Merge tag 'ctsm5.1.dev122' into zendersource_dev

Rework handling of evaporation constraint in SoilFluxes Occasionally, h2osoi_ice was going significantly negative in UpdateState_TopLayerFluxes - see ESCOMP#1979. As noted in that issue, this seems to be due to h2osoi_ice having a very different magnitude from h2osoi_liq, leading to greater-than-roundoff-level differences from zero final state in a relative sense (i.e., relative to the magnitude of h2osoi_ice) - I think because of the appearance of the sum (h2osoi_ice + h2osoi_liq) in the equations that limit fluxes. To try to deal with this, I have reworked the handling of the evaporation constraint to directly limit both the liqevap and solidevap, so that both of them should result in the equivalent liq or ice states going to 0 within roundoff. To do that, I needed to move the partitioning of the total flux into liquid and solid to earlier in the subroutine and then recalculate those partitioning fluxes in conditions where we're applying an evaporation constraint. Note that I applied a max of 0 to the new fluxes because many initial conditions files have roundoff-level negative H2OSOI_LIQ, so without this limit, we were getting roundoff-level negative fluxes. Resolves ESCOMP#1979
dmleung · Apr 28, 2023 · 7616b5c · 7616b5c
2 parents 4f5dcb9 + cdb6187
commit 7616b5c
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diff --git a/.config_files.xml b/.config_files.xml
@@ -5,31 +5,31 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for CTSM:
-       In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CLM:
+       In a standalone CLM 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 CTSM.
+       the value for CLM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"       >$SRCROOT</value>
-      <value component="ctsm"      >$SRCROOT</value>
-      <value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
-      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
-      <value component="slnd"  comp_interface="mct"     >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
-      <value component="xlnd" comp_interface="mct"      >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
-      <value component="slnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
-      <value component="xlnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/xcpl_comps_nuopc/xlnd</value>
+      <value component="clm"                         >$SRCROOT</value>
+      <value component="slim"                        >$SRCROOT/components/slim/</value>
+      <value component="dlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
+      <value component="slnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="xlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
+      <value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>
     <desc>Root directory of the case land model component  </desc>
-    <schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
+    <schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
   </entry>
 
 </entry_id>
diff --git a/Externals.cfg b/Externals.cfg
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.38
+tag = ccs_config_cesm0.0.58
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.45
+tag = cime6.0.100
 required = True
 
 [cmeps]
-tag = cmeps0.13.71
+tag = cmeps0.14.17
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.65
+tag = cdeps1.0.7
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.13
+tag = share1.0.16
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -84,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_7
+tag = pio2_5_10
 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.1.61.0_api.25.0.0
+tag = sci.1.65.3_api.25.4.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -2492,6 +2492,7 @@ sub setup_logic_dynamic_subgrid {
    setup_logic_do_transient_lakes($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_transient_urban($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl);
+   setup_logic_do_grossunrep($opts, $nl_flags, $definition, $defaults, $nl);
 
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_dynbal_baselines');
    if ( &value_is_true($nl->get_value('reset_dynbal_baselines')) &&
@@ -2837,6 +2838,63 @@ sub setup_logic_do_harvest {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_do_grossunrep {
+   #
+   # Set do_grossunrep default value, and perform error checking on do_grossunrep
+   #
+   # 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
+   # - use_cn
+   # - use_fates
+   #
+   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+   my $var = 'do_grossunrep';
+
+   # Start by assuming a default value of '.true.'. Then check a number of
+   # conditions under which do_grossunrep cannot be true. Under these
+   # conditions: (1) set default value to '.false.'; (2) make sure that the
+   # value is indeed false (e.g., that the user didn't try to set it to true).
+
+   my $default_val = ".false.";
+
+   # cannot_be_true will be set to a non-empty string in any case where
+   # do_grossunrep should not be true; if it turns out that do_grossunrep IS true
+   # in any of these cases, a fatal error will be generated
+   my $cannot_be_true = "";
+
+   if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
+      $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
+   }
+   elsif (&value_is_true($nl->get_value('use_fates'))) {
+      $cannot_be_true = "$var currently doesn't work with FATES";
+   }
+   elsif (!&value_is_true($nl->get_value('use_cn'))) {
+      $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)";
+   }
+
+   if ($cannot_be_true) {
+      $default_val = ".false.";
+   }
+
+   if (!$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, $var, val=>$default_val);
+   }
+
+   # 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);
+   }
+
+}
+
+#-------------------------------------------------------------------------------
 sub setup_logic_spinup {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -493,7 +493,7 @@ 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.25.0.0_12pft_c221128.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -2495,6 +2495,13 @@ If TRUE, apply harvest from flanduse_timeseries file.
 (Also, only valid for use_cn = true.)
 </entry>
 
