Merge pull request #6 from samsrabin/hs-uii-ssr

hs-uii: Merge in latest b4b-dev
samsrabin · Sep 16, 2024 · 149ffda · 149ffda
2 parents 822618e + e205e2e
commit 149ffda
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diff --git a/.gitmodules b/.gitmodules
@@ -92,7 +92,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.47
+fxtag = cdeps1.0.48
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -159,16 +159,20 @@ OPTIONS
  This turns on the namelist variable: use_crop
  -csmdata "dir" Root directory of CESM input data.
  Can also be set by using the CSMDATA environment variable.
- -drydep Produce a drydep_inparm namelist that will go into the
+ -drydep Produce a drydep_inparm namelist for testing that will go into the
  "drv_flds_in" file for the driver to pass dry-deposition to the atm.
+ This populates the namelist with valid drydep settings for testing.
  Default: -no-drydep
+ Note: Can always add drydep fields to user_nl_clm even with --no-drydep
  (Note: buildnml copies the file for use by the driver)
  -dynamic_vegetation Toggle for dynamic vegetation model. (default is off)
  (can ONLY be turned on when BGC type is 'bgc')
  This turns on the namelist variable: use_cndv
  (Deprecated, this will be removed)
- -fire_emis Produce a fire_emis_nl namelist that will go into the
+ -fire_emis Produce a fire_emis_nl namelist for testing that will go into the
  "drv_flds_in" file for the driver to pass fire emissions to the atm.
+ This populates the namelist with valid fire-emiss settings for testing.
+ Note: Can always add fire_emis fields to user_nl_clm even with --no-fire_emis
  (Note: buildnml copies the file for use by the driver)
  -glc_nec <name> Glacier number of elevation classes [0 | 3 | 5 | 10 | 36]
  (default is 0) (standard option with land-ice model is 10)
@@ -204,9 +208,11 @@ OPTIONS
  -namelist "namelist" Specify namelist settings directly on the commandline by supplying
  a string containing FORTRAN namelist syntax, e.g.,
  -namelist "&clm_inparm dt=1800 /"
- -no-megan DO NOT PRODUCE a megan_emis_nl namelist that will go into the
+ -no-megan DO NOT PRODUCE a megan_emis_nl namelist for testing that will go into the
  "drv_flds_in" file for the driver to pass VOCs to the atm.
  MEGAN (Model of Emissions of Gases and Aerosols from Nature)
+ This removes setting default values for testing MEGAN fields
+ Note: Can always add megan fields to user_nl_clm even with --no-megan
  (Note: buildnml copies the file for use by the driver)
  -[no-]note Add note to output namelist [do NOT add note] about the
  arguments to build-namelist.
@@ -1449,7 +1455,7 @@ sub setup_cmdl_vichydro {
 
 sub process_namelist_commandline_namelist {
  # Process the commandline '-namelist' arg.
- my ($opts, $definition, $nl, $envxml_ref) = @_;
+ my ($opts, $definition, $nl, $envxml_ref, %settings) = @_;
 
  if (defined $opts->{'namelist'}) {
  # Parse commandline namelist
@@ -1470,6 +1476,32 @@ sub process_namelist_commandline_namelist {
  }
 }
 
+sub process_namelist_infile {
+ my ($definition, $nl, $envxml_ref, $infile, %settings) = @_;
+
+ # Make sure a valid file was found
+ if ( -f "$infile" ) {
+ # Otherwise abort as a valid file doesn't exist
+ } else {
+ $log->fatal_error("input namelist file does NOT exist $infile.\n $@");
+ }
+ # Parse namelist input from the next file
+ my $nl_infile = Build::Namelist->new($infile);
+
+ # Validate input namelist -- trap exceptions
+ my $nl_infile_valid;
+ eval { $nl_infile_valid = $definition->validate($nl_infile); };
+ if ($@) {
+ $log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
+ }
+ # Go through all variables and expand any XML env settings in them
+ expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );
+
+ # Merge input values into namelist. Previously specified values have higher precedence
+ # and are not overwritten.
+ $nl->merge_nl($nl_infile_valid, %settings);
+}
+
 #-------------------------------------------------------------------------------
 
