alpha-ctsm5.4.CMIP7.02.ctsm5.3.055: Update default settings

.github/workflows/docs-omnibus.yml

@@ -51,4 +51,4 @@ jobs:
       # TODO: Split testing.sh tests into their own steps in this job
       - name: Text Sphinx builds with omnibus script
         run: |
-          cd doc && conda run -n ctsm_pylib ./testing.sh
+          cd doc && ./testing.sh

.github/workflows/fleximod_test.yaml

@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
       - id: run-fleximod
         run: |
-          $GITHUB_WORKSPACE/bin/git-fleximod update
+          $GITHUB_WORKSPACE/bin/git-fleximod update -o
           echo
           echo "Update complete, checking status"
           echo
@@ -32,4 +32,4 @@ jobs:
           echo
           echo "Checking if git fleximod matches expected externals"
           echo
-          git diff --exit-code
+          git add . && git diff --exit-code && git diff --cached --exit-code

.github/workflows/validate_xml.py

@@ -0,0 +1,67 @@
+"""
+Check that all XML files in our repo (except for those in submodules) are well-formed. Error if not.
+"""
+import sys
+import glob
+import os
+import subprocess
+import xml.etree.ElementTree as ET
+
+
+def get_submodule_paths():
+    """
+    Get list of submodules
+    """
+    cmd = "git config --file .gitmodules --get-regexp path | awk '{ print $2 }'"
+    result = subprocess.run(cmd, capture_output=True, text=True, shell=True, check=True)
+    result_list = result.stdout.split("\n")[:-1]
+    result_list = [x for x in result_list if x]
+    return result_list
+
+
+def is_in_submodule(file_path, submodule):
+    """
+    Return True if file is in given submodule, False otherwise
+    """
+    return os.path.commonpath([file_path, submodule]) == os.path.commonpath([submodule])
+
+
+def is_in_any_submodule(file_path, submodule_paths):
+    """
+    Return True if file is in any submodule, False otherwise
+    """
+    file_path = os.path.abspath(file_path)
+    submodule_paths = map(os.path.abspath, submodule_paths)
+    return any(is_in_submodule(file_path, submodule) for submodule in submodule_paths)
+
+
+def validate_xml(file_path):
+    """
+    Return True if XML file is well-formed, False otherwise
+    """
+    try:
+        ET.parse(file_path)
+    except ET.ParseError:
+        print(f"❌ {file_path} is NOT well-formed")
+        return False
+    print(f"✅ {file_path} is well-formed")
+    return True
+
+
+def main():
+    # pylint: disable=missing-function-docstring
+    submodule_paths = get_submodule_paths()
+    all_valid = True
+    for xml_file in glob.glob("**/*.xml", recursive=True):
+        if is_in_any_submodule(xml_file, submodule_paths):
+            continue
+        if not validate_xml(xml_file):
+            all_valid = False
+
+    if not all_valid:
+        print("\nUse xmllint to show problems in malformed files")
+
+    return all_valid
+
+
+sys.exit(0 if main() else 1)

.github/workflows/xml-check.yml

@@ -0,0 +1,20 @@
+name: Check that XML files are well-formed
+# 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, pull_request] # Trigger on push or pull request
+
+jobs:
+  check-xml:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Check XML files
+        run: python .github/workflows/validate_xml.py

.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 = cdeps1.0.73
+fxtag = cdeps1.0.75
 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
@@ -128,13 +128,3 @@ fxtag = v2.2.6
 fxrequired = ToplevelOptional
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/doc-builder
-
-# FTorch is an optional library useful for AI and Machine Learning
-# In order to use it -- it must be checked out with git-fleximod
-[submodule "FTorch"]
-path = libraries/FTorch
-url = https://github.com/ESCOMP/FTorch_interface
-fxtag = v0.0.5
-fxrequired = ToplevelOptional
-# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/ESCOMP/FTorch_interface

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");
     }

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -110,6 +110,17 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <stomatalcond_method               >Medlyn2011</stomatalcond_method>
 <stomatalcond_method phys="clm4_5" >Ball-Berry1987</stomatalcond_method>
 
