Merge tag 'ctsm5.1.dev111' into ctsm5.2.mksurfdata

Fixes for NEON cases Two sets of fixes for NEON cases: (1) Fixes for leap year handling when there are discrepancies between the model and the DATM forcing data in terms of whether the current year is a leap year. This involved updates to the share and cdeps externals from Jim Edwards. (2) Other fixes for NEON cases from Will Wieder, as documented in #1860 Conflicts: Externals.cfg src/biogeophys/test/Photosynthesis_test/test_Photosynthesis.pf src/main/clm_initializeMod.F90 src/main/clm_varpar.F90 tools/README tools/mkmapdata/mkmapdata.sh
ESCOMP · Oct 8, 2022 · 989584c · 989584c
2 parents 981247f + c6d8032
commit 989584c
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,9 @@
+# Ran python directory through black python formatter
+4cd83cb3ee6d85eb909403487abf5eeaf4d98911
+0aa2957c1f8603c63fa30b11295c06cfddff44a5
+2cdb380febb274478e84cd90945aee93f29fa2e6
+e44dc469439e02e9ee582dab274d890ebdfab104
+565e7bcacbb0bba20ff80d680d8ad769676641c6
+b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
+51c102c5df2e0ef971b5f8eeeb477567899af63a
+7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -0,0 +1,21 @@
+name: black check on push and PR
+#
+# Run the python formatting in check mode
+#
+on: [push, pull_request]
+
+jobs:
+  black-check:
+     runs-on: ubuntu-latest
+     steps:
+        # Checkout the code
+        - uses: actions/checkout@v2
+        # Use the latest stable version of the github action
+        - uses: psf/black@stable
+          with:
+             # Use options and version identical to the conda environment
+             # Using pyproject.toml makes sure this testing is consistent with our python directory testing
+             options: "--check --config python/pyproject.toml"
+             src:     "./python"
+             # Version should be coordinated with the ctsm_py conda environment under the python directory
+             version: "22.3.0"
diff --git a/Externals.cfg b/Externals.cfg
@@ -34,46 +34,43 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-#tag = ccs_config_cesm0.0.15
-#branch = update_for_mksurfdata_esmf_build
-hash = 29a06a80a5f411f3ed001d5b2cb34d2aab685cbe
+tag = ccs_config_cesm0.0.45
 protocol = git
-#repo_url = https://github.com/ESMCI/ccs_config_cesm.git
-repo_url = https://github.com/ekluzek/ccs_config_cesm.git
+repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.15
+tag = cime6.0.45
 required = True
 
 [cmeps]
-tag = cmeps0.13.47
+tag = cmeps0.13.71
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.41
+tag = cdeps0.12.65
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.12
+tag = cpl7.0.14
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.10
+tag = share1.0.13
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -87,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_6
+tag = pio2_5_7
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.55.4_api.22.1.0
+tag = sci.1.58.1_api.24.1.0
 required = True
 
 [externals_description]

diff --git a/README b/README
@@ -45,6 +45,7 @@ test -------------- CTSM Testing scripts for CTSM offline tools.
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 manage_externals -- Script to manage the external source directories
+py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere l
 
 Directory structure only for a CTSM checkout:

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -741,7 +741,7 @@ sub setup_cmdl_fates_mode {
 
     $var = "use_fates";
     if ( &value_is_true($nl_flags->{$var}) ) {
-      # This section is a place-holder to test for modules that are not allowed with ED
+      # This section is a place-holder to test for modules that are not allowed with FATES
       # the defaults which are set in the logic section of the namelist builder will
       # automatically set these correctly (well that is the assumption), but here we
       # want to set a catch to fail and warn users if they explicitly set incompatible user namelist
@@ -774,7 +774,7 @@ sub setup_cmdl_fates_mode {
        # dis-allow fates specific namelist items with non-fates runs
        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_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" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -863,16 +863,34 @@ sub setup_cmdl_bgc {
      }
   }
   #
+  # Set FATES-SP mode
+  #
+  if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_sp', 'use_fates'=>$nl_flags->{'use_fates'} );
+     if ( &value_is_true($nl->get_value('use_fates_sp')) ) {
+        $nl_flags->{'use_fates_sp'} = ".true.";
+     } else {
+        $nl_flags->{'use_fates_sp'} = ".false.";
+     }
+  } else {
+     $nl_flags->{'use_fates_sp'} = ".false.";
+  }
+  #
   # Determine Soil decomposition method
   #
   my $var = "soil_decomp_method";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
+              'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'},
+              'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
   my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( $var ) );
 
