Merge remote-tracking branch 'upstream/master' into noresm

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.67.2_api.27.0.0
+tag = sci.1.68.2_api.30.0.0
 required = True
 
 [externals_description]

bld/CLMBuildNamelist.pm

@@ -769,8 +769,8 @@ sub setup_cmdl_fates_mode {
        # dis-allow fates specific namelist items with non-fates runs
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
-		      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
-		      "fates_parteh_mode","use_fates_tree_damage" );
+                      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
+                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -4010,21 +4010,28 @@ sub setup_logic_cropcal_streams {
   # Option checks
   my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ;
   my $use_mxmat = $nl->get_value('use_mxmat') ;
-  my $sdate_file = $nl->get_value('stream_fldFileName_sdate') ;
+  my $swindow_start_file = $nl->get_value('stream_fldFileName_swindow_start') ;
+  my $swindow_end_file = $nl->get_value('stream_fldFileName_swindow_end') ;
   my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ;
   my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ;
+  if ( ($swindow_start_file eq '' and $swindow_start_file ne '') or ($swindow_start_file ne '' and $swindow_start_file eq '') ) {
+    $log->fatal_error("When specifying sowing window dates, you must provide both swindow_start_file and swindow_end_file. To specify exact sowing dates, use the same file." );
+  }
   if ( $generate_crop_gdds eq '.true.' ) {
       if ( $use_mxmat eq '.true.' ) {
           $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
       }
-      if ( $sdate_file eq '' ) {
-          $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_sdate")
+      if ( $swindow_start_file eq '' or $swindow_end_file eq '' ) {
+          $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_swindow_start and stream_fldFileName_swindow_end")
+      }
+      if ( $swindow_start_file ne $swindow_end_file ) {
+          $log->fatal_error("If generate_crop_gdds is true, you must specify exact sowing dates by setting stream_fldFileName_swindow_start and stream_fldFileName_swindow_end to the same file")
       }
       if ( $gdd_file ne '' ) {
           $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_cultivar_gdds")
       }
   }
-  if ( $mesh_file eq '' and ( $sdate_file ne '' or $gdd_file ne '' ) ) {
+  if ( $mesh_file eq '' and ( $swindow_start_file ne '' or $gdd_file ne '' ) ) {
       $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal")
   }
 }
@@ -4325,7 +4332,7 @@ sub setup_logic_fates {
     if (&value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
-                       "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp",
+                       "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
                        "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2714,6 +2714,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
+<fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true.">.true.</use_fates_nocomp>
 <use_fates_nocomp              use_fates=".true."                      >.false.</use_fates_nocomp>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -686,6 +686,17 @@ Switch deciding which nutrient model to use in FATES.
 (Only relevant if FATES is on)
 </entry>
 
+<entry id="fates_seeddisp_cadence" type="integer" category="physics"
+        group="clm_inparm" valid_values="0,1,2,3">
+Switch defining the cadence at which seeds are dispersed across
+gridcells.  Setting the switch value to zero turns off dispersal.
+Setting the switch to 1, 2, or 3 sets the dispersal cadence to
+daily, monthly or yearly.  The daily cadence is primarily
+recommended for test and debug only. Note that turning this
+feature on will result in more memory usage.
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="use_fates_tree_damage" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false."> 
 Toggle to turn on the tree damage module in FATES
@@ -1882,9 +1893,19 @@ Last year to loop over for crop calendar data
 Simulation year that aligns with stream_year_first_cropcal value
 </entry>
 
-<entry id="stream_fldfilename_sdate" type="char*256(30)" category="datasets"
+<entry id="allow_invalid_swindow_inputs" type="logical" category="datasets"
+       group="cropcal_streams" valid_values="" >
+By default, a value in stream_fldFileName_swindow_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead fall back on the paramfile sowing windows.
+</entry>
+
+<entry id="stream_fldFileName_swindow_start" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for date (day of year) of start of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history.
+</entry>
+
+<entry id="stream_fldFileName_swindow_end" type="char*256(30)" category="datasets"
        input_pathname="abs" group="cropcal_streams" valid_values="" >
-Filename of input stream data for sowing dates
+Filename of input stream data for date (day of year) of end of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history.
 </entry>
 
 <entry id="stream_fldfilename_cultivar_gdds" type="char*256(30)" category="datasets"

cime_config/SystemTests/rxcropmaturity.py

@@ -357,7 +357,8 @@ def _run_check_rxboth_run(self):
     def _modify_user_nl_allruns(self):
         nl_additions = [
             "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")),
-            "stream_fldFileName_sdate = '{}'".format(self._sdatefile),
+            "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile),
+            "stream_fldFileName_swindow_end   = '{}'".format(self._sdatefile),
             "stream_year_first_cropcal = 2000",
             "stream_year_last_cropcal = 2000",
             "model_year_align_cropcal = 2000",

cime_config/testdefs/ExpectedTestFails.xml

@@ -57,6 +57,13 @@
     </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">
@@ -109,7 +116,12 @@
     </phase>
   </test>
 
