Merge https://github.com/mvdebolskiy/CTSM into noresm

.git-blame-ignore-revs

@@ -11,11 +11,16 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 b771971e3299c4fa56534b93421f7a2b9c7282fd
 9de88bb57ea9855da408cbec1dc8acb9079eda47
 8bc4688e52ea23ef688e283698f70a44388373eb
+4ee49e3e516ca7dee5df378f65664f93a7db4415
+0207bc98dd5c75cd69a0e788bc53e41093712f5c
+e4d38681df23ccca0ae29581a45f8362574e0630
 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
 810cb346f05ac1aabfff931ab1a2b7b584add241
 5933b0018f8e29413e30dda9b906370d147bad45
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+0bc3f00115d86d026a977918661c93779b3b19f9
 540b256d1f3382f4619d7b0877c32d54ce5c40b6
 8a168bb0895f4f2421608dd2589398e13a6663e6
+6fccf682eaf718615407d9bacdd3903b8786a03d

Externals.cfg

@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_95
+tag = cismwrap_2_1_96
 externals = Externals_CISM.cfg
 required = True
 
@@ -44,26 +44,26 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.125
+tag = cime6.0.175
 required = True
 
 [cmeps]
-tag = cmeps0.14.21
+tag = cmeps0.14.43
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.13
+tag = cdeps1.0.24
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl77.0.5
+tag = cpl77.0.7
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
@@ -84,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_10
+tag = pio2_6_2
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.68.2_api.30.0.0
+tag = sci.1.68.2_api.31.0.0
 required = True
 
 [externals_description]

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" );
+     }
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4174,7 +4212,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fresh_snw_rds_max');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');

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/createMapEntry.pl

@@ -23,7 +23,7 @@
    my $scriptName;
    ($scriptName = $0) =~ s!(.*)/!!; # get name of script
    my $cwd = getcwd();
-   my $CSMDATA = "/glade/p/cesm/cseg/inputdata";
+   my $CSMDATA = "/glade/campaign/cesm/cesmdata/cseg/inputdata";
 
    if ($#ARGV != 0 ) {
       usage();