  !-----------------------------------------------------------------------
-  subroutine set_glc2lnd_fields(this, bounds, glc_present, x2l, &
-       index_x2l_Sg_ice_covered, index_x2l_Sg_topo, index_x2l_Flgg_hflx, &
-       index_x2l_Sg_icemask, index_x2l_Sg_icemask_coupled_fluxes)
-    !
-    ! !DESCRIPTION:
-    ! Set coupling fields sent from glc to lnd
-    !
-    ! If glc_present is true, then the given fields are all assumed to be valid; if
-    ! glc_present is false, then these fields are ignored.
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(inout) :: this
-    type(bounds_type)  , intent(in)    :: bounds
-    logical  , intent(in) :: glc_present                         ! true if running with a non-stub glc model
-    real(r8) , intent(in) :: x2l(:, bounds%begg: )               ! driver import state to land model [field, gridcell]
-    integer  , intent(in) :: index_x2l_Sg_ice_covered( 0: )      ! indices of ice-covered field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Sg_topo( 0: )             ! indices of topo field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Flgg_hflx( 0: )           ! indices of heat flux field in x2l, for each elevation class
-    integer  , intent(in) :: index_x2l_Sg_icemask                ! index of icemask field in x2l
-    integer  , intent(in) :: index_x2l_Sg_icemask_coupled_fluxes ! index of icemask_coupled_fluxes field in x2l
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g
-    integer :: icemec_class
-
-    character(len=*), parameter :: subname = 'set_glc2lnd_fields'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT((ubound(x2l, 2) == bounds%endg), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(index_x2l_Sg_ice_covered) == (/maxpatch_glcmec/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(index_x2l_Sg_topo) == (/maxpatch_glcmec/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(index_x2l_Flgg_hflx) == (/maxpatch_glcmec/)), errMsg(sourcefile, __LINE__))
-
-    if (glc_present) then
-       call endrun(' ERROR: SLIM can NOT run with an active ice sheet model' )
-    end if
-    if (glc_do_dynglacier) then
-       call endrun(' ERROR: With glc_present false (e.g., a stub glc model), glc_do_dynglacier must be false '// &
-            errMsg(sourcefile, __LINE__))
-    end if
-
-  end subroutine set_glc2lnd_fields
-
-  !-----------------------------------------------------------------------
-  subroutine for_test_set_glc2lnd_fields_directly(this, bounds, &
-       topo, icemask)
-    !
-    ! !DESCRIPTION:
-    ! Set glc2lnd fields directly in a unit testing context
-    !
-    ! This currently only provides a mechanism to set fields that are actually needed in
-    ! our unit tests. More could be added later.
-    !
-    ! Also: In contrast to the production version (set_glc2lnd_fields), this does NOT
-    ! currently update glc2lnd_dyn_runoff_routing (because doing so would require having a
-    ! sensible glc_behavior, which we may not have; and also, we currently don't need this
-    ! field in a unit testing context). (Note: If we eventually want/need to update
-    ! glc2lnd_dyn_runoff_routing, and thus need a fully sensible glc_behavior, then we
-    ! should extract the self-calls at the end of set_glc2lnd_fields
-    ! (check_glc2lnd_icemask, check_glc2lnd_icemask_coupled_fluxes,
-    ! update_glc2lnd_dyn_runoff_routing) into a private routine like
-    ! set_glc2lnd_fields_wrapup, which could be called by both set_glc2lnd_fields and this
-    ! routine.)
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(inout) :: this
-    type(bounds_type)  , intent(in)    :: bounds
-    real(r8), intent(in), optional :: topo( bounds%begg: , 0: )  ! topographic height [gridcell, elevclass]
-    real(r8), intent(in), optional :: icemask( bounds%begg: )
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'for_test_set_glc2lnd_fields_directly'
-    !-----------------------------------------------------------------------
-
-    if (present(topo)) then
-       SHR_ASSERT_ALL((ubound(topo) == (/bounds%endg, maxpatch_glcmec/)), errMsg(sourcefile, __LINE__))
-       this%topo_grc(bounds%begg:bounds%endg, 0:maxpatch_glcmec) = topo(bounds%begg:bounds%endg, 0:maxpatch_glcmec)
-    end if
-
-    if (present(icemask)) then
-       SHR_ASSERT_ALL((ubound(icemask) == (/bounds%endg/)), errMsg(sourcefile, __LINE__))
-       this%icemask_grc(bounds%begg:bounds%endg) = icemask(bounds%begg:bounds%endg)
-    end if
-
-  end subroutine for_test_set_glc2lnd_fields_directly
-
-  !-----------------------------------------------------------------------
-  subroutine check_glc2lnd_icemask(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Do a sanity check on the icemask received from CISM via coupler.
-    !
-    ! !USES:
-    use domainMod , only : ldomain
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(in) :: this
-    type(bounds_type)       , intent(in) :: bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g  ! grid cell index
-    
-    character(len=*), parameter :: subname = 'check_glc2lnd_icemask'
-    !-----------------------------------------------------------------------
-    
-    do g = bounds%begg, bounds%endg
-
-       if (this%icemask_grc(g) > 0._r8) then
-
-          ! Ensure that icemask is a subset of has_virtual_columns. This is needed because
-          ! we allocated memory based on has_virtual_columns, so it is a problem if the
-          ! ice sheet tries to expand beyond the area defined by has_virtual_columns.
-          if (.not. this%glc_behavior%has_virtual_columns_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask must be a subset of has_virtual_columns.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "virtual" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "virtual" in glacier_region_behavior.)'
-             call endrun(decomp_index=g, clmlevel=nameg, msg=errMsg(sourcefile, __LINE__))
-          end if
-
-          ! Ensure that icemask is a subset of melt_replaced_by_ice. This is needed
-          ! because we only compute SMB in the region given by melt_replaced_by_ice
-          ! (according to the logic for building the do_smb filter), and we need SMB
-          ! everywhere inside the icemask.
-          if (.not. this%glc_behavior%melt_replaced_by_ice_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask must be a subset of melt_replaced_by_ice.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_melt_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "replaced_by_ice" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "replaced_by_ice" in glacier_region_melt_behavior.)'
-             call endrun(decomp_index=g, clmlevel=nameg, msg=errMsg(sourcefile, __LINE__))
-          end if
-
-       end if
-    end do
-
-  end subroutine check_glc2lnd_icemask
-
-  !-----------------------------------------------------------------------
-  subroutine check_glc2lnd_icemask_coupled_fluxes(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Do a sanity check on the icemask_coupled_fluxes field received from CISM via coupler.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(in) :: this
-    type(bounds_type)  , intent(in) :: bounds ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g  ! grid cell index
-    
-    character(len=*), parameter :: subname = 'check_glc2lnd_icemask_coupled_fluxes'
-    !-----------------------------------------------------------------------
-
-    do g = bounds%begg, bounds%endg
-
-       ! Ensure that icemask_coupled_fluxes is a subset of icemask. Although there
-       ! currently is no code in CLM that depends on this relationship, it seems helpful
-       ! to ensure that this intuitive relationship holds, so that code developed in the
-       ! future can rely on it.
-       if (this%icemask_coupled_fluxes_grc(g) > 0._r8 .and. this%icemask_grc(g) == 0._r8) then
-          write(iulog,*) subname//' ERROR: icemask_coupled_fluxes must be a subset of icemask.'
-          call endrun(decomp_index=g, clmlevel=nameg, msg=errMsg(sourcefile, __LINE__))
-       end if
-
-    end do
-
-  end subroutine check_glc2lnd_icemask_coupled_fluxes
-
-  !-----------------------------------------------------------------------
-  subroutine update_glc2lnd_dyn_runoff_routing(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Update glc_dyn_runoff_routing field based on updated icemask_coupled_fluxes field
-    !
-    ! !USES:
-    use domainMod , only : ldomain
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type), intent(inout) :: this
-    type(bounds_type)  , intent(in) :: bounds ! bounds
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g  ! grid cell index
-    
-    character(len=*), parameter :: subname = 'update_glc2lnd_dyn_runoff_routing'
-    !-----------------------------------------------------------------------
-
-    ! Wherever we have an icesheet that is computing and sending fluxes to the coupler -
-    ! which particularly means it is computing a calving flux - we will use the
-    ! "glc_dyn_runoff_routing" scheme, with 0 < glc_dyn_runoff_routing <= 1. 
-    ! In these places, all or part of the snowcap flux goes to CISM rather than the runoff model.
-    ! In other places - including places where CISM is not running at all, as well as places 
-    ! where CISM is running in diagnostic-only mode and therefore is not sending a calving flux - 
-    ! we have glc_dyn_runoff_routing = 0, and the snowcap flux goes to the runoff model.
-    ! This is needed to conserve water correctly in the absence of a calving flux.
-
-    do g = bounds%begg, bounds%endg
-
-       ! Set glc_dyn_runoff_routing_grc(g) to a value in the range [0,1].
-       !
-       ! This value gives the grid cell fraction that is deemed to be coupled to the
-       ! dynamic ice sheet model. For this fraction of the grid cell, snowcap fluxes are
-       ! sent to the ice sheet model. The remainder of the grid cell sends snowcap fluxes
-       ! to the runoff model.
-       !
-       ! Note: The coupler (in prep_glc_mod.F90) assumes that the fraction coupled to the
-       !       dynamic ice sheet model is min(lfrac, Sg_icemask_l), where lfrac is the
-       !       "frac" component of fraction_lx, and Sg_icemask_l is obtained by mapping
-       !       Sg_icemask_g from the glc to the land grid. Here, ldomain%frac is
-       !       equivalent to lfrac, and this%icemask_grc is equivalent to Sg_icemask_l.
-       !       However, here we use icemask_coupled_fluxes_grc, so that we route all snow
-       !       capping to runoff in areas where the ice sheet is not generating calving
-       !       fluxes. In addition, here we need to divide by lfrac, because the coupler
-       !       multiplies by it later (and, for example, if lfrac = 0.1 and
-       !       icemask_coupled_fluxes = 1, we want all snow capping to go to the ice
-       !       sheet model, not to the runoff model).
-       !
-       ! Note: In regions where CLM overlaps the CISM domain, this%icemask_grc(g) typically
-       !       is nearly equal to ldomain%frac(g). So an alternative would be to simply set
-       !       glc_dyn_runoff_routing_grc(g) = icemask_grc(g).
-       !       The reason to cap glc_dyn_runoff_routing at lfrac is to avoid sending the
-       !       ice sheet model a greater mass of water (in the form of snowcap fluxes) 
-       !       than is allowed to fall on a CLM grid cell that is part ocean.
-
-       ! TODO(wjs, 2017-05-08) Ideally, we wouldn't have this duplication in logic
-       ! between the coupler and CLM. The best solution would be to have the coupler
-       ! itself do the partitioning of the snow capping flux between the ice sheet model
-       ! and the runoff model. A next-best solution would be to have the coupler send a
-       ! field to CLM telling it what fraction of snow capping should go to the runoff
-       ! model in each grid cell.
-
-       if (ldomain%frac(g) == 0._r8) then
-          ! Avoid divide by 0; note that, in this case, the amount going to runoff isn't
-          ! important for system-wide conservation, so we could really choose anything we
-          ! want.
-          this%glc_dyn_runoff_routing_grc(g) = this%icemask_coupled_fluxes_grc(g)
-       else
-          this%glc_dyn_runoff_routing_grc(g) = &
-               min(ldomain%frac(g), this%icemask_coupled_fluxes_grc(g)) / &
-               ldomain%frac(g)
-       end if
-
-       if (this%glc_dyn_runoff_routing_grc(g) > 0.0_r8) then
-
-          ! Ensure that glc_dyn_runoff_routing is a subset of melt_replaced_by_ice. This
-          ! is needed because glacial melt is only sent to the runoff stream in the region
-          ! given by melt_replaced_by_ice (because the latter is used to create the do_smb
-          ! filter, and the do_smb filter controls where glacial melt is computed).
-          if (.not. this%glc_behavior%melt_replaced_by_ice_grc(g)) then
-             write(iulog,'(a)') subname//' ERROR: icemask_coupled_fluxes must be a subset of melt_replaced_by_ice.'
-             write(iulog,'(a)') 'Ensure that the glacier_region_melt_behavior namelist item is set correctly.'
-             write(iulog,'(a)') '(It should specify "replaced_by_ice" for the region corresponding to the GLC domain.)'
-             write(iulog,'(a)') 'If glacier_region_behavior is set correctly, then you can fix this problem'
-             write(iulog,'(a)') 'by modifying GLACIER_REGION on the surface dataset.'
-             write(iulog,'(a)') '(Expand the region that corresponds to the GLC domain'
-             write(iulog,'(a)') '- i.e., the region specified as "replaced_by_ice" in glacier_region_melt_behavior.)'
-             call endrun(decomp_index=g, clmlevel=nameg, msg=errMsg(sourcefile, __LINE__))
-          end if
-       end if
-    end do
-
-  end subroutine update_glc2lnd_dyn_runoff_routing
-
-
-
-  !-----------------------------------------------------------------------
-  subroutine update_glc2lnd_topo(this, bounds, topo_col, needs_downscaling_col)
-    !
-    ! !DESCRIPTION:
-    ! Update column-level topographic heights based on input from GLC (via the coupler).
-    !
-    ! Also updates the logical array, needs_downscaling_col: Sets this array to true
-    ! anywhere where topo_col is updated, because these points will need downscaling.
-    ! (Leaves other array elements in needs_downscaling_col untouched.)
-    !
-    ! If glc_do_dynglacier is false, then both topographic heights and
-    ! needs_downscaling_col are left unchanged.
-    !
-    ! !USES:
-    use landunit_varcon , only : istice_mec
-    use column_varcon   , only : col_itype_to_icemec_class
-    !
-    ! !ARGUMENTS:
-    class(glc2lnd_type) , intent(in)    :: this
-    type(bounds_type)   , intent(in)    :: bounds                   ! bounds
-    real(r8)            , intent(inout) :: topo_col( bounds%begc: ) ! topographic height (m)
-    logical             , intent(inout) :: needs_downscaling_col( bounds%begc: )
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c, l, g      ! indices
-    integer :: icemec_class ! current icemec class (1..maxpatch_glcmec)
-
-    character(len=*), parameter :: subname = 'update_glc2lnd_topo'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(topo_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(needs_downscaling_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-    if (glc_do_dynglacier) then
-       do c = bounds%begc, bounds%endc
-          l = col%landunit(c)
-          g = col%gridcell(c)
-
-          ! Values from GLC are only valid within the icemask, so we only update CLM's topo values there
-          if (this%icemask_grc(g) > 0._r8) then
-             if (lun%itype(l) == istice_mec) then
-                icemec_class = col_itype_to_icemec_class(col%itype(c))
-             else
-                ! If not on a glaciated column, assign topography to the bare-land value determined by GLC.
-                icemec_class = 0
-             end if
-
-             ! Note that we do downscaling over all column types. This is for consistency:
-             ! interpretation of results would be difficult if some non-glacier column types
-             ! were downscaled but others were not.
-             !
-             ! BUG(wjs, 2016-11-15, bugz 2377) Actually, do not downscale over urban points:
-             ! this currently isn't allowed because the urban code references some
-             ! non-downscaled, gridcell-level atmospheric forcings
-             if (.not. lun%urbpoi(l)) then
-                topo_col(c) = this%topo_grc(g, icemec_class)
-                needs_downscaling_col(c) = .true.
-             end if
-          end if
-       end do
-    end if
-
-  end subroutine update_glc2lnd_topo
-
-end module glc2lndMod
-
diff --git a/src/main/glcBehaviorMod.F90 b/src/main/glcBehaviorMod.F90
index 2fa47857ea..a1f15f8c36 100644
--- a/src/main/glcBehaviorMod.F90
+++ b/src/main/glcBehaviorMod.F90
@@ -25,63 +25,12 @@ module glcBehaviorMod
   type, public :: glc_behavior_type
      private
 
-     ! ------------------------------------------------------------------------
-     ! Public data
-     ! ------------------------------------------------------------------------
-
-     ! If has_virtual_columns_grc(g) is true, then grid cell g has virtual columns for
-     ! all possible glc_mec columns.
-     !
-     ! For the sake of coupling with CISM, this should only be needed within the icemask,
-     ! where we need virtual columns for the sake of coupling with CISM. This is needed in
-     ! order to (1) provide SMB in all elevation classes, in case it is being used with
-     ! 1-way coupling (or to force a later TG run); (2) even with two-way coupling,
-     ! provide SMB in the elevation classes above and below existing elevation classes,
-     ! for the sake of vertical interpolation; (3) provide place-holder columns (which are
-     ! already spun-up) for dynamic landunits; (4) ensure that all glacier columns are
-     ! given spun-up initial conditions by init_interp.
-     !
-     ! More details on (4) (echoing the similar comment in subgridWeightsMod): We need all
-     ! glacier and vegetated points to be active in the icemask region for the sake of
-     ! init_interp - since we only interpolate onto active points, and we don't know which
-     ! points will have non-zero area until after initialization (as long as we can't send
-     ! information from glc to clm in initialization). (If we had an inactive glacier
-     ! point in the icemask region, according to the weights on the surface dataset, and
-     ! ran init_interp, this point would keep its cold start initialization values. Then,
-     ! in the first time step of the run loop, it's possible that this point would become
-     ! active because, according to glc, there is actually > 0% glacier in that grid
-     ! cell. We don't do any state / flux adjustments in the first time step after
-     ! init_interp due to glacier area changes, so this glacier column would remain at its
-     ! cold start initialization values, which would be a Bad Thing. Ensuring that all
-     ! glacier points within the icemask are active gets around this problem - as well as
-     ! having other benefits, as noted above.)
-     !
-     ! However, by making this part of the user-modifiable "glc behavior", we make it easy
-     ! for the user to add virtual columns, if this is desired for diagnostic
-     ! purposes. One important reason why this may be desired is to produce coupler
-     ! history forcings to force a later TG run, with SMB forcings outside the original
-     ! CISM area. (Also, we cannot use icemask for all purposes, because it isn't known at
-     ! initialization.)
-     logical, allocatable, public :: has_virtual_columns_grc(:)
-
      ! If allow_multiple_columns_grc(g) is true, then grid cell g may have multiple
      ! glacier columns, for the different elevation classes. If
      ! allow_multiple_columns_grc(g) is false, then grid cell g is guaranteed to have at
      ! most one glacier column.
      logical, allocatable, public :: allow_multiple_columns_grc(:)
 
-     ! If melt_replaced_by_ice_grc(g) is true, then any glacier ice melt in gridcell g
-     ! runs off and is replaced by ice. Note that SMB cannot be computed in gridcell g if
-     ! melt_replaced_by_ice_grc(g) is false, since we can't compute a sensible negative
-     ! smb in that case.
-     logical, allocatable, public :: melt_replaced_by_ice_grc(:)
-
-     ! If ice_runoff_melted_grc(g) is true, then ice runoff generated by the
-     ! CLM physics over glacier columns in gridcell g is melted (generating a negative
-     ! sensible heat flux) and runs off as liquid. If it is false, then ice runoff is
-     ! sent to the river model as ice (a crude parameterization of iceberg calving).
-     logical, allocatable, public :: ice_runoff_melted_grc(:)
-
      ! ------------------------------------------------------------------------
      ! Private data
      ! ------------------------------------------------------------------------
@@ -154,8 +103,7 @@ module glcBehaviorMod
 
   ! !PRIVATE MEMBER DATA:
 
-  ! Longest name allowed for glacier_region_behavior, glacier_region_melt_behavior and
-  ! glacier_region_ice_runoff_behavior
+  ! Longest name allowed for glacier_region_behavior
   integer, parameter :: max_behavior_name_len = 32
 
   ! Smallest and largest allowed values for a glacier region ID
@@ -190,27 +138,22 @@ subroutine Init(this, begg, endg, NLFilename)
     ! !LOCAL VARIABLES:
     integer, allocatable :: glacier_region_map(:)
     character(len=max_behavior_name_len) :: glacier_region_behavior(min_glacier_region_id:max_glacier_region_id)
-    character(len=max_behavior_name_len) :: glacier_region_melt_behavior(min_glacier_region_id:max_glacier_region_id)
-    character(len=max_behavior_name_len) :: glacier_region_ice_runoff_behavior(min_glacier_region_id:max_glacier_region_id)
 
     character(len=*), parameter :: subname = 'Init'
     !-----------------------------------------------------------------------
 
     allocate(glacier_region_map(begg:endg))
     call this%read_surface_dataset(begg, endg, glacier_region_map(begg:endg))
-    call this%read_namelist(NLFilename, glacier_region_behavior, &
-         glacier_region_melt_behavior, glacier_region_ice_runoff_behavior)
+    call this%read_namelist(NLFilename, glacier_region_behavior)
 
     call this%InitFromInputs(begg, endg, &
-         glacier_region_map(begg:endg), glacier_region_behavior, &
-         glacier_region_melt_behavior, glacier_region_ice_runoff_behavior)
+         glacier_region_map(begg:endg), glacier_region_behavior)
 
   end subroutine Init
 
   !-----------------------------------------------------------------------
   subroutine InitFromInputs(this, begg, endg, &
-       glacier_region_map, glacier_region_behavior_str, glacier_region_melt_behavior_str, &
-       glacier_region_ice_runoff_behavior_str)
+       glacier_region_map, glacier_region_behavior_str)
     !
     ! !DESCRIPTION:
     ! Initialize a glc_behavior_type object given a map of glacier region IDs and an
@@ -233,26 +176,11 @@ subroutine InitFromInputs(this, begg, endg, &
     ! allowed values are:
     ! - 'multiple': grid cells can potentially have multiple glacier elevation classes,
     !   but no virtual columns
-    ! - 'virtual': grid cells have virtual columns: values are computed for every glacier
-    !   elevation class, even those with 0 area
     ! - 'single_at_atm_topo': glacier landunits in these grid cells have a single column,
     !   whose elevation matches the atmosphere's topographic height (so that there is no
     !   adjustment due to downscaling)
     character(len=*), intent(in) :: glacier_region_behavior_str(min_glacier_region_id:)
 
-    ! string giving treatment of ice melt for each glacier region ID
-    ! allowed values are:
-    ! - 'replaced_by_ice'
-    ! - 'remains_in_place'
-    character(len=*), intent(in) :: glacier_region_melt_behavior_str(min_glacier_region_id:)
-
-    ! string giving treatment of ice runoff for each glacier region ID
-    ! allowed values are:
-    ! - 'remains_ice'
-    ! - 'melted'
-    character(len=*), intent(in) :: glacier_region_ice_runoff_behavior_str(min_glacier_region_id:)
-
-    !
     ! !LOCAL VARIABLES:
     ! whether each glacier region ID is present in the glacier_region_map
     logical :: glacier_region_present(min_glacier_region_id:max_glacier_region_id)
@@ -260,33 +188,15 @@ subroutine InitFromInputs(this, begg, endg, &
     ! integer codes corresponding to glacier_region_behavior_str
     integer :: glacier_region_behavior(min_glacier_region_id:max_glacier_region_id)
 
-    ! integer codes corresponding to glacier_region_melt_behavior_str
-    integer :: glacier_region_melt_behavior(min_glacier_region_id:max_glacier_region_id)
-
-    ! integer codes corresponding to glacier_region_ice_runoff_behavior_str
-    integer :: glacier_region_ice_runoff_behavior(min_glacier_region_id:max_glacier_region_id)
-
     integer :: g
     integer :: my_id
     integer :: my_behavior
-    integer :: my_melt_behavior
-    integer :: my_ice_runoff_behavior
 
     ! possible glacier_region_behavior codes
     integer, parameter :: BEHAVIOR_MULTIPLE = 1
-    integer, parameter :: BEHAVIOR_VIRTUAL = 2
     integer, parameter :: BEHAVIOR_SINGLE_AT_ATM_TOPO = 3
 
-    ! possible glacier_region_melt_behavior codes
-    integer, parameter :: MELT_BEHAVIOR_REPLACED_BY_ICE = 1
-    integer, parameter :: MELT_BEHAVIOR_REMAINS_IN_PLACE = 2
-
-    ! possible glacier_region_ice_runoff_behavior codes
-    integer, parameter :: ICE_RUNOFF_BEHAVIOR_REMAINS_ICE = 1
-    integer, parameter :: ICE_RUNOFF_BEHAVIOR_MELTED = 2
-
-    ! value indicating that a behavior code has not been set (for glacier_region_behavior,
-    ! glacier_region_melt_behavior or glacier_region_ice_runoff_behavior)
+    ! value indicating that a behavior code has not been set (for glacier_region_behavior)
     integer, parameter :: BEHAVIOR_UNSET = -1
 
     character(len=*), parameter :: subname = 'InitFromInputs'
@@ -299,39 +209,12 @@ subroutine InitFromInputs(this, begg, endg, &
     call determine_region_presence
 
     call translate_glacier_region_behavior
-    call translate_glacier_region_melt_behavior
-    call translate_glacier_region_ice_runoff_behavior
 
     call this%InitAllocate(begg, endg)
 
     do g = begg, endg
        my_id = glacier_region_map(g)
        my_behavior = glacier_region_behavior(my_id)
-       my_melt_behavior = glacier_region_melt_behavior(my_id)
-       my_ice_runoff_behavior = glacier_region_ice_runoff_behavior(my_id)
-
-       ! This should only happen due to a programming error, not due to a user input error
-       SHR_ASSERT(my_behavior /= BEHAVIOR_UNSET, errMsg(sourcefile, __LINE__))
-       SHR_ASSERT(my_melt_behavior /= BEHAVIOR_UNSET, errMsg(sourcefile, __LINE__))
-       SHR_ASSERT(my_ice_runoff_behavior /= BEHAVIOR_UNSET, errMsg(sourcefile, __LINE__))
-
-       if (my_behavior == BEHAVIOR_VIRTUAL) then
-          this%has_virtual_columns_grc(g) = .true.
-       else
-          this%has_virtual_columns_grc(g) = .false.
-       end if
-
-       if (my_melt_behavior == MELT_BEHAVIOR_REMAINS_IN_PLACE) then
-          this%melt_replaced_by_ice_grc(g) = .false.
-       else
-          this%melt_replaced_by_ice_grc(g) = .true.
-       end if
-
-       if (my_ice_runoff_behavior == ICE_RUNOFF_BEHAVIOR_MELTED) then
-          this%ice_runoff_melted_grc(g) = .true.
-       else
-          this%ice_runoff_melted_grc(g) = .false.
-       end if
 
        ! For now, allow_multiple_columns_grc is simply the opposite of
        ! collapse_to_atm_topo_grc. However, we maintain the separate
@@ -390,8 +273,6 @@ subroutine translate_glacier_region_behavior
             select case (glacier_region_behavior_str(i))
             case ('multiple')
                glacier_region_behavior(i) = BEHAVIOR_MULTIPLE
-            case ('virtual')
-               glacier_region_behavior(i) = BEHAVIOR_VIRTUAL
             case ('single_at_atm_topo')
                glacier_region_behavior(i) = BEHAVIOR_SINGLE_AT_ATM_TOPO
             case (behavior_str_unset)
@@ -400,87 +281,19 @@ subroutine translate_glacier_region_behavior
                call endrun(msg=' ERROR: glacier_region_behavior not specified for ID '// &
                     errMsg(sourcefile, __LINE__))
             case default
-               write(iulog,*) ' ERROR: Unknown glacier_region_behavior for ID ', i
-               write(iulog,*) glacier_region_behavior_str(i)
-               write(iulog,*) 'Allowable values are: multiple, virtual, single_at_atm_topo'
-               call endrun(msg=' ERROR: Unknown glacier_region_behavior'// &
-                    errMsg(sourcefile, __LINE__))
             end select
 
          end if
       end do
     end subroutine translate_glacier_region_behavior
 
-    subroutine translate_glacier_region_melt_behavior
-      integer :: i
-
-      do i = min_glacier_region_id, max_glacier_region_id
-         glacier_region_melt_behavior(i) = BEHAVIOR_UNSET
-
-         if (glacier_region_present(i)) then
-            SHR_ASSERT_ALL((ubound(glacier_region_melt_behavior_str) >= (/i/)), errMsg(sourcefile, __LINE__))
-
-            select case (glacier_region_melt_behavior_str(i))
-            case ('replaced_by_ice')
-               glacier_region_melt_behavior(i) = MELT_BEHAVIOR_REPLACED_BY_ICE
-            case ('remains_in_place')
-               glacier_region_melt_behavior(i) = MELT_BEHAVIOR_REMAINS_IN_PLACE
-            case (behavior_str_unset)
-               write(iulog,*) ' ERROR: glacier_region_melt_behavior not specified for ID ', i
-               write(iulog,*) 'You probably need to extend the glacier_region_melt_behavior namelist array'
-               call endrun(msg=' ERROR: glacier_region_melt_behavior not specified for ID '// &
-                    errMsg(sourcefile, __LINE__))
-            case default
-               write(iulog,*) ' ERROR: Unknown glacier_region_melt_behavior for ID ', i
-               write(iulog,*) glacier_region_melt_behavior_str(i)
-               write(iulog,*) 'Allowable values are: replaced_by_ice, remains_in_place'
-               call endrun(msg=' ERROR: Unknown glacier_region_melt_behavior'// &
-                    errMsg(sourcefile, __LINE__))
-            end select
-
-         end if
-      end do
-    end subroutine translate_glacier_region_melt_behavior
-
-    subroutine translate_glacier_region_ice_runoff_behavior
-      integer :: i
-
-      do i = min_glacier_region_id, max_glacier_region_id
-         glacier_region_ice_runoff_behavior(i) = BEHAVIOR_UNSET
-
-         if (glacier_region_present(i)) then
-            SHR_ASSERT_ALL((ubound(glacier_region_ice_runoff_behavior_str) >= (/i/)), errMsg(sourcefile, __LINE__))
-
-            select case (glacier_region_ice_runoff_behavior_str(i))
-            case ('remains_ice')
-               glacier_region_ice_runoff_behavior(i) = ICE_RUNOFF_BEHAVIOR_REMAINS_ICE
-            case('melted')
-               glacier_region_ice_runoff_behavior(i) = ICE_RUNOFF_BEHAVIOR_MELTED
-            case (behavior_str_unset)
-               write(iulog,*) ' ERROR: glacier_region_ice_runoff_behavior not specified for ID ', i
-               write(iulog,*) 'You probably need to extend the glacier_region_ice_runoff_behavior namelist array'
-               call endrun(msg=' ERROR: glacier_region_ice_runoff_behavior not specified for ID '// &
-                    errMsg(sourcefile, __LINE__))
-            case default
-               write(iulog,*) ' ERROR: Unknown glacier_region_ice_runoff_behavior for ID ', i
-               write(iulog,*) glacier_region_ice_runoff_behavior_str(i)
-               write(iulog,*) 'Allowable values are: remains_ice, melted'
-               call endrun(msg=' ERROR: Unknown glacier_region_ice_runoff_behavior'// &
-                    errMsg(sourcefile, __LINE__))
-            end select
-         end if
-      end do
-    end subroutine translate_glacier_region_ice_runoff_behavior
-
   end subroutine InitFromInputs
 
-
   !-----------------------------------------------------------------------
-  subroutine InitSetDirectly(this, begg, endg, &
-       has_virtual_columns, collapse_to_atm_topo)
+  subroutine InitSetDirectly(this, begg, endg, collapse_to_atm_topo)
     !
     ! !DESCRIPTION:
-    ! Initialize a glc_behavior_type object by directly setting has_virtual_columns and
+    ! Initialize a glc_behavior_type object by directly setting
     ! collapse_to_atm_topo
     !
     ! This version is meant for testing
@@ -491,19 +304,16 @@ subroutine InitSetDirectly(this, begg, endg, &
     class(glc_behavior_type), intent(inout) :: this
     integer, intent(in) :: begg  ! beginning gridcell index
     integer, intent(in) :: endg  ! ending gridcell index
-    logical, intent(in) :: has_virtual_columns(begg:)
     logical, intent(in) :: collapse_to_atm_topo(begg:)
     !
     ! !LOCAL VARIABLES:
 
-    character(len=*), parameter :: subname = 'InitForTesting'
+    character(len=*), parameter :: subname = 'InitSetDirectly'
     !-----------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(has_virtual_columns) == (/endg/)), errMsg(sourcefile, __LINE__))
     SHR_ASSERT_ALL((ubound(collapse_to_atm_topo) == (/endg/)), errMsg(sourcefile, __LINE__))
 
     call this%InitAllocate(begg, endg)
-    this%has_virtual_columns_grc(:) = has_virtual_columns(:)
     this%collapse_to_atm_topo_grc(:) = collapse_to_atm_topo(:)
 
   end subroutine InitSetDirectly
@@ -525,11 +335,8 @@ subroutine InitAllocate(this, begg, endg)
     character(len=*), parameter :: subname = 'InitAllocate'
     !-----------------------------------------------------------------------
 
-    allocate(this%has_virtual_columns_grc (begg:endg)); this%has_virtual_columns_grc (:) = .false.
     allocate(this%allow_multiple_columns_grc(begg:endg)); this%allow_multiple_columns_grc(:) = .false.
-    allocate(this%melt_replaced_by_ice_grc(begg:endg)); this%melt_replaced_by_ice_grc(:) = .false.
     allocate(this%collapse_to_atm_topo_grc(begg:endg)); this%collapse_to_atm_topo_grc(:) = .false.
-    allocate(this%ice_runoff_melted_grc(begg:endg)); this%ice_runoff_melted_grc(:) = .false.
 
   end subroutine InitAllocate
 
@@ -580,8 +387,7 @@ subroutine read_surface_dataset(begg, endg, glacier_region_map)
   end subroutine read_surface_dataset
 
   !-----------------------------------------------------------------------
-  subroutine read_namelist(NLFilename, glacier_region_behavior, &
-       glacier_region_melt_behavior, glacier_region_ice_runoff_behavior)
+  subroutine read_namelist(NLFilename, glacier_region_behavior)
     !
     ! !DESCRIPTION:
     ! Read local namelist items
@@ -597,10 +403,6 @@ subroutine read_namelist(NLFilename, glacier_region_behavior, &
     character(len=*), intent(in)  :: NLFilename ! Namelist filename
     character(len=max_behavior_name_len), intent(out) :: &
          glacier_region_behavior(min_glacier_region_id:max_glacier_region_id)
-    character(len=max_behavior_name_len), intent(out) :: &
-         glacier_region_melt_behavior(min_glacier_region_id:max_glacier_region_id)
-    character(len=max_behavior_name_len), intent(out) :: &
-         glacier_region_ice_runoff_behavior(min_glacier_region_id:max_glacier_region_id)
     !
     ! !LOCAL VARIABLES:
     integer :: unitn     ! unit for namelist file
@@ -609,14 +411,10 @@ subroutine read_namelist(NLFilename, glacier_region_behavior, &
     character(len=*), parameter :: subname = 'read_namelist'
     !-----------------------------------------------------------------------
 
-    namelist /clm_glacier_behavior/ &
-         glacier_region_behavior, glacier_region_melt_behavior, &
-         glacier_region_ice_runoff_behavior
+    namelist /clm_glacier_behavior/ glacier_region_behavior
 
     ! Initialize options to default values
     glacier_region_behavior(:) = behavior_str_unset
-    glacier_region_melt_behavior(:) = behavior_str_unset
-    glacier_region_ice_runoff_behavior(:) = behavior_str_unset
 
     if (masterproc) then
        unitn = getavu()
@@ -636,8 +434,6 @@ subroutine read_namelist(NLFilename, glacier_region_behavior, &
     endif
 
     call shr_mpi_bcast(glacier_region_behavior, mpicom)
-    call shr_mpi_bcast(glacier_region_melt_behavior, mpicom)
-    call shr_mpi_bcast(glacier_region_ice_runoff_behavior, mpicom)
 
     if (masterproc) then
        write(iulog,*) ' '
@@ -656,7 +452,6 @@ subroutine get_num_glc_mec_subgrid(this, gi, atm_topo, npatches, ncols, nlunits)
     ! Get number of subgrid units in glc_mec landunit on one grid cell
     !
     ! !USES:
-    use clm_varpar      , only : maxpatch_glcmec
     !
     ! !ARGUMENTS:
     class(glc_behavior_type), intent(in) :: this
@@ -676,7 +471,7 @@ subroutine get_num_glc_mec_subgrid(this, gi, atm_topo, npatches, ncols, nlunits)
 
     ncols = 0
 
-    do m = 1, maxpatch_glcmec
+    do m = 1, 10
        call this%glc_mec_col_exists(gi = gi, elev_class = m, atm_topo = atm_topo, &
             exists = col_exists, col_wt_lunit = col_wt_lunit)
        if (col_exists) then
@@ -762,9 +557,7 @@ subroutine glc_mec_col_exists(this, gi, elev_class, atm_topo, exists, col_wt_lun
        end if
 
     else  ! collapse_to_atm_topo_grc .false.
-       if (this%has_virtual_columns_grc(gi)) then
-          exists = .true.
-       else if (wt_lunit(gi, istice_mec) > 0.0_r8 .and. &
+       if (wt_lunit(gi, istice_mec) > 0.0_r8 .and. &
             wt_glc_mec(gi, elev_class) > 0.0_r8) then
           ! If the landunit has non-zero weight on the grid cell, and this column has
           ! non-zero weight on the landunit...
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 918b025940..0cfc010c96 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -12,9 +12,9 @@ module histFileMod
   use shr_sys_mod    , only : shr_sys_flush
   use spmdMod        , only : masterproc
   use abortutils     , only : endrun
-  use clm_varctl     , only : iulog, use_vertsoilc
-  use clm_varcon     , only : spval, ispval, dzsoi_decomp 
-  use clm_varcon     , only : grlnd, nameg, namel, namec, namep, nameCohort
+  use clm_varctl     , only : iulog
+  use clm_varcon     , only : spval, ispval
+  use clm_varcon     , only : grlnd, nameg, namel, namec, namep
   use decompMod      , only : get_proc_bounds, get_proc_global, bounds_type
   use GridcellType   , only : grc                
   use LandunitType   , only : lun                
@@ -107,7 +107,6 @@ module histFileMod
   ! !PUBLIC MEMBER FUNCTIONS:
   public :: hist_addfld1d        ! Add a 1d single-level field to the master field list
   public :: hist_addfld2d        ! Add a 2d multi-level field to the master field list
-  public :: hist_addfld_decomp   ! Add a 2d multi-level field to the master field list
   public :: hist_add_subscript   ! Add a 2d subscript dimension
   public :: hist_printflds       ! Print summary of master field list
   public :: hist_htapes_build    ! Initialize history file handler for initial or continue run
@@ -125,8 +124,6 @@ module histFileMod
   private :: htape_create              ! Define contents of history file t
   private :: htape_add_ltype_metadata  ! Add global metadata defining landunit types
   private :: htape_add_ctype_metadata  ! Add global metadata defining column types
-  private :: htape_add_natpft_metadata ! Add global metadata defining natpft types
-  private :: htape_add_cft_metadata    ! Add global metadata defining cft types
   private :: htape_timeconst           ! Write time constant values to history tape
   private :: htape_timeconst3D         ! Write time constant 3D values to primary history tape
   private :: hfields_normalize         ! Normalize history file fields by number of accumulations
@@ -162,7 +159,7 @@ module histFileMod
      character(len=max_chars)  :: units        ! units
      character(len=hist_dim_name_length) :: type1d                ! pointer to first dimension type from data type (nameg, etc)
      character(len=hist_dim_name_length) :: type1d_out            ! hbuf first dimension type from data type (nameg, etc)
-     character(len=hist_dim_name_length) :: type2d                ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)"]
+     character(len=hist_dim_name_length) :: type2d                ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","elevclas","subname(n)"]
      integer :: beg1d                          ! on-node 1d clm pointer start index
      integer :: end1d                          ! on-node 1d clm pointer end index
      integer :: num1d                          ! size of clm pointer first dimension (all nodes)
@@ -1025,7 +1022,7 @@ subroutine hist_update_hbuf(bounds)
     integer :: f                   ! field index
     integer :: num2d               ! size of second dimension (e.g. number of vertical levels)
     character(len=*),parameter :: subname = 'hist_update_hbuf'
-    character(len=hist_dim_name_length) :: type2d     ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)"]
+    character(len=hist_dim_name_length) :: type2d     ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","elevclas","subname(n)"]
     !-----------------------------------------------------------------------
 
     do t = 1,ntapes
@@ -1852,10 +1849,10 @@ subroutine htape_create (t, histrest)
     ! wrapper calls to define the history file contents.
     !
     ! !USES:
-    use clm_varpar      , only : nlevgrnd, nlevsno, nlevlak, nlevurb, numrad, nlevcan, nvegwcs,nlevsoi
-    use clm_varpar      , only : natpft_size, cft_size, maxpatch_glcmec, nlevdecomp_full
+    use clm_varpar      , only : nlevgrnd, nlevsno, nlevlak, nlevurb, numrad, nlevsoi
+    use clm_varpar      , only : natpft_size
     use landunit_varcon , only : max_lunit
-    use clm_varctl      , only : caseid, ctitle, fsurdat, finidat, paramfile
+    use clm_varctl      , only : caseid, ctitle, fsurdat, finidat
     use clm_varctl      , only : version, hostname, username, conventions, source
     use domainMod       , only : ldomain
     use fileutils       , only : get_filename
@@ -1973,8 +1970,6 @@ subroutine htape_create (t, histrest)
        str = get_filename(finidat)
     endif
     call ncd_putatt(lnfid, ncd_global, 'Initial_conditions_dataset', trim(str))
-    str = get_filename(paramfile)
-    call ncd_putatt(lnfid, ncd_global, 'PFT_physiological_constants_dataset', trim(str))
 
     ! Define dimensions.
     ! Time is an unlimited dimension. Character string is treated as an array of characters.
@@ -2003,26 +1998,18 @@ subroutine htape_create (t, histrest)
     call ncd_defdim(lnfid, 'numrad' , numrad , dimid)
     call ncd_defdim(lnfid, 'levsno' , nlevsno , dimid)
     call ncd_defdim(lnfid, 'ltype', max_lunit, dimid)
-    call ncd_defdim(lnfid, 'nlevcan',nlevcan, dimid)
-    call ncd_defdim(lnfid, 'nvegwcs',nvegwcs, dimid)
     call htape_add_ltype_metadata(lnfid)
     call htape_add_ctype_metadata(lnfid)
     call ncd_defdim(lnfid, 'natpft', natpft_size, dimid)
-    if (cft_size > 0) then
-       call ncd_defdim(lnfid, 'cft', cft_size, dimid)
-       call htape_add_cft_metadata(lnfid)
-    end if
-    call ncd_defdim(lnfid, 'glc_nec' , maxpatch_glcmec , dimid)
-    ! elevclas (in contrast to glc_nec) includes elevation class 0 (bare land)
+    ! elevclas includes elevation class 0 (bare land)
     ! (although on the history file it will go 1:(nec+1) rather than 0:nec)
-    call ncd_defdim(lnfid, 'elevclas' , maxpatch_glcmec + 1, dimid)
+    call ncd_defdim(lnfid, 'elevclas' , 11, dimid)
 
     do n = 1,num_subs
        call ncd_defdim(lnfid, subs_name(n), subs_dim(n), dimid)
     end do
     call ncd_defdim(lnfid, 'string_length', hist_dim_name_length, strlen_dimid)
     call ncd_defdim(lnfid, 'scale_type_string_length', scale_type_strlen, dimid)
-    call ncd_defdim( lnfid, 'levdcmp', nlevdecomp_full, dimid)
     ! MML: adding a mml soiz dimension:
     call ncd_defdim(lnfid, 'mml_lev', 10, dimid); ! hard-coded for 10 soil layers; make more clever.
     call ncd_defdim(lnfid, 'mml_dust', 4, dimid); ! hard-coded for 4 dust bins
@@ -2096,68 +2083,7 @@ subroutine htape_add_ctype_metadata(lnfid)
   end subroutine htape_add_ctype_metadata
 
   !-----------------------------------------------------------------------
-  subroutine htape_add_natpft_metadata(lnfid)
-    !
-    ! !DESCRIPTION:
-    ! Add global metadata defining natpft types
-    !
-    ! !USES:
-    use clm_varpar, only : natpft_lb, natpft_ub
-    use pftconMod , only : pftname_len, pftname
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t), intent(inout) :: lnfid ! local file id
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ptype  ! patch type
-    integer :: ptype_1_indexing ! patch type, translated to 1 indexing
-    character(len=*), parameter :: att_prefix = 'natpft_' ! prefix for attributes
-    character(len=len(att_prefix)+pftname_len) :: attname ! attribute name
-
-    character(len=*), parameter :: subname = 'htape_add_natpft_metadata'
-    !-----------------------------------------------------------------------
-    
-    do ptype = natpft_lb, natpft_ub
-       ptype_1_indexing = ptype + (1 - natpft_lb)
-       attname = att_prefix // pftname(ptype)
-       call ncd_putatt(lnfid, ncd_global, attname, ptype_1_indexing)
-    end do
-
-  end subroutine htape_add_natpft_metadata
-
-  !-----------------------------------------------------------------------
-  subroutine htape_add_cft_metadata(lnfid)
-    !
-    ! !DESCRIPTION:
-    ! Add global metadata defining natpft types
-    !
-    ! !USES:
-    use clm_varpar, only : cft_lb, cft_ub
-    use pftconMod , only : pftname_len, pftname
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t), intent(inout) :: lnfid ! local file id
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ptype  ! patch type
-    integer :: ptype_1_indexing ! patch type, translated to 1 indexing
-    character(len=*), parameter :: att_prefix = 'cft_'    ! prefix for attributes
-    character(len=len(att_prefix)+pftname_len) :: attname ! attribute name
-
-    character(len=*), parameter :: subname = 'htape_add_cft_metadata'
-    !-----------------------------------------------------------------------
-    
-    do ptype = cft_lb, cft_ub
-       ptype_1_indexing = ptype + (1 - cft_lb)
-       attname = att_prefix // pftname(ptype)
-       call ncd_putatt(lnfid, ncd_global, attname, ptype_1_indexing)
-    end do
-
-  end subroutine htape_add_cft_metadata
-
-  !-----------------------------------------------------------------------
-  subroutine htape_timeconst3D(t, &
-       bounds, watsat_col, sucsat_col, bsw_col, hksat_col, mode)
+  subroutine htape_timeconst3D(t, bounds, mode)
     !
     ! !DESCRIPTION:
     ! Write time constant 3D variables to history tapes.
@@ -2175,10 +2101,7 @@ subroutine htape_timeconst3D(t, &
     ! !ARGUMENTS:
     integer           , intent(in) :: t    ! tape index
     type(bounds_type) , intent(in) :: bounds           
-    real(r8)          , intent(in) :: watsat_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: sucsat_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: bsw_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: hksat_col( bounds%begc:,1: ) 
+!   real(r8)          , intent(in) :: watsat_col( bounds%begc:,1: ) 
     character(len=*)  , intent(in) :: mode ! 'define' or 'write'
     !
     ! !LOCAL VARIABLES:
@@ -2191,15 +2114,11 @@ subroutine htape_timeconst3D(t, &
     !
     real(r8), pointer :: histi(:,:)       ! temporary
     real(r8), pointer :: histo(:,:)       ! temporary
-    integer, parameter :: nflds = 6       ! Number of 3D time-constant fields
+    integer, parameter :: nflds = 2       ! Number of 3D time-constant fields
     character(len=*),parameter :: subname = 'htape_timeconst3D'
     character(len=*),parameter :: varnames(nflds) = (/ &
                                                         'ZSOI  ', &
-                                                        'DZSOI ', &
-                                                        'WATSAT', &
-                                                        'SUCSAT', &
-                                                        'BSW   ', &
-                                                        'HKSAT '  &
+                                                        'DZSOI '  &
                                                     /)
     real(r8), pointer :: histil(:,:)      ! temporary
     real(r8), pointer :: histol(:,:)
@@ -2210,10 +2129,7 @@ subroutine htape_timeconst3D(t, &
                                                       /)
     !-----------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(watsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(sucsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(bsw_col)    == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(hksat_col)  == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
+!   SHR_ASSERT_ALL((ubound(watsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
 
     !-------------------------------------------------------------------------------
     !***      Non-time varying 3D fields                    ***
@@ -2229,14 +2145,6 @@ subroutine htape_timeconst3D(t, &
              long_name='soil depth'; units = 'm'
           else if (ifld == 2) then
              long_name='soil thickness'; units = 'm'
-          else if (ifld == 3) then
-             long_name='saturated soil water content (porosity)';  units = 'mm3/mm3'
-          else if (ifld == 4) then
-             long_name='saturated soil matric potential'; units = 'mm'
-          else if (ifld == 5) then
-             long_name='slope of soil water retention curve'; units = 'unitless'
-          else if (ifld == 6) then
-             long_name='saturated hydraulic conductivity'; units = 'mm s-1'
           else
              call endrun(msg=' ERROR: bad 3D time-constant field index'//errMsg(sourcefile, __LINE__))
           end if
@@ -2292,14 +2200,6 @@ subroutine htape_timeconst3D(t, &
              l2g_scale_type = 'nonurb'
           else if (ifld == 2) then  ! DZSOI
              l2g_scale_type = 'nonurb'
-          else if (ifld == 3) then  ! WATSAT
-             l2g_scale_type = 'veg'
-          else if (ifld == 4) then  ! SUCSAT
-             l2g_scale_type = 'veg'
-          else if (ifld == 5) then  ! BSW
-             l2g_scale_type = 'veg'
-          else if (ifld == 6) then  ! HKSAT
-             l2g_scale_type = 'veg'
           end if
 
           histi(:,:) = spval
@@ -2309,10 +2209,6 @@ subroutine htape_timeconst3D(t, &
                    ! Field indices MUST match varnames array order above!
                    if (ifld ==1) histi(c,lev) = col%z(c,lev)
                    if (ifld ==2) histi(c,lev) = col%dz(c,lev)
-                   if (ifld ==3) histi(c,lev) = watsat_col(c,lev)
-                   if (ifld ==4) histi(c,lev) = sucsat_col(c,lev)
-                   if (ifld ==5) histi(c,lev) = bsw_col(c,lev)
-                   if (ifld ==6) histi(c,lev) = hksat_col(c,lev)
              end do
           end do
           if (tape(t)%dov2xy) then
@@ -2517,8 +2413,6 @@ subroutine htape_timeconst(t, mode)
           call ncd_defvar(varname='levlak', xtype=tape(t)%ncprec, &
                dim1name='levlak', &
                long_name='coordinate lake levels', units='m', ncid=nfid(t))
-          call ncd_defvar(varname='levdcmp', xtype=tape(t)%ncprec, dim1name='levdcmp', &
-               long_name='coordinate soil levels', units='m', ncid=nfid(t))
 
       	  ! Add MML soil layers
           call ncd_defvar(varname='mml_lev', xtype=tape(t)%ncprec, dim1name='mml_lev', &
@@ -2531,12 +2425,7 @@ subroutine htape_timeconst(t, mode)
           if ( masterproc ) write(iulog, *) ' zsoi:',zsoi
           call ncd_io(varname='levgrnd', data=zsoi, ncid=nfid(t), flag='write')
           call ncd_io(varname='levlak' , data=zlak, ncid=nfid(t), flag='write')
-          if (use_vertsoilc) then
-             call ncd_io(varname='levdcmp', data=zsoi, ncid=nfid(t), flag='write')
-          else
-             zsoi_1d(1) = 1._r8
-             call ncd_io(varname='levdcmp', data=zsoi_1d, ncid=nfid(t), flag='write')
-          end if
+          zsoi_1d(1) = 1._r8
 		   ! Add MML soil layers
           call ncd_io(varname='mml_lev', data=mml_zsoi, ncid=nfid(t), flag='write')
           
@@ -2713,28 +2602,6 @@ subroutine htape_timeconst(t, mode)
               long_name='land/ocean mask (0.=ocean and 1.=land)', ncid=nfid(t), &
               imissing_value=ispval, ifill_value=ispval)
        end if
-       if (ldomain%isgrid2d) then
-          call ncd_defvar(varname='pftmask' , xtype=ncd_int, &
-              dim1name='lon', dim2name='lat', &
-              long_name='pft real/fake mask (0.=fake and 1.=real)', ncid=nfid(t), &
-              imissing_value=ispval, ifill_value=ispval)
-       else
-          call ncd_defvar(varname='pftmask' , xtype=ncd_int, &
-              dim1name=grlnd, &
-              long_name='pft real/fake mask (0.=fake and 1.=real)', ncid=nfid(t), &
-              imissing_value=ispval, ifill_value=ispval)
-       end if
-       if (ldomain%isgrid2d) then
-          call ncd_defvar(varname='nbedrock' , xtype=ncd_int, &
-              dim1name='lon', dim2name='lat', &
-              long_name='index of shallowest bedrock layer', ncid=nfid(t), &
-              imissing_value=ispval, ifill_value=ispval)
-       else
-          call ncd_defvar(varname='nbedrock' , xtype=ncd_int, &
-              dim1name=grlnd, &
-              long_name='index of shallowest bedrock layer', ncid=nfid(t), &
-              imissing_value=ispval, ifill_value=ispval)
-       end if
 
     else if (mode == 'write') then
 
@@ -2751,8 +2618,6 @@ subroutine htape_timeconst(t, mode)
        call ncd_io(varname='area'    , data=ldomain%area, dim1name=grlnd, ncid=nfid(t), flag='write')
        call ncd_io(varname='landfrac', data=ldomain%frac, dim1name=grlnd, ncid=nfid(t), flag='write')
        call ncd_io(varname='landmask', data=ldomain%mask, dim1name=grlnd, ncid=nfid(t), flag='write')
-       call ncd_io(varname='pftmask' , data=ldomain%pftm, dim1name=grlnd, ncid=nfid(t), flag='write')
-       call ncd_io(varname='nbedrock' , data=grc%nbedrock, dim1name=grlnd, ncid=nfid(t), flag='write')
 
     end if  ! (define/write mode
 
@@ -3233,8 +3098,7 @@ subroutine hfields_1dinfo(t, mode)
   end subroutine hfields_1dinfo
 
   !-----------------------------------------------------------------------
-  subroutine hist_htapes_wrapup( rstwr, nlend, bounds, &
-       watsat_col, sucsat_col, bsw_col, hksat_col)
+  subroutine hist_htapes_wrapup( rstwr, nlend, bounds)
     !
     ! !DESCRIPTION:
     ! Write history tape(s)
@@ -3266,10 +3130,7 @@ subroutine hist_htapes_wrapup( rstwr, nlend, bounds, &
     logical, intent(in) :: rstwr    ! true => write restart file this step
     logical, intent(in) :: nlend    ! true => end of run on this step
     type(bounds_type) , intent(in) :: bounds           
-    real(r8)          , intent(in) :: watsat_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: sucsat_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: bsw_col( bounds%begc:,1: ) 
-    real(r8)          , intent(in) :: hksat_col( bounds%begc:,1: ) 
+!   real(r8)          , intent(in) :: watsat_col( bounds%begc:,1: ) 
     !
     ! !LOCAL VARIABLES:
     integer :: t                          ! tape index
@@ -3293,10 +3154,7 @@ subroutine hist_htapes_wrapup( rstwr, nlend, bounds, &
     character(len=*),parameter :: subname = 'hist_htapes_wrapup'
     !-----------------------------------------------------------------------
 
-    SHR_ASSERT_ALL((ubound(watsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(sucsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(bsw_col)    == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(hksat_col)  == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
+!   SHR_ASSERT_ALL((ubound(watsat_col) == (/bounds%endc, nlevgrnd/)), errMsg(sourcefile, __LINE__))
 
     ! get current step
 
@@ -3366,36 +3224,29 @@ subroutine hist_htapes_wrapup( rstwr, nlend, bounds, &
              ! Define time-constant field variables
              call htape_timeconst(t, mode='define')
 
-             !write(iulog,*)'MML define 3D'
-             ! Define 3D time-constant field variables only to first primary tape
-             if ( do_3Dtconst .and. t == 1 ) then
-                call htape_timeconst3D(t, &
-                     bounds, watsat_col, sucsat_col, bsw_col, hksat_col, mode='define')
-                TimeConst3DVars_Filename = trim(locfnh(t))
-             end if
+!            ! Define 3D time-constant field variables only to first primary tape
+!            if ( do_3Dtconst .and. t == 1 ) then
+!               call htape_timeconst3D(t, bounds, watsat_col, mode='define')
+!               TimeConst3DVars_Filename = trim(locfnh(t))
+!            end if
 
-             !write(iulog,*)'MML define model field vars'
              ! Define model field variables
              call hfields_write(t, mode='define')
 
-             !write(iulog,*)'MML run away'
              ! Exit define model
              call ncd_enddef(nfid(t))
              call t_stopf('hist_htapes_wrapup_define')
           endif
 
-          !write(iulog,*)'MML before htape_teimconst'
           call t_startf('hist_htapes_wrapup_tconst')
           ! Write time constant history variables
           call htape_timeconst(t, mode='write')
 
-          !write(iulog,*)'MML write 3D time const'
-          ! Write 3D time constant history variables only to first primary tape
-          if ( do_3Dtconst .and. t == 1 .and. tape(t)%ntimes == 1 )then
-             call htape_timeconst3D(t, &
-                  bounds, watsat_col, sucsat_col, bsw_col, hksat_col, mode='write')
-             do_3Dtconst = .false.
-          end if
+!         ! Write 3D time constant history variables only to first primary tape
+!         if ( do_3Dtconst .and. t == 1 .and. tape(t)%ntimes == 1 )then
+!            call htape_timeconst3D(t, bounds, watsat_col, mode='write')
+!            do_3Dtconst = .false.
+!         end if
 
           if (masterproc) then
              write(iulog,*)
@@ -3486,7 +3337,7 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate)
     use clm_varctl      , only : nsrest, caseid, inst_suffix, nsrStartup, nsrBranch
     use fileutils       , only : getfil
     use domainMod       , only : ldomain
-    use clm_varpar      , only : nlevgrnd, nlevlak, numrad, nlevdecomp_full
+    use clm_varpar      , only : nlevgrnd, nlevlak, numrad
     use clm_time_manager, only : is_restart
     use restUtilMod     , only : iflag_skip
     use pio
@@ -4612,8 +4463,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     ! initial or branch run to initialize the actual history tapes.
     !
     ! !USES:
-    use clm_varpar      , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevdecomp_full, nlevcan, nvegwcs,nlevsoi
-    use clm_varpar      , only : natpft_size, cft_size, maxpatch_glcmec
+    use clm_varpar      , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevsoi
+    use clm_varpar      , only : natpft_size, cft_size
     use landunit_varcon , only : max_lunit
     !
     ! !ARGUMENTS:
@@ -4692,8 +4543,6 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        num2d = nlevlak
     case ('numrad')
        num2d = numrad
-    case ('levdcmp')
-       num2d = nlevdecomp_full
     case ('ltype')
        num2d = max_lunit
     case ('natpft')
@@ -4706,27 +4555,21 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
                ' only valid for cft_size > 0'
           call endrun()
        end if
-    case ('glc_nec')
-       num2d = maxpatch_glcmec
     case ('elevclas')
-       ! add one because indexing starts at 0 (elevclas, unlike glc_nec, includes the
+       ! add one because indexing starts at 0 (elevclas includes the
        ! bare ground "elevation class")
-       num2d = maxpatch_glcmec + 1
+       num2d = 11
     case ('levsno')
        num2d = nlevsno
-    case ('nlevcan')
-        num2d = nlevcan 
     ! MML: adding my own 
     case ('mml_lev')
     	num2d = 10 !mml_nsoi ! mml_dim ! mml_nsoi not defined in this subroutine, so hard coding until I get more clever...
     case ('mml_dust')
     	num2d = 4
-    case ('nvegwcs')
-        num2d = nvegwcs
     case default
        write(iulog,*) trim(subname),' ERROR: unsupported 2d type ',type2d, &
           ' currently supported types for multi level fields are: ', &
-          '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs]'
+          '[levgrnd,levsoi,levlak,numrad,levtrc,ltype,natpft,cft,elevclas,levsno]'
        call endrun(msg=errMsg(sourcefile, __LINE__))
     end select
 
@@ -4882,94 +4725,6 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
 
   end subroutine hist_addfld2d
 
-  !-----------------------------------------------------------------------
-  subroutine hist_addfld_decomp (fname, type2d, units, avgflag, long_name, ptr_col, &
-       ptr_patch, l2g_scale_type, default)
-
-    !
-    ! !USES:
-    use clm_varpar  , only : nlevdecomp_full
-    use clm_varctl  , only : iulog
-    use abortutils  , only : endrun
-    use shr_log_mod , only : errMsg => shr_log_errMsg
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: fname                    ! field name
-    character(len=*), intent(in) :: type2d                   ! 2d output type
-    character(len=*), intent(in) :: units                    ! units of field
-    character(len=*), intent(in) :: avgflag                  ! time averaging flag
-    character(len=*), intent(in) :: long_name                ! long name of field
-    real(r8)        , optional, pointer    :: ptr_col(:,:)   ! pointer to column array
-    real(r8)        , optional, pointer    :: ptr_patch(:,:)   ! pointer to patch array
-    character(len=*), optional, intent(in) :: l2g_scale_type ! scale type for subgrid averaging of landunits to gridcells
-    character(len=*), optional, intent(in) :: default        ! if set to 'inactive, field will not appear on primary tape
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), pointer  :: ptr_1d(:)
-    !-----------------------------------------------------------------------
-
-    if (present(ptr_col)) then
-
-       ! column-level data
-       if (present(default)) then
-          if ( nlevdecomp_full > 1 ) then
-             call hist_addfld2d (fname=trim(fname), units=units, type2d=type2d, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_col=ptr_col, l2g_scale_type=l2g_scale_type, default=default)
-          else
-             ptr_1d => ptr_col(:,1)
-             call hist_addfld1d (fname=trim(fname), units=units, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_col=ptr_1d, l2g_scale_type=l2g_scale_type, default=default)
-          endif
-       else
-          if ( nlevdecomp_full > 1 ) then
-             call hist_addfld2d (fname=trim(fname), units=units, type2d=type2d, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_col=ptr_col, l2g_scale_type=l2g_scale_type)
-          else
-             ptr_1d => ptr_col(:,1)
-             call hist_addfld1d (fname=trim(fname), units=units, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_col=ptr_1d, l2g_scale_type=l2g_scale_type)
-          endif
-       endif
-
-    else if (present(ptr_patch)) then
-
-       ! patch-level data
-       if (present(default)) then
-          if ( nlevdecomp_full > 1 ) then
-             call hist_addfld2d (fname=trim(fname), units=units, type2d=type2d, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_patch=ptr_patch, l2g_scale_type=l2g_scale_type, default=default)
-          else
-             ptr_1d => ptr_patch(:,1)
-             call hist_addfld1d (fname=trim(fname), units=units, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_patch=ptr_1d, l2g_scale_type=l2g_scale_type, default=default)
-          endif
-       else
-          if ( nlevdecomp_full > 1 ) then
-             call hist_addfld2d (fname=trim(fname), units=units, type2d=type2d, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_patch=ptr_patch, l2g_scale_type=l2g_scale_type)
-          else
-             ptr_1d => ptr_patch(:,1)
-             call hist_addfld1d (fname=trim(fname), units=units, &
-                  avgflag=avgflag, long_name=long_name, &
-                  ptr_patch=ptr_1d, l2g_scale_type=l2g_scale_type)
-          endif
-       endif
-
-    else
-       write(iulog, *) ' error: hist_addfld_decomp needs either patch or column level pointer'
-       write(iulog, *) fname
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-
-  end subroutine hist_addfld_decomp
-
   !-----------------------------------------------------------------------
   integer function pointer_index ()
     !
diff --git a/src/main/initGridCellsMod.F90 b/src/main/initGridCellsMod.F90
index def9631a8a..238762fdb9 100644
--- a/src/main/initGridCellsMod.F90
+++ b/src/main/initGridCellsMod.F90
@@ -62,7 +62,6 @@ subroutine initGridcells(glc_behavior)
     use subgridWeightsMod , only : compute_higher_order_weights
     use landunit_varcon   , only : istsoil, istwet, istdlak, istice_mec
     use landunit_varcon   , only : isturb_tbd, isturb_hd, isturb_md, istcrop
-    use clm_varctl        , only : use_fates
     use shr_const_mod     , only : SHR_CONST_PI
     !
     ! !ARGUMENTS:
@@ -223,7 +222,7 @@ subroutine set_landunit_veg_compete (ltype, gi, li, ci, pi)
     ! !USES
     use clm_instur, only : wt_lunit, wt_nat_patch
     use subgridMod, only : subgrid_get_info_natveg
-    use clm_varpar, only : numpft, maxpatch_pft, natpft_lb, natpft_ub
+    use clm_varpar, only : natpft_lb, natpft_ub
     !
     ! !ARGUMENTS:
     integer , intent(in)    :: ltype             ! landunit type
@@ -270,7 +269,6 @@ subroutine set_landunit_wet_lake (ltype, gi, li, ci, pi)
     use clm_instur      , only : wt_lunit
     use landunit_varcon , only : istwet, istdlak
     use subgridMod      , only : subgrid_get_info_wetland, subgrid_get_info_lake
-    use pftconMod       , only : noveg
 
     !
     ! !ARGUMENTS:
@@ -317,7 +315,7 @@ subroutine set_landunit_wet_lake (ltype, gi, li, ci, pi)
        
        call add_landunit(li=li, gi=gi, ltype=ltype, wtgcell=wtlunit2gcell)
        call add_column(ci=ci, li=li, ctype=ltype, wtlunit=1.0_r8)
-       call add_patch(pi=pi, ci=ci, ptype=noveg, wtcol=1.0_r8)
+       call add_patch(pi=pi, ci=ci, ptype=0, wtcol=1.0_r8)
 
     endif       ! npatches > 0       
 
@@ -330,12 +328,10 @@ subroutine set_landunit_ice_mec(glc_behavior, ltype, gi, li, ci, pi)
     ! Initialize glacier_mec landunits
     !
     ! !USES:
-    use clm_varpar      , only : maxpatch_glcmec
     use clm_instur      , only : wt_lunit, wt_glc_mec
     use landunit_varcon , only : istice_mec
     use column_varcon   , only : icemec_class_to_col_itype
     use subgridMod      , only : subgrid_get_info_glacier_mec
-    use pftconMod       , only : noveg
     !
     ! !ARGUMENTS:
     type(glc_behavior_type), intent(in) :: glc_behavior
@@ -383,13 +379,13 @@ subroutine set_landunit_ice_mec(glc_behavior, ltype, gi, li, ci, pi)
        ! balance in each elevation class wherever the SMB is needed.
        
        type_is_dynamic = glc_behavior%cols_have_dynamic_type(gi)
-       do m = 1, maxpatch_glcmec
+       do m = 1, 10
           call glc_behavior%glc_mec_col_exists(gi = gi, elev_class = m, atm_topo = atm_topo, &
                exists = col_exists, col_wt_lunit = wtcol2lunit)
           if (col_exists) then
              call add_column(ci=ci, li=li, ctype=icemec_class_to_col_itype(m), &
                   wtlunit=wtcol2lunit, type_is_dynamic=type_is_dynamic)
-             call add_patch(pi=pi, ci=ci, ptype=noveg, wtcol=1.0_r8)
+             call add_patch(pi=pi, ci=ci, ptype=0, wtcol=1.0_r8)
           endif
        enddo
 
@@ -415,8 +411,7 @@ subroutine set_landunit_crop_noncompete (ltype, gi, li, ci, pi)
     use clm_instur      , only : wt_lunit, wt_cft
     use landunit_varcon , only : istcrop, istsoil
     use subgridMod      , only : subgrid_get_info_crop, crop_patch_exists
-    use clm_varpar      , only : maxpatch_pft, cft_lb, cft_ub
-    use clm_varctl      , only : create_crop_landunit
+    use clm_varpar      , only : cft_lb, cft_ub
     !
     ! !ARGUMENTS:
     integer , intent(in)    :: ltype             ! landunit type
@@ -444,16 +439,7 @@ subroutine set_landunit_crop_noncompete (ltype, gi, li, ci, pi)
 
        ! Note that we cannot simply use the 'ltype' argument to set itype here,
        ! because ltype will always indicate istcrop
-       if ( create_crop_landunit )then
-          my_ltype = ltype    ! Will always be istcrop
-          if ( ltype /= istcrop )then
-             write(iulog,*)' create_crop_landunit on and ltype is not istcrop: ', ltype
-             call endrun(msg=errMsg(sourcefile, __LINE__))
-          end if
-       else
-          my_ltype = istsoil
-       end if
-
+       my_ltype = ltype    ! Will always be istcrop
        call add_landunit(li=li, gi=gi, ltype=my_ltype, wtgcell=wtlunit2gcell)
        
        ! Set column and patch properties for this landunit 
@@ -487,7 +473,6 @@ subroutine set_landunit_urban (ltype, gi, li, ci, pi)
     use subgridMod      , only : subgrid_get_info_urban_md
     use UrbanParamsType , only : urbinp
     use decompMod       , only : ldecomp
-    use pftconMod       , only : noveg
     !
     ! !ARGUMENTS:
     integer , intent(in)    :: ltype             ! landunit type
@@ -561,7 +546,7 @@ subroutine set_landunit_urban (ltype, gi, li, ci, pi)
 
           call add_column(ci=ci, li=li, ctype=ctype, wtlunit=wtcol2lunit)
 
-          call add_patch(pi=pi, ci=ci, ptype=noveg, wtcol=1.0_r8)
+          call add_patch(pi=pi, ci=ci, ptype=0, wtcol=1.0_r8)
 
        end do   ! end of loop through urban columns-pfts
     end if
diff --git a/src/main/initSubgridMod.F90 b/src/main/initSubgridMod.F90
index 57384dc461..187d164123 100644
--- a/src/main/initSubgridMod.F90
+++ b/src/main/initSubgridMod.F90
@@ -10,7 +10,7 @@ module initSubgridMod
   use shr_log_mod    , only : errMsg => shr_log_errMsg
   use spmdMod        , only : masterproc
   use abortutils     , only : endrun
-  use clm_varctl     , only : iulog, use_fates
+  use clm_varctl     , only : iulog
   use clm_varcon     , only : namep, namec, namel
   use decompMod      , only : bounds_type
   use GridcellType   , only : grc                
@@ -455,11 +455,9 @@ subroutine add_patch(pi, ci, ptype, wtcol)
 
     ! TODO (MV, 10-17-14): The following must be commented out because
     ! currently patch%itype is used in CanopyTemperatureMod to calculate 
-    ! z0m(p) and displa(p) - and is still called even when fates is on
+    ! z0m(p) and displa(p)
 
-    !if (.not. use_fates) then
     patch%itype(pi) = ptype
-    !end if
 
     if (lun%itype(li) == istsoil .or. lun%itype(li) == istcrop) then
        lb_offset = 1 - natpft_lb
diff --git a/src/main/initVerticalMod.F90 b/src/main/initVerticalMod.F90
index c4f3f9a8cb..d444e6cc37 100644
--- a/src/main/initVerticalMod.F90
+++ b/src/main/initVerticalMod.F90
@@ -13,18 +13,13 @@ module initVerticalMod
   use decompMod         , only : bounds_type
   use spmdMod           , only : masterproc
   use clm_varpar        , only : nlevsno, nlevgrnd, nlevlak
-  use clm_varpar        , only : toplev_equalspace, nlev_equalspace
   use clm_varpar        , only : nlevsoi, nlevsoifl, nlevurb 
   use clm_varctl        , only : fsurdat, iulog
-  use clm_varctl        , only : use_vancouver, use_mexicocity, use_vertsoilc, use_extralakelayers
-  use clm_varctl        , only : use_bedrock, soil_layerstruct
-  use clm_varctl        , only : use_fates
-  use clm_varcon        , only : zlak, dzlak, zsoi, dzsoi, zisoi, dzsoi_decomp, spval, ispval, grlnd 
-  use column_varcon     , only : icol_roof, icol_sunwall, icol_shadewall, is_hydrologically_active
-  use landunit_varcon   , only : istdlak, istice_mec
+  use clm_varcon        , only : zlak, dzlak, zsoi, dzsoi, zisoi, spval, ispval, grlnd 
+  use column_varcon     , only : icol_roof, icol_sunwall, icol_shadewall
+  use landunit_varcon   , only : istdlak
   use fileutils         , only : getfil
   use LandunitType      , only : lun                
-  use GridcellType      , only : grc                
   use ColumnType        , only : col                
   use glcBehaviorMod    , only : glc_behavior_type
   use abortUtils        , only : endrun    
@@ -38,9 +33,6 @@ module initVerticalMod
   ! !PUBLIC MEMBER FUNCTIONS:
   public :: initVertical
   ! !PRIVATE MEMBER FUNCTIONS:
-  private :: ReadNL
-  private :: hasBedrock  ! true if the given column type includes bedrock layers
-  !
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -51,67 +43,11 @@ module initVerticalMod
 contains
 
   !------------------------------------------------------------------------
-  subroutine ReadNL( )
-    !
-    ! !DESCRIPTION:
-    ! Read namelist for SoilStateType
-    !
-    ! !USES:
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    use shr_log_mod    , only : errMsg => shr_log_errMsg
-    use fileutils      , only : getavu, relavu, opnfil
-    use clm_nlUtilsMod , only : find_nlgroup_name
-    use clm_varctl     , only : iulog
-    use spmdMod        , only : mpicom, masterproc
-    use controlMod     , only : NLFilename
-    !
-    ! !ARGUMENTS:
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    character(len=32) :: subname = 'InitVertical_readnl'  ! subroutine name
-    !-----------------------------------------------------------------------
-
-    character(len=*), parameter :: nl_name  = 'clm_inparm'  ! Namelist name
-                                                                      
-    ! MUST agree with name in namelist and read
-    namelist /clm_inparm/ use_bedrock
-
-    ! preset values
-
-    use_bedrock = .false.
-
-    if ( masterproc )then
-
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nl_name//' namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call find_nlgroup_name(unitn, nl_name, status=ierr)
-       if (ierr == 0) then
-          read(unit=unitn, nml=clm_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading '//nl_name//' namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR finding '//nl_name//' namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-
-    end if
-
-    call shr_mpi_bcast(use_bedrock, mpicom)
-
-  end subroutine ReadNL
-
-  !------------------------------------------------------------------------
-  subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof)
-    use clm_varcon, only : zmin_bedrock, n_melt_glcmec
+  subroutine initVertical(bounds, glc_behavior, thick_wall, thick_roof)
     !
     ! !ARGUMENTS:
     type(bounds_type)   , intent(in)    :: bounds
     type(glc_behavior_type), intent(in) :: glc_behavior
-    real(r8)            , intent(in)    :: snow_depth(bounds%begc:)
     real(r8)            , intent(in)    :: thick_wall(bounds%begl:)
     real(r8)            , intent(in)    :: thick_roof(bounds%begl:)
     !
@@ -121,15 +57,11 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
     logical               :: readvar 
     integer               :: dimid             ! dimension id
     character(len=256)    :: locfn             ! local filename
-    real(r8) ,pointer     :: std (:)           ! read in - topo_std 
-    real(r8) ,pointer     :: tslope (:)        ! read in - topo_slope 
     real(r8)              :: slope0            ! temporary
     real(r8)              :: slopebeta         ! temporary
     real(r8)              :: slopemax          ! temporary
     integer               :: ier               ! error status
     real(r8)              :: scalez = 0.025_r8 ! Soil layer thickness discretization (m)
-    real(r8)              :: thick_equal = 0.2
-    real(r8) ,pointer     :: zbedrock_in(:)   ! read in - z_bedrock
     real(r8) ,pointer     :: lakedepth_in(:)   ! read in - lakedepth 
     real(r8), allocatable :: zurb_wall(:,:)    ! wall (layer node depth)
     real(r8), allocatable :: zurb_roof(:,:)    ! roof (layer node depth)
@@ -140,33 +72,12 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
     real(r8)              :: depthratio        ! ratio of lake depth to standard deep lake depth 
     integer               :: begc, endc
     integer               :: begl, endl
-    integer               :: jmin_bedrock
 