 sub process_namelist_commandline_infile {
@@ -1479,27 +1511,7 @@ sub process_namelist_commandline_infile {
  if (defined $opts->{'infile'}) {
  my @infiles = split( /,/, $opts->{'infile'} );
  foreach my $infile ( @infiles ) {
- # Make sure a valid file was found
- if ( -f "$infile" ) {
- # Otherwise abort as a valid file doesn't exist
- } else {
- $log->fatal_error("input namelist file does NOT exist $infile.\n $@");
- }
- # Parse namelist input from the next file
- my $nl_infile = Build::Namelist->new($infile);
-
- # Validate input namelist -- trap exceptions
- my $nl_infile_valid;
- eval { $nl_infile_valid = $definition->validate($nl_infile); };
- if ($@) {
- $log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
- }
- # Go through all variables and expand any XML env settings in them
- expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );
-
- # Merge input values into namelist. Previously specified values have higher precedence
- # and are not overwritten.
- $nl->merge_nl($nl_infile_valid);
+ process_namelist_infile( $definition, $nl, $envxml_ref, $infile );
  }
  }
 }
@@ -1750,25 +1762,29 @@ sub process_namelist_inline_logic {
  ##################################
  setup_logic_lightning_streams($opts, $nl_flags, $definition, $defaults, $nl);
 
- #################################
- # namelist group: drydep_inparm #
- #################################
- setup_logic_dry_deposition($opts, $nl_flags, $definition, $defaults, $nl);
-
- #################################
- # namelist group: fire_emis_nl #
- #################################
- setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);
-
- ######################################
+ ############################################################################################
  # namelist options for dust emissions
- ######################################
+ # NOTE: This MUST be done before other drv_flds_in settings (megan, drydep, fire_emis etc.)
+ ############################################################################################
  setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
  setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);
 
- #################################
- # namelist group: megan_emis_nl #
- #################################
+ #####################################
+ # namelist group: drydep_inparm #
+ # NOTE: After setup_logic_dust_emis #
+ #####################################
+ setup_logic_dry_deposition($opts, $nl_flags, $definition, $defaults, $nl);
+
+ #####################################
+ # namelist group: fire_emis_nl #
+ # NOTE: After setup_logic_dust_emis #
+ #####################################
+ setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);
+
+ #####################################
+ # namelist group: megan_emis_nl #
+ # NOTE: After setup_logic_dust_emis #
+ #####################################
  setup_logic_megan($opts, $nl_flags, $definition, $defaults, $nl);
 
  ##################################
@@ -2266,7 +2282,9 @@ sub setup_logic_cnfire {
 
  my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c",
  "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel",
- "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd" );
+ "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd", "max_rh30_affecting_fuel",
+ "defo_fire_precip_thresh_bet", "defo_fire_precip_thresh_bdt",
+ "borpeat_fire_soilmoist_denom", "nonborpeat_fire_precip_denom" );
  if ( &value_is_true($nl->get_value('use_cn')) ) {
  foreach my $item ( @fire_consts ) {
  if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) {
@@ -3999,17 +4017,18 @@ sub setup_logic_lightning_streams {
 sub setup_logic_dry_deposition {
  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+ my @list = ( "drydep_list", "dep_data_file");
  if ($opts->{'drydep'} ) {
- if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
- $log->warning("DryDeposition can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
- " Use the '--no-drydep' option when '-bgc fates' is activated");
- }
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
- } else {
- if ( defined($nl->get_value('drydep_list')) ) {
- $log->fatal_error("drydep_list defined, but drydep option NOT set");
- }
+ }
+ if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+ foreach my $var ( @list ) {
+ if ( defined($nl->get_value($var)) ) {
+ $log->warning("DryDeposition $var is being set and can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
+ " Use the '--no-drydep' option when '-bgc fates' is activated");
+ }
+ }
  }
 }
 
@@ -4018,20 +4037,20 @@ sub setup_logic_dry_deposition {
 sub setup_logic_fire_emis {
  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+ my @list = ( "fire_emis_eleveated", "fire_emis_factors_file", "fire_emis_specifier");
+
  if ($opts->{'fire_emis'} ) {
- if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
- $log->warning("Fire emission can NOT be on when FATES is also on.\n" .
- " DON'T use the '-fire_emis' option when '-bgc fates' is activated");
- }
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file');
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier');
- } else {
- if ( defined($nl->get_value('fire_emis_elevated')) ||
- defined($nl->get_value('fire_emis_factors_file')) ||
- defined($nl->get_value('fire_emis_specifier')) ) {
- $log->fatal_error("fire_emission setting defined: fire_emis_elevated, fire_emis_factors_file, or fire_emis_specifier, but fire_emis option NOT set");
- }
  }
+ foreach my $var ( @list ) {
+ if ( defined($nl->get_value($var)) ) {
+ if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+ $log->warning("Fire emission option $var can NOT be on when FATES is also on.\n" .
+ " DON'T use the '--fire_emis' option when '--bgc fates' is activated");
+ }
+ }
+ }
 }
 
