Merge branch 'cropresidues3' into tillage-and-residues4

samsrabin · Jan 8, 2024 · cd6a021 · cd6a021
2 parents 2f69473 + 336f848
commit cd6a021
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -11,16 +11,20 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 b771971e3299c4fa56534b93421f7a2b9c7282fd
 9de88bb57ea9855da408cbec1dc8acb9079eda47
 8bc4688e52ea23ef688e283698f70a44388373eb
+c8bd4c6f98c0b411391b4355da449507db3aab4e
 4ee49e3e516ca7dee5df378f65664f93a7db4415
 0207bc98dd5c75cd69a0e788bc53e41093712f5c
 e4d38681df23ccca0ae29581a45f8362574e0630
 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
 810cb346f05ac1aabfff931ab1a2b7b584add241
 5933b0018f8e29413e30dda9b906370d147bad45
+025d5e7c2e80263717fb029101d65cbbf261c3c4
+a9d96219902cf609636886c7073a84407f450d9a
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
 0bc3f00115d86d026a977918661c93779b3b19f9
 540b256d1f3382f4619d7b0877c32d54ce5c40b6
 8a168bb0895f4f2421608dd2589398e13a6663e6
+183fc26a6691bbdf87f515dc47924a64be3ced9b
 6fccf682eaf718615407d9bacdd3903b8786a03d
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.1.68.2_api.31.0.0
+tag = sci.1.70.0_api.32.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -784,7 +784,7 @@ sub setup_cmdl_fates_mode {
        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","fates_seeddisp_cadence" );
+                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -2240,8 +2240,13 @@ sub setup_logic_crop_inparm {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting",
                  'use_crop'=>$nl->get_value('use_crop') );
+
+     my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
+     if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
+        $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
+     }
   } else {
-     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" );
+     error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept", "crop_residue_removal_frac" );
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' );
   }
 }
@@ -4386,7 +4391,7 @@ sub setup_logic_fates {
         add_default($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","fates_seeddisp_cadence",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
+                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
@@ -4414,21 +4419,34 @@ sub setup_logic_fates {
               # spit-fire can't be on with FATES SP mode is active
               if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
                     $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
+              }
            }
-	 }
         }
         my $var = "use_fates_inventory_init";
         if ( defined($nl->get_value($var))  ) {
            if ( &value_is_true($nl->get_value($var)) ) {
               $var = "fates_inventory_ctrl_filename";
-	      my $fname = substr $nl->get_value($var), 1, -1;  # ignore first and last positions of string because those are quote characters
+              my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
               if ( ! defined($nl->get_value($var))  ) {
                  $log->fatal_error("$var is required when use_fates_inventory_init is set" );
               } elsif ( ! -f "$fname" ) {
                  $log->fatal_error("$fname does NOT point to a valid filename" );
               }
            }
         }
+        my $var = "use_fates_luh";
+        if ( defined($nl->get_value($var))  ) {
+           if ( &value_is_true($nl->get_value($var)) ) {
+              $var = "fluh_timeseries";
+              add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
+              my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
+              if ( ! defined($nl->get_value($var))  ) {
+                 $log->fatal_error("$var is required when use_fates_luh is set" );
+              } elsif ( ! -f "$fname" ) {
+                 $log->fatal_error("$fname does NOT point to a valid filename" );
+              }
+           }
+        }
     }
 }
 

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -492,7 +492,7 @@ 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.25.5.0_12pft_c230628.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc</fates_paramfile>
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->
@@ -553,6 +553,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_grainproduct use_crop=".true." phys="clm5_0" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 <use_grainproduct use_crop=".true." phys="clm5_1" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 
+<crop_residue_removal_frac>0.d+0</crop_residue_removal_frac>
+
 <!-- Crop model options -->
 <baset_mapping           use_crop=".true." phys="clm4_5" >constant</baset_mapping>
 <baset_mapping           use_crop=".true." phys="clm5_0" >varytropicsbylat</baset_mapping>
@@ -1572,6 +1574,15 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2100" ssp_rcp="SSP5-3.4"
  use_crop=".false."   >lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_10x15_SSP5-3.4_16pfts_Irrig_CMIP6_simyr1850-2100_c190228.nc</flanduse_timeseries>
 