-    ! Possible values for levgrnd_class. The important thing is that, for a given column,
-    ! layers that are fundamentally different (e.g., soil vs bedrock) have different
-    ! values. This information is used in the vertical interpolation in init_interp.
-    !
-    ! IMPORTANT: These values should not be changed lightly. e.g., try to avoid changing
-    ! the values assigned to LEVGRND_CLASS_STANDARD, LEVGRND_CLASS_DEEP_BEDROCK, etc.  The
-    ! problem with changing these is that init_interp expects that layers with a value of
-    ! (e.g.) 1 on the source file correspond to layers with a value of 1 on the
-    ! destination file. So if you change the values of these constants, you either need to
-    ! adequately inform users of this change, or build in some translation mechanism in
-    ! init_interp (such as via adding more metadata to the restart file on the meaning of
-    ! these different values).
-    !
-    ! The distinction between "shallow" and "deep" bedrock is not made explicitly
-    ! elsewhere. But, since these classes have somewhat different behavior, they are
-    ! distinguished explicitly here.
-    integer, parameter :: LEVGRND_CLASS_STANDARD        = 1
-    integer, parameter :: LEVGRND_CLASS_DEEP_BEDROCK    = 2
-    integer, parameter :: LEVGRND_CLASS_SHALLOW_BEDROCK = 3
     !------------------------------------------------------------------------
 
     begc = bounds%begc; endc= bounds%endc
     begl = bounds%begl; endl= bounds%endl
 
-    SHR_ASSERT_ALL((ubound(snow_depth)  == (/endc/)), errMsg(sourcefile, __LINE__))
     SHR_ASSERT_ALL((ubound(thick_wall)  == (/endl/)), errMsg(sourcefile, __LINE__))
     SHR_ASSERT_ALL((ubound(thick_roof)  == (/endl/)), errMsg(sourcefile, __LINE__))
 
@@ -183,7 +94,6 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
     ! Soil layers and interfaces (assumed same for all non-lake patches)
     ! "0" refers to soil surface and "nlevsoi" refers to the bottom of model soil
 
-    if ( soil_layerstruct == '10SL_3.5m' ) then 
        do j = 1, nlevgrnd
           zsoi(j) = scalez*(exp(0.5_r8*(j-0.5_r8))-1._r8)    !node depths
        enddo
@@ -200,98 +110,10 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
        enddo
        zisoi(nlevgrnd) = zsoi(nlevgrnd) + 0.5_r8*dzsoi(nlevgrnd)
 
-    else if ( soil_layerstruct == '23SL_3.5m' )then
-       ! Soil layer structure that starts with standard exponential
-       ! and then has several evenly spaced layers, then finishes off exponential. 
-       ! this allows the upper soil to behave as standard, but then continues 
-       ! with higher resolution to a deeper depth, so that, for example, permafrost
-       ! dynamics are not lost due to an inability to resolve temperature, moisture, 
-       ! and biogeochemical dynamics at the base of the active layer
-       do j = 1, toplev_equalspace
-          zsoi(j) = scalez*(exp(0.5_r8*(j-0.5_r8))-1._r8)    !node depths
-       enddo
-
-       do j = toplev_equalspace+1,toplev_equalspace + nlev_equalspace
-          zsoi(j) = zsoi(j-1) + thick_equal
-       enddo
-
-       do j = toplev_equalspace + nlev_equalspace +1, nlevgrnd
-          zsoi(j) = scalez*(exp(0.5_r8*((j - nlev_equalspace)-0.5_r8))-1._r8) + nlev_equalspace * thick_equal
-       enddo
-
-       dzsoi(1) = 0.5_r8*(zsoi(1)+zsoi(2))             !thickness b/n two interfaces
-       do j = 2,nlevgrnd-1
-          dzsoi(j)= 0.5_r8*(zsoi(j+1)-zsoi(j-1))
-       enddo
-       dzsoi(nlevgrnd) = zsoi(nlevgrnd)-zsoi(nlevgrnd-1)
-
-       zisoi(0) = 0._r8
-       do j = 1, nlevgrnd-1
-       zisoi(j) = 0.5_r8*(zsoi(j)+zsoi(j+1))         !interface depths
-       enddo
-       zisoi(nlevgrnd) = zsoi(nlevgrnd) + 0.5_r8*dzsoi(nlevgrnd)
-
-    else if ( soil_layerstruct == '49SL_10m' ) then
-       !scs: 10 meter soil column, nlevsoi set to 49 in clm_varpar
-       do j = 1,10
-          dzsoi(j)= 1.e-2_r8     !10mm layers
-       enddo
-       do j = 11,19
-          dzsoi(j)= 1.e-1_r8     !100 mm layers
-       enddo
-       do j = 20,nlevsoi+1       !300 mm layers
-          dzsoi(j)= 3.e-1_r8
-       enddo
-       do j = nlevsoi+2,nlevgrnd !10 meter bedrock layers
-          dzsoi(j)= 10._r8
-       enddo
-       
-       zisoi(0) = 0._r8
-       do j = 1,nlevgrnd
-          zisoi(j)= sum(dzsoi(1:j))
-       enddo
-       
-       do j = 1, nlevgrnd
-          zsoi(j) = 0.5*(zisoi(j-1) + zisoi(j))
-       enddo
-
-    else if ( soil_layerstruct == '20SL_8.5m' ) then
-       do j = 1,4
-          dzsoi(j)= j*0.02_r8          ! linear increase in layer thickness of 2cm each layer
-       enddo
-       do j = 5,13
-          dzsoi(j)= dzsoi(4)+(j-4)*0.04_r8      ! linear increase in layer thickness of 2cm each layer
-       enddo
-       do j = 14,nlevsoi       
-          dzsoi(j)= dzsoi(13)+(j-13)*0.10_r8     ! linear increase in layer thickness of 2cm each layer
-       enddo
-       do j = nlevsoi+1,nlevgrnd !bedrock layers
-          dzsoi(j)= dzsoi(nlevsoi)+(((j-nlevsoi)*25._r8)**1.5_r8)/100._r8  ! bedrock layers
-       enddo
-       
-       zisoi(0) = 0._r8
-       do j = 1,nlevgrnd
-          zisoi(j)= sum(dzsoi(1:j))
-       enddo
-       
-       do j = 1, nlevgrnd
-          zsoi(j) = 0.5*(zisoi(j-1) + zisoi(j))
-       enddo
-    end if
-
-    ! define a vertical grid spacing such that it is the normal dzsoi if
-    ! nlevdecomp =nlevgrnd, or else 1 meter
-    if (use_vertsoilc) then
-       dzsoi_decomp = dzsoi            !thickness b/n two interfaces
-    else
-       dzsoi_decomp(1) = 1.
-    end if
-
     if (masterproc) then
        write(iulog, *) 'zsoi', zsoi(:) 
        write(iulog, *) 'zisoi: ', zisoi(:)
        write(iulog, *) 'dzsoi: ', dzsoi(:)
-       write(iulog, *) 'dzsoi_decomp: ',dzsoi_decomp
     end if
 
     if (nlevurb > 0) then
@@ -314,91 +136,6 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
 
        ! "0" refers to urban wall/roof surface and "nlevsoi" refers to urban wall/roof bottom
        if (lun%urbpoi(l)) then
-          if (use_vancouver) then       
-             zurb_wall(l,1) = 0.010_r8/2._r8
-             zurb_wall(l,2) = zurb_wall(l,1) + 0.010_r8/2._r8 + 0.020_r8/2._r8
-             zurb_wall(l,3) = zurb_wall(l,2) + 0.020_r8/2._r8 + 0.070_r8/2._r8
-             zurb_wall(l,4) = zurb_wall(l,3) + 0.070_r8/2._r8 + 0.070_r8/2._r8
-             zurb_wall(l,5) = zurb_wall(l,4) + 0.070_r8/2._r8 + 0.030_r8/2._r8
-
-             zurb_roof(l,1) = 0.010_r8/2._r8
-             zurb_roof(l,2) = zurb_roof(l,1) + 0.010_r8/2._r8 + 0.010_r8/2._r8
-             zurb_roof(l,3) = zurb_roof(l,2) + 0.010_r8/2._r8 + 0.010_r8/2._r8
-             zurb_roof(l,4) = zurb_roof(l,3) + 0.010_r8/2._r8 + 0.010_r8/2._r8
-             zurb_roof(l,5) = zurb_roof(l,4) + 0.010_r8/2._r8 + 0.030_r8/2._r8
-
-             dzurb_wall(l,1) = 0.010_r8
-             dzurb_wall(l,2) = 0.020_r8
-             dzurb_wall(l,3) = 0.070_r8
-             dzurb_wall(l,4) = 0.070_r8
-             dzurb_wall(l,5) = 0.030_r8
-             write(iulog,*)'Total thickness of wall: ',sum(dzurb_wall(l,:))
-             write(iulog,*)'Wall layer thicknesses: ',dzurb_wall(l,:)
-
-             dzurb_roof(l,1) = 0.010_r8
-             dzurb_roof(l,2) = 0.010_r8
-             dzurb_roof(l,3) = 0.010_r8
-             dzurb_roof(l,4) = 0.010_r8
-             dzurb_roof(l,5) = 0.030_r8
-             write(iulog,*)'Total thickness of roof: ',sum(dzurb_roof(l,:))
-             write(iulog,*)'Roof layer thicknesses: ',dzurb_roof(l,:)
-
-             ziurb_wall(l,0) = 0.
-             ziurb_wall(l,1) = dzurb_wall(l,1)
-             do j = 2,nlevurb
-                ziurb_wall(l,j) = sum(dzurb_wall(l,1:j))
-             end do
-             write(iulog,*)'Wall layer interface depths: ',ziurb_wall(l,:)
-
-             ziurb_roof(l,0) = 0.
-             ziurb_roof(l,1) = dzurb_roof(l,1)
-             do j = 2,nlevurb
-                ziurb_roof(l,j) = sum(dzurb_roof(l,1:j))
-             end do
-             write(iulog,*)'Roof layer interface depths: ',ziurb_roof(l,:)
-          else if (use_mexicocity) then
-             zurb_wall(l,1) = 0.015_r8/2._r8
-             zurb_wall(l,2) = zurb_wall(l,1) + 0.015_r8/2._r8 + 0.120_r8/2._r8
-             zurb_wall(l,3) = zurb_wall(l,2) + 0.120_r8/2._r8 + 0.150_r8/2._r8
-             zurb_wall(l,4) = zurb_wall(l,3) + 0.150_r8/2._r8 + 0.150_r8/2._r8
-             zurb_wall(l,5) = zurb_wall(l,4) + 0.150_r8/2._r8 + 0.015_r8/2._r8
-
-             zurb_roof(l,1) = 0.010_r8/2._r8
-             zurb_roof(l,2) = zurb_roof(l,1) + 0.010_r8/2._r8 + 0.050_r8/2._r8
-             zurb_roof(l,3) = zurb_roof(l,2) + 0.050_r8/2._r8 + 0.050_r8/2._r8
-             zurb_roof(l,4) = zurb_roof(l,3) + 0.050_r8/2._r8 + 0.050_r8/2._r8
-             zurb_roof(l,5) = zurb_roof(l,4) + 0.050_r8/2._r8 + 0.025_r8/2._r8
-
-             dzurb_wall(l,1) = 0.015_r8
-             dzurb_wall(l,2) = 0.120_r8
-             dzurb_wall(l,3) = 0.150_r8
-             dzurb_wall(l,4) = 0.150_r8
-             dzurb_wall(l,5) = 0.015_r8
-             write(iulog,*)'Total thickness of wall: ',sum(dzurb_wall(l,:))
-             write(iulog,*)'Wall layer thicknesses: ',dzurb_wall(l,:)
-
-             dzurb_roof(l,1) = 0.010_r8
-             dzurb_roof(l,2) = 0.050_r8
-             dzurb_roof(l,3) = 0.050_r8
-             dzurb_roof(l,4) = 0.050_r8
-             dzurb_roof(l,5) = 0.025_r8
-             write(iulog,*)'Total thickness of roof: ',sum(dzurb_roof(l,:))
-             write(iulog,*)'Roof layer thicknesses: ',dzurb_roof(l,:)
-
-             ziurb_wall(l,0) = 0.
-             ziurb_wall(l,1) = dzurb_wall(l,1)
-             do j = 2,nlevurb
-                ziurb_wall(l,j) = sum(dzurb_wall(l,1:j))
-             end do
-             write(iulog,*)'Wall layer interface depths: ',ziurb_wall(l,:)
-
-             ziurb_roof(l,0) = 0.
-             ziurb_roof(l,1) = dzurb_roof(l,1)
-             do j = 2,nlevurb
-                ziurb_roof(l,j) = sum(dzurb_roof(l,1:j))
-             end do
-             write(iulog,*)'Roof layer interface depths: ',ziurb_roof(l,:)
-          else
              do j = 1, nlevurb
                 zurb_wall(l,j) = (j-0.5)*(thick_wall(l)/float(nlevurb))  !node depths
              end do
@@ -429,7 +166,6 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
                 ziurb_roof(l,j) = 0.5*(zurb_roof(l,j)+zurb_roof(l,j+1))          !interface depths
              enddo
              ziurb_roof(l,nlevurb) = zurb_roof(l,nlevurb) + 0.5*dzurb_roof(l,nlevurb)
-          end if
        end if
     end do
 
@@ -471,53 +207,6 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
        deallocate(zurb_wall, zurb_roof, dzurb_wall, dzurb_roof, ziurb_wall, ziurb_roof)
     end if
 
-    !-----------------------------------------------
-    ! Set index defining depth to bedrock
-    !-----------------------------------------------
-
-    allocate(zbedrock_in(bounds%begg:bounds%endg))
-    if (use_bedrock) then
-       call ncd_io(ncid=ncid, varname='zbedrock', flag='read', data=zbedrock_in, dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          if (masterproc) then
-             call endrun( 'ERROR:: zbedrock not found on surface data set, and use_bedrock is true.'//errmsg(sourcefile, __LINE__) )
-          end if
-       end if
-
-    !  if use_bedrock = false, set zbedrock to lowest layer bottom interface
-    else
-       if (masterproc) write(iulog,*) 'not using use_bedrock!!'
-       zbedrock_in(:) = zisoi(nlevsoi)
-    endif
-
-    !  determine minimum index of minimum soil depth
-    jmin_bedrock = 3
-    do j = 3,nlevsoi 
-       if (zisoi(j-1) < zmin_bedrock .and. zisoi(j) >= zmin_bedrock) then
-          jmin_bedrock = j
-       endif
-    enddo
-
-    if (masterproc) write(iulog,*) 'jmin_bedrock: ', jmin_bedrock
-
-    !  Determine gridcell bedrock index
-    do g = bounds%begg,bounds%endg
-       grc%nbedrock(g) = nlevsoi
-       do j = jmin_bedrock,nlevsoi 
-          if (zisoi(j-1) < zbedrock_in(g) .and. zisoi(j) >= zbedrock_in(g)) then
-             grc%nbedrock(g) = j
-          end if
-       end do
-    end do
-
-    !  Set column bedrock index
-    do c = begc, endc
-       g = col%gridcell(c)
-       col%nbedrock(c) = grc%nbedrock(g) 
-    end do
-
-    deallocate(zbedrock_in)
-
     !-----------------------------------------------
     ! Set lake levels and layers (no interfaces)
     !-----------------------------------------------
@@ -538,60 +227,27 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
     deallocate(lakedepth_in)
 
     ! Lake layers
-    if (.not. use_extralakelayers) then
-       dzlak(1) = 0.1_r8
-       dzlak(2) = 1._r8
-       dzlak(3) = 2._r8
-       dzlak(4) = 3._r8
-       dzlak(5) = 4._r8
-       dzlak(6) = 5._r8
-       dzlak(7) = 7._r8
-       dzlak(8) = 7._r8
-       dzlak(9) = 10.45_r8
-       dzlak(10)= 10.45_r8
-
-       zlak(1) =  0.05_r8
-       zlak(2) =  0.6_r8
-       zlak(3) =  2.1_r8
-       zlak(4) =  4.6_r8
-       zlak(5) =  8.1_r8
-       zlak(6) = 12.6_r8
-       zlak(7) = 18.6_r8
-       zlak(8) = 25.6_r8
-       zlak(9) = 34.325_r8
-       zlak(10)= 44.775_r8
-    else
-       dzlak(1) =0.1_r8
-       dzlak(2) =0.25_r8
-       dzlak(3) =0.25_r8
-       dzlak(4) =0.25_r8
-       dzlak(5) =0.25_r8
-       dzlak(6) =0.5_r8
-       dzlak(7) =0.5_r8
-       dzlak(8) =0.5_r8
-       dzlak(9) =0.5_r8
-       dzlak(10) =0.75_r8
-       dzlak(11) =0.75_r8
-       dzlak(12) =0.75_r8
-       dzlak(13) =0.75_r8
-       dzlak(14) =2_r8
-       dzlak(15) =2_r8
-       dzlak(16) =2.5_r8
-       dzlak(17) =2.5_r8
-       dzlak(18) =3.5_r8
-       dzlak(19) =3.5_r8
-       dzlak(20) =3.5_r8
-       dzlak(21) =3.5_r8
-       dzlak(22) =5.225_r8
-       dzlak(23) =5.225_r8
-       dzlak(24) =5.225_r8
-       dzlak(25) =5.225_r8
-
-       zlak(1) = dzlak(1)/2._r8
-       do i=2,nlevlak
-          zlak(i) = zlak(i-1) + (dzlak(i-1)+dzlak(i))/2._r8
-       end do
-    end if
+    dzlak(1) = 0.1_r8
+    dzlak(2) = 1._r8
+    dzlak(3) = 2._r8
+    dzlak(4) = 3._r8
+    dzlak(5) = 4._r8
+    dzlak(6) = 5._r8
+    dzlak(7) = 7._r8
+    dzlak(8) = 7._r8
+    dzlak(9) = 10.45_r8
+    dzlak(10)= 10.45_r8
+
+    zlak(1) =  0.05_r8
+    zlak(2) =  0.6_r8
+    zlak(3) =  2.1_r8
+    zlak(4) =  4.6_r8
+    zlak(5) =  8.1_r8
+    zlak(6) = 12.6_r8
+    zlak(7) = 18.6_r8
+    zlak(8) = 25.6_r8
+    zlak(9) = 34.325_r8
+    zlak(10)= 44.775_r8
 
     do c = bounds%begc,bounds%endc
        l = col%landunit(c)
@@ -635,160 +291,8 @@ subroutine initVertical(bounds, glc_behavior, snow_depth, thick_wall, thick_roof
        end if
     end do
 
-    ! ------------------------------------------------------------------------
-    ! Set classes of layers
-    ! ------------------------------------------------------------------------
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (hasBedrock(col_itype=col%itype(c), lun_itype=lun%itype(l))) then
-          ! NOTE(wjs, 2015-10-17) We are assuming that points with bedrock have both
-          ! "shallow" and "deep" bedrock. Currently, this is not true for lake columns:
-          ! lakes do not distinguish between "shallow" bedrock and "normal" soil.
-          ! However, that was just due to an oversight that is supposed to be corrected
-          ! soon; so to keep things simple we assume that any point with bedrock
-          ! potentially has both shallow and deep bedrock.
-          col%levgrnd_class(c, 1:col%nbedrock(c)) = LEVGRND_CLASS_STANDARD
-          if (col%nbedrock(c) < nlevsoi) then
-             col%levgrnd_class(c, (col%nbedrock(c) + 1) : nlevsoi) = LEVGRND_CLASS_SHALLOW_BEDROCK
-          end if
-          col%levgrnd_class(c, (nlevsoi + 1) : nlevgrnd) = LEVGRND_CLASS_DEEP_BEDROCK
-       else
-          col%levgrnd_class(c, 1:nlevgrnd) = LEVGRND_CLASS_STANDARD
-       end if
-    end do
-
-    do j = 1, nlevgrnd
-       do c = bounds%begc, bounds%endc
-          if (col%z(c,j) == spval) then
-             col%levgrnd_class(c,j) = ispval
-          end if
-       end do
-    end do
-
-    !-----------------------------------------------
-    ! Set cold-start values for snow levels, snow layers and snow interfaces 
-    !-----------------------------------------------
-
-    !call InitSnowLayers(bounds, snow_depth(bounds%begc:bounds%endc))
-
-    !-----------------------------------------------
-    ! Read in topographic index and slope
-    !-----------------------------------------------
-
-    allocate(tslope(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='SLOPE', flag='read', data=tslope, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call shr_sys_abort(' ERROR: TOPOGRAPHIC SLOPE NOT on surfdata file'//&
-            errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = begc,endc
-       g = col%gridcell(c)
-       ! check for near zero slopes, set minimum value
-       col%topo_slope(c) = max(tslope(g), 0.2_r8)
-    end do
-    deallocate(tslope)
-
-    allocate(std(bounds%begg:bounds%endg))
-    call ncd_io(ncid=ncid, varname='STD_ELEV', flag='read', data=std, dim1name=grlnd, readvar=readvar)
-    if (.not. readvar) then
-       call shr_sys_abort(' ERROR: TOPOGRAPHIC STDdev (STD_ELEV) NOT on surfdata file'//&
-            errMsg(sourcefile, __LINE__)) 
-    end if
-    do c = begc,endc
-       g = col%gridcell(c)
-       ! Topographic variables
-       col%topo_std(c) = std(g)
-    end do
-    deallocate(std)
-
-    !-----------------------------------------------
-    ! SCA shape function defined
-    !-----------------------------------------------
-
-    do c = begc,endc
-       l = col%landunit(c)
-       g = col%gridcell(c)
-
-       if (lun%itype(l)==istice_mec .and. glc_behavior%allow_multiple_columns_grc(g)) then
-          ! ice_mec columns already account for subgrid topographic variability through
-          ! their use of multiple elevation classes; thus, to avoid double-accounting for
-          ! topographic variability in these columns, we ignore topo_std and use a fixed
-          ! value of n_melt.
-          col%n_melt(c) = n_melt_glcmec
-       else
-          col%n_melt(c) = 200.0/max(10.0_r8, col%topo_std(c))
-       end if
-
-       ! microtopographic parameter, units are meters (try smooth function of slope)
-
-       slopebeta = 3._r8
-       slopemax = 0.4_r8
-       slope0 = slopemax**(-1._r8/slopebeta)
-       col%micro_sigma(c) = (col%topo_slope(c) + slope0)**(-slopebeta)
-    end do
-
     call ncd_pio_closefile(ncid)
 
   end subroutine initVertical
 
-  !-----------------------------------------------------------------------
-  logical function hasBedrock(col_itype, lun_itype)
-    !
-    ! !DESCRIPTION:
-    ! Returns true if the given column type has a representation of bedrock - i.e., a set
-    ! of layers at the bottom of the column that are treated fundamentally differently
-    ! from the upper layers.
-    !
-    ! !USES:
-    use landunit_varcon, only : istice_mec, isturb_MIN, isturb_MAX
-    use column_varcon  , only : icol_road_perv
-    !
-    ! !ARGUMENTS:
-    integer, intent(in) :: col_itype  ! col%itype value
-    integer, intent(in) :: lun_itype  ! lun%itype value for the landunit on which this column sits
-    ! If we had an easy way to figure out which landunit a column was on based on
-    ! col_itype (which would be very helpful!), then we wouldn't need lun_itype.
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'hasBedrock'
-    !-----------------------------------------------------------------------
-
-    ! TODO(wjs, 2015-10-17) I don't like that the logic here implicitly duplicates logic
-    ! elsewhere in the code. For example, if there were a change in the lake code so that
-    ! it no longer treated the bottom layers as bedrock, then that change would need to be
-    ! reflected here. One solution would be to set some has_bedrock flag in one central
-    ! place, and then have the science code use that. But that could get messy in the
-    ! science code. Another solution would be to decentralize the definition of
-    ! hasBedrock, so that (for example) the lake code itself sets the value for lun_itype
-    ! == istdlak - that way, hasBedrock(lake) would be more likely to get updated
-    ! correctly if the lake logic changes.
-
-    if (lun_itype == istice_mec) then
-       hasBedrock = .false.
-    else if (lun_itype >= isturb_MIN .and. lun_itype <= isturb_MAX) then
-       if (col_itype == icol_road_perv) then
-          hasBedrock = .true.
-       else
-          hasBedrock = .false.
-       end if
-    else
-       hasBedrock = .true.
-    end if
-
-    ! As an independent check of the above logic, assert that, at the very least, any
-    ! hydrologically-active column is given hasBedrock = .true. This is to try to catch
-    ! problems with new column types being added that aren't handled properly by the
-    ! above logic, since (as noted in the todo note above) there is some implicit
-    ! duplication of logic between this routine and other parts of the code, which is
-    ! dangerous. For example, if a new "urban lawn" type is added, then it should have
-    ! hasBedrock = .true. - and this omission will hopefully be caught by this assertion.
-    if (is_hydrologically_active(col_itype=col_itype, lun_itype=lun_itype)) then
-       SHR_ASSERT(hasBedrock, "hasBedrock should be true for all hydrologically-active columns")
-    end if
-
-  end function hasBedrock
-
-
 end module initVerticalMod
diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90
index ebe7eea1f1..b1c68d38d7 100644
--- a/src/main/lnd2atmMod.F90
+++ b/src/main/lnd2atmMod.F90
@@ -9,28 +9,18 @@ module lnd2atmMod
   use shr_kind_mod         , only : r8 => shr_kind_r8
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use shr_log_mod          , only : errMsg => shr_log_errMsg
-  use shr_megan_mod        , only : shr_megan_mechcomps_n
   use clm_varpar           , only : numrad, ndst, nlevgrnd !ndst = number of dust bins.
   use clm_varcon           , only : rair, grav, cpair, hfus, tfrz, spval
   use clm_varctl           , only : iulog
-  use seq_drydep_mod       , only : n_drydep, drydep_method, DD_XLND
   use decompMod            , only : bounds_type
   use subgridAveMod        , only : p2g, c2g 
   use lnd2atmType          , only : lnd2atm_type
   use atm2lndType          , only : atm2lnd_type
-  use ch4Mod               , only : ch4_type
-  use DUSTMod              , only : dust_type
-  use DryDepVelocity       , only : drydepvel_type
-  use VocEmissionMod       , only : vocemis_type
   use EnergyFluxType       , only : energyflux_type
-  use FrictionVelocityMod  , only : frictionvel_type
-  use SolarAbsorbedType    , only : solarabs_type
   use SurfaceAlbedoType    , only : surfalb_type
   use TemperatureType      , only : temperature_type
-  use WaterFluxType        , only : waterflux_type
   use WaterstateType       , only : waterstate_type
   use glcBehaviorMod       , only : glc_behavior_type
-  use glc2lndMod           , only : glc2lnd_type
   use ColumnType           , only : col
   use LandunitType         , only : lun
   use GridcellType         , only : grc                
@@ -41,12 +31,9 @@ module lnd2atmMod
   private
   !
   ! !PUBLIC MEMBER FUNCTIONS:
-  public :: lnd2atm
   public :: lnd2atm_minimal
-
   !
   ! !PRIVATE MEMBER FUNCTIONS:
-  private :: handle_ice_runoff
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -91,11 +78,6 @@ subroutine lnd2atm_minimal(bounds, &
        lnd2atm_inst%h2osno_grc(g) = lnd2atm_inst%h2osno_grc(g)/1000._r8
     end do
 
-    call c2g(bounds, nlevgrnd, &
-         waterstate_inst%h2osoi_vol_col (bounds%begc:bounds%endc, :), &
-         lnd2atm_inst%h2osoi_vol_grc    (bounds%begg:bounds%endg, :), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity')
-
     call p2g(bounds, numrad, &
          surfalb_inst%albd_patch (bounds%begp:bounds%endp, :), &
          lnd2atm_inst%albd_grc   (bounds%begg:bounds%endg, :), &
@@ -111,340 +93,15 @@ subroutine lnd2atm_minimal(bounds, &
          lnd2atm_inst%eflx_lwrad_out_grc      (bounds%begg:bounds%endg), &
          p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
 
+    ! TODO slevis SLIM: Eliminating next assignment returns error:
+    ! Longwave down is <= 0, while eliminating and then changing the
+    ! initialization of t_rad_grc to tfrz in lnd2atmType works but changes
+    ! answers throughout, including in MML variables. See
+    ! /glade/scratch/slevis/ERS_D_Ld60.f19_g16.H_MML_2000_CAM5.cheyenne_gnu.clm-global_uniform_g16_SOM.C.20221207_111523_9gqwvp/ERS_D_Ld60.f19_g16.H_MML_2000_CAM5.cheyenne_gnu.clm-global_uniform_g16_SOM.C.20221207_111523_9gqwvp.clm2.h0.0001-03-02-00000.nc.cprnc.out
     do g = bounds%begg,bounds%endg
        lnd2atm_inst%t_rad_grc(g) = sqrt(sqrt(lnd2atm_inst%eflx_lwrad_out_grc(g)/sb))
     end do
 
   end subroutine lnd2atm_minimal
 
-  !------------------------------------------------------------------------
-  subroutine lnd2atm(bounds, &
-       atm2lnd_inst, surfalb_inst, temperature_inst, frictionvel_inst, &
-       waterstate_inst, waterflux_inst, energyflux_inst, &
-       solarabs_inst, drydepvel_inst,  &
-       vocemis_inst, dust_inst, ch4_inst, glc_behavior, &
-       lnd2atm_inst, &
-       net_carbon_exchange_grc) 
-    !
-    ! !DESCRIPTION:
-    ! Compute lnd2atm_inst component of gridcell derived type
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)           , intent(in)    :: bounds  
-    type(atm2lnd_type)          , intent(in)    :: atm2lnd_inst
-    type(surfalb_type)          , intent(in)    :: surfalb_inst
-    type(temperature_type)      , intent(in)    :: temperature_inst
-    type(frictionvel_type)      , intent(in)    :: frictionvel_inst
-    type(waterstate_type)       , intent(inout) :: waterstate_inst
-    type(waterflux_type)        , intent(inout) :: waterflux_inst
-    type(energyflux_type)       , intent(in)    :: energyflux_inst
-    type(solarabs_type)         , intent(in)    :: solarabs_inst
-    type(drydepvel_type)        , intent(in)    :: drydepvel_inst
-    type(vocemis_type)          , intent(in)    :: vocemis_inst
-    type(dust_type)             , intent(in)    :: dust_inst
-    type(ch4_type)              , intent(in)    :: ch4_inst
-    type(glc_behavior_type)     , intent(in)    :: glc_behavior
-    type(lnd2atm_type)          , intent(inout) :: lnd2atm_inst 
-    real(r8)                    , intent(in)    :: net_carbon_exchange_grc( bounds%begg: )  ! net carbon exchange between land and atmosphere, positive for source (gC/m2/s)
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c, g  ! indices
-    real(r8) :: qflx_ice_runoff_col(bounds%begc:bounds%endc) ! total column-level ice runoff
-    real(r8) :: eflx_sh_ice_to_liq_grc(bounds%begg:bounds%endg) ! sensible heat flux generated from the ice to liquid conversion, averaged to gridcell
-    real(r8), parameter :: amC   = 12.0_r8 ! Atomic mass number for Carbon
-    real(r8), parameter :: amO   = 16.0_r8 ! Atomic mass number for Oxygen
-    real(r8), parameter :: amCO2 = amC + 2.0_r8*amO ! Atomic mass number for CO2
-    ! The following converts g of C to kg of CO2
-    real(r8), parameter :: convertgC2kgCO2 = 1.0e-3_r8 * (amCO2/amC)
-    !------------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(net_carbon_exchange_grc) == (/bounds%endg/)), errMsg(sourcefile, __LINE__))
-
-    call handle_ice_runoff(bounds, waterflux_inst, glc_behavior, &
-         melt_non_icesheet_ice_runoff = lnd2atm_inst%params%melt_non_icesheet_ice_runoff, &
-         qflx_ice_runoff_col = qflx_ice_runoff_col(bounds%begc:bounds%endc), &
-         qflx_liq_from_ice_col = lnd2atm_inst%qflx_liq_from_ice_col(bounds%begc:bounds%endc), &
-         eflx_sh_ice_to_liq_col = lnd2atm_inst%eflx_sh_ice_to_liq_col(bounds%begc:bounds%endc))
-
-    !----------------------------------------------------
-    ! lnd -> atm
-    !----------------------------------------------------
-    
-    ! First, compute the "minimal" set of fields.
-    call lnd2atm_minimal(bounds, &
-         waterstate_inst, surfalb_inst, energyflux_inst, lnd2atm_inst)
-
-    call p2g(bounds, &
-         temperature_inst%t_ref2m_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%t_ref2m_grc       (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         waterstate_inst%q_ref2m_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%q_ref2m_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         frictionvel_inst%u10_clm_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%u_ref10m_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         energyflux_inst%taux_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%taux_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         energyflux_inst%tauy_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%tauy_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         waterflux_inst%qflx_evap_tot_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%qflx_evap_tot_grc     (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         solarabs_inst%fsa_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%fsa_grc    (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         frictionvel_inst%fv_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%fv_grc       (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g(bounds, &
-         frictionvel_inst%ram1_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%ram1_grc       (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-    call p2g( bounds, &
-         energyflux_inst%eflx_sh_tot_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%eflx_sh_tot_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity',c2l_scale_type='urbanf',l2g_scale_type='unity')
-    call c2g( bounds, &
-         energyflux_inst%eflx_sh_precip_conversion_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%eflx_sh_precip_conversion_grc    (bounds%begg:bounds%endg), &
-         c2l_scale_type='urbanf', l2g_scale_type='unity')
-    call c2g( bounds, &
-         lnd2atm_inst%eflx_sh_ice_to_liq_col(bounds%begc:bounds%endc), &
-         eflx_sh_ice_to_liq_grc(bounds%begg:bounds%endg), &
-         c2l_scale_type='urbanf', l2g_scale_type='unity')
-    do g = bounds%begg, bounds%endg
-       lnd2atm_inst%eflx_sh_tot_grc(g) =  lnd2atm_inst%eflx_sh_tot_grc(g) + &
-            lnd2atm_inst%eflx_sh_precip_conversion_grc(g) + &
-            eflx_sh_ice_to_liq_grc(g) - &
-            energyflux_inst%eflx_dynbal_grc(g) 
-    enddo
-
-    call p2g(bounds, &
-         energyflux_inst%eflx_lh_tot_patch (bounds%begp:bounds%endp), &
-         lnd2atm_inst%eflx_lh_tot_grc      (bounds%begg:bounds%endg), &
-         p2c_scale_type='unity', c2l_scale_type= 'urbanf', l2g_scale_type='unity')
-
-    do g = bounds%begg, bounds%endg
-       lnd2atm_inst%net_carbon_exchange_grc(g) = &
-            net_carbon_exchange_grc(g)
-    end do
-    ! Convert from gC/m2/s to kgCO2/m2/s
-    do g = bounds%begg,bounds%endg
-       lnd2atm_inst%net_carbon_exchange_grc(g) = &
-            lnd2atm_inst%net_carbon_exchange_grc(g)*convertgC2kgCO2
-    end do
-
-    ! drydepvel
-    if ( n_drydep > 0 .and. drydep_method == DD_XLND ) then
-       call p2g(bounds, n_drydep, &
-            drydepvel_inst%velocity_patch (bounds%begp:bounds%endp, :), &
-            lnd2atm_inst%ddvel_grc        (bounds%begg:bounds%endg, :), &
-            p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-    endif
-
-    ! voc emission flux
-    if (shr_megan_mechcomps_n>0) then
-       !call p2g(bounds, shr_megan_mechcomps_n, &
-            !vocemis_inst%vocflx_patch(bounds%begp:bounds%endp,:), &
-            !lnd2atm_inst%flxvoc_grc  (bounds%begg:bounds%endg,:), &
-            !p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-    end if
-
-    ! dust emission flux
-    call p2g(bounds, ndst, &
-         dust_inst%flx_mss_vrt_dst_patch(bounds%begp:bounds%endp, :), &
-         lnd2atm_inst%flxdst_grc        (bounds%begg:bounds%endg, :), &
-         p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity')
-
-
-    !----------------------------------------------------
-    ! lnd -> rof
-    !----------------------------------------------------
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_surf_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_qsur_grc   (bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_drain_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_qsub_grc   (bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    do c = bounds%begc, bounds%endc
-       if (col%active(c)) then
-          ! It's not entirely appropriate to put qflx_liq_from_ice_col into
-          ! qflx_qrgwl_col, since this isn't necessarily just glaciers, wetlands and
-          ! lakes. But since we put the liquid portion of snow capping into
-          ! qflx_qrgwl_col, it seems reasonable to put qflx_liq_from_ice_col there as
-          ! well.
-          waterflux_inst%qflx_qrgwl_col(c) = waterflux_inst%qflx_qrgwl_col(c) + &
-               lnd2atm_inst%qflx_liq_from_ice_col(c)
-
-          ! qflx_runoff is the sum of a number of terms, including qflx_qrgwl. Since we
-          ! are adjusting qflx_qrgwl above, we need to adjust qflx_runoff analogously.
-          waterflux_inst%qflx_runoff_col(c) = waterflux_inst%qflx_runoff_col(c) + &
-               lnd2atm_inst%qflx_liq_from_ice_col(c)
-       end if
-    end do
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_qrgwl_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_qgwl_grc   (bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_runoff_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_grc   (bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    do g = bounds%begg, bounds%endg
-       lnd2atm_inst%qflx_rofliq_qgwl_grc(g) = lnd2atm_inst%qflx_rofliq_qgwl_grc(g) - waterflux_inst%qflx_liq_dynbal_grc(g)
-       lnd2atm_inst%qflx_rofliq_grc(g) = lnd2atm_inst%qflx_rofliq_grc(g) - waterflux_inst%qflx_liq_dynbal_grc(g)
-    enddo
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_h2osfc_surf_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_h2osfc_grc(bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    call c2g( bounds, &
-         waterflux_inst%qflx_drain_perched_col (bounds%begc:bounds%endc), &
-         lnd2atm_inst%qflx_rofliq_drain_perched_grc(bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-
-    call c2g( bounds, &
-         qflx_ice_runoff_col(bounds%begc:bounds%endc),  &
-         lnd2atm_inst%qflx_rofice_grc(bounds%begg:bounds%endg),  & 
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-    do g = bounds%begg, bounds%endg
-       lnd2atm_inst%qflx_rofice_grc(g) = lnd2atm_inst%qflx_rofice_grc(g) - waterflux_inst%qflx_ice_dynbal_grc(g)          
-    enddo
-
-    ! calculate total water storage for history files
-    ! first set tws to gridcell total endwb
-    ! second add river storage as gridcell average depth (1.e-3 converts [m3/km2] to [mm])
-    ! TODO - this was in BalanceCheckMod - not sure where it belongs?
-
-    call c2g( bounds, &
-         waterstate_inst%endwb_col(bounds%begc:bounds%endc), &
-         waterstate_inst%tws_grc  (bounds%begg:bounds%endg), &
-         c2l_scale_type= 'urbanf', l2g_scale_type='unity' )
-    do g = bounds%begg, bounds%endg
-       waterstate_inst%tws_grc(g) = waterstate_inst%tws_grc(g) + atm2lnd_inst%volr_grc(g) / grc%area(g) * 1.e-3_r8
-    enddo
-
-  end subroutine lnd2atm
-
-  !-----------------------------------------------------------------------
-  subroutine handle_ice_runoff(bounds, waterflux_inst, glc_behavior, &
-       melt_non_icesheet_ice_runoff, &
-       qflx_ice_runoff_col, qflx_liq_from_ice_col, eflx_sh_ice_to_liq_col)
-    !
-    ! !DESCRIPTION:
-    ! Take column-level ice runoff and divide it between (a) ice runoff, and (b) liquid
-    ! runoff with a compensating negative sensible heat flux.
-    !
-    ! The rationale here is: Ice runoff is largely meant to represent a crude
-    ! parameterization of iceberg calving. Iceberg calving is mainly appropriate in
-    ! regions where an ice sheet terminates at the land-ocean boundary. Elsewhere, in
-    ! reality, we expect most ice runoff to flow downstream and melt before it reaches the
-    ! ocean. Furthermore, sending ice runoff directly to the ocean can lead to runaway sea
-    ! ice growth in some regions (around the Canadian archipelago, and possibly in more
-    ! wide-spread regions of the Arctic Ocean); melting this ice before it reaches the
-    ! ocean avoids this problem.
-    !
-    ! If the river model were able to melt ice, then we might not need this routine.
-    !
-    ! Note that this routine does NOT handle ice runoff generated via the dynamic
-    ! landunits adjustment fluxes (i.e., the fluxes that compensate for a difference in
-    ! ice content between the pre- and post-dynamic landunit areas). This is partly
-    ! because those gridcell-level dynamic landunits adjustment fluxes do not fit well
-    ! with this column-based infrastructure, and partly because either method of handling
-    ! these fluxes (i.e., sending an ice runoff or sending a liquid runoff with a
-    ! negative sensible heat flux) seems equally justifiable.
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(bounds_type), intent(in) :: bounds
-    type(waterflux_type), intent(in) :: waterflux_inst
-    type(glc_behavior_type), intent(in) :: glc_behavior
-    logical, intent(in) :: melt_non_icesheet_ice_runoff
-    real(r8), intent(out) :: qflx_ice_runoff_col( bounds%begc: ) ! total column-level ice runoff (mm H2O /s)
-    real(r8), intent(out) :: qflx_liq_from_ice_col( bounds%begc: ) ! liquid runoff from converted ice runoff (mm H2O /s)
-    real(r8), intent(out) :: eflx_sh_ice_to_liq_col( bounds%begc: ) ! sensible heat flux generated from the ice to liquid conversion (W/m2) (+ to atm)
-
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c, l, g
-    logical :: do_conversion
-
-    character(len=*), parameter :: subname = 'handle_ice_runoff'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(qflx_ice_runoff_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(qflx_liq_from_ice_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(eflx_sh_ice_to_liq_col) == (/bounds%endc/)), errMsg(sourcefile, __LINE__))
-
-    do c = bounds%begc, bounds%endc
-       if (col%active(c)) then
-          qflx_ice_runoff_col(c) = waterflux_inst%qflx_ice_runoff_snwcp_col(c) + &
-               waterflux_inst%qflx_ice_runoff_xs_col(c)
-          qflx_liq_from_ice_col(c) = 0._r8
-          eflx_sh_ice_to_liq_col(c) = 0._r8
-       end if
-    end do
-
-    if (melt_non_icesheet_ice_runoff) then
-       do c = bounds%begc, bounds%endc
-          if (col%active(c)) then
-             l = col%landunit(c)
-             g = col%gridcell(c)
-             do_conversion = .false.
-             if (lun%itype(l) /= istice_mec) then
-                do_conversion = .true.
-             else  ! istice_mec
-                if (glc_behavior%ice_runoff_melted_grc(g)) then
-                   do_conversion = .true.
-                else
-                   do_conversion = .false.
-                end if
-             end if
-             if (do_conversion) then
-                ! ice to liquid absorbs energy, so results in a negative heat flux to atm
-                ! Note that qflx_ice_runoff_col is in mm H2O/s, which is the same as kg
-                ! m-2 s-1, so we can simply multiply by hfus.
-                eflx_sh_ice_to_liq_col(c) = -qflx_ice_runoff_col(c) * hfus
-                qflx_liq_from_ice_col(c) = qflx_ice_runoff_col(c)
-                qflx_ice_runoff_col(c) = 0._r8
-             end if
-          end if
-       end do
-    end if
-
-  end subroutine handle_ice_runoff
-
-
 end module lnd2atmMod
diff --git a/src/main/lnd2atmType.F90 b/src/main/lnd2atmType.F90
index fbfab7b862..6cefaed1ee 100644
--- a/src/main/lnd2atmType.F90
+++ b/src/main/lnd2atmType.F90
@@ -13,26 +13,15 @@ module lnd2atmType
   use clm_varpar    , only : numrad, ndst, nlevgrnd !ndst = number of dust bins. 	! MML: ndst = 4 from clm varpar
   use clm_varcon    , only : spval
   use clm_varctl    , only : iulog
-  use shr_megan_mod , only : shr_megan_mechcomps_n
-  use shr_fire_emis_mod,only : shr_fire_emis_mechcomps_n
-  use seq_drydep_mod, only : n_drydep, drydep_method, DD_XLND
   !
   ! !PUBLIC TYPES:
   implicit none
   private
 
-  type, public :: lnd2atm_params_type
-     ! true => ice runoff generated from non-glacier columns and glacier columns outside
-     ! icesheet regions is converted to liquid, with an appropriate sensible heat flux
-     logical, public :: melt_non_icesheet_ice_runoff
-  end type lnd2atm_params_type
-
   ! ----------------------------------------------------
   ! land -> atmosphere variables structure
   !----------------------------------------------------
   type, public :: lnd2atm_type
-     type(lnd2atm_params_type) :: params
-
      ! lnd->atm
      real(r8), pointer :: t_rad_grc          (:)   => null() ! radiative temperature (Kelvin)
      ! MML check tech note for examples on how to calculate this; use MO theory
@@ -50,7 +39,6 @@ module lnd2atmType
      real(r8), pointer :: tauy_grc           (:)   => null() ! wind stress: n-s (kg/m/s**2)
      real(r8), pointer :: eflx_lh_tot_grc    (:)   => null() ! total latent HF (W/m**2)  [+ to atm]
      real(r8), pointer :: eflx_sh_tot_grc    (:)   => null() ! total sensible HF (W/m**2) [+ to atm]
-     real(r8), pointer :: eflx_sh_precip_conversion_grc(:) => null() ! sensible HF from precipitation conversion (W/m**2) [+ to atm]
      real(r8), pointer :: eflx_sh_ice_to_liq_col(:) => null() ! sensible HF generated from conversion of ice runoff to liquid (W/m**2) [+ to atm]
      real(r8), pointer :: eflx_lwrad_out_grc (:)   => null() ! IR (longwave) radiation (W/m**2)
      real(r8), pointer :: qflx_evap_tot_grc  (:)   => null() ! qflx_evap_soi + qflx_evap_can + qflx_tran_veg
@@ -61,10 +49,6 @@ module lnd2atmType
      real(r8), pointer :: fv_grc             (:)   => null() ! friction velocity (m/s) (for dust model)
      real(r8), pointer :: flxdst_grc         (:,:) => null() ! dust flux (size bins)
      real(r8), pointer :: ddvel_grc          (:,:) => null() ! dry deposition velocities
-     real(r8), pointer :: flxvoc_grc         (:,:) => null() ! VOC flux (size bins)
-     real(r8), pointer :: fireflx_grc        (:,:) => null() ! Wild Fire Emissions
-     real(r8), pointer :: fireztop_grc       (:)   => null() ! Wild Fire Emissions vertical distribution top
-     real(r8), pointer :: flux_ch4_grc       (:)   => null() ! net CH4 flux (kg C/m**2/s) [+ to atm]
      ! lnd->rof
      real(r8), pointer :: qflx_rofliq_grc         (:)   => null() ! rof liq forcing
      real(r8), pointer :: qflx_rofliq_qsur_grc    (:)   => null() ! rof liq -- surface runoff component
@@ -74,58 +58,29 @@ module lnd2atmType
      real(r8), pointer :: qflx_rofliq_drain_perched_grc    (:)   => null() ! rof liq -- perched water table runoff component
      real(r8), pointer :: qflx_rofice_grc    (:)   => null() ! rof ice forcing
      real(r8), pointer :: qflx_liq_from_ice_col(:) => null() ! liquid runoff from converted ice runoff
-     real(r8), pointer :: qirrig_grc         (:)   => null() ! irrigation flux
 
    contains
 
      procedure, public  :: Init
-     procedure, private :: ReadNamelist
      procedure, private :: InitAllocate 
      procedure, private :: InitHistory  
 
   end type lnd2atm_type
   !------------------------------------------------------------------------
 
-  interface lnd2atm_params_type
-     module procedure lnd2atm_params_constructor
-  end interface lnd2atm_params_type
-
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
   !------------------------------------------------------------------------
 
 contains
 
-  !-----------------------------------------------------------------------
-  function lnd2atm_params_constructor(melt_non_icesheet_ice_runoff) &
-       result(params)
-    !
-    ! !DESCRIPTION:
-    ! Creates a new instance of lnd2atm_params_type
-    !
-    ! !ARGUMENTS:
-    type(lnd2atm_params_type) :: params  ! function result
-    logical, intent(in) :: melt_non_icesheet_ice_runoff
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'lnd2atm_params_type'
-    !-----------------------------------------------------------------------
-
-    params%melt_non_icesheet_ice_runoff = melt_non_icesheet_ice_runoff
-
-  end function lnd2atm_params_constructor
-
-
   !------------------------------------------------------------------------
-  subroutine Init(this, bounds, NLFilename)
+  subroutine Init(this, bounds)
 
     class(lnd2atm_type) :: this
     type(bounds_type), intent(in) :: bounds  
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
 
     call this%InitAllocate(bounds)
-    call this%ReadNamelist(NLFilename)
     call this%InitHistory(bounds)
     
   end subroutine Init
@@ -161,7 +116,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%tauy_grc           (begg:endg))            ; this%tauy_grc           (:)   =ival
     allocate(this%eflx_lwrad_out_grc (begg:endg))            ; this%eflx_lwrad_out_grc (:)   =ival
     allocate(this%eflx_sh_tot_grc    (begg:endg))            ; this%eflx_sh_tot_grc    (:)   =ival
-    allocate(this%eflx_sh_precip_conversion_grc(begg:endg))  ; this%eflx_sh_precip_conversion_grc(:) = ival
     allocate(this%eflx_sh_ice_to_liq_col(begc:endc))         ; this%eflx_sh_ice_to_liq_col(:) = ival
     allocate(this%eflx_lh_tot_grc    (begg:endg))            ; this%eflx_lh_tot_grc    (:)   =ival
     allocate(this%qflx_evap_tot_grc  (begg:endg))            ; this%qflx_evap_tot_grc  (:)   =ival
@@ -171,7 +125,6 @@ subroutine InitAllocate(this, bounds)
     allocate(this%ram1_grc           (begg:endg))            ; this%ram1_grc           (:)   =ival
     allocate(this%fv_grc             (begg:endg))            ; this%fv_grc             (:)   =ival
     allocate(this%flxdst_grc         (begg:endg,1:ndst))     ; this%flxdst_grc         (:,:) =ival
-    allocate(this%flux_ch4_grc       (begg:endg))            ; this%flux_ch4_grc       (:)   =ival
     allocate(this%qflx_rofliq_grc    (begg:endg))            ; this%qflx_rofliq_grc    (:)   =ival
     allocate(this%qflx_rofliq_qsur_grc    (begg:endg))       ; this%qflx_rofliq_qsur_grc    (:)   =ival
     allocate(this%qflx_rofliq_qsub_grc    (begg:endg))       ; this%qflx_rofliq_qsub_grc    (:)   =ival
@@ -180,86 +133,9 @@ subroutine InitAllocate(this, bounds)
     allocate(this%qflx_rofliq_drain_perched_grc    (begg:endg))       ; this%qflx_rofliq_drain_perched_grc    (:)   =ival
     allocate(this%qflx_rofice_grc    (begg:endg))            ; this%qflx_rofice_grc    (:)   =ival
     allocate(this%qflx_liq_from_ice_col(begc:endc))          ; this%qflx_liq_from_ice_col(:) = ival
-    allocate(this%qirrig_grc         (begg:endg))            ; this%qirrig_grc         (:)   =ival
-
-    if (shr_megan_mechcomps_n>0) then
-       allocate(this%flxvoc_grc(begg:endg,1:shr_megan_mechcomps_n));  this%flxvoc_grc(:,:)=ival
-    endif
-    if (shr_fire_emis_mechcomps_n>0) then
-       allocate(this%fireflx_grc(begg:endg,1:shr_fire_emis_mechcomps_n))
-       this%fireflx_grc = ival
-       allocate(this%fireztop_grc(begg:endg))
-       this%fireztop_grc = ival
-    endif
-    if ( n_drydep > 0 .and. drydep_method == DD_XLND )then
-       allocate(this%ddvel_grc(begg:endg,1:n_drydep)); this%ddvel_grc(:,:)=ival
-    end if
 
   end subroutine InitAllocate
 
-  !-----------------------------------------------------------------------
-  subroutine ReadNamelist(this, NLFilename)
-    !
-    ! !DESCRIPTION:
-    ! Read the lnd2atm namelist
-    !
-    ! !USES:
-    use fileutils      , only : getavu, relavu, opnfil
-    use shr_nl_mod     , only : shr_nl_find_group_name
-    use spmdMod        , only : masterproc, mpicom
-    use shr_mpi_mod    , only : shr_mpi_bcast
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: NLFilename ! Namelist filename
-    class(lnd2atm_type), intent(inout) :: this
-    !
-    ! !LOCAL VARIABLES:
-
-    ! temporary variables corresponding to the components of lnd2atm_params_type
-    logical :: melt_non_icesheet_ice_runoff
-
-    integer :: ierr                 ! error code
-    integer :: unitn                ! unit for namelist file
-    character(len=*), parameter :: nmlname = 'lnd2atm_inparm'
-
-    character(len=*), parameter :: subname = 'ReadNamelist'
-    !-----------------------------------------------------------------------
-
-    namelist /lnd2atm_inparm/ melt_non_icesheet_ice_runoff
-
-    ! Initialize namelist variables to defaults
-    melt_non_icesheet_ice_runoff = .false.
-
-    if (masterproc) then
-       unitn = getavu()
-       write(iulog,*) 'Read in '//nmlname//'  namelist'
-       call opnfil (NLFilename, unitn, 'F')
-       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
-       if (ierr == 0) then
-          read(unitn, nml=lnd2atm_inparm, iostat=ierr)
-          if (ierr /= 0) then
-             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-          end if
-       else
-          call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
-       end if
-       call relavu( unitn )
-    end if
-
-    call shr_mpi_bcast(melt_non_icesheet_ice_runoff, mpicom)
-
-    if (masterproc) then
-       write(iulog,*)
-       write(iulog,*) nmlname, ' settings:'
-       write(iulog,nml=lnd2atm_inparm)
-       write(iulog,*) ' '
-    end if
-
-    this%params = lnd2atm_params_type( &
-         melt_non_icesheet_ice_runoff = melt_non_icesheet_ice_runoff)
-
-  end subroutine ReadNamelist
-
   !-----------------------------------------------------------------------
   subroutine InitHistory(this, bounds)
     !
@@ -271,11 +147,9 @@ subroutine InitHistory(this, bounds)
     type(bounds_type), intent(in) :: bounds  
     !
     ! !LOCAL VARIABLES:
-    integer  :: begc, endc
     integer  :: begg, endg
     !---------------------------------------------------------------------
 
-    begc = bounds%begc; endc = bounds%endc
     begg = bounds%begg; endg = bounds%endg
 
     this%eflx_sh_tot_grc(begg:endg) = 0._r8
@@ -285,37 +159,6 @@ subroutine InitHistory(this, bounds)
               &(includes corrections for land use change, rain/snow conversion and conversion of ice runoff to liquid)', &
          ptr_lnd=this%eflx_sh_tot_grc)
 
-    this%eflx_sh_ice_to_liq_col(begc:endc) = 0._r8
-    call hist_addfld1d (fname='FSH_RUNOFF_ICE_TO_LIQ', units='W/m^2', &
-         avgflag='A', &
-         long_name='sensible heat flux generated from conversion of ice runoff to liquid', &
-         ptr_col=this%eflx_sh_ice_to_liq_col)
-
-    this%qflx_rofliq_grc(begg:endg) = 0._r8
-    call hist_addfld1d (fname='QRUNOFF_TO_COUPLER',  units='mm/s',  &
-         avgflag='A', &
-         long_name='total liquid runoff sent to coupler (includes corrections for land use change)', &
-         ptr_lnd=this%qflx_rofliq_grc)
-
-    this%qflx_rofice_grc(begg:endg) = 0._r8
-    call hist_addfld1d (fname='QRUNOFF_ICE_TO_COUPLER',  units='mm/s',  &
-         avgflag='A', &
-         long_name='total ice runoff sent to coupler (includes corrections for land use change)', &
-         ptr_lnd=this%qflx_rofice_grc)
-
-    this%qflx_liq_from_ice_col(begc:endc) = 0._r8
-    call hist_addfld1d (fname='QRUNOFF_ICE_TO_LIQ', units='mm/s', &
-         avgflag='A', &
-         long_name='liquid runoff from converted ice runoff', &
-         ptr_col=this%qflx_liq_from_ice_col, default='inactive')
-
-    this%net_carbon_exchange_grc(begg:endg) = spval
-    call hist_addfld1d(fname='FCO2', units='kgCO2/m2/s', &
-         avgflag='A', &
-         long_name='CO2 flux to atmosphere (+ to atm)', &
-         ptr_lnd=this%net_carbon_exchange_grc, &
-         default='inactive')
-
   end subroutine InitHistory
 