 #-------------------------------------------------------------------------------
@@ -4041,6 +4060,8 @@ sub setup_logic_dust_emis {
  my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
  # Only set dust emission settings -- if not connected to CAM
+ # Longer term plan is to remove this logic and have CTSM just set it and for CAM to use what CLM decides
+ # See: https://github.com/ESCOMP/CTSM/issues/2713
  my $lnd_sets_dust = logical_to_fortran($envxml_ref->{'LND_SETS_DUST_EMIS_DRV_FLDS'});
  if ( &value_is_true( $lnd_sets_dust)) {
 
@@ -4093,6 +4114,14 @@ sub setup_logic_dust_emis {
  " connected to CAM as CAM should set them");
  }
  }
+ # Now process the CAM drv_flds_in to get the dust settings
+ # This requires that the CAM drv_flds_in namelist be created BEFORE CLM
+ # and that the path below NOT be changed. Hence, there's some fragility here
+ # to future changes.
+ my $infile = $opts->{'envxml_dir'} . "/Buildconf/camconf/drv_flds_in";
+ $log->verbose_message("Read in the drv_flds_in file generated by CAM's build-namelist");
+ # When merging the CAM namelist in -- die with an error if there's a conflict between CAM and CLM
+ process_namelist_infile( $definition, $nl, $envxml_ref, $infile, 'die_on_conflict'=>1 );
  }
 }
 
@@ -4113,17 +4142,15 @@ sub setup_logic_megan {
  }
 
  if ($nl_flags->{'megan'} ) {
- if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
- $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
- " Use the '-no-megan' option when '-bgc fates' is activated");
- }
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
- check_megan_spec( $opts, $nl, $definition );
  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file');
- } else {
-  if ( defined($nl->get_value('megan_specifier')) ||
+ }
+ if ( defined($nl->get_value('megan_specifier')) ||
  defined($nl->get_value('megan_factors_file')) ) {
- $log->fatal_error("megan_specifier or megan_factors_file defined, but megan option NOT set");
+ check_megan_spec( $opts, $nl, $definition );
+ if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+ $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
+ " Use the '-no-megan' option when '-bgc fates' is activated");
  }
  }
 }
@@ -5650,27 +5677,11 @@ sub check_megan_spec {
 
  my $megan_spec = $nl->get_value('megan_specifier');
  my @megan_spec_list = split( /\s*,\s*/, $megan_spec );
- foreach $megan_spec ( @megan_spec_list ) {
- if ( $megan_spec =~ /^['"]+[A-Za-z0-9]+\s*\=\s*([\sA-Za-z0-9+_-]+)["']+$/ ) {
- my $megan_list = $1;
- my @megan_cmpds = split( /\s*\+\s*/, $megan_list );
- my $var = "megan_cmpds";
- my $warn = 0;
- foreach my $megan_cmpd ( @megan_cmpds ) {
- if ( ! $definition->is_valid_value( $var, $megan_cmpd, 'noquotes'=>1 ) ) {
- $log->warning("megan_compound $megan_cmpd NOT found in list" );
- $warn++;
- }
- }
- if ( $warn > 0 ) {
- my @valid_values = $definition->get_valid_values( $var, 'noquotes'=>1 );
- $log->warning("list of megan compounds includes:\n" .
- "@valid_values\n" .
- "Does your megan_factors_file include more compounds?\n" .
- "If NOT your simulation will fail." );
- }
- } else {
- $log->fatal_error("Bad format for megan_specifier = $megan_spec");
+ foreach my $spec ( @megan_spec_list ) {
+ $megan_spec = remove_leading_and_trailing_quotes($spec);
+ # Do simple validation of the expressions to just check for valid characters
+ if ( $megan_spec !~ /^([\s=A-Za-z0-9_\+\.\*\(\)-]+)$/ ) {
+ $log->warning("Bad format for megan_specifier = $megan_spec");
  }
  }
 }