Merge pull request #1257 from glemieux/fma-merge-ctsm5.1.dev020

Merge ctsm5.1.dev020 tag into fates_main_api

.config_files.xml

@@ -5,19 +5,20 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for clm:
-       In a standalone clm checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CTSM:
+       In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
        rather than $SRCROOT/components/clm.
 
        However, because of the way overrides are handled, we need to
        re-specify the full information here rather than just overriding
-       the value for clm.
+       the value for CTSM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"      >$SRCROOT</value>
+      <value component="clm"       >$SRCROOT</value>
+      <value component="ctsm"      >$SRCROOT</value>
       <value component="dlnd" comp_interface="mct">$CIMEROOT/src/components/data_comps_mct/dlnd</value>
       <value component="dlnd" comp_interface="nuopc">$CIMEROOT/src/components/cdeps/dlnd</value>
       <value component="slnd"      >$CIMEROOT/src/components/stub_comps_$COMP_INTERFACE/slnd</value>

.gitignore

@@ -5,6 +5,7 @@ manage_externals.log
 /tools/PTCLM/
 /cime/
 /components/
+/doc/doc-builder/
 
 # ignore svn directories
 **/.svn/**
@@ -47,16 +48,6 @@ CMakeFiles/
 # unit testing directories
 /src/unit_tests.*
 
-# files generated by the unit test build
-/src/dyn_subgrid/dynVarMod.F90
-/src/dyn_subgrid/dynVarTimeInterpMod.F90
-/src/dyn_subgrid/dynVarTimeUninterpMod.F90
-/src/utils/array_utils.F90
-/src/unit_test_stubs/utils/restUtilMod_stub.F90
-/src/unit_test_stubs/main/ncdio_pio_fake.F90
-/src/unit_test_stubs/main/ncdio_var.F90
-/src/unit_test_shr/unittestArrayMod.F90
-
 # cime_config
 buildnmlc
 
@@ -72,6 +63,7 @@ buildnmlc
 /bld/unit_testers/drv_flds_in*
 /bld/unit_testers/temp_file.txt*
 /bld/unit_testers/user_nl_clm_real_parameters*
+/bld/unit_testers/user_nl_ctsm_real_parameters*
 /bld/unit_testers/env_run.xml
 
 # tools testing output
@@ -86,8 +78,8 @@ surfdata_*.namelist
 landuse.timeseries_*.namelist
 landuse.timeseries_*.log
 landuse_timeseries_*.txt
-clm.input_data_list
-clm.input_data_list.previous
+ctsm.input_data_list
+ctsm.input_data_list.previous
 *.stdout.txt.o*
 
 # mksurfdata unit tests

Externals.cfg

@@ -16,31 +16,51 @@ required = True
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_72
+tag = rtm1_0_73
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_37
+tag = mosart1_0_38
 required = True
 
-[cdeps]
-hash = 45b7a85
+[mizuRoute]
+local_path = components/mizuRoute
 protocol = git
-repo_url = https://github.com/ESCOMP/CDEPS.git
-local_path = components/cdeps
+repo_url = https://github.com/nmizukami/mizuRoute
+hash = 34723c2
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime5.8.32
-externals = ../Externals_cime.cfg
+tag = branch_tags/cime5.8.32_a02
+required = True
+
+[cmeps]
+local_path = cime/src/drivers/nuopc/
+protocol = git
+repo_url = https://github.com/ESCOMP/CMEPS.git
+hash = 7654038
+required = True
+
+[cdeps]
+local_path = components/cdeps
+protocol = git
+repo_url = https://github.com/ESCOMP/CDEPS.git
+hash = 45b7a85
 required = True
 
+[doc-builder]
+local_path = doc/doc-builder
+protocol = git
+repo_url = https://github.com/ESMCI/doc-builder
+tag = v1.0.5
+required = False
+
 [externals_description]
 schema_version = 1.0.0
 

bld/CLMBuildNamelist.pm

@@ -1010,24 +1010,6 @@ sub setup_cmdl_maxpft {
   }
   $nl_flags->{'maxpft'} = $val;
 
-  $var = "maxpatch_pft";
-  my $group = $definition->get_group_name($var);
-  if ( ! defined($nl->get_variable_value($group, $var)) ) {
-    $val = $nl_flags->{'maxpft'};
-    $nl->set_variable_value($group, $var, $val);
-  }
-  $val = $nl->get_variable_value($group, $var);
-  my @valid_values   = ($maxpatchpft{'.true.'}, $maxpatchpft{'.false.'}  );
-  my $found = 0;
-  foreach my $valid_val ( @valid_values ) {
-     if ( $val == $valid_val ) {
-       $found = 1;
-       last;
-     }
-  }
-  if ( ! $found ) {
-     $log->warning("$var has a value ($val) that is normally NOT valid. Normal valid values are: @valid_values");
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -1488,7 +1470,7 @@ sub process_namelist_inline_logic {
   ##############################
   # namelist group: clm_inparm #
   ##############################
-  setup_logic_site_specific($nl_flags, $definition, $nl);
+  setup_logic_site_specific($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_lnd_frac($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_co2_type($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl);
@@ -1516,6 +1498,7 @@ sub process_namelist_inline_logic {
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
 
   #########################################
   # namelist group: atm2lnd_inparm
@@ -1717,7 +1700,7 @@ sub process_namelist_inline_logic {
 
 sub setup_logic_site_specific {
   # site specific requirements
-  my ($nl_flags, $definition, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
   # res check prevents polluting the namelist with an unnecessary
   # false variable for every run
@@ -1748,6 +1731,9 @@ sub setup_logic_site_specific {
       $log->fatal_error("1x1_numaIA grids must use a compset with CN and CROP turned on.");
     }
   }
+  #  Set compname
+  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'compname',
+              'phys'=>$nl_flags->{'phys'} );
 }
 