-  if ( &value_is_true($nl_flags->{'use_cn'}) ||  &value_is_true($nl_flags->{'use_fates'}))  {
+  if (      &value_is_true($nl_flags->{'use_cn'}) ) {
+     if ( $soil_decomp_method eq "None" ) {
+        $log->fatal_error("$var must NOT be None if use_cn is on");
+     }
+  } elsif ( &value_is_true($nl_flags->{'use_fates'}) && (not &value_is_true($nl_flags->{'use_fates_sp'}))  )  {
      if ( $soil_decomp_method eq "None" ) {
-        $log->fatal_error("$var must NOT be None if use_cn or use_fates are on");
+        $log->fatal_error("$var must NOT be None if use_fates is on and use_fates_sp is not TRUE");
      }
   } elsif ( $soil_decomp_method ne "None" ) {
      $log->fatal_error("$var must be None if use_cn and use_fates are off");
@@ -901,6 +919,12 @@ sub setup_cmdl_bgc {
            $log->warning("$var normally use_nitrif_denitrif should only be FALSE if FATES is on, it has NOT been validated for being off for BGC mode" );
         }
      }
+     # if MIMICS is on and use_fates = .true. then use_lch4 must = .true.
+     if ( (! &value_is_true($nl_flags->{'use_lch4'})) && &value_is_true($nl_flags->{'use_fates'}) ) {
+        if ( $soil_decomp_method eq "MIMICSWieder2015" ) {
+           $log->warning("If MIMICS is on and use_fates = .true. then use_lch4 must be .true. and currently it's not" );
+        }
+     }
   }
   #
   # Set FUN for BGC
@@ -1143,7 +1167,7 @@ sub setup_cmdl_spinup {
      $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values");
   }
   if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} ))  && (not &value_is_true($nl_flags->{'use_fates'})) ) {
-     $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor ED is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'}).");
+     $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor FATES is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'}).");
   }
   if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) {
      $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
@@ -2022,6 +2046,10 @@ sub setup_logic_subgrid {
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_lake');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_wetland');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_urban');
+
+   if ( &value_is_true($nl_flags->{'use_fates'}) && $nl->get_value('n_dom_pfts') != 0 ) {
+      $log->fatal_error( "FATES and n_dom_pfts can NOT be set at the same time" );
+   }
 }
 
 #-------------------------------------------------------------------------------
@@ -2587,7 +2615,7 @@ sub setup_logic_do_transient_crops {
       # In principle, use_fates should be compatible with
       # 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 ED, so for now these two options cannot be combined";
+      $cannot_be_true = "$var has not been tested with FATES, so for now these two options cannot be combined";
    }
 
    if ($cannot_be_true) {
@@ -2705,8 +2733,8 @@ sub setup_logic_do_transient_urban {
    # for them to be unset if that will be their final state):
    # - flanduse_timeseries
    #
-   # NOTE(kwo, 2021-08-11) I based this function on setup_logic_do_transient_lakes. 
-   # As in NOTE(wjs, 2020-08-23) I'm not sure if all of the checks here are truly important 
+   # NOTE(kwo, 2021-08-11) I based this function on setup_logic_do_transient_lakes.
+   # As in NOTE(wjs, 2020-08-23) I'm not sure if all of the checks here are truly important
    # for transient urban (in particular, my guess is that collapse_urban could probably be done with transient
    # urban - as well as transient pfts and transient crops for that matter), but some of
    # the checks probably are needed, and it seems best to keep transient urban consistent
@@ -3650,12 +3678,15 @@ sub setup_logic_dry_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   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, $nl, 'drydep_method');
+    add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
   } else {
-    if ( defined($nl->get_value('drydep_list')) ||
-         defined($nl->get_value('drydep_method')) ) {
-      $log->fatal_error("drydep_list or drydep_method defined, but drydep option NOT set");
+    if ( defined($nl->get_value('drydep_list')) ) {
+      $log->fatal_error("drydep_list defined, but drydep option NOT set");
     }
   }
 }
@@ -3695,7 +3726,7 @@ sub setup_logic_megan {
 
   if ($nl_flags->{'megan'} ) {
     if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-       $log->fatal_error("MEGAN can NOT be on when ED is also on.\n" .
+       $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
                    "   Use the '-no-megan' option when '-bgc fates' is activated");
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
@@ -4095,15 +4126,9 @@ sub setup_logic_fates {
 
     if (&value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
-        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_sp', 'use_fates'=>$nl_flags->{'use_fates'} );
-        if ( &value_is_true($nl->get_value('use_fates_sp')) ) {
-           $nl_flags->{'use_fates_sp'} = ".true.";
-        } else {
-           $nl_flags->{'use_fates_sp'} = ".false.";
-        }
         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",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" );
+                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
         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'} );

diff --git a/bld/README b/bld/README
@@ -23,7 +23,7 @@ env_run.xml --- Sample case runtime environment variables, so build-namelist can
 listDefaultNamelist.pl -- List the files needed, for a list of resolutions,
                           to run CLM that are currently NOT on your machine.
                           This file can then be used by 
-                            cime/scripts/Tools/check_input_data
+                            cime/CIME/Tools/check_input_data
                           to retreive them from the inputdata repository.
                           Setting up cases with create_newcase also does
                           this -- but only for the exact configuration

diff --git a/bld/listDefaultNamelist.pl b/bld/listDefaultNamelist.pl
@@ -17,7 +17,7 @@
 #
 # To then get the files from the CESM SVN repository:
 #
-# ../cime/scripts/Tools/check_input_data --data-list-dir . --download
+# ../cime/CIME/Tools/check_input_data --data-list-dir . --download
 #
 #=======================================================================
 
