ESCOMP · ekluzek · Dec 31, 2023 · Jun 14, 2023 · Jun 14, 2023 · Jun 20, 2023
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($var)) ) {
@@ -4370,7 +4370,7 @@ sub setup_logic_fates {
         add_default($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'} );
@@ -4398,21 +4398,34 @@ 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                         -->
@@ -1572,6 +1572,15 @@ 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 +2764,7 @@ 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

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 #):

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,104 @@
 ===============================================================
+Tag name: ctsm5.1.dev160
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Sat 30 Dec 2023 11:23:47 PM MST
+One-line Summary: FATES landuse version 1
+
+Purpose and description of changes
+----------------------------------
+
+This tag enables FATES to utilize the state and transitions data
+from the Land Use Harmonization (https://luh.umd.edu/) data sets.
+This data has been preprocessed using tooling provided by FATES via
+a separate pull request (FATES#1032).  A new module has been added
+to the dyn_subgrid directory that largely adapts the dynHarvest
+module to import and read this minimially processed data, which is
+data is passed to fates.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+CTSM issues fixed (include CTSM Issue #):
+   #1077 -- Read in full LUH2 dataset for use by FATES
+   #2283 -- fates wood product flux not being correctly reported during CBalanceCheck endrun diagnostic output
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+   New namelist item: fluh_timeseries and use_fates_luh
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   FATES landuse testmod, FatesColdLUH2, added
+
+IMPORTANT NOTE ON BASELINES:
+   FATES baseline tests have a change in namelists because the fluh_timeseries file is listed in the baselines
+   but was removed in a last minute change. Compare to baseline other than that change are exact though.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS (66 FATES tests differ because of new fates param file)
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- PASS
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: yes, for FATES only
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
+
+  The fates tag update incorporates bug fixes and hydraulic mortality fixes, as well as the
+  restructured disturbance code necessary to accomodate the new landuse transitions capability.
+  As such, small differences were observed in testmods that engaged specific disturbance modes
+  or were long enough to trigger other default disturbances (e.g. fire)
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+  fates: sci.1.69.0_api.31.0.0 -> fates-sci.1.70.0_api.32.0.0
+
+Pull Requests that document the changes (include PR ids):
+  https://github.com/ESCOMP/ctsm/pull/2076
+  https://github.com/NGEET/fates/pull/1040
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev159
 Originator(s): multiple (slevis (Sam Levis), afoster (Adrianna Foster), erik (Erik Kluzek), wwieder (Will Wieder), glemieux (Greg Lemieux), oleson (Keith Oleson), sacks (Bill Sacks), samrabin (Sam Rabin), santos (Sean Patrick Santos))
 Date: Tue 12 Dec 2023 11:10:26 AM MST

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1
     ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates
     ctsm5.1.dev158     erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho
     ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho

diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90
@@ -258,7 +258,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
     real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)
     real(r8) :: gru_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)
     real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)
-    real(r8) :: fates_woodproduct_flux  ! Total carbon wood products flux from FATES to CLM [gC/m2/s]
 
     !-----------------------------------------------------------------------
 
@@ -309,11 +308,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
 
             s = clm_fates%f2hmap(ic)%hsites(c)
 
-
-            fates_woodproduct_flux = clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod10c + &
-                                     clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod100c
-
-            col_cinputs = fates_litter_flux(c) + fates_woodproduct_flux
+            col_cinputs = fates_litter_flux(c)
 
             ! calculate total column-level outputs
             ! fates has already exported burn losses and fluxes to the atm
@@ -372,7 +367,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
          write(iulog,*)'--- Inputs ---'
          if( col%is_fates(c) ) then
             write(iulog,*)'fates litter_flux        = ',fates_litter_flux(c)*dt
-            write(iulog,*)'fates wood product flux  = ',fates_woodproduct_flux*dt
          else
             write(iulog,*)'gpp                      = ',gpp(c)*dt
          end if