ESCOMP · ekluzek · Jun 21, 2022 · May 20, 2022 · May 23, 2022 · May 23, 2022
diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.56.0_api.23.0.0
+repo_url = https://github.com/rgknox/fates
+branch = params-maxpatch-logfinal
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -774,7 +774,7 @@ 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_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" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -3705,7 +3705,7 @@ sub setup_logic_megan {
 
   if ($nl_flags->{'megan'} ) {
     if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-       $log->fatal_error("MEGAN can NOT be on when ED is also on.\n" .
+       $log->warning("MEGAN can NOT be on when ED is also on.\n" .
                    "   Use the '-no-megan' option when '-bgc fates' is activated");
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
@@ -4107,7 +4107,7 @@ sub setup_logic_fates {
         add_default($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",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" );
+                       "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'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -491,7 +491,7 @@ 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.22.1.0_12pft_c220307.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.24.0.0_12pft_c220608.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->
@@ -2541,6 +2541,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <!-- ===== FATES DEFAULTS =========== -->
 <fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
+<use_fates_tree_damage         use_fates=".true.">.false.</use_fates_tree_damage>
 <use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
 <use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -648,6 +648,12 @@ Switch deciding which nutrient model to use in FATES.
 (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
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="fates_spitfire_mode" type="integer" category="physics"
         group="clm_inparm" valid_values="0,1,2,3,4,5" value=".false.">
 Turn on spitfire module to simulate fire by setting fates_spitfire_mode > 0.

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1804,6 +1804,24 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="SMS_D" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdDefDryDep">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Run a test with dry deposition on and regular FATES</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdDefTreeDamage">
+    <machines>
+      <machine name="cheyenne" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Ensure functionality of the tree damage option in FATES</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3_PS" grid="f09_g17" compset="I2000Clm50FatesRs" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -2060,7 +2078,7 @@
       <option name="comment">Short ERP debug FATES test for f19_g17 grid.</option>
     </options>
   </test>
-  <test name="ERP_D_P32x2_Ld3" grid="f19_g17" compset="I2000Clm50FatesCru" testmods="clm/FatesColdDef">
+  <test name="ERP_D_P36x2_Ld3" grid="f19_g17" compset="I2000Clm50FatesCru" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
     </machines>
@@ -2251,6 +2269,24 @@
       <option name="comment">Test with DEBUG on for FatesSP mode, NOTE: FatesSp has the largest difference in CTSM code for any FATES mode</option>
     </options>
   </test>
+  <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdDefDryDepReducedComplexSatPhen">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Run a test with dry deposition on and FATES-SP</option>
+    </options>
+  </test>
+  <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdDefMeganReducedComplexSatPhen">
+    <machines>
+      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Run a test with MEGAN on and FATES-SP</option>
+    </options>
+  </test>
 <!--    Don't active this test until #1722 is fixed
   <test name="SMS_Ld3" grid="f09_f09_mg17" compset="I2000Clm51FatesCruRsGs" testmods="clm/FatesColdDefReducedComplexSatPhen_prescribed">
     <machines>

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods
@@ -0,0 +1 @@
+../FatesColdDef
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/shell_commands
@@ -0,0 +1 @@
+./xmlchange CLM_BLDNML_OPTS='--drydep' --append
diff --git a/...nfig/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/...nfig/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods
@@ -0,0 +1,2 @@
+../FatesColdDefDryDep
+../FatesColdDefReducedComplexSatPhen
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods
@@ -0,0 +1 @@
+../FatesColdDef
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange CLM_BLDNML_OPTS='--megan' --append
+./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append
diff --git a/...onfig/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/...onfig/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods
@@ -0,0 +1,2 @@
+../FatesColdDefMegan
+../FatesColdDefReducedComplexSatPhen
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods
@@ -0,0 +1 @@
+../FatesColdDef
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/user_nl_clm
@@ -0,0 +1 @@
+use_fates_tree_damage=.true.
diff --git a/src/biogeochem/EDBGCDynMod.F90 b/src/biogeochem/EDBGCDynMod.F90
@@ -260,6 +260,17 @@ subroutine EDBGCDyn(bounds,                                                    &
        call t_stopf('SoilBiogeochemLittVertTransp')
     end if
 
+    !call FatesWrapWoodProducts(bounds, num_soilc, filter_soilc,c_products_inst)
+    !call t_startf('CNWoodProducts')
+    !call c_products_inst%UpdateProducts(bounds, &
+    !     num_soilp, filter_soilp, &
+    !     dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), &
+    !     wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), &
+    !     dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), &
+    !     crop_harvest_to_cropprod_patch = cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp))
+    !call t_stopf('CNWoodProducts')
+
+
     end associate
 
   end subroutine EDBGCDyn

diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
@@ -231,21 +231,32 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
           call t_stopf('interpMonthlyVeg')
        endif
 