@@ -84,7 +84,7 @@ sub usage {
 
   to then read the resulting clm.input_data_list file and retreive the files
 
-  ../cime/scripts/Tools/check_input_data --data-list-dir . --download
+  ../cime/CIME/Tools/check_input_data --data-list-dir . --download
 
 EOF
 }

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -491,7 +491,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.22.1.0_12pft_c220307.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.24.0.0_12pft_c220608.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->
@@ -2528,9 +2528,10 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
 
-<soil_decomp_method use_cn=".true."    >CENTURYKoven2013</soil_decomp_method>
-<soil_decomp_method use_fates=".true." >CENTURYKoven2013</soil_decomp_method>
-<soil_decomp_method                    >None</soil_decomp_method>
+<soil_decomp_method use_cn=".true."                          >CENTURYKoven2013</soil_decomp_method>
+<soil_decomp_method use_fates=".true."                       >CENTURYKoven2013</soil_decomp_method>
+<soil_decomp_method use_fates=".true." use_fates_sp=".true." >None</soil_decomp_method>
+<soil_decomp_method                                          >None</soil_decomp_method>
 
 <use_lch4            soil_decomp_method="None" >.false.</use_lch4>
 <use_lch4                                      >.true.</use_lch4>
@@ -2540,6 +2541,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <!-- ===== FATES DEFAULTS =========== -->
 <fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
+<use_fates_tree_damage         use_fates=".true.">.false.</use_fates_tree_damage>
 <use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
 <use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>

diff --git a/bld/namelist_files/namelist_defaults_drydep.xml b/bld/namelist_files/namelist_defaults_drydep.xml
@@ -17,7 +17,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <drydep_list>'O3','NO2','HNO3','NO','HO2NO2','CH3OOH','CH2O','CO','H2O2','CH3COOOH','PAN','MPAN','C2H5OOH','ONIT','POOH','C3H7OOH','ROOH','CH3COCHO','CH3COCH3','Pb','ONITR','MACROOH','XOOH','ISOPOOH','CH3OH','C2H5OH','CH3CHO','GLYALD','HYAC','HYDRALD','ALKOOH','MEKOOH','TOLOOH','TERPOOH','CH3COOH','CB1','CB2','OC1','OC2','SOA','SO2','SO4','NH3','NH4NO3'
 </drydep_list>
-<drydep_method>xactive_lnd</drydep_method>
+
+<!-- effective Henry's coef data for wet and dry deposition -->
+<dep_data_file>atm/cam/chem/trop_mozart/dvel/dep_data_c201019.nc</dep_data_file>
 
 <!-- Defaults for megan_emis_nl -->
 

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -8,16 +8,6 @@
 <!-- CLM Namelist -->
 <!-- ========================================================================================  -->
 
-<entry id="finidat_interp_dest" 
-       type="char*256" 
-       category="datasets"
-       input_pathname="abs" 
-       group="clm_inparm" 
-       valid_values="" >
-If use_init_interp is set to .true., interpinic will be called to interpolate
-the file given by finidat, creating the output file specified by finidat_interp_dest.
-</entry>
-
 <entry id="finidat" 
        type="char*256" 
        category="datasets"
@@ -648,6 +638,12 @@ Switch deciding which nutrient model to use in FATES.
 (Only relevant if FATES is on)
 </entry>
 
+<entry id="use_fates_tree_damage" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false."> 
+Toggle to turn on the tree damage module in FATES
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="fates_spitfire_mode" type="integer" category="physics"
         group="clm_inparm" valid_values="0,1,2,3,4,5" value=".false.">
 Turn on spitfire module to simulate fire by setting fates_spitfire_mode > 0.
@@ -2124,7 +2120,7 @@ Command line arguement for biogeochemistry mode for CLM4.5
         Nitrification/De-nitrification
         Methane model
         Vertically resolved Carbon
-   fates = FATES/ED ecosystem demography model with below ground BGC:
+   fates = FATES Functionally Assembled Terrestrial Ecosystem Simulator (ecosystem demography model with below ground BGC):
 </entry>
 
 <!-- ========================================================================================  -->