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
@@ -741,7 +741,7 @@ sub setup_cmdl_fates_mode {
 
     $var = "use_fates";
     if ( &value_is_true($nl_flags->{$var}) ) {
-      # This section is a place-holder to test for modules that are not allowed with ED
+      # This section is a place-holder to test for modules that are not allowed with FATES
       # the defaults which are set in the logic section of the namelist builder will
       # automatically set these correctly (well that is the assumption), but here we
       # want to set a catch to fail and warn users if they explicitly set incompatible user namelist
@@ -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)) ) {
@@ -1167,7 +1167,7 @@ sub setup_cmdl_spinup {
      $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values");
   }
   if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} ))  && (not &value_is_true($nl_flags->{'use_fates'})) ) {
-     $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor ED is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'}).");
+     $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor FATES is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'}).");
   }
   if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) {
      $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
@@ -2046,6 +2046,10 @@ sub setup_logic_subgrid {
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_lake');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_wetland');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'toosmall_urban');
+
+   if ( &value_is_true($nl_flags->{'use_fates'}) && $nl->get_value('n_dom_pfts') != 0 ) {
+      $log->fatal_error( "FATES and n_dom_pfts can NOT be set at the same time" );
+   }
 }
 
 #-------------------------------------------------------------------------------
@@ -2611,7 +2615,7 @@ sub setup_logic_do_transient_crops {
       # In principle, use_fates should be compatible with
       # do_transient_crops. However, this hasn't been tested, so to be safe,
       # we are not allowing this combination for now.
-      $cannot_be_true = "$var has not been tested with ED, so for now these two options cannot be combined";
+      $cannot_be_true = "$var has not been tested with FATES, so for now these two options cannot be combined";
    }
 
    if ($cannot_be_true) {
@@ -3660,6 +3664,10 @@ sub setup_logic_dry_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   if ($opts->{'drydep'} ) {
+    if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+       $log->warning("DryDeposition can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
+                     "   Use the '--no-drydep' option when '-bgc fates' is activated");
+    }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_method');
   } else {
@@ -3705,7 +3713,7 @@ 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" .
+       $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
                    "   Use the '-no-megan' option when '-bgc fates' is activated");
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
@@ -4107,7 +4115,7 @@ sub setup_logic_fates {
         add_default($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.
@@ -2124,7 +2130,7 @@ Command line arguement for biogeochemistry mode for CLM4.5
         Nitrification/De-nitrification
         Methane model
         Vertically resolved Carbon
-   fates = FATES/ED ecosystem demography model with below ground BGC:
+   fates = FATES Functionally Assembled Terrestrial Ecosystem Simulator (ecosystem demography model with below ground BGC):
 </entry>
 
 <!-- ========================================================================================  -->

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 = 1844;
+my $ntests = 1846;
 if ( defined($opts{'compare'}) ) {
    $ntests += 1254;
 }
@@ -956,6 +956,11 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "useFATESWn_dom_pft"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"n_dom_pfts = 1",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "useFATESWbMH"              =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_biomass_heat_storage=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1001,6 +1006,11 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "useDRYDEPwithFATES"        =>{ options=>"--bgc fates --envxml_dir . --no-megan --drydep",
+                                     namelst=>"",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm4_5",
+                                   },
      "useFATESSPWONOCOMP"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_fates_sp=T,use_fates_nocomp=F",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

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" compiler="intel" 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 +1,3 @@
+./xmlchange CLM_BLDNML_OPTS='--drydep' --append
+# The following would be required if you want to run with DryDep and FATES without Fates-SP mode
+#./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --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/DryDepVelocity.F90 b/src/biogeochem/DryDepVelocity.F90
@@ -103,9 +103,14 @@ Module DryDepVelocity
   !------------------------------------------------------------------------
   subroutine Init(this, bounds)
 
+    use clm_varctl     , only : use_fates, use_fates_sp
     class(drydepvel_type) :: this
     type(bounds_type), intent(in) :: bounds  
 