+    elseif(use_fates) then
+
+       ! FATES does not use any leaf/stem/htop data unless in satphen mode
+       if ( use_fates_sp) then
+          call t_startf('interpMonthlyVeg')
+          call interpMonthlyVeg(bounds_proc, canopystate_inst)
+          call t_stopf('interpMonthlyVeg')
+       end if
+
     else
+
        ! Determine weights for time interpolation of monthly vegetation data.
        ! This also determines whether it is time to read new monthly vegetation and
        ! obtain updated leaf area index [mlai1,mlai2], stem area index [msai1,msai2],
        ! vegetation top [mhvt1,mhvt2] and vegetation bottom [mhvb1,mhvb2]. The
        ! weights obtained here are used in subroutine SatellitePhenology to obtain time
        ! interpolated values.
-       if (doalb .or. ( n_drydep > 0 .and. drydep_method == DD_XLND ) .or. use_fates_sp) then
+       if ( doalb .or. ( n_drydep > 0 .and. drydep_method == DD_XLND ) )then
           call t_startf('interpMonthlyVeg')
           call interpMonthlyVeg(bounds_proc, canopystate_inst)
           call t_stopf('interpMonthlyVeg')
        end if
 
     end if
 
+
     ! ==================================================================================
     ! Determine decomp vertical profiles
     !

diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
@@ -26,7 +26,7 @@ module clm_initializeMod
   use PatchType             , only : patch         ! instance
   use reweightMod           , only : reweight_wrapup
   use filterMod             , only : allocFilters, filter, filter_inactive_and_active
-  use CLMFatesInterfaceMod  , only : CLMFatesGlobals
+  use CLMFatesInterfaceMod  , only : CLMFatesGlobals1,CLMFatesGlobals2
   use CLMFatesInterfaceMod  , only : CLMFatesTimesteps
   use dynSubgridControlMod  , only : dynSubgridControl_init, get_reset_dynbal_baselines
   use SelfTestDriver        , only : self_test_driver
@@ -40,7 +40,8 @@ module clm_initializeMod
   public :: initialize2  ! Phase two initialization
 
   integer :: actual_numcft  ! numcft from sfc dataset
-
+  integer :: actual_numpft  ! numpft from sfc dataset
+
 !-----------------------------------------------------------------------
 contains
 !-----------------------------------------------------------------------
@@ -96,8 +97,19 @@ subroutine initialize1(dtime)
 
     call control_init(dtime)
     call ncd_pio_init()
-    call surfrd_get_num_patches(fsurdat, actual_maxsoil_patches, actual_numcft)
-    call clm_varpar_init(actual_maxsoil_patches, actual_numcft)
+    call surfrd_get_num_patches(fsurdat, actual_maxsoil_patches, actual_numpft, actual_numcft)
+
+    if(use_fates) then
+
+       ! If fates is on, we override actual_maxsoil_patches. FATES dictates the
+       ! number of patches per column.  We still use numcft from the surface
+       ! file though...
+
+       call CLMFatesGlobals1(actual_numpft, actual_numcft, actual_maxsoil_patches)
+
+    end if
+
+    call clm_varpar_init(actual_maxsoil_patches, actual_numpft, actual_numcft)
     call decomp_cascade_par_init( NLFilename )
     call clm_varcon_init( IsSimpleBuildTemp() )
     call landunit_varcon_init()
@@ -119,6 +131,7 @@ subroutine initialize2(ni,nj)
     use clm_varcon                    , only : spval
     use clm_varpar                    , only : natpft_lb, natpft_ub, cft_lb, cft_ub, maxpatch_glc
     use clm_varpar                    , only : nlevsno
+    use clm_varpar                    , only : natpft_size,cft_size
     use clm_varctl                    , only : fsurdat
     use clm_varctl                    , only : finidat, finidat_interp_source, finidat_interp_dest, fsurdat
     use clm_varctl                    , only : use_cn, use_fates
@@ -210,36 +223,40 @@ subroutine initialize2(ni,nj)
     ! Allocate surface grid dynamic memory (just gridcell bounds dependent)
     allocate (wt_lunit     (begg:endg, max_lunit           ))
     allocate (urban_valid  (begg:endg                      ))
-    allocate (wt_nat_patch (begg:endg, natpft_lb:natpft_ub ))
     allocate (wt_cft       (begg:endg, cft_lb:cft_ub       ))
     allocate (fert_cft     (begg:endg, cft_lb:cft_ub       ))
     allocate (irrig_method (begg:endg, cft_lb:cft_ub       ))
     allocate (wt_glc_mec   (begg:endg, maxpatch_glc     ))
     allocate (topo_glc_mec (begg:endg, maxpatch_glc     ))
     allocate (haslake      (begg:endg                      ))
     allocate (pct_urban_max(begg:endg, numurbl             ))
-
+    allocate (wt_nat_patch (begg:endg, natpft_lb:natpft_ub ))
+
     ! Read list of Patches and their corresponding parameter values
     ! Independent of model resolution, Needs to stay before surfrd_get_data
     call pftcon%Init()
 
