Merge remote-tracking branch 'ekluzek/compset_fix' into mergetag-20231114

slevis-lmwg · slevis-lmwg · commit ed728bfccd06 · 2023-11-14T10:01:54.000-07:00
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -613,7 +613,7 @@ sub process_namelist_user_input {
   process_namelist_commandline_infile($opts, $definition, $nl, $envxml_ref);
 
   # Apply the commandline options and make sure the user didn't change it above
-  process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv);
 
   # The last two process command line arguments for usr_name and use_case
   # They require that process_namelist_commandline_options was called before this
@@ -634,10 +634,10 @@ sub process_namelist_commandline_options {
   # Obtain default values for the following build-namelist input arguments
   # : res, mask, ssp_rcp, sim_year, sim_year_range, and clm_accelerated_spinup.
 
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv) = @_;
 
   setup_cmdl_chk_res($opts, $defaults);
-  setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults);
+  setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults, $envxml_ref);
   setup_cmdl_mask($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_configuration_and_structure($opts, $nl_flags, $definition, $defaults, $nl);
   setup_cmdl_bgc($opts, $nl_flags, $definition, $defaults, $nl);
@@ -668,7 +668,7 @@ sub setup_cmdl_chk_res {
 }
 
 sub setup_cmdl_resolution {
-  my ($opts, $nl_flags, $definition, $defaults) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $envxml_ref) = @_;
 
   my $var = "res";
   my $val;
@@ -686,16 +686,30 @@ sub setup_cmdl_resolution {
     $val = &quote_string( $nl_flags->{'res'} );
     if (  ! $definition->is_valid_value( $var, $val ) ) {
       my @valid_values   = $definition->get_valid_values( $var );
-      if ( ! defined($opts->{'clm_usr_name'}) || $nl_flags->{'res'} ne $opts->{'clm_usr_name'} ) {
+      if ( $nl_flags->{'res'} ne "CLM_USRDAT" ) {
         $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
       }
     }
   }
+  if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) {
+    if ( ! defined($opts->{'clm_usr_name'}) ) {
+        $log->fatal_error("Resolution is CLM_USRDAT, but --clm_usr_name option is NOT set, and it is required for CLM_USRDAT resolutions");
+    }
+  }
+  #
   # For NEON sites
-  if ($nl_flags->{'res'} =~ /NEON/) {
-    $nl_flags->{'neon'} = ".true."
-  } else {
-    $nl_flags->{'neon'} = ".false."
+  #
+  $nl_flags->{'neon'} = ".false.";
+  $nl_flags->{'neonsite'} = "";
+  if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) {
+    if ( $opts->{'clm_usr_name'} eq "NEON" ) {
+       $nl_flags->{'neon'} = ".true.";
+       $nl_flags->{'neonsite'} = $envxml_ref->{'NEONSITE'};
+       $log->verbose_message( "This is a NEON site with NEONSITE = " . $nl_flags->{'neonsite'} );
+    }
+  }
+  if ( ! &value_is_true( $nl_flags->{'neon'} ) ) {
+    $log->verbose_message( "This is NOT a NEON site" );
   }
 
 }
@@ -1572,7 +1586,7 @@ sub process_namelist_inline_logic {
   setup_logic_grainproduct($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_soilstate($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl);
-  setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_dynamic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl);
   if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
     setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
@@ -2297,6 +2311,7 @@ sub setup_logic_demand {
   $settings{'use_lch4'}            = $nl_flags->{'use_lch4'};
   $settings{'use_nitrif_denitrif'} = $nl_flags->{'use_nitrif_denitrif'};
   $settings{'use_crop'}            = $nl_flags->{'use_crop'};
+  $settings{'neon'}                = $nl_flags->{'neon'};
 
   my $demand = $nl->get_value('clm_demand');
   if (defined($demand)) {
@@ -2349,7 +2364,7 @@ sub setup_logic_surface_dataset {
   # consistent with it
   # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set
   #
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_;
 
