Update ctsm5.2 branch to ctsm5.1.dev176 and some small updates

.gitignore

@@ -91,11 +91,10 @@ ctsm.input_data_list.previous
 /tools/mksurfdata_esmf/mksurfdata_in
 /tools/mksurfdata_esmf/surfdata_*.nc
 /tools/mksurfdata_esmf/landuse.timeseries_*.nc
-/tools/mksurfdata_esmf/mksurfdata_jobscript_multi
-/tools/mksurfdata_esmf/mksurfdata_jobscript_single
+/tools/mksurfdata_esmf/mksurfdata_jobscript_multi.sh
+/tools/mksurfdata_esmf/mksurfdata_jobscript_single.sh
 /tools/mksurfdata_esmf/pio_iotype.txt
 /tools/mksurfdata_esmf/*.sh
-/tools/mksurfdata_esmf/mksrf_*.o*
 /tools/mksurfdata_esmf/tool_bld
 /tools/mksurfdata_esmf/pio_iotype.txt
 

Externals.cfg

@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_97
+tag = cismwrap_2_1_99
 externals = Externals_CISM.cfg
 required = True
 

bld/CLMBuildNamelist.pm

@@ -651,9 +651,9 @@ sub process_namelist_commandline_options {
   setup_cmdl_dynamic_vegetation($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_fates_mode($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_vichydro($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_lnd_tuning($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_cmdl_run_type($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_output_reals($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_logic_lnd_tuning($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 }
 
 #-------------------------------------------------------------------------------
@@ -1265,6 +1265,8 @@ sub setup_cmdl_simulation_year {
 
 sub setup_cmdl_run_type {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  # Set the clm_start_type and the st_year, start year
+  # This MUST be done after lnd_tuning_mode is set
 
   my $val;
   my $var = "clm_start_type";
@@ -1279,20 +1281,19 @@ sub setup_cmdl_run_type {
     my $group = $definition->get_group_name($date);
     $nl->set_variable_value($group, $date, $ic_date );
   }
+  my $set = undef;
   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'}, 'use_fates'=>$nl_flags->{'use_fates'},
-                  'sim_year'=>$st_year, 'sim_year_range'=>$nl_flags->{'sim_year_range'},
-                  'bgc_spinup'=>$nl_flags->{'bgc_spinup'} );
-    } else {
+    if ($opts->{$var} ne "default" ) {
+      $set = 1;
       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'}, 'use_fates'=>$nl_flags->{'use_fates'},
-                  'sim_year'=>$st_year );
+  }
+  if ( ! defined $set ) {
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
+                 'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'},
+                 'sim_year'=>$st_year, 'sim_year_range'=>$nl_flags->{'sim_year_range'},
+                 'bgc_spinup'=>$nl_flags->{'bgc_spinup'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
   }
   $nl_flags->{'clm_start_type'} = $nl->get_value($var);
   $nl_flags->{'st_year'}        = $st_year;
@@ -1697,6 +1698,11 @@ sub process_namelist_inline_logic {
   #################################
   setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);
 
+  ######################################
+  # namelist options for dust emissions
+  ######################################
+  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl);
+
   #################################
   # namelist group: megan_emis_nl #
   #################################
@@ -3981,6 +3987,56 @@ sub setup_logic_fire_emis {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_dust_emis {
+  # Logic to handle the dust emissions
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+  # First get the dust emission method
+  my $var = "dust_emis_method";
+  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var );
+
+  my $dust_emis_method = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+
+  my @zender_files_in_lnd_opts = ( "stream_fldfilename_zendersoilerod", "stream_meshfile_zendersoilerod",
+                                   "zendersoilerod_mapalgo" );
+  if ( $dust_emis_method eq "Zender_2003" ) {
+     # get the zender_soil_erod_source
+     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+                 "zender_soil_erod_source", 'dust_emis_method'=>$dust_emis_method );
+
+     my $zender_source = remove_leading_and_trailing_quotes( $nl->get_value('zender_soil_erod_source') );
+     if ( $zender_source eq "lnd" ) {
+        foreach my $option ( @zender_files_in_lnd_opts ) {
+           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option,
+                       'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
+                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
+        }
+     } else {
+        foreach my $option ( @zender_files_in_lnd_opts ) {
+           if ( defined($nl->get_value($option)) ) {
+             $log->fatal_error("zender_soil_erod_source is NOT lnd, but the file option $option is being set" .
+                               " and should NOT be unless you want it handled here in the LAND model, " .
+                               "otherwise the equivalent option is set in CAM" );
+           }
+        }
+     }
+  } else {
+     # Verify that NONE of the Zender options are being set if Zender is NOT being used
+     push @zender_files_in_lnd_opts, "zender_soil_erod_source";
+     foreach my $option ( @zender_files_in_lnd_opts ) {
+        if ( defined($nl->get_value($option)) ) {
+          $log->fatal_error("dust_emis_method is NOT set to Zender_2003, but one of it's options " .
+                            "$option is being set, need to change one or the other" );
+        }
+     }
+     if ( $dust_emis_method eq "Leung_2023" ) {
+        $log->warning("dust_emis_method is Leung_2023 and that option has NOT been brought into CTSM yet");
+     }
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_megan {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -4665,6 +4721,7 @@ sub write_output_files {
   push @groups, "exice_streams";
   push @groups, "soilbgc_decomp";
   push @groups, "clm_canopy_inparm";
+  push @groups, "zendersoilerod";
   if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
      push @groups, "scf_swenson_lawrence_2012_inparm";
   }