Merge tag 'ctsm5.3.060' into merge-b4bdev-20250625

Preliminary update of ctsm54 defaults (answer changing)

Allows running coupled without having to adjust clm things manually. In particular, updates namelist defaults, including new IC files, that have been limited to the ctsm5.4 branch so far.

Author: slevis-lmwg

.github/workflows/check-clm6-aliases.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+set -e
+
+# Check that clm6* compset aliases return CLM6* longnames
+
+# Change to top level of clone
+cd "$(git rev-parse --show-toplevel)"
+
+# Check that query_config can run without error
+cime/scripts/query_config --compsets 1>/dev/null
+
+# Find bad compsets
+OLD_IFS=$IFS
+IFS='\n'
+set +e
+# Relies on case sensitivity here: Alias should have Clm6 and longname should have CLM6
+bad_compsets="$(cime/scripts/query_config --compsets | sort | uniq | grep Clm6 | grep -v CLM6)"
+set -e
+if [[ "${bad_compsets}" != "" ]]; then
+    echo "One or more compsets with Clm6 alias but not CLM6 longname:" >&2
+    echo $bad_compsets  >&2
+    exit 1
+fi
+
+exit 0

.github/workflows/check-clm6-aliases.yml

@@ -0,0 +1,40 @@
+name: Check that clm6* compset aliases return CLM6* longnames
+# Only check files in our repo that AREN'T in submodules
+# Use a Python command to check each file because xmllint isn't available on GH runners
+
+on:
+  push:
+    # Run when a change to these files is pushed to any branch. Without the "branches:" line, for some reason this will be run whenever a tag is pushed, even if the listed files aren't changed.
+    branches: ['*']
+    paths:
+      - '.github/workflows/check-clm6-aliases.sh'
+      - 'cime/**'
+      - 'cime_config/config_compsets.xml'
+
+  pull_request:
+    # Run on pull requests that change the listed files
+    paths:
+      - '.github/workflows/check-clm6-aliases.sh'
+      - 'cime/**'
+      - 'cime_config/config_compsets.xml'
+
+  workflow_dispatch:
+
+jobs:
+  check-clm6-aliases:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Checkout submodules
+        run: |
+          bin/git-fleximod update
+          
+      - name: Install xmllint for CIME
+        run: |
+          sudo apt-get update && sudo apt-get install --no-install-recommends -y libxml2-utils
+
+      - name: Check aliases
+        run: |
+          .github/workflows/check-clm6-aliases.sh

.gitmodules

@@ -58,8 +58,8 @@ fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
-path = components/mizuRoute
-url = https://github.com/ESCOMP/mizuRoute
+	path = components/mizuroute
+	url = https://github.com/ESCOMP/mizuRoute
 fxtag = cesm-coupling.n03_v2.2.0
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed

README

@@ -66,7 +66,7 @@ components/cmeps -------------------- CESM top level driver (for NUOPC driver [w
 components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
-components/mizuRoute ---------------- Reached based river transport model for water routing 
+components/mizuroute ---------------- Reached based river transport model for water routing 
                                       (allows both gridded river and Hydrologic Responce Unit river grids)
 components/rtm ---------------------- CESM River Transport Model.
 

bld/CLMBuildNamelist.pm

@@ -1688,6 +1688,7 @@ sub process_namelist_inline_logic {
   setup_logic_cnmatrix($opts,  $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_spinup($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
@@ -1737,7 +1738,6 @@ sub process_namelist_inline_logic {
   # namelist group: ch4par_in   #
   ###############################
   setup_logic_methane($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl);
 
   ###############################
   # namelist group: ndepdyn_nml #
@@ -3175,10 +3175,11 @@ sub setup_logic_do_grossunrep {
 
    my $var = 'do_grossunrep';
 
-   # Start by assuming a default value of '.true.'. Then check a number of
+   # Start by assuming a default value of '.false.'. Then check a number of
    # conditions under which do_grossunrep cannot be true. Under these
-   # conditions: (1) set default value to '.false.'; (2) make sure that the
+   # conditions: (1) set default value to '.false.' again; (2) make sure that the
    # value is indeed false (e.g., that the user didn't try to set it to true).
+   # Ideally the default value would be set in namelist_defaults
 
    my $default_val = ".false.";
 