   $nl_flags->{'flanduse_timeseries'} = "null";
   my $flanduse_timeseries = $nl->get_value('flanduse_timeseries');
@@ -2374,26 +2389,42 @@ sub setup_logic_surface_dataset {
   if ( !  &value_is_true($nl_flags->{'use_fates'}) ) {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'},
+                 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
                  'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'use_crop'=>".true.", 'glc_nec'=>$nl_flags->{'glc_nec'}, 'nofail'=>1);
+                 'use_crop'=>".true.", 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'}, 'nofail'=>1);
   }
   # If didn't find the crop version check for the exact match
-  if ( ! defined($nl->get_value($var) ) ) {
+  my $fsurdat = $nl->get_value($var);
+  if ( ! defined($fsurdat) ) {
      if ( !  &value_is_true($nl_flags->{'use_fates'}) ) {
         $log->verbose_message( "Crop version of $var NOT found, searching for an exact match" );
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'},
+                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, 'use_fates'=>$nl_flags->{'use_fates'},
+                 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
                  'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}, 'nofail'=>1 );
-     if ( ! defined($nl->get_value($var) ) ) {
+     if ( ! defined($fsurdat) ) {
         $log->verbose_message( "Exact match of $var NOT found, searching for version with irrigate true" );
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'},
-                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.",
+                 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_fates'=>$nl_flags->{'use_fates'}, 
+                 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'},
                  'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'} );
   }
+  #
+  # Expand the XML variables for NEON cases so that NEONSITE will be used
+  #
+  if ( &value_is_true($nl_flags->{'neon'}) ) {
+     my $fsurdat = $nl->get_value($var);
+     my $newval = SetupTools::expand_xml_var( $fsurdat, $xmlvar_ref );
+     if ( $newval ne $fsurdat ) {
+        my $group = $definition->get_group_name($var);
+        $nl->set_variable_value($group, $var, $newval);
+        $log->verbose_message( "This is a NEON site and the fsurdat file selected is: $newval" );
+     }
+  }
 }
 
 #-------------------------------------------------------------------------------
diff --git a/bld/env_run.xml b/bld/env_run.xml
@@ -9,5 +9,6 @@ Sample env_run.xml file that allows build-namelist to be run for testing in this
 -->
 <entry id="DIN_LOC_ROOT"         value="MYDINLOCROOT"  /> 
 <entry id="GLC_TWO_WAY_COUPLING" value="FALSE"         /> 
+<entry id="NEONSITE"             value=""              /> 
 
 </config_definition>
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -1290,8 +1290,25 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <fsurdat hgrid="0.9x1.25"     sim_year="PtVg" use_crop=".false." irrigate=".false."
 >lnd/clm2/surfdata_map/surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc</fsurdat>
 
+<!-- for NEON sites present day simulations - year 2000 -->
+<fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".true.">
+lnd/clm2/surfdata_map/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230120.nc</fsurdat>
+<fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false.">
+lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230601.nc</fsurdat>
+<!-- If there are cases where only a few datasets change - they can be listed here for the particular NEONSITE -->
+<!-- for example to override the above for the TOOL site do something like this...
+<fsurdat hgrid="CLM_USRDAT" neon=".true." sim_year="2018" use_fates=".false." neonsite="TOOL">
+lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c230699.nc</fsurdat>
+-->
+
 <!-- Dynamic PFT surface datasets (relative to {csmdata}) -->
 
+<!-- When NEON landuse datasets are available uncomment the following for something like this...
+     Also change the setting for clm_demand in the namelist_defaults_overall.xml file
+<flanduse_timeseries hgrid="CLM_USRDAT" neon=".true." sim_year_range="1850-2100">
+>lnd/clm2/surfdata_map/NEON/landuse.timeseries_NEON_${NEONSITE}_hist_78pfts_simyr2018-2023_c230931.nc</flanduse_timeseries>
+-->
+
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000" irrigate=".true." use_vichydro=".true."
  use_crop=".false." >lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="0.9x1.25"      sim_year_range="1850-2000" irrigate=".true." 
diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml
@@ -44,8 +44,10 @@ determine default values for namelists.
 
 
 <!-- For transient cases, turn on demand to set flanduse_timeseries -->
-<clm_demand sim_year_range="1850-2000">flanduse_timeseries</clm_demand>
-<clm_demand sim_year_range="1850-2100">flanduse_timeseries</clm_demand>
+<clm_demand sim_year_range="1850-2100" neon=".true." >null</clm_demand>    <!-- NEON sites don't have transient PFT datasets yet -->
+<clm_demand sim_year_range="constant"                >null</clm_demand>
+<clm_demand sim_year_range="1850-2000"               >flanduse_timeseries</clm_demand>
+<clm_demand sim_year_range="1850-2100"               >flanduse_timeseries</clm_demand>
 
