ctsm5.3.065: Merge b4bdev 20250725

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

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       - name: Checkout submodules
         run: |

.github/workflows/docker-image-build-publish.yml

@@ -42,7 +42,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       # Uses the `docker/login-action` action to log in to the Container registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
       - name: Log in to the Container registry
@@ -78,7 +78,7 @@ jobs:
 
       # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see [Using artifact attestations to establish provenance for builds](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds).
       - name: Generate artifact attestation
-        uses: actions/attest-build-provenance@v2
+        uses: actions/attest-build-provenance@e8998f949152b193b063cb0ec769d69d929409be  # v2
         with:
           subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           subject-digest: ${{ steps.push.outputs.digest }}

.github/workflows/docker-image-common.yml

@@ -30,14 +30,11 @@ jobs:
     # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
     permissions:
       contents: read
-      packages: write
-      attestations: write
-      id-token: write
 
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       # Ensure that the repository part of IMAGE_NAME is lowercase. This is needed because Docker requires image names to be entirely lowercase. Note that the *image name* part, set as IMAGE_BASENAME in the env block above, is *not* converted. This will cause the check-version job to fail if the IMAGE_BASENAME contains capitals. We don't want to silently fix that here; rather, we require the user to specify a lowercase IMAGE_BASENAME.
       - name: Get image name with lowercase repo

.github/workflows/docker-image-get-version.yml

@@ -42,7 +42,7 @@ jobs:
 
     steps:
       - name: Check out repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       - name: Get version number from Dockerfile and check it
         id: get-check-version

.github/workflows/docs-build-and-deploy.yml

@@ -40,13 +40,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           # Get all history, ensuring all branches are available for checkout
           fetch-depth: 0
 
       - name: Setup Pages
-        uses: actions/configure-pages@v5
+        uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b  # v5
 
       # Check out all submodules because we might :literalinclude: something from one
       - name: Checkout all submodules
@@ -60,11 +60,11 @@ jobs:
           ./build_docs_to_publish -d --site-root https://escomp.github.io/CTSM
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@0252fc4ba7626f0298f0cf00902a25c6afc77fa8  # v3
         with:
           # Upload publish dir
           path: 'doc/_publish'
 
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@f33f41b675f0ab2dc5a6863c9a170fe83af3571e  # v4

.github/workflows/docs-common.yml

@@ -21,7 +21,7 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
           lfs: true
@@ -35,12 +35,12 @@ jobs:
       # Based on  https://github.com/actions/cache/blob/main/examples.md#python---pip
       - name: Install python
         if: ${{ ! inputs.use_conda }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5.6.0
         with:
           python-version: '3.13.2'  # needs to be coordinated with version in python/conda_env_ctsm_py.txt
       - name: Cache pip
         if: ${{ ! inputs.use_conda }}
-        uses: actions/cache@v3
+        uses: actions/cache@2f8e54208210a422b2efd51efaa6bd6d7ca8920f  # v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('doc/ctsm-docs_container/requirements.txt') }}
@@ -54,7 +54,7 @@ jobs:
       # Do this if using conda
       - name: Set up conda environment
         if: ${{ inputs.use_conda }}
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ${{ inputs.conda_env_name }}
           environment-file: ${{ inputs.conda_env_file }}

.github/workflows/docs-omnibus.yml

@@ -24,7 +24,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
           lfs: true
@@ -36,7 +36,7 @@ jobs:
 
       # Set up conda
       - name: Set up conda environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ctsm_pylib
           environment-file: python/conda_env_ctsm_py.yml

.github/workflows/docs-update-ctsm_pylib.yml

@@ -53,7 +53,7 @@ jobs:
     needs: test-build-docs-ctsm_pylib
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       - name: Create issue
         uses: JasonEtco/create-an-issue@1b14a70e4d8dc185e5cc76d3bec9eab20257b2c5

.github/workflows/docs-update-dependency-common.yml

@@ -27,7 +27,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
           lfs: true
@@ -38,7 +38,7 @@ jobs:
           bin/git-fleximod update -o
 
       - name: Set up conda environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ${{ inputs.conda_env_name }}
           environment-file: ${{ inputs.conda_env_file }}
@@ -53,7 +53,7 @@ jobs:
   makefile-method:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
           lfs: true
@@ -64,7 +64,7 @@ jobs:
           bin/git-fleximod update -o
 
       - name: Set up conda environment
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ${{ inputs.conda_env_name }}
           environment-file: ${{ inputs.conda_env_file }}

.github/workflows/docs-update-doc-builder.yml

@@ -28,7 +28,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
         with:
           fetch-depth: 0
           lfs: true