 end module lnd2atmType
diff --git a/src/main/lnd2glcMod.F90 b/src/main/lnd2glcMod.F90
deleted file mode 100644
index 9de7eba3f3..0000000000
--- a/src/main/lnd2glcMod.F90
+++ /dev/null
@@ -1,304 +0,0 @@
-module lnd2glcMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Handle arrays used for exchanging data from land model to glc
-  ! For now glc datais send and received on the lnd grid and decomposition.
-  !
-  ! The fields sent from the lnd component to the glc component via
-  !  the coupler are labeled 's2x', or sno to coupler.
-  ! The fields received by the lnd component from the glc component
-  !  via the coupler are labeled 'x2s', or coupler to sno.
-  ! 'Sno' is a misnomer in that the exchanged data are related to
-  !  the ice beneath the snow, not the snow itself.  But by CESM convention,
-  ! 'ice' refers to sea ice, not land ice.
-  !
-  ! !USES:
-  use shr_kind_mod    , only : r8 => shr_kind_r8
-  use shr_infnan_mod  , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod     , only : errMsg => shr_log_errMsg
-  use decompMod       , only : get_proc_bounds, bounds_type
-  use domainMod       , only : ldomain
-  use clm_varpar      , only : maxpatch_glcmec
-  use clm_varctl      , only : iulog
-  use clm_varcon      , only : spval, tfrz, namec
-  use column_varcon   , only : col_itype_to_icemec_class
-  use landunit_varcon , only : istice_mec, istsoil
-  use abortutils      , only : endrun
-  use GlacierSurfaceMassBalanceMod, only : glacier_smb_type
-  use TemperatureType , only : temperature_type
-  use LandunitType    , only : lun                
-  use ColumnType      , only : col
-  use TopoMod         , only : topo_type
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  ! land -> glc variables structure
-  type, public :: lnd2glc_type
-     real(r8), pointer :: tsrf_grc(:,:) => null()
-     real(r8), pointer :: topo_grc(:,:) => null()
-     real(r8), pointer :: qice_grc(:,:) => null()
-
-   contains
-
-     procedure, public  :: Init
-     procedure, public  :: update_lnd2glc
-     procedure, private :: InitAllocate
-     procedure, private :: InitHistory
-
-  end type lnd2glc_type
-
-  ! !PUBLIC MEMBER FUNCTIONS:
-  
-  ! The following is public simply to support unit testing, and should not generally be
-  ! called from outside this module.
-  !
-  ! Note that it is not a type-bound procedure, because it doesn't actually involve the
-  ! lnd2glc_type. This suggests that perhaps it belongs in some other module.
-  public :: bareland_normalization ! compute normalization factor for fluxes from the bare land portion of the grid cell
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(lnd2glc_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate(bounds)
-    call this%InitHistory(bounds)
-    
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize land variables required by glc
-    !
-    ! !USES:
-    use clm_varcon , only : spval
-    use histFileMod, only : hist_addfld1d
-    !
-    ! !ARGUMENTS:
-    class(lnd2glc_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begg,endg 
-    !------------------------------------------------------------------------
-
-    begg = bounds%begg; endg = bounds%endg
-
-    allocate(this%tsrf_grc(begg:endg,0:maxpatch_glcmec)) ; this%tsrf_grc(:,:)=0.0_r8
-    allocate(this%topo_grc(begg:endg,0:maxpatch_glcmec)) ; this%topo_grc(:,:)=0.0_r8
-    allocate(this%qice_grc(begg:endg,0:maxpatch_glcmec)) ; this%qice_grc(:,:)=0.0_r8
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d,hist_addfld2d 
-    !
-    ! !ARGUMENTS:
-    class(lnd2glc_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), pointer :: data2dptr(:,:)
-    integer  :: begg, endg
-    !---------------------------------------------------------------------
-
-    begg = bounds%begg; endg = bounds%endg
-
-    this%qice_grc(begg:endg,0:maxpatch_glcmec) = spval
-    ! For this and the following fields, set up a pointer to the field simply for the
-    ! sake of changing the indexing, so that levels start with an index of 1, as is
-    ! assumed by histFileMod - so levels go 1:(nec+1) rather than 0:nec
-    data2dptr => this%qice_grc(:,0:maxpatch_glcmec)
-    call hist_addfld2d (fname='QICE_FORC', units='mm/s', type2d='elevclas', &
-         avgflag='A', long_name='qice forcing sent to GLC', &
-         ptr_lnd=data2dptr, default='inactive')
-
-    this%tsrf_grc(begg:endg,0:maxpatch_glcmec) = spval
-    data2dptr => this%tsrf_grc(:,0:maxpatch_glcmec)
-    call hist_addfld2d (fname='TSRF_FORC', units='K', type2d='elevclas', &
-         avgflag='A', long_name='surface temperature sent to GLC', &
-         ptr_lnd=data2dptr, default='inactive')
-
-    this%topo_grc(begg:endg,0:maxpatch_glcmec) = spval
-    data2dptr => this%topo_grc(:,0:maxpatch_glcmec)
-    call hist_addfld2d (fname='TOPO_FORC', units='m', type2d='elevclas', &
-         avgflag='A', long_name='topograephic height sent to GLC', &
-         ptr_lnd=data2dptr, default='inactive')
-
-  end subroutine InitHistory
-
-
-  !------------------------------------------------------------------------------
-  subroutine update_lnd2glc(this, bounds, num_do_smb_c, filter_do_smb_c, &
-       temperature_inst, glacier_smb_inst, topo_inst, init)
-    !
-    ! !DESCRIPTION:
-    ! Assign values to lnd2glc+
-    !
-    ! !ARGUMENTS:
-    class(lnd2glc_type)    , intent(inout) :: this
-    type(bounds_type)      , intent(in)    :: bounds  
-    integer                , intent(in)    :: num_do_smb_c       ! number of columns in filter_do_smb_c
-    integer                , intent(in)    :: filter_do_smb_c(:) ! column filter: columns where smb calculations are performed
-    type(temperature_type) , intent(in)    :: temperature_inst
-    type(glacier_smb_type) , intent(in)    :: glacier_smb_inst
-    type(topo_type)        , intent(in)    :: topo_inst
-    logical                , intent(in)    :: init               ! if true=>only set a subset of fields
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c, l, g, n, fc                   ! indices
-    logical, allocatable :: fields_assigned(:,:) ! tracks whether fields have already been assigned for each index [begg:endg, 0:maxpatch_glcmec]
-    real(r8) :: flux_normalization               ! factor by which fluxes should be normalized
-
-    character(len=*), parameter :: subname = 'update_lnd2glc'
-    !------------------------------------------------------------------------------
-
-    ! Initialize to reasonable defaults
-
-    this%qice_grc(bounds%begg : bounds%endg, :) = 0._r8
-    this%tsrf_grc(bounds%begg : bounds%endg, :) = tfrz
-    this%topo_grc(bounds%begg : bounds%endg, :) = 0._r8     
-  
-    ! Fill the lnd->glc data on the clm grid
-
-    allocate(fields_assigned(bounds%begg:bounds%endg, 0:maxpatch_glcmec))
-    fields_assigned(:,:) = .false.
-
-    do fc = 1, num_do_smb_c
-      c = filter_do_smb_c(fc)
-      l = col%landunit(c)
-      g = col%gridcell(c) 
-
-      ! Set vertical index and a flux normalization, based on whether the column in question is glacier or vegetated.  
-      if (lun%itype(l) == istice_mec) then
-         n = col_itype_to_icemec_class(col%itype(c))
-         flux_normalization = 1.0_r8
-      else if (lun%itype(l) == istsoil) then
-         n = 0  !0-level index (bareland information)
-         flux_normalization = bareland_normalization(c)
-      else
-         ! Other landunit types do not pass information in the lnd2glc fields.
-         ! Note: for this to be acceptable, we need virtual vegetated columns in any grid
-         ! cell that is made up solely of glacier plus some other special landunit (e.g.,
-         ! glacier + lake) -- otherwise CISM wouldn't have any information for the non-
-         ! glaciated portion of the grid cell.
-         cycle
-      end if
-
-      ! Make sure we haven't already assigned the coupling fields for this point
-      ! (this could happen, for example, if there were multiple columns in the
-      ! istsoil landunit, which we aren't prepared to handle)
-      if (fields_assigned(g,n)) then
-         write(iulog,*) subname//' ERROR: attempt to assign coupling fields twice for the same index.'
-         write(iulog,*) 'One possible cause is having multiple columns in the istsoil landunit,'
-         write(iulog,*) 'which this routine cannot handle.'
-         write(iulog,*) 'g, n = ', g, n
-         call endrun(decomp_index=c, clmlevel=namec, msg=errMsg(sourcefile, __LINE__))
-      end if
-
-      ! Send surface temperature, topography, and SMB flux (qice) to coupler.
-      ! t_soisno and topo_col are valid even in initialization, so tsrf and topo
-      ! are set here regardless of the value of init. But qflx_glcice is not valid
-      ! until the run loop; thus, in initialization, we will use the default value
-      ! for qice, as set above.
-      fields_assigned(g,n) = .true.
-      this%tsrf_grc(g,n) = temperature_inst%t_soisno_col(c,1)
-      this%topo_grc(g,n) = topo_inst%topo_col(c)
-      if (.not. init) then
-         this%qice_grc(g,n) = glacier_smb_inst%qflx_glcice_col(c) * flux_normalization
-
-         ! Check for bad values of qice
-         if ( abs(this%qice_grc(g,n)) > 1.0_r8) then
-            write(iulog,*) 'WARNING: qice out of bounds: g, n, qice =', g, n, this%qice_grc(g,n)
-         end if
-      end if
-
-    end do
-
-    deallocate(fields_assigned)
-                
-  end subroutine update_lnd2glc
-
-  !-----------------------------------------------------------------------
-  real(r8) function bareland_normalization(c)
-    !
-    ! !DESCRIPTION:
-    ! Compute normalization factor for fluxes from the bare land portion of the grid
-    ! cell. Fluxes should be multiplied by this factor before being sent to CISM.
-    !
-    ! The point of this is: CISM effectively has two land cover types: glaciated and
-    ! bare. CLM, on the other hand, subdivides the bare land portion of the grid cell into
-    ! multiple landunits. However, we currently don't do any sort of averaging of
-    ! quantities computed in the different "bare land" landunits - instead, we simply send
-    ! the values computed in the natural vegetated landunit - these fluxes (like SMB) are
-    ! 0 in the other landunits. To achieve conservation, we need to normalize these
-    ! natural veg. fluxes by the fraction of the "bare land" area accounted for by the
-    ! natural veg. landunit.
-    !
-    ! For example, consider a grid cell that is:
-    !   60% glacier_mec
-    !   30% natural veg
-    !   10% lake
-    !
-    ! According to CISM, this grid cell is 60% icesheet, 40% "bare land". Now suppose CLM
-    ! has an SMB flux of 1m in the natural veg landunit. If we simply sent 1m of ice to
-    ! CISM, conservation would be broken, since it would also apply 1m of ice to the 10%
-    ! of the grid cell that CLM says is lake. So, instead, we must multiply the 1m of ice
-    ! by (0.3/0.4), thus "spreading out" the SMB from the natural veg. landunit, so that
-    ! 0.75m of ice is grown throughout the bare land portion of CISM.
-    !
-    ! Note: If the non-glaciated area of the grid cell is 0, then we arbitrarily return a
-    ! normalization factor of 1.0, in order to avoid divide-by-zero errors.
-    !
-    ! Note: We currently aren't careful about how we would handle things if there are
-    ! multiple columns within the vegetated landunit. If that possibility were introduced,
-    ! this code - as well as the code in update_clm_s2x - may need to be reworked somewhat.
-    !
-    ! !USES:
-    use subgridWeightsMod , only : get_landunit_weight
-    !
-    ! !ARGUMENTS:
-    integer, intent(in) :: c  ! column index
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: g             ! grid cell index
-    real(r8) :: area_glacier  ! fractional area of the glacier_mec landunit in this grid cell
-    real(r8) :: area_this_col ! fractional area of column c in the grid cell
-
-    real(r8), parameter :: tol = 1.e-13_r8  ! tolerance for checking subgrid weight equality
-    character(len=*), parameter :: subname = 'bareland_normalization'
-    !-----------------------------------------------------------------------
-
-    g = col%gridcell(c)
-
-    area_glacier = get_landunit_weight(g, istice_mec)
-
-    if (abs(area_glacier - 1.0_r8) < tol) then
-       ! If the whole grid cell is glacier, then the normalization factor is arbitrary;
-       ! set it to 1 so we don't do any normalization in this case
-       bareland_normalization = 1.0_r8
-    else
-       area_this_col = col%wtgcell(c)
-       bareland_normalization = area_this_col / (1.0_r8 - area_glacier)
-    end if
-
-  end function bareland_normalization
-
-end module lnd2glcMod
-
diff --git a/src/main/ndepStreamMod.F90 b/src/main/ndepStreamMod.F90
deleted file mode 100644
index c6147255eb..0000000000
--- a/src/main/ndepStreamMod.F90
+++ /dev/null
@@ -1,126 +0,0 @@
-module ndepStreamMod
-
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION: 
-  ! Contains methods for reading in nitrogen deposition data file
-  ! Also includes functions for dynamic ndep file handling and 
-  ! interpolation.
-  !
-  ! !USES
-  use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl 
-  use mct_mod     , only: mct_ggrid
-  use spmdMod     , only: mpicom, iam
-  use clm_varctl  , only: iulog
-  use abortutils  , only: endrun
-  use decompMod   , only: bounds_type, gsmap_lnd_gdc2glo 
-  use domainMod   , only: ldomain
-
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-
-  public :: clm_domain_mct ! Sets up MCT domain for this resolution
-
-  ! ! PRIVATE TYPES
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !==============================================================================
-
-contains
-
- !==============================================================================
-  subroutine clm_domain_mct(bounds, dom_clm)
-
-    !-------------------------------------------------------------------
-    ! Set domain data type for internal clm grid
-    use clm_varcon  , only : re
-    use domainMod   , only : ldomain
-    use seq_flds_mod
-    use mct_mod     , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init
-    use mct_mod     , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr
-    use mct_mod     , only : mct_gGrid_importRAttr
-    implicit none
-    ! 
-    ! arguments
-    type(bounds_type), intent(in) :: bounds  
-    type(mct_ggrid), intent(out)   :: dom_clm     ! Output domain information for land model
-    !
-    ! local variables
-    integer :: g,i,j              ! index
-    integer :: lsize              ! land model domain data size
-    real(r8), pointer :: data(:)  ! temporary
-    integer , pointer :: idata(:) ! temporary
-    !-------------------------------------------------------------------
-    !
-    ! Initialize mct domain type
-    ! lat/lon in degrees,  area in radians^2, mask is 1 (land), 0 (non-land)
-    ! Note that in addition land carries around landfrac for the purposes of domain checking
-    ! 
-    lsize = mct_gsMap_lsize(gsmap_lnd_gdc2glo, mpicom)
-    call mct_gGrid_init( GGrid=dom_clm, CoordChars=trim(seq_flds_dom_coord), &
-                         OtherChars=trim(seq_flds_dom_other), lsize=lsize )
-    !
-    ! Allocate memory
-    !
-    allocate(data(lsize))
-    !
-    ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT
-    !
-    call mct_gsMap_orderedPoints(gsmap_lnd_gdc2glo, iam, idata)
-    call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize)
-    !
-    ! Determine domain (numbering scheme is: West to East and South to North to South pole)
-    ! Initialize attribute vector with special value
-    !
-    data(:) = -9999.0_R8 
-    call mct_gGrid_importRAttr(dom_clm,"lat"  ,data,lsize) 
-    call mct_gGrid_importRAttr(dom_clm,"lon"  ,data,lsize) 
-    call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize) 
-    call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize) 
-    data(:) = 0.0_R8     
-    call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize) 
-    !
-    ! Determine bounds
-    !
-    ! Fill in correct values for domain components
-    ! Note aream will be filled in in the atm-lnd mapper
-    !
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%lonc(g)
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lon",data,lsize) 
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%latc(g)
-    end do
-    call mct_gGrid_importRattr(dom_clm,"lat",data,lsize) 
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = ldomain%area(g)/(re*re)
-    end do
-    call mct_gGrid_importRattr(dom_clm,"area",data,lsize) 
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%mask(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_clm,"mask",data,lsize) 
-
-    do g = bounds%begg,bounds%endg
-       i = 1 + (g - bounds%begg)
-       data(i) = real(ldomain%frac(g), r8)
-    end do
-    call mct_gGrid_importRattr(dom_clm,"frac",data,lsize) 
-
-    deallocate(data)
-    deallocate(idata)
-
-  end subroutine clm_domain_mct
-    
-end module ndepStreamMod
-
diff --git a/src/main/organicFileMod.F90 b/src/main/organicFileMod.F90
deleted file mode 100644
index 3adbd5b6f1..0000000000
--- a/src/main/organicFileMod.F90
+++ /dev/null
@@ -1,113 +0,0 @@
-module organicFileMod
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !MODULE: organicFileMod
-!
-! !DESCRIPTION:
-! Contains methods for reading in organic matter data file which has 
-! organic matter density for each grid point and soil level 
-!
-! !USES
-  use abortutils   , only : endrun
-  use clm_varctl   , only : iulog
-  use shr_kind_mod , only : r8 => shr_kind_r8
-  use clm_varcon   , only : grlnd
-!
-! !PUBLIC TYPES:
-  implicit none
-  private
-  save
-!
-! !PUBLIC MEMBER FUNCTIONS:
-  public :: organicrd  ! Read organic matter dataset
-!
-! !REVISION HISTORY:
-! Created by David Lawrence, 4 May 2006
-! Revised by David Lawrence, 21 September 2007
-! Revised by David Lawrence, 14 October 2008
-!
-!EOP
-!
-!----------------------------------------------------------------------- 
-
-contains
-
-!-----------------------------------------------------------------------
-!BOP
-!
-! !IROUTINE: organicrd
-!
-! !INTERFACE:
-  subroutine organicrd(organic)
-!
-! !DESCRIPTION: 
-! Read the organic matter dataset.
-!
-! !USES:
-    use clm_varctl  , only : fsurdat, single_column
-    use fileutils   , only : getfil
-    use spmdMod     , only : masterproc
-    use domainMod   , only : ldomain
-    use ncdio_pio
-!
-! !ARGUMENTS:
-    implicit none
-    real(r8), pointer :: organic(:,:)         ! organic matter density (kg/m3)
-!
-! !CALLED FROM:
-! subroutine initialize in module initializeMod
-!
-! !REVISION HISTORY:
-! Created by David Lawrence, 4 May 2006
-! Revised by David Lawrence, 21 September 2007
-!
-!
-! !LOCAL VARIABLES:
-!EOP
-    character(len=256) :: locfn                 ! local file name
-    type(file_desc_t)  :: ncid                  ! netcdf id
-    integer            :: ni,nj,ns              ! dimension sizes  
-    logical            :: isgrid2d              ! true => file is 2d
-    logical            :: readvar               ! true => variable is on dataset
-    character(len=32)  :: subname = 'organicrd' ! subroutine name
-!-----------------------------------------------------------------------
-
-    ! Initialize data to zero - no organic matter dataset
-
-    organic(:,:)   = 0._r8
-       
-    ! Read data if file was specified in namelist
-       
-    if (fsurdat /= ' ') then
-       if (masterproc) then
-          write(iulog,*) 'Attempting to read organic matter data .....'
-	  write(iulog,*) subname,trim(fsurdat)
-       end if
-
-       call getfil (fsurdat, locfn, 0)
-       call ncd_pio_openfile (ncid, locfn, 0)
-
-       call ncd_inqfdims (ncid, isgrid2d, ni, nj, ns)
-       if (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj) then
-          write(iulog,*)trim(subname), 'ldomain and input file do not match dims '
-          write(iulog,*)trim(subname), 'ldomain%ni,ni,= ',ldomain%ni,ni
-          write(iulog,*)trim(subname), 'ldomain%nj,nj,= ',ldomain%nj,nj
-          write(iulog,*)trim(subname), 'ldomain%ns,ns,= ',ldomain%ns,ns
-          call endrun()
-       end if
-       
-       call ncd_io(ncid=ncid, varname='ORGANIC', flag='read', data=organic, &
-            dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) call endrun('organicrd: errror reading ORGANIC')
-
-       if ( masterproc )then
-          write(iulog,*) 'Successfully read organic matter data'
-          write(iulog,*)
-       end if
-    endif
-
-  end subroutine organicrd
-
-end module organicFileMod
diff --git a/src/main/paramUtilMod.F90 b/src/main/paramUtilMod.F90
deleted file mode 100644
index 96c95440e7..0000000000
--- a/src/main/paramUtilMod.F90
+++ /dev/null
@@ -1,291 +0,0 @@
-module paramUtilMod
-   !
-   ! module that deals with reading parameter files
-   !
-   use shr_kind_mod , only: r8 => shr_kind_r8
-   implicit none
-   save
-   private
-
-   interface readNcdio
-      module procedure readNcdioScalar
-      module procedure readNcdioArray1d
-      module procedure readNcdioArray2d
-      module procedure readNcdioScalarCheckDimensions
-      module procedure readNcdioArray1dCheckDimensions
-      module procedure readNcdioArray2dCheckDimensions
-   end interface
-
-   public :: readNcdioScalar
-   public :: readNcdioArray1d
-   public :: readNcdioArray2d
-   public :: readNcdioScalarCheckDimensions
-   public :: readNcdioArray1dCheckDimensions
-   public :: readNcdioArray2dCheckDimensions
-
-   public :: readNcdio
-
-   private :: checkDimensions
-   
-contains
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioScalar(ncid, varName, callingName, retVal)
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t,ncd_io
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-     logical            :: readv     ! has variable been read in or not
-
-     !
-     ! netcdf read here
-     !
-
-     call ncd_io(varname=trim(varName),data=retVal, flag='read', ncid=ncid, readvar=readv)
-
-     if ( .not. readv ) then
-        call endrun(trim(callingName)//trim(subname)//trim(errCode)//trim(varName))
-     endif
-
-  end subroutine readNcdioScalar
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioArray1d(ncid, varName, callingName, retVal) 
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t,ncd_io
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal( 1: )
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-     logical            :: readv     ! has variable been read in or not
-
-     !
-     ! netcdf read here
-     !
-
-     call ncd_io(varname=trim(varName),data=retVal, flag='read', ncid=ncid, readvar=readv)
-
-     if ( .not. readv ) then
-        call endrun(trim(callingName)//trim(subname)//trim(errCode)//trim(varName))
-     endif
-
-  end subroutine readNcdioArray1d
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioArray2d(ncid, varName, callingName, retVal) 
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t,ncd_io
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal( 1: , :)
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-     logical            :: readv     ! has variable been read in or not
-
-     !
-     ! netcdf read here
-     !
-
-     call ncd_io(varname=trim(varName),data=retVal, flag='read', ncid=ncid, readvar=readv)
-
-     if ( .not. readv ) then
-        call endrun(trim(callingName)//trim(subname)//trim(errCode)//trim(varName))
-     endif
-
-  end subroutine readNcdioArray2d
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioScalarCheckDimensions(ncid, varName, expected_numDims, expected_dimNames, &
-       callingName, retVal) 
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     integer, intent(in) :: expected_numDims
-     character(len=*), intent(in)    :: expected_dimNames(:) ! expected dimension name
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-
-     !
-     ! netcdf read here
-     !
-     call checkDimensions(ncid, varName, expected_numDims, expected_dimNames, subname)
-     call readNcdio(ncid, varName, callingName, retVal)
-
-   end subroutine readNcdioScalarCheckDimensions
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioArray1dCheckDimensions(ncid, varName, expected_numDims, expected_dimNames, &
-       callingName, retVal) 
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     integer, intent(in) :: expected_numDims
-     character(len=*), intent(in)    :: expected_dimNames(:) ! expected dimension name
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal( 1: )
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-     !
-     ! netcdf read here
-     !
-     call checkDimensions(ncid, varName, expected_numDims, expected_dimNames, subname)
-     call readNcdio(ncid, varName, callingName, retVal)
-
-   end subroutine readNcdioArray1dCheckDimensions
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine readNcdioArray2dCheckDimensions(ncid, varName, expected_numDims, expected_dimNames, &
-       callingName, retVal) 
-     !
-     ! read the netcdf file...generic, could be used for any parameter read
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     integer, intent(in) :: expected_numDims
-     character(len=*), intent(in)    :: expected_dimNames(:) ! expected dimension name
-     character(len=*), intent(in)    :: callingName ! calling routine
-     real(r8), intent(inout) :: retVal(1:, : )
-
-     ! local vars
-     character(len=32)  :: subname = 'readNcdio::'
-     character(len=100) :: errCode = ' - Error reading.  Var: '
-     !
-     ! netcdf read here
-     !
-     call checkDimensions(ncid, varName, expected_numDims, expected_dimNames, subname)
-     call readNcdio(ncid, varName, callingName, retVal)
-
-   end subroutine readNcdioArray2dCheckDimensions
-  !-----------------------------------------------------------------------
-
-  !-----------------------------------------------------------------------
-  !
-  !-----------------------------------------------------------------------
-  subroutine checkDimensions(ncid, varName, expected_numDims, expected_dimNames, callingName) 
-     !
-     ! Assert that the expected number of dimensions and dimension
-     ! names for a variable match the actual names on the file.
-     !
-     use abortutils   , only : endrun
-     use ncdio_pio    , only : file_desc_t, var_desc_t, check_var, ncd_inqvdname, ncd_inqvdims
-
-     implicit none
-
-     ! arguments
-     type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-     character(len=*), intent(in)    :: varName ! variable we are reading
-     integer,          intent(in)    :: expected_numDims ! number of expected dimensions on the variable
-     character(len=*), intent(in)    :: expected_dimNames(:) ! expected dimension names
-     character(len=*), intent(in)    :: callingName ! calling routine
-     integer                         :: error_num
-
-     ! local vars
-     character(len=32)  :: subname = 'checkDimensions::'
-     type(Var_desc_t)   :: var_desc        ! variable descriptor
-     logical            :: readvar        ! whether the variable was found
-     character(len=100) :: received_dimName
-     integer            :: d, num_dims
-     character(len=256) :: msg
-
-     call check_var(ncid, varName, var_desc, readvar)
-     if (readvar) then
-        call ncd_inqvdims(ncid, num_dims, var_desc)
-        if (num_dims /= expected_numDims) then
-           write(msg, *) trim(callingName)//trim(subname)//trim(varname)//":: expected number of dimensions = ", &
-                expected_numDims, "   num dimensions received from file = ", num_dims
-           call endrun(msg)
-        end if
-        do d = 1, num_dims
-           received_dimName = ''
-           call ncd_inqvdname(ncid, varname=trim(varName), dimnum=d, dname=received_dimName, err_code=error_num)
-           if (trim(expected_dimNames(d)) /= trim(received_dimName)) then
-              write(msg, *) trim(callingName)//trim(subname)//trim(varname)//":: dimension ", d, &
-                   " expected dimension name '"//trim(expected_dimNames(d))//&
-                   "' dimension name received from file '"//trim(received_dimName)//"'." 
-              call endrun(msg)
-           end if
-        end do
-     end if
-
-   end subroutine checkDimensions
-  !-----------------------------------------------------------------------
-
-end module paramUtilMod
diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90
deleted file mode 100644
index 4714fca0f9..0000000000
--- a/src/main/pftconMod.F90
+++ /dev/null
@@ -1,1374 +0,0 @@
-module pftconMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module containing vegetation constants and method to
-  ! read and initialize vegetation (PFT) constants.
-  !
-  ! !USES:
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use abortutils  , only : endrun
-  use clm_varpar  , only : mxpft, numrad, ivis, inir, cft_lb, cft_ub
-  use clm_varctl  , only : iulog, use_cndv, use_vertsoilc, use_crop
-  !
-  ! !PUBLIC TYPES:
-  implicit none
-  !
-  ! Vegetation type constants
-  !
-  integer :: noveg                  ! value for not vegetated 
-  integer :: ndllf_evr_tmp_tree     ! value for Needleleaf evergreen temperate tree
-  integer :: ndllf_evr_brl_tree     ! value for Needleleaf evergreen boreal tree
-  integer :: ndllf_dcd_brl_tree     ! value for Needleleaf deciduous boreal tree
-  integer :: nbrdlf_evr_trp_tree    ! value for Broadleaf evergreen tropical tree
-  integer :: nbrdlf_evr_tmp_tree    ! value for Broadleaf evergreen temperate tree
-  integer :: nbrdlf_dcd_trp_tree    ! value for Broadleaf deciduous tropical tree
-  integer :: nbrdlf_dcd_tmp_tree    ! value for Broadleaf deciduous temperate tree
-  integer :: nbrdlf_dcd_brl_tree    ! value for Broadleaf deciduous boreal tree
-  integer :: ntree                  ! value for last type of tree
-  integer :: nbrdlf_evr_shrub       ! value for Broadleaf evergreen shrub
-  integer :: nbrdlf_dcd_tmp_shrub   ! value for Broadleaf deciduous temperate shrub
-  integer :: nbrdlf_dcd_brl_shrub   ! value for Broadleaf deciduous boreal shrub
-  integer :: nc3_arctic_grass       ! value for C3 arctic grass
-  integer :: nc3_nonarctic_grass    ! value for C3 non-arctic grass
-  integer :: nc4_grass              ! value for C4 grass
-  integer :: npcropmin              ! value for first crop
-  integer :: ntmp_corn              ! value for temperate corn, rain fed (rf)
-  integer :: nirrig_tmp_corn        ! value for temperate corn, irrigated (ir)
-  integer :: nswheat                ! value for spring temperate cereal (rf)
-  integer :: nirrig_swheat          ! value for spring temperate cereal (ir)
-  integer :: nwwheat                ! value for winter temperate cereal (rf)
-  integer :: nirrig_wwheat          ! value for winter temperate cereal (ir)
-  integer :: ntmp_soybean           ! value for temperate soybean (rf)
-  integer :: nirrig_tmp_soybean     ! value for temperate soybean (ir)
-  integer :: nbarley                ! value for spring barley (rf)
-  integer :: nirrig_barley          ! value for spring barley (ir)
-  integer :: nwbarley               ! value for winter barley (rf)
-  integer :: nirrig_wbarley         ! value for winter barley (ir)
-  integer :: nrye                   ! value for spring rye (rf)
-  integer :: nirrig_rye             ! value for spring rye (ir)
-  integer :: nwrye                  ! value for winter rye (rf)
-  integer :: nirrig_wrye            ! value for winter rye (ir)
-  integer :: ncassava               ! ...and so on
-  integer :: nirrig_cassava
-  integer :: ncitrus
-  integer :: nirrig_citrus
-  integer :: ncocoa
-  integer :: nirrig_cocoa
-  integer :: ncoffee
-  integer :: nirrig_coffee
-  integer :: ncotton
-  integer :: nirrig_cotton
-  integer :: ndatepalm
-  integer :: nirrig_datepalm
-  integer :: nfoddergrass
-  integer :: nirrig_foddergrass
-  integer :: ngrapes
-  integer :: nirrig_grapes
-  integer :: ngroundnuts
-  integer :: nirrig_groundnuts
-  integer :: nmillet
-  integer :: nirrig_millet
-  integer :: noilpalm
-  integer :: nirrig_oilpalm
-  integer :: npotatoes
-  integer :: nirrig_potatoes
-  integer :: npulses
-  integer :: nirrig_pulses
-  integer :: nrapeseed
-  integer :: nirrig_rapeseed
-  integer :: nrice
-  integer :: nirrig_rice
-  integer :: nsorghum
-  integer :: nirrig_sorghum
-  integer :: nsugarbeet
-  integer :: nirrig_sugarbeet
-  integer :: nsugarcane
-  integer :: nirrig_sugarcane
-  integer :: nsunflower
-  integer :: nirrig_sunflower
-  integer :: nmiscanthus
-  integer :: nirrig_miscanthus
-  integer :: nswitchgrass
-  integer :: nirrig_switchgrass
-  integer :: ntrp_corn              !value for tropical corn (rf)
-  integer :: nirrig_trp_corn        !value for tropical corn (ir)
-  integer :: ntrp_soybean           !value for tropical soybean (rf)
-  integer :: nirrig_trp_soybean     !value for tropical soybean (ir)
-  integer :: npcropmax              ! value for last prognostic crop in list
-  integer :: nc3crop                ! value for generic crop (rf)
-  integer :: nc3irrig               ! value for irrigated generic crop (ir)
-
-  ! Number of crop functional types actually used in the model. This includes each CFT for
-  ! which is_pft_known_to_model is true. Note that this includes irrigated crops even if
-  ! irrigation is turned off in this run: it just excludes crop types that aren't handled
-  ! at all, as given by the mergetoclmpft list.
-  integer :: num_cfts_known_to_model
-
-  ! !PUBLIC TYPES:
-  type, public :: pftcon_type
-
-     integer , allocatable :: noveg         (:)   ! value for not vegetated
-     integer , allocatable :: tree          (:)   ! tree or not?
-
-     real(r8), allocatable :: dleaf         (:)   ! characteristic leaf dimension (m)
-     real(r8), allocatable :: c3psn         (:)   ! photosynthetic pathway: 0. = c4, 1. = c3
-     real(r8), allocatable :: xl            (:)   ! leaf/stem orientation index
-     real(r8), allocatable :: rhol          (:,:) ! leaf reflectance: 1=vis, 2=nir
-     real(r8), allocatable :: rhos          (:,:) ! stem reflectance: 1=vis, 2=nir
-     real(r8), allocatable :: taul          (:,:) ! leaf transmittance: 1=vis, 2=nir
-     real(r8), allocatable :: taus          (:,:) ! stem transmittance: 1=vis, 2=nir
-     real(r8), allocatable :: z0mr          (:)   ! ratio of momentum roughness length to canopy top height (-)
-     real(r8), allocatable :: displar       (:)   ! ratio of displacement height to canopy top height (-)
-     real(r8), allocatable :: roota_par     (:)   ! CLM rooting distribution parameter [1/m]
-     real(r8), allocatable :: rootb_par     (:)   ! CLM rooting distribution parameter [1/m]
-     real(r8), allocatable :: crop          (:)   ! crop pft: 0. = not crop, 1. = crop pft
-     real(r8), allocatable :: irrigated     (:)   ! irrigated pft: 0. = not, 1. = irrigated
-     real(r8), allocatable :: smpso         (:)   ! soil water potential at full stomatal opening (mm)
-     real(r8), allocatable :: smpsc         (:)   ! soil water potential at full stomatal closure (mm)
-     real(r8), allocatable :: fnitr         (:)   ! foliage nitrogen limitation factor (-)
-
-     !  CN code
-     real(r8), allocatable :: dwood         (:)   ! wood density (gC/m3)
-     real(r8), allocatable :: slatop        (:)   ! SLA at top of canopy [m^2/gC]
-     real(r8), allocatable :: dsladlai      (:)   ! dSLA/dLAI [m^2/gC]
-     real(r8), allocatable :: leafcn        (:)   ! leaf C:N [gC/gN]
-     real(r8), allocatable :: flnr          (:)   ! fraction of leaf N in Rubisco [no units]
-     real(r8), allocatable :: woody         (:)   ! woody lifeform flag (0 or 1)
-     real(r8), allocatable :: lflitcn       (:)   ! leaf litter C:N (gC/gN)
-     real(r8), allocatable :: frootcn       (:)   ! fine root C:N (gC/gN)
-     real(r8), allocatable :: livewdcn      (:)   ! live wood (phloem and ray parenchyma) C:N (gC/gN)
-     real(r8), allocatable :: deadwdcn      (:)   ! dead wood (xylem and heartwood) C:N (gC/gN)
-     real(r8), allocatable :: grperc        (:)   ! growth respiration parameter
-     real(r8), allocatable :: grpnow        (:)   ! growth respiration parameter
-     real(r8), allocatable :: rootprof_beta (:,:) ! CLM rooting distribution parameter for C and N inputs [unitless]
-     real(r8), allocatable :: root_radius   (:)   ! root radius (m)
-     real(r8), allocatable :: root_density  (:)   ! root density (gC/m3)
-
-     !  crop
-
-     ! These arrays give information about the merge of unused crop types to the types CLM
-     ! knows about. mergetoclmpft(m) gives the crop type that CLM uses to simulate input
-     ! type m (and mergetoclmpft(m) == m implies that CLM simulates crop type m
-     ! directly). is_pft_known_to_model(m) is true if CLM simulates crop type m, and false
-     ! otherwise. Note that these do NOT relate to whether irrigation is on or off in a
-     ! given simulation - that is handled separately.
-     integer , allocatable :: mergetoclmpft         (:)
-     logical , allocatable :: is_pft_known_to_model (:)
-
-     real(r8), allocatable :: graincn       (:)   ! grain C:N (gC/gN)
-     real(r8), allocatable :: mxtmp         (:)   ! parameter used in accFlds
-     real(r8), allocatable :: baset         (:)   ! parameter used in accFlds
-     real(r8), allocatable :: declfact      (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: bfact         (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: aleaff        (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: arootf        (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: astemf        (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: arooti        (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: fleafi        (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: allconsl      (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: allconss      (:)   ! parameter used in CNAllocation
-     real(r8), allocatable :: ztopmx        (:)   ! parameter used in CNVegStructUpdate
-     real(r8), allocatable :: laimx         (:)   ! parameter used in CNVegStructUpdate
-     real(r8), allocatable :: gddmin        (:)   ! parameter used in CNPhenology
-     real(r8), allocatable :: hybgdd        (:)   ! parameter used in CNPhenology
-     real(r8), allocatable :: lfemerg       (:)   ! parameter used in CNPhenology
-     real(r8), allocatable :: grnfill       (:)   ! parameter used in CNPhenology
-     integer , allocatable :: mxmat         (:)   ! parameter used in CNPhenology
-     real(r8), allocatable :: mbbopt        (:)   ! Ball-Berry equation slope used in Photosynthesis
-     real(r8), allocatable :: medlynslope   (:)   ! Medlyn equation slope used in Photosynthesis
-     real(r8), allocatable :: medlynintercept(:)  ! Medlyn equation intercept used in Photosynthesis
-     integer , allocatable :: mnNHplantdate (:)   ! minimum planting date for NorthHemisphere (YYYYMMDD)
-     integer , allocatable :: mxNHplantdate (:)   ! maximum planting date for NorthHemisphere (YYYYMMDD)
-     integer , allocatable :: mnSHplantdate (:)   ! minimum planting date for SouthHemisphere (YYYYMMDD)
-     integer , allocatable :: mxSHplantdate (:)   ! maximum planting date for SouthHemisphere (YYYYMMDD)
-     real(r8), allocatable :: planttemp     (:)   ! planting temperature used in CNPhenology (K)
-     real(r8), allocatable :: minplanttemp  (:)   ! mininum planting temperature used in CNPhenology (K)
-     real(r8), allocatable :: froot_leaf    (:)   ! allocation parameter: new fine root C per new leaf C (gC/gC) 
-     real(r8), allocatable :: stem_leaf     (:)   ! allocation parameter: new stem c per new leaf C (gC/gC)
-     real(r8), allocatable :: croot_stem    (:)   ! allocation parameter: new coarse root C per new stem C (gC/gC)
-     real(r8), allocatable :: flivewd       (:)   ! allocation parameter: fraction of new wood that is live (phloem and ray parenchyma) (no units)
-     real(r8), allocatable :: fcur          (:)   ! allocation parameter: fraction of allocation that goes to currently displayed growth, remainder to storage
-     real(r8), allocatable :: fcurdv        (:)   ! alternate fcur for use with cndv
-     real(r8), allocatable :: lf_flab       (:)   ! leaf litter labile fraction
-     real(r8), allocatable :: lf_fcel       (:)   ! leaf litter cellulose fraction
-     real(r8), allocatable :: lf_flig       (:)   ! leaf litter lignin fraction
-     real(r8), allocatable :: fr_flab       (:)   ! fine root litter labile fraction
-     real(r8), allocatable :: fr_fcel       (:)   ! fine root litter cellulose fraction
-     real(r8), allocatable :: fr_flig       (:)   ! fine root litter lignin fraction
-     real(r8), allocatable :: leaf_long     (:)   ! leaf longevity (yrs)
-     real(r8), allocatable :: evergreen     (:)   ! binary flag for evergreen leaf habit (0 or 1)
-     real(r8), allocatable :: stress_decid  (:)   ! binary flag for stress-deciduous leaf habit (0 or 1)
-     real(r8), allocatable :: season_decid  (:)   ! binary flag for seasonal-deciduous leaf habit (0 or 1)
-     real(r8), allocatable :: pconv         (:)   ! proportion of deadstem to conversion flux
-     real(r8), allocatable :: pprod10       (:)   ! proportion of deadstem to 10-yr product pool
-     real(r8), allocatable :: pprod100      (:)   ! proportion of deadstem to 100-yr product pool
-     real(r8), allocatable :: pprodharv10   (:)   ! harvest mortality proportion of deadstem to 10-yr pool
-
-     ! pft paraemeters for fire code
-     real(r8), allocatable :: cc_leaf       (:)
-     real(r8), allocatable :: cc_lstem      (:)
-     real(r8), allocatable :: cc_dstem      (:)
-     real(r8), allocatable :: cc_other      (:)
-     real(r8), allocatable :: fm_leaf       (:)
-     real(r8), allocatable :: fm_lstem      (:)
-     real(r8), allocatable :: fm_dstem      (:)
-     real(r8), allocatable :: fm_other      (:)
-     real(r8), allocatable :: fm_root       (:)
-     real(r8), allocatable :: fm_lroot      (:)
-     real(r8), allocatable :: fm_droot      (:)
-     real(r8), allocatable :: fsr_pft       (:)
-     real(r8), allocatable :: fd_pft        (:)
-
-     ! pft parameters for crop code
-     real(r8), allocatable :: manunitro     (:)   ! manure
-     real(r8), allocatable :: fleafcn       (:)   ! C:N during grain fill; leaf
-     real(r8), allocatable :: ffrootcn      (:)   ! C:N during grain fill; fine root
-     real(r8), allocatable :: fstemcn       (:)   ! C:N during grain fill; stem
-
-     real(r8), allocatable :: i_vcad        (:)   
-     real(r8), allocatable :: s_vcad        (:)   
-     real(r8), allocatable :: i_flnr        (:)   
-     real(r8), allocatable :: s_flnr        (:)     
-
-     ! pft parameters for CNDV code (from LPJ subroutine pftparameters)
-     real(r8), allocatable :: pftpar20      (:)   ! tree maximum crown area (m2)
-     real(r8), allocatable :: pftpar28      (:)   ! min coldest monthly mean temperature
-     real(r8), allocatable :: pftpar29      (:)   ! max coldest monthly mean temperature
-     real(r8), allocatable :: pftpar30      (:)   ! min growing degree days (>= 5 deg C)
-     real(r8), allocatable :: pftpar31      (:)   ! upper limit of temperature of the warmest month (twmax)
-     
-     ! pft parameters for FUN
-     real(r8), allocatable :: a_fix         (:)   ! A BNF parameter
-     real(r8), allocatable :: b_fix         (:)   ! A BNF parameter
-     real(r8), allocatable :: c_fix         (:)   ! A BNF parameter
-     real(r8), allocatable :: s_fix         (:)   ! A BNF parameter
-     real(r8), allocatable :: akc_active    (:)   ! A mycorrhizal uptake parameter
-     real(r8), allocatable :: akn_active    (:)   ! A mycorrhizal uptake parameter
-     real(r8), allocatable :: ekc_active    (:)   ! A mycorrhizal uptake parameter
-     real(r8), allocatable :: ekn_active    (:)   ! A mycorrhizal uptake parameter
-     real(r8), allocatable :: kc_nonmyc     (:)   ! A non-mycorrhizal uptake parameter
-     real(r8), allocatable :: kn_nonmyc     (:)   ! A non-mycorrhizal uptake parameter
-     real(r8), allocatable :: kr_resorb     (:)   ! A retrasnlcation parameter
-     real(r8), allocatable :: perecm        (:)   ! The fraction of ECM-associated PFT 
-     real(r8), allocatable :: fun_cn_flex_a (:)   ! Parameter a of FUN-flexcn link code (def 5)
-     real(r8), allocatable :: fun_cn_flex_b (:)   ! Parameter b of FUN-flexcn link code (def 200)
-     real(r8), allocatable :: fun_cn_flex_c (:)   ! Parameter b of FUN-flexcn link code (def 80)         
-     real(r8), allocatable :: FUN_fracfixers(:)   ! Fraction of C that can be used for fixation.    
-
-
-     ! pft parameters for dynamic root code
-     real(r8), allocatable :: root_dmx(:)     !maximum root depth
-
-   contains
-
-     procedure, public  :: Init
-     procedure, public  :: InitForTesting ! version of Init meant for unit testing
-     procedure, public  :: Clean
-     procedure, private :: InitAllocate   
-     procedure, private :: InitRead
-     procedure, private :: set_is_pft_known_to_model   ! Set is_pft_known_to_model based on mergetoclmpft
-     procedure, private :: set_num_cfts_known_to_model ! Set the module-level variable, num_cfts_known_to_model
-
-  end type pftcon_type
-
-  type(pftcon_type), public :: pftcon ! pft type constants structure
-
-  integer, parameter :: pftname_len = 40         ! max length of pftname       
-  character(len=pftname_len) :: pftname(0:mxpft) ! PFT description
-
-  real(r8), parameter :: reinickerp = 1.6_r8     ! parameter in allometric equation
-  real(r8), parameter :: dwood  = 2.5e5_r8       ! cn wood density (gC/m3); lpj:2.0e5
-  real(r8), parameter :: allom1 = 100.0_r8       ! parameters in
-  real(r8), parameter :: allom2 =  40.0_r8       ! ...allometric
-  real(r8), parameter :: allom3 =   0.5_r8       ! ...equations
-  real(r8), parameter :: allom1s = 250.0_r8      ! modified for shrubs by
-  real(r8), parameter :: allom2s =   8.0_r8      ! X.D.Z
-! root radius, density from Bonan, GMD, 2014
-  real(r8), parameter :: root_density = 0.31e06_r8 !(g biomass / m3 root)
-  real(r8), parameter :: root_radius = 0.29e-03_r8 !(m)
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this)
-
-    class(pftcon_type) :: this
-
-    call this%InitAllocate()
-    call this%InitRead()
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitForTesting(this)
-    ! Version of Init meant for unit testing
-    !
-    ! Allocate arrays, but don't try to read from file.
-    !
-    ! Values can then be set by tests as needed
-
-    class(pftcon_type) :: this
-
-    call this%InitAllocate()
-
-  end subroutine InitForTesting
-
-  !-----------------------------------------------------------------------
-  subroutine InitAllocate (this)
-    !
-    ! !DESCRIPTION:
-    ! Read and initialize vegetation (PFT) constants
-    !
-    ! !USES:
-    use clm_varpar  ,  only: nvariants
-    implicit none
-    !
-    ! !ARGUMENTS:
-    class(pftcon_type) :: this
-    !-----------------------------------------------------------------------
-
-    allocate( this%noveg         (0:mxpft)); this%noveg (:)   =huge(1)
-    allocate( this%tree          (0:mxpft)); this%tree  (:)   =huge(1)
-
-    allocate( this%dleaf         (0:mxpft) )       
-    allocate( this%c3psn         (0:mxpft) )       
-    allocate( this%xl            (0:mxpft) )          
-    allocate( this%rhol          (0:mxpft,numrad) ) 
-    allocate( this%rhos          (0:mxpft,numrad) ) 
-    allocate( this%taul          (0:mxpft,numrad) ) 
-    allocate( this%taus          (0:mxpft,numrad) ) 
-    allocate( this%z0mr          (0:mxpft) )        
-    allocate( this%displar       (0:mxpft) )     
-    allocate( this%roota_par     (0:mxpft) )   
-    allocate( this%rootb_par     (0:mxpft) )   
-    allocate( this%crop          (0:mxpft) )        
-    allocate( this%mergetoclmpft (0:mxpft) )
-    allocate( this%is_pft_known_to_model  (0:mxpft) )
-    allocate( this%irrigated     (0:mxpft) )   
-    allocate( this%smpso         (0:mxpft) )       
-    allocate( this%smpsc         (0:mxpft) )       
-    allocate( this%fnitr         (0:mxpft) )       
-    allocate( this%slatop        (0:mxpft) )      
-    allocate( this%dsladlai      (0:mxpft) )    
-    allocate( this%leafcn        (0:mxpft) )      
-    allocate( this%flnr          (0:mxpft) )        
-    allocate( this%woody         (0:mxpft) )       
-    allocate( this%lflitcn       (0:mxpft) )      
-    allocate( this%frootcn       (0:mxpft) )      
-    allocate( this%livewdcn      (0:mxpft) )     
-    allocate( this%deadwdcn      (0:mxpft) )     
-    allocate( this%grperc        (0:mxpft) )       
-    allocate( this%grpnow        (0:mxpft) )       
-    allocate( this%rootprof_beta (0:mxpft,nvariants) )
-    allocate( this%graincn       (0:mxpft) )      
-    allocate( this%mxtmp         (0:mxpft) )        
-    allocate( this%baset         (0:mxpft) )        
-    allocate( this%declfact      (0:mxpft) )     
-    allocate( this%bfact         (0:mxpft) )        
-    allocate( this%aleaff        (0:mxpft) )       
-    allocate( this%arootf        (0:mxpft) )       
-    allocate( this%astemf        (0:mxpft) )       
-    allocate( this%arooti        (0:mxpft) )       
-    allocate( this%fleafi        (0:mxpft) )       
-    allocate( this%allconsl      (0:mxpft) )     
-    allocate( this%allconss      (0:mxpft) )     
-    allocate( this%ztopmx        (0:mxpft) )       
-    allocate( this%laimx         (0:mxpft) )        
-    allocate( this%gddmin        (0:mxpft) )       
-    allocate( this%hybgdd        (0:mxpft) )       
-    allocate( this%lfemerg       (0:mxpft) )      
-    allocate( this%grnfill       (0:mxpft) )      
-    allocate( this%mbbopt        (0:mxpft) )      
-    allocate( this%medlynslope   (0:mxpft) )      
-    allocate( this%medlynintercept(0:mxpft) )      
-    allocate( this%mxmat         (0:mxpft) )        
-    allocate( this%mnNHplantdate (0:mxpft) )
-    allocate( this%mxNHplantdate (0:mxpft) )
-    allocate( this%mnSHplantdate (0:mxpft) )
-    allocate( this%mxSHplantdate (0:mxpft) )
-    allocate( this%planttemp     (0:mxpft) )    
-    allocate( this%minplanttemp  (0:mxpft) ) 
-    allocate( this%froot_leaf    (0:mxpft) )   
-    allocate( this%stem_leaf     (0:mxpft) )    
-    allocate( this%croot_stem    (0:mxpft) )   
-    allocate( this%flivewd       (0:mxpft) )      
-    allocate( this%fcur          (0:mxpft) )         
-    allocate( this%fcurdv        (0:mxpft) )       
-    allocate( this%lf_flab       (0:mxpft) )      
-    allocate( this%lf_fcel       (0:mxpft) )      
-    allocate( this%lf_flig       (0:mxpft) )      
-    allocate( this%fr_flab       (0:mxpft) )      
-    allocate( this%fr_fcel       (0:mxpft) )      
-    allocate( this%fr_flig       (0:mxpft) )      
-    allocate( this%leaf_long     (0:mxpft) )
-    allocate( this%evergreen     (0:mxpft) )    
-    allocate( this%stress_decid  (0:mxpft) ) 
-    allocate( this%season_decid  (0:mxpft) ) 
-    allocate( this%dwood         (0:mxpft) )
-    allocate( this%root_density  (0:mxpft) )
-    allocate( this%root_radius   (0:mxpft) )
-    allocate( this%pconv         (0:mxpft) )        
-    allocate( this%pprod10       (0:mxpft) )      
-    allocate( this%pprod100      (0:mxpft) )     
-    allocate( this%pprodharv10   (0:mxpft) )  
-    allocate( this%cc_leaf       (0:mxpft) )
-    allocate( this%cc_lstem      (0:mxpft) )
-    allocate( this%cc_dstem      (0:mxpft) )
-    allocate( this%cc_other      (0:mxpft) )
-    allocate( this%fm_leaf       (0:mxpft) )
-    allocate( this%fm_lstem      (0:mxpft) )
-    allocate( this%fm_dstem      (0:mxpft) )
-    allocate( this%fm_other      (0:mxpft) )
-    allocate( this%fm_root       (0:mxpft) )
-    allocate( this%fm_lroot      (0:mxpft) )
-    allocate( this%fm_droot      (0:mxpft) )
-    allocate( this%fsr_pft       (0:mxpft) )
-    allocate( this%fd_pft        (0:mxpft) )
-    allocate( this%manunitro     (0:mxpft) )
-    allocate( this%fleafcn       (0:mxpft) )  
-    allocate( this%ffrootcn      (0:mxpft) ) 
-    allocate( this%fstemcn       (0:mxpft) )  
-    allocate( this%i_vcad        (0:mxpft) )
-    allocate( this%s_vcad        (0:mxpft) )
-    allocate( this%i_flnr        (0:mxpft) )
-    allocate( this%s_flnr        (0:mxpft) )
-    allocate( this%pftpar20      (0:mxpft) )   
-    allocate( this%pftpar28      (0:mxpft) )   
-    allocate( this%pftpar29      (0:mxpft) )   
-    allocate( this%pftpar30      (0:mxpft) )   
-    allocate( this%pftpar31      (0:mxpft) )   
-    allocate( this%a_fix         (0:mxpft) )
-    allocate( this%b_fix         (0:mxpft) )
-    allocate( this%c_fix         (0:mxpft) )
-    allocate( this%s_fix         (0:mxpft) )
-    allocate( this%akc_active    (0:mxpft) )
-    allocate( this%akn_active    (0:mxpft) )
-    allocate( this%ekc_active    (0:mxpft) )
-    allocate( this%ekn_active    (0:mxpft) )  
-    allocate( this%kc_nonmyc     (0:mxpft) )
-    allocate( this%kn_nonmyc     (0:mxpft) )
-    allocate( this%kr_resorb     (0:mxpft) )
-    allocate( this%perecm        (0:mxpft) )
-    allocate( this%root_dmx      (0:mxpft) )
-    allocate( this%fun_cn_flex_a (0:mxpft) )
-    allocate( this%fun_cn_flex_b (0:mxpft) )
-    allocate( this%fun_cn_flex_c (0:mxpft) )
-    allocate( this%FUN_fracfixers(0:mxpft) )
-    
- 
-  end subroutine InitAllocate
-
-  !-----------------------------------------------------------------------
-  subroutine InitRead(this)
-    !
-    ! !DESCRIPTION:
-    ! Read and initialize vegetation (PFT) constants
-    !
-    ! !USES:
-    use shr_log_mod , only : errMsg => shr_log_errMsg
-    use fileutils   , only : getfil
-    use ncdio_pio   , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t
-    use ncdio_pio   , only : ncd_inqdid, ncd_inqdlen
-    use clm_varctl  , only : paramfile, use_flexibleCN, use_dynroot
-    use spmdMod     , only : masterproc
-    !
-    ! !ARGUMENTS:
-    class(pftcon_type) :: this
-    !
-    ! !LOCAL VARIABLES:
-    character(len=256) :: locfn                ! local file name
-    integer            :: i,n,m                ! loop indices
-    integer            :: ier                  ! error code
-    type(file_desc_t)  :: ncid                 ! pio netCDF file id
-    integer            :: dimid                ! netCDF dimension id
-    integer            :: npft                 ! number of pfts on pft-physiology file
-    logical            :: readv                ! read variable in or not
-    character(len=32)  :: subname = 'InitRead' ! subroutine name
-    character(len=pftname_len) :: expected_pftnames(0:mxpft) 
-    character(len=512) :: msg
-    !-----------------------------------------------------------------------
-    !
-    ! Expected PFT names: The names expected on the paramfile file and the order they are expected to be in.
-    ! NOTE: similar types are assumed to be together, first trees (ending with broadleaf_deciduous_boreal_tree
-    !       then shrubs, ending with broadleaf_deciduous_boreal_shrub, then grasses starting with c3_arctic_grass
-    !       and finally crops, ending with irrigated_tropical_soybean
-    ! DO NOT CHANGE THE ORDER -- WITHOUT MODIFYING OTHER PARTS OF THE CODE WHERE THE ORDER MATTERS!
-
-    expected_pftnames( 0) = 'not_vegetated                      '
-    expected_pftnames( 1) = 'needleleaf_evergreen_temperate_tree'
-    expected_pftnames( 2) = 'needleleaf_evergreen_boreal_tree   '
-    expected_pftnames( 3) = 'needleleaf_deciduous_boreal_tree   '
-    expected_pftnames( 4) = 'broadleaf_evergreen_tropical_tree  '
-    expected_pftnames( 5) = 'broadleaf_evergreen_temperate_tree '
-    expected_pftnames( 6) = 'broadleaf_deciduous_tropical_tree  '
-    expected_pftnames( 7) = 'broadleaf_deciduous_temperate_tree '
-    expected_pftnames( 8) = 'broadleaf_deciduous_boreal_tree    '
-    expected_pftnames( 9) = 'broadleaf_evergreen_shrub          '
-    expected_pftnames(10) = 'broadleaf_deciduous_temperate_shrub'
-    expected_pftnames(11) = 'broadleaf_deciduous_boreal_shrub   '
-    expected_pftnames(12) = 'c3_arctic_grass                    '
-    expected_pftnames(13) = 'c3_non-arctic_grass                '
-    expected_pftnames(14) = 'c4_grass                           '
-    expected_pftnames(15) = 'c3_crop                            '
-    expected_pftnames(16) = 'c3_irrigated                       '
-    expected_pftnames(17) = 'temperate_corn                     '
-    expected_pftnames(18) = 'irrigated_temperate_corn           '
-    expected_pftnames(19) = 'spring_wheat                       '
-    expected_pftnames(20) = 'irrigated_spring_wheat             '
-    expected_pftnames(21) = 'winter_wheat                       '
-    expected_pftnames(22) = 'irrigated_winter_wheat             '
-    expected_pftnames(23) = 'temperate_soybean                  '
-    expected_pftnames(24) = 'irrigated_temperate_soybean        '
-    expected_pftnames(25) = 'barley                             '
-    expected_pftnames(26) = 'irrigated_barley                   '
-    expected_pftnames(27) = 'winter_barley                      '
-    expected_pftnames(28) = 'irrigated_winter_barley            '
-    expected_pftnames(29) = 'rye                                '
-    expected_pftnames(30) = 'irrigated_rye                      '
-    expected_pftnames(31) = 'winter_rye                         '
-    expected_pftnames(32) = 'irrigated_winter_rye               '
-    expected_pftnames(33) = 'cassava                            '
-    expected_pftnames(34) = 'irrigated_cassava                  '
-    expected_pftnames(35) = 'citrus                             '
-    expected_pftnames(36) = 'irrigated_citrus                   '
-    expected_pftnames(37) = 'cocoa                              '
-    expected_pftnames(38) = 'irrigated_cocoa                    '
-    expected_pftnames(39) = 'coffee                             '
-    expected_pftnames(40) = 'irrigated_coffee                   '
-    expected_pftnames(41) = 'cotton                             '
-    expected_pftnames(42) = 'irrigated_cotton                   '
-    expected_pftnames(43) = 'datepalm                           '
-    expected_pftnames(44) = 'irrigated_datepalm                 '
-    expected_pftnames(45) = 'foddergrass                        '
-    expected_pftnames(46) = 'irrigated_foddergrass              '
-    expected_pftnames(47) = 'grapes                             '
-    expected_pftnames(48) = 'irrigated_grapes                   '
-    expected_pftnames(49) = 'groundnuts                         '
-    expected_pftnames(50) = 'irrigated_groundnuts               '
-    expected_pftnames(51) = 'millet                             '
-    expected_pftnames(52) = 'irrigated_millet                   '
-    expected_pftnames(53) = 'oilpalm                            '
-    expected_pftnames(54) = 'irrigated_oilpalm                  '
-    expected_pftnames(55) = 'potatoes                           '
-    expected_pftnames(56) = 'irrigated_potatoes                 '
-    expected_pftnames(57) = 'pulses                             '
-    expected_pftnames(58) = 'irrigated_pulses                   '
-    expected_pftnames(59) = 'rapeseed                           '
-    expected_pftnames(60) = 'irrigated_rapeseed                 '
-    expected_pftnames(61) = 'rice                               '
-    expected_pftnames(62) = 'irrigated_rice                     '
-    expected_pftnames(63) = 'sorghum                            '
-    expected_pftnames(64) = 'irrigated_sorghum                  '
-    expected_pftnames(65) = 'sugarbeet                          '
-    expected_pftnames(66) = 'irrigated_sugarbeet                '
-    expected_pftnames(67) = 'sugarcane                          '
-    expected_pftnames(68) = 'irrigated_sugarcane                '
-    expected_pftnames(69) = 'sunflower                          '
-    expected_pftnames(70) = 'irrigated_sunflower                '
-    expected_pftnames(71) = 'miscanthus                         '
-    expected_pftnames(72) = 'irrigated_miscanthus               '
-    expected_pftnames(73) = 'switchgrass                        '
-    expected_pftnames(74) = 'irrigated_switchgrass              '
-    expected_pftnames(75) = 'tropical_corn                      '
-    expected_pftnames(76) = 'irrigated_tropical_corn            '
-    expected_pftnames(77) = 'tropical_soybean                   '
-    expected_pftnames(78) = 'irrigated_tropical_soybean         '
-
-    ! Set specific vegetation type values
-
-    if (masterproc) then
-       write(iulog,*) 'Attempting to read PFT physiological data .....'
-    end if
-    call getfil (paramfile, locfn, 0)
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-    call ncd_inqdid(ncid, 'pft', dimid)
-    call ncd_inqdlen(ncid, dimid, npft)
-
-    if (npft - 1 /= mxpft) then
-       ! NOTE(bja, 201503) need to subtract 1 because of indexing.
-       ! NOTE(bja, 201503) fail early because one of the io libs
-       ! throws a useless abort error message deep inside the stack
-       ! instead of returning readv so we can get a useful line
-       ! number.
-       write(msg, '(a, i4, a, i4, a)') "ERROR: The number of pfts in the input netcdf file (", &
-            npft, ") does not equal the expected number of pfts (", mxpft, "). "
-       call endrun(msg=trim(msg)//errMsg(sourcefile, __LINE__))
-    end if
-
-    call ncd_io('pftname',pftname, 'read', ncid, readvar=readv, posNOTonfile=.true.) 
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('displar', this%displar, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('dleaf', this%dleaf, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('c3psn', this%c3psn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rholvis', this%rhol(:,ivis), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rholnir', this%rhol(:,inir), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rhosvis', this%rhos(:,ivis), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rhosnir', this% rhos(:,inir), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('taulvis', this%taul(:,ivis), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('taulnir', this%taul(:,inir), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('tausvis', this%taus(:,ivis), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('tausnir', this%taus(:,inir), 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('xl', this%xl, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('roota_par', this%roota_par, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rootb_par', this%rootb_par, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('slatop', this%slatop, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('dsladlai', this%dsladlai, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('leafcn', this%leafcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('flnr', this%flnr, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('smpso', this%smpso, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('smpsc', this%smpsc, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fnitr', this%fnitr, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('woody', this%woody, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('lflitcn', this%lflitcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('frootcn', this%frootcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('livewdcn', this%livewdcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('deadwdcn', this%deadwdcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('grperc', this%grperc, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('grpnow', this%grpnow, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('froot_leaf', this%froot_leaf, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('stem_leaf', this%stem_leaf, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('croot_stem', this%croot_stem, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('flivewd', this%flivewd, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fcur', this%fcur, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fcurdv', this%fcurdv, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('lf_flab', this%lf_flab, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('lf_fcel', this%lf_fcel, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('lf_flig', this%lf_flig, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fr_flab', this%fr_flab, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fr_fcel', this%fr_fcel, 'read', ncid, readvar=readv, posNOTonfile=.true.)    
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fr_flig', this%fr_flig, 'read', ncid, readvar=readv, posNOTonfile=.true.)    
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('leaf_long', this%leaf_long, 'read', ncid, readvar=readv, posNOTonfile=.true.)    
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('evergreen', this%evergreen, 'read', ncid, readvar=readv, posNOTonfile=.true.)    
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('stress_decid', this%stress_decid, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('season_decid', this%season_decid, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pftpar20', this%pftpar20, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pftpar28', this%pftpar28, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pftpar29', this%pftpar29, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pftpar30', this%pftpar30, 'read', ncid, readvar=readv, posNOTonfile=.true.)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pftpar31', this%pftpar31, 'read', ncid, readvar=readv, posNOTonfile=.true.)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('a_fix', this%a_fix, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-   
-    call ncd_io('b_fix', this%b_fix, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-    
-    call ncd_io('c_fix', this%c_fix, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-    
-    call ncd_io('s_fix', this%s_fix, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('akc_active', this%akc_active, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('akn_active', this%akn_active, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('ekc_active', this%ekc_active, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('ekn_active', this%ekn_active, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('kc_nonmyc', this%kc_nonmyc, 'read', ncid, readvar=readv,   posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-   
-    call ncd_io('kn_nonmyc', this%kn_nonmyc, 'read', ncid, readvar=readv,   posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('kr_resorb', this%kr_resorb, 'read', ncid, readvar=readv,   posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('perecm', this%perecm, 'read', ncid, readvar=readv,         posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fun_cn_flex_a', this%fun_cn_flex_a, 'read', ncid, readvar=readv,         posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fun_cn_flex_b', this%fun_cn_flex_b, 'read', ncid, readvar=readv,         posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fun_cn_flex_c', this%fun_cn_flex_c, 'read', ncid, readvar=readv,         posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-  
-    call ncd_io('FUN_fracfixers', this%FUN_fracfixers, 'read', ncid, readvar=readv,         posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('manunitro', this%manunitro, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fleafcn', this%fleafcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('ffrootcn', this%ffrootcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fstemcn', this%fstemcn, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('rootprof_beta', this%rootprof_beta, 'read', ncid, readvar=readv, posNOTonfile=.true.)
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pconv', this%pconv, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pprod10', this%pprod10, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pprodharv10', this%pprodharv10, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('pprod100', this%pprod100, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('graincn', this%graincn, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('mxtmp', this%mxtmp, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('baset', this%baset, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('declfact', this%declfact, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('bfact', this%bfact, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('aleaff', this%aleaff, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('arootf', this%arootf, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('astemf', this%astemf, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('arooti', this%arooti, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fleafi', this%fleafi, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('allconsl', this%allconsl, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('allconss', this%allconss, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('crop', this%crop, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('mergetoclmpft', this%mergetoclmpft, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) then
-       call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-    end if
-
-    call ncd_io('irrigated', this%irrigated, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('ztopmx', this%ztopmx, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('laimx', this%laimx, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('gddmin', this%gddmin, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('hybgdd', this%hybgdd, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('lfemerg', this%lfemerg, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('grnfill', this%grnfill, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('mbbopt', this%mbbopt, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('medlynslope', this%medlynslope, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('medlynintercept', this%medlynintercept, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('mxmat', this%mxmat, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('cc_leaf', this% cc_leaf, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('cc_lstem', this%cc_lstem, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('cc_dstem', this%cc_dstem, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('cc_other', this%cc_other, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_leaf', this% fm_leaf, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_lstem', this%fm_lstem, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_dstem', this%fm_dstem, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_other', this%fm_other, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_root', this% fm_root, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_lroot', this%fm_lroot, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fm_droot', this%fm_droot, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fsr_pft', this% fsr_pft, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('fd_pft', this%  fd_pft, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('planting_temp', this%planttemp, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('min_planting_temp', this%minplanttemp, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('min_NH_planting_date', this%mnNHplantdate, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('min_SH_planting_date', this%mnSHplantdate, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('max_NH_planting_date', this%mxNHplantdate, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    call ncd_io('max_SH_planting_date', this%mxSHplantdate, 'read', ncid, readvar=readv)  
-    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-
-    !
-    ! Constants
-    !
-    !MV (10-08-14) TODO is this right - used to be numpft - is it okay to set it to mxpft?
-    do m = 0,mxpft 
-       this%dwood(m) = dwood
-       this%root_radius(m)  = root_radius
-       this%root_density(m) = root_density
-
-       if (m <= ntree) then
-          this%tree(m) = 1
-       else
-          this%tree(m) = 0
-       end if
-    end do
-    !
-    ! clm 5 nitrogen variables
-    !
-    if (use_flexibleCN) then
-       call ncd_io('i_vcad', this%i_vcad, 'read', ncid, readvar=readv) 
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) 
-       
-       call ncd_io('s_vcad', this%s_vcad, 'read', ncid, readvar=readv) 
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) 
-       
-       call ncd_io('i_flnr', this%i_flnr, 'read', ncid, readvar=readv) 
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) 
-       
-       call ncd_io('s_flnr', this%s_flnr, 'read', ncid, readvar=readv) 
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) 
-    end if
-
-    !
-    ! Dynamic Root variables for crops
-    !
-    if ( use_crop .and. use_dynroot )then
-       call ncd_io('root_dmx', this%root_dmx, 'read', ncid, readvar=readv)
-       if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
-    end if
-   
-    call ncd_pio_closefile(ncid)
-
-    do i = 0, mxpft
-       if ( trim(adjustl(pftname(i))) /= trim(expected_pftnames(i)) )then
-          write(iulog,*)'pftconrd: pftname is NOT what is expected, name = ', &
-               trim(pftname(i)), ', expected name = ', trim(expected_pftnames(i))
-          call endrun(msg='pftconrd: bad name for pft on paramfile dataset'//errMsg(sourcefile, __LINE__))
-       end if
-
-       if ( trim(pftname(i)) == 'not_vegetated'                       ) noveg                = i
-       if ( trim(pftname(i)) == 'needleleaf_evergreen_temperate_tree' ) ndllf_evr_tmp_tree   = i
-       if ( trim(pftname(i)) == 'needleleaf_evergreen_boreal_tree'    ) ndllf_evr_brl_tree   = i
-       if ( trim(pftname(i)) == 'needleleaf_deciduous_boreal_tree'    ) ndllf_dcd_brl_tree   = i
-       if ( trim(pftname(i)) == 'broadleaf_evergreen_tropical_tree'   ) nbrdlf_evr_trp_tree  = i
-       if ( trim(pftname(i)) == 'broadleaf_evergreen_temperate_tree'  ) nbrdlf_evr_tmp_tree  = i
-       if ( trim(pftname(i)) == 'broadleaf_deciduous_tropical_tree'   ) nbrdlf_dcd_trp_tree  = i
-       if ( trim(pftname(i)) == 'broadleaf_deciduous_temperate_tree'  ) nbrdlf_dcd_tmp_tree  = i
-       if ( trim(pftname(i)) == 'broadleaf_deciduous_boreal_tree'     ) nbrdlf_dcd_brl_tree  = i
-       if ( trim(pftname(i)) == 'broadleaf_evergreen_shrub'           ) nbrdlf_evr_shrub     = i
-       if ( trim(pftname(i)) == 'broadleaf_deciduous_temperate_shrub' ) nbrdlf_dcd_tmp_shrub = i
-       if ( trim(pftname(i)) == 'broadleaf_deciduous_boreal_shrub'    ) nbrdlf_dcd_brl_shrub = i
-       if ( trim(pftname(i)) == 'c3_arctic_grass'                     ) nc3_arctic_grass     = i
-       if ( trim(pftname(i)) == 'c3_non-arctic_grass'                 ) nc3_nonarctic_grass  = i
-       if ( trim(pftname(i)) == 'c4_grass'                            ) nc4_grass            = i
-       if ( trim(pftname(i)) == 'c3_crop'                             ) nc3crop              = i
-       if ( trim(pftname(i)) == 'c3_irrigated'                        ) nc3irrig             = i
-       if ( trim(pftname(i)) == 'temperate_corn'                      ) ntmp_corn            = i
-       if ( trim(pftname(i)) == 'irrigated_temperate_corn'            ) nirrig_tmp_corn      = i
-       if ( trim(pftname(i)) == 'spring_wheat'                        ) nswheat              = i
-       if ( trim(pftname(i)) == 'irrigated_spring_wheat'              ) nirrig_swheat        = i
-       if ( trim(pftname(i)) == 'winter_wheat'                        ) nwwheat              = i
-       if ( trim(pftname(i)) == 'irrigated_winter_wheat'              ) nirrig_wwheat        = i
-       if ( trim(pftname(i)) == 'temperate_soybean'                   ) ntmp_soybean         = i
-       if ( trim(pftname(i)) == 'irrigated_temperate_soybean'         ) nirrig_tmp_soybean   = i
-       if ( trim(pftname(i)) == 'barley'                              ) nbarley              = i
-       if ( trim(pftname(i)) == 'irrigated_barley'                    ) nirrig_barley        = i
-       if ( trim(pftname(i)) == 'winter_barley'                       ) nwbarley             = i
-       if ( trim(pftname(i)) == 'irrigated_winter_barley'             ) nirrig_wbarley       = i
-       if ( trim(pftname(i)) == 'rye'                                 ) nrye                 = i
-       if ( trim(pftname(i)) == 'irrigated_rye'                       ) nirrig_rye           = i
-       if ( trim(pftname(i)) == 'winter_rye'                          ) nwrye                = i
-       if ( trim(pftname(i)) == 'irrigated_winter_rye'                ) nirrig_wrye          = i
-       if ( trim(pftname(i)) == 'cassava'                             ) ncassava             = i
-       if ( trim(pftname(i)) == 'irrigated_cassava'                   ) nirrig_cassava       = i
-       if ( trim(pftname(i)) == 'citrus'                              ) ncitrus              = i
-       if ( trim(pftname(i)) == 'irrigated_citrus'                    ) nirrig_citrus        = i
-       if ( trim(pftname(i)) == 'cocoa'                               ) ncocoa               = i
-       if ( trim(pftname(i)) == 'irrigated_cocoa'                     ) nirrig_cocoa         = i
-       if ( trim(pftname(i)) == 'coffee'                              ) ncoffee              = i
-       if ( trim(pftname(i)) == 'irrigated_coffee'                    ) nirrig_coffee        = i
-       if ( trim(pftname(i)) == 'cotton'                              ) ncotton              = i
-       if ( trim(pftname(i)) == 'irrigated_cotton'                    ) nirrig_cotton        = i
-       if ( trim(pftname(i)) == 'datepalm'                            ) ndatepalm            = i
-       if ( trim(pftname(i)) == 'irrigated_datepalm'                  ) nirrig_datepalm      = i
-       if ( trim(pftname(i)) == 'foddergrass'                         ) nfoddergrass         = i
-       if ( trim(pftname(i)) == 'irrigated_foddergrass'               ) nirrig_foddergrass   = i
-       if ( trim(pftname(i)) == 'grapes'                              ) ngrapes              = i
-       if ( trim(pftname(i)) == 'irrigated_grapes'                    ) nirrig_grapes        = i
-       if ( trim(pftname(i)) == 'groundnuts'                          ) ngroundnuts          = i
-       if ( trim(pftname(i)) == 'irrigated_groundnuts'                ) nirrig_groundnuts    = i
-       if ( trim(pftname(i)) == 'millet'                              ) nmillet              = i
-       if ( trim(pftname(i)) == 'irrigated_millet'                    ) nirrig_millet        = i
-       if ( trim(pftname(i)) == 'oilpalm'                             ) noilpalm             = i
-       if ( trim(pftname(i)) == 'irrigated_oilpalm'                   ) nirrig_oilpalm       = i
-       if ( trim(pftname(i)) == 'potatoes'                            ) npotatoes            = i
-       if ( trim(pftname(i)) == 'irrigated_potatoes'                  ) nirrig_potatoes      = i
-       if ( trim(pftname(i)) == 'pulses'                              ) npulses              = i
-       if ( trim(pftname(i)) == 'irrigated_pulses'                    ) nirrig_pulses        = i
-       if ( trim(pftname(i)) == 'rapeseed'                            ) nrapeseed            = i
-       if ( trim(pftname(i)) == 'irrigated_rapeseed'                  ) nirrig_rapeseed      = i
-       if ( trim(pftname(i)) == 'rice'                                ) nrice                = i
-       if ( trim(pftname(i)) == 'irrigated_rice'                      ) nirrig_rice          = i
-       if ( trim(pftname(i)) == 'sorghum'                             ) nsorghum             = i
-       if ( trim(pftname(i)) == 'irrigated_sorghum'                   ) nirrig_sorghum       = i
-       if ( trim(pftname(i)) == 'sugarbeet'                           ) nsugarbeet           = i
-       if ( trim(pftname(i)) == 'irrigated_sugarbeet'                 ) nirrig_sugarbeet     = i
-       if ( trim(pftname(i)) == 'sugarcane'                           ) nsugarcane           = i
-       if ( trim(pftname(i)) == 'irrigated_sugarcane'                 ) nirrig_sugarcane     = i
-       if ( trim(pftname(i)) == 'sunflower'                           ) nsunflower           = i
-       if ( trim(pftname(i)) == 'irrigated_sunflower'                 ) nirrig_sunflower     = i
-       if ( trim(pftname(i)) == 'miscanthus'                          ) nmiscanthus          = i
-       if ( trim(pftname(i)) == 'irrigated_miscanthus'                ) nirrig_miscanthus    = i
-       if ( trim(pftname(i)) == 'switchgrass'                         ) nswitchgrass         = i
-       if ( trim(pftname(i)) == 'irrigated_switchgrass'               ) nirrig_switchgrass   = i
-       if ( trim(pftname(i)) == 'tropical_corn'                       ) ntrp_corn            = i
-       if ( trim(pftname(i)) == 'irrigated_tropical_corn'             ) nirrig_trp_corn      = i
-       if ( trim(pftname(i)) == 'tropical_soybean'                    ) ntrp_soybean         = i
-       if ( trim(pftname(i)) == 'irrigated_tropical_soybean'          ) nirrig_trp_soybean   = i
-    end do
-
-    ntree                = nbrdlf_dcd_brl_tree  ! value for last type of tree
-    npcropmin            = ntmp_corn            ! first prognostic crop
-    npcropmax            = mxpft                ! last prognostic crop in list
-
-    call this%set_is_pft_known_to_model()
-    call this%set_num_cfts_known_to_model()
-
-    if (use_cndv) then
-       this%fcur(:) = this%fcurdv(:)
-    end if
-    !
-    ! Do some error checking.
-    !
-    ! FIX(SPM,032414) double check if some of these should be on...
-
-    if ( npcropmax /= mxpft )then
-       call endrun(msg=' ERROR: npcropmax is NOT the last value'//errMsg(sourcefile, __LINE__))
-    end if
-    do i = 0, mxpft
-       if ( this%irrigated(i) == 1.0_r8 .and.                              &
-            (i == nc3irrig               .or.                              &
-             i == nirrig_tmp_corn        .or.                              &
-             i == nirrig_swheat          .or. i == nirrig_wwheat      .or. &
-             i == nirrig_tmp_soybean     .or.                              &
-             i == nirrig_barley          .or. i == nirrig_wbarley     .or. &
-             i == nirrig_rye             .or. i == nirrig_wrye        .or. &
-             i == nirrig_cassava         .or.                              &
-             i == nirrig_citrus          .or.                              &
-             i == nirrig_cocoa           .or. i == nirrig_coffee      .or. &
-             i == nirrig_cotton          .or.                              &
-             i == nirrig_datepalm        .or.                              &
-             i == nirrig_foddergrass     .or.                              &
-             i == nirrig_grapes          .or. i == nirrig_groundnuts  .or. &
-             i == nirrig_millet          .or.                              &
-             i == nirrig_oilpalm         .or.                              &
-             i == nirrig_potatoes        .or. i == nirrig_pulses      .or. &
-             i == nirrig_rapeseed        .or. i == nirrig_rice        .or. &
-             i == nirrig_sorghum         .or.                              &
-             i == nirrig_sugarbeet       .or. i == nirrig_sugarcane   .or. &
-             i == nirrig_sunflower       .or.                              &
-             i == nirrig_miscanthus      .or. i == nirrig_switchgrass .or. &
-             i == nirrig_trp_corn        .or.                              &
-             i == nirrig_trp_soybean) )then
-             ! correct
-          else if ( this%irrigated(i) == 0.0_r8 )then
-             ! correct
-          else
-          call endrun(msg=' ERROR: irrigated has wrong values'//errMsg(sourcefile, __LINE__))
-       end if
-       if (      this%crop(i) == 1.0_r8 .and. (i >= nc3crop .and. i <= npcropmax) )then
-          ! correct
-       else if ( this%crop(i) == 0.0_r8 )then
-          ! correct
-       else
-          call endrun(msg=' ERROR: crop has wrong values'//errMsg(sourcefile, __LINE__))
-       end if
-       if ( (i /= noveg) .and. (i < npcropmin) .and. &
-            abs(this%pconv(i) + this%pprod10(i) + this%pprod100(i) - 1.0_r8) > 1.e-7_r8 )then
-          call endrun(msg=' ERROR: pconv+pprod10+pprod100 do NOT sum to one.'//errMsg(sourcefile, __LINE__))
-       end if
-       if ( this%pprodharv10(i) > 1.0_r8 .or. this%pprodharv10(i) < 0.0_r8 )then
-          call endrun(msg=' ERROR: pprodharv10 outside of range.'//errMsg(sourcefile, __LINE__))
-       end if
-    end do
-
-    if (masterproc) then
-       write(iulog,*) 'Successfully read PFT physiological data'
-       write(iulog,*)
-    end if
-
-  end subroutine InitRead
-
-  !-----------------------------------------------------------------------
-  subroutine set_is_pft_known_to_model(this)
-    !
-    ! !DESCRIPTION:
-    ! Set is_pft_known_to_model based on mergetoclmpft
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(pftcon_type), intent(inout) :: this
-    !
-    ! !LOCAL VARIABLES:
-    integer :: m, merge_type
-
-    character(len=*), parameter :: subname = 'set_is_pft_known_to_model'
-    !-----------------------------------------------------------------------
-
-    this%is_pft_known_to_model(:) = .false.
-
-    ! NOTE(wjs, 2015-10-04) Currently, type 0 has mergetoclmpft = _FillValue in the file,
-    ! so we can't handle it in the general loop below. But CLM always uses type 0, so
-    ! handle it specially here.
-    this%is_pft_known_to_model(0) = .true.
-
-    ! NOTE(wjs, 2015-10-04) Currently, mergetoclmpft is only used for crop types.
-    ! However, we handle it more generally here (treating ALL pft types), in case its use
-    ! is ever extended to work with non-crop types as well.
-    do m = 1, mxpft
-       merge_type = this%mergetoclmpft(m)
-       this%is_pft_known_to_model(merge_type) = .true.
-    end do
-
-  end subroutine set_is_pft_known_to_model
-
-  !-----------------------------------------------------------------------
-  subroutine set_num_cfts_known_to_model(this)
-    !
-    ! !DESCRIPTION:
-    ! Set the module-level variable, num_cfts_known_to_model
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(pftcon_type), intent(in) :: this
-    !
-    ! !LOCAL VARIABLES:
-    integer :: m
-
-    character(len=*), parameter :: subname = 'set_num_cfts_known_to_model'
-    !-----------------------------------------------------------------------
-
-    num_cfts_known_to_model = 0
-    do m = cft_lb, cft_ub
-       if (this%is_pft_known_to_model(m)) then
-          num_cfts_known_to_model = num_cfts_known_to_model + 1
-       end if
-    end do
-
-  end subroutine set_num_cfts_known_to_model
-
-  !-----------------------------------------------------------------------
-  subroutine Clean(this)
-    !
-    ! !DESCRIPTION:
-    ! Deallocate memory
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(pftcon_type), intent(inout) :: this
-    !
-    ! !LOCAL VARIABLES:
-
-    character(len=*), parameter :: subname = 'Clean'
-    !-----------------------------------------------------------------------
-
-    deallocate( this%noveg)
-    deallocate( this%tree)
-
-    deallocate( this%dleaf)
-    deallocate( this%c3psn)
-    deallocate( this%xl)
-    deallocate( this%rhol)
-    deallocate( this%rhos)
-    deallocate( this%taul)
-    deallocate( this%taus)
-    deallocate( this%z0mr)
-    deallocate( this%displar)
-    deallocate( this%roota_par)
-    deallocate( this%rootb_par)
-    deallocate( this%crop)
-    deallocate( this%mergetoclmpft)
-    deallocate( this%is_pft_known_to_model)
-    deallocate( this%irrigated)
-    deallocate( this%smpso)
-    deallocate( this%smpsc)
-    deallocate( this%fnitr)
-    deallocate( this%slatop)
-    deallocate( this%dsladlai)
-    deallocate( this%leafcn)
-    deallocate( this%flnr)
-    deallocate( this%woody)
-    deallocate( this%lflitcn)
-    deallocate( this%frootcn)
-    deallocate( this%livewdcn)
-    deallocate( this%deadwdcn)
-    deallocate( this%grperc)
-    deallocate( this%grpnow)
-    deallocate( this%rootprof_beta)
-    deallocate( this%graincn)
-    deallocate( this%mxtmp)
-    deallocate( this%baset)
-    deallocate( this%declfact)
-    deallocate( this%bfact)
-    deallocate( this%aleaff)
-    deallocate( this%arootf)
-    deallocate( this%astemf)
-    deallocate( this%arooti)
-    deallocate( this%fleafi)
-    deallocate( this%allconsl)
-    deallocate( this%allconss)
-    deallocate( this%ztopmx)
-    deallocate( this%laimx)
-    deallocate( this%gddmin)
-    deallocate( this%hybgdd)
-    deallocate( this%lfemerg)
-    deallocate( this%grnfill)
-    deallocate( this%mbbopt)
-    deallocate( this%medlynslope)
-    deallocate( this%medlynintercept)
-    deallocate( this%mxmat)
-    deallocate( this%mnNHplantdate)
-    deallocate( this%mxNHplantdate)
-    deallocate( this%mnSHplantdate)
-    deallocate( this%mxSHplantdate)
-    deallocate( this%planttemp)
-    deallocate( this%minplanttemp)
-    deallocate( this%froot_leaf)
-    deallocate( this%stem_leaf)
-    deallocate( this%croot_stem)
-    deallocate( this%flivewd)
-    deallocate( this%fcur)
-    deallocate( this%fcurdv)
-    deallocate( this%lf_flab)
-    deallocate( this%lf_fcel)
-    deallocate( this%lf_flig)
-    deallocate( this%fr_flab)
-    deallocate( this%fr_fcel)
-    deallocate( this%fr_flig)
-    deallocate( this%leaf_long)
-    deallocate( this%evergreen)
-    deallocate( this%stress_decid)
-    deallocate( this%season_decid)
-    deallocate( this%dwood)
-    deallocate( this%root_density)
-    deallocate( this%root_radius)
-    deallocate( this%pconv)
-    deallocate( this%pprod10)
-    deallocate( this%pprod100)
-    deallocate( this%pprodharv10)
-    deallocate( this%cc_leaf)
-    deallocate( this%cc_lstem)
-    deallocate( this%cc_dstem)
-    deallocate( this%cc_other)
-    deallocate( this%fm_leaf)
-    deallocate( this%fm_lstem)
-    deallocate( this%fm_dstem)
-    deallocate( this%fm_other)
-    deallocate( this%fm_root)
-    deallocate( this%fm_lroot)
-    deallocate( this%fm_droot)
-    deallocate( this%fsr_pft)
-    deallocate( this%fd_pft)
-    deallocate( this%manunitro)
-    deallocate( this%fleafcn)
-    deallocate( this%ffrootcn)
-    deallocate( this%fstemcn)
-    deallocate( this%i_vcad)
-    deallocate( this%s_vcad)
-    deallocate( this%i_flnr)
-    deallocate( this%s_flnr)
-    deallocate( this%pftpar20)
-    deallocate( this%pftpar28)
-    deallocate( this%pftpar29)
-    deallocate( this%pftpar30)
-    deallocate( this%pftpar31)
-    deallocate( this%a_fix)
-    deallocate( this%b_fix)
-    deallocate( this%c_fix)
-    deallocate( this%s_fix)
-    deallocate( this%akc_active)
-    deallocate( this%akn_active)
-    deallocate( this%ekc_active)
-    deallocate( this%ekn_active)
-    deallocate( this%kc_nonmyc)
-    deallocate( this%kn_nonmyc)
-    deallocate( this%kr_resorb)
-    deallocate( this%perecm)
-    deallocate( this%root_dmx)
-    deallocate( this%fun_cn_flex_a)
-    deallocate( this%fun_cn_flex_b)
-    deallocate( this%fun_cn_flex_c)
-    deallocate( this%FUN_fracfixers)
-    
-  end subroutine Clean
-
-end module pftconMod
-
diff --git a/src/main/readParamsMod.F90 b/src/main/readParamsMod.F90
deleted file mode 100644
index d2c2393e0f..0000000000
--- a/src/main/readParamsMod.F90
+++ /dev/null
@@ -1,100 +0,0 @@
-module readParamsMod
-
-  !-----------------------------------------------------------------------
-  !
-  ! Read parameters
-  ! module used to read parameters for individual modules and/or for some 
-  ! well defined functionality (eg. ED).
-  !
-  ! ! USES:
-  use clm_varctl , only : paramfile, iulog, use_fates, use_cn
-  use spmdMod    , only : masterproc
-  use fileutils  , only : getfil
-  use ncdio_pio  , only : ncd_pio_closefile, ncd_pio_openfile
-  use ncdio_pio  , only : file_desc_t , ncd_inqdid, ncd_inqdlen
-
-  implicit none
-  private
-  !
-  public :: readParameters
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParameters (photosyns_inst)
-    !
-    ! ! USES:
-    use CNSharedParamsMod                 , only : CNParamsReadShared
-    use CNGapMortalityMod                 , only : readCNGapMortParams                    => readParams
-    use CNMRespMod                        , only : readCNMRespParams                      => readParams
-    use CNPhenologyMod                    , only : readCNPhenolParams                     => readParams
-    use SoilBiogeochemNLeachingMod        , only : readSoilBiogeochemNLeachingParams      => readParams
-    use SoilBiogeochemNitrifDenitrifMod   , only : readSoilBiogeochemNitrifDenitrifParams => readParams
-    use SoilBiogeochemLittVertTranspMod   , only : readSoilBiogeochemLittVertTranspParams => readParams
-    use SoilBiogeochemPotentialMod        , only : readSoilBiogeochemPotentialParams      => readParams
-    use SoilBiogeochemDecompMod           , only : readSoilBiogeochemDecompParams         => readParams
-    use SoilBiogeochemDecompCascadeBGCMod , only : readSoilBiogeochemDecompBgcParams      => readParams
-    use SoilBiogeochemDecompCascadeCNMod  , only : readSoilBiogeochemDecompCnParams       => readParams
-    !use ch4Mod                            , only : readCH4Params                          => readParams
-    use clm_varctl,                         only : NLFilename_in
-    use PhotosynthesisMod                 , only : photosyns_type
-    !
-    ! !ARGUMENTS:
-    type(photosyns_type)                   , intent(in) :: photosyns_inst
-    !
-    ! !LOCAL VARIABLES:
-    character(len=256) :: locfn ! local file name
-    type(file_desc_t)  :: ncid  ! pio netCDF file id
-    integer            :: dimid ! netCDF dimension id
-    integer            :: npft  ! number of pfts on pft-physiology file
-    character(len=32)  :: subname = 'readParameters'
-    !-----------------------------------------------------------------------
-
-    if (masterproc) then
-       write(iulog,*) 'paramMod.F90::'//trim(subname)//' :: reading CLM '//' parameters '
-    end if
-
-    call getfil (paramfile, locfn, 0)
-    call ncd_pio_openfile (ncid, trim(locfn), 0)
-    call ncd_inqdid(ncid,'pft',dimid) 
-    call ncd_inqdlen(ncid,dimid,npft) 
-
-    !
-    ! Above ground biogeochemistry...
-    !
-    if (use_cn) then
-       call readCNGapMortParams(ncid)
-       call readCNMRespParams(ncid)
-       call readCNPhenolParams(ncid)
-    end if
-
-    !
-    ! Soil biogeochemistry...
-    !
-    if (use_cn .or. use_fates) then
-       call readSoilBiogeochemDecompBgcParams(ncid)
-       call readSoilBiogeochemDecompCnParams(ncid)
-       call readSoilBiogeochemDecompParams(ncid)
-       call readSoilBiogeochemLittVertTranspParams(ncid)
-       call readSoilBiogeochemNitrifDenitrifParams(ncid)
-       call readSoilBiogeochemNLeachingParams(ncid)
-       call readSoilBiogeochemPotentialParams(ncid)
-       call CNParamsReadShared(ncid, NLFilename_in)  ! this is called CN params but really is for the soil biogeochem parameters
-
-       !call readCH4Params (ncid)
-    end if
-
-    !
-    ! Biogeophysics
-    !
-    call photosyns_inst%ReadParams( ncid )
-
-
-    !
-    call ncd_pio_closefile(ncid)
-
-  end subroutine readParameters
-
-end module readParamsMod
diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90
index d30d59a853..c5e2610e93 100644
--- a/src/main/restFileMod.F90
+++ b/src/main/restFileMod.F90
@@ -17,9 +17,8 @@ module restFileMod
   use accumulMod       , only : accumulRest
   use clm_instMod      , only : clm_instRest
   use histFileMod      , only : hist_restart_ncd
-  use clm_varctl       , only : iulog, use_fates, use_hydrstress
-  use clm_varctl       , only : create_crop_landunit, irrigate
-  use clm_varcon       , only : nameg, namel, namec, namep, nameCohort
+  use clm_varctl       , only : iulog
+  use clm_varcon       , only : nameg, namel, namec, namep
   use ncdio_pio        , only : file_desc_t, ncd_pio_createfile, ncd_pio_openfile, ncd_global
   use ncdio_pio        , only : ncd_pio_closefile, ncd_defdim, ncd_putatt, ncd_enddef, check_dim
   use ncdio_pio        , only : check_att, ncd_getatt
@@ -47,7 +46,6 @@ module restFileMod
   private :: restFile_add_flag_metadata ! Add global metadata for some logical flag
   private :: restFile_add_ilun_metadata ! Add global metadata defining landunit types
   private :: restFile_add_icol_metadata ! Add global metadata defining column types
-  private :: restFile_add_ipft_metadata ! Add global metadata defining patch types
   private :: restFile_dimcheck
   private :: restFile_enddef
   private :: restFile_check_consistency   ! Perform consistency checks on the restart file
@@ -185,7 +183,7 @@ subroutine restFile_read( bounds_proc, file, glc_behavior )
     !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
     do nc = 1, nclumps
        call get_clump_bounds(nc, bounds_clump)
-       call reweight_wrapup(bounds_clump, glc_behavior)
+       call reweight_wrapup(bounds_clump)
     end do
     !$OMP END PARALLEL DO
 