     ! Read surface dataset and set up subgrid weight arrays
     call surfrd_get_data(begg, endg, ldomain, fsurdat, actual_numcft)
 
-    ! Ask Fates to evaluate its own dimensioning needs.
-    ! This determines the total amount of space it requires in its largest
-    ! dimension.  We are currently calling that the "cohort" dimension, but
-    ! it is really a utility dimension that captures the models largest
-    ! size need.
-    ! Sets:
-    !   fates_maxElementsPerPatch
-    !   fates_maxElementsPerSite (where a site is roughly equivalent to a column)
-    ! (Note: fates_maxELementsPerSite is the critical variable used by CLM
-    ! to allocate space)
-    ! This also sets up various global constants in FATES
-    ! ------------------------------------------------------------------------
-
-    call CLMFatesGlobals()
+    if(use_fates) then
+
+       ! Ask Fates to evaluate its own dimensioning needs.
+       ! This determines the total amount of space it requires in its largest
+       ! dimension.  We are currently calling that the "cohort" dimension, but
+       ! it is really a utility dimension that captures the models largest
+       ! size need.
+       ! Sets:
+       !   fates_maxElementsPerPatch
+       !   fates_maxElementsPerSite (where a site is roughly equivalent to a column)
+       ! (Note: fates_maxELementsPerSite is the critical variable used by CLM
+       ! to allocate space)
+       ! This also sets up various global constants in FATES
+       ! ------------------------------------------------------------------------
+
+       call CLMFatesGlobals2()
+
+    end if
 
     ! Determine decomposition of subgrid scale landunits, columns, patches
     call decompInit_clumps(ni, nj, glc_behavior)
@@ -425,12 +442,17 @@ subroutine initialize2(ni,nj)
        if ( use_c13 .and. use_c13_timeseries ) then
           call C13_init_TimeSeries()
        end if
+
     else
-       call SatellitePhenologyInit(bounds_proc)
+       ! FATES OR Satellite phenology
+
+       if(use_fates_sp .or. .not.use_fates)then
+          call SatellitePhenologyInit(bounds_proc)
+       end if
 
        ! fates_spitfire_mode is assigned an integer value in the namelist
        ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
-       if (fates_spitfire_mode > scalar_lightning) then
+       if(use_fates .and. (fates_spitfire_mode > scalar_lightning)) then
           call clm_fates%Init2(bounds_proc, NLFilename)
        end if
     end if
@@ -591,7 +613,7 @@ subroutine initialize2(ni,nj)
     ! Read monthly vegetation
     ! Even if CN is on, and dry-deposition is active, read CLMSP annual vegetation
     ! to get estimates of monthly LAI
-    if ( n_drydep > 0 .and. drydep_method == DD_XLND )then
+    if ( n_drydep > 0 .and. drydep_method == DD_XLND .and. .not.use_fates )then
        call readAnnualVegetation(bounds_proc, canopystate_inst)
        if (nsrest == nsrStartup .and. finidat /= ' ') then
           ! Call interpMonthlyVeg for dry-deposition so that mlaidiff will be calculated
@@ -601,9 +623,9 @@ subroutine initialize2(ni,nj)
     ! If fates has satellite phenology enabled, get the monthly veg values
     ! prior to the first call to SatellitePhenology()
     elseif ( use_fates_sp ) then
-          call interpMonthlyVeg(bounds_proc, canopystate_inst)
+       call interpMonthlyVeg(bounds_proc, canopystate_inst)
     end if
-
+    
     ! Determine gridcell averaged properties to send to atm
     if (nsrest == nsrStartup) then
        call t_startf('init_map2gc')

diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
@@ -259,6 +259,7 @@ module clm_varctl
   integer, public            :: fates_spitfire_mode = 0                
   ! 0 for no fire; 1 for constant ignitions; > 1 for external data (lightning and/or anthropogenic ignitions)
   ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
+  logical, public            :: use_fates_tree_damage = .false.        ! true => turn on tree damage module
   logical, public            :: use_fates_logging = .false.            ! true => turn on logging module
   logical, public            :: use_fates_planthydro = .false.         ! true => turn on fates hydro
   logical, public            :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking