Merge branch 'master' into feature/add_dglc

mvertens · Apr 1, 2024 · 79d431f · 79d431f
2 parents ef7de61 + 1bab27e
commit 79d431f
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -11,16 +11,24 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 b771971e3299c4fa56534b93421f7a2b9c7282fd
 9de88bb57ea9855da408cbec1dc8acb9079eda47
 8bc4688e52ea23ef688e283698f70a44388373eb
+c8bd4c6f98c0b411391b4355da449507db3aab4e
 4ee49e3e516ca7dee5df378f65664f93a7db4415
 0207bc98dd5c75cd69a0e788bc53e41093712f5c
 e4d38681df23ccca0ae29581a45f8362574e0630
 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
 810cb346f05ac1aabfff931ab1a2b7b584add241
 5933b0018f8e29413e30dda9b906370d147bad45
+025d5e7c2e80263717fb029101d65cbbf261c3c4
+a9d96219902cf609636886c7073a84407f450d9a
+d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
 0bc3f00115d86d026a977918661c93779b3b19f9
 540b256d1f3382f4619d7b0877c32d54ce5c40b6
 8a168bb0895f4f2421608dd2589398e13a6663e6
+183fc26a6691bbdf87f515dc47924a64be3ced9b
 6fccf682eaf718615407d9bacdd3903b8786a03d
+2500534eb0a83cc3aff94b30fb62e915054030bf
+78d05967c2b027dc9776a884716597db6ef7f57c
diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
@@ -0,0 +1,23 @@
+name: Auto Assign to Project(s)
+
+on:
+  issues:
+    types: [opened, labeled]
+  pull_request:
+    types: [opened, labeled]
+  issue_comment:
+    types: [created]
+
+jobs:
+  assign_high_priority:
+    runs-on: ubuntu-latest
+    name: Assign to High Priority project
+    steps:
+    - name: Assign issues and pull requests with priority-high label to project 25
+      uses: srggrs/[email protected]
+      if: |
+        contains(github.event.issue.labels.*.name, 'priority: high') ||
+        contains(github.event.pull_request.labels.*.name, 'priority: high')
+      with:
+        project: 'https://github.com/ESCOMP/CTSM/projects/25'
+        column_name: 'Needs triage'
diff --git a/.gitignore b/.gitignore
@@ -111,6 +111,7 @@ unit_test_build
 /tools/site_and_regional/????.ad/
 /tools/site_and_regional/????.postad/
 /tools/site_and_regional/????.transient/
+/tools/site_and_regional/archive/
 
 # build output
 *.o

diff --git a/Externals.cfg b/Externals.cfg
@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_96
+tag = cismwrap_2_1_97
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_78
+tag = rtm1_0_79
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_48
+tag = mosart1_0_49
 required = True
 
 [mizuRoute]
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.84
+tag = ccs_config_cesm0.0.92
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.175
+tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.14.43
+tag = cmeps0.14.50
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.24
+tag = cdeps1.0.28
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.17
+tag = share1.0.18
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.70.0_api.32.0.0
+repo_url = https://github.com/rgknox/fates
+tag = sci.1.72.2_api.34.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -784,7 +784,8 @@ sub setup_cmdl_fates_mode {
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
-                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
+                      "fates_parteh_mode","use_fates_tree_damage","fates_history_dimlevel","fates_seeddisp_cadence",
+		      "use_fates_luh","fluh_timeseries" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -1571,11 +1572,13 @@ sub process_namelist_inline_logic {
   setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_start_type($opts, $nl_flags, $nl);
   setup_logic_decomp_performance($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_roughness_methods($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_snicar_methods($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl,  $envxml_ref);
   setup_logic_dynamic_plant_nitrogen_alloc($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_luna($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  setup_logic_hillslope($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_o3_veg_stress_method($opts, $nl_flags, $definition, $defaults, $nl,$physv);
   setup_logic_hydrstress($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_dynamic_roots($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
@@ -1633,6 +1636,11 @@ sub process_namelist_inline_logic {
   ###############################
   setup_logic_crop_inparm($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ###############################
+  # namelist group: tillage     #
+  ###############################
+  setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+
   ###############################
   # namelist group: ch4par_in   #
   ###############################
@@ -1997,6 +2005,25 @@ sub setup_logic_decomp_performance {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_roughness_methods {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method',
+              'phys'=>$nl_flags->{'phys'} );
+
+  my $var = remove_leading_and_trailing_quotes( $nl->get_value("z0param_method") );
+  if ( $var ne "Meier2022" && $var ne "ZengWang2007" ) {
+    $log->fatal_error("$var is incorrect entry for the namelist variable z0param_method; expected Meier2022 or ZengWang2007");
+  }
+  my $phys = $physv->as_string();
+  if ( $phys eq "clm4_5" || $phys eq "clm5_0" ) {
+    if ( $var eq "Meier2022" ) {
+      $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm5_1 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file");
+    }
+  }
+}
+#-------------------------------------------------------------------------------
+
 sub setup_logic_snicar_methods {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -2011,7 +2038,7 @@ sub setup_logic_snicar_methods {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' );
 
   # Error checking in loop
-  my %supportedSettings = ( 'snicar_solarspec' => "'mid_latitude_winter'", 'snicar_dust_optics' => "'sahara'", 'snicar_numrad_snw' => '5', 'snicar_snobc_intmix' => '.false.', 'snicar_snodst_intmix' => '.false.', 'snicar_use_aerosol' => '.true.', 'do_sno_oc' => '.false.' );
+  my %supportedSettings = ( 'snicar_solarspec' => "'mid_latitude_winter'", 'snicar_dust_optics' => "'sahara'", 'snicar_numrad_snw' => '5', 'snicar_snodst_intmix' => '.false.', 'snicar_use_aerosol' => '.true.', 'do_sno_oc' => '.false.' );
   keys %supportedSettings;
   while ( my ($key, $val) = each %supportedSettings ) {
     my $var = $nl->get_value($key);
@@ -2029,13 +2056,13 @@ sub setup_logic_snicar_methods {
     $log->warning("$key1=$val1a and $val1b are supported; $var1 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!");
   }
 
-  # snicar_snobc_intmix and snicar_snodst_intmix cannot both be true
+  # snicar_snobc_intmix and snicar_snodst_intmix cannot both be true, however, they can both be false
   my $key1 = 'snicar_snobc_intmix';
   my $key2 = 'snicar_snodst_intmix';
   my $var1 = $nl->get_value($key1);
   my $var2 = $nl->get_value($key2);
-  my $val1 = $supportedSettings{$key1};  # supported value for this option
-  if (($var1 eq $var2) && ($var1 ne $val1)) {
+  my $val2 = $supportedSettings{$key2};  # supported value for this option
+  if (($var1 eq $var2) && ($var2 ne $val2)) {
     $log->warning("$key1 = $var1 and $key2 = $var2 do not work together!");
   }
 }
@@ -2235,12 +2262,32 @@ sub setup_logic_crop_inparm {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting",
                  'use_crop'=>$nl->get_value('use_crop') );
+
+     my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_residue_removal_frac' );
+     if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
+        $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
+     }
   } else {
-     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" );
+     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept", "crop_residue_removal_frac" );
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' );
   }
 }
 
+#-------------------------------------------------------------------------------
+
+sub setup_logic_tillage {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode',
+              'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() );
+
+  my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) );
+  if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl_flags->{'use_crop'}) ) {
+      $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." );
+  }
+}
+
 #-------------------------------------------------------------------------------
 sub error_if_set {
    # do a fatal_error and exit if any of the input variable names are set
@@ -2661,6 +2708,8 @@ sub setup_logic_do_transient_pfts {
       $cannot_be_true = "$var cannot be combined with use_cndv";
    } elsif (&value_is_true($nl->get_value('use_fates'))) {
       $cannot_be_true = "$var cannot be combined with use_fates";
+   } elsif (&value_is_true($nl->get_value('use_hillslope'))) {
+      $cannot_be_true = "$var cannot be combined with use_hillslope";
    }
 
    if ($cannot_be_true) {
@@ -2736,6 +2785,8 @@ sub setup_logic_do_transient_crops {
       # do_transient_crops. However, this hasn't been tested, so to be safe,
       # we are not allowing this combination for now.
       $cannot_be_true = "$var has not been tested with FATES, so for now these two options cannot be combined";
+   } elsif (&value_is_true($nl->get_value('use_hillslope'))) {
+      $cannot_be_true = "$var cannot be combined with use_hillslope";
    }
 