@@ -483,8 +481,7 @@ subroutine restFile_dimset( ncid )
     use clm_time_manager     , only : get_nstep
     use clm_varctl           , only : caseid, ctitle, version, username, hostname, fsurdat
     use clm_varctl           , only : conventions, source
-    use clm_varpar           , only : numrad, nlevlak, nlevsno, nlevgrnd, nlevurb, nlevcan
-    use clm_varpar           , only : maxpatch_glcmec, nvegwcs
+    use clm_varpar           , only : numrad, nlevlak, nlevsno, nlevgrnd, nlevurb
     use decompMod            , only : get_proc_global
     !
     ! !ARGUMENTS:
@@ -513,7 +510,6 @@ subroutine restFile_dimset( ncid )
     call ncd_defdim(ncid , namel      , numl           ,  dimid)
     call ncd_defdim(ncid , namec      , numc           ,  dimid)
     call ncd_defdim(ncid , namep      , nump           ,  dimid)
-    call ncd_defdim(ncid , nameCohort , numCohort      ,  dimid)
 
     call ncd_defdim(ncid , 'levgrnd' , nlevgrnd       ,  dimid)
     call ncd_defdim(ncid , 'levurb'  , nlevurb        ,  dimid)
@@ -522,12 +518,7 @@ subroutine restFile_dimset( ncid )
     call ncd_defdim(ncid , 'levsno1' , nlevsno+1      ,  dimid)
     call ncd_defdim(ncid , 'levtot'  , nlevsno+nlevgrnd, dimid)
     call ncd_defdim(ncid , 'numrad'  , numrad         ,  dimid)
-    call ncd_defdim(ncid , 'levcan'  , nlevcan        ,  dimid)
-    if ( use_hydrstress ) then
-      call ncd_defdim(ncid , 'vegwcs'  , nvegwcs        ,  dimid)
-    end if
     call ncd_defdim(ncid , 'string_length', 64        ,  dimid)
-    call ncd_defdim(ncid , 'glc_nec', maxpatch_glcmec, dimid)
 	
 	! mml add my soil dimension
     call ncd_defdim(ncid , 'mml_lev'  , 10        ,  dimid) ! mml: hard coded for six soil layers
@@ -551,8 +542,6 @@ subroutine restFile_dimset( ncid )
     call ncd_putatt(ncid, NCD_GLOBAL, 'surface_dataset', trim(fsurdat))
     call ncd_putatt(ncid, NCD_GLOBAL, 'title', 'CLM Restart information')
 
-    call restFile_add_flag_metadata(ncid, create_crop_landunit, 'create_crop_landunit')
-    call restFile_add_flag_metadata(ncid, irrigate, 'irrigate')
     ! BACKWARDS_COMPATIBILITY(wjs, 2017-12-13) created_glacier_mec_landunits is always
     ! true now. However, we can't remove the read of this field from init_interp until we
     ! can reliably assume that all initial conditions files that might be used in
@@ -560,7 +549,6 @@ subroutine restFile_dimset( ncid )
     ! hard-coded .true. value.
     call restFile_add_flag_metadata(ncid, .true., 'created_glacier_mec_landunits')
 
-    call restFile_add_ipft_metadata(ncid)
     call restFile_add_icol_metadata(ncid)
     call restFile_add_ilun_metadata(ncid)
 
@@ -642,37 +630,6 @@ subroutine restFile_add_icol_metadata(ncid)
 
   end subroutine restFile_add_icol_metadata
 
-  !-----------------------------------------------------------------------
-  subroutine restFile_add_ipft_metadata(ncid)
-    !
-    ! !DESCRIPTION:
-    ! Add global metadata defining patch types
-    !
-    ! !USES:
-    use clm_varpar, only : natpft_lb, mxpft, cft_lb, cft_ub
-    use pftconMod , only : pftname_len, pftname
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t), intent(inout) :: ncid ! local file id
-    !
-    ! !LOCAL VARIABLES:
-    integer :: ptype  ! patch type
-    character(len=*), parameter :: att_prefix = 'ipft_'   ! prefix for attributes
-    character(len=len(att_prefix)+pftname_len) :: attname ! attribute name
-
-    character(len=*), parameter :: subname = 'restFile_add_ipft_metadata'
-    !-----------------------------------------------------------------------
-    
-    do ptype = natpft_lb, mxpft
-       attname = att_prefix // pftname(ptype)
-       call ncd_putatt(ncid, ncd_global, attname, ptype)
-    end do
-
-    call ncd_putatt(ncid, ncd_global, 'cft_lb', cft_lb)
-    call ncd_putatt(ncid, ncd_global, 'cft_ub', cft_ub)
-
-  end subroutine restFile_add_ipft_metadata
-
   !-----------------------------------------------------------------------
   subroutine restFile_dimcheck( ncid )
     !
@@ -714,7 +671,6 @@ subroutine restFile_dimcheck( ncid )
        call check_dim(ncid, namel, numl, msg=msg)
        call check_dim(ncid, namec, numc, msg=msg)
        call check_dim(ncid, namep, nump, msg=msg)
-       if ( use_fates ) call check_dim(ncid, nameCohort  , numCohort, msg=msg)
     end if
     call check_dim(ncid, 'levsno'  , nlevsno, &
          msg = 'You can deal with this mismatch by rerunning with ' // &
diff --git a/src/main/reweightMod.F90 b/src/main/reweightMod.F90
index 5816fa1d1b..23ad038de0 100644
--- a/src/main/reweightMod.F90
+++ b/src/main/reweightMod.F90
@@ -29,7 +29,7 @@ module reweightMod
 contains
 
   !-----------------------------------------------------------------------
-  subroutine reweight_wrapup(bounds, glc_behavior)
+  subroutine reweight_wrapup(bounds)
     !
     ! !DESCRIPTION:
     ! Do additional modifications and error-checks that should be done after modifying subgrid
@@ -42,19 +42,17 @@ subroutine reweight_wrapup(bounds, glc_behavior)
     use filterMod         , only : setFilters
     use subgridWeightsMod , only : set_active, check_weights
     use decompMod         , only : bounds_type, BOUNDS_LEVEL_CLUMP
-    use glcBehaviorMod    , only : glc_behavior_type
     !
     ! !ARGUMENTS:
     type(bounds_type) , intent(in) :: bounds                      ! clump bounds
-    type(glc_behavior_type), intent(in) :: glc_behavior
     !------------------------------------------------------------------------
 
     SHR_ASSERT(bounds%level == BOUNDS_LEVEL_CLUMP, errMsg(sourcefile, __LINE__))
 
-    call set_active(bounds, glc_behavior)
+    call set_active(bounds)
     call check_weights(bounds, active_only=.false.)
     call check_weights(bounds, active_only=.true.)
-    call setFilters(bounds, glc_behavior)
+    call setFilters(bounds)
 
   end subroutine reweight_wrapup
 
diff --git a/src/main/subgridMod.F90 b/src/main/subgridMod.F90
index f844033aee..efc79616e8 100644
--- a/src/main/subgridMod.F90
+++ b/src/main/subgridMod.F90
@@ -428,13 +428,8 @@ function crop_patch_exists(gi, cft) result(exists)
     ! Returns true if a patch should be created in memory for the given crop functional
     ! type in this grid cell.
     !
-    ! This just applies to the crop landunit: it always returns .false. if
-    ! create_crop_landunit is .false.
-    !
     ! !USES:
     use clm_varpar           , only : cft_lb, cft_ub
-    use clm_varctl           , only : create_crop_landunit
-    use pftconmod            , only : pftcon
     use landunit_varcon      , only : istcrop
     !
     ! !ARGUMENTS:
@@ -447,10 +442,6 @@ function crop_patch_exists(gi, cft) result(exists)
     character(len=*), parameter :: subname = 'crop_patch_exists'
     !-----------------------------------------------------------------------
 
-    if (create_crop_landunit) then
-       SHR_ASSERT(cft >= cft_lb, errMsg(sourcefile, __LINE__))
-       SHR_ASSERT(cft <= cft_ub, errMsg(sourcefile, __LINE__))
-
        ! For a run without transient crops, only allocate memory for crops that are
        ! actually present in this run. (This will require running init_interp when
        ! changing between a transient crop run and a non-transient run.)
@@ -460,10 +451,6 @@ function crop_patch_exists(gi, cft) result(exists)
           exists = .false.
        end if
 
-    else  ! create_crop_landunit false
-       exists = .false.
-    end if
-
   end function crop_patch_exists
 
 
diff --git a/src/main/subgridRestMod.F90 b/src/main/subgridRestMod.F90
index 725db50351..6319f1f6eb 100644
--- a/src/main/subgridRestMod.F90
+++ b/src/main/subgridRestMod.F90
@@ -302,11 +302,6 @@ subroutine subgridRest_write_only(bounds, ncid, flag)
          long_name='column active flag (1=active, 0=inactive)', units=' ',          &
          interpinic_flag='skip', readvar=readvar, data=icarr)
 
-    call restartvar(ncid=ncid, flag=flag, varname='LEVGRND_CLASS', xtype=ncd_int,   &
-         dim1name='column', dim2name='levgrnd', switchdim=.true.,                   &
-         long_name='class in which each layer falls', units=' ',                    &
-         interpinic_flag='skip', readvar=readvar, data=col%levgrnd_class)
-
     allocate(temp2d_r(bounds%begc:bounds%endc, 1:nlevgrnd))
     temp2d_r(bounds%begc:bounds%endc, 1:nlevgrnd) = col%z(bounds%begc:bounds%endc, 1:nlevgrnd)
     call restartvar(ncid=ncid, flag=flag, varname='COL_Z', xtype=ncd_double,  & 
@@ -412,17 +407,6 @@ subroutine subgridRest_write_only(bounds, ncid, flag)
          long_name='pft active flag (1=active, 0=inactive)', units='',            &
          interpinic_flag='skip', readvar=readvar, data=iparr)
 
-    allocate(temp2d_i(bounds%begp:bounds%endp, 1:nlevgrnd))
-    do p=bounds%begp,bounds%endp
-       c = patch%column(p)
-       temp2d_i(p, 1:nlevgrnd) = col%levgrnd_class(c, 1:nlevgrnd)
-    end do
-    call restartvar(ncid=ncid, flag=flag, varname='LEVGRND_CLASS_p', xtype=ncd_int, &
-         dim1name='pft', dim2name='levgrnd', switchdim=.true., &
-         long_name='class in which each layer falls, patch-level', units=' ', &
-         interpinic_flag='skip', readvar=readvar, data=temp2d_i)
-    deallocate(temp2d_i)
-
     allocate(temp2d_r(bounds%begp:bounds%endp, 1:nlevgrnd))
     do p=bounds%begp,bounds%endp
        c = patch%column(p)
@@ -595,7 +579,7 @@ logical function do_check_weights()
       ! Return true if we should check weights
       !
       ! !USES:
-      use clm_varctl, only : nsrest, nsrContinue, use_cndv, use_fates
+      use clm_varctl, only : nsrest, nsrContinue
       !
       ! !ARGUMENTS:
       !
@@ -611,14 +595,6 @@ logical function do_check_weights()
          ! maintaining the logic that used to be in BiogeophysRestMod regarding these
          ! weight checks
          do_check_weights = .false.
-      else if (use_cndv) then
-         ! Don't check weights for a cndv case, because the weights will almost certainly
-         ! differ from the surface dataset in this case
-         do_check_weights = .false.
-      else if (use_fates) then
-         ! Don't check weights for a fates case, because the weights will almost certainly
-         ! differ from the surface dataset in this case
-         do_check_weights = .false.
       else
          do_check_weights = .true.
       end if
diff --git a/src/main/subgridWeightsMod.F90 b/src/main/subgridWeightsMod.F90
index d496c620f5..05dead68f0 100644
--- a/src/main/subgridWeightsMod.F90
+++ b/src/main/subgridWeightsMod.F90
@@ -92,14 +92,13 @@ module subgridWeightsMod
   use shr_kind_mod , only : r8 => shr_kind_r8
   use shr_log_mod  , only : errMsg => shr_log_errMsg
   use abortutils   , only : endrun
-  use clm_varctl   , only : iulog, all_active, use_fates
+  use clm_varctl   , only : iulog
   use clm_varcon   , only : nameg, namel, namec, namep
   use decompMod    , only : bounds_type
   use GridcellType , only : grc                
   use LandunitType , only : lun                
   use ColumnType   , only : col                
   use PatchType    , only : patch                
-  use glcBehaviorMod , only : glc_behavior_type
   !
   ! PUBLIC TYPES:
   implicit none
@@ -155,7 +154,7 @@ subroutine init_subgrid_weights_mod(bounds)
     !
     ! !USES:
     use landunit_varcon, only : max_lunit
-    use clm_varpar     , only : maxpatch_glcmec, natpft_size, cft_size
+    use clm_varpar     , only : natpft_size, cft_size
     use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
     use decompMod      , only : BOUNDS_LEVEL_PROC
     use histFileMod    , only : hist_addfld2d
@@ -183,7 +182,7 @@ subroutine init_subgrid_weights_mod(bounds)
     subgrid_weights_diagnostics%pct_nat_pft(:,:) = nan
     allocate(subgrid_weights_diagnostics%pct_cft(bounds%begg:bounds%endg, 1:cft_size))
     subgrid_weights_diagnostics%pct_cft(:,:) = nan
-    allocate(subgrid_weights_diagnostics%pct_glc_mec(bounds%begg:bounds%endg, 1:maxpatch_glcmec))
+    allocate(subgrid_weights_diagnostics%pct_glc_mec(bounds%begg:bounds%endg, 1:10))
     subgrid_weights_diagnostics%pct_glc_mec(:,:) = nan
 
     ! ------------------------------------------------------------------------
@@ -194,22 +193,10 @@ subroutine init_subgrid_weights_mod(bounds)
          avgflag='A', long_name='% of each landunit on grid cell', &
          ptr_lnd=subgrid_weights_diagnostics%pct_landunit, default='inactive')
 
-    if(.not.use_fates) then
-       call hist_addfld2d (fname='PCT_NAT_PFT', units='%', type2d='natpft', &
-             avgflag='A', long_name='% of each PFT on the natural vegetation (i.e., soil) landunit', &
-             ptr_lnd=subgrid_weights_diagnostics%pct_nat_pft, default='inactive')
-    end if
+    call hist_addfld2d (fname='PCT_NAT_PFT', units='%', type2d='natpft', &
+          avgflag='A', long_name='% of each PFT on the natural vegetation (i.e., soil) landunit', &
+          ptr_lnd=subgrid_weights_diagnostics%pct_nat_pft, default='inactive')
        
-    if (cft_size > 0) then
-       call hist_addfld2d (fname='PCT_CFT', units='%', type2d='cft', &
-            avgflag='A', long_name='% of each crop on the crop landunit', &
-            ptr_lnd=subgrid_weights_diagnostics%pct_cft, default='inactive')
-    end if
-
-    call hist_addfld2d (fname='PCT_GLC_MEC', units='%', type2d='glc_nec', &
-         avgflag='A', long_name='% of each GLC elevation class on the glc_mec landunit', &
-         ptr_lnd=subgrid_weights_diagnostics%pct_glc_mec, default='inactive')
-
   end subroutine init_subgrid_weights_mod
 
 
@@ -243,7 +230,7 @@ subroutine compute_higher_order_weights(bounds)
   end subroutine compute_higher_order_weights
 
   !-----------------------------------------------------------------------
-  subroutine set_active(bounds, glc_behavior)
+  subroutine set_active(bounds)
     !
     ! !DESCRIPTION:
     ! Set 'active' flags at the pft, column and landunit level
@@ -260,7 +247,6 @@ subroutine set_active(bounds, glc_behavior)
     ! !ARGUMENTS:
     implicit none
     type(bounds_type), intent(in) :: bounds  ! bounds
-    type(glc_behavior_type), intent(in) :: glc_behavior
     !
     ! !LOCAL VARIABLES:
     integer :: l,c,p       ! loop counters
@@ -269,12 +255,12 @@ subroutine set_active(bounds, glc_behavior)
     !------------------------------------------------------------------------
 
     do l = bounds%begl,bounds%endl
-       lun%active(l) = is_active_l(l, glc_behavior)
+       lun%active(l) = is_active_l(l)
     end do
 
     do c = bounds%begc,bounds%endc
        l = col%landunit(c)
-       col%active(c) = is_active_c(c, glc_behavior)
+       col%active(c) = is_active_c(c)
        if (col%active(c) .and. .not. lun%active(l)) then
           write(iulog,*) trim(subname),' ERROR: active column found on inactive landunit', &
                          'at c = ', c, ', l = ', l
@@ -295,7 +281,7 @@ subroutine set_active(bounds, glc_behavior)
   end subroutine set_active
 
   !-----------------------------------------------------------------------
-  logical function is_active_l(l, glc_behavior)
+  logical function is_active_l(l)
     !
     ! !DESCRIPTION:
     ! Determine whether the given landunit is active
@@ -306,16 +292,11 @@ logical function is_active_l(l, glc_behavior)
     ! !ARGUMENTS:
     implicit none
     integer, intent(in) :: l   ! landunit index
-    type(glc_behavior_type), intent(in) :: glc_behavior
     !
     ! !LOCAL VARIABLES:
     integer :: g  ! grid cell index
     !------------------------------------------------------------------------
 
-    if (all_active) then
-       is_active_l = .true.
-
-    else
        g =lun%gridcell(l)
 
        is_active_l = .false.
@@ -326,15 +307,6 @@ logical function is_active_l(l, glc_behavior)
        ! ------------------------------------------------------------------------
        if (lun%wtgcell(l) > 0) is_active_l = .true.
 
-       ! ------------------------------------------------------------------------
-       ! Conditions under which is_active_p is set to true because we want extra virtual landunits:
-       ! ------------------------------------------------------------------------
-
-       if (lun%itype(l) == istice_mec .and. &
-            glc_behavior%has_virtual_columns_grc(g)) then
-          is_active_l = .true.
-       end if
-
        ! In general, include a virtual natural vegetation landunit. This aids
        ! initialization of a new landunit; and for runs that are coupled to CISM, this
        ! provides bare land SMB forcing even if there is no vegetated area.
@@ -357,12 +329,10 @@ logical function is_active_l(l, glc_behavior)
           is_active_l = .true.
        end if
 
-    end if
-
   end function is_active_l
 
   !-----------------------------------------------------------------------
-  logical function is_active_c(c, glc_behavior)
+  logical function is_active_c(c)
     !
     ! !DESCRIPTION:
     ! Determine whether the given column is active
@@ -373,17 +343,12 @@ logical function is_active_c(c, glc_behavior)
     ! !ARGUMENTS:
     implicit none
     integer, intent(in) :: c   ! column index
-    type(glc_behavior_type), intent(in) :: glc_behavior
     !
     ! !LOCAL VARIABLES:
     integer :: l  ! landunit index
     integer :: g  ! grid cell index
     !------------------------------------------------------------------------
 
-    if (all_active) then
-       is_active_c = .true.
-
-    else
        l =col%landunit(c)
        g =col%gridcell(c)
 
@@ -395,15 +360,6 @@ logical function is_active_c(c, glc_behavior)
        ! ------------------------------------------------------------------------
        if (lun%active(l) .and. col%wtlunit(c) > 0._r8) is_active_c = .true.
 
-       ! ------------------------------------------------------------------------
-       ! Conditions under which is_active_c is set to true because we want extra virtual columns:
-       ! ------------------------------------------------------------------------
-
-       if (lun%itype(l) == istice_mec .and. &
-            glc_behavior%has_virtual_columns_grc(g)) then
-          is_active_c = .true.
-       end if
-
        ! We don't really need to run over 0-weight urban columns. But because of some
        ! messiness in the urban code (many loops are over the landunit filter, then drill
        ! down to columns - so we would need to add 'col%active(c)' conditionals in many
@@ -413,7 +369,6 @@ logical function is_active_c(c, glc_behavior)
        if (lun%active(l) .and. (lun%itype(l) >= isturb_MIN .and. lun%itype(l) <= isturb_MAX)) then
           is_active_c = .true.
        end if
-    end if
 
   end function is_active_c
 
@@ -433,10 +388,6 @@ logical function is_active_p(p)
     integer :: c  ! column index
     !------------------------------------------------------------------------
 
-    if (all_active) then
-       is_active_p = .true.
-
-    else
        c =patch%column(p)
     
        is_active_p = .false.
@@ -447,8 +398,6 @@ logical function is_active_p(p)
        ! ------------------------------------------------------------------------
        if (col%active(c) .and. patch%wtcol(p) > 0._r8) is_active_p = .true.
 
-    end if
-
   end function is_active_p
 
   !-----------------------------------------------------------------------
@@ -733,8 +682,6 @@ subroutine set_subgrid_diagnostic_fields(bounds)
     
     call set_pct_landunit_diagnostics(bounds)
 
-    ! Note: (MV, 10-17-14): The following has an use_fates if-block around it since
-    ! the pct_pft_diagnostics referens to patch%itype(p) which is not used by ED
     ! Note: (SPM, 10-20-15): If this isn't set then debug mode with intel and 
     ! yellowstone will fail when trying to write pct_nat_pft since it contains
     ! all NaN's.
@@ -845,7 +792,7 @@ subroutine set_pct_pft_diagnostics(bounds)
        g = patch%gridcell(p)
        l = patch%landunit(p)
        ptype = patch%itype(p)
-       if (lun%itype(l) == istsoil .and. (.not.use_fates) ) then
+       if (lun%itype(l) == istsoil) then
           ptype_1indexing = ptype + (1 - natpft_lb)
           subgrid_weights_diagnostics%pct_nat_pft(g, ptype_1indexing) = patch%wtlunit(p) * 100._r8
        else if (lun%itype(l) == istcrop) then
diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index ef593b1a6e..3aac15ea8f 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -14,8 +14,7 @@ module surfrdMod
   use landunit_varcon , only : numurbl
   use clm_varcon      , only : grlnd
   use clm_varctl      , only : iulog, scmlat, scmlon, single_column
-  use clm_varctl      , only : use_cndv, use_crop
-  use surfrdUtilsMod  , only : check_sums_equal_1, collapse_crop_types
+  use surfrdUtilsMod  , only : check_sums_equal_1
   use ncdio_pio       , only : file_desc_t, var_desc_t, ncd_pio_openfile, ncd_pio_closefile
   use ncdio_pio       , only : ncd_io, check_var, ncd_inqfdims, check_dim, ncd_inqdid
   use pio
@@ -33,7 +32,6 @@ module surfrdMod
   ! !PRIVATE MEMBER FUNCTIONS:
   private :: surfrd_special             ! Read the special landunits
   private :: surfrd_veg_all             ! Read all of the vegetated landunits
-  private :: surfrd_veg_dgvm            ! Read vegetated landunits for DGVM mode
   private :: surfrd_pftformat           ! Read crop pfts in file format where they are part of the vegetated land unit
   private :: surfrd_cftformat           ! Read crop pfts in file format where they are on their own landunit
   !
@@ -305,7 +303,6 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat)
     !    o real % abundance PFTs (as a percent of vegetated area)
     !
     ! !USES:
-    use clm_varctl  , only : create_crop_landunit
     use fileutils   , only : getfil
     use domainMod   , only : domain_type, domain_init, domain_clean
     use clm_instur  , only : wt_lunit, topo_glc_mec
@@ -418,10 +415,6 @@ subroutine surfrd_get_data (begg, endg, ldomain, lfsurdat)
 
     call surfrd_veg_all(begg, endg, ncid, ldomain%ns)
 
-    if (use_cndv) then
-       call surfrd_veg_dgvm(begg, endg)
-    end if
-
     call ncd_pio_closefile(ncid)
 
     call check_sums_equal_1(wt_lunit, begg, 'wt_lunit', subname)
@@ -441,10 +434,9 @@ subroutine surfrd_special(begg, endg, ncid, ns)
     ! as soil color and percent sand and clay
     !
     ! !USES:
-    use clm_varpar      , only : maxpatch_glcmec, nlevurb
+    use clm_varpar      , only : nlevurb
     use landunit_varcon , only : isturb_MIN, isturb_MAX, istdlak, istwet, istice_mec
     use clm_instur      , only : wt_lunit, urban_valid, wt_glc_mec, topo_glc_mec
-    use UrbanParamsType , only : CheckUrban
     !
     ! !ARGUMENTS:
     integer          , intent(in)    :: begg, endg 
@@ -472,6 +464,10 @@ subroutine surfrd_special(begg, endg, ncid, ns)
     integer, parameter :: urban_invalid_region = 0   ! urban_region_id indicating invalid point
 !-----------------------------------------------------------------------
 
+    ! TODO slevis SLIM: Attempted to not read special landunits, leave their
+    ! wt_lunit = 0, and remove calls to check_sums and check_weights that were
+    ! triggered. Outcome was an error in the sea-ice model:
+    ! "ice_therm_mushy solver failure"
     allocate(pctgla(begg:endg))
     allocate(pctlak(begg:endg))
     allocate(pctwet(begg:endg))
@@ -531,8 +527,8 @@ subroutine surfrd_special(begg, endg, ncid, ns)
 
     ! Read glacier info
 
-    call check_dim(ncid, 'nglcec',   maxpatch_glcmec   )
-    call check_dim(ncid, 'nglcecp1', maxpatch_glcmec+1 )
+    call check_dim(ncid, 'nglcec',   10)
+    call check_dim(ncid, 'nglcecp1', 11)
 
     call ncd_io(ncid=ncid, varname='PCT_GLC_MEC', flag='read', data=wt_glc_mec, &
          dim1name=grlnd, readvar=readvar)
@@ -582,8 +578,6 @@ subroutine surfrd_special(begg, endg, ncid, ns)
 
     end do
 
-    call CheckUrban(begg, endg, pcturb(begg:endg,:), subname)
-
     deallocate(pctgla,pctlak,pctwet,pcturb,pcturb_tot,urban_region_id,pctspec)
 
   end subroutine surfrd_special
@@ -595,7 +589,7 @@ subroutine surfrd_cftformat( ncid, begg, endg, wt_cft, cftsize, natpft_size )
     !     Handle generic crop types for file format where they are on their own
     !     crop landunit and read in as Crop Function Types.
     ! !USES:
-    use clm_instur      , only : fert_cft, wt_nat_patch
+    use clm_instur      , only : wt_nat_patch
     use clm_varpar      , only : cft_size, cft_lb, natpft_lb
     ! !ARGUMENTS:
     implicit none
@@ -622,18 +616,6 @@ subroutine surfrd_cftformat( ncid, begg, endg, wt_cft, cftsize, natpft_size )
             dim1name=grlnd, readvar=readvar)
     if (.not. readvar) call endrun( msg=' ERROR: PCT_CFT NOT on surfdata file'//errMsg(sourcefile, __LINE__)) 
 
-    if ( cft_size > 0 )then
-       call ncd_io(ncid=ncid, varname='CONST_FERTNITRO_CFT', flag='read', data=fert_cft, &
-               dim1name=grlnd, readvar=readvar)
-       if (.not. readvar) then
-          if ( masterproc ) &
-                write(iulog,*) ' WARNING: CONST_FERTNITRO_CFT NOT on surfdata file zero out'
-          fert_cft = 0.0_r8
-       end if
-    else
-       fert_cft = 0.0_r8
-    end if
-
     allocate( array2D(begg:endg,1:natpft_size) )
     call ncd_io(ncid=ncid, varname='PCT_NAT_PFT', flag='read', data=array2D, &
          dim1name=grlnd, readvar=readvar)
@@ -650,7 +632,7 @@ subroutine surfrd_pftformat( begg, endg, ncid )
     !     Handle generic crop types for file format where they are part of the
     !     natural vegetation landunit.
     ! !USES:
-    use clm_instur      , only : fert_cft, wt_nat_patch
+    use clm_instur      , only : wt_nat_patch
     use clm_varpar      , only : natpft_size, cft_size, natpft_lb
     ! !ARGUMENTS:
     implicit none
@@ -678,15 +660,6 @@ subroutine surfrd_pftformat( begg, endg, ncid )
                ' must also have a separate crop landunit, and vice versa)'//&
                errMsg(sourcefile, __LINE__))
     end if
-    call ncd_io(ncid=ncid, varname='CONST_FERTNITRO_CFT', flag='read', data=fert_cft, &
-            dim1name=grlnd, readvar=readvar)
-    if (readvar) then
-       call endrun( msg= ' ERROR: unexpectedly found CONST_FERTNITRO_CFT on dataset when cft_size=0'// &
-               ' (if the surface dataset has a separate crop landunit, then the code'// &
-               ' must also have a separate crop landunit, and vice versa)'//&
-               errMsg(sourcefile, __LINE__))
-    end if
-    fert_cft = 0.0_r8
 
     call ncd_io(ncid=ncid, varname='PCT_NAT_PFT', flag='read', data=wt_nat_patch, &
          dim1name=grlnd, readvar=readvar)
@@ -701,11 +674,9 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns)
     ! Determine weight arrays for non-dynamic landuse mode
     !
     ! !USES:
-    use clm_varctl      , only : create_crop_landunit, use_fates
     use clm_varpar      , only : natpft_lb, natpft_ub, natpft_size, cft_size, cft_lb
-    use clm_instur      , only : wt_lunit, wt_nat_patch, wt_cft, fert_cft
+    use clm_instur      , only : wt_lunit, wt_nat_patch, wt_cft
     use landunit_varcon , only : istsoil, istcrop
-    use surfrdUtilsMod  , only : convert_cft_to_pft
     !
     ! !ARGUMENTS:
     implicit none
@@ -746,25 +717,7 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns)
 
     ! Check the file format for CFT's and handle accordingly
     call ncd_inqdid(ncid, 'cft', dimid, cft_dim_exists)
-    if ( cft_dim_exists .and. create_crop_landunit )then
-       call surfrd_cftformat( ncid, begg, endg, wt_cft, cft_size, natpft_size )  ! Format where CFT's is read in a seperate landunit
-    else if ( (.not. cft_dim_exists) .and. (.not. create_crop_landunit) )then
-       if ( masterproc ) write(iulog,*) "WARNING: The PFT format is an unsupported format that will be removed in th future!"
-       call surfrd_pftformat( begg, endg, ncid )                                 ! Format where crop is part of the natural veg. landunit
-    else if ( cft_dim_exists .and. .not. create_crop_landunit )then
-       if ( masterproc ) write(iulog,*) "WARNING: New CFT-based format surface datasets should be run with create_crop_landunit=T"
-       if ( use_fates ) then
-          if ( masterproc ) write(iulog,*) "WARNING: When fates is on we allow new CFT based surface datasets ", &
-                                           "to be used with create_crop_land FALSE"
-          cftsize = 2
-          allocate(array2D(begg:endg,cft_lb:cftsize-1+cft_lb))
-          call surfrd_cftformat( ncid, begg, endg, array2D, cftsize, natpft_size-cftsize ) ! Read crops in as CFT's
-          call convert_cft_to_pft( begg, endg, cftsize, array2D )                          ! Convert from CFT to natural veg. landunit
-          deallocate(array2D)
-       else
-          call endrun( msg=' ERROR: New format surface datasets require create_crop_landunit TRUE'//errMsg(sourcefile, __LINE__))
-       end if
-    end if
+    call surfrd_cftformat( ncid, begg, endg, wt_cft, cft_size, natpft_size )  ! Format where CFT's is read in a seperate landunit
 
     ! Do some checking
     
@@ -784,36 +737,6 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns)
     wt_nat_patch(begg:endg,:)   = wt_nat_patch(begg:endg,:) / 100._r8
     call check_sums_equal_1(wt_nat_patch, begg, 'wt_nat_patch', subname)
 
-    ! Collapse crop landunits down when prognostic crops are on
-    if (use_crop) then
-       call collapse_crop_types(wt_cft(begg:endg, :), fert_cft(begg:endg, :), begg, endg, verbose=.true.)
-    end if
-
   end subroutine surfrd_veg_all
 
-  !-----------------------------------------------------------------------
-  subroutine surfrd_veg_dgvm(begg, endg)
-    !
-    ! !DESCRIPTION:
-    ! Determine weights for CNDV mode.
-    !
-    ! !USES:
-    use pftconMod , only : noveg
-    use clm_instur, only : wt_nat_patch
-    !
-    ! !ARGUMENTS:
-    integer, intent(in) :: begg, endg  
-    !
-    ! !LOCAL VARIABLES:
-    character(len=*), parameter :: subname = 'surfrd_veg_dgvm'
-    !-----------------------------------------------------------------------
-
-    ! Bare ground gets 100% weight; all other natural patches are zeroed out
-    wt_nat_patch(begg:endg, :)     = 0._r8
-    wt_nat_patch(begg:endg, noveg) = 1._r8
-
-    call check_sums_equal_1(wt_nat_patch, begg, 'wt_nat_patch', subname)
-
-  end subroutine surfrd_veg_dgvm
-
 end module surfrdMod
diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90
index 45fbf9ebe1..0ca58f71f7 100644
--- a/src/main/surfrdUtilsMod.F90
+++ b/src/main/surfrdUtilsMod.F90
@@ -20,8 +20,6 @@ module surfrdUtilsMod
   ! !PUBLIC MEMBER FUNCTIONS:
   public :: check_sums_equal_1  ! Confirm that sum(arr(n,:)) == 1 for all n
   public :: renormalize         ! Renormalize an array
-  public :: convert_cft_to_pft  ! Conversion of crop CFT to natural veg PFT:w
-  public :: collapse_crop_types ! Collapse unused crop types into types used in this run
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -100,144 +98,4 @@ subroutine renormalize(arr, lb, normal)
 
   end subroutine renormalize
 
-!-----------------------------------------------------------------------
-  subroutine convert_cft_to_pft( begg, endg, cftsize, wt_cft )
-    !
-    ! !DESCRIPTION:
-    !        Convert generic crop types that were read in as seperate CFT's on
-    !        a crop landunit, and put them on the vegetated landunit.
-    ! !USES:
-    use clm_instur      , only : wt_lunit, wt_nat_patch, fert_cft
-    use clm_varpar      , only : cft_size, natpft_size
-    use pftconMod       , only : nc3crop
-    use landunit_varcon , only : istsoil, istcrop
-    ! !ARGUMENTS:
-    implicit none
-    integer          , intent(in)    :: begg, endg
-    integer          , intent(in)    :: cftsize          ! CFT size
-    real(r8)         , intent(inout) :: wt_cft(begg:,:)  ! CFT weights
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g    ! index
-!-----------------------------------------------------------------------
-    SHR_ASSERT_ALL((ubound(wt_cft) == (/endg, cftsize/)), errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(wt_nat_patch) == (/endg, nc3crop+cftsize-1/)), errMsg(sourcefile, __LINE__))
-
-    do g = begg, endg
-       if ( wt_lunit(g,istcrop) > 0.0_r8 )then
-          ! Move CFT over to PFT and do weighted average of the crop and soil parts
-          wt_nat_patch(g,:) = wt_nat_patch(g,:) * wt_lunit(g,istsoil)
-          wt_cft(g,:)       = wt_cft(g,:) * wt_lunit(g,istcrop)
-          wt_nat_patch(g,nc3crop:) = wt_cft(g,:)      ! Add crop CFT's to end of natural veg PFT's
-          wt_lunit(g,istsoil) = (wt_lunit(g,istsoil) + wt_lunit(g,istcrop)) ! Add crop landunit to soil landunit
-          wt_nat_patch(g,:)   =  wt_nat_patch(g,:) / wt_lunit(g,istsoil)
-          wt_lunit(g,istcrop) = 0.0_r8                ! Zero out crop CFT's
-       else
-          wt_nat_patch(g,nc3crop:) = 0.0_r8    ! Make sure generic crops are zeroed out
-       end if
-    end do
-
-  end subroutine convert_cft_to_pft
-
-  !-----------------------------------------------------------------------
-  subroutine collapse_crop_types(wt_cft, fert_cft, begg, endg, verbose)
-    !
-    ! !DESCRIPTION:
-    ! Collapse unused crop types into types used in this run.
-    !
-    ! Should only be called if using prognostic crops - otherwise, wt_cft is meaningless
-    !
-    ! !USES:
-    use clm_varctl , only : irrigate
-    use clm_varpar , only : cft_lb, cft_ub, cft_size
-    use pftconMod  , only : nc3crop, nc3irrig, npcropmax, pftcon
-    !
-    ! !ARGUMENTS:
-
-    ! Note that we use begg and endg rather than 'bounds', because bounds may not be
-    ! available yet when this is called
-    integer, intent(in) :: begg     ! Beginning grid cell index
-    integer, intent(in) :: endg     ! Ending grid cell index
-
-    ! Weight and fertilizer of each CFT in each grid cell; dimensioned [g, cft_lb:cft_ub]
-    ! This array is modified in-place
-    real(r8), intent(inout) :: wt_cft(begg:, cft_lb:)
-    real(r8), intent(inout) :: fert_cft(begg:, cft_lb:)
-
-    logical, intent(in) :: verbose  ! If true, print some extra information
-    !
-    ! !LOCAL VARIABLES:
-    integer :: g
-    integer :: m
-    real(r8) :: wt_cft_to
-    real(r8) :: wt_cft_from
-    real(r8) :: wt_cft_merge
-
-    character(len=*), parameter :: subname = 'collapse_crop_types'
-    !-----------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(wt_cft) == (/endg, cft_ub/)), errMsg(sourcefile, __LINE__))
-
-    if (cft_size <= 0) then
-       call endrun(msg = subname//' can only be called if cft_size > 0' // &
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    ! ------------------------------------------------------------------------
-    ! If not using irrigation, merge irrigated CFTs into rainfed CFTs
-    ! ------------------------------------------------------------------------
-
-    if (.not. irrigate) then
-       if (verbose .and. masterproc) then
-          write(iulog,*) trim(subname)//' crop=.T. and irrigate=.F., so merging irrigated pfts with rainfed'
-       end if
-
-       do g = begg, endg
-          ! Left Hand Side: merged rainfed+irrigated crop pfts from nc3crop to
-          !                 npcropmax-1, stride 2
-          ! Right Hand Side: rainfed crop pfts from nc3crop to npcropmax-1,
-          !                  stride 2
-          ! plus             irrigated crop pfts from nc3irrig to npcropmax,
-          !                  stride 2
-          ! where stride 2 means "every other"
-          wt_cft(g, nc3crop:npcropmax-1:2) = &
-               wt_cft(g, nc3crop:npcropmax-1:2) + wt_cft(g, nc3irrig:npcropmax:2)
-          wt_cft(g, nc3irrig:npcropmax:2)  = 0._r8
-       end do
-
-       call check_sums_equal_1(wt_cft, begg, 'wt_cft', subname//': irrigation')
-    end if
-
-    ! ------------------------------------------------------------------------
-    ! Merge CFTs into the list of crops that CLM knows how to model
-    ! ------------------------------------------------------------------------
-
-    if (verbose .and. masterproc) then
-       write(iulog, *) trim(subname) // ' merging wheat, barley, and rye into temperate cereals'
-       write(iulog, *) trim(subname) // ' clm knows how to model corn, temperate cereals, and soybean'
-       write(iulog, *) trim(subname) // ' all other crops are lumped with the generic crop pft'
-    end if
-
-    do g = begg, endg
-       do m = 1, npcropmax
-          if (m /= pftcon%mergetoclmpft(m)) then
-             wt_cft_to = wt_cft(g, pftcon%mergetoclmpft(m))
-             wt_cft_from = wt_cft(g, m)
-             wt_cft_merge = wt_cft_to + wt_cft_from
-             wt_cft(g, pftcon%mergetoclmpft(m)) = wt_cft_merge
-             wt_cft(g, m) = 0._r8
-             if (wt_cft_merge > 0._r8) then
-                fert_cft(g,pftcon%mergetoclmpft(m)) = (wt_cft_to * fert_cft(g,pftcon%mergetoclmpft(m)) + &
-                                                      wt_cft_from * fert_cft(g,m)) / wt_cft_merge
-             end if
-          end if
-       end do
-
-    end do
-
-    call check_sums_equal_1(wt_cft, begg, 'wt_cft', subname//': mergetoclmpft')
-
-  end subroutine collapse_crop_types
-
-
 end module surfrdUtilsMod
diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
deleted file mode 100644
index d4d296256e..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
+++ /dev/null
@@ -1,825 +0,0 @@
-module SoilBiogeochemCarbonFluxType
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use decompMod                          , only : bounds_type
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan
-  use clm_varpar                         , only : nlevdecomp_full, nlevgrnd, nlevdecomp, nlevsoi
-  use clm_varcon                         , only : spval, ispval, dzsoi_decomp
-  use landunit_varcon                    , only : istsoil, istcrop, istdlak 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use ColumnType                         , only : col                
-  use LandunitType                       , only : lun
-  use clm_varctl                         , only : use_fates
-  
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  type, public :: soilbiogeochem_carbonflux_type
-
-     ! fire fluxes
-     real(r8), pointer :: somc_fire_col                             (:)     ! (gC/m2/s) carbon emissions due to peat burning
-
-     ! decomposition fluxes
-     real(r8), pointer :: decomp_cpools_sourcesink_col              (:,:,:) ! change in decomposing c pools. Used to update concentrations concurrently with vertical transport (gC/m3/timestep)  
-     real(r8), pointer :: decomp_cascade_hr_vr_col                  (:,:,:) ! vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
-     real(r8), pointer :: decomp_cascade_hr_col                     (:,:)   ! vertically-integrated (diagnostic) het. resp. from decomposing C pools (gC/m2/s)
-     real(r8), pointer :: decomp_cascade_ctransfer_vr_col           (:,:,:) ! vertically-resolved C transferred along deomposition cascade (gC/m3/s)
-     real(r8), pointer :: decomp_cascade_ctransfer_col              (:,:)   ! vertically-integrated (diagnostic) C transferred along decomposition cascade (gC/m2/s)
-     real(r8), pointer :: decomp_k_col                              (:,:,:) ! rate constant for decomposition (1./sec)
-     real(r8), pointer :: hr_vr_col                                 (:,:)   ! (gC/m3/s) total vertically-resolved het. resp. from decomposing C pools 
-     real(r8), pointer :: o_scalar_col                              (:,:)   ! fraction by which decomposition is limited by anoxia
-     real(r8), pointer :: w_scalar_col                              (:,:)   ! fraction by which decomposition is limited by moisture availability
-     real(r8), pointer :: t_scalar_col                              (:,:)   ! fraction by which decomposition is limited by temperature
-     real(r8), pointer :: som_c_leached_col                         (:)     ! (gC/m^2/s) total SOM C loss from vertical transport 
-     real(r8), pointer :: decomp_cpools_leached_col                 (:,:)   ! (gC/m^2/s) C loss from vertical transport from each decomposing C pool 
-     real(r8), pointer :: decomp_cpools_transport_tendency_col      (:,:,:) ! (gC/m^3/s) C tendency due to vertical transport in decomposing C pools 
-
-     ! nitrif_denitrif
-     real(r8), pointer :: phr_vr_col                                (:,:)   ! (gC/m3/s) potential hr (not N-limited) 
-     real(r8), pointer :: fphr_col                                  (:,:)   ! fraction of potential heterotrophic respiration
-
-     real(r8), pointer :: hr_col                                    (:)     ! (gC/m2/s) total heterotrophic respiration
-     real(r8), pointer :: lithr_col                                 (:)     ! (gC/m2/s) litter heterotrophic respiration 
-     real(r8), pointer :: somhr_col                                 (:)     ! (gC/m2/s) soil organic matter heterotrophic res   
-     real(r8), pointer :: soilc_change_col                          (:)     ! (gC/m2/s) FUN used soil C
-
-     ! fluxes to receive carbon inputs from FATES
-     real(r8), pointer :: FATES_c_to_litr_lab_c_col                 (:,:)   ! total labile    litter coming from ED. gC/m3/s
-     real(r8), pointer :: FATES_c_to_litr_cel_c_col                 (:,:)   ! total cellulose    litter coming from ED. gC/m3/s
-     real(r8), pointer :: FATES_c_to_litr_lig_c_col                 (:,:)   ! total lignin    litter coming from ED. gC/m3/s
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory
-     procedure , private :: InitCold
-     procedure , public  :: Restart
-     procedure , public  :: SetValues
-     procedure , public  :: Summary
-
-  end type soilbiogeochem_carbonflux_type
-  !------------------------------------------------------------------------
-
-contains
-   
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, carbon_type)
-
-     class(soilbiogeochem_carbonflux_type) :: this
-     type(bounds_type), intent(in) :: bounds  
-     character(len=3) , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-
-     call this%InitAllocate ( bounds)
-     call this%InitHistory ( bounds, carbon_type )
-     call this%InitCold (bounds )
-
-   end subroutine Init
-
-   !------------------------------------------------------------------------
-   subroutine InitAllocate(this, bounds)
-     !
-     ! !ARGUMENTS:
-     class (soilbiogeochem_carbonflux_type) :: this 
-     type(bounds_type), intent(in)    :: bounds 
-     !
-     ! !LOCAL VARIABLES:
-     integer           :: begp,endp
-     integer           :: begc,endc
-     !------------------------------------------------------------------------
-
-     begp = bounds%begp; endp = bounds%endp
-     begc = bounds%begc; endc = bounds%endc
-
-     allocate(this%t_scalar_col      (begc:endc,1:nlevdecomp_full)); this%t_scalar_col      (:,:) =spval
-     allocate(this%w_scalar_col      (begc:endc,1:nlevdecomp_full)); this%w_scalar_col      (:,:) =spval
-     allocate(this%o_scalar_col      (begc:endc,1:nlevdecomp_full)); this%o_scalar_col      (:,:) =spval
-     allocate(this%phr_vr_col        (begc:endc,1:nlevdecomp_full)); this%phr_vr_col        (:,:) =nan 
-     allocate(this%fphr_col          (begc:endc,1:nlevgrnd))       ; this%fphr_col          (:,:) =nan 
-     allocate(this%som_c_leached_col (begc:endc))                  ; this%som_c_leached_col (:)   =nan
-     allocate(this%somc_fire_col     (begc:endc))                  ; this%somc_fire_col     (:)   =nan
-     allocate(this%hr_vr_col         (begc:endc,1:nlevdecomp_full)); this%hr_vr_col         (:,:) =nan
-
-     allocate(this%decomp_cpools_sourcesink_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))                  
-     this%decomp_cpools_sourcesink_col(:,:,:)= nan
-
-     allocate(this%decomp_cascade_hr_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions))        
-     this%decomp_cascade_hr_vr_col(:,:,:)= spval
-
-     allocate(this%decomp_cascade_hr_col(begc:endc,1:ndecomp_cascade_transitions))                             
-     this%decomp_cascade_hr_col(:,:)= nan
-
-     allocate(this%decomp_cascade_ctransfer_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions)) 
-     this%decomp_cascade_ctransfer_vr_col(:,:,:)= nan
-
-     allocate(this%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions))                      
-     this%decomp_cascade_ctransfer_col(:,:)= nan
-
-     allocate(this%decomp_k_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions))                    
-     this%decomp_k_col(:,:,:)= spval
-
-     allocate(this%decomp_cpools_leached_col(begc:endc,1:ndecomp_pools))              
-     this%decomp_cpools_leached_col(:,:)= nan
-
-     allocate(this%decomp_cpools_transport_tendency_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))          
-     this%decomp_cpools_transport_tendency_col(:,:,:)= nan
-
-     allocate(this%hr_col                  (begc:endc)) ; this%hr_col                  (:) = nan
-     allocate(this%lithr_col               (begc:endc)) ; this%lithr_col               (:) = nan
-     allocate(this%somhr_col               (begc:endc)) ; this%somhr_col               (:) = nan
-     allocate(this%soilc_change_col        (begc:endc)) ; this%soilc_change_col        (:) = nan
-
-     if ( use_fates ) then
-        ! initialize these variables to be zero rather than a bad number since they are not zeroed every timestep (due to a need for them to persist)
-
-        allocate(this%FATES_c_to_litr_lab_c_col(begc:endc,1:nlevdecomp_full))
-        this%FATES_c_to_litr_lab_c_col(begc:endc,1:nlevdecomp_full) = 0._r8
-        
-        allocate(this%FATES_c_to_litr_cel_c_col(begc:endc,1:nlevdecomp_full))
-        this%FATES_c_to_litr_cel_c_col(begc:endc,1:nlevdecomp_full) = 0._r8
-        
-        allocate(this%FATES_c_to_litr_lig_c_col(begc:endc,1:nlevdecomp_full))
-        this%FATES_c_to_litr_lig_c_col(begc:endc,1:nlevdecomp_full) = 0._r8
-
-     endif
-     
-   end subroutine InitAllocate 
-
-   !------------------------------------------------------------------------
-   subroutine InitHistory(this, bounds, carbon_type)
-     !
-     ! !DESCRIPTION:
-     ! add history fields for all CN variables, always set as default='inactive'
-     !
-     ! !USES:
-     use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools
-     use clm_varpar , only : nlevdecomp, nlevdecomp_full
-     use clm_varctl , only : hist_wrtch4diag
-     use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
-     !
-     ! !ARGUMENTS:
-     class(soilbiogeochem_carbonflux_type) :: this    
-     type(bounds_type)         , intent(in) :: bounds 
-     character(len=3)          , intent(in) :: carbon_type ! one of ['c12', c13','c14']
-     !
-     ! !LOCAL VARIABLES:
-     integer           :: k,l,ii,jj,c
-     character(8)      :: vr_suffix
-     character(10)     :: active
-     integer           :: begp,endp
-     integer           :: begc,endc
-     character(24)     :: fieldname
-     character(100)    :: longname
-     real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-     real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays
-     !---------------------------------------------------------------------
-
-     begp = bounds%begp; endp = bounds%endp
-     begc = bounds%begc; endc = bounds%endc
-
-     if (nlevdecomp > 1) then
-        vr_suffix = "_vr"
-     else 
-        vr_suffix = ""
-     endif
-
-     !-------------------------------
-     ! C flux variables - native to column 
-     !-------------------------------
-
-     ! add history fields for all CLAMP CN variables
-
-     if (carbon_type == 'c12') then
-
-        this%hr_col(begc:endc) = spval
-        call hist_addfld1d (fname='HR', units='gC/m^2/s', &
-             avgflag='A', long_name='total heterotrophic respiration', &
-             ptr_col=this%hr_col, default='inactive')
-
-        this%lithr_col(begc:endc) = spval
-        call hist_addfld1d (fname='LITTERC_HR', units='gC/m^2/s', &
-             avgflag='A', long_name='litter C heterotrophic respiration', &
-             ptr_col=this%lithr_col, default='inactive')
-
-        this%somhr_col(begc:endc) = spval
-        call hist_addfld1d (fname='SOILC_HR', units='gC/m^2/s', &
-             avgflag='A', long_name='soil C heterotrophic respiration', &
-             ptr_col=this%somhr_col, default='inactive')
-
-        if (hist_wrtch4diag) then
-           this%fphr_col(begc:endc,1:nlevgrnd) = spval
-           call hist_addfld_decomp (fname='FPHR'//trim(vr_suffix), units='unitless', type2d='levdcmp', &
-                avgflag='A', long_name='fraction of potential HR due to N limitation', &
-                ptr_col=this%fphr_col, default='inactive')
-        end if
-
-        this%somc_fire_col(begc:endc) = spval
-        call hist_addfld1d (fname='SOMC_FIRE', units='gC/m^2/s', &
-             avgflag='A', long_name='C loss due to peat burning', &
-             ptr_col=this%somc_fire_col, default='inactive')
-
-        do k = 1, ndecomp_pools
-           ! decomposition k
-           data2dptr => this%decomp_k_col(:,:,k)
-           fieldname = 'K_'//trim(decomp_cascade_con%decomp_pool_name_history(k))
-           longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' potential loss coefficient'
-           call hist_addfld_decomp (fname=fieldname, units='1/s',  type2d='levdcmp', &
-                avgflag='A', long_name=longname, &
-                ptr_col=data2dptr, default='inactive')
-        end do
-
-        this%decomp_cascade_hr_col(begc:endc,:)             = spval
-        this%decomp_cascade_hr_vr_col(begc:endc,:,:)        = spval
-        this%decomp_cascade_ctransfer_col(begc:endc,:)      = spval
-        this%decomp_cascade_ctransfer_vr_col(begc:endc,:,:) = spval
-        do l = 1, ndecomp_cascade_transitions
-
-           ! output the vertically integrated fluxes only as  default
-           !-- HR fluxes (none from CWD)
-           if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-              data1dptr => this%decomp_cascade_hr_col(:,l)
-              ! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
-              ii = 0
-              do jj = 1, ndecomp_cascade_transitions
-                 if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
-              end do
-              if ( ii == 1 ) then
-                 fieldname = &
-                      trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_HR'
-              else
-                 fieldname = &
-                      trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_HR_'//&
-                      trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))
-              endif
-              longname =  'Het. Resp. from '//&
-                   trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
-              call hist_addfld1d (fname=fieldname, units='gC/m^2/s',  &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data1dptr, default='inactive')
-           endif
-
-           !-- transfer fluxes (none from terminal pool, if present)
-           if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-              data1dptr => this%decomp_cascade_ctransfer_col(:,l)
-              fieldname = &
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'C_TO_'//&
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'C'
-              longname =  'decomp. of '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                   ' C to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C'
-              call hist_addfld1d (fname=fieldname, units='gC/m^2/s', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data1dptr, default='inactive')
-           endif
-
-           ! output the vertically resolved fluxes 
-           if ( nlevdecomp_full > 1 ) then  
-              !-- HR fluxes (none from CWD)
-              if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-                 data2dptr => this%decomp_cascade_hr_vr_col(:,:,l)
-                 ! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
-                 ii = 0
-                 do jj = 1, ndecomp_cascade_transitions
-                    if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
-                 end do
-                 if ( ii == 1 ) then
-                    fieldname = &
-                         trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                         //'_HR'//trim(vr_suffix)
-                 else
-                    fieldname = &
-                         trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_HR_'//&
-                         trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))&
-                         //trim(vr_suffix)
-                 endif
-                 longname =  'Het. Resp. from '//&
-                      trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
-                 call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s',  type2d='levdcmp', &
-                      avgflag='A', long_name=longname, &
-                      ptr_col=data2dptr, default='inactive')
-              endif
-
-              !-- transfer fluxes (none from terminal pool, if present)
-              if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-                 data2dptr => this%decomp_cascade_ctransfer_vr_col(:,:,l)
-                 fieldname = &
-                      trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'C_TO_'//&
-                      trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))&
-                      //'C'//trim(vr_suffix)
-                 longname =  'decomp. of '//&
-                      trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                      ' C to '//&
-                      trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C'
-                 call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s',  type2d='levdcmp', &
-                      avgflag='A', long_name=longname, &
-                      ptr_col=data2dptr, default='inactive')
-              endif
-           end if
-
-        end do
-
-        if ( nlevdecomp_full > 1 ) then  
-           data2dptr => this%t_scalar_col(begc:endc,1:nlevsoi)
-           call hist_addfld_decomp (fname='T_SCALAR', units='unitless',  type2d='levsoi', &
-                avgflag='A', long_name='temperature inhibition of decomposition', &
-                ptr_col=data2dptr, default='inactive')
-
-           data2dptr => this%w_scalar_col(begc:endc,1:nlevsoi)
-           call hist_addfld_decomp (fname='W_SCALAR', units='unitless',  type2d='levsoi', &
-                avgflag='A', long_name='Moisture (dryness) inhibition of decomposition', &
-                ptr_col=data2dptr, default='inactive')
-
-           data2dptr => this%o_scalar_col(begc:endc,1:nlevsoi)
-           call hist_addfld_decomp (fname='O_SCALAR', units='unitless', type2d='levsoi', &
-                avgflag='A', long_name='fraction by which decomposition is reduced due to anoxia', &
-                ptr_col=data2dptr, default='inactive')
-        end if
-        
-        this%som_c_leached_col(begc:endc) = spval
-        call hist_addfld1d (fname='SOM_C_LEACHED', units='gC/m^2/s', &
-             avgflag='A', long_name='total flux of C from SOM pools due to leaching', &
-             ptr_col=this%som_c_leached_col, default='inactive')
-
-        this%decomp_cpools_leached_col(begc:endc,:) = spval
-        this%decomp_cpools_transport_tendency_col(begc:endc,:,:) = spval
-        do k = 1, ndecomp_pools
-           if ( .not. decomp_cascade_con%is_cwd(k) ) then
-              data1dptr => this%decomp_cpools_leached_col(:,k)
-              fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_LEACHING'
-              longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' C leaching loss'
-              call hist_addfld1d (fname=fieldname, units='gC/m^2/s', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data1dptr, default='inactive')
-
-              data2dptr => this%decomp_cpools_transport_tendency_col(:,:,k)
-              fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TNDNCY_VERT_TRANSPORT'
-              longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' C tendency due to vertical transport'
-              call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s',  type2d='levdcmp', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data2dptr, default='inactive')
-           endif
-        end do
-
-        if ( nlevdecomp_full > 1 ) then
-           data2dptr => this%hr_vr_col(begc:endc,1:nlevsoi)
-           call hist_addfld2d (fname='HR_vr', units='gC/m^3/s', type2d='levsoi', &
-                avgflag='A', long_name='total vertically resolved heterotrophic respiration', &
-                ptr_col=data2dptr, default='inactive')
-        endif
-
-     end if
-
-     !-------------------------------
-     ! C13 flux variables - native to column 
-     !-------------------------------
-
-     if ( carbon_type == 'c13' ) then
-
-        this%hr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_HR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 total heterotrophic respiration', &
-             ptr_col=this%hr_col, default='inactive')
-
-        this%lithr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_LITTERC_HR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 fine root C litterfall to litter 3 C', &
-             ptr_col=this%lithr_col, default='inactive')
-
-        this%somhr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C13_SOILC_HR', units='gC13/m^2/s', &
-             avgflag='A', long_name='C13 soil organic matter heterotrophic respiration', &
-             ptr_col=this%somhr_col, default='inactive')
-
-
-        this%decomp_cascade_hr_col(begc:endc,:)             = spval
-        this%decomp_cascade_hr_vr_col(begc:endc,:,:)        = spval
-        this%decomp_cascade_ctransfer_col(begc:endc,:)      = spval
-        this%decomp_cascade_ctransfer_vr_col(begc:endc,:,:) = spval
-        do l = 1, ndecomp_cascade_transitions
-           !-- HR fluxes (none from CWD)
-           if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-              data2dptr => this%decomp_cascade_hr_vr_col(:,:,l)
-              ! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
-              ii = 0
-              do jj = 1, ndecomp_cascade_transitions
-                 if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
-              end do
-              if ( ii == 1 ) then
-                 fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                      //'_HR'//trim(vr_suffix)
-              else
-                 fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                      //'_HR_'//&
-                      trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))//&
-                      trim(vr_suffix)
-              endif
-              longname =  'C13 Het. Resp. from '&
-                   //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
-              call hist_addfld_decomp (fname=fieldname, units='gC13/m^3',  type2d='levdcmp', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data2dptr, default='inactive')
-           endif
-           !-- transfer fluxes (none from terminal pool, if present)
-           if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-              data2dptr => this%decomp_cascade_ctransfer_vr_col(:,:,l)
-              fieldname = 'C13_'//&
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                   //'C_TO_'//&
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))&
-                   //'C'//trim(vr_suffix)
-              longname =  'C13 decomp. of '&
-                   //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))&
-                   //' C to '//&
-                   trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C'
-              call hist_addfld_decomp (fname=fieldname, units='gC13/m^3',  type2d='levdcmp', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data2dptr, default='inactive')
-           endif
-        end do
-
-     end if
-
-     !-------------------------------
-     ! C14 flux variables - native to column 
-     !-------------------------------
-
-     if (carbon_type == 'c14') then
-
-        this%hr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_HR', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 total heterotrophic respiration', &
-             ptr_col=this%hr_col, default='inactive')
-
-        this%lithr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_LITTERC_HR', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 litter carbon heterotrophic respiration', &
-             ptr_col=this%lithr_col, default='inactive')
-
-        this%somhr_col(begc:endc) = spval
-        call hist_addfld1d (fname='C14_SOILC_HR', units='gC14/m^2/s', &
-             avgflag='A', long_name='C14 soil organic matter heterotrophic respiration', &
-             ptr_col=this%somhr_col, default='inactive')
-
-        this%decomp_cascade_hr_col(begc:endc,:)             = spval
-        this%decomp_cascade_hr_vr_col(begc:endc,:,:)        = spval
-        this%decomp_cascade_ctransfer_col(begc:endc,:)      = spval
-        this%decomp_cascade_ctransfer_vr_col(begc:endc,:,:) = spval
-
-        do l = 1, ndecomp_cascade_transitions
-           !-- HR fluxes (none from CWD)
-           if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-              data2dptr => this%decomp_cascade_hr_vr_col(:,:,l)
-
-              ! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
-              ii = 0
-              do jj = 1, ndecomp_cascade_transitions
-                 if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
-              end do
-              if ( ii == 1 ) then
-                 fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                      //'_HR'//trim(vr_suffix)
-              else
-                 fieldname = 'C14_'//&
-                      trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                      //'_HR_'//&
-                      trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))&
-                      //trim(vr_suffix)
-              endif
-              longname =  'C14 Het. Resp. from '&
-                   //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
-              call hist_addfld_decomp (fname=fieldname, units='gC14/m^3',  type2d='levdcmp', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data2dptr, default='inactive')
-           endif
-
-           !-- transfer fluxes (none from terminal pool, if present)
-           if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-              data2dptr => this%decomp_cascade_ctransfer_vr_col(:,:,l)
-
-              fieldname = 'C14_'//&
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                   //'C_TO_'//&
-                   trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))&
-                   //'C'//trim(vr_suffix)
-              longname =  'C14 decomp. of '&
-                   //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                   ' C to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C'
-              call hist_addfld_decomp (fname=fieldname, units='gC14/m^3',  type2d='levdcmp', &
-                   avgflag='A', long_name=longname, &
-                   ptr_col=data2dptr, default='inactive')
-           endif
-        end do
-
-     end if
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       this%fphr_col(c,nlevdecomp+1:nlevgrnd) = 0._r8 !used to be in ch4Mod
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          this%fphr_col(c,nlevdecomp+1:nlevgrnd) = 0._r8 
-       else  ! Inactive CH4 columns
-          this%fphr_col(c,:) = spval
-       end if
-
-    end do
-
-    if ( use_fates ) then
-
-       call hist_addfld_decomp(fname='FATES_c_to_litr_lab_c', units='gC/m^3/s',  type2d='levdcmp', &
-                   avgflag='A', long_name='litter labile carbon flux from FATES to BGC', &
-                   ptr_col=this%FATES_c_to_litr_lab_c_col, default='inactive')
-
-       call hist_addfld_decomp(fname='FATES_c_to_litr_cel_c', units='gC/m^3/s',  type2d='levdcmp', &
-                   avgflag='A', long_name='litter celluluse carbon flux from FATES to BGC', &
-                   ptr_col=this%FATES_c_to_litr_cel_c_col, default='inactive')
-
-       call hist_addfld_decomp(fname='FATES_c_to_litr_lig_c', units='gC/m^3/s',  type2d='levdcmp', &
-                   avgflag='A', long_name='litter lignin carbon flux from FATES to BGC', &
-                   ptr_col=this%FATES_c_to_litr_lig_c_col, default='inactive')
-
-     endif
-
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_carbonflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,l
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: special_col(bounds%endc-bounds%begc+1)    ! special landunit filter - columns
-    !-----------------------------------------------------------------------
-
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    ! initialize fields for special filters
-
-    call this%SetValues (num_column=num_special_col, filter_column=special_col, &
-         value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !USES:
-    use restUtilMod
-    use ncdio_pio
-    use clm_varctl, only : use_vertsoilc
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_carbonflux_type) :: this
-    type(bounds_type) , intent(in)        :: bounds  
-    type(file_desc_t) , intent(inout)     :: ncid   ! netcdf id
-    character(len=*)  , intent(in)        :: flag   !'read', 'write', 'define'
-    !
-    ! local vars
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    logical  :: readvar
-    !-----------------------------------------------------------------------
-
-    !
-    ! if  FATES is enabled, need to restart the variables used to transfer from FATES to CLM as they
-    ! are persistent between daily FATES dynamics calls and half-hourly CLM timesteps
-    !
-    if ( use_fates ) then
-       
-       if (use_vertsoilc) then
-          ptr2d => this%FATES_c_to_litr_lab_c_col
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lab_c_col', xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-          
-          ptr2d => this%FATES_c_to_litr_cel_c_col
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_cel_c_col', xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-          
-          ptr2d => this%FATES_c_to_litr_lig_c_col
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lig_c_col', xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-          
-       else
-          ptr1d => this%FATES_c_to_litr_lab_c_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lab_c_col', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d) 
-          
-          ptr1d => this%FATES_c_to_litr_cel_c_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_cel_c_col', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d) 
-          
-          ptr1d => this%FATES_c_to_litr_lig_c_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lig_c_col', xtype=ncd_double,  &
-               dim1name='column', long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d) 
-          
-       end if
-       
-    end if
-    
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set carbon fluxes
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_carbonflux_type) :: this
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i     ! loop index
-    integer :: j,k,l    ! indices
-    !------------------------------------------------------------------------
-
-    do l = 1, ndecomp_cascade_transitions
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_cascade_hr_col(i,l)             = value_column
-             this%decomp_cascade_hr_vr_col(i,j,l)        = value_column
-             this%decomp_cascade_ctransfer_col(i,l)      = value_column
-             this%decomp_cascade_ctransfer_vr_col(i,j,l) = value_column
-             this%decomp_k_col(i,j,l)                    = value_column
-          end do
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%decomp_cpools_leached_col(i,k) = value_column
-       end do
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_cpools_transport_tendency_col(i,j,k) = value_column
-             this%decomp_cpools_sourcesink_col(i,j,k)         = value_column  
-          end do
-       end do
-    end do
-
-    do j = 1, nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%hr_vr_col(i,j) = value_column
-       end do
-    end do
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-       this%hr_col(i)            = value_column
-       this%somc_fire_col(i)     = value_column  
-       this%som_c_leached_col(i) = value_column
-       this%somhr_col(i)         = value_column
-       this%lithr_col(i)         = value_column
-       this%soilc_change_col(i)  = value_column
-    end do
-
-    ! NOTE: do not zero the fates to BGC C flux variables since they need to persist from the daily fates timestep s to the half-hourly BGC timesteps.  I.e. FATES_c_to_litr_lab_c_col, FATES_c_to_litr_cel_c_col, FATES_c_to_litr_lig_c_col
-    
-  end subroutine SetValues
-
-  !-----------------------------------------------------------------------
-  subroutine Summary(this, bounds, num_soilc, filter_soilc)
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, column-level carbon summary calculations
-    !
-    ! !USES:
-    ! !ARGUMENTS:
-    class(soilbiogeochem_carbonflux_type)           :: this
-    type(bounds_type)               , intent(in)    :: bounds          
-    integer                         , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                         , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,j,k,l
-    integer  :: fc       
-    !-----------------------------------------------------------------------
-
-    do fc = 1,num_soilc
-       c = filter_soilc(fc)
-       this%som_c_leached_col(c) = 0._r8
-    end do
-
-    ! vertically integrate HR and decomposition cascade fluxes
-    do k = 1, ndecomp_cascade_transitions
-       do j = 1,nlevdecomp
-          do fc = 1,num_soilc
-             c = filter_soilc(fc)
-             this%decomp_cascade_hr_col(c,k) = &
-                  this%decomp_cascade_hr_col(c,k) + &
-                  this%decomp_cascade_hr_vr_col(c,j,k) * dzsoi_decomp(j) 
-
-             this%decomp_cascade_ctransfer_col(c,k) = &
-                  this%decomp_cascade_ctransfer_col(c,k) + &
-                  this%decomp_cascade_ctransfer_vr_col(c,j,k) * dzsoi_decomp(j) 
-          end do
-       end do
-    end do
-
-    ! total heterotrophic respiration, vertically resolved (HR)
-    do j = 1,nlevdecomp
-       do fc = 1,num_soilc
-          c = filter_soilc(fc)
-          this%hr_vr_col(c,j) = 0._r8
-       end do
-    end do
-    do k = 1, ndecomp_cascade_transitions
-       do j = 1,nlevdecomp
-          do fc = 1,num_soilc
-             c = filter_soilc(fc)
-             this%hr_vr_col(c,j) = &
-                  this%hr_vr_col(c,j) + &
-                  this%decomp_cascade_hr_vr_col(c,j,k)
-          end do
-       end do
-    end do
-
-    ! add up all vertical transport tendency terms and calculate total som leaching loss as the sum of these
-    do l = 1, ndecomp_pools
-       do fc = 1,num_soilc
-          c = filter_soilc(fc)
-          this%decomp_cpools_leached_col(c,l) = 0._r8
-       end do
-       do j = 1, nlevdecomp
-          do fc = 1,num_soilc
-             c = filter_soilc(fc)
-             this%decomp_cpools_leached_col(c,l) = this%decomp_cpools_leached_col(c,l) + &
-                  this%decomp_cpools_transport_tendency_col(c,j,l) * dzsoi_decomp(j)
-          end do
-       end do
-       do fc = 1,num_soilc
-          c = filter_soilc(fc)
-          this%som_c_leached_col(c) = this%som_c_leached_col(c) + this%decomp_cpools_leached_col(c,l)
-       end do
-    end do
-
-    ! soil organic matter heterotrophic respiration 
-    associate(is_soil => decomp_cascade_con%is_soil) ! TRUE => pool is a soil pool  
-      do k = 1, ndecomp_cascade_transitions
-         if ( is_soil(decomp_cascade_con%cascade_donor_pool(k)) ) then
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               this%somhr_col(c) = this%somhr_col(c) + this%decomp_cascade_hr_col(c,k)
-            end do
-         end if
-      end do
-    end associate
-
-    ! litter heterotrophic respiration (LITHR)
-    associate(is_litter => decomp_cascade_con%is_litter) ! TRUE => pool is a litter pool
-      do k = 1, ndecomp_cascade_transitions
-         if ( is_litter(decomp_cascade_con%cascade_donor_pool(k)) ) then
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               this%lithr_col(c) = this%lithr_col(c) + this%decomp_cascade_hr_col(c,k)
-            end do
-         end if
-      end do
-    end associate
-
-    ! total heterotrophic respiration (HR)
-    do fc = 1,num_soilc
-       c = filter_soilc(fc)
-       
-          this%hr_col(c) = &
-               this%lithr_col(c) + &
-               this%somhr_col(c)
-       
-    end do
-
-  end subroutine Summary
-
-end module SoilBiogeochemCarbonFluxType
-
-
diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
deleted file mode 100644
index 7d2c814a53..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
+++ /dev/null
@@ -1,942 +0,0 @@
-module SoilBiogeochemCarbonStateType
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use decompMod                          , only : bounds_type
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp, nlevsoi
-  use clm_varcon                         , only : spval, ispval, dzsoi_decomp, zisoi, zsoi, c3_r2
-  use clm_varctl                         , only : iulog, use_vertsoilc, spinup_state, use_fates 
-  use landunit_varcon                    , only : istcrop, istsoil
-  use abortutils                         , only : endrun
-  use spmdMod                            , only : masterproc 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  use GridcellType                       , only : grc
-  use SoilBiogeochemStateType            , only : get_spinup_latitude_term
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  type, public :: soilbiogeochem_carbonstate_type
-     
-     ! all c pools involved in decomposition
-     real(r8), pointer :: decomp_cpools_vr_col (:,:,:) ! (gC/m3) vertically-resolved decomposing (litter, cwd, soil) c pools
-     real(r8), pointer :: ctrunc_vr_col        (:,:)   ! (gC/m3) vertically-resolved column-level sink for C truncation
-
-     ! summary (diagnostic) state variables, not involved in mass balance
-     real(r8), pointer :: ctrunc_col               (:) ! (gC/m2) column-level sink for C truncation
-     real(r8), pointer :: totlitc_col          (:)     ! (gC/m2) total litter carbon
-     real(r8), pointer :: totlitc_1m_col       (:)     ! (gC/m2) total litter carbon to 1 meter
-     real(r8), pointer :: totsomc_col          (:)     ! (gC/m2) total soil organic matter carbon
-     real(r8), pointer :: totsomc_1m_col       (:)     ! (gC/m2) total soil organic matter carbon to 1 meter
-     real(r8), pointer :: cwdc_col             (:)     ! (gC/m2) coarse woody debris C (diagnostic)
-     real(r8), pointer :: decomp_cpools_1m_col (:,:)   ! (gC/m2)  Diagnostic: decomposing (litter, cwd, soil) c pools to 1 meter
-     real(r8), pointer :: decomp_cpools_col    (:,:)   ! (gC/m2)  decomposing (litter, cwd, soil) c pools
-     real(r8), pointer :: dyn_cbal_adjustments_col (:) ! (gC/m2) adjustments to each column made in this timestep via dynamic column area adjustments (note: this variable only makes sense at the column-level: it is meaningless if averaged to the gridcell-level)
-     integer  :: restart_file_spinup_state             ! spinup state as read from restart file, for determining whether to enter or exit spinup mode.
-     real(r8)          :: totvegcthresh                ! threshold for total vegetation carbon to zero out decomposition pools
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: SetValues 
-     procedure , public  :: Restart
-     procedure , public  :: Summary
-     procedure , public  :: SetTotVgCThresh
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory  
-     procedure , private :: InitCold     
-
-
-  end type soilbiogeochem_carbonstate_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds, carbon_type, ratio, c12_soilbiogeochem_carbonstate_inst)
-
-    class(soilbiogeochem_carbonstate_type)                       :: this
-    type(bounds_type)                     , intent(in)           :: bounds  
-    character(len=3)                      , intent(in)           :: carbon_type
-    real(r8)                              , intent(in)           :: ratio
-    type(soilbiogeochem_carbonstate_type) , intent(in), optional :: c12_soilbiogeochem_carbonstate_inst
-
-    this%totvegcthresh = nan
-    call this%InitAllocate ( bounds)
-    call this%InitHistory ( bounds, carbon_type )
-    if (present(c12_soilbiogeochem_carbonstate_inst)) then
-       call this%InitCold  ( bounds, ratio, c12_soilbiogeochem_carbonstate_inst )
-    else
-       call this%InitCold  ( bounds, ratio) 
-    end if
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_carbonstate_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begc,endc
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    allocate( this%decomp_cpools_col    (begc :endc,1:ndecomp_pools))   ; this%decomp_cpools_col    (:,:) = nan
-    allocate( this%decomp_cpools_1m_col (begc :endc,1:ndecomp_pools))   ; this%decomp_cpools_1m_col (:,:) = nan
-
-    allocate( this%ctrunc_vr_col(begc :endc,1:nlevdecomp_full)) ; 
-    this%ctrunc_vr_col        (:,:) = nan
-
-    allocate(this%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))  
-    this%decomp_cpools_vr_col(:,:,:)= nan
-
-    allocate(this%ctrunc_col     (begc :endc)) ; this%ctrunc_col     (:) = nan
-    if ( .not. use_fates ) then
-       allocate(this%cwdc_col       (begc :endc)) ; this%cwdc_col       (:) = nan
-    endif
-    allocate(this%totlitc_col    (begc :endc)) ; this%totlitc_col    (:) = nan
-    allocate(this%totsomc_col    (begc :endc)) ; this%totsomc_col    (:) = nan
-    allocate(this%totlitc_1m_col (begc :endc)) ; this%totlitc_1m_col (:) = nan
-    allocate(this%totsomc_1m_col (begc :endc)) ; this%totsomc_1m_col (:) = nan
-    allocate(this%dyn_cbal_adjustments_col (begc:endc)) ; this%dyn_cbal_adjustments_col (:) = nan
-
-    this%restart_file_spinup_state = huge(1)
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds, carbon_type) 
-    !
-    ! !USES:
-    use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_carbonstate_type) :: this
-    type(bounds_type) , intent(in)          :: bounds 
-    character(len=3)  , intent(in)          :: carbon_type
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: l
-    integer           :: begc ,endc
-    character(24)     :: fieldname
-    character(100)    :: longname
-    real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    !-------------------------------
-    ! C12 state variables - column
-    !-------------------------------
-
-    if (carbon_type == 'c12') then
-
-       this%decomp_cpools_col(begc:endc,:) = spval
-       do l  = 1, ndecomp_pools
-          if ( nlevdecomp_full > 1 ) then
-             data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l)
-             fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr'
-             longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)'
-             call hist_addfld2d (fname=fieldname, units='gC/m^3',  type2d='levsoi', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data2dptr, default='inactive')
-          endif
-
-          data1dptr => this%decomp_cpools_col(:,l)
-          fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' C'
-          call hist_addfld1d (fname=fieldname, units='gC/m^2', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-
-          if ( nlevdecomp_full > 1 ) then
-             data1dptr => this%decomp_cpools_1m_col(:,l)
-             fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_1m'
-             longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' C to 1 meter'
-             call hist_addfld1d (fname=fieldname, units='gC/m^2', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data1dptr, default='inactive')
-          endif
-       end do
- 
-       this%totlitc_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTLITC', units='gC/m^2', &
-            avgflag='A', long_name='total litter carbon', &
-            ptr_col=this%totlitc_col, default='inactive')
-
-       this%totsomc_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTSOMC', units='gC/m^2', &
-            avgflag='A', long_name='total soil organic matter carbon', &
-            ptr_col=this%totsomc_col, default='inactive')
-
-       if ( nlevdecomp_full > 1 ) then
-          this%totlitc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='TOTLITC_1m', units='gC/m^2', &
-               avgflag='A', long_name='total litter carbon to 1 meter depth', &
-               ptr_col=this%totlitc_1m_col, default='inactive')
-       end if
-
-       if ( nlevdecomp_full > 1 ) then
-          this%totsomc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='TOTSOMC_1m', units='gC/m^2', &
-               avgflag='A', long_name='total soil organic matter carbon to 1 meter depth', &
-               ptr_col=this%totsomc_1m_col, default='inactive')
-       end if
-
-       this%ctrunc_col(begc:endc) = spval
-       call hist_addfld1d (fname='COL_CTRUNC', units='gC/m^2',  &
-            avgflag='A', long_name='column-level sink for C truncation', &
-            ptr_col=this%ctrunc_col, default='inactive')
-
-       this%dyn_cbal_adjustments_col(begc:endc) = spval
-       call hist_addfld1d (fname='DYN_COL_SOIL_ADJUSTMENTS_C', units='gC/m^2', &
-            avgflag='SUM', &
-            long_name='Adjustments in soil carbon due to dynamic column areas; &
-            &only makes sense at the column level: should not be averaged to gridcell', &
-            ptr_col=this%dyn_cbal_adjustments_col, default='inactive')
-
-   end if
-
-    !-------------------------------
-    ! C13 state variables - column
-    !-------------------------------
-
-    if ( carbon_type == 'c13' ) then
-
-       this%decomp_cpools_vr_col(begc:endc,:,:) = spval
-       do l = 1, ndecomp_pools
-          if ( nlevdecomp_full > 1 ) then
-             data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l)
-             fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr'
-             longname =  'C13 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)'
-             call hist_addfld2d (fname=fieldname, units='gC13/m^3',  type2d='levsoi', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data2dptr, default='inactive')
-          endif
-
-          data1dptr => this%decomp_cpools_col(:,l)
-          fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C'
-          longname =  'C13 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C'
-          call hist_addfld1d (fname=fieldname, units='gC13/m^2', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-       end do
-
-       this%totlitc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_TOTLITC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total litter carbon', &
-            ptr_col=this%totlitc_col, default='inactive')
-
-       this%totsomc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_TOTSOMC', units='gC13/m^2', &
-            avgflag='A', long_name='C13 total soil organic matter carbon', &
-            ptr_col=this%totsomc_col, default='inactive')
-
-       if ( nlevdecomp_full > 1 ) then
-          this%totlitc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='C13_TOTLITC_1m', units='gC13/m^2', &
-               avgflag='A', long_name='C13 total litter carbon to 1 meter', &
-               ptr_col=this%totlitc_1m_col, default='inactive')
-       end if
-
-       if ( nlevdecomp_full > 1 ) then
-          this%totsomc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='C13_TOTSOMC_1m', units='gC13/m^2', &
-               avgflag='A', long_name='C13 total soil organic matter carbon to 1 meter', &
-               ptr_col=this%totsomc_1m_col, default='inactive')
-       endif
-
-       this%ctrunc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_COL_CTRUNC', units='gC13/m^2',  &
-            avgflag='A', long_name='C13 column-level sink for C truncation', &
-            ptr_col=this%ctrunc_col, default='inactive')
-
-       this%dyn_cbal_adjustments_col(begc:endc) = spval
-       call hist_addfld1d (fname='C13_DYN_COL_SOIL_ADJUSTMENTS_C', units='gC13/m^2', &
-            avgflag='SUM', &
-            long_name='C13 adjustments in soil carbon due to dynamic column areas; &
-            &only makes sense at the column level: should not be averaged to gridcell', &
-            ptr_col=this%dyn_cbal_adjustments_col, default='inactive')
-    endif
-
-    !-------------------------------
-    ! C14 state variables - column
-    !-------------------------------
-
-    if ( carbon_type == 'c14' ) then
-
-       this%decomp_cpools_vr_col(begc:endc,:,:) = spval
-       do l = 1, ndecomp_pools
-          if ( nlevdecomp_full > 1 ) then
-             data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l)
-             fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr'
-             longname =  'C14 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)'
-             call hist_addfld2d (fname=fieldname, units='gC14/m^3',  type2d='levsoi', &
-                  avgflag='A', long_name=longname, ptr_col=data2dptr, default='inactive')
-          endif
-
-          data1dptr => this%decomp_cpools_col(:,l)
-          fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C'
-          longname =  'C14 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C'
-          call hist_addfld1d (fname=fieldname, units='gC14/m^2', &
-               avgflag='A', long_name=longname, ptr_col=data1dptr, default='inactive')
-
-          if ( nlevdecomp_full > 1 ) then
-             data1dptr => this%decomp_cpools_1m_col(:,l)
-             fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_1m'
-             longname =  'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C to 1 meter'
-             call hist_addfld1d (fname=fieldname, units='gC/m^2', &
-                  avgflag='A', long_name=longname, ptr_col=data1dptr, default='inactive')
-          endif
-       end do
-
-       this%totlitc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_TOTLITC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total litter carbon', &
-            ptr_col=this%totlitc_col, default='inactive')
-
-       this%totsomc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_TOTSOMC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 total soil organic matter carbon', &
-            ptr_col=this%totsomc_col, default='inactive')
-
-       if ( nlevdecomp_full > 1 ) then       
-          this%totlitc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='C14_TOTLITC_1m', units='gC14/m^2', &
-               avgflag='A', long_name='C14 total litter carbon to 1 meter', &
-               ptr_col=this%totlitc_1m_col, default='inactive')
-
-          this%totsomc_1m_col(begc:endc) = spval
-          call hist_addfld1d (fname='C14_TOTSOMC_1m', units='gC14/m^2', &
-               avgflag='A', long_name='C14 total soil organic matter carbon to 1 meter', &
-               ptr_col=this%totsomc_1m_col, default='inactive')
-       endif
-
-       this%ctrunc_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_COL_CTRUNC', units='gC14/m^2', &
-            avgflag='A', long_name='C14 column-level sink for C truncation', &
-            ptr_col=this%ctrunc_col, default='inactive')
-
-       this%dyn_cbal_adjustments_col(begc:endc) = spval
-       call hist_addfld1d (fname='C14_DYN_COL_SOIL_ADJUSTMENTS_C', units='gC14/m^2', &
-            avgflag='SUM', &
-            long_name='C14 adjustments in soil carbon due to dynamic column areas; &
-            &only makes sense at the column level: should not be averaged to gridcell', &
-            ptr_col=this%dyn_cbal_adjustments_col, default='inactive')
-    endif
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, ratio, c12_soilbiogeochem_carbonstate_inst)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_carbonstate_type) :: this 
-    type(bounds_type) , intent(in)         :: bounds  
-    real(r8)          , intent(in)         :: ratio
-    type(soilbiogeochem_carbonstate_type), intent(in), optional :: c12_soilbiogeochem_carbonstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: p,c,l,j,k
-    integer :: fc                                        ! filter index
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: special_col(bounds%endc-bounds%begc+1)    ! special landunit filter - columns
-    !-----------------------------------------------------------------------
-
-    ! initialize column-level variables
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          if (.not. present(c12_soilbiogeochem_carbonstate_inst)) then !c12
-
-             do j = 1, nlevdecomp
-                do k = 1, ndecomp_pools
-                   if (zsoi(j) < decomp_cascade_con%initial_stock_soildepth ) then  !! only initialize upper soil column
-                      this%decomp_cpools_vr_col(c,j,k) = decomp_cascade_con%initial_stock(k)
-                   else
-                      this%decomp_cpools_vr_col(c,j,k) = 0._r8
-                   endif
-                end do
-                this%ctrunc_vr_col(c,j) = 0._r8
-             end do
-             if ( nlevdecomp > 1 ) then
-                do j = nlevdecomp+1, nlevdecomp_full
-                   do k = 1, ndecomp_pools
-                      this%decomp_cpools_vr_col(c,j,k) = 0._r8
-                   end do
-                   this%ctrunc_vr_col(c,j) = 0._r8
-                end do
-             end if
-             this%decomp_cpools_col(c,1:ndecomp_pools)    = decomp_cascade_con%initial_stock(1:ndecomp_pools)
-             this%decomp_cpools_1m_col(c,1:ndecomp_pools) = decomp_cascade_con%initial_stock(1:ndecomp_pools)
-
-          else
-
-             do j = 1, nlevdecomp
-                do k = 1, ndecomp_pools
-                   this%decomp_cpools_vr_col(c,j,k) = c12_soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(c,j,k) * ratio
-                end do
-                this%ctrunc_vr_col(c,j) = c12_soilbiogeochem_carbonstate_inst%ctrunc_vr_col(c,j) * ratio
-             end do
-             if ( nlevdecomp > 1 ) then
-                do j = nlevdecomp+1, nlevdecomp_full
-                   do k = 1, ndecomp_pools
-                      this%decomp_cpools_vr_col(c,j,k) = 0._r8
-                   end do
-                   this%ctrunc_vr_col(c,j) = 0._r8
-                end do
-             end if
-             do k = 1, ndecomp_pools
-                this%decomp_cpools_col(c,k)    = c12_soilbiogeochem_carbonstate_inst%decomp_cpools_col(c,k) * ratio
-                this%decomp_cpools_1m_col(c,k) = c12_soilbiogeochem_carbonstate_inst%decomp_cpools_1m_col(c,k) * ratio
-             end do
-
-          endif
-       end if
-
-       if ( .not. use_fates ) then
-          if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-             if (present(c12_soilbiogeochem_carbonstate_inst)) then
-                this%cwdc_col(c)    = c12_soilbiogeochem_carbonstate_inst%cwdc_col(c) * ratio
-             else
-                this%cwdc_col(c)    = 0._r8
-             end if
-             this%ctrunc_col(c)     = 0._r8
-             this%totlitc_col(c)    = 0._r8
-             this%totsomc_col(c)    = 0._r8
-             this%totlitc_1m_col(c) = 0._r8
-             this%totsomc_1m_col(c) = 0._r8
-          end if
-       end if
-    end do
-
-    ! now loop through special filters and explicitly set the variables that
-    ! have to be in place for biogeophysics
-    
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    ! initialize fields for special filters
-
-    call this%SetValues (num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart ( this,  bounds, ncid, flag, carbon_type, totvegc_col, c12_soilbiogeochem_carbonstate_inst )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon state
-    !
-    ! !USES:
-    use shr_infnan_mod       , only : isnan => shr_infnan_isnan, nan => shr_infnan_nan, assignment(=)
-    use clm_time_manager     , only : is_restart, get_nstep
-    use shr_const_mod        , only : SHR_CONST_PDB
-    use clm_varcon           , only : c14ratio
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_carbonstate_type)                      :: this
-    type(bounds_type)                     , intent(in)           :: bounds 
-    type(file_desc_t)                     , intent(inout)        :: ncid   ! netcdf id
-    character(len=*)                      , intent(in)           :: flag   !'read' or 'write'
-    character(len=3)                      , intent(in)           :: carbon_type ! 'c12' or 'c13' or 'c14'
-    real(r8)                              , intent(in)           :: totvegc_col(bounds%begc:bounds%endc) ! (gC/m2) total 
-                                                                                                         ! vegetation carbon
-    type(soilbiogeochem_carbonstate_type) , intent(in), optional :: c12_soilbiogeochem_carbonstate_inst
-
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: i,j,k,l,c
-    real(r8) :: m                   ! multiplier for the exit_spinup code
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    character(len=128) :: varname   ! temporary
-    logical  :: readvar
-    integer  :: idata
-    logical  :: exit_spinup  = .false.
-    logical  :: enter_spinup = .false.
-    ! flags for comparing the model and restart decomposition cascades
-    integer  :: decomp_cascade_state, restart_file_decomp_cascade_state 
-    !------------------------------------------------------------------------
-
-    if (carbon_type == 'c12') then
-
-       do k = 1, ndecomp_pools
-          varname=trim(decomp_cascade_con%decomp_pool_name_restart(k))//'c'
-          if (use_vertsoilc) then
-             ptr2d => this%decomp_cpools_vr_col(:,:,k)
-             call restartvar(ncid=ncid, flag=flag, varname=trim(varname)//"_vr", xtype=ncd_double,  &
-                  dim1name='column', dim2name='levgrnd', switchdim=.true., &
-                  long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp', readvar=readvar, data=ptr2d)
-          else
-             ptr1d => this%decomp_cpools_vr_col(:,1,k) ! nlevdecomp = 1; so treat as 1D variable
-             call restartvar(ncid=ncid, flag=flag, varname=varname, xtype=ncd_double,  &
-                  dim1name='column', long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-          end if
-          if (flag=='read' .and. .not. readvar) then
-             call endrun(msg='ERROR:: '//trim(varname)//' is required on an initialization dataset'//&
-                  errMsg(sourcefile, __LINE__))
-          end if
-       end do
-
-       if (use_vertsoilc) then
-          ptr2d => this%ctrunc_vr_col
-          call restartvar(ncid=ncid, flag=flag, varname='col_ctrunc_vr', xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d)
-       else
-          ptr1d => this%ctrunc_vr_col(:,1) ! nlevdecomp = 1; so treat as 1D variable
-          call restartvar(ncid=ncid, flag=flag, varname='col_ctrunc', xtype=ncd_double,  &
-               dim1name='column', long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg='ERROR:: '//trim(varname)//' is required on an initialization dataset'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-
-    end if
-
-    !--------------------------------
-    ! C13 column carbon state variables
-    !--------------------------------
-
-    if ( carbon_type == 'c13' ) then
-
-       do k = 1, ndecomp_pools
-          varname = trim(decomp_cascade_con%decomp_pool_name_restart(k))//'c_13'
-          if (use_vertsoilc) then
-             ptr2d => this%decomp_cpools_vr_col(:,:,k)
-             call restartvar(ncid=ncid, flag=flag, varname=trim(varname)//"_vr", xtype=ncd_double,  &
-                  dim1name='column', dim2name='levgrnd', switchdim=.true., &
-                  long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp', readvar=readvar, data=ptr2d)
-          else
-             ptr1d => this%decomp_cpools_vr_col(:,1,k) ! nlevdecomp = 1; so treat as 1D variable
-             call restartvar(ncid=ncid, flag=flag, varname=varname, xtype=ncd_double,  &
-                  dim1name='column', long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-          end if
-          if (flag=='read' .and. .not. readvar) then
-             write(iulog,*) 'initializing soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col' &
-                  // ' with atmospheric c13 value for: '//trim(varname)
-             do i = bounds%begc,bounds%endc
-                do j = 1, nlevdecomp
-                   if (this%decomp_cpools_vr_col(i,j,k) /= spval .and. .not. isnan(this%decomp_cpools_vr_col(i,j,k)) ) then
-                      this%decomp_cpools_vr_col(i,j,k) = c12_soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(i,j,k) * c3_r2
-                   endif
-                end do
-             end do
-          end if
-       end do
-
-       if (use_vertsoilc) then
-          ptr2d => this%ctrunc_vr_col
-          call restartvar(ncid=ncid, flag=flag, varname="col_ctrunc_c13_vr", xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d)
-       else
-          ptr1d => this%ctrunc_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname="col_ctrunc_c13", xtype=ncd_double,  &
-               dim1name='column', long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-       end if
-    end if
-
-    !--------------------------------
-    ! C14 column carbon state variables
-    !--------------------------------
-
-    if ( carbon_type == 'c14' ) then
-
-       do k = 1, ndecomp_pools
-          varname = trim(decomp_cascade_con%decomp_pool_name_restart(k))//'c_14'
-          if (use_vertsoilc) then
-             ptr2d => this%decomp_cpools_vr_col(:,:,k)
-             call restartvar(ncid=ncid, flag=flag, varname=trim(varname)//"_vr", xtype=ncd_double,  &
-                  dim1name='column', dim2name='levgrnd', switchdim=.true., &
-                  long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp', readvar=readvar, data=ptr2d)
-          else
-             ptr1d => this%decomp_cpools_vr_col(:,1,k) ! nlevdecomp = 1; so treat as 1D variable
-             call restartvar(ncid=ncid, flag=flag, varname=varname, xtype=ncd_double,  &
-                  dim1name='column', &
-                  long_name='',  units='', fill_value=spval, &
-                  interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-          end if
-          if (flag=='read' .and. .not. readvar) then
-             write(iulog,*) 'initializing soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col with atmospheric c14 value for: '//&
-                  trim(varname)
-             do i = bounds%begc,bounds%endc
-                do j = 1, nlevdecomp
-                   if (this%decomp_cpools_vr_col(i,j,k) /= spval .and. .not. isnan(this%decomp_cpools_vr_col(i,j,k)) ) then
-                      this%decomp_cpools_vr_col(i,j,k) = c12_soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(i,j,k) * c3_r2
-                   endif
-                end do
-             end do
-          end if
-       end do
-
-       if (use_vertsoilc) then 
-          ptr2d => this%ctrunc_vr_col
-          call restartvar(ncid=ncid, flag=flag, varname="col_ctrunc_c14_vr", xtype=ncd_double,  &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d)
-       else
-          ptr1d => this%ctrunc_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname="col_ctrunc_c14", xtype=ncd_double,  &
-               dim1name='column', long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-       end if
-
-    end if
-
-    !--------------------------------
-    ! Spinup state
-    !--------------------------------
-
-       
-        if (carbon_type == 'c12') then
-           if (flag == 'write') idata = spinup_state
-           call restartvar(ncid=ncid, flag=flag, varname='spinup_state', xtype=ncd_int,  &
-             long_name='Spinup state of the model that wrote this restart file: ' &
-             // ' 0 = normal model mode, 1 = AD spinup', units='', &
-             interpinic_flag='copy', readvar=readvar,  data=idata)
-           if (flag == 'read') then
-              if (readvar) then
-                 this%restart_file_spinup_state = idata
-              else
-                 call endrun(msg=' CNRest: spinup_state was not on the restart file and is required' // &
-                   errMsg(sourcefile, __LINE__))
-              end if
-           end if
-        else
-           this%restart_file_spinup_state = c12_soilbiogeochem_carbonstate_inst%restart_file_spinup_state
-        endif
-
-        ! now compare the model and restart file spinup states, and either take the 
-        ! model into spinup mode or out of it if they are not identical
-        ! taking model out of spinup mode requires multiplying each decomposing pool 
-        ! by the associated AD factor.
-        ! putting model into spinup mode requires dividing each decomposing pool 
-        ! by the associated AD factor.
-        ! only allow this to occur on first timestep of model run.
-        
-        if (flag == 'read' .and. spinup_state /= this%restart_file_spinup_state ) then
-           if (spinup_state == 0 .and. this%restart_file_spinup_state >= 1 ) then
-              if ( masterproc ) write(iulog,*) ' CNRest: taking ',carbon_type,' SOM pools out of AD spinup mode'
-              exit_spinup = .true.
-           else if (spinup_state >= 1 .and. this%restart_file_spinup_state == 0 ) then
-              if ( masterproc ) write(iulog,*) ' CNRest: taking ',carbon_type,' SOM pools into AD spinup mode'
-              enter_spinup = .true.
-           else
-              call endrun(msg=' CNRest: error in entering/exiting spinup.  spinup_state ' &
-                   // ' != restart_file_spinup_state, but do not know what to do'//&
-                   errMsg(sourcefile, __LINE__))
-           end if
-           if (get_nstep() >= 2) then
-              call endrun(msg=' CNRest: error in entering/exiting spinup - should occur only when nstep = 1'//&
-                   errMsg(sourcefile, __LINE__))
-           endif
-           if ( exit_spinup .and. isnan(this%totvegcthresh) )then
-              call endrun(msg=' CNRest: error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//&
-                   errMsg(sourcefile, __LINE__))
-           end if
-           do k = 1, ndecomp_pools
-              if ( exit_spinup ) then
-                 m = decomp_cascade_con%spinup_factor(k)
-              else if ( enter_spinup ) then
-                 m = 1. / decomp_cascade_con%spinup_factor(k)
-              end if
-              do c = bounds%begc, bounds%endc
-                 l = col%landunit(c)
-                 do j = 1, nlevdecomp_full
-                    if ( abs(m - 1._r8) .gt. 0.000001_r8 .and. exit_spinup) then
-                       this%decomp_cpools_vr_col(c,j,k) = this%decomp_cpools_vr_col(c,j,k) * m * &
-                            get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
-                       ! If there is no vegetation carbon, implying that all vegetation has died, then 
-                       ! reset decomp pools to near zero during exit_spinup to avoid very 
-                       ! large and inert soil carbon stocks; note that only pools with spinup factor > 1 
-                       ! will be affected, which means that total SOMC and LITC pools will not be set to 0.
-                       if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then 
-                         this%decomp_cpools_vr_col(c,j,k) = 0.0_r8
-                       endif
-                    elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then
-                       this%decomp_cpools_vr_col(c,j,k) = this%decomp_cpools_vr_col(c,j,k) * m / &
-                            get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
-                    else
-                       this%decomp_cpools_vr_col(c,j,k) = this%decomp_cpools_vr_col(c,j,k) * m 
-                    endif
-                 end do
-              end do
-           end do
-        end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set carbon state variables
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_carbonstate_type) :: this
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i,j,k,l     ! loop index
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-       if ( .not. use_fates ) then
-          this%cwdc_col(i)       = value_column
-       end if
-       this%ctrunc_col(i)     = value_column
-       this%totlitc_col(i)    = value_column
-       this%totlitc_1m_col(i) = value_column
-       this%totsomc_col(i)    = value_column
-       this%totsomc_1m_col(i) = value_column
-    end do
-
-    do j = 1,nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%ctrunc_vr_col(i,j) = value_column
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%decomp_cpools_col(i,k) = value_column
-          this%decomp_cpools_1m_col(i,k) = value_column
-       end do
-    end do
-
-    do j = 1,nlevdecomp_full
-       do k = 1, ndecomp_pools
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_cpools_vr_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-  end subroutine SetValues
-
-  !-----------------------------------------------------------------------
-  subroutine Summary(this, bounds, num_allc, filter_allc)
-    !
-    ! !DESCRIPTION:
-    ! Perform column-level carbon summary calculations
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_carbonstate_type)          :: this
-    type(bounds_type)               , intent(in)    :: bounds          
-    integer                         , intent(in)    :: num_allc       ! number of columns in allc filter
-    integer                         , intent(in)    :: filter_allc(:) ! filter for all active columns
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c,j,k,l       ! indices
-    integer  :: fc            ! filter indices
-    real(r8) :: maxdepth      ! depth to integrate soil variables
-    !-----------------------------------------------------------------------
-
-    ! vertically integrate each of the decomposing C pools
-    do l = 1, ndecomp_pools
-       do fc = 1,num_allc
-          c = filter_allc(fc)
-          this%decomp_cpools_col(c,l) = 0._r8
-       end do
-    end do
-    do l = 1, ndecomp_pools
-       do j = 1, nlevdecomp
-          do fc = 1,num_allc
-             c = filter_allc(fc)
-             this%decomp_cpools_col(c,l) = &
-                  this%decomp_cpools_col(c,l) + &
-                  this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j)
-          end do
-       end do
-    end do
-
-    if ( nlevdecomp > 1) then
-
-       ! vertically integrate each of the decomposing C pools to 1 meter
-       maxdepth = 1._r8
-       do l = 1, ndecomp_pools
-          do fc = 1,num_allc
-             c = filter_allc(fc)
-             this%decomp_cpools_1m_col(c,l) = 0._r8
-          end do
-       end do
-       do l = 1, ndecomp_pools
-          do j = 1, nlevdecomp
-             if ( zisoi(j) <= maxdepth ) then
-                do fc = 1,num_allc
-                   c = filter_allc(fc)
-                   this%decomp_cpools_1m_col(c,l) = &
-                        this%decomp_cpools_1m_col(c,l) + &
-                        this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j)
-                end do
-             elseif ( zisoi(j-1) < maxdepth ) then
-                do fc = 1,num_allc
-                   c = filter_allc(fc)
-                   this%decomp_cpools_1m_col(c,l) = &
-                        this%decomp_cpools_1m_col(c,l) + &
-                        this%decomp_cpools_vr_col(c,j,l) * (maxdepth - zisoi(j-1))
-                end do
-             endif
-          end do
-       end do
-
-    endif
-
-    ! truncation carbon
-    do fc = 1,num_allc
-       c = filter_allc(fc)
-       this%ctrunc_col(c) = 0._r8
-    end do
-    do j = 1, nlevdecomp
-       do fc = 1,num_allc
-          c = filter_allc(fc)
-          this%ctrunc_col(c) = &
-               this%ctrunc_col(c) + &
-               this%ctrunc_vr_col(c,j) * dzsoi_decomp(j)
-       end do
-    end do
-
-    ! total litter carbon in the top meter (TOTLITC_1m)
-    if ( nlevdecomp > 1) then
-       do fc = 1,num_allc
-          c = filter_allc(fc)
-          this%totlitc_1m_col(c) = 0._r8
-       end do
-       do l = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_litter(l) ) then
-             do fc = 1,num_allc
-                c = filter_allc(fc)
-                this%totlitc_1m_col(c) = this%totlitc_1m_col(c) + &
-                     this%decomp_cpools_1m_col(c,l)
-             end do
-          endif
-       end do
-    end if
-
-    ! total soil organic matter carbon in the top meter (TOTSOMC_1m)
-    if ( nlevdecomp > 1) then
-       do fc = 1,num_allc
-          c = filter_allc(fc)
-          this%totsomc_1m_col(c) = 0._r8
-       end do
-       do l = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_soil(l) ) then
-             do fc = 1,num_allc
-                c = filter_allc(fc)
-                this%totsomc_1m_col(c) = this%totsomc_1m_col(c) + this%decomp_cpools_1m_col(c,l)
-             end do
-          end if
-       end do
-    end if
-
-    ! total litter carbon (TOTLITC)
-    do fc = 1,num_allc
-       c = filter_allc(fc)
-       this%totlitc_col(c) = 0._r8
-    end do
-    do l = 1, ndecomp_pools
-       if ( decomp_cascade_con%is_litter(l) ) then
-          do fc = 1,num_allc
-             c = filter_allc(fc)
-             this%totlitc_col(c) = this%totlitc_col(c) + this%decomp_cpools_col(c,l)
-          end do
-       endif
-    end do
-
-    ! total soil organic matter carbon (TOTSOMC)
-    do fc = 1,num_allc
-       c = filter_allc(fc)
-       this%totsomc_col(c) = 0._r8
-    end do
-    do l = 1, ndecomp_pools
-       if ( decomp_cascade_con%is_soil(l) ) then
-          do fc = 1,num_allc
-             c = filter_allc(fc)
-             this%totsomc_col(c) = this%totsomc_col(c) + this%decomp_cpools_col(c,l)
-          end do
-       end if
-    end do
-
-    ! coarse woody debris carbon
-    if (.not. use_fates ) then
-       do fc = 1,num_allc
-          c = filter_allc(fc)
-          this%cwdc_col(c) = 0._r8
-       end do
-       do l = 1, ndecomp_pools
-          if ( decomp_cascade_con%is_cwd(l) ) then
-             do fc = 1,num_allc
-                c = filter_allc(fc)
-                this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l)
-             end do
-          end if
-       end do
-       
-    end if
-
-  end subroutine Summary
-
-  !------------------------------------------------------------------------
-  subroutine SetTotVgCThresh(this, totvegcthresh)
-
-    class(soilbiogeochem_carbonstate_type)                       :: this
-    real(r8)                              , intent(in)           :: totvegcthresh
-
-    if ( totvegcthresh <= 0.0_r8 )then
-        call endrun(msg=' ERROR totvegcthresh is zero or negative and should be > 0'//&
-               errMsg(sourcefile, __LINE__))
-    end if
-    this%totvegcthresh = totvegcthresh
-
-  end subroutine SetTotVgCThresh
-
-end module SoilBiogeochemCarbonStateType
diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
deleted file mode 100644
index e636fd3085..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
+++ /dev/null
@@ -1,578 +0,0 @@
-module SoilBiogeochemDecompCascadeBGCMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Sets the coeffiecients used in the decomposition cascade submodel.  
-  ! This uses the CENTURY/BGC parameters
-  !
-  ! !USES:
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_const_mod                      , only : SHR_CONST_TKFRZ
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varpar                         , only : nlevsoi, nlevgrnd, nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : i_met_lit, i_cel_lit, i_lig_lit, i_cwd
-  use clm_varctl                         , only : iulog, spinup_state, anoxia, use_vertsoilc, use_fates
-  use clm_varcon                         , only : zsoi
-  use decompMod                          , only : bounds_type
-  use spmdMod                            , only : masterproc
-  use abortutils                         , only : endrun
-  use CNSharedParamsMod                  , only : CNParamsShareInst, anoxia_wtsat, nlev_soildecomp_standard 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
-  use SoilStateType                      , only : soilstate_type
-  use CanopyStateType                    , only : canopystate_type
-  use TemperatureType                    , only : temperature_type 
-  use ch4Mod                             , only : ch4_type
-  use ColumnType                         , only : col                
-  use GridcellType                       , only : grc
-  use SoilBiogeochemStateType            , only : get_spinup_latitude_term
-
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams                      ! Read in parameters from params file
-  public :: init_decompcascade_bgc          ! Initialization
-  !
-  ! !PUBLIC DATA MEMBERS 
-  logical , public :: normalize_q10_to_century_tfunc = .true.! do we normalize the century decomp. rates so that they match the CLM Q10 at a given tep?
-  logical , public :: use_century_tfunc = .false.
-  real(r8), public :: normalization_tref = 15._r8            ! reference temperature for normalizaion (degrees C)
-  !
-  ! !PRIVATE DATA MEMBERS 
-
-  integer, private            :: i_soil1   = -9         ! Soil Organic Matter (SOM) first pool
-  integer, private            :: i_soil2   = -9         ! SOM second pool
-  integer, private            :: i_soil3   = -9         ! SOM third pool
-  integer, private, parameter :: nsompools = 3          ! Number of SOM pools
-  integer, private, parameter :: i_litr1   = i_met_lit  ! First litter pool, metobolic
-  integer, private, parameter :: i_litr2   = i_cel_lit  ! Second litter pool, cellulose
-  integer, private, parameter :: i_litr3   = i_lig_lit  ! Third litter pool, lignin
-
-  type, private :: params_type
-     real(r8):: cn_s1_bgc     !C:N for SOM 1
-     real(r8):: cn_s2_bgc     !C:N for SOM 2
-     real(r8):: cn_s3_bgc     !C:N for SOM 3
-
-     real(r8):: rf_l1s1_bgc   !respiration fraction litter 1 -> SOM 1
-     real(r8):: rf_l2s1_bgc
-     real(r8):: rf_l3s2_bgc
-
-     real(r8):: rf_s2s1_bgc    
-     real(r8):: rf_s2s3_bgc    
-     real(r8):: rf_s3s1_bgc    
-
-     real(r8):: rf_cwdl2_bgc 
-     real(r8):: rf_cwdl3_bgc
-
-     real(r8):: tau_l1_bgc    ! turnover time of  litter 1 (yr)
-     real(r8):: tau_l2_l3_bgc ! turnover time of  litter 2 and litter 3 (yr)
-     real(r8):: tau_s1_bgc    ! turnover time of  SOM 1 (yr)
-     real(r8):: tau_s2_bgc    ! turnover time of  SOM 2 (yr)
-     real(r8):: tau_s3_bgc    ! turnover time of  SOM 3 (yr)
-     real(r8):: tau_cwd_bgc   ! corrected fragmentation rate constant CWD
-
-     real(r8) :: cwd_fcel_bgc !cellulose fraction for CWD
-     real(r8) :: cwd_flig_bgc !
-
-     real(r8) :: k_frag_bgc   !fragmentation rate for CWD
-     real(r8) :: minpsi_bgc   !minimum soil water potential for heterotrophic resp
-     real(r8) :: maxpsi_bgc   !maximum soil water potential for heterotrophic resp
-
-     real(r8) :: initial_Cstocks(nsompools) ! Initial Carbon stocks for a cold-start
-     real(r8) :: initial_Cstocks_depth      ! Soil depth for initial Carbon stocks for a cold-start
-     
-  end type params_type
-  !
-  type(params_type), private :: params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    !
-    ! !USES:
-    use ncdio_pio    , only: file_desc_t,ncd_io
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNDecompBgcParamsType'
-    character(len=100) :: errCode = 'Error reading in CN const file '
-    logical            :: readv   ! has variable been read in or not
-    real(r8)           :: tempr   ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    ! Read off of netcdf file
-    tString='tau_l1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_l1_bgc=tempr
-
-    tString='tau_l2_l3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_l2_l3_bgc=tempr
-
-    tString='tau_s1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_s1_bgc=tempr
-
-    tString='tau_s2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_s2_bgc=tempr
-
-    tString='tau_s3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_s3_bgc=tempr
-
-    tString='tau_cwd'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%tau_cwd_bgc=tempr
-
-    tString='cn_s1_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s1_bgc=tempr
-
-    tString='cn_s2_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s2_bgc=tempr
-
-    tString='cn_s3_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s3_bgc=tempr
-
-    tString='rf_l1s1_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l1s1_bgc=tempr
-
-    tString='rf_l2s1_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l2s1_bgc=tempr
-
-    tString='rf_l3s2_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l3s2_bgc=tempr   
-
-    tString='rf_s2s1_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s2s1_bgc=tempr
-
-    tString='rf_s2s3_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s2s3_bgc=tempr
-
-    tString='rf_s3s1_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s3s1_bgc=tempr
-
-    tString='rf_cwdl2_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_cwdl2_bgc=tempr
-
-    tString='rf_cwdl3_bgc'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_cwdl3_bgc=tempr
-
-    tString='cwd_fcel'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cwd_fcel_bgc=tempr
-
-    tString='k_frag'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_frag_bgc=tempr
-
-    tString='minpsi_hr'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%minpsi_bgc=tempr 
-
-    tString='maxpsi_hr'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%maxpsi_bgc=tempr 
-
-    tString='cwd_flig'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cwd_flig_bgc=tempr 
-    
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_inst )
-    !
-    ! !DESCRIPTION:
-    !  initialize rate constants and decomposition pathways following the decomposition cascade of the BGC model.
-    !  written by C. Koven 
-    !
-    ! !USES:
-    use clm_time_manager , only : get_step_size
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)               , intent(in)    :: bounds  
-    type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst
-    type(soilstate_type)            , intent(in)    :: soilstate_inst
-    !
-    ! !LOCAL VARIABLES
-    !-- properties of each decomposing pool
-    real(r8) :: rf_l1s1
-    real(r8) :: rf_l2s1
-    real(r8) :: rf_l3s2
-    !real(r8) :: rf_s1s2(bounds%begc:bounds%endc,1:nlevdecomp)
-    !real(r8) :: rf_s1s3(bounds%begc:bounds%endc,1:nlevdecomp)
-    real(r8), allocatable :: rf_s1s2(:,:)
-    real(r8), allocatable :: rf_s1s3(:,:)
-    real(r8) :: rf_s2s1
-    real(r8) :: rf_s2s3
-    real(r8) :: rf_s3s1
-    real(r8) :: rf_cwdl2
-    real(r8) :: rf_cwdl3
-    real(r8) :: cwd_fcel
-    real(r8) :: cwd_flig
-    real(r8) :: cn_s1
-    real(r8) :: cn_s2
-    real(r8) :: cn_s3
-    !real(r8) :: f_s1s2(bounds%begc:bounds%endc,1:nlevdecomp)
-    !real(r8) :: f_s1s3(bounds%begc:bounds%endc,1:nlevdecomp)
-    real(r8), allocatable :: f_s1s2(:,:)
-    real(r8), allocatable :: f_s1s3(:,:)
-    real(r8) :: f_s2s1
-    real(r8) :: f_s2s3
-
-    integer :: i_l1s1
-    integer :: i_l2s1
-    integer :: i_l3s2
-    integer :: i_s1s2
-    integer :: i_s1s3
-    integer :: i_s2s1
-    integer :: i_s2s3
-    integer :: i_s3s1
-    integer :: i_cwdl2
-    integer :: i_cwdl3
-    real(r8):: speedup_fac                  ! acceleration factor, higher when vertsoilc = .true.
-
-    integer  :: c, j    ! indices
-    real(r8) :: t       ! temporary variable
-    !-----------------------------------------------------------------------
-
-    associate(                                                                                     &
-         rf_decomp_cascade              => soilbiogeochem_state_inst%rf_decomp_cascade_col       , & ! Input:  [real(r8)          (:,:,:) ]  respired fraction in decomposition step (frac)       
-         pathfrac_decomp_cascade        => soilbiogeochem_state_inst%pathfrac_decomp_cascade_col , & ! Input:  [real(r8)          (:,:,:) ]  what fraction of C leaving a given pool passes through a given transition (frac)
-
-         cellsand                       => soilstate_inst%cellsand_col                           , & ! Input:  [real(r8)          (:,:)   ]  column 3D sand                                         
-         
-         cascade_step_name              => decomp_cascade_con%cascade_step_name                  , & ! Output: [character(len=8)  (:)     ]  name of transition                               