+<!-- Land Use Harmonization unified data sets for dynamic FATES land use change -->
+
+<fluh_timeseries hgrid="4x5" sim_year_range="1850-2000" use_fates=".true."
+ >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
+
+<!-- This one is just for testing until Issue #2304 is resolved -->
+<fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
+ >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
+
 <!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
 <use_fun phys="clm5_1"  use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
 <use_fun phys="clm5_0"  use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
@@ -2755,6 +2766,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_logging             use_fates=".true.">.false.</use_fates_logging>
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
+<use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
 

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -777,6 +777,22 @@ Full pathname to the inventory initialization control file.
 (Only relevant if FATES is on).
 </entry>
 
+<!-- This may eventually migrate to the dynamic_subgrid group-->
+<entry id="use_fates_luh" type="logical" category="physics"
+       group="clm_inparm" valid_values="" >
+If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file.
+(Also, only valid for use_fates = true and is incompatible with transient runs currently.)
+</entry>
+
+<!-- This could eventually be included in the "dynamic_subgrid" -->
+<entry id="fluh_timeseries" type="char*256" category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname of unified land use harmonization (LUH) data file. This causes the land-use
+types to vary over time.
+(Required, if use_fates_luh=T)
+(Only relevant if FATES is on).
+</entry>
+
 <entry id="use_luna" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen
@@ -1148,6 +1164,13 @@ Toggle to turn on the prognostic fertilizer for crop model
 Toggle to turn on the 1-year grain product pool in the crop model 
 </entry>
 
+<entry id="crop_residue_removal_frac" type="real" category="physics"
+       group="clm_inparm" valid_values="" value="0.0d00">
+Fraction of post-harvest crop residues (leaf and stem) to move to 
+1-year product pool instead of letting them fall as litter.
+<default>Default: 0.0</default>
+</entry>
+
 <entry id="baset_mapping" type="char*20" category="physics"
        group="crop_inparm" valid_values="constant,varytropicsbylat" value="constant">
 Type of mapping to use for base temperature for prognostic crop model

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -1061,6 +1061,16 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "useinventorybutnotfile"    =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"use_fates_luh=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm4_5",
+                                   },
+     "inventoryfileDNE"          =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_luh=.true., fluh_timeseries='zztop'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm4_5",
+                                   },
      "useMEGANwithFATES"         =>{ options=>"-bgc fates -envxml_dir . -megan",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -2900,6 +2900,16 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdLUH2">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3" grid="f19_g17" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesCold">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -16,10 +16,8 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
-'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
-'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
+'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
-'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
 'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
 'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
 'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
@@ -28,4 +26,5 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
 'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
-'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC'
+'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
+'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods
@@ -0,0 +1 @@
+../FatesCold
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -0,0 +1 @@
+use_fates_luh = .true.
diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm
@@ -21,9 +21,8 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLD
               'FATES_SEEDS_IN_EXTERN_EL', 'FATES_SEED_GERM_EL', 'FATES_SEED_DECAY_EL', 'FATES_STOREC', 'FATES_VEGC',
               'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 
               'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
-              'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S',
               'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
-              'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
+              'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
               'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
               'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 
               'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ',

diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template
@@ -27,8 +27,8 @@ Does this tag change answers significantly for any of the following physics conf
 [ ] clm4_5
 
 
-Bugs fixed or introduced
-------------------------
+Bugs fixed
+----------
 [Remove any lines that don't apply. Remove entire section if nothing applies.]
 
 CTSM issues fixed (include CTSM Issue #):