 
 <!-- Default location of {csmdata} -->
diff --git a/bld/namelist_files/use_cases/2018-PD_transient.xml b/bld/namelist_files/use_cases/2018-PD_transient.xml
@@ -1,8 +1,12 @@
 <?xml version="1.0"?>
 
+<!-- This use-case is mainly in use for NEON sites -->
+
 <namelist_defaults>
 
-<use_case_desc>Simulate transient land-use, and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data</use_case_desc>
+<use_case_desc use_cn=".true.">Simulate transient Nitrogen-deposition, aerosol deposition, urban, and fire related (pop-density, lightning) changes from 2018 to current day with a mix of historical data, and future scenario data</use_case_desc>
+<use_case_desc use_cn=".false." use_fates=".true.">Simulate transient Nitrogen-deposition, aerosol deposition, urban, and fire related (pop-density, lightning) changes from 2018 to current day with a mix of historical data, and future scenario data</use_case_desc>
+<use_case_desc use_cn=".false." use_fates=".false.">Simulate transient urban and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data</use_case_desc>
 
 <!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
      set in a namelist_defaults xml file -->
diff --git a/bld/namelist_files/use_cases/2018_control.xml b/bld/namelist_files/use_cases/2018_control.xml
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 
+
+<!-- This use-case is mainly in use for NEON sites -->
+
 <namelist_defaults>
 
 <use_case_desc>Conditions to simulate 2018 land-use</use_case_desc>
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};
@@ -381,7 +381,7 @@ sub cat_and_create_namelistinfile {
                    "JORN", "LAJA", "MOAB", "OAES", "OSBS", "SCBI", "SOAP", "STER", "TOOL",
                    "UNDE", "YELL"
  ) {
-   &make_env_run();
+   &make_env_run( NEONSITE=>"$site" );
    #
    # Concatonate  default usermods and specific sitetogether expanding env variables while doing that
    #
@@ -400,7 +400,7 @@ sub cat_and_create_namelistinfile {
    #
    # Now run  the site
    #
-   my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2018 -infile $namelistfile";
+   my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc bgc --use_case 2018_control --infile $namelistfile";
    eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
    $cfiles->checkfilesexist( "$options", $mode );
diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -136,7 +136,6 @@ def buildnml(case, caseroot, compname):
     clmusr = ""
     if lnd_grid == "CLM_USRDAT":
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
-        lnd_grid = clm_usrdat_name
         clmusr = " -clm_usr_name %s " % clm_usrdat_name
         # Write warning about initial condition data
         if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands
@@ -32,7 +32,7 @@ else
 fi
 
 # If needed for SP simulations: & set history file variables
-if [[ $compset =~ .*CLM[0-9]+%.*SP.* ]]; then
+if [[ $compset =~ .*CLM[0-9]+%[^_]*SP.* ]]; then
   if [[ $TEST != "TRUE" ]]; then
     ./xmlchange STOP_OPTION=nyears
   fi

Original file line number	Diff line number	Diff line change
`@@ -42,7 +42,7 @@ sub make_env_run {`
`42`	`42`	`my %settings = @_;`
`43`	`43`
`44`	`44`	`# Set default settings`
`45`		`- my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE" );`
	`45`	`+ my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" );`
`46`	`46`	`# Set any settings that came in from function call`
`47`	`47`	`foreach my $item ( keys(%settings) ) {`
`48`	`48`	`$env_vars{$item} = $settings{$item};`
`@@ -381,7 +381,7 @@ sub cat_and_create_namelistinfile {`
`381`	`381`	`"JORN", "LAJA", "MOAB", "OAES", "OSBS", "SCBI", "SOAP", "STER", "TOOL",`
`382`	`382`	`"UNDE", "YELL"`
`383`	`383`	`) {`
`384`		`- &make_env_run();`
	`384`	`+ &make_env_run( NEONSITE=>"$site" );`
`385`	`385`	`#`
`386`	`386`	`# Concatonate default usermods and specific sitetogether expanding env variables while doing that`
`387`	`387`	`#`
`@@ -400,7 +400,7 @@ sub cat_and_create_namelistinfile {`
`400`	`400`	`#`
`401`	`401`	`# Now run the site`
`402`	`402`	`#`
`403`		`- my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2018 -infile $namelistfile";`
	`403`	`+ my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc bgc --use_case 2018_control --infile $namelistfile";`
`404`	`404`	`eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };`
`405`	`405`	`is( $@, '', "options: $options" );`
`406`	`406`	`$cfiles->checkfilesexist( "$options", $mode );`