+<!-- Carbon isotope settings -->
+<use_c13>.false.</use_c13>
+<use_c14>.false.</use_c14>
+<use_c13_timeseries>.false.</use_c13_timeseries>
+<use_c14_bombspike>.false.</use_c14_bombspike>
+
+<use_c13 phys="clm6_0" bgc_mode="bgc" >.true.</use_c13>
+<use_c14 phys="clm6_0" bgc_mode="bgc" >.true.</use_c14>
+<use_c13_timeseries phys="clm6_0" bgc_mode="bgc" >.true.</use_c13_timeseries>
+<use_c14_bombspike phys="clm6_0" bgc_mode="bgc" >.true.</use_c14_bombspike>
+
 <!-- Carbon isotope concentration files -->
 <atm_c13_filename use_c13=".true." use_c13_timeseries=".true." ssp_rcp="hist"     >lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_v2.0_c190528.nc</atm_c13_filename>
 <atm_c13_filename use_c13=".true." use_c13_timeseries=".true." ssp_rcp="SSP1-1.9" >lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP119_1850-2100_yearly_c181209.nc</atm_c13_filename>
@@ -484,13 +495,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <snow_thermal_cond_method>Jordan1991</snow_thermal_cond_method>
 <snow_thermal_cond_method phys="clm6_0">Sturm1997</snow_thermal_cond_method>
 
-<!-- TODO change clm6 to Jordan with answer changing tag for glacier mass ballance -->
 <snow_thermal_cond_glc_method>Jordan1991</snow_thermal_cond_glc_method>
-<snow_thermal_cond_glc_method phys="clm6_0">Sturm1997</snow_thermal_cond_glc_method>
+<snow_thermal_cond_glc_method phys="clm6_0">Jordan1991</snow_thermal_cond_glc_method>
 
-<!-- TODO change clm6 to Sturm with answer changing tag -->
 <snow_thermal_cond_lake_method>Jordan1991</snow_thermal_cond_lake_method>
-<snow_thermal_cond_lake_method phys="clm6_0">Jordan1991</snow_thermal_cond_lake_method>
+<snow_thermal_cond_lake_method phys="clm6_0">Sturm1997</snow_thermal_cond_lake_method>
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
@@ -532,7 +541,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- 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="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c250311.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm5.3.041.Nfix_params.v13.c250221_upplim250.nc</paramfile>
 <paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c250311.nc</paramfile>
 <paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c250311.nc</paramfile>
 
@@ -1283,14 +1292,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          phys="clm6_0"
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53019_f09_BNF_pSASU.clm2.r.0161-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.4/ctsm53041_54surfdata_snowTherm_100_pSASU.clm2.r.0161-01-01-00000_64bitoffset.nc
 </finidat>
 <!-- Corresponding ne30 -->
 <finidat hgrid="ne30np4.pg3" mask="tx2_3v2" use_cn=".true." use_cndv=".false." use_fates=".false."
          sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          use_crop=".true." irrigate=".false."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53019_f09_BNF_pSASU.clm2.r.0161-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.4/ctsm53041_54surfdata_ne30_102_pSASU.clm2.r.0081-01-01-00000_64bitoffset.nc
 </finidat>
 <!-- Corresponding f19 -->
 <finidat hgrid="1.9x2.5" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
@@ -1425,13 +1434,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53019_f09_BNF_hist.clm2.r.2000-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.4/ctsm53041_54surfdata_ne30_102_HIST.clm2.r.2000-01-01-00000.nc
 </finidat>
 <finidat hgrid="ne30np4.pg3"    maxpft="79"  mask="tx2_3v2" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          phys="clm6_0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm53019_f09_BNF_hist.clm2.r.2000-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.4/ctsm53041_54surfdata_ne30_102_HIST.clm2.r.2000-01-01-00000.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1700,7 +1709,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_4x5_hist_1850_16pfts_c241007.nc</fsurd
 <fsurdat hgrid="360x720cru"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_360x720cru_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="0.9x1.25"    sim_year="1850" >
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_0.9x1.25_hist_1850_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.4.0/surfdata_0.9x1.25_hist_1850_78pfts_c250428.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"     sim_year="1850" use_crop=".true.">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1.9x2.5_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="10x15"       sim_year="1850" >
@@ -1718,7 +1727,7 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4_hist_1850_78pfts_c240908.nc</f
 <fsurdat hgrid="ne30np4.pg2" sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne30np4.pg3" sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
+lnd/clm2/surfdata_esmf/ctsm5.4.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c250428.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 
@@ -1778,7 +1787,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 
 <!-- 78-pft landuse files -->
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000"
- >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_0.9x1.25_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
+ >lnd/clm2/surfdata_esmf/ctsm5.4.0/landuse.timeseries_0.9x1.25_hist_1850-2023_78pfts_c250428.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1.9x2.5"       sim_year_range="1850-2000" use_crop=".true."
  >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_1.9x2.5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne0np4.ARCTICGRIS.ne30x8" sim_year_range="1850-2000"
@@ -1808,7 +1817,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne16np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne30np4.pg3"   sim_year_range="1850-2000"
->lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_esmf/ctsm5.4.0/landuse.timeseries_ne30np4.pg3_hist_1850-2023_78pfts_c250428.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="C96"           sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>