.github/workflows/docs.yml

@@ -51,7 +51,7 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       # Check out all submodules because we might :literalinclude: something from one
       - name: Checkout all submodules

.github/workflows/python-tests.yml

@@ -22,10 +22,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the code
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       # Set up the conda environment
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ctsm_pylib
           environment-file: python/conda_env_ctsm_py.yml
@@ -42,10 +42,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the code
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       # Set up the conda environment
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@2defc80cc6f4028b1780c50faf08dd505d698976  # v3
         with:
           activate-environment: ctsm_pylib
           environment-file: python/conda_env_ctsm_py.yml

.github/workflows/xml-check.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5.6.0
         with:
           python-version: '3.x'
 

.gitmodules

@@ -44,15 +44,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_87
+fxtag = rtm1_0_88
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.09
+fxtag = mosart1.1.10
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
@@ -68,31 +68,31 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.43
+fxtag = ccs_config_cesm1.0.48
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.102
+fxtag = cime6.1.107
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.48
+fxtag = cmeps1.1.2
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.75
+fxtag = cdeps1.0.79
 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
@@ -108,7 +108,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_4
+fxtag = pio2_6_6
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO

bld/CLMBuildNamelist.pm

@@ -994,7 +994,7 @@ sub setup_cmdl_bgc {
   # Set soil matrix (which is needed later for spinup)
   $var = "use_soil_matrixcn";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              , 'use_fates'=>$nl_flags->{'use_fates'}, 
+              , 'use_fates'=>$nl_flags->{'use_fates'},
               , 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'},
               , 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
   if ( &value_is_true($nl->get_value($var)) ) {
@@ -1230,7 +1230,7 @@ sub setup_cmdl_spinup {
   if ( &value_is_true($nl_flags->{'use_cn'}) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
                 $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'},
-                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, 
+                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
                 use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} );
     if ( $nl->get_value("spinup_state") ne 0 ) {
        $nl_flags->{'bgc_spinup'} = "on";
@@ -1803,6 +1803,7 @@ sub process_namelist_inline_logic {
   # NOTE: After setup_logic_dust_emis #
   #####################################
   setup_logic_megan($opts, $nl_flags, $definition, $defaults, $nl);
+  setup_logic_megan_opts($opts, $nl_flags, $definition, $defaults, $nl);
 
   ##################################
   # namelist group: lai_streams  #
@@ -4176,6 +4177,7 @@ sub setup_logic_dust_emis {
 
 sub setup_logic_megan {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  # Setup megan_emis_nl namelist for drv_flds_in
 
   my $var   = "megan";
 
@@ -4205,6 +4207,29 @@ sub setup_logic_megan {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_megan_opts {
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  # Setup megan_opts namelist
+  # This should be set when megan is turned on by CTSM, but also when CAM has turned it on
+
+  if ($nl_flags->{'megan'} ) {
+    add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_use_gamma_sm');
+    if ( &value_is_true( $nl->get_value('megan_use_gamma_sm') ) ) {
+       add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_min_gamma_sm');
+    } elsif ( defined($nl->get_value('megan_min_gamma_sm')) ) {
+       $log->fatal_error("megan_min_gamma_sm should NOT be set when megan_use_gamma_sm NOT TRUE.\n" );
+    }
+  }
+  else {
+     if ( defined($nl->get_value('megan_use_gamma_sm')) ||
+          defined($nl->get_value('megan_min_gamma_sm')) ) {
+          $log->fatal_error("MEGAN options should NOT be set when MEGAN is NOT in use.\n" );
+     }
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_soilm_streams {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
@@ -5016,7 +5041,7 @@ sub setup_logic_exice {
   # excess ice streams, must be set before initial conditions
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string());
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   # Put use_exice into nl_flags so can be referenced later
   if ( value_is_true($use_exice) ) {
@@ -5230,7 +5255,7 @@ sub write_output_files {
 
   @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams
                soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology
-               cropcal_streams
+               cropcal_streams megan_opts
                clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate
                finidat_consistency_checks dynpft_consistency_checks
                clm_initinterp_inparm century_soilbgcdecompcascade

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -152,6 +152,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <megan clm_accelerated_spinup="sasu">0</megan>
 <megan configuration="nwp"          >0</megan>
 
+<!-- Setting to TRUE replicates previous ctsm5.3.063 answers, setting to false turns the soil moisture effect off -->
+<megan_use_gamma_sm>.true.</megan_use_gamma_sm>
+<megan_min_gamma_sm>0.0d00</megan_min_gamma_sm>
+
 <!-- Supplmental Nitrogen mode -->
 <suplnitro use_cn=".true." >NONE</suplnitro>
 <suplnitro use_fates=".true." >ALL</suplnitro>