PR for merging several PRs at once

.git-blame-ignore-revs

@@ -11,11 +11,15 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 b771971e3299c4fa56534b93421f7a2b9c7282fd
 9de88bb57ea9855da408cbec1dc8acb9079eda47
 8bc4688e52ea23ef688e283698f70a44388373eb
+4ee49e3e516ca7dee5df378f65664f93a7db4415
+0207bc98dd5c75cd69a0e788bc53e41093712f5c
+e4d38681df23ccca0ae29581a45f8362574e0630
 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
 810cb346f05ac1aabfff931ab1a2b7b584add241
 5933b0018f8e29413e30dda9b906370d147bad45
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+0bc3f00115d86d026a977918661c93779b3b19f9
 540b256d1f3382f4619d7b0877c32d54ce5c40b6
 8a168bb0895f4f2421608dd2589398e13a6663e6

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, $physv);
@@ -2031,6 +2045,13 @@ sub setup_logic_snicar_methods {
 sub setup_logic_snow {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_thermal_cond_method' );
+
+  my $var = $nl->get_value('snow_thermal_cond_method');
+  if ( $var ne "'Jordan1991'" && $var ne "'Sturm1997'" ) {
+    $log->fatal_error("$var is incorrect entry for the namelist variable snow_thermal_cond_method; expected Jordan1991 or Sturm1997");
+  }
+
   my $numrad_snw = $nl->get_value('snicar_numrad_snw');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics',
                 'snicar_numrad_snw' => $numrad_snw);
@@ -2290,6 +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)) {
@@ -2342,7 +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 = $nl->get_value('flanduse_timeseries');
@@ -2367,26 +2389,42 @@ sub setup_logic_surface_dataset {
   if ( !  &value_is_true($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" );
+     }
+  }
 }
 
 #-------------------------------------------------------------------------------

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>

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -445,6 +445,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <reset_snow_glc_ela>1.e9</reset_snow_glc_ela>
 
 <snow_cover_fraction_method>SwensonLawrence2012</snow_cover_fraction_method>
+<snow_thermal_cond_method>Jordan1991</snow_thermal_cond_method>
 
 <!-- Default glacier behavior is:
      Mountain glaciers: single_at_atm_topo
@@ -1289,8 +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." 

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} -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -2845,6 +2845,11 @@ NiuYang2007: Niu and Yang 2007
 SwensonLawrence2012: Swenson and Lawrence 2012
 </entry>
 
+<entry id="snow_thermal_cond_method" type="char*25" category="clm_physics"
+       group="clm_inparm" valid_values="Jordan1991,Sturm1997" >
+Parameterization to use for snow thermal conductivity
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- Namelist options related to water tracers                                                 -->
 <!-- ========================================================================================  -->

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 -->

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>

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 );

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":

cime_config/testdefs/ExpectedTestFails.xml

@@ -57,13 +57,6 @@
     </phase>
   </test>
 
-  <test name="ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>#2236</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">

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