-
+  <test name="PEM_D_Ld15.5x5_amazon.I2000Clm50FatesRs.cheyenne_gnu.clm-FatesColdSeedDisp">
+    <phase name="COMPARE_base_modpes">
+      <status>FAIL</status>
+      <issue>FATES#1089</issue>
+    </phase>
+  </test>
 
 
 </expectedFails>

cime_config/testdefs/testlist_clm.xml

@@ -1563,6 +1563,19 @@
       <option name="comment"  >Add at least one test of a NEON site with PRISM precipitation</option>
     </options>
   </test>
+
+  <test name="ERS_P144x1_Lm25" grid="f10_f10_mg37" compset="I2000Clm51Fates" testmods="clm/FatesColdNoComp">
+       <machines>
+	 <!-- no izumi tests since this has a pe layout specific for cheyenne -->
+	 <machine name="cheyenne" compiler="intel"   category="aux_clm"/>
+	 <machine name="cheyenne" compiler="intel"   category="fates"/>
+       </machines>
+       <options>
+	 <option name="wallclock">00:60:00</option>
+	 <option name="comment"  >This is a long fates test on full dynamics. The 144 count is designed to minimize wall time.</option>
+       </options>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -1836,6 +1849,24 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >This test should be convered to an ERP test once the PEM version of this test is passing COMPARE_base_modpes.</option>
+    </options>
+  </test>
+  <test name="PEM_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment"  >This checks that the FATES seed dispersal MPI communication is consistent when the PE layout changes.</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTreeDamage">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>

cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README

@@ -0,0 +1,26 @@
+Testing FATES cross grid seed dispersal is activated by enabling the 
+namelist switch option fates_seeddisp_cadence as well as providing reasonable
+values to the fates parameter file for the following variables:
+
+fates_seed_dispersal_fraction
+fates_seed_dispersal_max_dist
+fates_seed_dispersal_pdf_scale
+fates_seed_dispersal_pdf_shape
+
+Given that the default fates parameter file has the above variables as unset,
+a custom fates parameter file must be supplied to appropriately test this mode.
+This testmod itself addresses CTSM issue 2151: https://github.com/ESCOMP/CTSM/issues/2151
+Note that to avoid exceeding the filename string length maximu, the parameter
+file generated on the fly is placed in the $SRCROOT/src/fates/parameter_files
+directory.  This may still run into problems is the $SRCROOT string is too long.
+
+The max_dist value will impact the size of the 'neighborhood' of gridcells
+that fates will attempt to distribute seeds to.  To limit the neighborhood to
+something tractable for a regression test, the user_nl_clm file points to a 
+specific fates parameter file that was generated to work with a 5x5_amazon 
+resolution.
+
+The main downside of this method is that this file will require a custom update
+for every fates parameter file API update.  Addressing CTSM issue #2126 will alleviate
+this issue as it will provide the capability to build the fates parameter file on 
+the fly which with the appropriate values for this test.

cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/include_user_mods

@@ -0,0 +1 @@
+../FatesCold

cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands

@@ -0,0 +1,11 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESROOT=$SRCDIR/src/fates/
+FATESPARAMFILE=$FATESROOT/parameter_files/fates_params_seeddisp_4x5.nc
+
+ncgen -o $FATESPARAMFILE $FATESROOT/parameter_files/fates_params_default.cdl
+
+$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts
+$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts
+$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts
+$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts

cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm

@@ -0,0 +1,3 @@
+fates_paramfile = '$SRCROOT/src/fates/parameter_files/fates_params_seeddisp_4x5.nc'
+fates_seeddisp_cadence = 1
+hist_fincl1       = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF'

cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm

@@ -1,7 +1,7 @@
  hist_fincl1   += 'GDD0', 'GDD8', 'GDD10', 
                   'GDD020', 'GDD820', 'GDD1020',
                   'GDDACCUM', 'GDDTSOI', 'A5TMIN', 'A10TMIN',
-                  'HUI'
+                  'HUI', 'GRAINN_TO_FOOD'
 
 ! The main point of including this field is to test the SUM history field infrastructure
 ! This is in the crop testmods because this field is mainly useful in transient crop runs
@@ -10,7 +10,7 @@ hist_fincl2  += 'DYN_COL_SOIL_ADJUSTMENTS_C'
 
 
 ! Annual crop variables on per-sowing/per-harvest axes, per PFT.
-hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'
+hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS'
 hist_nhtfrq(3) = 17520
 hist_mfilt(3) = 1
 hist_type1d_pertape(3) = 'PFTS'

cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods

@@ -0,0 +1 @@
+../default

cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm

@@ -0,0 +1,5 @@
+stream_fldFileName_swindow_start = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
+stream_fldFileName_swindow_end = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc'
+stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc'
+stream_year_first_cropcal = 2000
+stream_year_last_cropcal = 2000