    if ($cannot_be_true) {
@@ -2831,6 +2882,8 @@ sub setup_logic_do_transient_lakes {
    if (&value_is_true($nl->get_value($var))) {
       if (&value_is_true($nl->get_value('collapse_urban'))) {
          $log->fatal_error("$var cannot be combined with collapse_urban");
+      } elsif (&value_is_true($nl->get_value('use_hillslope'))) {
+         $log->fatal_error("$var cannot be combined with use_hillslope");
       }
       if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) {
          $log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8");
@@ -2894,6 +2947,8 @@ sub setup_logic_do_transient_urban {
    if (&value_is_true($nl->get_value($var))) {
       if (&value_is_true($nl->get_value('collapse_urban'))) {
          $log->fatal_error("$var cannot be combined with collapse_urban");
+      } elsif (&value_is_true($nl->get_value('use_hillslope'))) {
+         $log->fatal_error("$var cannot be combined with use_hillslope");
       }
       if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) {
          $log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8");
@@ -3223,12 +3278,8 @@ sub setup_logic_hydrology_switches {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_subgrid_fluxes');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_cover_fraction_method');
   my $subgrid    = $nl->get_value('use_subgrid_fluxes' );
-  my $origflag   = $nl->get_value('origflag'    );
   my $h2osfcflag = $nl->get_value('h2osfcflag'  );
   my $scf_method = $nl->get_value('snow_cover_fraction_method');
-  if ( $origflag == 1 && &value_is_true($subgrid) ) {
-    $log->fatal_error("if origflag is ON, use_subgrid_fluxes can NOT also be on!");
-  }
   if ( $h2osfcflag == 1 && ! &value_is_true($subgrid) ) {
     $log->fatal_error("if h2osfcflag is ON, use_subgrid_fluxes can NOT be off!");
   }
@@ -3252,9 +3303,6 @@ sub setup_logic_hydrology_switches {
   if ( defined($use_vic) && defined($lower) && (&value_is_true($use_vic)) && $lower != 3 && $lower != 4) {
      $log->fatal_error( "If use_vichydro is on -- lower_boundary_condition can only be table or aquifer" );
   }
-  if ( defined($origflag) && defined($use_vic) && (&value_is_true($use_vic)) && $origflag == 1 ) {
-     $log->fatal_error( "If use_vichydro is on -- origflag can NOT be equal to 1" );
-  }
   if ( defined($h2osfcflag) && defined($lower) && $h2osfcflag == 0 && $lower != 4 ) {
      $log->fatal_error( "If h2osfcflag is 0 lower_boundary_condition can only be aquifer" );
   }
@@ -3436,6 +3484,28 @@ sub setup_logic_luna {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_hillslope {
+  #
+  # Hillslope model
+  #
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'downscale_hillslope_meteorology' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_head_gradient_method' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_transmissivity_method' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_pft_distribution_method' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_soil_profile_method' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope_routing', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
+  my $use_hillslope = $nl->get_value('use_hillslope');
+  my $use_hillslope_routing = $nl->get_value('use_hillslope_routing');
+  if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
+      $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_hydrstress {
   #
   # Plant hydraulic stress model
@@ -4164,7 +4234,6 @@ sub setup_logic_soil_resis {
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soil_resis_method' );
 }
-#-------------------------------------------------------------------------------
 
 sub setup_logic_canopyfluxes {
   #
@@ -4370,7 +4439,8 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
+                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
+		       "use_fates_luh","fates_history_dimlevel" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
@@ -4540,6 +4610,7 @@ sub write_output_files {
 
   # CLM component
   my @groups;
+
   @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
@@ -4549,9 +4620,9 @@ sub write_output_files {
                soilhydrology_inparm luna friction_velocity mineral_nitrogen_dynamics
                soilwater_movement_inparm rooting_profile_inparm
                soil_resis_inparm  bgc_shared canopyfluxes_inparm aerosol
-               clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm
+               clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm hillslope_hydrology_inparm hillslope_properties_inparm
                cnprecision_inparm clm_glacier_behavior crop_inparm irrigation_inparm
-               surfacealbedo_inparm water_tracers_inparm);
+               surfacealbedo_inparm water_tracers_inparm tillage_inparm);
 
   #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm
   #             finidat_consistency_checks dynpft_consistency_checks);