 #-------------------------------------------------------------------------------
@@ -2378,6 +2364,7 @@ sub setup_logic_dynamic_subgrid {
 
    setup_logic_do_transient_pfts($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_transient_crops($opts, $nl_flags, $definition, $defaults, $nl);
+   setup_logic_do_transient_lakes($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl);
 
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_dynbal_baselines');
@@ -2543,6 +2530,69 @@ sub setup_logic_do_transient_crops {
    }
 }
 
+sub setup_logic_do_transient_lakes {
+   #
+   # Set do_transient_lakes default value, and perform error checking on do_transient_lakes
+   #
+   # Assumes the following are already set in the namelist (although it's okay
+   # for them to be unset if that will be their final state):
+   # - flanduse_timeseries
+   #
+   # NOTE(wjs, 2020-08-23) I based this function on setup_logic_do_transient_crops. I'm
+   # not sure if all of the checks here are truly important for transient lakes (in
+   # particular, my guess is that collapse_urban could probably be done with transient
+   # lakes - 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 lakes consistent
+   # with other transient areas in this respect.
+   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+   my $var = 'do_transient_lakes';
+
+   # cannot_be_true will be set to a non-empty string in any case where
+   # do_transient_lakes should not be true; if it turns out that
+   # do_transient_lakes IS true in any of these cases, a fatal error will be
+   # generated
+   my $cannot_be_true = "";
+
+   my $n_dom_pfts = $nl->get_value( 'n_dom_pfts' );
+   my $n_dom_landunits = $nl->get_value( 'n_dom_landunits' );
+   my $toosmall_soil = $nl->get_value( 'toosmall_soil' );
+   my $toosmall_crop = $nl->get_value( 'toosmall_crop' );
+   my $toosmall_glacier = $nl->get_value( 'toosmall_glacier' );
+   my $toosmall_lake = $nl->get_value( 'toosmall_lake' );
+   my $toosmall_wetland = $nl->get_value( 'toosmall_wetland' );
+   my $toosmall_urban = $nl->get_value( 'toosmall_urban' );
+
+   if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
+      $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
+   }
+
+   if (!$cannot_be_true) {
+      # Note that, if the variable cannot be true, we don't call add_default
+      # - so that we don't clutter up the namelist with variables that don't
+      # matter for this case
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+   }
+
+   # Make sure the value is false when it needs to be false - i.e., that the
+   # user hasn't tried to set a true value at an inappropriate time.
+
+   if (&value_is_true($nl->get_value($var)) && $cannot_be_true) {
+      $log->fatal_error($cannot_be_true);
+   }
+
+   # if do_transient_lakes is .true. and any of these (n_dom_* or toosmall_*)
+   # are > 0 or collapse_urban = .true., then give fatal error
+   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");
+      }
+      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");
+      }
+   }
+}
+
 sub setup_logic_do_harvest {
    #
    # Set do_harvest default value, and perform error checking on do_harvest
@@ -3420,7 +3470,7 @@ sub setup_logic_megan {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_soilm_streams {
-  # prescribed soil moisture streams require clm4_5/clm5_0
+  # prescribed soil moisture streams require clm4_5/clm5_0/clm5_1
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_soil_moisture_streams');
@@ -3833,6 +3883,18 @@ sub setup_logic_fates {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_misc {
+   #
+   # Set some misc options
+   #
+   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_run_ncdiopio_tests');
+   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file');
+}
+
+#-------------------------------------------------------------------------------
+
 sub write_output_files {
   my ($opts, $nl_flags, $defaults, $nl) = @_;
 

bld/config_files/clm_phys_vers.pm

@@ -28,7 +28,7 @@ use bigint;
 #use warnings;
 #use diagnostics;
 
-my @version_strings = ("clm4_5", "clm5_0");
+my @version_strings = ("clm4_5", "clm5_0", "clm5_1");
 
 #-------------------------------------------------------------------------------
 
@@ -83,12 +83,12 @@ if ( ! defined(caller) && $#ARGV == -1 ) {
    require Test::More;
    Test::More->import( );
 
-   plan( tests=>2 );
+   plan( tests=>3 );
 
    sub testit {
       print "unit tester\n";
       my %lastv;
-      my @vers_list = ( "clm4_5", "clm5_0" );
+      my @vers_list = ( "clm4_5", "clm5_0", "clm5_1" );
       foreach my $vers ( @vers_list ) {
          my $phys = config_files::clm_phys_vers->new($vers);
          isa_ok($phys, "config_files::clm_phys_vers", "created clm_phys_vers object");

bld/config_files/config_definition_ctsm.xml

@@ -5,10 +5,10 @@
 <config_definition>
 
 <entry id="phys" 
-       valid_values="clm4_5,clm5_0"
+       valid_values="clm4_5,clm5_0,clm5_1"
        value="clm4_5"
        category="physics">
-Specifies either clm4_5 or clm5_0 physics
+Specifies either clm4_5, clm5_0, or clm5_1 physics
 </entry>
 
 <entry id="clm_root" 

bld/listDefaultNamelist.pl

@@ -97,7 +97,7 @@ sub make_config_cache {
 <?xml version="1.0"?>
 <config_definition>
 <commandline></commandline>
-<entry id="phys" value="$phys" list="" valid_values="clm4_5,clm5_0">Specifies clm physics</entry>
+<entry id="phys" value="$phys" list="" valid_values="clm4_5,clm5_0,clm5_1">Specifies clm physics</entry>
 </config_definition>
 EOF
    $fh->close();