+    if ( (.not. use_fates_sp) .and. use_fates .and. (n_drydep > 0 .and. drydep_method == DD_XLND) )then
+       call endrun( msg='ERROR: Dry-deposition currently does NOT work with FATES outside of FATES-SP mode (see github issue #1044)'//&
+                    errMsg(sourcefile, __LINE__))
+    end if
     call this%InitAllocate(bounds)
     call this%InitHistory(bounds)
 

diff --git a/src/biogeochem/EDBGCDynMod.F90 b/src/biogeochem/EDBGCDynMod.F90
@@ -260,6 +260,25 @@ subroutine EDBGCDyn(bounds,                                                    &
        call t_stopf('SoilBiogeochemLittVertTransp')
     end if
 
+    ! Wood product fluxes will eventually be added to FATES-CLM. However
+    ! it is likely this will be implemented during or after we break away from
+    ! using this module. This module and the current coupling stategy bypasses
+    ! a number of processes in CLM, which includes the wood product modules.
+    ! Therefore the following call is a placeholder so that the wood-product 
+    ! wrapper code can be copied from here and applied at the right place when the time comes.
+    ! RGK 06-2022
+
+    !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/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90
@@ -84,10 +84,15 @@ module VOCEmissionMod
   !------------------------------------------------------------------------
   subroutine Init(this, bounds)
 
+    use clm_varctl     , only : use_fates, use_fates_sp
     class(vocemis_type) :: this
     type(bounds_type), intent(in)    :: bounds  
 
     if ( shr_megan_mechcomps_n > 0) then
+       if ( use_fates .and. (.not. use_fates_sp) ) then
+           call endrun( msg='ERROR: MEGAN currently does NOT work with FATES outside of FATES-SP mode (see github issue #115)'//&
+                     errMsg(sourcefile, __LINE__))
+       end if
        call this%InitAllocate(bounds) 
        call this%InitHistory(bounds)
        call this%InitCold(bounds)

diff --git a/src/biogeophys/test/Photosynthesis_test/test_Photosynthesis.pf b/src/biogeophys/test/Photosynthesis_test/test_Photosynthesis.pf
@@ -38,7 +38,7 @@ contains
     soil_layerstruct_predefined = '20SL_8.5m'
 
     call setup_ncells_single_veg_patch(ncells=1, pft_type=1)
-    call clm_varpar_init( actual_maxsoil_patches=17, actual_numcft=2 )
+    call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2 )
     call this%photo%Init( bounds )
     call this%photo%setParamsForTesting( )
 

diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
@@ -221,24 +221,41 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
     ! ============================================================================
     ! Specified phenology
+    ! Done in SP mode, FATES-SP mode and also when dry-deposition is active
     ! ============================================================================
 
     if (use_cn) then
        ! For dry-deposition need to call CLMSP so that mlaidiff is obtained
+       ! NOTE: This is also true of FATES below
        if ( n_drydep > 0 .and. drydep_method == DD_XLND ) then
           call t_startf('interpMonthlyVeg')
           call interpMonthlyVeg(bounds_proc, canopystate_inst)
           call t_stopf('interpMonthlyVeg')
        endif
 
+    elseif(use_fates) then
+
+       ! For FATES-Specified phenology mode interpolate the weights for
+       ! time-interpolation of monthly vegetation data (as in SP mode below)
+       ! Also for FATES with dry-deposition as above need to call CLMSP so that mlaidiff is obtained
+       !if ( use_fates_sp .or. (n_drydep > 0 .and. drydep_method == DD_XLND ) ) then    ! Replace with this when we have dry-deposition working
+       ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022
+       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
+       ! This is also done for FATES-SP mode above
+       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')
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		../FatesColdDefDryDep
		../FatesColdDefReducedComplexSatPhen
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		./xmlchange CLM_BLDNML_OPTS='--megan' --append
		./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		../FatesColdDefMegan
		../FatesColdDefReducedComplexSatPhen