+<entry id="do_grossunrep" type="logical" category="physics"
+       group="dynamic_subgrid" valid_values="" >
+If TRUE, apply gross unrepresented landuse/land-cover change from flanduse_timeseries file.
+(Only valid for transient runs, where there is a flanduse_timeseries file.)
+(Also, only valid for use_cn = true.)
+</entry>
+
 <entry id="reset_dynbal_baselines" type="logical" category="physics"
        group="dynamic_subgrid" valid_values="">
 If TRUE, reset baseline values of total column water and energy in the

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1847;
+my $ntests = 1850;
 if ( defined($opts{'compare'}) ) {
    $ntests += 1254;
 }
@@ -1061,6 +1061,21 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "dogrossandsp"               =>{ options=>"--envxml_dir . --bgc sp --use_case 20thC_transient",
+                                     namelst=>"do_grossunrep=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "dogrossandfates"            =>{ options=>"--envxml_dir . --bgc fates --use_case 20thC_transient --no-megan",
+                                     namelst=>"do_grossunrep=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "dogrossandnottrans"         =>{ options=>"--envxml_dir . --bgc bgc --use_case 2000_control",
+                                     namelst=>"do_grossunrep=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "nocropwfert"                =>{ options=>"-envxml_dir . -bgc sp -no-crop",
                                      namelst=>"use_fertilizer=T",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1444,7 +1459,7 @@ sub cat_and_create_namelistinfile {
 my $usecase  = "20thC_transient";
 my $GLC_NEC         = 10;
 foreach my $res ( @tran_res ) {
-   $options = "-res $res -use_case $usecase -envxml_dir . -namelist '&a start_ymd=18500101/'";
+   $options = "-res $res -use_case $usecase -envxml_dir . -namelist '&a start_ymd=18500101/' -bgc bgc -crop -namelist '&a do_grossunrep=T/'";
    &make_env_run();
    eval{ system( "$bldnml $options > $tempfile 2>&1 " ); };
    is( $@, '', "$options" );

diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py
@@ -89,6 +89,7 @@ def _run_modify_fsurdat(self):
             print("getting an error within the fsurdat_modifier tool itself. ")
             print("Default error message: ")
             print(error.output)
+            raise
         except:
             print("ERROR trying to run fsurdat_modifier tool.")
             raise

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -88,7 +88,7 @@
     </phase>
   </test>
 
-  <test name="ERP_P144x2_Ld30.f45_f45_mg37.I2000Clm50FatesRs.cheyenne_intel.clm-mimicsFatesCold">
+  <test name="ERP_P72x2_Ld30.f45_f45_mg37.I2000Clm50FatesRs.cheyenne_intel.clm-mimicsFatesCold">
     <phase name="SHAREDLIB_BUILD">
       <status>PEND</status>
       <issue>#1045</issue>

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -327,7 +327,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment">Want one C96 test in the aux_clm test suite; just a short smoke test to make sure it can get off the ground. Use a PE layout that (1) has threading, because CAM uses threading at this resolution; and (2) has a smaller-than-standard task count in order to get through the queue faster.</option>
     </options>
   </test>
@@ -467,8 +467,17 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Transient case with isotopes with a december start</option>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >Transient case with isotopes with a December start</option>
+    </options>
+  </test>
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
     </options>
   </test>
   <test name="ERP_D_Ld10_P36x2_Vmct" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_decStart">
@@ -1867,7 +1876,7 @@
       <machine name="cheyenne" compiler="gnu" category="fates"/>
     </machines>
     <options>
-      <option name="wallclock">00:40:00</option>
+      <option name="wallclock">00:50:00</option>
     </options>
   </test>
   <test name="ERS_Lm13" grid="f45_f45_mg37" compset="I2000Clm50Fates" testmods="clm/FatesColdNoComp">
@@ -2007,7 +2016,7 @@
       <option name="comment">30 day exact restart test activating FATES size and age mortality mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="ERP_P144x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/mimicsFatesCold">
+  <test name="ERP_P72x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/mimicsFatesCold">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="fates"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands
@@ -0,0 +1,3 @@
+./xmlchange RUN_STARTDATE=1990-12-30
+# Ignore warnings because we are using crop, but starting from a different date than the initial conditions were for
+./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm
@@ -0,0 +1,5 @@
+ ! Specify a dataset that has non-zero Gross Unrepresented Land Use change fields on it
+ ! And turn it on
+ flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1700-2021_c220825.nc'
+ fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr1700_c220825.nc'
+ do_grossunrep = .true.
diff --git a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands
@@ -1,3 +1,5 @@
 #!/bin/bash
 ./xmlchange CLM_FORCE_COLDSTART="on"
 
+# We use this testmod in a _Ln1 test; this requires forcing the ROF coupling frequency to every time step
+./xmlchange ROF_NCPL=48