@@ -3703,63 +3704,53 @@ sub setup_logic_c_isotope {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
   my $use_c13 = $nl->get_value('use_c13');
   my $use_c14 = $nl->get_value('use_c14');
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" ) {
     if ( $nl_flags->{'bgc_mode'} ne "bgc" ) {
-      if ( defined($use_c13) && &value_is_true($use_c13) ) {
+      if ( &value_is_true($use_c13) ) {
         $log->warning("use_c13 is ONLY scientifically validated with the bgc=BGC configuration" );
       }
-      if ( defined($use_c14) && &value_is_true($use_c14) ) {
+      if ( &value_is_true($use_c14) ) {
         $log->warning("use_c14 is ONLY scientifically validated with the bgc=BGC configuration" );
       }
     }
-    if ( defined($use_c14) ) {
-      if ( &value_is_true($use_c14) ) {
-        my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
-        if ( defined($use_c14_bombspike) && &value_is_true($use_c14_bombspike) ) {
-           add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
-                   'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
-                   'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
-        }
-      } else {
-        if ( defined($nl->get_value('use_c14_bombspike')) ||
-             defined($nl->get_value('atm_c14_filename')) ) {
-          $log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
-        }
+    if ( &value_is_true($use_c14) ) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+      my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
+      if ( &value_is_true($use_c14_bombspike) ) {
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
+                 'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
+                 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
       }
     } else {
       if ( defined($nl->get_value('use_c14_bombspike')) ||
            defined($nl->get_value('atm_c14_filename')) ) {
-        $log->fatal_error("use_c14 NOT set to .true., but use_c14_bompspike/atm_c14_filename defined.");
+        $log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
       }
     }
-    if ( defined($use_c13) ) {
-      if ( &value_is_true($use_c13) ) {
-        my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
-        if ( defined($use_c13_timeseries) && &value_is_true($use_c13_timeseries) ) {
-           add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
-                   'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
-                   'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
-        }
-      } else {
-        if ( defined($nl->get_value('use_c13_timeseries')) ||
-             defined($nl->get_value('atm_c13_filename')) ) {
-          $log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
-        }
+    if ( &value_is_true($use_c13) ) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+      my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
+      if ( &value_is_true($use_c13_timeseries) ) {
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
+                 'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
+                 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
       }
     } else {
       if ( defined($nl->get_value('use_c13_timeseries')) ||
            defined($nl->get_value('atm_c13_filename')) ) {
-        $log->fatal_error("use_c13 NOT set to .true., but use_c13_bompspike/atm_c13_filename defined.");
+        $log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
       }
     }
   } else {
-    if ( defined($use_c13) ||
-         defined($use_c14) ||
-         defined($nl->get_value('use_c14_bombspike')) ||
+    if ( &value_is_true($use_c13) ||
+         &value_is_true($use_c14) ||
+         &value_is_true($nl->get_value('use_c14_bombspike')) ||
          defined($nl->get_value('atm_c14_filename'))  ||
-         defined($nl->get_value('use_c13_timeseries')) ||
+         &value_is_true($nl->get_value('use_c13_timeseries')) ||
          defined($nl->get_value('atm_c13_filename')) ) {
            $log->fatal_error("bgc=sp and C isotope  namelist variables were set, both can't be used at the same time");
     }
@@ -4071,7 +4062,16 @@ sub setup_logic_fire_emis {
         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");
-       }
+        } elsif ( ! &value_is_true( $nl_flags->{'use_cn'} ) ) {
+          $log->fatal_error("Fire emission option $var can NOT be on when BGC SP (i.e. Satellite Phenology) is also on.\n" .
+                           "  DON'T use the '--fire_emis' option when '--bgc sp' is activated");
+        } elsif ( &value_is_true( $nl_flags->{'use_cn'}) ) {
+          my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
+          if ( $fire_method eq "nofire" ) {
+             $log->fatal_error("Fire emission option $var can NOT be on with BGC and fire_method=='nofire'.\n" .
+                              "  DON'T use the '--fire_emis' option when fire_method is nofire");
+          }
+        }
      }
    }
 }
@@ -4235,7 +4235,7 @@ sub setup_logic_lai_streams {
   if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams'))  ) {
     $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
   }
-  if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) {
+  if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl_flags->{'use_fates_sp'}) )) {
      if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
@@ -4749,29 +4749,26 @@ sub setup_logic_fates {
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
         #
-        my $var = "use_fates_sp";
-        if ( defined($nl->get_value($var))  ) {
-           if ( &value_is_true($nl->get_value($var)) ) {
-              my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
-              foreach my $var ( @list ) {
-                 if ( ! &value_is_true($nl->get_value($var)) ) {
-                    $log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
-                 }
-              }
-              # spit-fire can't be on with FATES SP mode is active
-              if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
-                    $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
-              }
+        if ( &value_is_true($nl_flags->{'use_fates_sp'}) ) {
+           my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
+           foreach my $var ( @list ) {
+                if ( ! &value_is_true($nl->get_value($var)) ) {
+                   $log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
+                }
+           }
+           # spit-fire can't be on with FATES SP mode is active
+           if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
+                 $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
+           }
 
-              # fates landuse can't be on with FATES SP mode is active
-              if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
-                   $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
-              }
+           # fates landuse can't be on with FATES SP mode is active
+           if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
+                $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+           }
 
-              # hydro isn't currently supported to work when FATES SP mode is active
-              if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
-                    $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
-              }
+           # hydro isn't currently supported to work when FATES SP mode is active
+           if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
+                 $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
            }
         }
         my $var = "use_fates_inventory_init";
@@ -4796,6 +4793,13 @@ sub setup_logic_fates {
             }
           }
         }
+        # Check that both FaTES-SP and FATES ST3 aren't both on
+        my $var = "use_fates_ed_st3";
+        if ( defined($nl->get_value($var))  ) {
+           if ( &value_is_true($nl->get_value($var)) && &value_is_true($nl_flags->{'use_fates_sp'}) ) {
+              $log->fatal_error("$var can NOT also be true with use_fates_sp true" );
+           }
+        }
         # check that fates landuse change mode has the necessary luh2 landuse timeseries data
         # and add the default if not defined.  Do not add default if use_fates_potentialveg is true.
         # If fixed biogeography is on, make sure that flandusepftdat is avilable.