-         cascade_donor_pool             => decomp_cascade_con%cascade_donor_pool                 , & ! Output: [integer           (:)     ]  which pool is C taken from for a given decomposition step 
-         cascade_receiver_pool          => decomp_cascade_con%cascade_receiver_pool              , & ! Output: [integer           (:)     ]  which pool is C added to for a given decomposition step   
-         floating_cn_ratio_decomp_pools => decomp_cascade_con%floating_cn_ratio_decomp_pools     , & ! Output: [logical           (:)     ]  TRUE => pool has fixed C:N ratio                          
-         decomp_pool_name_restart       => decomp_cascade_con%decomp_pool_name_restart           , & ! Output: [character(len=8)  (:)     ]  name of pool for restart files                   
-         decomp_pool_name_history       => decomp_cascade_con%decomp_pool_name_history           , & ! Output: [character(len=8)  (:)     ]  name of pool for history files                   
-         decomp_pool_name_long          => decomp_cascade_con%decomp_pool_name_long              , & ! Output: [character(len=20) (:)     ]  name of pool for netcdf long names              
-         decomp_pool_name_short         => decomp_cascade_con%decomp_pool_name_short             , & ! Output: [character(len=8)  (:)     ]  name of pool for netcdf short names              
-         is_litter                      => decomp_cascade_con%is_litter                          , & ! Output: [logical           (:)     ]  TRUE => pool is a litter pool                             
-         is_soil                        => decomp_cascade_con%is_soil                            , & ! Output: [logical           (:)     ]  TRUE => pool is a soil pool                               
-         is_cwd                         => decomp_cascade_con%is_cwd                             , & ! Output: [logical           (:)     ]  TRUE => pool is a cwd pool                                
-         initial_cn_ratio               => decomp_cascade_con%initial_cn_ratio                   , & ! Output: [real(r8)          (:)     ]  c:n ratio for initialization of pools                    
-         initial_stock                  => decomp_cascade_con%initial_stock                      , & ! Output: [real(r8)          (:)     ]  initial concentration for seeding at spinup              
-         initial_stock_soildepth        => decomp_cascade_con%initial_stock_soildepth            , & ! Output: [real(r8)          (:)     ]  soil depth for initial concentration for seeding at spinup              
-         is_metabolic                   => decomp_cascade_con%is_metabolic                       , & ! Output: [logical           (:)     ]  TRUE => pool is metabolic material                        
-         is_cellulose                   => decomp_cascade_con%is_cellulose                       , & ! Output: [logical           (:)     ]  TRUE => pool is cellulose                                 
-         is_lignin                      => decomp_cascade_con%is_lignin                          , & ! Output: [logical           (:)     ]  TRUE => pool is lignin                                    
-         spinup_factor                  => decomp_cascade_con%spinup_factor                        & ! Output: [real(r8)          (:)     ]  factor for AD spinup associated with each pool           
-
-         )
-
-      allocate(rf_s1s2(bounds%begc:bounds%endc,1:nlevdecomp))
-      allocate(rf_s1s3(bounds%begc:bounds%endc,1:nlevdecomp))
-      allocate(f_s1s2(bounds%begc:bounds%endc,1:nlevdecomp))
-      allocate(f_s1s3(bounds%begc:bounds%endc,1:nlevdecomp))
-
-      !------- time-constant coefficients ---------- !
-      ! set soil organic matter compartment C:N ratios
-      cn_s1 = params_inst%cn_s1_bgc
-      cn_s2 = params_inst%cn_s2_bgc
-      cn_s3 = params_inst%cn_s3_bgc
-
-      ! set respiration fractions for fluxes between compartments
-      rf_l1s1 = params_inst%rf_l1s1_bgc
-      rf_l2s1 = params_inst%rf_l2s1_bgc
-      rf_l3s2 = params_inst%rf_l3s2_bgc
-      rf_s2s1 = params_inst%rf_s2s1_bgc
-      rf_s2s3 = params_inst%rf_s2s3_bgc
-      rf_s3s1 = params_inst%rf_s3s1_bgc
-
-      rf_cwdl2 = params_inst%rf_cwdl2_bgc
-      rf_cwdl3 = params_inst%rf_cwdl3_bgc
-
-      ! set the cellulose and lignin fractions for coarse woody debris
-      cwd_fcel = params_inst%cwd_fcel_bgc
-      cwd_flig = params_inst%cwd_flig_bgc
-
-      ! set path fractions
-      f_s2s1 = 0.42_r8/(0.45_r8)
-      f_s2s3 = 0.03_r8/(0.45_r8)
-
-      ! some of these are dependent on the soil texture properties
-      do c = bounds%begc, bounds%endc
-         do j = 1, nlevdecomp
-            t = 0.85_r8 - 0.68_r8 * 0.01_r8 * (100._r8 - cellsand(c,j))
-            f_s1s2(c,j) = 1._r8 - .004_r8 / (1._r8 - t)
-            f_s1s3(c,j) = .004_r8 / (1._r8 - t)
-            rf_s1s2(c,j) = t
-            rf_s1s3(c,j) = t
-         end do
-      end do
-      initial_stock_soildepth = params_inst%initial_Cstocks_depth
-
-      !-------------------  list of pools and their attributes  ------------
-      floating_cn_ratio_decomp_pools(i_litr1) = .true.
-      decomp_pool_name_restart(i_litr1) = 'litr1'
-      decomp_pool_name_history(i_litr1) = 'LITR1'
-      decomp_pool_name_long(i_litr1) = 'litter 1'
-      decomp_pool_name_short(i_litr1) = 'L1'
-      is_litter(i_litr1) = .true.
-      is_soil(i_litr1) = .false.
-      is_cwd(i_litr1) = .false.
-      initial_cn_ratio(i_litr1) = 90._r8
-      initial_stock(i_litr1) = 0._r8
-      is_metabolic(i_litr1) = .true.
-      is_cellulose(i_litr1) = .false.
-      is_lignin(i_litr1) = .false.
-
-      floating_cn_ratio_decomp_pools(i_litr2) = .true.
-      decomp_pool_name_restart(i_litr2) = 'litr2'
-      decomp_pool_name_history(i_litr2) = 'LITR2'
-      decomp_pool_name_long(i_litr2) = 'litter 2'
-      decomp_pool_name_short(i_litr2) = 'L2'
-      is_litter(i_litr2) = .true.
-      is_soil(i_litr2) = .false.
-      is_cwd(i_litr2) = .false.
-      initial_cn_ratio(i_litr2) = 90._r8
-      initial_stock(i_litr2) = 0._r8
-      is_metabolic(i_litr2) = .false.
-      is_cellulose(i_litr2) = .true.
-      is_lignin(i_litr2) = .false.
-
-      floating_cn_ratio_decomp_pools(i_litr3) = .true.
-      decomp_pool_name_restart(i_litr3) = 'litr3'
-      decomp_pool_name_history(i_litr3) = 'LITR3'
-      decomp_pool_name_long(i_litr3) = 'litter 3'
-      decomp_pool_name_short(i_litr3) = 'L3'
-      is_litter(i_litr3) = .true.
-      is_soil(i_litr3) = .false.
-      is_cwd(i_litr3) = .false.
-      initial_cn_ratio(i_litr3) = 90._r8
-      initial_stock(i_litr3) = 0._r8
-      is_metabolic(i_litr3) = .false.
-      is_cellulose(i_litr3) = .false.
-      is_lignin(i_litr3) = .true.
-
-      if (.not. use_fates) then
-         ! CWD
-         floating_cn_ratio_decomp_pools(i_cwd) = .true.
-         decomp_pool_name_restart(i_cwd) = 'cwd'
-         decomp_pool_name_history(i_cwd) = 'CWD'
-         decomp_pool_name_long(i_cwd) = 'coarse woody debris'
-         decomp_pool_name_short(i_cwd) = 'CWD'
-         is_litter(i_cwd) = .false.
-         is_soil(i_cwd) = .false.
-         is_cwd(i_cwd) = .true.
-         initial_cn_ratio(i_cwd) = 90._r8
-         initial_stock(i_cwd) = 0._r8
-         is_metabolic(i_cwd) = .false.
-         is_cellulose(i_cwd) = .false.
-         is_lignin(i_cwd) = .false.
-      endif
-
-      if (.not. use_fates) then
-         i_soil1 = 5
-      else
-         i_soil1 = 4
-      endif
-      floating_cn_ratio_decomp_pools(i_soil1) = .false.
-      decomp_pool_name_restart(i_soil1) = 'soil1'
-      decomp_pool_name_history(i_soil1) = 'SOIL1'
-      decomp_pool_name_long(i_soil1) = 'soil 1'
-      decomp_pool_name_short(i_soil1) = 'S1'
-      is_litter(i_soil1) = .false.
-      is_soil(i_soil1) = .true.
-      is_cwd(i_soil1) = .false.
-      initial_cn_ratio(i_soil1) = cn_s1
-      initial_stock(i_soil1) = params_inst%initial_Cstocks(1)
-      is_metabolic(i_soil1) = .false.
-      is_cellulose(i_soil1) = .false.
-      is_lignin(i_soil1) = .false.
-
-      if (.not. use_fates) then
-         i_soil2 = 6
-      else
-         i_soil2 = 5
-      endif
-      floating_cn_ratio_decomp_pools(i_soil2) = .false.
-      decomp_pool_name_restart(i_soil2) = 'soil2'
-      decomp_pool_name_history(i_soil2) = 'SOIL2'
-      decomp_pool_name_long(i_soil2) = 'soil 2'
-      decomp_pool_name_short(i_soil2) = 'S2'
-      is_litter(i_soil2) = .false.
-      is_soil(i_soil2) = .true.
-      is_cwd(i_soil2) = .false.
-      initial_cn_ratio(i_soil2) = cn_s2
-      initial_stock(i_soil2) = params_inst%initial_Cstocks(2)
-      is_metabolic(i_soil2) = .false.
-      is_cellulose(i_soil2) = .false.
-      is_lignin(i_soil2) = .false.
-
-      if (.not. use_fates) then
-         i_soil3 = 7
-      else
-         i_soil3 = 6
-      endif
-      floating_cn_ratio_decomp_pools(i_soil3) = .false.
-      decomp_pool_name_restart(i_soil3) = 'soil3'
-      decomp_pool_name_history(i_soil3) = 'SOIL3'
-      decomp_pool_name_long(i_soil3) = 'soil 3'
-      decomp_pool_name_short(i_soil3) = 'S3'
-      is_litter(i_soil3) = .false.
-      is_soil(i_soil3) = .true.
-      is_cwd(i_soil3) = .false.
-      initial_cn_ratio(i_soil3) = cn_s3
-      initial_stock(i_soil3) = params_inst%initial_Cstocks(3)
-      is_metabolic(i_soil3) = .false.
-      is_cellulose(i_soil3) = .false.
-      is_lignin(i_soil3) = .false.
-
-
-      speedup_fac = 1._r8
-
-      !lit1
-      spinup_factor(i_litr1) = 1._r8
-      !lit2,3
-      spinup_factor(i_litr2) = 1._r8
-      spinup_factor(i_litr3) = 1._r8
-      !CWD
-      if (.not. use_fates) then
-         spinup_factor(i_cwd) = max(1._r8, (speedup_fac * params_inst%tau_cwd_bgc / 2._r8 ))
-      end if
-      !som1
-      spinup_factor(i_soil1) = 1._r8
-      !som2,3
-      spinup_factor(i_soil2) = max(1._r8, (speedup_fac * params_inst%tau_s2_bgc))
-      spinup_factor(i_soil3) = max(1._r8, (speedup_fac * params_inst%tau_s3_bgc))
-
-      if ( masterproc ) then
-         write(iulog,*) 'Spinup_state ',spinup_state
-         write(iulog,*) 'Spinup factors ',spinup_factor
-      end if
-
-      !----------------  list of transitions and their time-independent coefficients  ---------------!
-      i_l1s1 = 1
-      cascade_step_name(i_l1s1) = 'L1S1'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = rf_l1s1
-      cascade_donor_pool(i_l1s1) = i_litr1
-      cascade_receiver_pool(i_l1s1) = i_soil1
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = 1.0_r8
-
-      i_l2s1 = 2
-      cascade_step_name(i_l2s1) = 'L2S1'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s1) = rf_l2s1
-      cascade_donor_pool(i_l2s1) = i_litr2
-      cascade_receiver_pool(i_l2s1) = i_soil1
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s1)= 1.0_r8
-
-      i_l3s2 = 3
-      cascade_step_name(i_l3s2) = 'L3S2'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s2) = rf_l3s2
-      cascade_donor_pool(i_l3s2) = i_litr3
-      cascade_receiver_pool(i_l3s2) = i_soil2
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s2) = 1.0_r8
-
-      i_s1s2 = 4
-      cascade_step_name(i_s1s2) = 'S1S2'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s2) = rf_s1s2(bounds%begc:bounds%endc,1:nlevdecomp)
-      cascade_donor_pool(i_s1s2) = i_soil1
-      cascade_receiver_pool(i_s1s2) = i_soil2
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s2) = f_s1s2(bounds%begc:bounds%endc,1:nlevdecomp)
-
-      i_s1s3 = 5
-      cascade_step_name(i_s1s3) = 'S1S3'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s3) = rf_s1s3(bounds%begc:bounds%endc,1:nlevdecomp)
-      cascade_donor_pool(i_s1s3) = i_soil1
-      cascade_receiver_pool(i_s1s3) = i_soil3
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s3) = f_s1s3(bounds%begc:bounds%endc,1:nlevdecomp)
-
-      i_s2s1 = 6
-      cascade_step_name(i_s2s1) = 'S2S1'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s1) = rf_s2s1
-      cascade_donor_pool(i_s2s1) = i_soil2
-      cascade_receiver_pool(i_s2s1) = i_soil1
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s1) = f_s2s1
-
-      i_s2s3 = 7 
-      cascade_step_name(i_s2s3) = 'S2S3'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s3) = rf_s2s3
-      cascade_donor_pool(i_s2s3) = i_soil2
-      cascade_receiver_pool(i_s2s3) = i_soil3
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s3) = f_s2s3
-
-      i_s3s1 = 8
-      cascade_step_name(i_s3s1) = 'S3S1'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s1) = rf_s3s1
-      cascade_donor_pool(i_s3s1) = i_soil3
-      cascade_receiver_pool(i_s3s1) = i_soil1
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s1) = 1.0_r8
-
-      if (.not. use_fates) then
-         i_cwdl2 = 9
-         cascade_step_name(i_cwdl2) = 'CWDL2'
-         rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl2) = rf_cwdl2
-         cascade_donor_pool(i_cwdl2) = i_cwd
-         cascade_receiver_pool(i_cwdl2) = i_litr2
-         pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl2) = cwd_fcel
-         
-         i_cwdl3 = 10
-         cascade_step_name(i_cwdl3) = 'CWDL3'
-         rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl3) = rf_cwdl3
-         cascade_donor_pool(i_cwdl3) = i_cwd
-         cascade_receiver_pool(i_cwdl3) = i_litr3
-         pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl3) = cwd_flig
-      end if
-
-      deallocate(rf_s1s2)
-      deallocate(rf_s1s3)
-      deallocate(f_s1s2)
-      deallocate(f_s1s3)
-
-    end associate
-
-  end subroutine init_decompcascade_bgc
-
-end module SoilBiogeochemDecompCascadeBGCMod
diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeCNMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeCNMod.F90
deleted file mode 100644
index 2c4d3b182c..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeCNMod.F90
+++ /dev/null
@@ -1,894 +0,0 @@
-module SoilBiogeochemDecompCascadeCNMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Sets the coeffiecients used in the decomposition cascade submodel.  
-  ! This uses the CN parameters as in CLMCN 4.0
-  !
-  ! !USES:
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_const_mod                      , only : SHR_CONST_TKFRZ
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varpar                         , only : nlevsoi, nlevgrnd, nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : i_met_lit, i_cel_lit, i_lig_lit, i_cwd
-  use clm_varctl                         , only : iulog, spinup_state, anoxia, use_vertsoilc, use_fates
-  use clm_varcon                         , only : zsoi
-  use decompMod                          , only : bounds_type
-  use abortutils                         , only : endrun
-  use CNSharedParamsMod                  , only : CNParamsShareInst, anoxia_wtsat, nlev_soildecomp_standard 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
-  use SoilStateType                      , only : soilstate_type
-  use CanopyStateType                    , only : canopystate_type
-  use TemperatureType                    , only : temperature_type 
-  use ch4Mod                             , only : ch4_type
-  use ColumnType                         , only : col                
-
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams
-  public :: init_decompcascade_cn
-  public :: decomp_rate_constants_cn
-
-  type, private :: params_type
-     real(r8):: cn_s1_cn        !C:N for SOM 1
-     real(r8):: cn_s2_cn        !C:N for SOM 2
-     real(r8):: cn_s3_cn        !C:N for SOM 3
-     real(r8):: cn_s4_cn        !C:N for SOM 4
-
-     real(r8):: rf_l1s1_cn      !respiration fraction litter 1 -> SOM 1
-     real(r8):: rf_l2s2_cn      !respiration fraction litter 2 -> SOM 2
-     real(r8):: rf_l3s3_cn      !respiration fraction litter 3 -> SOM 3
-     real(r8):: rf_s1s2_cn      !respiration fraction SOM 1 -> SOM 2
-     real(r8):: rf_s2s3_cn      !respiration fraction SOM 2 -> SOM 3
-     real(r8):: rf_s3s4_cn      !respiration fraction SOM 3 -> SOM 4
-
-     real(r8) :: cwd_fcel_cn    !cellulose fraction for CWD
-     real(r8) :: cwd_flig_cn    !
-
-     real(r8) :: k_l1_cn        !decomposition rate for litter 1
-     real(r8) :: k_l2_cn        !decomposition rate for litter 2
-     real(r8) :: k_l3_cn        !decomposition rate for litter 3
-     real(r8) :: k_s1_cn        !decomposition rate for SOM 1
-     real(r8) :: k_s2_cn        !decomposition rate for SOM 2
-     real(r8) :: k_s3_cn        !decomposition rate for SOM 3
-     real(r8) :: k_s4_cn        !decomposition rate for SOM 4
-
-     real(r8) :: k_frag_cn      !fragmentation rate for CWD
-     real(r8) :: minpsi_cn      !minimum soil water potential for heterotrophic resp
-     real(r8) :: maxpsi_cn      !maximum soil water potential for heterotrophic resp
-
-     integer  :: nsompools = 4 
-     real(r8), allocatable :: spinup_vector(:) ! multipliers for soil decomp during accelerated spinup
-
-  end type params_type
-  !
-  type(params_type), private :: params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !USES:
-    use ncdio_pio , only : file_desc_t,ncd_io
-    !
-    ! !ARGUMENTS:
-    implicit none
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !CALLED FROM:   readParamsMod.F90::CNParamsReadFile
-    !
-    ! !REVISION HISTORY:
-    !  Dec 3 2012 : Created by S. Muszala
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'SoilBiogeochemDecompCnParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-
-    !EOP
-    !-----------------------------------------------------------------------
-
-    ! These are not read off of netcdf file
-    allocate(params_inst%spinup_vector(params_inst%nsompools))
-    params_inst%spinup_vector(:) = (/ 1.0_r8, 1.0_r8, 5.0_r8, 70.0_r8 /)
-
-    ! Read off of netcdf file
-    tString='cn_s1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s1_cn=tempr
-
-    tString='cn_s2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s2_cn=tempr
-
-    tString='cn_s3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s3_cn=tempr
-
-    tString='cn_s4'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cn_s4_cn=tempr
-
-    tString='rf_l1s1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l1s1_cn=tempr
-
-    tString='rf_l2s2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l2s2_cn=tempr
-
-    tString='rf_l3s3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_l3s3_cn=tempr
-
-    tString='rf_s1s2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s1s2_cn=tempr
-
-    tString='rf_s2s3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s2s3_cn=tempr
-
-    tString='rf_s3s4'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rf_s3s4_cn=tempr
-
-    tString='cwd_fcel'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cwd_fcel_cn=tempr
-
-    tString='k_l1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_l1_cn=tempr
-
-    tString='k_l2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_l2_cn=tempr
-
-    tString='k_l3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_l3_cn=tempr
-
-    tString='k_s1'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_s1_cn=tempr
-
-    tString='k_s2'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_s2_cn=tempr
-
-    tString='k_s3'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_s3_cn=tempr
-
-    tString='k_s4'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_s4_cn=tempr
-
-    tString='k_frag'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%k_frag_cn=tempr
-
-    tString='minpsi_hr'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%minpsi_cn=tempr 
-
-    tString='maxpsi_hr'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%maxpsi_cn=tempr 
-
-    tString='cwd_flig'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%cwd_flig_cn=tempr
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine init_decompcascade_cn(bounds, soilbiogeochem_state_inst)
-    !
-    ! !DESCRIPTION:
-    !  initialize rate constants and decomposition pathways for the BGC model originally implemented in CLM-CN
-    !  written by C. Koven based on original CLM4 decomposition cascade by P. Thornton
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)               , intent(in)    :: bounds  
-    type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst
-    !
-    !-- properties of each pathway along decomposition cascade 
-    !-- properties of each decomposing pool
-    real(r8) :: rf_l1s1      !respiration fraction litter 1 -> SOM 1
-    real(r8) :: rf_l2s2      !respiration fraction litter 2 -> SOM 2
-    real(r8) :: rf_l3s3      !respiration fraction litter 3 -> SOM 3
-    real(r8) :: rf_s1s2      !respiration fraction SOM 1 -> SOM 2
-    real(r8) :: rf_s2s3      !respiration fraction SOM 2 -> SOM 3
-    real(r8) :: rf_s3s4      !respiration fraction SOM 3 -> SOM 4
-    real(r8) :: cwd_fcel
-    real(r8) :: cwd_flig
-    real(r8) :: cn_s1
-    real(r8) :: cn_s2
-    real(r8) :: cn_s3
-    real(r8) :: cn_s4
-
-    integer :: i_litr1
-    integer :: i_litr2
-    integer :: i_litr3
-    integer :: i_soil1
-    integer :: i_soil2
-    integer :: i_soil3
-    integer :: i_soil4
-    integer :: i_atm
-    integer :: i_l1s1
-    integer :: i_l2s2
-    integer :: i_l3s3
-    integer :: i_s1s2
-    integer :: i_s2s3
-    integer :: i_s3s4
-    integer :: i_s4atm
-    integer :: i_cwdl2
-    integer :: i_cwdl3
-    !-----------------------------------------------------------------------
-
-    associate(                                                                                        &
-         rf_decomp_cascade              =>    soilbiogeochem_state_inst%rf_decomp_cascade_col       , & ! Output:  [real(r8)           (:,:,:) ]  respired fraction in decomposition step (frac)       
-         pathfrac_decomp_cascade        =>    soilbiogeochem_state_inst%pathfrac_decomp_cascade_col , & ! Output:  [real(r8)           (:,:,:) ]  what fraction of C leaving a given pool passes through a given transition (frac)
-         
-         cascade_step_name              =>    decomp_cascade_con%cascade_step_name                  , & ! Output:   [character(len=8)  (:)     ]  name of transition                               
-         cascade_donor_pool             =>    decomp_cascade_con%cascade_donor_pool                 , & ! Output:   [integer           (:)     ]  which pool is C taken from for a given decomposition step 
-         cascade_receiver_pool          =>    decomp_cascade_con%cascade_receiver_pool              , & ! Output:   [integer           (:)     ]  which pool is C added to for a given decomposition step   
-         floating_cn_ratio_decomp_pools =>    decomp_cascade_con%floating_cn_ratio_decomp_pools     , & ! Output:   [logical           (:)     ]  TRUE => pool has fixed C:N ratio                          
-         decomp_pool_name_restart       =>    decomp_cascade_con%decomp_pool_name_restart           , & ! Output:   [character(len=8)  (:)     ]  name of pool for restart files                   
-         decomp_pool_name_history       =>    decomp_cascade_con%decomp_pool_name_history           , & ! Output:   [character(len=8)  (:)     ]  name of pool for history files                   
-         decomp_pool_name_long          =>    decomp_cascade_con%decomp_pool_name_long              , & ! Output:   [character(len=20) (:)     ]  name of pool for netcdf long names              
-         decomp_pool_name_short         =>    decomp_cascade_con%decomp_pool_name_short             , & ! Output:   [character(len=8)  (:)     ]  name of pool for netcdf short names              
-         is_litter                      =>    decomp_cascade_con%is_litter                          , & ! Output:   [logical           (:)     ]  TRUE => pool is a litter pool                             
-         is_soil                        =>    decomp_cascade_con%is_soil                            , & ! Output:   [logical           (:)     ]  TRUE => pool is a soil pool                               
-         is_cwd                         =>    decomp_cascade_con%is_cwd                             , & ! Output:   [logical           (:)     ]  TRUE => pool is a cwd pool                                
-         initial_cn_ratio               =>    decomp_cascade_con%initial_cn_ratio                   , & ! Output:   [real(r8)          (:)     ]  c:n ratio for initialization of pools                    
-         initial_stock                  =>    decomp_cascade_con%initial_stock                      , & ! Output:   [real(r8)          (:)     ]  initial concentration for seeding at spinup              
-         is_metabolic                   =>    decomp_cascade_con%is_metabolic                       , & ! Output:   [logical           (:)     ]  TRUE => pool is metabolic material                        
-         is_cellulose                   =>    decomp_cascade_con%is_cellulose                       , & ! Output:   [logical           (:)     ]  TRUE => pool is cellulose                                 
-         is_lignin                      =>    decomp_cascade_con%is_lignin                          , & ! Output:   [logical           (:)     ]  TRUE => pool is lignin                                    
-         spinup_factor                  =>    decomp_cascade_con%spinup_factor                        & ! Output:   [real(r8)          (:)     ]  factor for AD spinup associated with each pool           
-         )
-      
-      !------- time-constant coefficients ---------- !
-      ! set soil organic matter compartment C:N ratios (from Biome-BGC v4.2.0)
-      cn_s1=params_inst%cn_s1_cn
-      cn_s2=params_inst%cn_s2_cn
-      cn_s3=params_inst%cn_s3_cn
-      cn_s4=params_inst%cn_s4_cn
-
-      ! set respiration fractions for fluxes between compartments
-      ! (from Biome-BGC v4.2.0)
-      rf_l1s1=params_inst%rf_l1s1_cn
-      rf_l2s2=params_inst%rf_l2s2_cn
-      rf_l3s3=params_inst%rf_l3s3_cn
-      rf_s1s2=params_inst%rf_s1s2_cn
-      rf_s2s3=params_inst%rf_s2s3_cn
-      rf_s3s4=params_inst%rf_s3s4_cn
-
-      ! set the cellulose and lignin fractions for coarse woody debris
-      cwd_fcel=params_inst%cwd_fcel_cn
-      cwd_flig=params_inst%cwd_flig_cn
-
-      !-------------------  list of pools and their attributes  ------------
-
-      i_litr1 = i_met_lit
-      floating_cn_ratio_decomp_pools(i_litr1) = .true.
-      decomp_pool_name_restart(i_litr1) = 'litr1'
-      decomp_pool_name_history(i_litr1) = 'LITR1'
-      decomp_pool_name_long(i_litr1) = 'litter 1'
-      decomp_pool_name_short(i_litr1) = 'L1'
-      is_litter(i_litr1) = .true.
-      is_soil(i_litr1) = .false.
-      is_cwd(i_litr1) = .false.
-      initial_cn_ratio(i_litr1) = 90._r8
-      initial_stock(i_litr1) = 0._r8
-      is_metabolic(i_litr1) = .true.
-      is_cellulose(i_litr1) = .false.
-      is_lignin(i_litr1) = .false.
-
-      i_litr2 = i_cel_lit
-      floating_cn_ratio_decomp_pools(i_litr2) = .true.
-      decomp_pool_name_restart(i_litr2) = 'litr2'
-      decomp_pool_name_history(i_litr2) = 'LITR2'
-      decomp_pool_name_long(i_litr2) = 'litter 2'
-      decomp_pool_name_short(i_litr2) = 'L2'
-      is_litter(i_litr2) = .true.
-      is_soil(i_litr2) = .false.
-      is_cwd(i_litr2) = .false.
-      initial_cn_ratio(i_litr2) = 90._r8
-      initial_stock(i_litr2) = 0._r8
-      is_metabolic(i_litr2) = .false.
-      is_cellulose(i_litr2) = .true.
-      is_lignin(i_litr2) = .false.
-
-      i_litr3 = i_lig_lit
-      floating_cn_ratio_decomp_pools(i_litr3) = .true.
-      decomp_pool_name_restart(i_litr3) = 'litr3'
-      decomp_pool_name_history(i_litr3) = 'LITR3'
-      decomp_pool_name_long(i_litr3) = 'litter 3'
-      decomp_pool_name_short(i_litr3) = 'L3'
-      is_litter(i_litr3) = .true.
-      is_soil(i_litr3) = .false.
-      is_cwd(i_litr3) = .false.
-      initial_cn_ratio(i_litr3) = 90._r8
-      initial_stock(i_litr3) = 0._r8
-      is_metabolic(i_litr3) = .false.
-      is_cellulose(i_litr3) = .false.
-      is_lignin(i_litr3) = .true.
-
-      if (.not. use_fates) then
-         floating_cn_ratio_decomp_pools(i_cwd) = .true.
-         decomp_pool_name_restart(i_cwd) = 'cwd'
-         decomp_pool_name_history(i_cwd) = 'CWD'
-         decomp_pool_name_long(i_cwd) = 'coarse woody debris'
-         decomp_pool_name_short(i_cwd) = 'CWD'
-         is_litter(i_cwd) = .false.
-         is_soil(i_cwd) = .false.
-         is_cwd(i_cwd) = .true.
-         initial_cn_ratio(i_cwd) = 500._r8
-         initial_stock(i_cwd) = 0._r8
-         is_metabolic(i_cwd) = .false.
-         is_cellulose(i_cwd) = .false.
-         is_lignin(i_cwd) = .false.
-      end if
-
-      if ( .not. use_fates ) then
-         i_soil1 = 5
-      else
-         i_soil1 = 4
-      endif
-      floating_cn_ratio_decomp_pools(i_soil1) = .false.
-      decomp_pool_name_restart(i_soil1) = 'soil1'
-      decomp_pool_name_history(i_soil1) = 'SOIL1'
-      decomp_pool_name_long(i_soil1) = 'soil 1'
-      decomp_pool_name_short(i_soil1) = 'S1'
-      is_litter(i_soil1) = .false.
-      is_soil(i_soil1) = .true.
-      is_cwd(i_soil1) = .false.
-      initial_cn_ratio(i_soil1) = cn_s1
-      initial_stock(i_soil1) = 0._r8
-      is_metabolic(i_soil1) = .false.
-      is_cellulose(i_soil1) = .false.
-      is_lignin(i_soil1) = .false.
-
-      if ( .not. use_fates ) then
-         i_soil2 = 6
-      else
-         i_soil2 = 5
-      endif
-      floating_cn_ratio_decomp_pools(i_soil2) = .false.
-      decomp_pool_name_restart(i_soil2) = 'soil2'
-      decomp_pool_name_history(i_soil2) = 'SOIL2'
-      decomp_pool_name_long(i_soil2) = 'soil 2'
-      decomp_pool_name_short(i_soil2) = 'S2'
-      is_litter(i_soil2) = .false.
-      is_soil(i_soil2) = .true.
-      is_cwd(i_soil2) = .false.
-      initial_cn_ratio(i_soil2) = cn_s2
-      initial_stock(i_soil2) = 0._r8
-      is_metabolic(i_soil2) = .false.
-      is_cellulose(i_soil2) = .false.
-      is_lignin(i_soil2) = .false.
-
-      if ( .not. use_fates ) then
-         i_soil3 = 7
-      else
-         i_soil3 = 6
-      endif
-      floating_cn_ratio_decomp_pools(i_soil3) = .false.
-      decomp_pool_name_restart(i_soil3) = 'soil3'
-      decomp_pool_name_history(i_soil3) = 'SOIL3'
-      decomp_pool_name_long(i_soil3) = 'soil 3'
-      decomp_pool_name_short(i_soil3) = 'S3'
-      is_litter(i_soil3) = .false.
-      is_soil(i_soil3) = .true.
-      is_cwd(i_soil3) = .false.
-      initial_cn_ratio(i_soil3) = cn_s3
-      initial_stock(i_soil3) = 0._r8
-      is_metabolic(i_soil3) = .false.
-      is_cellulose(i_soil3) = .false.
-      is_lignin(i_soil3) = .false.
-
-      if ( .not. use_fates ) then
-         i_soil4 = 8
-      else
-         i_soil4 = 7
-      endif
-      floating_cn_ratio_decomp_pools(i_soil4) = .false.
-      decomp_pool_name_restart(i_soil4) = 'soil4'
-      decomp_pool_name_history(i_soil4) = 'SOIL4'
-      decomp_pool_name_long(i_soil4) = 'soil 4'
-      decomp_pool_name_short(i_soil4) = 'S4'
-      is_litter(i_soil4) = .false.
-      is_soil(i_soil4) = .true.
-      is_cwd(i_soil4) = .false.
-      initial_cn_ratio(i_soil4) = cn_s4
-      initial_stock(i_soil4) = 10._r8
-      is_metabolic(i_soil4) = .false.
-      is_cellulose(i_soil4) = .false.
-      is_lignin(i_soil4) = .false.
-
-      i_atm = 0  !! for terminal pools (i.e. 100% respiration)
-      floating_cn_ratio_decomp_pools(i_atm) = .false.
-      decomp_pool_name_restart(i_atm) = 'atmosphere'
-      decomp_pool_name_history(i_atm) = 'atmosphere'
-      decomp_pool_name_long(i_atm) = 'atmosphere'
-      decomp_pool_name_short(i_atm) = ''
-      is_litter(i_atm) = .true.
-      is_soil(i_atm) = .false.
-      is_cwd(i_atm) = .false.
-      initial_cn_ratio(i_atm) = 0._r8
-      initial_stock(i_atm) = 0._r8
-      is_metabolic(i_atm) = .false.
-      is_cellulose(i_atm) = .false.
-      is_lignin(i_atm) = .false.
-
-
-      spinup_factor(i_litr1) = 1._r8
-      spinup_factor(i_litr2) = 1._r8
-      spinup_factor(i_litr3) = 1._r8
-      if (.not. use_fates) then
-         spinup_factor(i_cwd) = 1._r8
-      end if
-      spinup_factor(i_soil1) = params_inst%spinup_vector(1)
-      spinup_factor(i_soil2) = params_inst%spinup_vector(2)
-      spinup_factor(i_soil3) = params_inst%spinup_vector(3)
-      spinup_factor(i_soil4) = params_inst%spinup_vector(4)
-
-
-      !----------------  list of transitions and their time-independent coefficients  ---------------!
-      i_l1s1 = 1
-      cascade_step_name(i_l1s1) = 'L1S1'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = rf_l1s1
-      cascade_donor_pool(i_l1s1) = i_litr1
-      cascade_receiver_pool(i_l1s1) = i_soil1
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = 1.0_r8
-
-      i_l2s2 = 2
-      cascade_step_name(i_l2s2) = 'L2S2'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s2) = rf_l2s2
-      cascade_donor_pool(i_l2s2) = i_litr2
-      cascade_receiver_pool(i_l2s2) = i_soil2
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s2) = 1.0_r8
-
-      i_l3s3 = 3
-      cascade_step_name(i_l3s3) = 'L3S3'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s3) = rf_l3s3
-      cascade_donor_pool(i_l3s3) = i_litr3
-      cascade_receiver_pool(i_l3s3) = i_soil3
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s3) = 1.0_r8
-
-      i_s1s2 = 4
-      cascade_step_name(i_s1s2) = 'S1S2'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s2) = rf_s1s2
-      cascade_donor_pool(i_s1s2) = i_soil1
-      cascade_receiver_pool(i_s1s2) = i_soil2
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s2) = 1.0_r8
-
-      i_s2s3 = 5
-      cascade_step_name(i_s2s3) = 'S2S3'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s3) = rf_s2s3
-      cascade_donor_pool(i_s2s3) = i_soil2
-      cascade_receiver_pool(i_s2s3) = i_soil3
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s3) = 1.0_r8
-
-      i_s3s4 = 6 
-      cascade_step_name(i_s3s4) = 'S3S4'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s4) = rf_s3s4
-      cascade_donor_pool(i_s3s4) = i_soil3
-      cascade_receiver_pool(i_s3s4) = i_soil4
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s4) = 1.0_r8
-
-      i_s4atm = 7
-      cascade_step_name(i_s4atm) = 'S4'
-      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s4atm) = 1.
-      cascade_donor_pool(i_s4atm) = i_soil4
-      cascade_receiver_pool(i_s4atm) = i_atm
-      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s4atm) = 1.0_r8
-
-      if (.not. use_fates) then
-         i_cwdl2 = 8
-         cascade_step_name(i_cwdl2) = 'CWDL2'
-         rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl2) = 0._r8
-         cascade_donor_pool(i_cwdl2) = i_cwd
-         cascade_receiver_pool(i_cwdl2) = i_litr2
-         pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl2) = cwd_fcel
-         
-         i_cwdl3 = 9
-         cascade_step_name(i_cwdl3) = 'CWDL3'
-         rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl3) = 0._r8
-         cascade_donor_pool(i_cwdl3) = i_cwd
-         cascade_receiver_pool(i_cwdl3) = i_litr3
-         pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_cwdl3) = cwd_flig
-      end if
-
-    end associate
-
-   end subroutine init_decompcascade_cn
-
-   !-----------------------------------------------------------------------
-   subroutine decomp_rate_constants_cn(bounds, &
-        num_soilc, filter_soilc, &
-        canopystate_inst, soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst)
-     !
-     ! !DESCRIPTION:
-     ! calculate rate constants and decomposition pathways for the BGC model 
-     ! originally implemented in CLM-CN  
-     ! written by C. Koven based on original CLM4 decomposition cascade by P. Thornton
-     !
-     ! !USES:
-     use clm_time_manager, only : get_step_size
-     use clm_varcon      , only : secspday
-     use clm_varpar      , only : i_cwd
-     !
-     ! !ARGUMENTS:
-     type(bounds_type)                    , intent(in)    :: bounds          
-     integer                              , intent(in)    :: num_soilc       ! number of soil columns in filter
-     integer                              , intent(in)    :: filter_soilc(:) ! filter for soil columns
-     type(canopystate_type)               , intent(in)    :: canopystate_inst
-     type(soilstate_type)                 , intent(in)    :: soilstate_inst
-     type(temperature_type)               , intent(in)    :: temperature_inst 
-     type(ch4_type)                       , intent(in)    :: ch4_inst
-     type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst
-     !
-     ! !LOCAL VARIABLES:
-     real(r8):: dt                           ! decomp timestep (seconds)   
-     real(r8):: dtd                          ! decomp timestep (days)
-     real(r8):: frw(bounds%begc:bounds%endc) ! rooting fraction weight
-     real(r8), allocatable:: fr(:,:)         ! column-level rooting fraction by soil depth
-     real(r8):: minpsi, maxpsi               ! limits for soil water scalar for decomp
-     real(r8):: psi                          ! temporary soilpsi for water scalar
-     real(r8):: rate_scalar                  ! combined rate scalar for decomp
-     real(r8):: k_l1                         ! decomposition rate constant litter 1
-     real(r8):: k_l2                         ! decomposition rate constant litter 2
-     real(r8):: k_l3                         ! decomposition rate constant litter 3
-     real(r8):: k_s1                         ! decomposition rate constant SOM 1
-     real(r8):: k_s2                         ! decomposition rate constant SOM 2
-     real(r8):: k_s3                         ! decomposition rate constant SOM 3
-     real(r8):: k_s4                         ! decomposition rate constant SOM 4
-     real(r8):: k_frag                       ! fragmentation rate constant CWD
-     real(r8):: ck_l1                        ! corrected decomposition rate constant litter 1
-     real(r8):: ck_l2                        ! corrected decomposition rate constant litter 2
-     real(r8):: ck_l3                        ! corrected decomposition rate constant litter 3
-     real(r8):: ck_s1                        ! corrected decomposition rate constant SOM 1
-     real(r8):: ck_s2                        ! corrected decomposition rate constant SOM 2
-     real(r8):: ck_s3                        ! corrected decomposition rate constant SOM 3
-     real(r8):: ck_s4                        ! corrected decomposition rate constant SOM 4
-     real(r8):: ck_frag                      ! corrected fragmentation rate constant CWD
-     real(r8):: cwdc_loss                    ! fragmentation rate for CWD carbon (gC/m2/s)
-     real(r8):: cwdn_loss                    ! fragmentation rate for CWD nitrogen (gN/m2/s)
-     integer :: i_litr1
-     integer :: i_litr2
-     integer :: i_litr3
-     integer :: i_soil1
-     integer :: i_soil2
-     integer :: i_soil3
-     integer :: i_soil4
-     integer :: c, fc, j, k, l
-     real(r8):: Q10                          ! temperature dependence
-     real(r8):: froz_q10                     ! separate q10 for frozen soil respiration rates.  default to same as above zero rates
-     real(r8):: decomp_depth_efolding        ! (meters) e-folding depth for reduction in decomposition [
-     real(r8):: depth_scalar(bounds%begc:bounds%endc,1:nlevdecomp) 
-     real(r8) :: mino2lim                    ! minimum anaerobic decomposition rate as a
-     ! fraction of potential aerobic rate
-     !-----------------------------------------------------------------------
-
-     associate(                                                           &
-          dz             => col%dz                                      , & ! Input:  [real(r8) (:,:)   ]  soil layer thickness (m)                               
-
-          soilpsi        => soilstate_inst%soilpsi_col                  , & ! Input:  [real(r8) (:,:)   ]  soil water potential in each soil layer (MPa)          
-
-          alt_indx       => canopystate_inst%alt_indx_col               , & ! Input:  [integer  (:)     ]  current depth of thaw                                     
-
-          t_soisno       => temperature_inst%t_soisno_col               , & ! Input:  [real(r8) (:,:)   ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)       
-
-          o2stress_sat   => ch4_inst%o2stress_sat_col                   , & ! Input:  [real(r8) (:,:)   ]  Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
-          o2stress_unsat => ch4_inst%o2stress_unsat_col                 , & ! Input:  [real(r8) (:,:)   ]  Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
-          finundated     => ch4_inst%finundated_col                     , & ! Input:  [real(r8) (:)     ]  fractional inundated area (excluding dedicated wetland columns)
-          
-          t_scalar       => soilbiogeochem_carbonflux_inst%t_scalar_col , & ! Output: [real(r8) (:,:)   ]  soil temperature scalar for decomp                     
-          w_scalar       => soilbiogeochem_carbonflux_inst%w_scalar_col , & ! Output: [real(r8) (:,:)   ]  soil water scalar for decomp                           
-          o_scalar       => soilbiogeochem_carbonflux_inst%o_scalar_col , & ! Output: [real(r8) (:,:)   ]  fraction by which decomposition is limited by anoxia   
-          decomp_k       => soilbiogeochem_carbonflux_inst%decomp_k_col   & ! Output: [real(r8) (:,:,:) ]  rate constant for decomposition (1./sec)             
-          )
-
-       mino2lim = CNParamsShareInst%mino2lim
-
-       ! set time steps
-       dt = real( get_step_size(), r8 )
-       dtd = dt/secspday
-
-       ! set initial base rates for decomposition mass loss (1/day)
-       ! (from Biome-BGC v4.2.0, using three SOM pools)
-       ! Value inside log function is the discrete-time values for a
-       ! daily time step model, and the result of the log function is
-       ! the corresponding continuous-time decay rate (1/day), following
-       ! Olson, 1963.
-       k_l1=params_inst%k_l1_cn
-       k_l2=params_inst%k_l2_cn
-       k_l3=params_inst%k_l3_cn
-
-       k_s1=params_inst%k_s1_cn
-       k_s2=params_inst%k_s2_cn
-       k_s3=params_inst%k_s3_cn
-       k_s4=params_inst%k_s4_cn
-
-       k_frag=params_inst%k_frag_cn
-
-       ! calculate the new discrete-time decay rate for model timestep
-       k_l1 = 1.0_r8-exp(-k_l1*dtd)
-       k_l2 = 1.0_r8-exp(-k_l2*dtd)
-       k_l3 = 1.0_r8-exp(-k_l3*dtd)
-
-       k_s1 = 1.0_r8-exp(-k_s1*dtd)
-       k_s2 = 1.0_r8-exp(-k_s2*dtd)
-       k_s3 = 1.0_r8-exp(-k_s3*dtd)
-       k_s4 = 1.0_r8-exp(-k_s4*dtd)
-
-       k_frag = 1.0_r8-exp(-k_frag*dtd)
-
-       minpsi = params_inst%minpsi_cn
-       maxpsi = params_inst%maxpsi_cn
-
-       Q10 = CNParamsShareInst%Q10
-
-       ! set "froz_q10" parameter
-       froz_q10  = CNParamsShareInst%froz_q10
-
-       if (use_vertsoilc) then
-          ! Set "decomp_depth_efolding" parameter
-          decomp_depth_efolding = CNParamsShareInst%decomp_depth_efolding
-       end if
-
-       ! The following code implements the acceleration part of the AD spinup
-       ! algorithm, by multiplying all of the SOM decomposition base rates by 10.0.
-
-       if ( spinup_state .eq. 1 ) then
-          k_s1 = k_s1 * params_inst%spinup_vector(1)
-          k_s2 = k_s2 * params_inst%spinup_vector(2)
-          k_s3 = k_s3 * params_inst%spinup_vector(3)
-          k_s4 = k_s4 * params_inst%spinup_vector(4)
-       endif
-
-       i_litr1 = 1
-       i_litr2 = 2
-       i_litr3 = 3
-       if (use_fates) then
-          i_soil1 = 4
-          i_soil2 = 5
-          i_soil3 = 6
-          i_soil4 = 7
-       else
-          i_soil1 = 5
-          i_soil2 = 6
-          i_soil3 = 7
-          i_soil4 = 8
-       endif
-
-       !--- time dependent coefficients-----!
-       if ( nlevdecomp .eq. 1 ) then
-
-          ! calculate function to weight the temperature and water potential scalars
-          ! for decomposition control.  
-
-
-          ! the following normalizes values in fr so that they
-          ! sum to 1.0 across top nlevdecomp levels on a column
-          frw(bounds%begc:bounds%endc) = 0._r8
-          nlev_soildecomp_standard=5
-          allocate(fr(bounds%begc:bounds%endc,nlev_soildecomp_standard))
-          do j=1,nlev_soildecomp_standard
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                frw(c) = frw(c) + dz(c,j)
-             end do
-          end do
-          do j = 1,nlev_soildecomp_standard
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                if (frw(c) /= 0._r8) then
-                   fr(c,j) = dz(c,j) / frw(c)
-                else
-                   fr(c,j) = 0._r8
-                end if
-             end do
-          end do
-
-          ! calculate rate constant scalar for soil temperature
-          ! assuming that the base rate constants are assigned for non-moisture
-          ! limiting conditions at 25 C. 
-          ! Peter Thornton: 3/13/09
-          ! Replaced the Lloyd and Taylor function with a Q10 formula, with Q10 = 1.5
-          ! as part of the modifications made to improve the seasonal cycle of 
-          ! atmospheric CO2 concentration in global simulations. This does not impact
-          ! the base rates at 25 C, which are calibrated from microcosm studies.
-          do j = 1,nlev_soildecomp_standard
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                if (j==1) t_scalar(c,:) = 0._r8
-                !! use separate (possibly equal) t funcs above and below freezing point
-                !! t_scalar(c,1)=t_scalar(c,1) + (1.5**((t_soisno(c,j)-(SHR_CONST_TKFRZ+25._r8))/10._r8))*fr(c,j)
-                if (t_soisno(c,j) >= SHR_CONST_TKFRZ) then
-                   t_scalar(c,1)=t_scalar(c,1) + &
-                        (Q10**((t_soisno(c,j)-(SHR_CONST_TKFRZ+25._r8))/10._r8))*fr(c,j)
-                else
-                   t_scalar(c,1)=t_scalar(c,1) + &
-                        (Q10**(-25._r8/10._r8))*(froz_q10**((t_soisno(c,j)-SHR_CONST_TKFRZ)/10._r8))*fr(c,j)
-                endif
-             end do
-          end do
-
-          ! calculate the rate constant scalar for soil water content.
-          ! Uses the log relationship with water potential given in
-          ! Andren, O., and K. Paustian, 1987. Barley straw decomposition in the field:
-          ! a comparison of models. Ecology, 68(5):1190-1200.
-          ! and supported by data in
-          ! Orchard, V.A., and F.J. Cook, 1983. Relationship between soil respiration
-          ! and soil moisture. Soil Biol. Biochem., 15(4):447-453.
-
-          do j = 1,nlev_soildecomp_standard
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                if (j==1) w_scalar(c,:) = 0._r8
-                psi = min(soilpsi(c,j),maxpsi)
-                ! decomp only if soilpsi is higher than minpsi
-                if (psi > minpsi) then
-                   w_scalar(c,1) = w_scalar(c,1) + (log(minpsi/psi)/log(minpsi/maxpsi))*fr(c,j)
-                end if
-             end do
-          end do
-
-          o_scalar(bounds%begc:bounds%endc,1:nlevdecomp) = 1._r8
-
-          deallocate(fr)
-
-       else
-
-          ! calculate rate constant scalar for soil temperature
-          ! assuming that the base rate constants are assigned for non-moisture
-          ! limiting conditions at 25 C. 
-          ! Peter Thornton: 3/13/09
-          ! Replaced the Lloyd and Taylor function with a Q10 formula, with Q10 = 1.5
-          ! as part of the modifications made to improve the seasonal cycle of 
-          ! atmospheric CO2 concentration in global simulations. This does not impact
-          ! the base rates at 25 C, which are calibrated from microcosm studies.
-
-          do j = 1, nlevdecomp
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                !! use separate (possibly equal) t funcs above and below freezing point
-                !! t_scalar(c,j)= (1.5**((t_soisno(c,j)-(SHR_CONST_TKFRZ+25._r8))/10._r8))
-                if (t_soisno(c,j) >= SHR_CONST_TKFRZ) then
-                   t_scalar(c,j)= (Q10**((t_soisno(c,j)-(SHR_CONST_TKFRZ+25._r8))/10._r8))
-                else
-                   t_scalar(c,j)= (Q10**(-25._r8/10._r8))*(froz_q10**((t_soisno(c,j)-SHR_CONST_TKFRZ)/10._r8))
-                endif
-             end do
-          end do
-
-
-          ! calculate the rate constant scalar for soil water content.
-          ! Uses the log relationship with water potential given in
-          ! Andren, O., and K. Paustian, 1987. Barley straw decomposition in the field:
-          ! a comparison of models. Ecology, 68(5):1190-1200.
-          ! and supported by data in
-          ! Orchard, V.A., and F.J. Cook, 1983. Relationship between soil respiration
-          ! and soil moisture. Soil Biol. Biochem., 15(4):447-453.
-
-          do j = 1,nlevdecomp
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                psi = min(soilpsi(c,j),maxpsi)
-                ! decomp only if soilpsi is higher than minpsi
-                if (psi > minpsi) then
-                   w_scalar(c,j) = (log(minpsi/psi)/log(minpsi/maxpsi))
-                else
-                   w_scalar(c,j) = 0._r8
-                end if
-             end do
-          end do
-
-       end if
-
-       o_scalar(bounds%begc:bounds%endc,1:nlevdecomp) = 1._r8
-
-       if (use_vertsoilc) then
-          ! add a term to reduce decomposition rate at depth
-          ! for now used a fixed e-folding depth
-          do j = 1, nlevdecomp
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                depth_scalar(c,j) = exp(-zsoi(j)/decomp_depth_efolding)
-             end do
-          end do
-       end if
-
-      ! calculate rate constants for all litter and som pools
-       if (use_vertsoilc) then
-          do j = 1,nlevdecomp
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                decomp_k(c,j,i_litr1) = k_l1 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_litr2) = k_l2 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_litr3) = k_l3 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil1) = k_s1 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil2) = k_s2 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil3) = k_s3 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil4) = k_s4 * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-             end do
-          end do
-       else
-          do j = 1,nlevdecomp
-             do fc = 1,num_soilc
-                c = filter_soilc(fc)
-                decomp_k(c,j,i_litr1) = k_l1 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_litr2) = k_l2 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_litr3) = k_l3 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil1) = k_s1 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil2) = k_s2 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil3) = k_s3 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                decomp_k(c,j,i_soil4) = k_s4 * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-             end do
-          end do
-       end if
-
-      ! do the same for cwd, but only if fates is not enabled (because fates handles CWD on its own structure
-       if (.not. use_fates) then
-          if (use_vertsoilc) then
-             do j = 1,nlevdecomp
-                do fc = 1,num_soilc
-                   c = filter_soilc(fc)
-                   decomp_k(c,j,i_cwd) = k_frag * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * o_scalar(c,j) / dt
-                end do
-             end do
-          else
-             do j = 1,nlevdecomp
-                do fc = 1,num_soilc
-                   c = filter_soilc(fc)
-                   decomp_k(c,j,i_cwd) = k_frag * t_scalar(c,j) * w_scalar(c,j) * o_scalar(c,j) / dt
-                end do
-             end do
-          end if
-       end if
-
-     end associate
-
-   end subroutine decomp_rate_constants_cn
-
- end module SoilBiogeochemDecompCascadeCNMod
diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90
deleted file mode 100644
index 8a8e2f8dfa..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90
+++ /dev/null
@@ -1,104 +0,0 @@
-module SoilBiogeochemDecompCascadeConType
-
-  !------------------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Decomposition Cascade Type
-  !
-  ! !USES:
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use clm_varpar     , only : ndecomp_cascade_transitions, ndecomp_pools
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: init_decomp_cascade_constants
-  !
-  type, public :: decomp_cascade_type
-     !-- properties of each pathway along decomposition cascade 
-     character(len=8)  , pointer :: cascade_step_name(:)               ! name of transition
-     integer           , pointer :: cascade_donor_pool(:)              ! which pool is C taken from for a given decomposition step
-     integer           , pointer :: cascade_receiver_pool(:)           ! which pool is C added to for a given decomposition step
-
-     !-- properties of each decomposing pool
-     logical           , pointer  :: floating_cn_ratio_decomp_pools(:) ! TRUE => pool has fixed C:N ratio
-     character(len=8)  , pointer  :: decomp_pool_name_restart(:)       ! name of pool for restart files
-     character(len=8)  , pointer  :: decomp_pool_name_history(:)       ! name of pool for history files
-     character(len=20) , pointer  :: decomp_pool_name_long(:)          ! name of pool for netcdf long names
-     character(len=8)  , pointer  :: decomp_pool_name_short(:)         ! name of pool for netcdf short names
-     logical           , pointer  :: is_litter(:)                      ! TRUE => pool is a litter pool
-     logical           , pointer  :: is_soil(:)                        ! TRUE => pool is a soil pool
-     logical           , pointer  :: is_cwd(:)                         ! TRUE => pool is a cwd pool
-     real(r8)          , pointer  :: initial_cn_ratio(:)               ! c:n ratio for initialization of pools
-     real(r8)          , pointer  :: initial_stock(:)                  ! initial concentration for seeding at spinup
-     real(r8)                     :: initial_stock_soildepth           ! soil depth for initial concentration for seeding at spinup
-     logical           , pointer  :: is_metabolic(:)                   ! TRUE => pool is metabolic material
-     logical           , pointer  :: is_cellulose(:)                   ! TRUE => pool is cellulose
-     logical           , pointer  :: is_lignin(:)                      ! TRUE => pool is lignin
-     real(r8)          , pointer  :: spinup_factor(:)                  ! factor by which to scale AD and relevant processes by
-  end type decomp_cascade_type
-
-  type(decomp_cascade_type), public :: decomp_cascade_con
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine init_decomp_cascade_constants()
-    !
-    ! !DESCRIPTION:
-    ! Initialize decomposition cascade state
-    !------------------------------------------------------------------------
-
-    !-- properties of each pathway along decomposition cascade 
-    allocate(decomp_cascade_con%cascade_step_name(1:ndecomp_cascade_transitions))
-    allocate(decomp_cascade_con%cascade_donor_pool(1:ndecomp_cascade_transitions))
-    allocate(decomp_cascade_con%cascade_receiver_pool(1:ndecomp_cascade_transitions))
-
-    ! NOTE(bja, 2015-10) according to Dave Lawrence and Charlie Koven,
-    ! the indexing of decomposing pools from 0:ndecomp_pools is a
-    ! bug. The lower bound should be 1. The index zero data shouldn't
-    ! be used.
-    
-    !-- properties of each decomposing pool
-    allocate(decomp_cascade_con%floating_cn_ratio_decomp_pools(0:ndecomp_pools))
-    allocate(decomp_cascade_con%decomp_pool_name_restart(0:ndecomp_pools))
-    allocate(decomp_cascade_con%decomp_pool_name_history(0:ndecomp_pools))
-    allocate(decomp_cascade_con%decomp_pool_name_long(0:ndecomp_pools))
-    allocate(decomp_cascade_con%decomp_pool_name_short(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_litter(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_soil(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_cwd(0:ndecomp_pools))
-    allocate(decomp_cascade_con%initial_cn_ratio(0:ndecomp_pools))
-    allocate(decomp_cascade_con%initial_stock(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_metabolic(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_cellulose(0:ndecomp_pools))
-    allocate(decomp_cascade_con%is_lignin(0:ndecomp_pools))
-    allocate(decomp_cascade_con%spinup_factor(1:ndecomp_pools))
-
-    !-- properties of each pathway along decomposition cascade 
-    decomp_cascade_con%cascade_step_name(1:ndecomp_cascade_transitions) = ''
-    decomp_cascade_con%cascade_donor_pool(1:ndecomp_cascade_transitions) = 0
-    decomp_cascade_con%cascade_receiver_pool(1:ndecomp_cascade_transitions) = 0
-
-    !-- first initialization of properties of each decomposing pool
-    decomp_cascade_con%floating_cn_ratio_decomp_pools(0:ndecomp_pools) = .false.
-    decomp_cascade_con%decomp_pool_name_history(0:ndecomp_pools)       = ''
-    decomp_cascade_con%decomp_pool_name_restart(0:ndecomp_pools)       = ''
-    decomp_cascade_con%decomp_pool_name_long(0:ndecomp_pools)          = ''
-    decomp_cascade_con%decomp_pool_name_short(0:ndecomp_pools)         = ''
-    decomp_cascade_con%is_litter(0:ndecomp_pools)                      = .false.
-    decomp_cascade_con%is_soil(0:ndecomp_pools)                        = .false.
-    decomp_cascade_con%is_cwd(0:ndecomp_pools)                         = .false.
-    decomp_cascade_con%initial_cn_ratio(0:ndecomp_pools)               = nan
-    decomp_cascade_con%initial_stock(0:ndecomp_pools)                  = nan
-    decomp_cascade_con%initial_stock_soildepth                         = 0.3
-    decomp_cascade_con%is_metabolic(0:ndecomp_pools)                   = .false.
-    decomp_cascade_con%is_cellulose(0:ndecomp_pools)                   = .false.
-    decomp_cascade_con%is_lignin(0:ndecomp_pools)                      = .false.
-    decomp_cascade_con%spinup_factor(1:ndecomp_pools)                  = nan
-
-  end subroutine init_decomp_cascade_constants
-
-end module SoilBiogeochemDecompCascadeConType
diff --git a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompMod.F90
deleted file mode 100644
index 7906d8a85c..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90
+++ /dev/null
@@ -1,245 +0,0 @@
-module SoilBiogeochemDecompMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module holding routines used in litter and soil decomposition model
-  !
-  ! !USES:
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use decompMod                          , only : bounds_type
-  use clm_varpar                         , only : nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varctl                         , only : use_nitrif_denitrif, use_fates
-  use clm_varcon                         , only : dzsoi_decomp
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
-  use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
-  use SoilBiogeochemNitrogenStateType    , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemNitrogenFluxType     , only : soilbiogeochem_nitrogenflux_type
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams
-  public :: SoilBiogeochemDecomp
-  !
-  type, private :: params_type
-     real(r8) :: dnp         !denitrification proportion
-  end type params_type
-  !
-  type(params_type), private ::  params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    ! Read parameters
-    !
-    ! !USES:
-    use ncdio_pio    , only: file_desc_t,ncd_io
-    use abortutils   , only: endrun
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    tString='dnp'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%dnp=tempr 
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc,                                &
-       soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, &
-       soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, &
-       cn_decomp_pools, p_decomp_cpool_loss, pmnf_decomp_cascade)
-    !
-    ! !USES:
-    !
-    ! !ARGUMENT:
-    type(bounds_type)                       , intent(in)    :: bounds   
-    integer                                 , intent(in)    :: num_soilc          ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:)    ! filter for soil columns
-    type(soilbiogeochem_state_type)         , intent(inout) :: soilbiogeochem_state_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(in)    :: soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(inout) :: soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
-    real(r8)                                , intent(inout) :: cn_decomp_pools(bounds%begc:,1:,1:)     ! c:n ratios of applicable pools
-    real(r8)                                , intent(inout) :: p_decomp_cpool_loss(bounds%begc:,1:,1:) ! potential C loss from one pool to another
-    real(r8)                                , intent(inout) :: pmnf_decomp_cascade(bounds%begc:,1:,1:) ! potential mineral N flux from one pool to another
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,j,k,l,m                                    ! indices
-    integer :: fc                                           ! lake filter column index
-    integer :: begc,endc                                    ! bounds 
-    integer, parameter :: i_atm = 0 !TODO - this appears in two places - move it to 1
-    !  For methane code
-    real(r8):: hrsum(bounds%begc:bounds%endc,1:nlevdecomp)  ! sum of HR (gC/m2/s) 
-    !-----------------------------------------------------------------------
-   
-    begc = bounds%begc; endc = bounds%endc
-    
-    SHR_ASSERT_ALL((ubound(cn_decomp_pools)     == (/endc,nlevdecomp,ndecomp_pools/))               , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(p_decomp_cpool_loss) == (/endc,nlevdecomp,ndecomp_cascade_transitions/)) , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(pmnf_decomp_cascade) == (/endc,nlevdecomp,ndecomp_cascade_transitions/)) , errMsg(sourcefile, __LINE__))
-
-    associate(                                                                                                          & 
-         cascade_donor_pool               =>    decomp_cascade_con%cascade_donor_pool                                 , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
-         cascade_receiver_pool            =>    decomp_cascade_con%cascade_receiver_pool                              , & ! Input:  [integer  (:)     ]  which pool is C added to for a given decomposition step
-         floating_cn_ratio_decomp_pools   =>    decomp_cascade_con%floating_cn_ratio_decomp_pools                     , & ! Input:  [logical  (:)     ]  TRUE => pool has fixed C:N ratio                   
-         initial_cn_ratio                 =>    decomp_cascade_con%initial_cn_ratio                                   , & ! Input:  [real(r8) (:)     ]  c:n ratio for initialization of pools             
-
-         fpi_vr                           =>    soilbiogeochem_state_inst%fpi_vr_col                                  , & ! Input:  [real(r8) (:,:)   ]  fraction of potential immobilization (no units) 
-         rf_decomp_cascade                =>    soilbiogeochem_state_inst%rf_decomp_cascade_col                       , & ! Input:  [real(r8) (:,:,:) ]  respired fraction in decomposition step (frac)
-         pathfrac_decomp_cascade          =>    soilbiogeochem_state_inst%pathfrac_decomp_cascade_col                 , & ! Input:  [real(r8) (:,:,:) ]  what fraction of C leaving a given pool passes through a given transition (frac)
-
-         decomp_npools_vr                 =>    soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col                , & ! Input:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) N pools
-         decomp_cpools_vr                 =>    soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col                  , & ! Input:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) c pools
-
-         decomp_cascade_ntransfer_vr      =>    soilbiogeochem_nitrogenflux_inst%decomp_cascade_ntransfer_vr_col      , & ! Output: [real(r8) (:,:,:) ]  vert-res transfer of N from donor to receiver pool along decomp. cascade (gN/m3/s)
-         decomp_cascade_sminn_flux_vr     =>    soilbiogeochem_nitrogenflux_inst%decomp_cascade_sminn_flux_vr_col     , & ! Output: [real(r8) (:,:,:) ]  vert-res mineral N flux for transition along decomposition cascade (gN/m3/s)
-         potential_immob_vr               =>    soilbiogeochem_nitrogenflux_inst%potential_immob_vr_col               , & ! Output: [real(r8) (:,:)   ]                                                  
-         sminn_to_denit_decomp_cascade_vr =>    soilbiogeochem_nitrogenflux_inst%sminn_to_denit_decomp_cascade_vr_col , & ! Output: [real(r8) (:,:,:) ] 
-         gross_nmin_vr                    =>    soilbiogeochem_nitrogenflux_inst%gross_nmin_vr_col                    , & ! Output: [real(r8) (:,:)   ]                                                  
-         net_nmin_vr                      =>    soilbiogeochem_nitrogenflux_inst%net_nmin_vr_col                      , & ! Output: [real(r8) (:,:)   ]                                                  
-         gross_nmin                       =>    soilbiogeochem_nitrogenflux_inst%gross_nmin_col                       , & ! Output: [real(r8) (:)     ]  gross rate of N mineralization (gN/m2/s)          
-         net_nmin                         =>    soilbiogeochem_nitrogenflux_inst%net_nmin_col                         , & ! Output: [real(r8) (:)     ]  net rate of N mineralization (gN/m2/s)            
-         
-         w_scalar                         =>    soilbiogeochem_carbonflux_inst%w_scalar_col                           , & ! Input:  [real(r8) (:,:)   ]  fraction by which decomposition is limited by moisture availability
-         decomp_cascade_hr_vr             =>    soilbiogeochem_carbonflux_inst%decomp_cascade_hr_vr_col               , & ! Output: [real(r8) (:,:,:) ]  vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
-         decomp_cascade_ctransfer_vr      =>    soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_vr_col        , & ! Output: [real(r8) (:,:,:) ]  vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
-         decomp_k                         =>    soilbiogeochem_carbonflux_inst%decomp_k_col                           , & ! Output: [real(r8) (:,:,:) ]  rate constant for decomposition (1./sec)      
-         phr_vr                           =>    soilbiogeochem_carbonflux_inst%phr_vr_col                             , & ! Input:  [real(r8) (:,:)   ]  potential HR (gC/m3/s)                           
-         fphr                             =>    soilbiogeochem_carbonflux_inst%fphr_col                                 & ! Output: [real(r8) (:,:)   ]  fraction of potential SOM + LITTER heterotrophic
-         )
-
-      ! column loop to calculate actual immobilization and decomp rates, following
-      ! resolution of plant/heterotroph  competition for mineral N
-
-   if ( .not. use_fates) then
-      ! calculate c:n ratios of applicable pools
-      do l = 1, ndecomp_pools
-         if ( floating_cn_ratio_decomp_pools(l) ) then
-            do j = 1,nlevdecomp
-               do fc = 1,num_soilc
-                  c = filter_soilc(fc)
-                  if ( decomp_npools_vr(c,j,l) > 0._r8 ) then
-                     cn_decomp_pools(c,j,l) = decomp_cpools_vr(c,j,l) / decomp_npools_vr(c,j,l)
-                  end if
-               end do
-            end do
-         else
-            do j = 1,nlevdecomp
-               do fc = 1,num_soilc
-                  c = filter_soilc(fc)
-                  cn_decomp_pools(c,j,l) = initial_cn_ratio(l)
-               end do
-            end do
-         end if
-      end do
-
-      ! column loop to calculate actual immobilization and decomp rates, following
-      ! resolution of plant/heterotroph  competition for mineral N
-      
-      ! upon return from SoilBiogeochemCompetition, the fraction of potential immobilization
-      ! has been set (soilbiogeochem_state_inst%fpi_vr_col). now finish the decomp calculations.
-      ! Only the immobilization steps are limited by fpi_vr (pmnf > 0)
-      ! Also calculate denitrification losses as a simple proportion
-      ! of mineralization flux.
-
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-
-               if (decomp_cpools_vr(c,j,cascade_donor_pool(k)) > 0._r8) then
-                  if ( pmnf_decomp_cascade(c,j,k) > 0._r8 ) then
-                     p_decomp_cpool_loss(c,j,k) = p_decomp_cpool_loss(c,j,k) * fpi_vr(c,j)
-                     pmnf_decomp_cascade(c,j,k) = pmnf_decomp_cascade(c,j,k) * fpi_vr(c,j)
-                     if (.not. use_nitrif_denitrif) then
-                        sminn_to_denit_decomp_cascade_vr(c,j,k) = 0._r8
-                     end if
-                  else
-                     if (.not. use_nitrif_denitrif) then
-                        sminn_to_denit_decomp_cascade_vr(c,j,k) = -params_inst%dnp * pmnf_decomp_cascade(c,j,k)
-                     end if
-                  end if
-                  decomp_cascade_hr_vr(c,j,k) = rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k)
-                  decomp_cascade_ctransfer_vr(c,j,k) = (1._r8 - rf_decomp_cascade(c,j,k)) * p_decomp_cpool_loss(c,j,k)
-                  if (decomp_npools_vr(c,j,cascade_donor_pool(k)) > 0._r8 .and. cascade_receiver_pool(k) /= i_atm) then
-                     decomp_cascade_ntransfer_vr(c,j,k) = p_decomp_cpool_loss(c,j,k) / cn_decomp_pools(c,j,cascade_donor_pool(k))
-                  else
-                     decomp_cascade_ntransfer_vr(c,j,k) = 0._r8
-                  endif
-                  if ( cascade_receiver_pool(k) /= 0 ) then
-                     decomp_cascade_sminn_flux_vr(c,j,k) = pmnf_decomp_cascade(c,j,k)
-                  else  ! keep sign convention negative for terminal pools
-                     decomp_cascade_sminn_flux_vr(c,j,k) = - pmnf_decomp_cascade(c,j,k)
-                  endif
-                  net_nmin_vr(c,j) = net_nmin_vr(c,j) - pmnf_decomp_cascade(c,j,k)
-               else
-                  decomp_cascade_ntransfer_vr(c,j,k) = 0._r8
-                  if (.not. use_nitrif_denitrif) then
-                     sminn_to_denit_decomp_cascade_vr(c,j,k) = 0._r8
-                  end if
-                  decomp_cascade_sminn_flux_vr(c,j,k) = 0._r8
-               end if
-
-            end do
-         end do
-      end do
-   else
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               !
-               decomp_cascade_hr_vr(c,j,k) = rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k)
-               !
-               decomp_cascade_ctransfer_vr(c,j,k) = (1._r8 - rf_decomp_cascade(c,j,k)) * p_decomp_cpool_loss(c,j,k)
-               !
-            end do
-         end do
-      end do
-   end if
-
-      
-      ! vertically integrate net and gross mineralization fluxes for diagnostic output                                     
-
-     do fc = 1,num_soilc
-       c = filter_soilc(fc)
-         do j = 1,nlevdecomp
-            if(.not.use_fates)then
-              net_nmin(c) = net_nmin(c) + net_nmin_vr(c,j) * dzsoi_decomp(j)
-              gross_nmin(c) = gross_nmin(c) + gross_nmin_vr(c,j) * dzsoi_decomp(j)
-            ! else
-            !   net_nmin(c) = 0.0_r8
-            !   gross_nmin(c) = 0.0_r8
-            endif
-         end do
-      end do
-
-    end associate
-
-  end subroutine SoilBiogeochemDecomp
- 
-end module SoilBiogeochemDecompMod
diff --git a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90
deleted file mode 100644
index c9482667bc..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90
+++ /dev/null
@@ -1,494 +0,0 @@
-module SoilBiogeochemLittVertTranspMod
-
-  !-----------------------------------------------------------------------
-  ! calculate vertical mixing of all decomposing C and N pools
-  !
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varctl                         , only : iulog, spinup_state, use_vertsoilc, use_fates, use_cn
-  use clm_varcon                         , only : secspday
-  use decompMod                          , only : bounds_type
-  use abortutils                         , only : endrun
-  use CanopyStateType                    , only : canopystate_type
-  use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
-  use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
-  use SoilBiogeochemNitrogenFluxType     , only : soilbiogeochem_nitrogenflux_type
-  use SoilBiogeochemNitrogenStateType    , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use ColumnType                         , only : col                
-  use GridcellType                       , only : grc
-  use SoilBiogeochemStateType            , only : get_spinup_latitude_term
-  !
-  implicit none
-  private
-  !
-  public :: readParams
-  public :: SoilBiogeochemLittVertTransp
-
-  type, private :: params_type
-     real(r8) :: som_diffus                 ! Soil organic matter diffusion
-     real(r8) :: cryoturb_diffusion_k       ! The cryoturbation diffusive constant cryoturbation to the active layer thickness
-     real(r8) :: max_altdepth_cryoturbation ! (m) maximum active layer thickness for cryoturbation to occur
-  end type params_type
-
-  type(params_type), private :: params_inst
-  !
-  real(r8), public :: som_adv_flux =  0._r8
-  real(r8), public :: max_depth_cryoturb = 3._r8   ! (m) this is the maximum depth of cryoturbation
-  real(r8) :: som_diffus                   ! [m^2/sec] = 1 cm^2 / yr
-  real(r8) :: cryoturb_diffusion_k         ! [m^2/sec] = 5 cm^2 / yr = 1m^2 / 200 yr
-  real(r8) :: max_altdepth_cryoturbation   ! (m) maximum active layer thickness for cryoturbation to occur
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------  
-  subroutine readParams ( ncid )
-    !
-    use ncdio_pio   , only : file_desc_t,ncd_io
-    !
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    character(len=32)  :: subname = 'SoilBiogeochemLittVertTranspType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-    !
-    ! read in parameters
-    !
-
-     tString='som_diffus'
-     call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-     !soilbiogeochem_litt_verttransp_params_inst%som_diffus=tempr
-     ! FIX(SPM,032414) - can't be pulled out since division makes things not bfb
-     params_inst%som_diffus = 1e-4_r8 / (secspday * 365._r8)  
-
-     tString='cryoturb_diffusion_k'
-     call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-     !soilbiogeochem_litt_verttransp_params_inst%cryoturb_diffusion_k=tempr
-     !FIX(SPM,032414) Todo.  This constant cannot be on file since the divide makes things
-     !SPM Todo.  This constant cannot be on file since the divide makes things
-     !not bfb
-     params_inst%cryoturb_diffusion_k = 5e-4_r8 / (secspday * 365._r8)  ! [m^2/sec] = 5 cm^2 / yr = 1m^2 / 200 yr
-
-     tString='max_altdepth_cryoturbation'
-     call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-     if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-     params_inst%max_altdepth_cryoturbation=tempr
-    
-   end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc,      &
-       canopystate_inst, soilbiogeochem_state_inst,                     &
-       soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, &
-       c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, &
-       c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, &
-       soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! Calculate vertical mixing of soil and litter pools.  Also reconcile sources and sinks of these pools 
-    ! calculated in the CStateUpdate1 and NStateUpdate1 subroutines.
-    ! Advection-diffusion code based on algorithm in Patankar (1980)
-    ! Initial code by C. Koven and W. Riley
-    !
-    ! !USES:
-    use clm_time_manager , only : get_step_size
-    use clm_varpar       , only : nlevdecomp, ndecomp_pools, nlevdecomp_full
-    use clm_varcon       , only : zsoi, dzsoi_decomp, zisoi
-    use TridiagonalMod   , only : Tridiagonal
-    use ColumnType       , only : col
-    use clm_varctl       , only : use_bedrock
-
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                       , intent(in)    :: bounds 
-    integer                                 , intent(in)    :: num_soilc        ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:)  ! filter for soil columns
-    type(canopystate_type)                  , intent(in)    :: canopystate_inst
-    type(soilbiogeochem_state_type)         , intent(inout) :: soilbiogeochem_state_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(inout) :: soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c13_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(inout) :: c13_soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c14_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(inout) :: c14_soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: diffus (bounds%begc:bounds%endc,1:nlevdecomp+1)                    ! diffusivity (m2/s)  (includes spinup correction, if any)
-    real(r8) :: adv_flux(bounds%begc:bounds%endc,1:nlevdecomp+1)                   ! advective flux (m/s)  (includes spinup correction, if any)
-    real(r8) :: aaa                                                                ! "A" function in Patankar
-    real(r8) :: pe                                                                 ! Pe for "A" function in Patankar
-    real(r8) :: w_m1, w_p1                                                         ! Weights for calculating harmonic mean of diffusivity
-    real(r8) :: d_m1, d_p1                                                         ! Harmonic mean of diffusivity
-    real(r8) :: a_tri(bounds%begc:bounds%endc,0:nlevdecomp+1)                      ! "a" vector for tridiagonal matrix
-    real(r8) :: b_tri(bounds%begc:bounds%endc,0:nlevdecomp+1)                      ! "b" vector for tridiagonal matrix
-    real(r8) :: c_tri(bounds%begc:bounds%endc,0:nlevdecomp+1)                      ! "c" vector for tridiagonal matrix
-    real(r8) :: r_tri(bounds%begc:bounds%endc,0:nlevdecomp+1)                      ! "r" vector for tridiagonal solution
-    real(r8) :: d_p1_zp1(bounds%begc:bounds%endc,1:nlevdecomp+1)                   ! diffusivity/delta_z for next j  (set to zero for no diffusion)
-    real(r8) :: d_m1_zm1(bounds%begc:bounds%endc,1:nlevdecomp+1)                   ! diffusivity/delta_z for previous j (set to zero for no diffusion)
-    real(r8) :: f_p1(bounds%begc:bounds%endc,1:nlevdecomp+1)                       ! water flux for next j
-    real(r8) :: f_m1(bounds%begc:bounds%endc,1:nlevdecomp+1)                       ! water flux for previous j
-    real(r8) :: pe_p1(bounds%begc:bounds%endc,1:nlevdecomp+1)                      ! Peclet # for next j
-    real(r8) :: pe_m1(bounds%begc:bounds%endc,1:nlevdecomp+1)                      ! Peclet # for previous j
-    real(r8) :: dz_node(1:nlevdecomp+1)                                            ! difference between nodes
-    real(r8) :: epsilon_t (bounds%begc:bounds%endc,1:nlevdecomp+1,1:ndecomp_pools) !
-    real(r8) :: conc_trcr(bounds%begc:bounds%endc,0:nlevdecomp+1)                  !
-    real(r8) :: a_p_0
-    real(r8) :: deficit
-    integer  :: ntype
-    integer  :: i_type,s,fc,c,j,l                                                  ! indices
-    integer  :: jtop(bounds%begc:bounds%endc)                                      ! top level at each column
-    real(r8) :: dtime                                                              ! land model time step (sec)
-    integer  :: zerolev_diffus
-    real(r8) :: spinup_term                                                        ! spinup accelerated decomposition factor, used to accelerate transport as well
-    real(r8) :: epsilon                                                            ! small number
-    real(r8), pointer :: conc_ptr(:,:,:)                                           ! pointer, concentration state variable being transported
-    real(r8), pointer :: source(:,:,:)                                             ! pointer, source term
-    real(r8), pointer :: trcr_tendency_ptr(:,:,:)                                  ! poiner, store the vertical tendency (gain/loss due to vertical transport)
-    !-----------------------------------------------------------------------
-
-    ! Set statement functions
-    aaa (pe) = max (0._r8, (1._r8 - 0.1_r8 * abs(pe))**5)  ! A function from Patankar, Table 5.2, pg 95
-  
-    associate(                                                             &
-         is_cwd           => decomp_cascade_con%is_cwd                  ,  & ! Input:  [logical (:)    ]  TRUE => pool is a cwd pool                                
-         spinup_factor    => decomp_cascade_con%spinup_factor           ,  & ! Input:  [real(r8) (:)   ]  spinup accelerated decomposition factor, used to accelerate transport as well
-
-         altmax           => canopystate_inst%altmax_col                ,  & ! Input:  [real(r8) (:)   ]  maximum annual depth of thaw                             
-         altmax_lastyear  => canopystate_inst%altmax_lastyear_col       ,  & ! Input:  [real(r8) (:)   ]  prior year maximum annual depth of thaw                  
-
-         som_adv_coef     => soilbiogeochem_state_inst%som_adv_coef_col ,  & ! Output: [real(r8) (:,:) ]  SOM advective flux (m/s)                               
-         som_diffus_coef  => soilbiogeochem_state_inst%som_diffus_coef_col & ! Output: [real(r8) (:,:) ]  SOM diffusivity due to bio/cryo-turbation (m2/s)       
-         )
-
-      !Set parameters of vertical mixing of SOM
-      som_diffus                 = params_inst%som_diffus 
-      cryoturb_diffusion_k       = params_inst%cryoturb_diffusion_k 
-      max_altdepth_cryoturbation = params_inst%max_altdepth_cryoturbation 
-
-      dtime = get_step_size()
-
-      ntype = 2
-      if ( use_fates ) then
-         ntype = 1
-      endif
-      spinup_term = 1._r8
-      epsilon = 1.e-30
-
-      if (use_vertsoilc) then
-         !------ first get diffusivity / advection terms -------!
-         ! use different mixing rates for bioturbation and cryoturbation, with fixed bioturbation and cryoturbation set to a maximum depth
-         do fc = 1, num_soilc
-            c = filter_soilc (fc)
-            if  (( max(altmax(c), altmax_lastyear(c)) <= max_altdepth_cryoturbation ) .and. &
-                 ( max(altmax(c), altmax_lastyear(c)) > 0._r8) ) then
-               ! use mixing profile modified slightly from Koven et al. (2009): constant through active layer, linear decrease from base of active layer to zero at a fixed depth
-               do j = 1,nlevdecomp+1
-                  if ( j <= col%nbedrock(c)+1 ) then
-                     if ( zisoi(j) < max(altmax(c), altmax_lastyear(c)) ) then
-                        som_diffus_coef(c,j) = cryoturb_diffusion_k 
-                        som_adv_coef(c,j) = 0._r8
-                     else
-                        som_diffus_coef(c,j) = max(cryoturb_diffusion_k * & 
-                          ( 1._r8 - ( zisoi(j) - max(altmax(c), altmax_lastyear(c)) ) / &
-                          ( min(max_depth_cryoturb, zisoi(col%nbedrock(c)+1)) - max(altmax(c), altmax_lastyear(c)) ) ), 0._r8)  ! go linearly to zero between ALT and max_depth_cryoturb
-                        som_adv_coef(c,j) = 0._r8
-                     endif
-                  else
-                     som_adv_coef(c,j) = 0._r8
-                     som_diffus_coef(c,j) = 0._r8
-                  endif
-               end do
-            elseif (  max(altmax(c), altmax_lastyear(c)) > 0._r8 ) then
-               ! constant advection, constant diffusion
-               do j = 1,nlevdecomp+1
-                  if ( j <= col%nbedrock(c)+1 ) then
-                     som_adv_coef(c,j) = som_adv_flux 
-                     som_diffus_coef(c,j) = som_diffus
-                  else
-                     som_adv_coef(c,j) = 0._r8
-                     som_diffus_coef(c,j) = 0._r8
-                  endif
-               end do
-            else
-               ! completely frozen soils--no mixing
-               do j = 1,nlevdecomp+1
-                  som_adv_coef(c,j) = 0._r8
-                  som_diffus_coef(c,j) = 0._r8
-               end do
-            endif
-         end do
-
-         ! Set the distance between the node and the one ABOVE it   
-         dz_node(1) = zsoi(1)
-         do j = 2,nlevdecomp+1
-            dz_node(j)= zsoi(j) - zsoi(j-1)
-         enddo
-
-      endif
-
-      !------ loop over litter/som types
-      do i_type = 1, ntype
-
-         select case (i_type)
-         case (1)  ! C
-            conc_ptr          => soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col
-            source            => soilbiogeochem_carbonflux_inst%decomp_cpools_sourcesink_col
-            trcr_tendency_ptr => soilbiogeochem_carbonflux_inst%decomp_cpools_transport_tendency_col
-         case (2)  ! N
-            if (use_cn ) then
-               conc_ptr          => soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col
-               source            => soilbiogeochem_nitrogenflux_inst%decomp_npools_sourcesink_col
-               trcr_tendency_ptr => soilbiogeochem_nitrogenflux_inst%decomp_npools_transport_tendency_col
-            endif
-         case (3)
-            write(iulog,*) 'error.  ncase = 4, but c13 and c14 not both enabled.'
-            call endrun(msg=errMsg(sourcefile, __LINE__))
-         case (4)
-            write(iulog,*) 'error.  ncase = 4, but c13 and c14 not both enabled.'
-            call endrun(msg=errMsg(sourcefile, __LINE__))
-         end select
-
-         if (use_vertsoilc) then
-
-            do s = 1, ndecomp_pools
-
-               if ( .not. is_cwd(s) ) then
-
-                  do j = 1,nlevdecomp+1
-                     do fc = 1, num_soilc
-                        c = filter_soilc (fc)
-                        !
-                        if ( spinup_state >= 1 ) then
-                           ! increase transport (both advection and diffusion) by the same factor as accelerated decomposition for a given pool
-                           spinup_term = spinup_factor(s)
-                        else
-                           spinup_term = 1._r8
-                        endif
-
-                        if (abs(spinup_term - 1._r8) > .000001_r8 ) then
-                           spinup_term = spinup_term * get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
-                        endif
-
-                        if ( abs(som_adv_coef(c,j)) * spinup_term < epsilon ) then
-                           adv_flux(c,j) = epsilon
-                        else
-                           adv_flux(c,j) = som_adv_coef(c,j) * spinup_term
-                        endif
-                        !
-                        if ( abs(som_diffus_coef(c,j)) * spinup_term < epsilon ) then
-                           diffus(c,j) = epsilon
-                        else
-                           diffus(c,j) = som_diffus_coef(c,j) * spinup_term
-                        endif
-                        !
-                     end do
-                  end do
-
-                  ! Set Pe (Peclet #) and D/dz throughout column
-
-                  do fc = 1, num_soilc ! dummy terms here
-                     c = filter_soilc (fc)
-                     conc_trcr(c,0) = 0._r8
-                     conc_trcr(c,col%nbedrock(c)+1:nlevdecomp+1) = 0._r8
-                  end do
-
-
-                  do j = 1,nlevdecomp+1
-                     do fc = 1, num_soilc
-                        c = filter_soilc (fc)
-
-                        conc_trcr(c,j) = conc_ptr(c,j,s)
-                  
-                        ! dz_tracer below is the difference between gridcell edges  (dzsoi_decomp)
-                        ! dz_node_tracer is difference between cell centers 
-
-                        ! Calculate the D and F terms in the Patankar algorithm
-                        if (j == 1) then
-                           d_m1_zm1(c,j) = 0._r8
-                           w_p1 = (zsoi(j+1) - zisoi(j)) / dz_node(j+1)
-                           if ( diffus(c,j+1) > 0._r8 .and. diffus(c,j) > 0._r8) then
-                              d_p1 = 1._r8 / ((1._r8 - w_p1) / diffus(c,j) + w_p1 / diffus(c,j+1)) ! Harmonic mean of diffus
-                           else
-                              d_p1 = 0._r8
-                           endif
-                           d_p1_zp1(c,j) = d_p1 / dz_node(j+1)
-                           f_m1(c,j) = adv_flux(c,j)  ! Include infiltration here
-                           f_p1(c,j) = adv_flux(c,j+1)
-                           pe_m1(c,j) = 0._r8
-                           pe_p1(c,j) = f_p1(c,j) / d_p1_zp1(c,j) ! Peclet #
-                        elseif (j >= col%nbedrock(c)+1) then
-                           ! At the bottom, assume no gradient in d_z (i.e., they're the same)
-                           w_m1 = (zisoi(j-1) - zsoi(j-1)) / dz_node(j)
-                           if ( diffus(c,j) > 0._r8 .and. diffus(c,j-1) > 0._r8) then
-                              d_m1 = 1._r8 / ((1._r8 - w_m1) / diffus(c,j) + w_m1 / diffus(c,j-1)) ! Harmonic mean of diffus
-                           else
-                              d_m1 = 0._r8
-                           endif
-                           d_m1_zm1(c,j) = d_m1 / dz_node(j)
-                           d_p1_zp1(c,j) = d_m1_zm1(c,j) ! Set to be the same
-                           f_m1(c,j) = adv_flux(c,j)
-                           !f_p1(c,j) = adv_flux(c,j+1)
-                           f_p1(c,j) = 0._r8
-                           pe_m1(c,j) = f_m1(c,j) / d_m1_zm1(c,j) ! Peclet #
-                           pe_p1(c,j) = f_p1(c,j) / d_p1_zp1(c,j) ! Peclet #
-                        else
-                           ! Use distance from j-1 node to interface with j divided by distance between nodes
-                           w_m1 = (zisoi(j-1) - zsoi(j-1)) / dz_node(j)
-                           if ( diffus(c,j-1) > 0._r8 .and. diffus(c,j) > 0._r8) then
-                              d_m1 = 1._r8 / ((1._r8 - w_m1) / diffus(c,j) + w_m1 / diffus(c,j-1)) ! Harmonic mean of diffus
-                           else
-                              d_m1 = 0._r8
-                           endif
-                           w_p1 = (zsoi(j+1) - zisoi(j)) / dz_node(j+1)
-                           if ( diffus(c,j+1) > 0._r8 .and. diffus(c,j) > 0._r8) then
-                              d_p1 = 1._r8 / ((1._r8 - w_p1) / diffus(c,j) + w_p1 / diffus(c,j+1)) ! Harmonic mean of diffus
-                           else
-                              d_p1 = (1._r8 - w_m1) * diffus(c,j) + w_p1 * diffus(c,j+1) ! Arithmetic mean of diffus
-                           endif
-                           d_m1_zm1(c,j) = d_m1 / dz_node(j)
-                           d_p1_zp1(c,j) = d_p1 / dz_node(j+1)
-                           f_m1(c,j) = adv_flux(c,j)
-                           f_p1(c,j) = adv_flux(c,j+1)
-                           pe_m1(c,j) = f_m1(c,j) / d_m1_zm1(c,j) ! Peclet #
-                           pe_p1(c,j) = f_p1(c,j) / d_p1_zp1(c,j) ! Peclet #
-                        end if
-                     enddo ! fc
-                  enddo ! j; nlevdecomp
-
-
-                  ! Calculate the tridiagonal coefficients
-                  do j = 0,nlevdecomp +1
-                     do fc = 1, num_soilc
-                        c = filter_soilc (fc)
-                        ! g = cgridcell(c)
-
-                        if (j > 0 .and. j < nlevdecomp+1) then
-                           a_p_0 =  dzsoi_decomp(j) / dtime
-                        endif
-
-                        if (j == 0) then ! top layer (atmosphere)
-                           a_tri(c,j) = 0._r8
-                           b_tri(c,j) = 1._r8
-                           c_tri(c,j) = -1._r8
-                           r_tri(c,j) = 0._r8
-                        elseif (j == 1) then
-                           a_tri(c,j) = -(d_m1_zm1(c,j) * aaa(pe_m1(c,j)) + max( f_m1(c,j), 0._r8)) ! Eqn 5.47 Patankar
-                           c_tri(c,j) = -(d_p1_zp1(c,j) * aaa(pe_p1(c,j)) + max(-f_p1(c,j), 0._r8))
-                           b_tri(c,j) = -a_tri(c,j) - c_tri(c,j) + a_p_0
-                           r_tri(c,j) = source(c,j,s) * dzsoi_decomp(j) /dtime + (a_p_0 - adv_flux(c,j)) * conc_trcr(c,j) 
-                        elseif (j < nlevdecomp+1) then
-                           a_tri(c,j) = -(d_m1_zm1(c,j) * aaa(pe_m1(c,j)) + max( f_m1(c,j), 0._r8)) ! Eqn 5.47 Patankar
-                           c_tri(c,j) = -(d_p1_zp1(c,j) * aaa(pe_p1(c,j)) + max(-f_p1(c,j), 0._r8))
-                           b_tri(c,j) = -a_tri(c,j) - c_tri(c,j) + a_p_0
-                           r_tri(c,j) = source(c,j,s) * dzsoi_decomp(j) /dtime + a_p_0 * conc_trcr(c,j)
-                        else ! j==nlevdecomp+1; 0 concentration gradient at bottom
-                           a_tri(c,j) = -1._r8
-                           b_tri(c,j) = 1._r8
-                           c_tri(c,j) = 0._r8 
-                           r_tri(c,j) = 0._r8
-                        endif
-                     enddo ! fc; column
-                  enddo ! j; nlevdecomp
-
-                  do fc = 1, num_soilc
-                     c = filter_soilc (fc)
-                     jtop(c) = 0
-                  enddo
-
-                  ! subtract initial concentration and source terms for tendency calculation
-                  do fc = 1, num_soilc
-                     c = filter_soilc (fc)
-                     do j = 1, nlevdecomp
-                        trcr_tendency_ptr(c,j,s) = 0.-(conc_trcr(c,j) + source(c,j,s))
-                     end do
-                  end do
-
-                  ! Solve for the concentration profile for this time step
-                  call Tridiagonal(bounds, 0, nlevdecomp+1, &
-                       jtop(bounds%begc:bounds%endc), &
-                       num_soilc, filter_soilc, &
-                       a_tri(bounds%begc:bounds%endc, :), &
-                       b_tri(bounds%begc:bounds%endc, :), &
-                       c_tri(bounds%begc:bounds%endc, :), &
-                       r_tri(bounds%begc:bounds%endc, :), &
-                       conc_trcr(bounds%begc:bounds%endc,0:nlevdecomp+1))
-
-                  ! add post-transport concentration to calculate tendency term
-                  do fc = 1, num_soilc
-                     c = filter_soilc (fc)
-                     do j = 1, nlevdecomp
-                        trcr_tendency_ptr(c,j,s) = trcr_tendency_ptr(c,j,s) + conc_trcr(c,j)
-                        trcr_tendency_ptr(c,j,s) = trcr_tendency_ptr(c,j,s) / dtime
-                     end do
-                  end do
-
-               else
-                  ! for CWD pools, just add
-                  do j = 1,nlevdecomp
-                     do fc = 1, num_soilc
-                        c = filter_soilc (fc)
-                        conc_trcr(c,j) = conc_ptr(c,j,s) + source(c,j,s)
-                        if (j > col%nbedrock(c) .and. source(c,j,s) > 0._r8) then 
-                           write(iulog,*) 'source >0',c,j,s,source(c,j,s)
-                        end if
-                        if (j > col%nbedrock(c) .and. conc_ptr(c,j,s) > 0._r8) then
-                           write(iulog,*) 'conc_ptr >0',c,j,s,conc_ptr(c,j,s)
-                        end if
-
-                     end do
-                  end do
-
-               end if ! not CWD
-
-               do j = 1,nlevdecomp
-                  do fc = 1, num_soilc
-                     c = filter_soilc (fc)
-                     conc_ptr(c,j,s) = conc_trcr(c,j) 
-                     ! Correct for small amounts of carbon that leak into bedrock
-                     if (j > col%nbedrock(c)) then 
-                        conc_ptr(c,col%nbedrock(c),s) = conc_ptr(c,col%nbedrock(c),s) + &
-                           conc_trcr(c,j) * (dzsoi_decomp(j) / dzsoi_decomp(col%nbedrock(c)))
-                        conc_ptr(c,j,s) = 0._r8
-                     end if
-                  end do
-               end do
-
-            end do ! s (pool loop)
-
-         else
-
-            !! for single level case, no transport; just update the fluxes calculated in the StateUpdate1 subroutines
-            do l = 1, ndecomp_pools
-               do j = 1,nlevdecomp
-                  do fc = 1, num_soilc
-                     c = filter_soilc (fc)
-
-                     conc_ptr(c,j,l) = conc_ptr(c,j,l) + source(c,j,l)
-
-                     trcr_tendency_ptr(c,j,l) = 0._r8
-
-                  end do
-               end do
-            end do
-
-         endif
-
-      end do  ! i_type
-   
-    end associate
-
-  end subroutine SoilBiogeochemLittVertTransp
- 
-end module SoilBiogeochemLittVertTranspMod
diff --git a/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90 b/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90
deleted file mode 100644
index 3a0cb0c91b..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90
+++ /dev/null
@@ -1,289 +0,0 @@
-module SoilBiogeochemNLeachingMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Module for mineral nitrogen dynamics (deposition, fixation, leaching)
-  ! for coupled carbon-nitrogen code.
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use decompMod                       , only : bounds_type
-  use clm_varcon                      , only : dzsoi_decomp, zisoi
-  use clm_varctl                      , only : use_nitrif_denitrif, use_vertsoilc
-  use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemNitrogenFluxType  , only : soilbiogeochem_nitrogenflux_type
-  use WaterStateType                  , only : waterstate_type
-  use WaterFluxType                   , only : waterflux_type
-  use ColumnType                      , only : col                
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams
-  public :: SoilBiogeochemNLeaching
-  !
-  ! !PRIVATE DATA:
-  type, private :: params_type
-     real(r8):: sf        ! soluble fraction of mineral N (unitless)
-     real(r8):: sf_no3    ! soluble fraction of NO3 (unitless)
-  end type params_type
-  
-  type(params_type), private ::  params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    ! Read in parameters
-    !
-    ! !USES:
-    use ncdio_pio   , only : file_desc_t,ncd_io
-    use abortutils  , only : endrun
-    use shr_log_mod , only : errMsg => shr_log_errMsg
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNNDynamicsParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-    
-    tString='sf_minn'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%sf=tempr
-
-    tString='sf_no3'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%sf_no3=tempr
-   
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, &
-       waterstate_inst, waterflux_inst, &
-       soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    ! On the radiation time step, update the nitrogen leaching rate
-    ! as a function of soluble mineral N and total soil water outflow.
-    !
-    ! !USES:
-    use clm_varpar       , only : nlevdecomp, nlevsoi
-    use clm_time_manager , only : get_step_size
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                       , intent(in)    :: bounds  
-    integer                                 , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(waterstate_type)                   , intent(in)    :: waterstate_inst
-    type(waterflux_type)                    , intent(in)    :: waterflux_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(in)    :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst 
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: j,c,fc                                 ! indices
-    real(r8) :: dt                                     ! radiation time step (seconds)
-    real(r8) :: sf                                     ! soluble fraction of mineral N (unitless)
-    real(r8) :: sf_no3                                 ! soluble fraction of NO3 (unitless)
-    real(r8) :: disn_conc                              ! dissolved mineral N concentration (gN/kg water)
-    real(r8) :: tot_water(bounds%begc:bounds%endc)     ! total column liquid water (kg water/m2)
-    real(r8) :: surface_water(bounds%begc:bounds%endc) ! liquid water to shallow surface depth (kg water/m2)
-    real(r8) :: drain_tot(bounds%begc:bounds%endc)     ! total drainage flux (mm H2O /s)
-    real(r8), parameter :: depth_runoff_Nloss = 0.05   ! (m) depth over which runoff mixes with soil water for N loss to runoff
-    !-----------------------------------------------------------------------
-
-    associate(                                                                             & 
-         h2osoi_liq          => waterstate_inst%h2osoi_liq_col                           , & ! Input:  [real(r8) (:,:) ]  liquid water (kg/m2) (new) (-nlevsno+1:nlevgrnd)
-
-         qflx_drain          => waterflux_inst%qflx_drain_col                            , & ! Input:  [real(r8) (:)   ]  sub-surface runoff (mm H2O /s)                    
-         qflx_surf           => waterflux_inst%qflx_surf_col                             , & ! Input:  [real(r8) (:)   ]  surface runoff (mm H2O /s)                        
-         
-         sminn_vr            => soilbiogeochem_nitrogenstate_inst%sminn_vr_col           , & ! Input:  [real(r8) (:,:) ]  (gN/m3) soil mineral N                          
-         smin_no3_vr         => soilbiogeochem_nitrogenstate_inst%smin_no3_vr_col        , & ! Input:  [real(r8) (:,:) ]                                                  
-
-         sminn_leached_vr    => soilbiogeochem_nitrogenflux_inst%sminn_leached_vr_col    , & ! Output: [real(r8) (:,:) ]  rate of mineral N leaching (gN/m3/s)            
-         smin_no3_leached_vr => soilbiogeochem_nitrogenflux_inst%smin_no3_leached_vr_col , & ! Output: [real(r8) (:,:) ]  rate of mineral NO3 leaching (gN/m3/s)          
-         smin_no3_runoff_vr  => soilbiogeochem_nitrogenflux_inst%smin_no3_runoff_vr_col    & ! Output: [real(r8) (:,:) ]  rate of mineral NO3 loss with runoff (gN/m3/s)  
-         )
-
-      ! set time steps
-      dt = real( get_step_size(), r8 )
-
-      if (.not. use_nitrif_denitrif) then
-         ! set constant sf 
-         sf = params_inst%sf
-      else
-         ! Assume that 100% of the soil NO3 is in a soluble form
-         sf_no3 =  params_inst%sf_no3 
-      end if
-
-      ! calculate the total soil water
-      tot_water(bounds%begc:bounds%endc) = 0._r8
-      do j = 1,nlevsoi
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            tot_water(c) = tot_water(c) + h2osoi_liq(c,j)
-         end do
-      end do
-
-      ! for runoff calculation; calculate total water to a given depth
-      surface_water(bounds%begc:bounds%endc) = 0._r8
-      do j = 1,nlevsoi
-         if ( zisoi(j) <= depth_runoff_Nloss)  then
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               surface_water(c) = surface_water(c) + h2osoi_liq(c,j)
-            end do
-         elseif ( zisoi(j-1) < depth_runoff_Nloss)  then
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               surface_water(c) = surface_water(c) + h2osoi_liq(c,j) * ( (depth_runoff_Nloss - zisoi(j-1)) / col%dz(c,j))
-            end do
-         endif
-      end do
-
-      ! Loop through columns
-      do fc = 1,num_soilc
-         c = filter_soilc(fc)
-         drain_tot(c) = qflx_drain(c)
-      end do
-
-
-      if (.not. use_nitrif_denitrif) then
-
-         !----------------------------------------
-         ! --------- NITRIF_NITRIF OFF------------
-         !----------------------------------------
-
-         do j = 1,nlevdecomp
-            ! Loop through columns
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-
-               if (.not. use_vertsoilc) then
-                  ! calculate the dissolved mineral N concentration (gN/kg water)
-                  ! assumes that 10% of mineral nitrogen is soluble
-                  disn_conc = 0._r8
-                  if (tot_water(c) > 0._r8) then
-                     disn_conc = (sf * sminn_vr(c,j) ) / tot_water(c)
-                  end if
-
-                  ! calculate the N leaching flux as a function of the dissolved
-                  ! concentration and the sub-surface drainage flux
-                  sminn_leached_vr(c,j) = disn_conc * drain_tot(c)
-               else
-                  ! calculate the dissolved mineral N concentration (gN/kg water)
-                  ! assumes that 10% of mineral nitrogen is soluble
-                  disn_conc = 0._r8
-                  if (h2osoi_liq(c,j) > 0._r8) then
-                     disn_conc = (sf * sminn_vr(c,j) * col%dz(c,j) )/(h2osoi_liq(c,j) )
-                  end if
-
-                  ! calculate the N leaching flux as a function of the dissolved
-                  ! concentration and the sub-surface drainage flux
-                  sminn_leached_vr(c,j) = disn_conc * drain_tot(c) * h2osoi_liq(c,j) / ( tot_water(c) * col%dz(c,j) )
-
-               end if
-
-               ! limit the flux based on current sminn state
-               ! only let at most the assumed soluble fraction
-               ! of sminn be leached on any given timestep
-               sminn_leached_vr(c,j) = min(sminn_leached_vr(c,j), (sf * sminn_vr(c,j))/dt)
-
-               ! limit the flux to a positive value
-               sminn_leached_vr(c,j) = max(sminn_leached_vr(c,j), 0._r8)
-
-            end do
-         end do
-
-      else     
-
-         !----------------------------------------
-         ! --------- NITRIF_NITRIF ON-------------
-         !----------------------------------------
-
-         do j = 1,nlevdecomp
-            ! Loop through columns
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-
-               if (.not. use_vertsoilc) then
-                  ! calculate the dissolved mineral N concentration (gN/kg water)
-                  ! assumes that 10% of mineral nitrogen is soluble
-                  disn_conc = 0._r8
-                  if (tot_water(c) > 0._r8) then
-                     disn_conc = (sf_no3 * smin_no3_vr(c,j) )/tot_water(c)
-                  end if
-
-                  ! calculate the N leaching flux as a function of the dissolved
-                  ! concentration and the sub-surface drainage flux
-                  smin_no3_leached_vr(c,j) = disn_conc * drain_tot(c)
-               else
-                  ! calculate the dissolved mineral N concentration (gN/kg water)
-                  ! assumes that 10% of mineral nitrogen is soluble
-                  disn_conc = 0._r8
-                  if (h2osoi_liq(c,j) > 0._r8) then
-                     disn_conc = (sf_no3 * smin_no3_vr(c,j) * col%dz(c,j) )/(h2osoi_liq(c,j) )
-                  end if
-                  !
-                  ! calculate the N leaching flux as a function of the dissolved
-                  ! concentration and the sub-surface drainage flux
-                  smin_no3_leached_vr(c,j) = disn_conc * drain_tot(c) * h2osoi_liq(c,j) / ( tot_water(c) * col%dz(c,j) )
-                  !
-                  ! ensure that leaching rate isn't larger than soil N pool
-                  smin_no3_leached_vr(c,j) = min(smin_no3_leached_vr(c,j), smin_no3_vr(c,j) / dt )
-                  !
-                  ! limit the leaching flux to a positive value
-                  smin_no3_leached_vr(c,j) = max(smin_no3_leached_vr(c,j), 0._r8)
-                  !
-                  !
-                  ! calculate the N loss from surface runoff, assuming a shallow mixing of surface waters into soil and removal based on runoff
-                  if ( zisoi(j) <= depth_runoff_Nloss )  then
-                     smin_no3_runoff_vr(c,j) = disn_conc * qflx_surf(c) * &
-                          h2osoi_liq(c,j) / ( surface_water(c) * col%dz(c,j) )
-                  elseif ( zisoi(j-1) < depth_runoff_Nloss )  then
-                     smin_no3_runoff_vr(c,j) = disn_conc * qflx_surf(c) * &
-                          h2osoi_liq(c,j) * ((depth_runoff_Nloss - zisoi(j-1)) / &
-                          col%dz(c,j)) / ( surface_water(c) * (depth_runoff_Nloss-zisoi(j-1) ))
-                  else
-                     smin_no3_runoff_vr(c,j) = 0._r8
-                  endif
-                  !
-                  ! ensure that runoff rate isn't larger than soil N pool
-                  smin_no3_runoff_vr(c,j) = min(smin_no3_runoff_vr(c,j), smin_no3_vr(c,j) / dt - smin_no3_leached_vr(c,j))
-                  !
-                  ! limit the flux to a positive value
-                  smin_no3_runoff_vr(c,j) = max(smin_no3_runoff_vr(c,j), 0._r8)
-
-
-               endif
-               ! limit the flux based on current smin_no3 state
-               ! only let at most the assumed soluble fraction
-               ! of smin_no3 be leached on any given timestep
-               smin_no3_leached_vr(c,j) = min(smin_no3_leached_vr(c,j), (sf_no3 * smin_no3_vr(c,j))/dt)
-
-               ! limit the flux to a positive value
-               smin_no3_leached_vr(c,j) = max(smin_no3_leached_vr(c,j), 0._r8)
-
-            end do
-         end do
-      endif
-
-    end associate
-
-  end subroutine SoilBiogeochemNLeaching
-
-end module SoilBiogeochemNLeachingMod
diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90
deleted file mode 100644
index 08bbac9241..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90
+++ /dev/null
@@ -1,337 +0,0 @@
-module SoilBiogeochemNitrifDenitrifMod
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculate nitrification and denitrification rates
-  !
-  !
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use shr_const_mod                   , only : SHR_CONST_TKFRZ
-  use shr_log_mod                     , only : errMsg => shr_log_errMsg
-  use clm_varpar                      , only : nlevdecomp
-  use clm_varcon                      , only : rpi, grav
-  use clm_varcon                      , only : d_con_g, d_con_w, secspday
-  use abortutils                      , only : endrun
-  use decompMod                       , only : bounds_type
-  use SoilStatetype                   , only : soilstate_type
-  use WaterStateType                  , only : waterstate_type
-  use TemperatureType                 , only : temperature_type
-  use SoilBiogeochemCarbonFluxType    , only : soilbiogeochem_carbonflux_type
-  use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemNitrogenFluxType  , only : soilbiogeochem_nitrogenflux_type
-  use ch4Mod                          , only : ch4_type
-  use ColumnType                      , only : col                
-  !
-  implicit none
-  private
-  !
-  public :: readParams                      ! Read in parameters from params file
-  public :: SoilBiogeochemNitrifDenitrif    ! Calculate nitrification and 
-  !
-  type, private :: params_type
-     real(r8) :: k_nitr_max            ! maximum nitrification rate constant (1/s)
-     real(r8) :: surface_tension_water ! surface tension of water(J/m^2), Arah an and Vinten 1995
-     real(r8) :: rij_kro_a             ! Arah and Vinten 1995)
-     real(r8) :: rij_kro_alpha         ! parameter to calculate anoxic fraction of soil  (Arah and Vinten 1995)
-     real(r8) :: rij_kro_beta          ! (Arah and Vinten 1995)
-     real(r8) :: rij_kro_gamma         ! (Arah and Vinten 1995)
-     real(r8) :: rij_kro_delta         ! (Arah and Vinten 1995)
-     real(r8) :: denitrif_respiration_coefficient ! Multiplier for heterotrophic respiration for max denitrif rates
-     real(r8) :: denitrif_respiration_exponent    ! Exponents for heterotrophic respiration for max denitrif rates
-     real(r8) :: denitrif_nitrateconc_coefficient ! Multiplier for nitrate concentration for max denitrif rates
-     real(r8) :: denitrif_nitrateconc_exponent    ! Exponent for nitrate concentration for max denitrif rates
-  end type params_type
-
-  type(params_type), private :: params_inst
-
-  logical, public :: no_frozen_nitrif_denitrif = .false.  ! stop nitrification and denitrification in frozen soils
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------  
-  subroutine readParams ( ncid )
-    !
-    use ncdio_pio, only: file_desc_t,ncd_io
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNNitrifDenitrifParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-    !
-    ! read in constants
-    !
-    tString='surface_tension_water'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%surface_tension_water=tempr
-
-    tString='rij_kro_a'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rij_kro_a=tempr
-
-    tString='rij_kro_alpha'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rij_kro_alpha=tempr
-
-    tString='rij_kro_beta'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rij_kro_beta=tempr
-
-    tString='rij_kro_gamma'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rij_kro_gamma=tempr
-
-    tString='rij_kro_delta'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%rij_kro_delta=tempr
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, &
-       soilstate_inst, waterstate_inst, temperature_inst, ch4_inst, &
-       soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
-    !
-    ! !DESCRIPTION:
-    !  calculate nitrification and denitrification rates
-    !
-    ! !USES:
-    use clm_time_manager  , only : get_curr_date, get_step_size
-    use CNSharedParamsMod , only : anoxia_wtsat, CNParamsShareInst
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)                       , intent(in)    :: bounds  
-    integer                                 , intent(in)    :: num_soilc         ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:)   ! filter for soil columns
-    type(soilstate_type)                    , intent(in)    :: soilstate_inst
-    type(waterstate_type)                   , intent(in)    :: waterstate_inst
-    type(temperature_type)                  , intent(in)    :: temperature_inst
-    type(ch4_type)                          , intent(in)    :: ch4_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(in)    :: soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(in)    :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer  :: c, fc, reflev, j
-    real(r8) :: soil_hr_vr(bounds%begc:bounds%endc,1:nlevdecomp) ! total soil respiration rate (g C / m3 / s)
-    real(r8) :: g_per_m3__to__ug_per_gsoil
-    real(r8) :: g_per_m3_sec__to__ug_per_gsoil_day
-    real(r8) :: mu, sigma
-    real(r8) :: t
-    real(r8) :: pH(bounds%begc:bounds%endc)
-    !debug-- put these type structure for outing to hist files
-    real(r8) :: co2diff_con(2)                      ! diffusion constants for CO2
-    real(r8) :: eps
-    real(r8) :: f_a
-    real(r8) :: surface_tension_water ! (J/m^2), Arah and Vinten 1995
-    real(r8) :: rij_kro_a             !  Arah and Vinten 1995
-    real(r8) :: rij_kro_alpha         !  Arah and Vinten 1995
-    real(r8) :: rij_kro_beta          !  Arah and Vinten 1995
-    real(r8) :: rij_kro_gamma         !  Arah and Vinten 1995
-    real(r8) :: rij_kro_delta         !  Arah and Vinten 1995
-    real(r8) :: rho_w  = 1.e3_r8                   ! (kg/m3)
-    real(r8) :: r_max
-    real(r8) :: r_min(bounds%begc:bounds%endc,1:nlevdecomp)
-    real(r8) :: ratio_diffusivity_water_gas(bounds%begc:bounds%endc,1:nlevdecomp)
-    real(r8) :: om_frac
-    real(r8) :: anaerobic_frac_sat, r_psi_sat, r_min_sat ! scalar values in sat portion for averaging
-    real(r8) :: organic_max              ! organic matter content (kg/m3) where
-                                         ! soil is assumed to act like peat
-    character(len=32) :: subname='nitrif_denitrif' ! subroutine name
-    !-----------------------------------------------------------------------
-
-    associate(                                                                                                    & 
-         watsat                        =>    soilstate_inst%watsat_col                                          , & ! Input:  [real(r8) (:,:)  ]  volumetric soil water at saturation (porosity) (nlevgrnd)
-         watfc                         =>    soilstate_inst%watfc_col                                           , & ! Input:  [real(r8) (:,:)  ]  volumetric soil water at field capacity (nlevsoi)
-         bd                            =>    soilstate_inst%bd_col                                              , & ! Input:  [real(r8) (:,:)  ]  bulk density of dry soil material [kg/m3]       
-         bsw                           =>    soilstate_inst%bsw_col                                             , & ! Input:  [real(r8) (:,:)  ]  Clapp and Hornberger "b" (nlevgrnd)             
-         cellorg                       =>    soilstate_inst%cellorg_col                                         , & ! Input:  [real(r8) (:,:)  ]  column 3D org (kg/m3 organic matter) (nlevgrnd) 
-         sucsat                        =>    soilstate_inst%sucsat_col                                          , & ! Input:  [real(r8) (:,:)  ]  minimum soil suction (mm)                       
-         soilpsi                       =>    soilstate_inst%soilpsi_col                                         , & ! Input:  [real(r8) (:,:)  ]  soil water potential in each soil layer (MPa)   
-         
-         h2osoi_vol                    =>    waterstate_inst%h2osoi_vol_col                                     , & ! Input:  [real(r8) (:,:)  ]  volumetric soil water (0<=h2osoi_vol<=watsat) [m3/m3]  (nlevgrnd)
-         h2osoi_liq                    =>    waterstate_inst%h2osoi_liq_col                                     , & ! Input:  [real(r8) (:,:)  ]  liquid water (kg/m2) (new) (-nlevsno+1:nlevgrnd)
-         
-         t_soisno                      =>    temperature_inst%t_soisno_col                                      , & ! Input:  [real(r8) (:,:)  ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
-         
-         o2_decomp_depth_unsat         =>    ch4_inst%o2_decomp_depth_unsat_col                                 , & ! Input:  [real(r8) (:,:)  ]  O2 consumption during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-         conc_o2_unsat                 =>    ch4_inst%conc_o2_unsat_col                                         , & ! Input:  [real(r8) (:,:)  ]  O2 conc in each soil layer (mol/m3) (nlevsoi)   
-         o2_decomp_depth_sat           =>    ch4_inst%o2_decomp_depth_sat_col                                   , & ! Input:  [real(r8) (:,:)  ]  O2 consumption during decomposition in each soil layer (nlevsoi) (mol/m3/s)
-         conc_o2_sat                   =>    ch4_inst%conc_o2_sat_col                                           , & ! Input:  [real(r8) (:,:)  ]  O2 conc in each soil layer (mol/m3) (nlevsoi)   
-         finundated                    =>    ch4_inst%finundated_col                                            , & ! Input:  [real(r8) (:)    ]  fractional inundated area in soil column (excluding dedicated wetland columns)
-
-         smin_nh4_vr                   =>    soilbiogeochem_nitrogenstate_inst%smin_nh4_vr_col                  , & ! Input:  [real(r8) (:,:)  ]  (gN/m3) soil mineral NH4 pool                   
-         smin_no3_vr                   =>    soilbiogeochem_nitrogenstate_inst%smin_no3_vr_col                  , & ! Input:  [real(r8) (:,:)  ]  (gN/m3) soil mineral NO3 pool                   
-
-         phr_vr                        =>    soilbiogeochem_carbonflux_inst%phr_vr_col                          , & ! Input:  [real(r8) (:,:)  ]  potential hr (not N-limited)                    
-         w_scalar                      =>    soilbiogeochem_carbonflux_inst%w_scalar_col                        , & ! Input:  [real(r8) (:,:)  ]  soil water scalar for decomp                    
-         t_scalar                      =>    soilbiogeochem_carbonflux_inst%t_scalar_col                        , & ! Input:  [real(r8) (:,:)  ]  temperature scalar for decomp                   
-         denit_resp_coef               =>    params_inst%denitrif_respiration_coefficient                       , & ! Input:  [real(r8)        ]  coefficient for max denitrification rate based on respiration
-         denit_resp_exp                =>    params_inst%denitrif_respiration_exponent                          , & ! Input:  [real(r8)        ] exponent for max denitrification rate based on respiration
-         denit_nitrate_coef            =>    params_inst%denitrif_nitrateconc_coefficient                       , & ! Input:  [real(r8)        ] coefficient for max denitrification rate based on nitrate concentration
-         denit_nitrate_exp             =>    params_inst%denitrif_nitrateconc_exponent                          , & ! Input:  [real(r8)        ] exponent for max denitrification rate based on nitrate concentration
-         k_nitr_max                    =>    params_inst%k_nitr_max                                             , & ! Input:
-
-         r_psi                         =>    soilbiogeochem_nitrogenflux_inst%r_psi_col                         , & ! Output:  [real(r8) (:,:)  ]                                                  
-         anaerobic_frac                =>    soilbiogeochem_nitrogenflux_inst%anaerobic_frac_col                , & ! Output:  [real(r8) (:,:)  ]                                                  
-         ! ! subsets of the n flux calcs (for diagnostic/debugging purposes)
-         smin_no3_massdens_vr          =>    soilbiogeochem_nitrogenflux_inst%smin_no3_massdens_vr_col          , & ! Output:  [real(r8) (:,:) ]  (ugN / g soil) soil nitrate concentration       
-         k_nitr_t_vr                   =>    soilbiogeochem_nitrogenflux_inst%k_nitr_t_vr_col                   , & ! Output:  [real(r8) (:,:) ]                                                  
-         k_nitr_ph_vr                  =>    soilbiogeochem_nitrogenflux_inst%k_nitr_ph_vr_col                  , & ! Output:  [real(r8) (:,:) ]                                                  
-         k_nitr_h2o_vr                 =>    soilbiogeochem_nitrogenflux_inst%k_nitr_h2o_vr_col                 , & ! Output:  [real(r8) (:,:) ]                                                  
-         k_nitr_vr                     =>    soilbiogeochem_nitrogenflux_inst%k_nitr_vr_col                     , & ! Output:  [real(r8) (:,:) ]                                                  
-         wfps_vr                       =>    soilbiogeochem_nitrogenflux_inst%wfps_vr_col                       , & ! Output:  [real(r8) (:,:) ]                                                  
-         fmax_denit_carbonsubstrate_vr =>    soilbiogeochem_nitrogenflux_inst%fmax_denit_carbonsubstrate_vr_col , & ! Output:  [real(r8) (:,:) ]                                                  
-         fmax_denit_nitrate_vr         =>    soilbiogeochem_nitrogenflux_inst%fmax_denit_nitrate_vr_col         , & ! Output:  [real(r8) (:,:) ]                                                  
-         f_denit_base_vr               =>    soilbiogeochem_nitrogenflux_inst%f_denit_base_vr_col               , & ! Output:  [real(r8) (:,:) ]                                                  
-         diffus                        =>    soilbiogeochem_nitrogenflux_inst%diffus_col                        , & ! Output:  [real(r8) (:,:) ] diffusivity (unitless fraction of total diffusivity)
-         ratio_k1                      =>    soilbiogeochem_nitrogenflux_inst%ratio_k1_col                      , & ! Output:  [real(r8) (:,:) ]                                                  
-         ratio_no3_co2                 =>    soilbiogeochem_nitrogenflux_inst%ratio_no3_co2_col                 , & ! Output:  [real(r8) (:,:) ]                                                  
-         soil_co2_prod                 =>    soilbiogeochem_nitrogenflux_inst%soil_co2_prod_col                 , & ! Output:  [real(r8) (:,:) ]  (ug C / g soil / day)                           
-         fr_WFPS                       =>    soilbiogeochem_nitrogenflux_inst%fr_WFPS_col                       , & ! Output:  [real(r8) (:,:) ]                                                  
-         soil_bulkdensity              =>    soilbiogeochem_nitrogenflux_inst%soil_bulkdensity_col              , & ! Output:  [real(r8) (:,:) ]  (kg soil / m3) bulk density of soil (including water)
-         pot_f_nit_vr                  =>    soilbiogeochem_nitrogenflux_inst%pot_f_nit_vr_col                  , & ! Output:  [real(r8) (:,:) ]  (gN/m3/s) potential soil nitrification flux     
-
-         pot_f_denit_vr                =>    soilbiogeochem_nitrogenflux_inst%pot_f_denit_vr_col                , & ! Output:  [real(r8) (:,:) ]  (gN/m3/s) potential soil denitrification flux   
-         n2_n2o_ratio_denit_vr         =>    soilbiogeochem_nitrogenflux_inst%n2_n2o_ratio_denit_vr_col           & ! Output:  [real(r8) (:,:) ]  ratio of N2 to N2O production by denitrification [gN/gN]
-         )
-
-      surface_tension_water = params_inst%surface_tension_water
-
-      ! Set parameters from simple-structure model to calculate anoxic fratction (Arah and Vinten 1995)
-      rij_kro_a     = params_inst%rij_kro_a
-      rij_kro_alpha = params_inst%rij_kro_alpha
-      rij_kro_beta  = params_inst%rij_kro_beta
-      rij_kro_gamma = params_inst%rij_kro_gamma
-      rij_kro_delta = params_inst%rij_kro_delta
-
-      organic_max = CNParamsShareInst%organic_max
-
-      pH(bounds%begc:bounds%endc) = 6.5  !!! set all soils with the same pH as placeholder here
-      co2diff_con(1) =   0.1325_r8
-      co2diff_con(2) =   0.0009_r8
-
-      do j = 1, nlevdecomp
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-
-            !---------------- calculate soil anoxia state
-            ! calculate gas diffusivity of soil at field capacity here
-            ! use expression from methane code, but neglect OM for now
-            f_a = 1._r8 - watfc(c,j) / watsat(c,j)
-            eps =  watsat(c,j)-watfc(c,j) ! Air-filled fraction of total soil volume
-
-            ! NITRIF_DENITRIF requires Methane model to be active, 
-            ! otherwise diffusivity will be zeroed out here. EBK CDK 10/18/2011
-            anaerobic_frac(c,j) = 0._r8
-            diffus (c,j) = 0._r8
-            !call endrun(msg=' ERROR: NITRIF_DENITRIF requires Methane model to be active'//errMsg(sourcefile, __LINE__) )
-
-
-            !---------------- nitrification
-            ! follows CENTURY nitrification scheme (Parton et al., (2001, 1996))
-
-            ! assume nitrification temp function equal to the HR scalar
-            k_nitr_t_vr(c,j) = min(t_scalar(c,j), 1._r8)
-
-            ! ph function from Parton et al., (2001, 1996)
-            k_nitr_ph_vr(c,j) = 0.56 + atan(rpi * 0.45 * (-5.+ pH(c)))/rpi
-
-            ! moisture function-- assume the same moisture function as limits heterotrophic respiration
-            ! Parton et al. base their nitrification- soil moisture rate constants based on heterotrophic rates-- can we do the same?
-            k_nitr_h2o_vr(c,j) = w_scalar(c,j)
-
-            ! nitrification constant is a set scalar * temp, moisture, and ph scalars
-            k_nitr_vr(c,j) = k_nitr_max * k_nitr_t_vr(c,j) * k_nitr_h2o_vr(c,j) * k_nitr_ph_vr(c,j)
-
-            ! first-order decay of ammonium pool with scalar defined above
-            pot_f_nit_vr(c,j) = max(smin_nh4_vr(c,j) * k_nitr_vr(c,j), 0._r8)
-
-            ! limit to oxic fraction of soils
-            pot_f_nit_vr(c,j)  = pot_f_nit_vr(c,j) * (1._r8 - anaerobic_frac(c,j))
-
-            ! limit to non-frozen soil layers
-            if ( t_soisno(c,j) <= SHR_CONST_TKFRZ .and. no_frozen_nitrif_denitrif) then
-               pot_f_nit_vr(c,j) = 0._r8
-            endif
-
-
-            !---------------- denitrification
-            ! first some input variables an unit conversions
-            soil_hr_vr(c,j) = phr_vr(c,j)
-
-            ! CENTURY papers give denitrification in units of per gram soil; need to convert from volumetric to mass-based units here
-            soil_bulkdensity(c,j) = bd(c,j) + h2osoi_liq(c,j)/col%dz(c,j)         
-
-            g_per_m3__to__ug_per_gsoil = 1.e3_r8 / soil_bulkdensity(c,j)
-
-            g_per_m3_sec__to__ug_per_gsoil_day = g_per_m3__to__ug_per_gsoil * secspday
-
-            smin_no3_massdens_vr(c,j) = max(smin_no3_vr(c,j), 0._r8) * g_per_m3__to__ug_per_gsoil
-
-            soil_co2_prod(c,j) = (soil_hr_vr(c,j) * (g_per_m3_sec__to__ug_per_gsoil_day))
-
-            !! maximum potential denitrification rates based on heterotrophic respiration rates or nitrate concentrations, 
-            !! from (del Grosso et al., 2000)
-            fmax_denit_carbonsubstrate_vr(c,j) = (denit_resp_coef * (soil_co2_prod(c,j)**denit_resp_exp)) &
-                 / g_per_m3_sec__to__ug_per_gsoil_day
-            !  
-            fmax_denit_nitrate_vr(c,j) = (denit_nitrate_coef * smin_no3_massdens_vr(c,j)**denit_nitrate_exp)  &
-                 / g_per_m3_sec__to__ug_per_gsoil_day
-
-            ! find limiting denitrification rate
-            f_denit_base_vr(c,j) = max(min(fmax_denit_carbonsubstrate_vr(c,j), fmax_denit_nitrate_vr(c,j)),0._r8) 
-
-            ! limit to non-frozen soil layers
-            if ( t_soisno(c,j) <= SHR_CONST_TKFRZ .and. no_frozen_nitrif_denitrif ) then
-               f_denit_base_vr(c,j) = 0._r8
-            endif
-
-            ! limit to anoxic fraction of soils
-            pot_f_denit_vr(c,j) = f_denit_base_vr(c,j) * anaerobic_frac(c,j)
-
-            ! now calculate the ratio of N2O to N2 from denitrifictaion, following Del Grosso et al., 2000
-            ! diffusivity constant (figure 6b)
-            ratio_k1(c,j) = max(1.7_r8, 38.4_r8 - 350._r8 * diffus(c,j))
-
-            ! ratio function (figure 7c)
-            if ( soil_co2_prod(c,j) > 0 ) then
-               ratio_no3_co2(c,j) = smin_no3_massdens_vr(c,j) / soil_co2_prod(c,j)
-            else
-               ! fucntion saturates at large no3/co2 ratios, so set as some nominally large number
-               ratio_no3_co2(c,j) = 100._r8
-            endif
-
-            ! total water limitation function (Del Grosso et al., 2000, figure 7a)
-            wfps_vr(c,j) = max(min(h2osoi_vol(c,j)/watsat(c, j), 1._r8), 0._r8) * 100._r8
-            fr_WFPS(c,j) = max(0.1_r8, 0.015_r8 * wfps_vr(c,j) - 0.32_r8)
-
-            ! final ratio expression 
-            n2_n2o_ratio_denit_vr(c,j) = max(0.16*ratio_k1(c,j), ratio_k1(c,j)*exp(-0.8 * ratio_no3_co2(c,j))) * fr_WFPS(c,j)
-
-         end do
-
-      end do
-
-    end associate
-
-  end subroutine SoilBiogeochemNitrifDenitrif
-
-end module SoilBiogeochemNitrifDenitrifMod
diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90
deleted file mode 100644
index cf962de91b..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90
+++ /dev/null
@@ -1,1099 +0,0 @@
-module SoilBiogeochemNitrogenFluxType
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp
-  use clm_varcon                         , only : spval, ispval, dzsoi_decomp
-  use decompMod                          , only : bounds_type
-  use clm_varctl                         , only : use_nitrif_denitrif, use_vertsoilc, use_crop
-  use CNSharedParamsMod                  , only : use_fun
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use abortutils                         , only : endrun
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  type, public :: SoilBiogeochem_nitrogenflux_type
-
-     ! deposition fluxes
-     real(r8), pointer :: ndep_to_sminn_col                         (:)     ! col atmospheric N deposition to soil mineral N (gN/m2/s)
-     real(r8), pointer :: nfix_to_sminn_col                         (:)     ! col symbiotic/asymbiotic N fixation to soil mineral N (gN/m2/s) 
-     real(r8), pointer :: ffix_to_sminn_col                         (:)     ! col free living N fixation to soil mineral N (gN/m2/s)  
-     real(r8), pointer :: fert_to_sminn_col                         (:)     ! col fertilizer N to soil mineral N (gN/m2/s)
-     real(r8), pointer :: soyfixn_to_sminn_col                      (:)     ! col soybean fixation to soil mineral N (gN/m2/s)
-
-     ! decomposition fluxes
-     real(r8), pointer :: decomp_cascade_ntransfer_vr_col           (:,:,:) ! col vert-res transfer of N from donor to receiver pool along decomp. cascade (gN/m3/s)
-     real(r8), pointer :: decomp_cascade_ntransfer_col              (:,:)   ! col vert-int (diagnostic) transfer of N from donor to receiver pool along decomp. cascade (gN/m2/s)
-     real(r8), pointer :: decomp_cascade_sminn_flux_vr_col          (:,:,:) ! col vert-res mineral N flux for transition along decomposition cascade (gN/m3/s)
-     real(r8), pointer :: decomp_cascade_sminn_flux_col             (:,:)   ! col vert-int (diagnostic) mineral N flux for transition along decomposition cascade (gN/m2/s)
-
-     ! Used to update concentrations concurrently with vertical transport
-     ! vertically-resolved immobilization fluxes
-     real(r8), pointer :: potential_immob_vr_col                    (:,:)   ! col vertically-resolved potential N immobilization (gN/m3/s) at each level
-     real(r8), pointer :: potential_immob_col                       (:)     ! col vert-int (diagnostic) potential N immobilization (gN/m2/s)
-     real(r8), pointer :: actual_immob_vr_col                       (:,:)   ! col vertically-resolved actual N immobilization (gN/m3/s) at each level
-     real(r8), pointer :: actual_immob_col                          (:)     ! col vert-int (diagnostic) actual N immobilization (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_vr_col                     (:,:)   ! col vertically-resolved plant uptake of soil mineral N (gN/m3/s)
-     real(r8), pointer :: sminn_to_plant_col                        (:)     ! col vert-int (diagnostic) plant uptake of soil mineral N (gN/m2/s)
-     real(r8), pointer :: supplement_to_sminn_vr_col                (:,:)   ! col vertically-resolved supplemental N supply (gN/m3/s)
-     real(r8), pointer :: supplement_to_sminn_col                   (:)     ! col vert-int (diagnostic) supplemental N supply (gN/m2/s)
-     real(r8), pointer :: gross_nmin_vr_col                         (:,:)   ! col vertically-resolved gross rate of N mineralization (gN/m3/s)
-     real(r8), pointer :: gross_nmin_col                            (:)     ! col vert-int (diagnostic) gross rate of N mineralization (gN/m2/s)
-     real(r8), pointer :: net_nmin_vr_col                           (:,:)   ! col vertically-resolved net rate of N mineralization (gN/m3/s)
-     real(r8), pointer :: net_nmin_col                              (:)     ! col vert-int (diagnostic) net rate of N mineralization (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_col                    (:)     ! col total soil N uptake of FUN        (gN/m2/s)
-     ! ---------- NITRIF_DENITRIF  ---------------------
-
-     ! nitrification / denitrification fluxes
-     real(r8), pointer :: f_nit_vr_col                              (:,:)   ! col (gN/m3/s) soil nitrification flux
-     real(r8), pointer :: f_denit_vr_col                            (:,:)   ! col (gN/m3/s) soil denitrification flux
-     real(r8), pointer :: f_nit_col                                 (:)     ! col (gN/m2/s) soil nitrification flux
-     real(r8), pointer :: f_denit_col                               (:)     ! col (gN/m2/s) soil denitrification flux
-
-     real(r8), pointer :: pot_f_nit_vr_col                          (:,:)   ! col (gN/m3/s) potential soil nitrification flux
-     real(r8), pointer :: pot_f_denit_vr_col                        (:,:)   ! col (gN/m3/s) potential soil denitrification flux
-     real(r8), pointer :: pot_f_nit_col                             (:)     ! col (gN/m2/s) potential soil nitrification flux
-     real(r8), pointer :: pot_f_denit_col                           (:)     ! col (gN/m2/s) potential soil denitrification flux
-     real(r8), pointer :: n2_n2o_ratio_denit_vr_col                 (:,:)   ! col ratio of N2 to N2O production by denitrification [gN/gN]
-     real(r8), pointer :: f_n2o_denit_vr_col                        (:,:)   ! col flux of N2o from denitrification [gN/m^3/s]
-     real(r8), pointer :: f_n2o_denit_col                           (:)     ! col flux of N2o from denitrification [gN/m^2/s]
-     real(r8), pointer :: f_n2o_nit_vr_col                          (:,:)   ! col flux of N2o from nitrification [gN/m^3/s]
-     real(r8), pointer :: f_n2o_nit_col                             (:)     ! col flux of N2o from nitrification [gN/m^2/s]
-
-     ! immobilization / uptake fluxes
-     real(r8), pointer :: actual_immob_no3_vr_col                   (:,:)   ! col vertically-resolved actual immobilization of NO3 (gN/m3/s)
-     real(r8), pointer :: actual_immob_nh4_vr_col                   (:,:)   ! col vertically-resolved actual immobilization of NH4 (gN/m3/s)
-     real(r8), pointer :: smin_no3_to_plant_vr_col                  (:,:)   ! col vertically-resolved plant uptake of soil NO3 (gN/m3/s)
-     real(r8), pointer :: smin_nh4_to_plant_vr_col                  (:,:)   ! col vertically-resolved plant uptake of soil NH4 (gN/m3/s)
-     real(r8), pointer :: actual_immob_no3_col                      (:)     ! col actual immobilization of NO3 (gN/m2/s)
-     real(r8), pointer :: actual_immob_nh4_col                      (:)     ! col actual immobilization of NH4 (gN/m2/s)
-     real(r8), pointer :: smin_no3_to_plant_col                     (:)     ! col plant uptake of soil NO3 (gN/m2/s)
-     real(r8), pointer :: smin_nh4_to_plant_col                     (:)     ! col plant uptake of soil Nh4 (gN/m2/s)
-
-     ! leaching fluxes
-     real(r8), pointer :: smin_no3_leached_vr_col                   (:,:)   ! col vertically-resolved soil mineral NO3 loss to leaching (gN/m3/s)
-     real(r8), pointer :: smin_no3_leached_col                      (:)     ! col soil mineral NO3 pool loss to leaching (gN/m2/s)
-     real(r8), pointer :: smin_no3_runoff_vr_col                    (:,:)   ! col vertically-resolved rate of mineral NO3 loss with runoff (gN/m3/s)
-     real(r8), pointer :: smin_no3_runoff_col                       (:)     ! col soil mineral NO3 pool loss to runoff (gN/m2/s)
-
-     ! nitrification /denitrification diagnostic quantities
-     real(r8), pointer :: smin_no3_massdens_vr_col                  (:,:)   ! col (ugN / g soil) soil nitrate concentration
-     real(r8), pointer :: soil_bulkdensity_col                      (:,:)   ! col (kg soil / m3) bulk density of soil
-     real(r8), pointer :: k_nitr_t_vr_col                           (:,:)
-     real(r8), pointer :: k_nitr_ph_vr_col                          (:,:)
-     real(r8), pointer :: k_nitr_h2o_vr_col                         (:,:)
-     real(r8), pointer :: k_nitr_vr_col                             (:,:)
-     real(r8), pointer :: wfps_vr_col                               (:,:)
-     real(r8), pointer :: fmax_denit_carbonsubstrate_vr_col         (:,:)
-     real(r8), pointer :: fmax_denit_nitrate_vr_col                 (:,:)
-     real(r8), pointer :: f_denit_base_vr_col                       (:,:)   ! col nitrification and denitrification fluxes
-     real(r8), pointer :: diffus_col                                (:,:)   ! col diffusivity (m2/s)
-     real(r8), pointer :: ratio_k1_col                              (:,:)
-     real(r8), pointer :: ratio_no3_co2_col                         (:,:)
-     real(r8), pointer :: soil_co2_prod_col                         (:,:)
-     real(r8), pointer :: fr_WFPS_col                               (:,:)
-
-     real(r8), pointer :: r_psi_col                                 (:,:)
-     real(r8), pointer :: anaerobic_frac_col                        (:,:)
-     real(r8), pointer :: sminn_to_plant_fun_no3_vr_col             (:,:)   ! col total layer no3 uptake of FUN     (gN/m2/s)
-     real(r8), pointer :: sminn_to_plant_fun_nh4_vr_col             (:,:)   ! col total layer nh4 uptake of FUN     (gN/m2/s)
-     !----------- no NITRIF_DENITRIF--------------
-
-     ! denitrification fluxes
-     real(r8), pointer :: sminn_to_denit_decomp_cascade_vr_col      (:,:,:) ! col vertically-resolved denitrification along decomp cascade (gN/m3/s) 
-     real(r8), pointer :: sminn_to_denit_decomp_cascade_col         (:,:)   ! col vertically-integrated (diagnostic) denitrification along decomp cascade (gN/m2/s) 
-     real(r8), pointer :: sminn_to_denit_excess_vr_col              (:,:)   ! col vertically-resolved denitrification from excess mineral N pool (gN/m3/s)
-     real(r8), pointer :: sminn_to_denit_excess_col                 (:)     ! col vertically-integrated (diagnostic) denitrification from excess mineral N pool (gN/m2/s)
-
-     ! leaching fluxes
-     real(r8), pointer :: sminn_leached_vr_col                      (:,:)   ! col vertically-resolved soil mineral N pool loss to leaching (gN/m3/s)
-     real(r8), pointer :: sminn_leached_col                         (:)     ! col soil mineral N pool loss to leaching (gN/m2/s)
-
-     ! summary (diagnostic) flux variables, not involved in mass balance
-     real(r8), pointer :: denit_col                                 (:)     ! col total rate of denitrification (gN/m2/s)
-     real(r8), pointer :: ninputs_col                               (:)     ! col column-level N inputs (gN/m2/s)
-     real(r8), pointer :: noutputs_col                              (:)     ! col column-level N outputs (gN/m2/s)
-     real(r8), pointer :: som_n_leached_col                         (:)     ! col total SOM N loss from vertical transport (gN/m^2/s)
-     real(r8), pointer :: decomp_npools_leached_col                 (:,:)   ! col N loss from vertical transport from each decomposing N pool (gN/m^2/s)
-     real(r8), pointer :: decomp_npools_transport_tendency_col      (:,:,:) ! col N tendency due to vertical transport in decomposing N pools (gN/m^3/s)
-
-     ! all n pools involved in decomposition
-     real(r8), pointer :: decomp_npools_sourcesink_col              (:,:,:) ! col (gN/m3) change in decomposing n pools 
-                                                                            ! (sum of all additions and subtractions from stateupdate1).  
-          real(r8), pointer :: sminn_to_plant_fun_vr_col                 (:,:)   ! col total layer soil N uptake of FUN  (gN/m2/s)
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: Restart
-     procedure , public  :: SetValues
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory
-     procedure , private :: InitCold
-
-  end type SoilBiogeochem_nitrogenflux_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate (bounds)
-    call this%InitHistory (bounds)
-    call this%InitCold (bounds)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize nitrogen flux
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begc,endc
-!   integer           :: begp,endp
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-!   begp = bounds%begp; endp = bounds%endp
-    allocate(this%ndep_to_sminn_col                 (begc:endc))                   ; this%ndep_to_sminn_col          (:)   = nan
-    allocate(this%nfix_to_sminn_col                 (begc:endc))                   ; this%nfix_to_sminn_col          (:)   = nan
-    allocate(this%ffix_to_sminn_col                 (begc:endc))                   ; this%ffix_to_sminn_col          (:)   = nan
-    allocate(this%fert_to_sminn_col                 (begc:endc))                   ; this%fert_to_sminn_col          (:)   = nan
-    allocate(this%soyfixn_to_sminn_col              (begc:endc))                   ; this%soyfixn_to_sminn_col       (:)   = nan
-    allocate(this%sminn_to_plant_col                (begc:endc))                   ; this%sminn_to_plant_col         (:)   = nan
-    allocate(this%potential_immob_col               (begc:endc))                   ; this%potential_immob_col        (:)   = nan
-    allocate(this%actual_immob_col                  (begc:endc))                   ; this%actual_immob_col           (:)   = nan
-    allocate(this%gross_nmin_col                    (begc:endc))                   ; this%gross_nmin_col             (:)   = nan
-    allocate(this%net_nmin_col                      (begc:endc))                   ; this%net_nmin_col               (:)   = nan
-    allocate(this%denit_col                         (begc:endc))                   ; this%denit_col                  (:)   = nan
-    allocate(this%supplement_to_sminn_col           (begc:endc))                   ; this%supplement_to_sminn_col    (:)   = nan
-    allocate(this%ninputs_col                       (begc:endc))                   ; this%ninputs_col                (:)   = nan
-    allocate(this%noutputs_col                      (begc:endc))                   ; this%noutputs_col               (:)   = nan
-    allocate(this%som_n_leached_col                 (begc:endc))                   ; this%som_n_leached_col          (:)   = nan
-
-    allocate(this%r_psi_col                         (begc:endc,1:nlevdecomp_full)) ; this%r_psi_col                  (:,:) = spval
-    allocate(this%anaerobic_frac_col                (begc:endc,1:nlevdecomp_full)) ; this%anaerobic_frac_col         (:,:) = spval
-    allocate(this%potential_immob_vr_col            (begc:endc,1:nlevdecomp_full)) ; this%potential_immob_vr_col     (:,:) = nan
-    allocate(this%actual_immob_vr_col               (begc:endc,1:nlevdecomp_full)) ; this%actual_immob_vr_col        (:,:) = nan
-    allocate(this%sminn_to_plant_vr_col             (begc:endc,1:nlevdecomp_full)) ; this%sminn_to_plant_vr_col      (:,:) = nan
-    allocate(this%supplement_to_sminn_vr_col        (begc:endc,1:nlevdecomp_full)) ; this%supplement_to_sminn_vr_col (:,:) = nan
-    allocate(this%gross_nmin_vr_col                 (begc:endc,1:nlevdecomp_full)) ; this%gross_nmin_vr_col          (:,:) = nan
-    allocate(this%net_nmin_vr_col                   (begc:endc,1:nlevdecomp_full)) ; this%net_nmin_vr_col            (:,:) = nan
-    allocate(this%sminn_to_plant_fun_col            (begc:endc))                   ; this%sminn_to_plant_fun_col     (:)     = nan
-    allocate(this%sminn_to_plant_fun_vr_col         (begc:endc,1:nlevdecomp_full)) ; this%sminn_to_plant_fun_vr_col  (:,:)   = nan
-    allocate(this%sminn_to_plant_fun_no3_vr_col     (begc:endc,1:nlevdecomp_full)) ; this%sminn_to_plant_fun_no3_vr_col(:,:) = nan
-    allocate(this%sminn_to_plant_fun_nh4_vr_col     (begc:endc,1:nlevdecomp_full)) ; this%sminn_to_plant_fun_nh4_vr_col(:,:) = nan
-    allocate(this%f_nit_vr_col                      (begc:endc,1:nlevdecomp_full)) ; this%f_nit_vr_col               (:,:) = nan
-    allocate(this%f_denit_vr_col                    (begc:endc,1:nlevdecomp_full)) ; this%f_denit_vr_col             (:,:) = nan
-    allocate(this%smin_no3_leached_vr_col           (begc:endc,1:nlevdecomp_full)) ; this%smin_no3_leached_vr_col    (:,:) = nan
-    allocate(this%smin_no3_leached_col              (begc:endc))                   ; this%smin_no3_leached_col       (:)   = nan
-    allocate(this%smin_no3_runoff_vr_col            (begc:endc,1:nlevdecomp_full)) ; this%smin_no3_runoff_vr_col     (:,:) = nan
-    allocate(this%smin_no3_runoff_col               (begc:endc))                   ; this%smin_no3_runoff_col        (:)   = nan
-    allocate(this%pot_f_nit_vr_col                  (begc:endc,1:nlevdecomp_full)) ; this%pot_f_nit_vr_col           (:,:) = nan
-    allocate(this%pot_f_nit_col                     (begc:endc))                   ; this%pot_f_nit_col              (:)   = nan
-    allocate(this%pot_f_denit_vr_col                (begc:endc,1:nlevdecomp_full)) ; this%pot_f_denit_vr_col         (:,:) = nan
-    allocate(this%pot_f_denit_col                   (begc:endc))                   ; this%pot_f_denit_col            (:)   = nan
-    allocate(this%actual_immob_no3_vr_col           (begc:endc,1:nlevdecomp_full)) ; this%actual_immob_no3_vr_col    (:,:) = nan
-    allocate(this%actual_immob_nh4_vr_col           (begc:endc,1:nlevdecomp_full)) ; this%actual_immob_nh4_vr_col    (:,:) = nan
-    allocate(this%smin_no3_to_plant_vr_col          (begc:endc,1:nlevdecomp_full)) ; this%smin_no3_to_plant_vr_col   (:,:) = nan
-    allocate(this%smin_nh4_to_plant_vr_col          (begc:endc,1:nlevdecomp_full)) ; this%smin_nh4_to_plant_vr_col   (:,:) = nan
-    allocate(this%f_nit_col                         (begc:endc))                   ; this%f_nit_col                  (:)   = nan
-    allocate(this%f_denit_col                       (begc:endc))                   ; this%f_denit_col                (:)   = nan
-    allocate(this%n2_n2o_ratio_denit_vr_col         (begc:endc,1:nlevdecomp_full)) ; this%n2_n2o_ratio_denit_vr_col  (:,:) = nan
-    allocate(this%f_n2o_denit_col                   (begc:endc))                   ; this%f_n2o_denit_col            (:)   = nan
-    allocate(this%f_n2o_denit_vr_col                (begc:endc,1:nlevdecomp_full)) ; this%f_n2o_denit_vr_col         (:,:) = nan
-    allocate(this%f_n2o_nit_col                     (begc:endc))                   ; this%f_n2o_nit_col              (:)   = nan
-    allocate(this%f_n2o_nit_vr_col                  (begc:endc,1:nlevdecomp_full)) ; this%f_n2o_nit_vr_col           (:,:) = nan
-
-    allocate(this%smin_no3_massdens_vr_col          (begc:endc,1:nlevdecomp_full)) ; this%smin_no3_massdens_vr_col   (:,:) = nan
-    allocate(this%soil_bulkdensity_col              (begc:endc,1:nlevdecomp_full)) ; this%soil_bulkdensity_col       (:,:) = nan
-    allocate(this%k_nitr_t_vr_col                   (begc:endc,1:nlevdecomp_full)) ; this%k_nitr_t_vr_col            (:,:) = nan
-    allocate(this%k_nitr_ph_vr_col                  (begc:endc,1:nlevdecomp_full)) ; this%k_nitr_ph_vr_col           (:,:) = nan
-    allocate(this%k_nitr_h2o_vr_col                 (begc:endc,1:nlevdecomp_full)) ; this%k_nitr_h2o_vr_col          (:,:) = nan
-    allocate(this%k_nitr_vr_col                     (begc:endc,1:nlevdecomp_full)) ; this%k_nitr_vr_col              (:,:) = nan
-    allocate(this%wfps_vr_col                       (begc:endc,1:nlevdecomp_full)) ; this%wfps_vr_col                (:,:) = nan
-    allocate(this%f_denit_base_vr_col               (begc:endc,1:nlevdecomp_full)) ; this%f_denit_base_vr_col        (:,:) = nan
-    allocate(this%diffus_col                        (begc:endc,1:nlevdecomp_full)) ; this%diffus_col                 (:,:) = spval
-    allocate(this%ratio_k1_col                      (begc:endc,1:nlevdecomp_full)) ; this%ratio_k1_col               (:,:) = nan
-    allocate(this%ratio_no3_co2_col                 (begc:endc,1:nlevdecomp_full)) ; this%ratio_no3_co2_col          (:,:) = spval
-    allocate(this%soil_co2_prod_col                 (begc:endc,1:nlevdecomp_full)) ; this%soil_co2_prod_col          (:,:) = nan
-    allocate(this%fr_WFPS_col                       (begc:endc,1:nlevdecomp_full)) ; this%fr_WFPS_col                (:,:) = spval
-
-    allocate(this%fmax_denit_carbonsubstrate_vr_col (begc:endc,1:nlevdecomp_full)) ; 
-    this%fmax_denit_carbonsubstrate_vr_col (:,:) = nan
-    allocate(this%fmax_denit_nitrate_vr_col         (begc:endc,1:nlevdecomp_full)) ; 
-    this%fmax_denit_nitrate_vr_col         (:,:) = nan
-
-    allocate(this%decomp_cascade_ntransfer_vr_col   (begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions ))
-    allocate(this%decomp_cascade_sminn_flux_vr_col  (begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions ))
-    allocate(this%decomp_cascade_ntransfer_col      (begc:endc,1:ndecomp_cascade_transitions                   ))
-    allocate(this%decomp_cascade_sminn_flux_col     (begc:endc,1:ndecomp_cascade_transitions                   ))
-
-    this%decomp_cascade_ntransfer_vr_col  (:,:,:) = nan
-    this%decomp_cascade_sminn_flux_vr_col (:,:,:) = nan
-    this%decomp_cascade_ntransfer_col     (:,:)   = nan
-    this%decomp_cascade_sminn_flux_col    (:,:)   = nan
-
-    allocate(this%sminn_to_denit_decomp_cascade_vr_col (begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions ))
-    allocate(this%sminn_to_denit_decomp_cascade_col    (begc:endc,1:ndecomp_cascade_transitions                   ))
-    allocate(this%sminn_to_denit_excess_vr_col         (begc:endc,1:nlevdecomp_full                               ))
-    allocate(this%sminn_to_denit_excess_col            (begc:endc                                                 ))
-    allocate(this%sminn_leached_vr_col                 (begc:endc,1:nlevdecomp_full                               ))
-    allocate(this%sminn_leached_col                    (begc:endc                                                 ))
-    allocate(this%decomp_npools_leached_col            (begc:endc,1:ndecomp_pools                                 ))
-    allocate(this%decomp_npools_transport_tendency_col (begc:endc,1:nlevdecomp_full,1:ndecomp_pools               ))
-
-    this%sminn_to_denit_decomp_cascade_vr_col (:,:,:) = nan
-    this%sminn_to_denit_decomp_cascade_col    (:,:)   = nan
-    this%sminn_to_denit_excess_vr_col         (:,:)   = nan
-    this%sminn_to_denit_excess_col            (:)     = nan
-    this%sminn_leached_vr_col                 (:,:)   = nan
-    this%sminn_leached_col                    (:)     = nan
-    this%decomp_npools_leached_col            (:,:)   = nan
-    this%decomp_npools_transport_tendency_col (:,:,:) = nan  
-
-    allocate(this%decomp_npools_sourcesink_col (begc:endc,1:nlevdecomp_full,1:ndecomp_pools))
-    this%decomp_npools_sourcesink_col (:,:,:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use histFileMod    , only : hist_addfld1d, hist_addfld_decomp
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer        :: k,l
-    integer        :: begc, endc
-    character(24)  :: fieldname
-    character(100) :: longname
-    character(8)   :: vr_suffix
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc= bounds%endc
-
-    ! add suffix if number of soil decomposition depths is greater than 1
-    if (nlevdecomp > 1) then
-       vr_suffix = "_vr"
-    else 
-       vr_suffix = ""
-    endif
-
-    !-------------------------------
-    ! N flux variables - native to column
-    !-------------------------------
-
-    this%ndep_to_sminn_col(begc:endc) = spval
-    call hist_addfld1d (fname='NDEP_TO_SMINN', units='gN/m^2/s', &
-         avgflag='A', long_name='atmospheric N deposition to soil mineral N', &
-         ptr_col=this%ndep_to_sminn_col, default='inactive')
-
-    this%nfix_to_sminn_col(begc:endc) = spval
-    call hist_addfld1d (fname='NFIX_TO_SMINN', units='gN/m^2/s', &
-         avgflag='A', long_name='symbiotic/asymbiotic N fixation to soil mineral N', &
-         ptr_col=this%nfix_to_sminn_col, default='inactive')
-
-    this%ffix_to_sminn_col(begc:endc) = spval
-    call hist_addfld1d (fname='FFIX_TO_SMINN', units='gN/m^2/s', &
-         avgflag='A', long_name='free living  N fixation to soil mineral N', &
-         ptr_col=this%ffix_to_sminn_col, default='inactive')
-
-    do l = 1, ndecomp_cascade_transitions
-       ! vertically integrated fluxes
-       !-- mineralization/immobilization fluxes (none from CWD)
-       if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-          this%decomp_cascade_sminn_flux_col(begc:endc,l) = spval
-          data1dptr => this%decomp_cascade_sminn_flux_col(:,l)
-          if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-             fieldname = 'SMINN_TO_'//&
-                  trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'N_'//&
-                  trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_donor_pool(l)))
-             longname =  'mineral N flux for decomp. of '&
-                  //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//&
-                  'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))
-          else
-             fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                  //'N_TO_SMINN'
-             longname =  'mineral N flux for decomp. of '&
-                  //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))
-          endif
-          call hist_addfld1d (fname=fieldname, units='gN/m^2', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-       end if
-
-       !-- transfer fluxes (none from terminal pool, if present)
-       if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-          this%decomp_cascade_ntransfer_col(begc:endc,l) = spval
-          data1dptr => this%decomp_cascade_ntransfer_col(:,l)
-          fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'N_TO_'//&
-               trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'N'
-          longname =  'decomp. of '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-               ' N to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' N'
-          call hist_addfld1d (fname=fieldname, units='gN/m^2',  &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-       end if
-
-       ! vertically resolved fluxes
-       if ( nlevdecomp_full > 1 ) then
-          !-- mineralization/immobilization fluxes (none from CWD)
-          if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-             this%decomp_cascade_sminn_flux_vr_col(begc:endc,:,l) = spval
-             data2dptr => this%decomp_cascade_sminn_flux_vr_col(:,:,l)
-             if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-                fieldname = 'SMINN_TO_'&
-                     //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'N_'//&
-                     trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_donor_pool(l)))//trim(vr_suffix)
-                longname =  'mineral N flux for decomp. of '&
-                     //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//&
-                     'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))
-             else
-                fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
-                     //'N_TO_SMINN'//trim(vr_suffix)
-                longname =  'mineral N flux for decomp. of '&
-                     //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))
-             endif
-             call hist_addfld_decomp (fname=fieldname, units='gN/m^3',  type2d='levdcmp', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data2dptr, default='inactive')
-          endif
-
-          !-- transfer fluxes (none from terminal pool, if present)
-          if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
-             this%decomp_cascade_ntransfer_vr_col(begc:endc,:,l) = spval
-             data2dptr => this%decomp_cascade_ntransfer_vr_col(:,:,l)
-             fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'N_TO_'//&
-                  trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))&
-                  //'N'//trim(vr_suffix)
-             longname =  'decomp. of '&
-                  //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                  ' N to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' N'
-             call hist_addfld_decomp (fname=fieldname, units='gN/m^3',  type2d='levdcmp', &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data2dptr, default='inactive')
-          endif
-
-       endif
-    end do
-
-    this%denit_col(begc:endc) = spval
-    call hist_addfld1d (fname='DENIT', units='gN/m^2/s', &
-         avgflag='A', long_name='total rate of denitrification', &
-         ptr_col=this%denit_col, default='inactive')
-
-    this%som_n_leached_col(begc:endc) = spval
-    call hist_addfld1d (fname='SOM_N_LEACHED', units='gN/m^2/s', &
-         avgflag='A', long_name='total flux of N from SOM pools due to leaching', &
-         ptr_col=this%som_n_leached_col, default='inactive')
-
-    do k = 1, ndecomp_pools
-       if ( .not. decomp_cascade_con%is_cwd(k) ) then
-          this%decomp_npools_leached_col(begc:endc,k) = spval
-          data1dptr => this%decomp_npools_leached_col(:,k)
-          fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_LEACHING'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' N leaching loss'
-          call hist_addfld1d (fname=fieldname, units='gN/m^2/s', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default='inactive')
-
-          this%decomp_npools_transport_tendency_col(begc:endc,:,k) = spval
-          data2dptr => this%decomp_npools_transport_tendency_col(:,:,k)
-          fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TNDNCY_VERT_TRANSPORT'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_long(k))//' N tendency due to vertical transport'
-          call hist_addfld_decomp (fname=fieldname, units='gN/m^3/s',  type2d='levdcmp', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data2dptr, default='inactive')
-       end if
-    end do
-
-    if (.not. use_nitrif_denitrif) then
-       do l = 1, ndecomp_cascade_transitions
-          !-- denitrification fluxes (none from CWD)
-          if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-             this%sminn_to_denit_decomp_cascade_col(begc:endc,l) = spval
-             data1dptr => this%sminn_to_denit_decomp_cascade_col(:,l)
-             fieldname = 'SMINN_TO_DENIT_'//trim(decomp_cascade_con%cascade_step_name(l))
-             longname =  'denitrification for decomp. of '&
-                  //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                  'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))
-             call hist_addfld1d (fname=fieldname, units='gN/m^2',  &
-                  avgflag='A', long_name=longname, &
-                  ptr_col=data1dptr, default='inactive')
-          endif
-
-          if ( nlevdecomp_full > 1 ) then       
-             !-- denitrification fluxes (none from CWD)
-             if ( .not. decomp_cascade_con%is_cwd(decomp_cascade_con%cascade_donor_pool(l)) ) then
-                this%sminn_to_denit_decomp_cascade_vr_col(begc:endc,:,l) = spval
-                data2dptr => this%sminn_to_denit_decomp_cascade_vr_col(:,:,l)
-                fieldname = 'SMINN_TO_DENIT_'//trim(decomp_cascade_con%cascade_step_name(l))//trim(vr_suffix)
-                longname =  'denitrification for decomp. of '&
-                     //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//&
-                     'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))
-                call hist_addfld_decomp (fname=fieldname, units='gN/m^3',  type2d='levdcmp', &
-                     avgflag='A', long_name=longname, &
-                     ptr_col=data2dptr, default='inactive')
-             endif
-          endif
-       end do
-    end if
-
-    if (.not. use_nitrif_denitrif) then
-       this%sminn_to_denit_excess_col(begc:endc) = spval
-       call hist_addfld1d (fname='SMINN_TO_DENIT_EXCESS', units='gN/m^2/s',  &
-            avgflag='A', long_name='denitrification from excess mineral N pool', &
-            ptr_col=this%sminn_to_denit_excess_col, default='inactive')
-    end if
-
-    if (.not. use_nitrif_denitrif) then
-       this%sminn_leached_col(begc:endc) = spval
-       call hist_addfld1d (fname='SMINN_LEACHED', units='gN/m^2/s',   &
-            avgflag='A', long_name='soil mineral N pool loss to leaching', &
-            ptr_col=this%sminn_leached_col, default='inactive')
-    end if
-
-    if (.not. use_nitrif_denitrif) then
-       if ( nlevdecomp_full > 1 ) then  
-          this%sminn_to_denit_excess_vr_col(begc:endc,:) = spval
-          call hist_addfld_decomp (fname='SMINN_TO_DENIT_EXCESS'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-               avgflag='A', long_name='denitrification from excess mineral N pool', &
-               ptr_col=this%sminn_to_denit_excess_vr_col, default='inactive')   
-
-          this%sminn_leached_vr_col(begc:endc,:) = spval
-          call hist_addfld_decomp (fname='SMINN_LEACHED'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-               avgflag='A', long_name='soil mineral N pool loss to leaching', &
-               ptr_col=this%sminn_leached_vr_col, default='inactive')
-       endif
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%f_nit_col(begc:endc) = spval
-       call hist_addfld1d (fname='F_NIT', units='gN/m^2/s',  &
-            avgflag='A', long_name='nitrification flux', &
-            ptr_col=this%f_nit_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%f_denit_col(begc:endc) = spval
-       call hist_addfld1d (fname='F_DENIT', units='gN/m^2/s', &
-            avgflag='A', long_name='denitrification flux', &
-            ptr_col=this%f_denit_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%pot_f_nit_col(begc:endc) = spval
-       call hist_addfld1d (fname='POT_F_NIT', units='gN/m^2/s', &
-            avgflag='A', long_name='potential nitrification flux', &
-            ptr_col=this%pot_f_nit_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%pot_f_denit_col(begc:endc) = spval
-       call hist_addfld1d (fname='POT_F_DENIT', units='gN/m^2/s', &
-            avgflag='A', long_name='potential denitrification flux', &
-            ptr_col=this%pot_f_denit_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%smin_no3_leached_col(begc:endc) = spval
-       call hist_addfld1d (fname='SMIN_NO3_LEACHED', units='gN/m^2/s', &
-            avgflag='A', long_name='soil NO3 pool loss to leaching', &
-            ptr_col=this%smin_no3_leached_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%smin_no3_runoff_col(begc:endc) = spval
-       call hist_addfld1d (fname='SMIN_NO3_RUNOFF', units='gN/m^2/s', &
-            avgflag='A', long_name='soil NO3 pool loss to runoff', &
-            ptr_col=this%smin_no3_runoff_col, default='inactive')
-    end if
-       
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%f_nit_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='F_NIT'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='nitrification flux', &
-            ptr_col=this%f_nit_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%f_denit_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='F_DENIT'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='denitrification flux', &
-            ptr_col=this%f_denit_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%pot_f_nit_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='POT_F_NIT'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='potential nitrification flux', &
-            ptr_col=this%pot_f_nit_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%pot_f_denit_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='POT_F_DENIT'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='potential denitrification flux', &
-            ptr_col=this%pot_f_denit_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%smin_no3_leached_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMIN_NO3_LEACHED'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='soil NO3 pool loss to leaching', &
-            ptr_col=this%smin_no3_leached_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif .and.  nlevdecomp_full > 1 ) then 
-       this%smin_no3_runoff_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMIN_NO3_RUNOFF'//trim(vr_suffix), units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='soil NO3 pool loss to runoff', &
-            ptr_col=this%smin_no3_runoff_vr_col, default='inactive')
-    endif
-
-    if (use_nitrif_denitrif) then
-       this%n2_n2o_ratio_denit_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='n2_n2o_ratio_denit', units='gN/gN', type2d='levdcmp', &
-            avgflag='A', long_name='n2_n2o_ratio_denit', &
-            ptr_col=this%n2_n2o_ratio_denit_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%actual_immob_no3_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='ACTUAL_IMMOB_NO3', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='immobilization of NO3', &
-            ptr_col=this%actual_immob_no3_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%actual_immob_nh4_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='ACTUAL_IMMOB_NH4', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='immobilization of NH4', &
-            ptr_col=this%actual_immob_nh4_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%smin_no3_to_plant_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMIN_NO3_TO_PLANT', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='plant uptake of NO3', &
-            ptr_col=this%smin_no3_to_plant_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%smin_nh4_to_plant_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMIN_NH4_TO_PLANT', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='plant uptake of NH4', &
-            ptr_col=this%smin_nh4_to_plant_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%smin_no3_massdens_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMIN_NO3_MASSDENS', units='ugN/cm^3 soil', type2d='levdcmp', &
-            avgflag='A', long_name='SMIN_NO3_MASSDENS', &
-            ptr_col=this%smin_no3_massdens_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%k_nitr_t_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='K_NITR_T', units='unitless', type2d='levdcmp', &
-            avgflag='A', long_name='K_NITR_T', &
-            ptr_col=this%k_nitr_t_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%k_nitr_ph_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='K_NITR_PH', units='unitless', type2d='levdcmp', &
-            avgflag='A', long_name='K_NITR_PH', &
-            ptr_col=this%k_nitr_ph_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%k_nitr_h2o_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='K_NITR_H2O', units='unitless', type2d='levdcmp', &
-            avgflag='A', long_name='K_NITR_H2O', &
-            ptr_col=this%k_nitr_h2o_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%k_nitr_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='K_NITR', units='1/s', type2d='levdcmp', &
-            avgflag='A', long_name='K_NITR', &
-            ptr_col=this%k_nitr_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%wfps_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='WFPS', units='percent', type2d='levdcmp', &
-            avgflag='A', long_name='WFPS', &
-            ptr_col=this%wfps_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%fmax_denit_carbonsubstrate_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='FMAX_DENIT_CARBONSUBSTRATE', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='FMAX_DENIT_CARBONSUBSTRATE', &
-            ptr_col=this%fmax_denit_carbonsubstrate_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%fmax_denit_nitrate_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='FMAX_DENIT_NITRATE', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='FMAX_DENIT_NITRATE', &
-            ptr_col=this%fmax_denit_nitrate_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%f_denit_base_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='F_DENIT_BASE', units='gN/m^3/s', type2d='levdcmp', &
-            avgflag='A', long_name='F_DENIT_BASE', &
-            ptr_col=this%f_denit_base_vr_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%diffus_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='diffus', units='m^2/s', type2d='levdcmp', &
-            avgflag='A', long_name='diffusivity', &
-            ptr_col=this%diffus_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%ratio_k1_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='ratio_k1', units='none', type2d='levdcmp', &
-            avgflag='A', long_name='ratio_k1', &
-            ptr_col=this%ratio_k1_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%ratio_no3_co2_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='ratio_no3_co2', units='ratio', type2d='levdcmp', &
-            avgflag='A', long_name='ratio_no3_co2', &
-            ptr_col=this%ratio_no3_co2_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%soil_co2_prod_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='soil_co2_prod', units='ug C / g soil / day', type2d='levdcmp', &
-            avgflag='A', long_name='soil_co2_prod', &
-            ptr_col=this%soil_co2_prod_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%fr_WFPS_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='fr_WFPS', units='fraction', type2d='levdcmp', &
-            avgflag='A', long_name='fr_WFPS', &
-            ptr_col=this%fr_WFPS_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%soil_bulkdensity_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='soil_bulkdensity', units='kg/m3', type2d='levdcmp', &
-            avgflag='A', long_name='soil_bulkdensity', &
-            ptr_col=this%soil_bulkdensity_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%anaerobic_frac_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='anaerobic_frac', units='m3/m3', type2d='levdcmp', &
-            avgflag='A', long_name='anaerobic_frac', &
-            ptr_col=this%anaerobic_frac_col, default='inactive')
-    end if
-
-    if (use_nitrif_denitrif) then
-       this%r_psi_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='r_psi', units='m', type2d='levdcmp', &
-            avgflag='A', long_name='r_psi', &
-            ptr_col=this%r_psi_col, default='inactive')
-    end if
-
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%potential_immob_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='POTENTIAL_IMMOB'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='potential N immobilization', &
-            ptr_col=this%potential_immob_vr_col, default='inactive')
-    end if
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%actual_immob_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='ACTUAL_IMMOB'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='actual N immobilization', &
-            ptr_col=this%actual_immob_vr_col, default='inactive')
-    end if
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%sminn_to_plant_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SMINN_TO_PLANT'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='plant uptake of soil mineral N', &
-            ptr_col=this%sminn_to_plant_vr_col, default='inactive')
-    end if
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%supplement_to_sminn_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='SUPPLEMENT_TO_SMINN'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='supplemental N supply', &
-            ptr_col=this%supplement_to_sminn_vr_col, default='inactive')
-    end if
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%gross_nmin_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='GROSS_NMIN'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='gross rate of N mineralization', &
-            ptr_col=this%gross_nmin_vr_col, default='inactive')
-    end if
-
-    if ( use_nitrif_denitrif .and. nlevdecomp_full > 1 ) then
-       this%net_nmin_vr_col(begc:endc,:) = spval
-       call hist_addfld_decomp (fname='NET_NMIN'//trim(vr_suffix), units='gN/m^3/s',  type2d='levdcmp', &
-            avgflag='A', long_name='net rate of N mineralization', &
-            ptr_col=this%net_nmin_vr_col, default='inactive')
-    end if
-
-    this%potential_immob_col(begc:endc) = spval
-    call hist_addfld1d (fname='POTENTIAL_IMMOB', units='gN/m^2/s', &
-         avgflag='A', long_name='potential N immobilization', &
-         ptr_col=this%potential_immob_col, default='inactive')
-
-    this%actual_immob_col(begc:endc) = spval
-    call hist_addfld1d (fname='ACTUAL_IMMOB', units='gN/m^2/s', &
-         avgflag='A', long_name='actual N immobilization', &
-         ptr_col=this%actual_immob_col, default='inactive')
-
-    this%sminn_to_plant_col(begc:endc) = spval
-    call hist_addfld1d (fname='SMINN_TO_PLANT', units='gN/m^2/s', &
-         avgflag='A', long_name='plant uptake of soil mineral N', &
-         ptr_col=this%sminn_to_plant_col, default='inactive')
-
-    this%supplement_to_sminn_col(begc:endc) = spval
-    call hist_addfld1d (fname='SUPPLEMENT_TO_SMINN', units='gN/m^2/s', &
-         avgflag='A', long_name='supplemental N supply', &
-         ptr_col=this%supplement_to_sminn_col, default='inactive')
-
-    this%gross_nmin_col(begc:endc) = spval
-    call hist_addfld1d (fname='GROSS_NMIN', units='gN/m^2/s', &
-         avgflag='A', long_name='gross rate of N mineralization', &
-         ptr_col=this%gross_nmin_col, default='inactive')
-
-    this%net_nmin_col(begc:endc) = spval
-    call hist_addfld1d (fname='NET_NMIN', units='gN/m^2/s', &
-         avgflag='A', long_name='net rate of N mineralization', &
-         ptr_col=this%net_nmin_col, default='inactive')
-
-    if (use_nitrif_denitrif) then
-       this%f_n2o_nit_col(begc:endc) = spval
-       call hist_addfld1d (fname='F_N2O_NIT', units='gN/m^2/s', &
-            avgflag='A', long_name='nitrification N2O flux', &
-            ptr_col=this%f_n2o_nit_col, default='inactive')
-
-       this%f_n2o_denit_col(begc:endc) = spval
-       call hist_addfld1d (fname='F_N2O_DENIT', units='gN/m^2/s', &
-            avgflag='A', long_name='denitrification N2O flux', &
-            ptr_col=this%f_n2o_denit_col, default='inactive')
-    end if
-
-    if (use_crop) then
-       this%fert_to_sminn_col(begc:endc) = spval
-       call hist_addfld1d (fname='FERT_TO_SMINN', units='gN/m^2/s', &
-            avgflag='A', long_name='fertilizer to soil mineral N', &
-            ptr_col=this%fert_to_sminn_col, default='inactive')
-    end if
-
-    if (use_crop .and. .not. use_fun) then
-       this%soyfixn_to_sminn_col(begc:endc) = spval
-       call hist_addfld1d (fname='SOYFIXN_TO_SMINN', units='gN/m^2/s', &
-            avgflag='A', long_name='Soybean fixation to soil mineral N', &
-            ptr_col=this%soyfixn_to_sminn_col, default='inactive')
-    end if
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    ! !USES:
-    use landunit_varcon , only : istsoil, istcrop
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,l
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: special_col(bounds%endc-bounds%begc+1)    ! special landunit filter - columns
-    !---------------------------------------------------------------------
-
-    ! Set column filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    !-----------------------------------------------
-    ! initialize nitrogen flux variables
-    !-----------------------------------------------
-
-    call this%SetValues (&
-         num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart (this,  bounds, ncid, flag )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for carbon state
-    !
-    ! !USES:
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    type(bounds_type) , intent(in)    :: bounds 
-    type(file_desc_t) , intent(inout) :: ncid   ! netcdf id
-    character(len=*)  , intent(in)    :: flag   !'read' or 'write'
-    !
-    ! !LOCAL VARIABLES:
-    integer :: j,c ! indices
-    logical :: readvar      ! determine if variable is on initial file
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    if (use_nitrif_denitrif) then
-       ! pot_f_nit_vr
-       if (use_vertsoilc) then
-          ptr2d => this%pot_f_nit_vr_col(:,:)
-          call restartvar(ncid=ncid, flag=flag, varname='pot_f_nit_vr_vr', xtype=ncd_double, &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='potential soil nitrification flux', units='gN/m3/s', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d)
-       else
-          ptr1d => this%pot_f_nit_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='pot_f_nit_vr', xtype=ncd_double, &
-               dim1name='column', &
-               long_name='soil nitrification flux', units='gN/m3/s', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg= 'ERROR:: pot_f_nit_vr'//' is required on an initialization dataset' )
-       end if
-    end if
-
-    if (use_nitrif_denitrif) then
-       ! f_nit_vr
-       if (use_vertsoilc) then
-          ptr2d => this%f_nit_vr_col(:,:)
-          call restartvar(ncid=ncid, flag=flag, varname='f_nit_vr_vr', xtype=ncd_double, &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='soil nitrification flux', units='gN/m3/s', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-       else
-          ptr1d => this%f_nit_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='f_nit_vr', xtype=ncd_double, &
-               dim1name='column', &
-               long_name='soil nitrification flux', units='gN/m3/s', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg='ERROR:: f_nit_vr'//' is required on an initialization dataset'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-    end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, &
-       num_column, filter_column, value_column)
-    !
-    ! !DESCRIPTION:
-    ! Set nitrogen flux variables
-    !
-    ! !ARGUMENTS:
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenflux_type) :: this
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i,j,k,l     ! loop index
-    !------------------------------------------------------------------------
-
-    do j = 1, nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-
-          if (.not. use_nitrif_denitrif) then
-             this%sminn_to_denit_excess_vr_col(i,j)      = value_column
-             this%sminn_leached_vr_col(i,j)              = value_column
-             this%sminn_to_plant_fun_vr_col(i,j)         = value_column
-          else
-             this%f_nit_vr_col(i,j)                      = value_column
-             this%f_denit_vr_col(i,j)                    = value_column
-             this%smin_no3_leached_vr_col(i,j)           = value_column
-             this%smin_no3_runoff_vr_col(i,j)            = value_column 
-             this%n2_n2o_ratio_denit_vr_col(i,j)         = value_column
-             this%pot_f_nit_vr_col(i,j)                  = value_column
-             this%pot_f_denit_vr_col(i,j)                = value_column
-             this%actual_immob_no3_vr_col(i,j)           = value_column
-             this%actual_immob_nh4_vr_col(i,j)           = value_column
-             this%smin_no3_to_plant_vr_col(i,j)          = value_column
-             this%smin_nh4_to_plant_vr_col(i,j)          = value_column
-             this%f_n2o_denit_vr_col(i,j)                = value_column
-             this%f_n2o_nit_vr_col(i,j)                  = value_column
-
-             this%smin_no3_massdens_vr_col(i,j)          = value_column
-             this%k_nitr_t_vr_col(i,j)                   = value_column
-             this%k_nitr_ph_vr_col(i,j)                  = value_column
-             this%k_nitr_h2o_vr_col(i,j)                 = value_column
-             this%k_nitr_vr_col(i,j)                     = value_column 
-             this%wfps_vr_col(i,j)                       = value_column 
-             this%fmax_denit_carbonsubstrate_vr_col(i,j) = value_column 
-             this%fmax_denit_nitrate_vr_col(i,j)         = value_column 
-             this%f_denit_base_vr_col(i,j)               = value_column
-
-             this%diffus_col(i,j)                        = value_column
-             this%ratio_k1_col(i,j)                      = value_column
-             this%ratio_no3_co2_col(i,j)                 = value_column
-             this%soil_co2_prod_col(i,j)                 = value_column
-             this%fr_WFPS_col(i,j)                       = value_column
-             this%soil_bulkdensity_col(i,j)              = value_column
-
-             this%r_psi_col(i,j)                         = value_column
-             this%anaerobic_frac_col(i,j)                = value_column
-          end if
-          this%potential_immob_vr_col(i,j)               = value_column
-          this%actual_immob_vr_col(i,j)                  = value_column
-          this%sminn_to_plant_vr_col(i,j)                = value_column
-          this%supplement_to_sminn_vr_col(i,j)           = value_column
-          this%gross_nmin_vr_col(i,j)                    = value_column
-          this%net_nmin_vr_col(i,j)                      = value_column
-          this%sminn_to_plant_fun_no3_vr_col(i,j)        = value_column
-          this%sminn_to_plant_fun_nh4_vr_col(i,j)        = value_column
-       end do
-    end do
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-
-       this%ndep_to_sminn_col(i)             = value_column
-       this%nfix_to_sminn_col(i)             = value_column
-       this%ffix_to_sminn_col(i)             = value_column
-       this%fert_to_sminn_col(i)             = value_column
-       this%soyfixn_to_sminn_col(i)          = value_column
-       this%potential_immob_col(i)           = value_column
-       this%actual_immob_col(i)              = value_column
-       this%sminn_to_plant_col(i)            = value_column
-       this%supplement_to_sminn_col(i)       = value_column
-       this%gross_nmin_col(i)                = value_column
-       this%net_nmin_col(i)                  = value_column
-       this%denit_col(i)                     = value_column
-       this%sminn_to_plant_fun_col(i)        = value_column
-       if (use_nitrif_denitrif) then
-          this%f_nit_col(i)                  = value_column
-          this%pot_f_nit_col(i)              = value_column
-          this%f_denit_col(i)                = value_column
-          this%pot_f_denit_col(i)            = value_column
-          this%f_n2o_denit_col(i)            = value_column
-          this%f_n2o_nit_col(i)              = value_column
-          this%smin_no3_leached_col(i)       = value_column
-          this%smin_no3_runoff_col(i)        = value_column
-       else
-          this%sminn_to_denit_excess_col(i)  = value_column
-          this%sminn_leached_col(i)          = value_column
-       end if
-       this%ninputs_col(i)                   = value_column
-       this%noutputs_col(i)                  = value_column
-       this%som_n_leached_col(i)             = value_column
-    end do
-
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%decomp_npools_leached_col(i,k) = value_column
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_npools_transport_tendency_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-    do l = 1, ndecomp_cascade_transitions
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%decomp_cascade_ntransfer_col(i,l) = value_column
-          this%decomp_cascade_sminn_flux_col(i,l) = value_column
-          if (.not. use_nitrif_denitrif) then
-             this%sminn_to_denit_decomp_cascade_col(i,l) = value_column
-          end if
-       end do
-    end do
-
-    do l = 1, ndecomp_cascade_transitions
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_cascade_ntransfer_vr_col(i,j,l) = value_column
-             this%decomp_cascade_sminn_flux_vr_col(i,j,l) = value_column
-             if (.not. use_nitrif_denitrif) then
-                this%sminn_to_denit_decomp_cascade_vr_col(i,j,l) = value_column
-             end if
-          end do
-       end do
-    end do
-
-    do k = 1, ndecomp_pools
-       do j = 1, nlevdecomp_full
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_npools_sourcesink_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-  end subroutine SetValues
-
-end module soilbiogeochemNitrogenFluxType
-
diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
deleted file mode 100644
index 9403bd6c83..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
+++ /dev/null
@@ -1,717 +0,0 @@
-module SoilBiogeochemNitrogenStateType
-
-#include "shr_assert.h"
-
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use shr_infnan_mod                     , only : nan => shr_infnan_nan, assignment(=)
-  use shr_log_mod                        , only : errMsg => shr_log_errMsg
-  use decompMod                          , only : bounds_type
-  use abortutils                         , only : endrun
-  use spmdMod                            , only : masterproc 
-  use clm_varpar                         , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan
-  use clm_varpar                         , only : nlevdecomp_full, nlevdecomp, nlevsoi
-  use clm_varcon                         , only : spval, dzsoi_decomp, zisoi
-  use clm_varctl                         , only : use_nitrif_denitrif, use_vertsoilc, use_century_decomp
-  use clm_varctl                         , only : iulog, override_bgc_restart_mismatch_dump, spinup_state
-  use landunit_varcon                    , only : istcrop, istsoil 
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use LandunitType                       , only : lun                
-  use ColumnType                         , only : col                
-  use GridcellType                       , only : grc
-  use SoilBiogeochemStateType            , only : get_spinup_latitude_term
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-
-  type, public :: soilbiogeochem_nitrogenstate_type
-
-     real(r8), pointer :: decomp_npools_vr_col         (:,:,:) ! col (gN/m3) vertically-resolved decomposing (litter, cwd, soil) N pools
-     real(r8), pointer :: sminn_vr_col                 (:,:)   ! col (gN/m3) vertically-resolved soil mineral N
-     real(r8), pointer :: ntrunc_vr_col                (:,:)   ! col (gN/m3) vertically-resolved column-level sink for N truncation
-
-     ! nitrif_denitrif
-     real(r8), pointer :: smin_no3_vr_col              (:,:)   ! col (gN/m3) vertically-resolved soil mineral NO3
-     real(r8), pointer :: smin_no3_col                 (:)     ! col (gN/m2) soil mineral NO3 pool
-     real(r8), pointer :: smin_nh4_vr_col              (:,:)   ! col (gN/m3) vertically-resolved soil mineral NH4
-     real(r8), pointer :: smin_nh4_col                 (:)     ! col (gN/m2) soil mineral NH4 pool
-
-     ! summary (diagnostic) state variables, not involved in mass balance
-     real(r8), pointer :: decomp_npools_col            (:,:)   ! col (gN/m2)  decomposing (litter, cwd, soil) N pools
-     real(r8), pointer :: decomp_npools_1m_col         (:,:)   ! col (gN/m2)  diagnostic: decomposing (litter, cwd, soil) N pools to 1 meter
-     real(r8), pointer :: sminn_col                    (:)     ! col (gN/m2) soil mineral N
-     real(r8), pointer :: ntrunc_col                   (:)     ! col (gN/m2) column-level sink for N truncation
-     real(r8), pointer :: cwdn_col                     (:)     ! col (gN/m2) Diagnostic: coarse woody debris N
-     real(r8), pointer :: totlitn_col                  (:)     ! col (gN/m2) total litter nitrogen
-     real(r8), pointer :: totsomn_col                  (:)     ! col (gN/m2) total soil organic matter nitrogen
-     real(r8), pointer :: totlitn_1m_col               (:)     ! col (gN/m2) total litter nitrogen to 1 meter
-     real(r8), pointer :: totsomn_1m_col               (:)     ! col (gN/m2) total soil organic matter nitrogen to 1 meter
-     real(r8), pointer :: dyn_nbal_adjustments_col (:) ! (gN/m2) adjustments to each column made in this timestep via dynamic column adjustments (note: this variable only makes sense at the column-level: it is meaningless if averaged to the gridcell-level)
-
-     ! Track adjustments to no3 and nh4 pools separately, since those aren't included in
-     ! the N balance check
-     real(r8), pointer :: dyn_no3bal_adjustments_col (:) ! (gN/m2) NO3 adjustments to each column made in this timestep via dynamic column area adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level)
-     real(r8), pointer :: dyn_nh4bal_adjustments_col (:) ! (gN/m2) NH4 adjustments to each column made in this timestep via dynamic column adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level)
-     real(r8)          :: totvegcthresh                  ! threshold for total vegetation carbon to zero out decomposition pools
-
-   contains
-
-     procedure , public  :: Init   
-     procedure , public  :: Restart
-     procedure , public  :: SetValues
-     procedure , private :: InitAllocate 
-     procedure , private :: InitHistory  
-     procedure , private :: InitCold     
-
-  end type soilbiogeochem_nitrogenstate_type
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds,                           &
-       decomp_cpools_vr_col, decomp_cpools_col, decomp_cpools_1m_col)
-
-    class(soilbiogeochem_nitrogenstate_type)         :: this
-    type(bounds_type) , intent(in)    :: bounds  
-    real(r8)          , intent(in)    :: decomp_cpools_vr_col (bounds%begc:, 1:, 1:)
-    real(r8)          , intent(in)    :: decomp_cpools_col    (bounds%begc:, 1:)
-    real(r8)          , intent(in)    :: decomp_cpools_1m_col (bounds%begc:, 1:)
-
-    this%totvegcthresh = nan
-    call this%InitAllocate (bounds )
-
-    call this%InitHistory (bounds)
-
-    call this%InitCold ( bounds, & 
-         decomp_cpools_vr_col, decomp_cpools_col, decomp_cpools_1m_col)
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_nitrogenstate_type) :: this
-    type(bounds_type) , intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begc,endc
-    !------------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    allocate(this%sminn_vr_col         (begc:endc,1:nlevdecomp_full)) ; this%sminn_vr_col         (:,:) = nan
-    allocate(this%ntrunc_vr_col        (begc:endc,1:nlevdecomp_full)) ; this%ntrunc_vr_col        (:,:) = nan
-    allocate(this%smin_no3_vr_col      (begc:endc,1:nlevdecomp_full)) ; this%smin_no3_vr_col      (:,:) = nan
-    allocate(this%smin_nh4_vr_col      (begc:endc,1:nlevdecomp_full)) ; this%smin_nh4_vr_col      (:,:) = nan
-    allocate(this%smin_no3_col         (begc:endc))                   ; this%smin_no3_col         (:)   = nan
-    allocate(this%smin_nh4_col         (begc:endc))                   ; this%smin_nh4_col         (:)   = nan
-    allocate(this%cwdn_col             (begc:endc))                   ; this%cwdn_col             (:)   = nan
-    allocate(this%sminn_col            (begc:endc))                   ; this%sminn_col            (:)   = nan
-    allocate(this%ntrunc_col           (begc:endc))                   ; this%ntrunc_col           (:)   = nan
-    allocate(this%totlitn_col          (begc:endc))                   ; this%totlitn_col          (:)   = nan
-    allocate(this%totsomn_col          (begc:endc))                   ; this%totsomn_col          (:)   = nan
-    allocate(this%totlitn_1m_col       (begc:endc))                   ; this%totlitn_1m_col       (:)   = nan
-    allocate(this%totsomn_1m_col       (begc:endc))                   ; this%totsomn_1m_col       (:)   = nan
-    allocate(this%dyn_nbal_adjustments_col (begc:endc)) ; this%dyn_nbal_adjustments_col (:) = nan
-    allocate(this%dyn_no3bal_adjustments_col (begc:endc)) ; this%dyn_no3bal_adjustments_col (:) = nan
-    allocate(this%dyn_nh4bal_adjustments_col (begc:endc)) ; this%dyn_nh4bal_adjustments_col (:) = nan
-    allocate(this%decomp_npools_col    (begc:endc,1:ndecomp_pools))   ; this%decomp_npools_col    (:,:) = nan
-    allocate(this%decomp_npools_1m_col (begc:endc,1:ndecomp_pools))   ; this%decomp_npools_1m_col (:,:) = nan
-
-    allocate(this%decomp_npools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools));
-    this%decomp_npools_vr_col(:,:,:)= nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! add history fields for all CN variables, always set as default='inactive'
-    !
-    ! !USES:
-    use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools
-    use clm_varpar , only : nlevdecomp, nlevdecomp_full, nlevgrnd
-    use histFileMod, only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp 
-    use decompMod  , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenstate_type) :: this
-    type(bounds_type)         , intent(in) :: bounds 
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: k,l,ii,jj 
-    character(10)     :: active
-    character(8)      :: vr_suffix
-    integer           :: begc,endc
-    character(24)     :: fieldname
-    character(100)    :: longname
-    real(r8), pointer :: data1dptr(:)   ! temp. pointer for slicing larger arrays
-    real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays
-    !---------------------------------------------------------------------
-
-    begc = bounds%begc; endc = bounds%endc
-
-    if ( nlevdecomp_full > 1 ) then
-       this%decomp_npools_vr_col(begc:endc,:,:) = spval
-       this%decomp_npools_1m_col(begc:endc,:) = spval
-    end if
-    this%decomp_npools_col(begc:endc,:) = spval
-    do l  = 1, ndecomp_pools
-       if ( nlevdecomp_full > 1 ) then
-          data2dptr => this%decomp_npools_vr_col(:,:,l)
-          fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N_vr'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' N (vertically resolved)'
-          call hist_addfld2d (fname=fieldname, units='gN/m^3',  type2d='levdcmp', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data2dptr, default='inactive')
-       endif
-
-       data1dptr => this%decomp_npools_col(:,l)
-       fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N'
-       longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' N'
-       call hist_addfld1d (fname=fieldname, units='gN/m^2', &
-            avgflag='A', long_name=longname, &
-            ptr_col=data1dptr, default='inactive')
-
-       if ( nlevdecomp_full > 1 ) then
-          data1dptr => this%decomp_npools_1m_col(:,l)
-          fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N_1m'
-          longname =  trim(decomp_cascade_con%decomp_pool_name_history(l))//' N to 1 meter'
-          call hist_addfld1d (fname=fieldname, units='gN/m^2', &
-               avgflag='A', long_name=longname, &
-               ptr_col=data1dptr, default = 'inactive')
-       endif
-    end do
-
-
-    if ( nlevdecomp_full > 1 ) then
-
-       this%sminn_col(begc:endc) = spval
-       call hist_addfld1d (fname='SMINN', units='gN/m^2', &
-            avgflag='A', long_name='soil mineral N', &
-            ptr_col=this%sminn_col, default='inactive')
-
-       this%totlitn_1m_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTLITN_1m', units='gN/m^2', &
-            avgflag='A', long_name='total litter N to 1 meter', &
-            ptr_col=this%totlitn_1m_col, default='inactive')
-
-       this%totsomn_1m_col(begc:endc) = spval
-       call hist_addfld1d (fname='TOTSOMN_1m', units='gN/m^2', &
-            avgflag='A', long_name='total soil organic matter N to 1 meter', &
-            ptr_col=this%totsomn_1m_col, default='inactive')
-    endif
-
-    this%ntrunc_col(begc:endc) = spval
-    call hist_addfld1d (fname='COL_NTRUNC', units='gN/m^2',  &
-         avgflag='A', long_name='column-level sink for N truncation', &
-         ptr_col=this%ntrunc_col, default='inactive')
-
-    ! add suffix if number of soil decomposition depths is greater than 1
-    if (nlevdecomp > 1) then
-       vr_suffix = "_vr"
-    else 
-       vr_suffix = ""
-    endif
-
-    if (use_nitrif_denitrif) then
-       if ( nlevdecomp_full > 1 ) then
-          data2dptr => this%smin_no3_vr_col(begc:endc,1:nlevsoi)
-          call hist_addfld_decomp (fname='SMIN_NO3'//trim(vr_suffix), units='gN/m^3',  type2d='levsoi', &
-               avgflag='A', long_name='soil mineral NO3 (vert. res.)', &
-               ptr_col=data2dptr, default='inactive')
-
-          data2dptr => this%smin_nh4_vr_col(begc:endc,1:nlevsoi)
-          call hist_addfld_decomp (fname='SMIN_NH4'//trim(vr_suffix), units='gN/m^3',  type2d='levsoi', &
-               avgflag='A', long_name='soil mineral NH4 (vert. res.)', &
-               ptr_col=data2dptr, default='inactive')
-
-          data2dptr => this%sminn_vr_col(begc:endc,1:nlevsoi)
-          call hist_addfld_decomp (fname='SMINN'//trim(vr_suffix), units='gN/m^3',  type2d='levsoi', &
-               avgflag='A', long_name='soil mineral N', &
-               ptr_col=data2dptr, default='inactive')
-
-          this%smin_no3_col(begc:endc) = spval
-          call hist_addfld1d (fname='SMIN_NO3', units='gN/m^2', &
-               avgflag='A', long_name='soil mineral NO3', &
-               ptr_col=this%smin_no3_col, default='inactive')
-
-          this%smin_nh4_col(begc:endc) = spval
-          call hist_addfld1d (fname='SMIN_NH4', units='gN/m^2', &
-               avgflag='A', long_name='soil mineral NH4', &
-               ptr_col=this%smin_nh4_col, default='inactive')
-       endif
-    else
-       if ( nlevdecomp_full > 1 ) then
-          data2dptr => this%sminn_vr_col(begc:endc,1:nlevsoi) 
-          call hist_addfld_decomp (fname='SMINN'//trim(vr_suffix), units='gN/m^3', type2d='levsoi', &
-               avgflag='A', long_name='soil mineral N', &
-               ptr_col=data2dptr, default='inactive')
-       end if
-
-    end if
-
-    this%totlitn_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTLITN', units='gN/m^2', &
-         avgflag='A', long_name='total litter N', &
-         ptr_col=this%totlitn_col, default='inactive')
-
-    this%totsomn_col(begc:endc) = spval
-    call hist_addfld1d (fname='TOTSOMN', units='gN/m^2', &
-         avgflag='A', long_name='total soil organic matter N', &
-         ptr_col=this%totsomn_col, default='inactive')
-
-    this%dyn_nbal_adjustments_col(begc:endc) = spval
-    call hist_addfld1d (fname='DYN_COL_SOIL_ADJUSTMENTS_N', units='gN/m^2', &
-         avgflag='SUM', &
-         long_name='Adjustments in soil nitrogen due to dynamic column areas; &
-         &only makes sense at the column level: should not be averaged to gridcell', &
-         ptr_col=this%dyn_nbal_adjustments_col, default='inactive')
-
-    if (use_nitrif_denitrif) then
-       call hist_addfld1d (fname='DYN_COL_SOIL_ADJUSTMENTS_NO3', units='gN/m^2', &
-            avgflag='SUM', &
-            long_name='Adjustments in soil NO3 due to dynamic column areas; &
-            &only makes sense at the column level: should not be averaged to gridcell', &
-            ptr_col=this%dyn_no3bal_adjustments_col, default='inactive')
-
-       call hist_addfld1d (fname='DYN_COL_SOIL_ADJUSTMENTS_NH4', units='gN/m^2', &
-            avgflag='SUM', &
-            long_name='Adjustments in soil NH4 due to dynamic column areas; &
-            &only makes sense at the column level: should not be averaged to gridcell', &
-            ptr_col=this%dyn_nh4bal_adjustments_col, default='inactive')
-    end if
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine InitCold(this, bounds, &
-       decomp_cpools_vr_col, decomp_cpools_col, decomp_cpools_1m_col)
-    !
-    ! !DESCRIPTION:
-    ! Initializes time varying variables used only in coupled carbon-nitrogen mode (CN):
-    !
-    ! !USES:
-    use decompMod      , only : bounds_type
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_nitrogenstate_type)      :: this
-    type(bounds_type) , intent(in) :: bounds  
-    real(r8)          , intent(in) :: decomp_cpools_vr_col(bounds%begc:,:,:)
-    real(r8)          , intent(in) :: decomp_cpools_col(bounds%begc:,:)
-    real(r8)          , intent(in) :: decomp_cpools_1m_col(bounds%begc:,:)
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fc,g,l,c,j,k                              ! indices
-    integer :: num_special_col                           ! number of good values in special_col filter
-    integer :: special_col   (bounds%endc-bounds%begc+1) ! special landunit filter - columns
-    !------------------------------------------------------------------------
-
-    SHR_ASSERT_ALL((ubound(decomp_cpools_col)    == (/bounds%endc,ndecomp_pools/)),                 errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(decomp_cpools_1m_col) == (/bounds%endc,ndecomp_pools/)),                 errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(decomp_cpools_vr_col) == (/bounds%endc,nlevdecomp_full,ndecomp_pools/)), errMsg(sourcefile, __LINE__))
-
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-
-          ! column nitrogen state variables
-          this%ntrunc_col(c) = 0._r8
-          this%sminn_col(c) = 0._r8
-          do j = 1, nlevdecomp
-             do k = 1, ndecomp_pools
-                this%decomp_npools_vr_col(c,j,k) = decomp_cpools_vr_col(c,j,k) / decomp_cascade_con%initial_cn_ratio(k)
-             end do
-             this%sminn_vr_col(c,j) = 0._r8
-             this%ntrunc_vr_col(c,j) = 0._r8
-          end do
-          if ( nlevdecomp > 1 ) then
-             do j = nlevdecomp+1, nlevdecomp_full
-                do k = 1, ndecomp_pools
-                   this%decomp_npools_vr_col(c,j,k) = 0._r8
-                end do
-                this%sminn_vr_col(c,j) = 0._r8
-                this%ntrunc_vr_col(c,j) = 0._r8
-             end do
-          end if
-          do k = 1, ndecomp_pools
-             this%decomp_npools_col(c,k)    = decomp_cpools_col(c,k)    / decomp_cascade_con%initial_cn_ratio(k)
-             this%decomp_npools_1m_col(c,k) = decomp_cpools_1m_col(c,k) / decomp_cascade_con%initial_cn_ratio(k)
-          end do
-
-          if (use_nitrif_denitrif) then
-             do j = 1, nlevdecomp_full
-                this%smin_nh4_vr_col(c,j) = 0._r8
-                this%smin_no3_vr_col(c,j) = 0._r8
-             end do
-             this%smin_nh4_col(c) = 0._r8
-             this%smin_no3_col(c) = 0._r8
-          end if
-          this%totlitn_col(c)    = 0._r8
-          this%totsomn_col(c)    = 0._r8
-          this%totlitn_1m_col(c) = 0._r8
-          this%totsomn_1m_col(c) = 0._r8
-          this%cwdn_col(c)       = 0._r8
-
-       end if
-    end do
-
-    ! initialize fields for special filters
-
-    num_special_col = 0
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          num_special_col = num_special_col + 1
-          special_col(num_special_col) = c
-       end if
-    end do
-
-    call this%SetValues (num_column=num_special_col, filter_column=special_col, value_column=0._r8)
-
-  end subroutine InitCold
-
-  !-----------------------------------------------------------------------
-  subroutine Restart ( this,  bounds, ncid, flag, totvegc_col )
-    !
-    ! !DESCRIPTION: 
-    ! Read/write CN restart data for nitrogen state
-    !
-    ! !USES:
-    use shr_infnan_mod       , only : isnan => shr_infnan_isnan, nan => shr_infnan_nan, assignment(=)
-    use clm_time_manager     , only : is_restart, get_nstep
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_nitrogenstate_type) :: this
-    type(bounds_type)          , intent(in)    :: bounds 
-    type(file_desc_t)          , intent(inout) :: ncid   
-    character(len=*)           , intent(in)    :: flag   !'read' or 'write' or 'define'
-    real(r8)                   , intent(in)    :: totvegc_col(bounds%begc:bounds%endc) ! (gC/m2) total vegetation carbon
-
-    !
-    ! !LOCAL VARIABLES:
-    integer            :: i,j,k,l,c
-    logical            :: readvar
-    integer            :: idata
-    logical            :: exit_spinup = .false.
-    logical            :: enter_spinup = .false.
-    real(r8)           :: m          ! multiplier for the exit_spinup code
-    real(r8), pointer  :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer  :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    character(len=128) :: varname    ! temporary
-    integer            :: itemp      ! temporary 
-    integer , pointer  :: iptemp(:)  ! pointer to memory to be allocated
-    ! spinup state as read from restart file, for determining whether to enter or exit spinup mode.
-    integer            :: restart_file_spinup_state 
-    ! flags for comparing the model and restart decomposition cascades
-    integer            :: decomp_cascade_state, restart_file_decomp_cascade_state 
-    !------------------------------------------------------------------------
-
-    ! sminn
-    if (use_vertsoilc) then
-       ptr2d => this%sminn_vr_col
-       call restartvar(ncid=ncid, flag=flag, varname="sminn_vr", xtype=ncd_double,  &
-            dim1name='column', dim2name='levgrnd', switchdim=.true., &
-            long_name='',  units='', fill_value=spval, &
-            interpinic_flag='interp', readvar=readvar, data=ptr2d)
-    else
-       ptr1d => this%sminn_vr_col(:,1)
-       call restartvar(ncid=ncid, flag=flag, varname="sminn", xtype=ncd_double,  &
-            dim1name='column', &
-            long_name='',  units='', fill_value=spval, &
-            interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-    end if
-    if (flag=='read' .and. .not. readvar) then
-       call endrun(msg='ERROR::'//trim(varname)//' is required on an initialization dataset'//&
-            errMsg(sourcefile, __LINE__))
-    end if
-
-    ! decomposing N pools
-    do k = 1, ndecomp_pools
-       varname=trim(decomp_cascade_con%decomp_pool_name_restart(k))//'n'
-       if (use_vertsoilc) then
-          ptr2d => this%decomp_npools_vr_col(:,:,k)
-          call restartvar(ncid=ncid, flag=flag, varname=trim(varname)//"_vr", xtype=ncd_double, &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-       else
-          ptr1d => this%decomp_npools_vr_col(:,1,k)
-          call restartvar(ncid=ncid, flag=flag, varname=varname, xtype=ncd_double,  &
-               dim1name='column', &
-               long_name='',  units='', fill_value=spval, &
-               interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg='ERROR:: '//trim(varname)//' is required on an initialization dataset'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-    end do
-
-    if (use_vertsoilc) then
-       ptr2d => this%ntrunc_vr_col
-       call restartvar(ncid=ncid, flag=flag, varname="col_ntrunc_vr", xtype=ncd_double,  &
-            dim1name='column', dim2name='levgrnd', switchdim=.true., &
-            long_name='',  units='', fill_value=spval, &
-            interpinic_flag='interp', readvar=readvar, data=ptr2d)
-    else
-       ptr1d => this%ntrunc_vr_col(:,1)
-       call restartvar(ncid=ncid, flag=flag, varname="col_ntrunc", xtype=ncd_double,  &
-            dim1name='column', &
-            long_name='',  units='', fill_value=spval, &
-            interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-    end if
-
-    if (use_nitrif_denitrif) then
-       ! smin_no3_vr
-       if (use_vertsoilc) then
-          ptr2d => this%smin_no3_vr_col(:,:)
-          call restartvar(ncid=ncid, flag=flag, varname='smin_no3_vr', xtype=ncd_double, &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d)
-       else
-          ptr1d => this%smin_no3_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='smin_no3', xtype=ncd_double, &
-               dim1name='column', &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg= 'ERROR:: smin_no3_vr'//' is required on an initialization dataset' )
-       end if
-    end if
-
-    if (use_nitrif_denitrif) then
-       ! smin_nh4
-       if (use_vertsoilc) then
-          ptr2d => this%smin_nh4_vr_col(:,:)
-          call restartvar(ncid=ncid, flag=flag, varname='smin_nh4_vr', xtype=ncd_double, &
-               dim1name='column', dim2name='levgrnd', switchdim=.true., &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr2d) 
-       else
-          ptr1d => this%smin_nh4_vr_col(:,1)
-          call restartvar(ncid=ncid, flag=flag, varname='smin_nh4', xtype=ncd_double, &
-               dim1name='column', &
-               long_name='', units='', &
-               interpinic_flag='interp', readvar=readvar, data=ptr1d)
-       end if
-       if (flag=='read' .and. .not. readvar) then
-          call endrun(msg= 'ERROR:: smin_nh4_vr'//' is required on an initialization dataset' )
-       end if
-    end if
-
-    ! decomp_cascade_state - the purpose of this is to check to make sure the bgc used 
-    ! matches what the restart file was generated with.  
-    ! add info about the SOM decomposition cascade
-
-    if (use_century_decomp) then
-       decomp_cascade_state = 1
-    else
-       decomp_cascade_state = 0
-    end if
-    ! add info about the nitrification / denitrification state
-    if (use_nitrif_denitrif) then
-       decomp_cascade_state = decomp_cascade_state + 10
-    end if
-    if (flag == 'write') itemp = decomp_cascade_state    
-    call restartvar(ncid=ncid, flag=flag, varname='decomp_cascade_state', xtype=ncd_int,  &
-         long_name='BGC of the model that wrote this restart file:' &
-         // '  1s column: 0 = CLM-CN cascade, 1 = Century cascade;' &
-         // ' 10s column: 0 = CLM-CN denitrification, 10 = Century denitrification', units='', &
-         interpinic_flag='skip', readvar=readvar, data=itemp)
-    if (flag=='read') then
-       if (.not. readvar) then
-          ! assume, for sake of backwards compatibility, that if decomp_cascade_state 
-          ! is not in the restart file, then the current model state is the same as 
-          ! the prior model state
-          restart_file_decomp_cascade_state = decomp_cascade_state
-          if ( masterproc ) write(iulog,*) ' CNRest: WARNING!  Restart file does not ' &
-               // ' contain info on decomp_cascade_state used to generate the restart file.  '
-          if ( masterproc ) write(iulog,*) '   Assuming the same as current setting: ', decomp_cascade_state
-       else
-          restart_file_decomp_cascade_state = itemp  
-          if (decomp_cascade_state /= restart_file_decomp_cascade_state ) then
-             if ( masterproc ) then
-                write(iulog,*) 'CNRest: ERROR--the decomposition cascade differs between the current ' &
-                     // ' model state and the model that wrote the restart file. '
-                write(iulog,*) 'The model will be horribly out of equilibrium until after a lengthy spinup. '
-                write(iulog,*) 'Stopping here since this is probably an error in configuring the run. '
-                write(iulog,*) 'If you really wish to proceed, then override by setting '
-                write(iulog,*) 'override_bgc_restart_mismatch_dump to .true. in the namelist'
-                if ( .not. override_bgc_restart_mismatch_dump ) then
-                   call endrun(msg= ' CNRest: Stopping. Decomposition cascade mismatch error.'//&
-                        errMsg(sourcefile, __LINE__))
-                endif
-             endif
-          endif
-       end if
-    end if
-
-    !--------------------------------
-    ! Spinup state
-    !--------------------------------
-
-    ! Do nothing for write
-    ! Note that the call to write spinup_state out was done in soilbiogeochem_carbonstate_inst and
-    ! cannot be called again because it will try to define the variable twice
-    ! when the flag below is set to define
-    if (flag == 'read') then
-       call restartvar(ncid=ncid, flag=flag, varname='spinup_state', xtype=ncd_int,  &
-            long_name='Spinup state of the model that wrote this restart file: ' &
-            // ' 0 = normal model mode, 1 = AD spinup', units='', &
-            interpinic_flag='copy', readvar=readvar,  data=idata)
-       if (readvar) then
-          restart_file_spinup_state = idata
-       else
-          ! assume, for sake of backwards compatibility, that if spinup_state is not in 
-          ! the restart file then current model state is the same as prior model state
-          restart_file_spinup_state = spinup_state
-          if ( masterproc ) then
-             write(iulog,*) ' WARNING!  Restart file does not contain info ' &
-                  // ' on spinup state used to generate the restart file. '
-             write(iulog,*) '   Assuming the same as current setting: ', spinup_state
-          end if
-       end if
-    end if
-
-    ! now compare the model and restart file spinup states, and either take the 
-    ! model into spinup mode or out of it if they are not identical
-    ! taking model out of spinup mode requires multiplying each decomposing pool 
-    ! by the associated AD factor.
-    ! putting model into spinup mode requires dividing each decomposing pool 
-    ! by the associated AD factor.
-    ! only allow this to occur on first timestep of model run.
-
-    if (flag == 'read' .and. spinup_state /= restart_file_spinup_state ) then
-       if (spinup_state == 0 .and. restart_file_spinup_state >= 1 ) then
-          if ( masterproc ) write(iulog,*) ' NitrogenStateType Restart: taking SOM pools out of AD spinup mode'
-          exit_spinup = .true.
-       else if (spinup_state >= 1 .and. restart_file_spinup_state == 0 ) then
-          if ( masterproc ) write(iulog,*) ' NitrogenStateType Restart: taking SOM pools into AD spinup mode'
-          enter_spinup = .true.
-       else
-          call endrun(msg=' Error in entering/exiting spinup.  spinup_state ' &
-               // ' != restart_file_spinup_state, but do not know what to do'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-       if (get_nstep() >= 2) then
-          call endrun(msg=' Error in entering/exiting spinup - should occur only when nstep = 1'//&
-               errMsg(sourcefile, __LINE__))
-       endif
-       if ( exit_spinup .and. isnan(this%totvegcthresh) )then
-          call endrun(msg=' Error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//&
-               errMsg(sourcefile, __LINE__))
-       end if
-       do k = 1, ndecomp_pools
-          if ( exit_spinup ) then
-             m = decomp_cascade_con%spinup_factor(k)
-          else if ( enter_spinup ) then
-             m = 1. / decomp_cascade_con%spinup_factor(k)
-          end if
-          do c = bounds%begc, bounds%endc
-             l = col%landunit(c)
-             do j = 1, nlevdecomp
-                if ( abs(m - 1._r8) .gt. 0.000001_r8 .and. exit_spinup) then
-                   this%decomp_npools_vr_col(c,j,k) = this%decomp_npools_vr_col(c,j,k) * m * &
-                        get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
-                   ! If there is no vegetation nitrogen,
-                   ! implying that all vegetation has
-                   ! died, then 
-                   ! reset decomp pools to near zero during exit_spinup to
-                   ! avoid very 
-                   ! large and inert soil carbon stocks; note that only
-                   ! pools with spinup factor > 1 
-                   ! will be affected, which means that total SOMN and LITN
-                   ! pools will not be set to 0.
-                   if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then 
-                      this%decomp_npools_vr_col(c,j,k) = 0._r8
-                   endif
-                elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then
-                   this%decomp_npools_vr_col(c,j,k) = this%decomp_npools_vr_col(c,j,k) * m / &
-                        get_spinup_latitude_term(grc%latdeg(col%gridcell(c)))
-                else
-                   this%decomp_npools_vr_col(c,j,k) = this%decomp_npools_vr_col(c,j,k) * m 
-                endif
-             end do
-          end do
-       end do
-    end if
-
-  end subroutine Restart
-
-  !-----------------------------------------------------------------------
-  subroutine SetValues ( this, num_column, filter_column, value_column )
-    !
-    ! !DESCRIPTION:
-    ! Set nitrogen state variables
-    !
-    ! !ARGUMENTS:
-    class (soilbiogeochem_nitrogenstate_type) :: this
-    integer , intent(in) :: num_column
-    integer , intent(in) :: filter_column(:)
-    real(r8), intent(in) :: value_column
-    !
-    ! !LOCAL VARIABLES:
-    integer :: fi,i     ! loop index
-    integer :: j,k      ! indices
-    !------------------------------------------------------------------------
-
-    do fi = 1,num_column
-       i = filter_column(fi)
-
-       this%sminn_col(i)       = value_column
-       this%ntrunc_col(i)      = value_column
-       this%cwdn_col(i)        = value_column
-       if (use_nitrif_denitrif) then
-          this%smin_no3_col(i) = value_column
-          this%smin_nh4_col(i) = value_column
-       end if
-       this%totlitn_col(i)     = value_column
-       this%totsomn_col(i)     = value_column
-       this%totsomn_1m_col(i)  = value_column
-       this%totlitn_1m_col(i)  = value_column
-    end do
-
-    do j = 1,nlevdecomp_full
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%sminn_vr_col(i,j)       = value_column
-          this%ntrunc_vr_col(i,j)      = value_column
-          if (use_nitrif_denitrif) then
-             this%smin_no3_vr_col(i,j) = value_column
-             this%smin_nh4_vr_col(i,j) = value_column
-          end if
-       end do
-    end do
-
-    ! column and decomp_pools
-    do k = 1, ndecomp_pools
-       do fi = 1,num_column
-          i = filter_column(fi)
-          this%decomp_npools_col(i,k)    = value_column
-          this%decomp_npools_1m_col(i,k) = value_column
-       end do
-    end do
-
-    ! column levdecomp, and decomp_pools
-    do j = 1,nlevdecomp_full
-       do k = 1, ndecomp_pools
-          do fi = 1,num_column
-             i = filter_column(fi)
-             this%decomp_npools_vr_col(i,j,k) = value_column
-          end do
-       end do
-    end do
-
-  end subroutine SetValues
-
-end module SoilBiogeochemNitrogenStateType
diff --git a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 b/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90
deleted file mode 100644
index 2349a63fd4..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90
+++ /dev/null
@@ -1,266 +0,0 @@
-module SoilBiogeochemPotentialMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  ! Calculate potential decomp rates and total immobilization demand.
-  !
-  ! !USES:
-  use shr_kind_mod                       , only : r8 => shr_kind_r8
-  use decompMod                          , only : bounds_type
-  use clm_varpar                         , only : nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
-  use SoilBiogeochemStateType            , only : soilbiogeochem_state_type
-  use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
-  use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
-  use SoilBiogeochemNitrogenStateType    , only : soilbiogeochem_nitrogenstate_type
-  use SoilBiogeochemNitrogenFluxType     , only : soilbiogeochem_nitrogenflux_type
-  use clm_varctl                         , only : use_fates, iulog
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: readParams
-  public :: SoilBiogeochemPotential
-  !
-  type, private :: params_type
-     real(r8) :: dnp         !denitrification proportion
-  end type Params_type
-  !
-  type(params_type), private :: params_inst
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine readParams ( ncid )
-    !
-    ! !DESCRIPTION:
-    ! Read parameters
-    !
-    ! !USES:
-    use ncdio_pio    , only: file_desc_t,ncd_io
-    use abortutils   , only: endrun
-    use shr_log_mod  , only: errMsg => shr_log_errMsg
-    !
-    ! !ARGUMENTS:
-    type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
-    !
-    ! !LOCAL VARIABLES:
-    character(len=32)  :: subname = 'CNDecompParamsType'
-    character(len=100) :: errCode = '-Error reading in parameters file:'
-    logical            :: readv ! has variable been read in or not
-    real(r8)           :: tempr ! temporary to read in constant
-    character(len=100) :: tString ! temp. var for reading
-    !-----------------------------------------------------------------------
-
-    tString='dnp'
-    call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv)
-    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%dnp=tempr 
-
-  end subroutine readParams
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, &
-       soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,  &
-       soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, &
-       cn_decomp_pools, p_decomp_cpool_loss, pmnf_decomp_cascade)
-    !
-    ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    !
-    ! !ARGUMENT:
-    type(bounds_type)                       , intent(in)    :: bounds   
-    integer                                 , intent(in)    :: num_soilc          ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:)    ! filter for soil columns
-    type(soilbiogeochem_state_type)         , intent(inout) :: soilbiogeochem_state_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(in)    :: soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonflux_type)    , intent(inout) :: soilbiogeochem_carbonflux_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
-    type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
-    real(r8)                                , intent(out)   :: cn_decomp_pools(bounds%begc:,1:,1:)     ! c:n ratios of applicable pools
-    real(r8)                                , intent(out)   :: p_decomp_cpool_loss(bounds%begc:,1:,1:) ! potential C loss from one pool to another
-    real(r8)                                , intent(out)   :: pmnf_decomp_cascade(bounds%begc:,1:,1:) ! potential mineral N flux, from one pool to another
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,j,k,l,m                                    !indices
-    integer :: fc                                           !filter column index
-    integer :: begc,endc                                    !bounds 
-    real(r8):: immob(bounds%begc:bounds%endc,1:nlevdecomp)  !potential N immobilization
-    real(r8):: ratio                                        !temporary variable
-    integer, parameter :: i_atm = 0 !TODO - this appears in two places - move it to 1
-    !-----------------------------------------------------------------------
-   
-    begc = bounds%begc; endc = bounds%endc
-
-    SHR_ASSERT_ALL((ubound(cn_decomp_pools)     == (/endc,nlevdecomp,ndecomp_pools/))               , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(p_decomp_cpool_loss) == (/endc,nlevdecomp,ndecomp_cascade_transitions/)) , errMsg(sourcefile, __LINE__))
-    SHR_ASSERT_ALL((ubound(pmnf_decomp_cascade) == (/endc,nlevdecomp,ndecomp_cascade_transitions/)) , errMsg(sourcefile, __LINE__))
-
-    associate(                                                                                                          & 
-         cascade_donor_pool               => decomp_cascade_con%cascade_donor_pool                                 , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
-         cascade_receiver_pool            => decomp_cascade_con%cascade_receiver_pool                              , & ! Input:  [integer  (:)     ]  which pool is C added to for a given decomposition step
-         floating_cn_ratio_decomp_pools   => decomp_cascade_con%floating_cn_ratio_decomp_pools                     , & ! Input:  [logical  (:)     ]  TRUE => pool has fixed C:N ratio                   
-         initial_cn_ratio                 => decomp_cascade_con%initial_cn_ratio                                   , & ! Input:  [real(r8) (:)     ]  c:n ratio for initialization of pools             
-
-         fpi_vr                           => soilbiogeochem_state_inst%fpi_vr_col                                  , & ! Input:  [real(r8) (:,:)   ]  fraction of potential immobilization (no units) 
-         rf_decomp_cascade                => soilbiogeochem_state_inst%rf_decomp_cascade_col                       , & ! Input:  [real(r8) (:,:,:) ]  respired fraction in decomposition step (frac)
-         pathfrac_decomp_cascade          => soilbiogeochem_state_inst%pathfrac_decomp_cascade_col                 , & ! Input:  [real(r8) (:,:,:) ]  what fraction of C leaving a given pool passes through a given transition (frac)
-
-         decomp_npools_vr                 => soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col                , & ! Input:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) N pools
-
-         decomp_cpools_vr                 => soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col                  , & ! Input:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) c pools
-
-         decomp_cascade_ntransfer_vr      => soilbiogeochem_nitrogenflux_inst%decomp_cascade_ntransfer_vr_col      , & ! Output: [real(r8) (:,:,:) ]  vert-res transfer of N from donor to receiver pool along decomp. cascade (gN/m3/s)
-         decomp_cascade_sminn_flux_vr     => soilbiogeochem_nitrogenflux_inst%decomp_cascade_sminn_flux_vr_col     , & ! Output: [real(r8) (:,:,:) ]  vert-res mineral N flux for transition along decomposition cascade (gN/m3/s)
-         potential_immob_vr               => soilbiogeochem_nitrogenflux_inst%potential_immob_vr_col               , & ! Output: [real(r8) (:,:)   ]                                                  
-         sminn_to_denit_decomp_cascade_vr => soilbiogeochem_nitrogenflux_inst%sminn_to_denit_decomp_cascade_vr_col , & ! Output: [real(r8) (:,:,:) ] 
-         gross_nmin_vr                    => soilbiogeochem_nitrogenflux_inst%gross_nmin_vr_col                    , & ! Output: [real(r8) (:,:)   ]                                                  
-         net_nmin_vr                      => soilbiogeochem_nitrogenflux_inst%net_nmin_vr_col                      , & ! Output: [real(r8) (:,:)   ]                                                  
-         gross_nmin                       => soilbiogeochem_nitrogenflux_inst%gross_nmin_col                       , & ! Output: [real(r8) (:)     ]  gross rate of N mineralization (gN/m2/s)          
-         net_nmin                         => soilbiogeochem_nitrogenflux_inst%net_nmin_col                         , & ! Output: [real(r8) (:)     ]  net rate of N mineralization (gN/m2/s)            
-         
-         w_scalar                         => soilbiogeochem_carbonflux_inst%w_scalar_col                           , & ! Input:  [real(r8) (:,:)   ]  fraction by which decomposition is limited by moisture availability
-         decomp_cascade_hr_vr             => soilbiogeochem_carbonflux_inst%decomp_cascade_hr_vr_col               , & ! Output: [real(r8) (:,:,:) ]  vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
-         decomp_cascade_ctransfer_vr      => soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_vr_col        , & ! Output: [real(r8) (:,:,:) ]  vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
-         decomp_k                         => soilbiogeochem_carbonflux_inst%decomp_k_col                           , & ! Output: [real(r8) (:,:,:) ]  rate constant for decomposition (1./sec)      
-         phr_vr                           => soilbiogeochem_carbonflux_inst%phr_vr_col                             , & ! Output: [real(r8) (:,:)   ]  potential HR (gC/m3/s)                           
-         fphr                             => soilbiogeochem_carbonflux_inst%fphr_col                                 & ! Output: [real(r8) (:,:)   ]  fraction of potential SOM + LITTER heterotrophic
-         )
-   
-   if ( .not. use_fates ) then
-      ! set initial values for potential C and N fluxes
-      p_decomp_cpool_loss(begc:endc, :, :) = 0._r8
-      pmnf_decomp_cascade(begc:endc, :, :) = 0._r8
-
-      ! column loop to calculate potential decomp rates and total immobilization demand
-
-      !! calculate c:n ratios of applicable pools
-      do l = 1, ndecomp_pools
-         if ( floating_cn_ratio_decomp_pools(l) ) then
-            do j = 1,nlevdecomp
-               do fc = 1,num_soilc
-                  c = filter_soilc(fc)
-                  if ( decomp_npools_vr(c,j,l) > 0._r8 ) then
-                     cn_decomp_pools(c,j,l) = decomp_cpools_vr(c,j,l) / decomp_npools_vr(c,j,l)
-                  end if
-               end do
-            end do
-         else
-            do j = 1,nlevdecomp
-               do fc = 1,num_soilc
-                  c = filter_soilc(fc)
-                  cn_decomp_pools(c,j,l) = initial_cn_ratio(l)
-               end do
-            end do
-         end if
-      end do
-
-      ! calculate the non-nitrogen-limited fluxes
-      ! these fluxes include the  "/ dt" term to put them on a
-      ! per second basis, since the rate constants have been
-      ! calculated on a per timestep basis.
-
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-
-               if (decomp_cpools_vr(c,j,cascade_donor_pool(k)) > 0._r8 .and. &
-                    decomp_k(c,j,cascade_donor_pool(k)) > 0._r8 ) then
-                  p_decomp_cpool_loss(c,j,k) = decomp_cpools_vr(c,j,cascade_donor_pool(k)) &
-                       * decomp_k(c,j,cascade_donor_pool(k))  * pathfrac_decomp_cascade(c,j,k)
-                  if ( .not. floating_cn_ratio_decomp_pools(cascade_receiver_pool(k)) ) then  !! not transition of cwd to litter
-
-                     if (cascade_receiver_pool(k) /= i_atm ) then  ! not 100% respiration
-                        ratio = 0._r8
-
-                        if (decomp_npools_vr(c,j,cascade_donor_pool(k)) > 0._r8) then
-                           ratio = cn_decomp_pools(c,j,cascade_receiver_pool(k))/cn_decomp_pools(c,j,cascade_donor_pool(k))
-                        endif
-
-                        pmnf_decomp_cascade(c,j,k) = (p_decomp_cpool_loss(c,j,k) * (1.0_r8 - rf_decomp_cascade(c,j,k) - ratio) &
-                             / cn_decomp_pools(c,j,cascade_receiver_pool(k)) )
-
-                     else   ! 100% respiration
-                        pmnf_decomp_cascade(c,j,k) = - p_decomp_cpool_loss(c,j,k) / cn_decomp_pools(c,j,cascade_donor_pool(k))
-                     endif
-
-                  else   ! CWD -> litter
-                     pmnf_decomp_cascade(c,j,k) = 0._r8
-                  end if
-               end if
-            end do
-
-         end do
-      end do
-
-      ! Sum up all the potential immobilization fluxes (positive pmnf flux)
-      ! and all the mineralization fluxes (negative pmnf flux)
-      do j = 1,nlevdecomp
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            immob(c,j) = 0._r8
-         end do
-      end do
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               if (pmnf_decomp_cascade(c,j,k) > 0._r8) then
-                  immob(c,j) = immob(c,j) + pmnf_decomp_cascade(c,j,k)
-               else
-                  gross_nmin_vr(c,j) = gross_nmin_vr(c,j) - pmnf_decomp_cascade(c,j,k)
-               end if
-            end do
-         end do
-      end do
-
-      do j = 1,nlevdecomp
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            potential_immob_vr(c,j) = immob(c,j)
-         end do
-      end do
-   else  ! use_fates
-      ! As a first step we are making this a C-only model, so no N downregulation of fluxes. 
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               !
-               p_decomp_cpool_loss(c,j,k) = decomp_cpools_vr(c,j,cascade_donor_pool(k)) &
-                    * decomp_k(c,j,cascade_donor_pool(k))  * pathfrac_decomp_cascade(c,j,k)
-               !
-            end do
-         end do
-      end do
-   end if
-
-      ! Add up potential hr for methane calculations
-      do j = 1,nlevdecomp
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            phr_vr(c,j) = 0._r8
-         end do
-      end do
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               phr_vr(c,j) = phr_vr(c,j) + rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k)
-            end do
-         end do
-      end do
-
-    end associate
-
-  end subroutine SoilBiogeochemPotential
- 
-end module SoilBiogeochemPotentialMod
diff --git a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90
deleted file mode 100644
index c50bbd49ef..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90
+++ /dev/null
@@ -1,173 +0,0 @@
-module SoilBiogeochemPrecisionControlMod
-
-  !----------------------------------------------------------------------- 
-  ! !DESCRIPTION:
-  ! controls on very low values in critical state variables 
-  ! 
-  ! !USES:
-  use shr_kind_mod                    , only : r8 => shr_kind_r8
-  use clm_varpar                      , only : ndecomp_pools
-  use SoilBiogeochemCarbonStateType   , only : soilbiogeochem_carbonstate_type
-  use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type
-  use ColumnType                      , only : col
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public:: SoilBiogeochemPrecisionControlInit ! Initialization
-  public:: SoilBiogeochemPrecisionControl     ! Apply precision control to soil biogeochemistry carbon and nitrogen states
-
-  ! !PUBLIC DATA:
-  real(r8), public :: ccrit                   ! critical carbon state value for truncation (gC/m2)
-  real(r8), public :: ncrit                   ! critical nitrogen state value for truncation (gN/m2)
-  !----------------------------------------------------------------------- 
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemPrecisionControlInit( soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, &
-       c14_soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst)
-
-    !
-    ! !DESCRIPTION: 
-    ! Initialization of soil biogeochemistry precision control
-    !
-    ! !USES:
-    !
-    ! !ARGUMENTS:
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c13_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c14_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    real(r8), parameter :: totvegcthresh = 0.1_r8   ! Total vegetation carbon threshold to zero out decomposition pools
-    !-----------------------------------------------------------------------
-    ccrit    =  1.e-8_r8              ! critical carbon state value for truncation (gC/m2)
-    ncrit    =  1.e-8_r8              ! critical nitrogen state value for truncation (gN/m2)
-
-    !call soilbiogeochem_carbonstate_inst%setTotVgCThresh( totvegcthresh )
-    !call soilbiogeochem_nitrogenstate_inst%setTotVgCThresh( totvegcthresh )
-
-  end subroutine SoilBiogeochemPrecisionControlInit
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, &
-       soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, &
-       c14_soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst)
-
-    !
-    ! !DESCRIPTION: 
-    ! On the radiation time step, force leaf and deadstem c and n to 0 if
-    ! they get too small.
-    !
-    ! !USES:
-    use clm_varctl , only : iulog, use_nitrif_denitrif, use_cn
-    use clm_varpar , only : nlevdecomp
-    use CNSharedParamsMod, only: use_fun
-    !
-    ! !ARGUMENTS:
-    integer                                 , intent(in)    :: num_soilc       ! number of soil columns in filter
-    integer                                 , intent(in)    :: filter_soilc(:) ! filter for soil columns
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c13_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_carbonstate_type)   , intent(inout) :: c14_soilbiogeochem_carbonstate_inst
-    type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst
-    !
-    ! !LOCAL VARIABLES:
-    integer :: c,j,k ! indices
-    integer :: fc    ! filter indices
-    real(r8):: cc,cn ! truncation terms for column-level corrections
-    real(r8):: cc13  ! truncation terms for column-level corrections
-    real(r8):: cc14  ! truncation terms for column-level corrections
-    !-----------------------------------------------------------------------
-
-    ! soilbiogeochem_carbonstate_inst%ctrunc_vr_col          Output:  [real(r8) (:,:)   ]  (gC/m3) column-level sink for C truncation      
-    ! soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col   Output:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) c pools
-
-    ! soilbiogeochem_nitrogenstate_inst%ntrunc_vr_col        Output:  [real(r8) (:,:)   ]  (gN/m3) column-level sink for N truncation      
-    ! soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col Output:  [real(r8) (:,:,:) ]  (gC/m3)  vertically-resolved decomposing (litter, cwd, soil) N pools
-    ! soilbiogeochem_nitrogenstate_inst%smin_nh4_vr_col      Output:  [real(r8) (:,:)   ]  (gN/m3) soil mineral NH4                        
-    ! soilbiogeochem_nitrogenstate_inst%smin_no3_vr_col      Output:  [real(r8) (:,:)   ]  (gN/m3) soil mineral NO3                        
-
-    associate(&
-         cs    => soilbiogeochem_carbonstate_inst     , &
-         ns    => soilbiogeochem_nitrogenstate_inst   , & 
-         c13cs => c13_soilbiogeochem_carbonstate_inst , &
-         c14cs => c14_soilbiogeochem_carbonstate_inst   &
-         )
-
-      ! column loop
-      do fc = 1,num_soilc
-         c = filter_soilc(fc)
-
-         do j = 1,nlevdecomp
-            ! initialize the column-level C and N truncation terms
-            cc = 0._r8
-            cn = 0._r8
-
-            ! do tests on state variables for precision control
-            ! for linked C-N state variables, perform precision test on
-            ! the C component, but truncate both C and N components
-
-
-            ! all decomposing pools C and N
-            do k = 1, ndecomp_pools
-
-               if (abs(cs%decomp_cpools_vr_col(c,j,k)) < ccrit) then
-                  cc = cc + cs%decomp_cpools_vr_col(c,j,k)
-                  cs%decomp_cpools_vr_col(c,j,k) = 0._r8
-
-                  if (use_cn) then
-                     cn = cn + ns%decomp_npools_vr_col(c,j,k)
-                     ns%decomp_npools_vr_col(c,j,k) = 0._r8
-                  endif
-
-               end if
-
-            end do
-
-            ! not doing precision control on soil mineral N, since it will
-            ! be getting the N truncation flux anyway.
-
-            cs%ctrunc_vr_col(c,j) = cs%ctrunc_vr_col(c,j) + cc
-
-            if (use_cn) then
-               ns%ntrunc_vr_col(c,j) = ns%ntrunc_vr_col(c,j) + cn
-            endif
-         end do
-
-      end do   ! end of column loop
-
-     if(.not.use_fun)then
-      if (use_nitrif_denitrif) then
-         ! remove small negative perturbations for stability purposes, if any should arise.
-        
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            do j = 1,nlevdecomp
-               if (abs(ns%smin_no3_vr_col(c,j)) < ncrit/1e4_r8) then
-                  if ( ns%smin_no3_vr_col(c,j)  < 0._r8 ) then
-                     !write(iulog, *) '-10^-12 < smin_no3 < 0. resetting to zero.'
-                     !write(iulog, *) 'smin_no3_vr_col(c,j), c, j: ', ns%smin_no3_vr_col(c,j), c, j
-                     ns%smin_no3_vr_col(c,j) = 0._r8
-                  endif
-               end if
-               if (abs(ns%smin_nh4_vr_col(c,j)) < ncrit/1e4_r8) then
-                  if ( ns%smin_nh4_vr_col(c,j)  < 0._r8 ) then
-                     !write(iulog, *) '-10^-12 < smin_nh4 < 0. resetting to zero.'
-                     !write(iulog, *) 'smin_nh4_vr_col(c,j), c, j: ', ns%smin_nh4_vr_col(c,j), c, j
-                     ns%smin_nh4_vr_col(c,j) = 0._r8
-                  endif
-               end if
-            end do
-         end do
-      endif
-     endif
-
-    end associate
-
-  end subroutine SoilBiogeochemPrecisionControl
-
-end module SoilBiogeochemPrecisionControlMod
diff --git a/src/soilbiogeochem/SoilBiogeochemStateType.F90 b/src/soilbiogeochem/SoilBiogeochemStateType.F90
deleted file mode 100644
index 46586ef393..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemStateType.F90
+++ /dev/null
@@ -1,336 +0,0 @@
-module SoilBiogeochemStateType
-
-  use shr_kind_mod   , only : r8 => shr_kind_r8
-  use shr_log_mod    , only : errMsg => shr_log_errMsg
-  use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-  use decompMod      , only : bounds_type
-  use abortutils     , only : endrun
-  use spmdMod        , only : masterproc
-  use clm_varpar     , only : nlevsno, nlevgrnd, nlevlak, nlevsoifl, nlevsoi
-  use clm_varpar     , only : ndecomp_cascade_transitions, nlevdecomp, nlevdecomp_full
-  use clm_varcon     , only : spval, ispval, c14ratio, grlnd
-  use landunit_varcon, only : istsoil, istcrop
-  use clm_varpar     , only : nlevsno, nlevgrnd, nlevlak
-  use clm_varctl     , only : use_vertsoilc, use_cn 
-  use clm_varctl     , only : iulog
-  use LandunitType   , only : lun                
-  use ColumnType     , only : col                
-  ! 
-  ! !PUBLIC TYPES:
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public :: get_spinup_latitude_term  
-  !
-  ! !PUBLIC TYPES:
-  type, public :: soilbiogeochem_state_type
-
-     real(r8) , pointer :: leaf_prof_patch             (:,:)   ! (1/m) profile of leaves (vertical profiles for calculating fluxes)
-     real(r8) , pointer :: froot_prof_patch            (:,:)   ! (1/m) profile of fine roots (vertical profiles for calculating fluxes)
-     real(r8) , pointer :: croot_prof_patch            (:,:)   ! (1/m) profile of coarse roots (vertical profiles for calculating fluxes)
-     real(r8) , pointer :: stem_prof_patch             (:,:)   ! (1/m) profile of stems (vertical profiles for calculating fluxes)
-     real(r8) , pointer :: fpi_vr_col                  (:,:)   ! (no units) fraction of potential immobilization 
-     real(r8) , pointer :: fpi_col                     (:)     ! (no units) fraction of potential immobilization 
-     real(r8),  pointer :: fpg_col                     (:)     ! (no units) fraction of potential gpp 
-     real(r8) , pointer :: rf_decomp_cascade_col       (:,:,:) ! (frac) respired fraction in decomposition step 
-     real(r8) , pointer :: pathfrac_decomp_cascade_col (:,:,:) ! (frac) what fraction of C leaving a given pool passes through a given transition 
-     real(r8) , pointer :: nfixation_prof_col          (:,:)   ! (1/m) profile for N fixation additions 
-     real(r8) , pointer :: ndep_prof_col               (:,:)   ! (1/m) profile for N fixation additions 
-     real(r8) , pointer :: som_adv_coef_col            (:,:)   ! (m2/s) SOM advective flux 
-     real(r8) , pointer :: som_diffus_coef_col         (:,:)   ! (m2/s) SOM diffusivity due to bio/cryo-turbation 
-     real(r8) , pointer :: plant_ndemand_col           (:)     ! column-level plant N demand
-
-   contains
-
-     procedure, public  :: Init         
-     procedure, public  :: Restart      
-     procedure, private :: InitAllocate 
-     procedure, private :: InitHistory  
-     procedure, private :: InitCold     
-
-  end type soilbiogeochem_state_type
-  !------------------------------------------------------------------------
-
-contains
-
-  !------------------------------------------------------------------------
-  subroutine Init(this, bounds)
-
-    class(soilbiogeochem_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-
-    call this%InitAllocate ( bounds )
-    if (use_cn) then
-       call this%InitHistory ( bounds )
-    end if
-    call this%InitCold ( bounds ) 
-
-  end subroutine Init
-
-  !------------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer :: begp, endp
-    integer :: begc, endc
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    allocate(this%leaf_prof_patch     (begp:endp,1:nlevdecomp_full)) ; this%leaf_prof_patch     (:,:) = spval
-    allocate(this%froot_prof_patch    (begp:endp,1:nlevdecomp_full)) ; this%froot_prof_patch    (:,:) = spval
-    allocate(this%croot_prof_patch    (begp:endp,1:nlevdecomp_full)) ; this%croot_prof_patch    (:,:) = spval
-    allocate(this%stem_prof_patch     (begp:endp,1:nlevdecomp_full)) ; this%stem_prof_patch     (:,:) = spval
-    allocate(this%fpi_vr_col          (begc:endc,1:nlevdecomp_full)) ; this%fpi_vr_col          (:,:) = nan
-    allocate(this%fpi_col             (begc:endc))                   ; this%fpi_col             (:)   = nan
-    allocate(this%fpg_col             (begc:endc))                   ; this%fpg_col             (:)   = nan
-    allocate(this%nfixation_prof_col  (begc:endc,1:nlevdecomp_full)) ; this%nfixation_prof_col  (:,:) = spval
-    allocate(this%ndep_prof_col       (begc:endc,1:nlevdecomp_full)) ; this%ndep_prof_col       (:,:) = spval
-    allocate(this%som_adv_coef_col    (begc:endc,1:nlevdecomp_full)) ; this%som_adv_coef_col    (:,:) = spval
-    allocate(this%som_diffus_coef_col (begc:endc,1:nlevdecomp_full)) ; this%som_diffus_coef_col (:,:) = spval
-    allocate(this%plant_ndemand_col   (begc:endc))                   ; this%plant_ndemand_col   (:)   = nan
-
-    allocate(this%rf_decomp_cascade_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions)); 
-    this%rf_decomp_cascade_col(:,:,:) = nan
-
-    allocate(this%pathfrac_decomp_cascade_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions));     
-    this%pathfrac_decomp_cascade_col(:,:,:) = nan
-
-  end subroutine InitAllocate
-
-  !------------------------------------------------------------------------
-  subroutine InitHistory(this, bounds)
-    !
-    ! !DESCRIPTION:
-    ! Initialize module data structure
-    !
-    ! !USES:
-    use shr_infnan_mod    , only : nan => shr_infnan_nan, assignment(=)
-    use histFileMod       , only : hist_addfld1d, hist_addfld2d, hist_addfld_decomp, no_snow_normal
-    use CNSharedParamsMod , only : use_fun
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_state_type) :: this
-    type(bounds_type), intent(in) :: bounds  
-    !
-    ! !LOCAL VARIABLES:
-    integer           :: begp, endp
-    integer           :: begc, endc
-    character(8)      :: vr_suffix
-    character(10)     :: active
-    real(r8), pointer :: data2dptr(:,:), data1dptr(:) ! temp. pointers for slicing larger arrays
-    !------------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    this%croot_prof_patch(begp:endp,:) = spval
-    call hist_addfld_decomp (fname='CROOT_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for litter C and N inputs from coarse roots', &
-         ptr_patch=this%croot_prof_patch, default='inactive')
-
-    this%froot_prof_patch(begp:endp,:) = spval
-    call hist_addfld_decomp (fname='FROOT_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for litter C and N inputs from fine roots', &
-         ptr_patch=this%froot_prof_patch, default='inactive')
-
-    this%leaf_prof_patch(begp:endp,:) = spval
-    call hist_addfld_decomp (fname='LEAF_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for litter C and N inputs from leaves', &
-         ptr_patch=this%leaf_prof_patch, default='inactive')
-
-    this%stem_prof_patch(begp:endp,:) = spval
-    call hist_addfld_decomp (fname='STEM_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for litter C and N inputs from stems', &
-         ptr_patch=this%stem_prof_patch, default='inactive')
-
-    this%nfixation_prof_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='NFIXATION_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for biological N fixation', &
-         ptr_col=this%nfixation_prof_col, default='inactive')
-
-    this%ndep_prof_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='NDEP_PROF', units='1/m',  type2d='levdcmp', &
-         avgflag='A', long_name='profile for atmospheric N  deposition', &
-         ptr_col=this%ndep_prof_col, default='inactive')
-
-    this%som_adv_coef_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='SOM_ADV_COEF', units='m/s',  type2d='levdcmp', &
-         avgflag='A', long_name='advection term for vertical SOM translocation', &
-         ptr_col=this%som_adv_coef_col, default='inactive')
-
-    this%som_diffus_coef_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='SOM_DIFFUS_COEF', units='m^2/s',  type2d='levdcmp', &
-         avgflag='A', long_name='diffusion coefficient for vertical SOM translocation', &
-         ptr_col=this%som_diffus_coef_col, default='inactive')
-
-    if ( nlevdecomp_full > 1 ) then
-       this%fpi_col(begc:endc) = spval
-       call hist_addfld1d (fname='FPI', units='proportion', &
-            avgflag='A', long_name='fraction of potential immobilization', &
-            ptr_col=this%fpi_col, default='inactive')
-    endif
-   
-    if (.not. use_fun) then
-       this%fpg_col(begc:endc) = spval
-       call hist_addfld1d (fname='FPG', units='proportion', &
-            avgflag='A', long_name='fraction of potential gpp', &
-            ptr_col=this%fpg_col, default='inactive')
-    end if
-
-    if (nlevdecomp > 1) then
-       vr_suffix = "_vr"
-    else 
-       vr_suffix = ""
-    endif
-    this%fpi_vr_col(begc:endc,:) = spval
-    call hist_addfld_decomp (fname='FPI'//trim(vr_suffix), units='proportion', type2d='levdcmp', & 
-         avgflag='A', long_name='fraction of potential immobilization', &
-         ptr_col=this%fpi_vr_col, default='inactive')
-
-  end subroutine InitHistory
-
-  !-----------------------------------------------------------------------
-  subroutine initCold(this, bounds)
-    !
-    ! !USES:
-    use spmdMod    , only : masterproc
-    use fileutils  , only : getfil
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_state_type) :: this
-    type(bounds_type), intent(in) :: bounds   
-    !
-    ! !LOCAL VARIABLES:
-    integer               :: g,l,c,p,n,j,m            ! indices
-    integer               :: dimid                    ! dimension id
-    integer               :: ier                      ! error status
-    logical               :: readvar 
-    integer               :: begc, endc
-    !-----------------------------------------------------------------------
-
-    begc = bounds%begc; endc= bounds%endc
-
-    ! --------------------------------------------------------------------
-    ! Initialize terms needed for dust model
-    ! --------------------------------------------------------------------
-       
-    do c = bounds%begc, bounds%endc
-       l = col%landunit(c)
-       if (lun%ifspecial(l)) then
-          this%fpi_col (c) = spval
-          this%fpg_col (c) = spval
-          do j = 1,nlevdecomp_full
-             this%fpi_vr_col(c,j) = spval
-          end do
-       end if
-
-       if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then
-          ! initialize fpi_vr so that levels below nlevsoi are not nans
-          this%fpi_vr_col(c,1:nlevdecomp_full)          = 0._r8 
-          this%som_adv_coef_col(c,1:nlevdecomp_full)    = 0._r8 
-          this%som_diffus_coef_col(c,1:nlevdecomp_full) = 0._r8 
-
-          ! initialize the profiles for converting to vertically resolved carbon pools
-          this%nfixation_prof_col(c,1:nlevdecomp_full)  = 0._r8 
-          this%ndep_prof_col(c,1:nlevdecomp_full)       = 0._r8 
-       end if
-    end do
-
-  end subroutine initCold
-
-  !------------------------------------------------------------------------
-  subroutine Restart(this, bounds, ncid, flag)
-    !
-    ! !USES:
-    use shr_log_mod, only : errMsg => shr_log_errMsg
-    use spmdMod    , only : masterproc
-    use abortutils , only : endrun
-    use restUtilMod
-    use ncdio_pio
-    !
-    ! !ARGUMENTS:
-    class(soilbiogeochem_state_type) :: this
-    type(bounds_type), intent(in)    :: bounds 
-    type(file_desc_t), intent(inout) :: ncid   
-    character(len=*) , intent(in)    :: flag   
-    !
-    ! !LOCAL VARIABLES:
-    integer, pointer  :: temp1d(:)  ! temporary
-    integer           :: p,j,c,i    ! indices
-    logical           :: readvar    ! determine if variable is on initial file
-    real(r8), pointer :: ptr2d(:,:) ! temp. pointers for slicing larger arrays
-    real(r8), pointer :: ptr1d(:)   ! temp. pointers for slicing larger arrays
-    !-----------------------------------------------------------------------
-  
-    if (use_vertsoilc) then
-       ptr2d => this%fpi_vr_col
-       call restartvar(ncid=ncid, flag=flag, varname='fpi_vr', xtype=ncd_double,  &
-            dim1name='column',dim2name='levgrnd', switchdim=.true., &
-            long_name='fraction of potential immobilization',  units='unitless', &
-            interpinic_flag='interp', readvar=readvar, data=ptr2d)
-    else
-       ptr1d => this%fpi_vr_col(:,1) ! nlevdecomp = 1; so treat as 1D variable
-       call restartvar(ncid=ncid, flag=flag, varname='fpi', xtype=ncd_double,  &
-            dim1name='column', &
-            long_name='fraction of potential immobilization',  units='unitless', &
-            interpinic_flag='interp' , readvar=readvar, data=ptr1d)
-    end if
-
-    if (use_vertsoilc) then
-       ptr2d => this%som_adv_coef_col
-       call restartvar(ncid=ncid, flag=flag, varname='som_adv_coef_vr', xtype=ncd_double,  &
-            dim1name='column',dim2name='levgrnd', switchdim=.true., &
-            long_name='SOM advective flux', units='m/s', fill_value=spval, &
-            interpinic_flag='interp', readvar=readvar, data=ptr2d)
-    end if
-    
-    if (use_vertsoilc) then
-       ptr2d => this%som_diffus_coef_col
-       call restartvar(ncid=ncid, flag=flag, varname='som_diffus_coef_vr', xtype=ncd_double,  &
-            dim1name='column',dim2name='levgrnd', switchdim=.true., &
-            long_name='SOM diffusivity due to bio/cryo-turbation',  units='m^2/s', fill_value=spval, &
-            interpinic_flag='interp', readvar=readvar, data=ptr2d)
-    end if
-
-    call restartvar(ncid=ncid, flag=flag, varname='fpg', xtype=ncd_double,  &
-         dim1name='column', &
-         long_name='', units='', &
-         interpinic_flag='interp', readvar=readvar, data=this%fpg_col) 
-
-  end subroutine Restart
-
-
-  function get_spinup_latitude_term(latitude) result(ans)
-
-    !!DESCRIPTION:
-    ! calculate a logistic function to scale spinup factors so that spinup is more accelerated in high latitude regions
-    !
-    ! !REVISION HISTORY
-    ! charlie koven, nov. 2015
-    !
-    ! !ARGUMENTS:
-    real(r8), intent(in) :: latitude
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: ans
-
-    ans = 1._r8 + 50._r8 / ( 1._r8 + exp(-0.15_r8 * (abs(latitude) - 60._r8) ) )
-    
-    return
-  end function get_spinup_latitude_term
-
-end module SoilBiogeochemStateType
diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90
deleted file mode 100644
index 94c8c55d6a..0000000000
--- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90
+++ /dev/null
@@ -1,277 +0,0 @@
-module SoilBiogeochemVerticalProfileMod
-
-#include "shr_assert.h"
-
-  !-----------------------------------------------------------------------
-  ! !DESCRIPTION:
-  !  Calculate vertical profiles for distributing soil and litter C and N
-  !
-  ! !USES:
-  use shr_kind_mod, only: r8 => shr_kind_r8
-  !
-  implicit none
-  private
-  !
-  ! !PUBLIC MEMBER FUNCTIONS:
-  public:: SoilBiogeochemVerticalProfile
-  !
-  real(r8), public :: surfprof_exp  = 10. ! how steep profile is for surface components (1/ e_folding depth) (1/m)      
-
-  character(len=*), parameter, private :: sourcefile = &
-       __FILE__
-  !-----------------------------------------------------------------------
-
-contains
-
-  !-----------------------------------------------------------------------
-  subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soilp,filter_soilp, &
-       canopystate_inst, soilstate_inst, soilbiogeochem_state_inst)
-    !
-    ! !DESCRIPTION:
-    !  calculate vertical profiles for distributing soil and litter C and N
-    !
-    !  BUG(wjs, 2014-12-15, bugz 2107) 
-    !  Because of this routine's placement in the driver sequence (it is
-    !  called very early in each timestep, before weights are adjusted and filters are
-    !  updated), it may be necessary for this routine to compute values over inactive as well
-    !  as active points (since some inactive points may soon become active) - so that's what
-    !  is done now. Currently, it seems to be okay to do this, because the variables computed
-    !  here seem to only depend on quantities that are valid over inactive as well as active
-    !  points. However, note that this routine is (mistakenly) called from two places
-    !  currently - the above note applies to its call from the driver, but its call from
-    !  CNDecompMod uses the standard filters that just apply over active points
-    ! 
-    ! !USES:
-    use shr_log_mod             , only : errMsg => shr_log_errMsg
-    use decompMod               , only : bounds_type
-    use abortutils              , only : endrun
-    use clm_varcon              , only : zsoi, dzsoi, zisoi, dzsoi_decomp, zmin_bedrock
-    use clm_varpar              , only : nlevdecomp, nlevgrnd, nlevdecomp_full, maxpatch_pft
-    use clm_varctl              , only : use_vertsoilc, iulog, use_bedrock
-    use pftconMod               , only : noveg, pftcon
-    use SoilBiogeochemStateType , only : soilbiogeochem_state_type
-    use CanopyStateType         , only : canopystate_type
-    use SoilStateType           , only : soilstate_type
-    use ColumnType              , only : col                
-    use PatchType               , only : patch                
-    !
-    ! !ARGUMENTS:
-    type(bounds_type)               , intent(in)    :: bounds  
-    integer                         , intent(in)    :: num_soilc                               ! number of soil columns in filter
-    integer                         , intent(in)    :: filter_soilc(:)                         ! filter for soil columns
-    integer                         , intent(in)    :: num_soilp                               ! number of soil patches in filter
-    integer                         , intent(in)    :: filter_soilp(:)                         ! filter for soil patches
-    type(canopystate_type)          , intent(in)    :: canopystate_inst
-    type(soilstate_type)            , intent(in)    :: soilstate_inst				    
-    type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst
-    !
-    ! !LOCAL VARIABLES:
-    real(r8) :: surface_prof(1:nlevdecomp)
-    real(r8) :: surface_prof_tot
-    real(r8) :: rootfr_tot
-    real(r8) :: cinput_rootfr(bounds%begp:bounds%endp, 1:nlevdecomp_full)      ! pft-native root fraction used for calculating inputs
-    real(r8) :: col_cinput_rootfr(bounds%begc:bounds%endc, 1:nlevdecomp_full)  ! col-native root fraction used for calculating inputs
-    integer  :: c, j, fc, p, fp, pi
-    integer  :: alt_ind
-    ! debugging temp variables
-    real(r8) :: froot_prof_sum
-    real(r8) :: croot_prof_sum
-    real(r8) :: leaf_prof_sum
-    real(r8) :: stem_prof_sum
-    real(r8) :: ndep_prof_sum
-    real(r8) :: nfixation_prof_sum
-    real(r8) :: delta = 1.e-10
-    integer  :: begp, endp
-    integer  :: begc, endc
-    character(len=32) :: subname = 'SoilBiogeochemVerticalProfile'
-    !-----------------------------------------------------------------------
-
-    begp = bounds%begp; endp= bounds%endp
-    begc = bounds%begc; endc= bounds%endc
-
-    associate(                                                                  & 
-         altmax_lastyear_indx => canopystate_inst%altmax_lastyear_indx_col    , & ! Input:  [integer   (:)   ]  frost table depth (m)                              
-
-         crootfr              => soilstate_inst%crootfr_patch                 , & ! Input:  [real(r8)  (:,:) ]  fraction of roots in each soil layer  (nlevgrnd)
-         
-         nfixation_prof       => soilbiogeochem_state_inst%nfixation_prof_col , & ! Input  :  [real(r8) (:,:) ]  (1/m) profile for N fixation additions          
-         ndep_prof            => soilbiogeochem_state_inst%ndep_prof_col      , & ! Input  :  [real(r8) (:,:) ]  (1/m) profile for N fixation additions          
-         leaf_prof            => soilbiogeochem_state_inst%leaf_prof_patch    , & ! Output :  [real(r8) (:,:) ]  (1/m) profile of leaves                         
-         froot_prof           => soilbiogeochem_state_inst%froot_prof_patch   , & ! Output :  [real(r8) (:,:) ]  (1/m) profile of fine roots                     
-         croot_prof           => soilbiogeochem_state_inst%croot_prof_patch   , & ! Output :  [real(r8) (:,:) ]  (1/m) profile of coarse roots                   
-         stem_prof            => soilbiogeochem_state_inst%stem_prof_patch      & ! Output :  [real(r8) (:,:) ]  (1/m) profile of stems                          
-         )
-
-      if (use_vertsoilc) then
-
-         ! define a single shallow surface profile for surface additions (leaves, stems, and N deposition)
-         surface_prof(:) = 0._r8
-         do j = 1, nlevdecomp
-            surface_prof(j) = exp(-surfprof_exp * zsoi(j)) / dzsoi_decomp(j)
-            if (use_bedrock) then 
-               if (zsoi(j) > zmin_bedrock) then
-                 surface_prof(j) = 0._r8
-               end if
-            end if
-         end do
-
-         ! initialize profiles to zero
-         leaf_prof(begp:endp, :)      = 0._r8
-         froot_prof(begp:endp, :)     = 0._r8
-         croot_prof(begp:endp, :)     = 0._r8
-         stem_prof(begp:endp, :)      = 0._r8
-         nfixation_prof(begc:endc, :) = 0._r8
-         ndep_prof(begc:endc, :)      = 0._r8
-
-         cinput_rootfr(begp:endp, :)     = 0._r8
-         col_cinput_rootfr(begc:endc, :) = 0._r8
-
-         do fp = 1,num_soilp
-            p = filter_soilp(fp)
-            c = patch%column(p)
-            if (patch%itype(p) /= noveg) then
-               do j = 1, nlevdecomp
-                  cinput_rootfr(p,j) = crootfr(p,j) / dzsoi_decomp(j)
-               end do
-
-            else
-               cinput_rootfr(p,1) = 0.
-            endif
-         end do
-
-         do fp = 1,num_soilp
-            p = filter_soilp(fp)
-            c = patch%column(p)
-            ! integrate rootfr over active layer of soil column
-            rootfr_tot = 0._r8
-            surface_prof_tot = 0._r8
-            do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp)
-               rootfr_tot = rootfr_tot + cinput_rootfr(p,j) * dzsoi_decomp(j)
-               surface_prof_tot = surface_prof_tot + surface_prof(j)  * dzsoi_decomp(j)
-            end do
-            if ( (altmax_lastyear_indx(c) > 0) .and. (rootfr_tot > 0._r8) .and. (surface_prof_tot > 0._r8) ) then
-               ! where there is not permafrost extending to the surface, integrate the profiles over the active layer
-               ! this is equivalnet to integrating over all soil layers outside of permafrost regions
-               do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp)
-                  froot_prof(p,j) = cinput_rootfr(p,j) / rootfr_tot
-                  croot_prof(p,j) = cinput_rootfr(p,j) / rootfr_tot
-
-                  if (j > col%nbedrock(c) .and. cinput_rootfr(p,j) > 0._r8) then 
-                     write(iulog,*) 'cinput_rootfr > 0 in bedrock'
-                  end if
-                  ! set all surface processes to shallower profile
-                  leaf_prof(p,j) = surface_prof(j)/ surface_prof_tot
-                  stem_prof(p,j) = surface_prof(j)/ surface_prof_tot
-               end do
-            else
-               ! if fully frozen, or no roots, put everything in the top layer
-               froot_prof(p,1) = 1./dzsoi_decomp(1)
-               croot_prof(p,1) = 1./dzsoi_decomp(1)
-               leaf_prof(p,1) = 1./dzsoi_decomp(1)
-               stem_prof(p,1) = 1./dzsoi_decomp(1)
-            endif
-
-         end do
-
-         !! aggregate root profile to column
-         ! call p2c (decomp, nlevdecomp_full, &
-         !      cinput_rootfr(bounds%begp:bounds%endp, :), &
-         !      col_cinput_rootfr(bounds%begc:bounds%endc, :), &
-         !      'unity')
-         do pi = 1,maxpatch_pft
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               if (pi <=  col%npatches(c)) then
-                  p = col%patchi(c) + pi - 1
-                  do j = 1,nlevdecomp
-                     col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p)
-                  end do
-               end if
-            end do
-         end do
-
-         ! repeat for column-native profiles: Ndep and Nfix
-         do fc = 1,num_soilc
-            c = filter_soilc(fc)
-            rootfr_tot = 0._r8
-            surface_prof_tot = 0._r8
-            ! redo column ntegration over active layer for column-native profiles
-            do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp)
-               rootfr_tot = rootfr_tot + col_cinput_rootfr(c,j) * dzsoi_decomp(j)
-               surface_prof_tot = surface_prof_tot + surface_prof(j) * dzsoi_decomp(j)
-            end do
-            if ( (altmax_lastyear_indx(c) > 0) .and. (rootfr_tot > 0._r8) .and. (surface_prof_tot > 0._r8) ) then
-               do j = 1,  min(max(altmax_lastyear_indx(c), 1), nlevdecomp)
-                  nfixation_prof(c,j) = col_cinput_rootfr(c,j) / rootfr_tot
-                  ndep_prof(c,j) = surface_prof(j)/ surface_prof_tot
-               end do
-            else
-               nfixation_prof(c,1) = 1./dzsoi_decomp(1)
-               ndep_prof(c,1) = 1./dzsoi_decomp(1)
-            endif
-         end do
-
-      else
-
-         ! for one layer decomposition model, set profiles to unity
-         leaf_prof(begp:endp, :) = 1._r8
-         froot_prof(begp:endp, :) = 1._r8
-         croot_prof(begp:endp, :) = 1._r8
-         stem_prof(begp:endp, :) = 1._r8
-         nfixation_prof(begc:endc, :) = 1._r8
-         ndep_prof(begc:endc, :) = 1._r8
-
-      end if
-
-
-      ! check to make sure integral of all profiles = 1.
-      do fc = 1,num_soilc
-         c = filter_soilc(fc)
-         ndep_prof_sum = 0.
-         nfixation_prof_sum = 0.
-         do j = 1, nlevdecomp
-            ndep_prof_sum = ndep_prof_sum + ndep_prof(c,j) *  dzsoi_decomp(j)
-            nfixation_prof_sum = nfixation_prof_sum + nfixation_prof(c,j) *  dzsoi_decomp(j)
-         end do
-         if ( ( abs(ndep_prof_sum - 1._r8) > delta ) .or.  ( abs(nfixation_prof_sum - 1._r8) > delta ) ) then
-            write(iulog, *) 'profile sums: ', ndep_prof_sum, nfixation_prof_sum
-            write(iulog, *) 'c: ', c
-            write(iulog, *) 'altmax_lastyear_indx: ', altmax_lastyear_indx(c)
-            write(iulog, *) 'nfixation_prof: ', nfixation_prof(c,:)
-            write(iulog, *) 'ndep_prof: ', ndep_prof(c,:)
-            write(iulog, *) 'cinput_rootfr: ', cinput_rootfr(c,:)
-            write(iulog, *) 'dzsoi_decomp: ', dzsoi_decomp(:)
-            write(iulog, *) 'surface_prof: ', surface_prof(:)
-            write(iulog, *) 'npfts(c): ', col%npatches(c)
-            do p = col%patchi(c), col%patchi(c) + col%npatches(c) -1
-               write(iulog, *) 'p, itype(p), wtcol(p): ', p, patch%itype(p), patch%wtcol(p)
-               write(iulog, *) 'cinput_rootfr(p,:): ', cinput_rootfr(p,:)
-            end do
-            call endrun(msg=" ERROR: _prof_sum-1>delta"//errMsg(sourcefile, __LINE__))
-         endif
-      end do
-
-      do fp = 1,num_soilp
-         p = filter_soilp(fp)
-         froot_prof_sum = 0.
-         croot_prof_sum = 0.
-         leaf_prof_sum = 0.
-         stem_prof_sum = 0.
-         do j = 1, nlevdecomp
-            froot_prof_sum = froot_prof_sum + froot_prof(p,j) *  dzsoi_decomp(j)
-            croot_prof_sum = croot_prof_sum + croot_prof(p,j) *  dzsoi_decomp(j)
-            leaf_prof_sum = leaf_prof_sum + leaf_prof(p,j) *  dzsoi_decomp(j)
-            stem_prof_sum = stem_prof_sum + stem_prof(p,j) *  dzsoi_decomp(j)
-         end do
-         if ( ( abs(froot_prof_sum - 1._r8) > delta ) .or.  ( abs(croot_prof_sum - 1._r8) > delta ) .or. &
-              ( abs(stem_prof_sum - 1._r8) > delta ) .or.  ( abs(leaf_prof_sum - 1._r8) > delta ) ) then
-            write(iulog, *) 'profile sums: ', froot_prof_sum, croot_prof_sum, leaf_prof_sum, stem_prof_sum
-            call endrun(msg=' ERROR: sum-1 > delta'//errMsg(sourcefile, __LINE__))
-         endif
-      end do
-
-    end associate
-
-  end subroutine SoilBiogeochemVerticalProfile
-  
-end module SoilBiogeochemVerticalProfileMod