ctsm5.4.039: add new fates namelist switch for dbh init when nocomp is on

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.92.4_api.45.0.0
+fxtag = sci.1.92.5_api.46.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates

bld/CLMBuildNamelist.pm

@@ -816,7 +816,7 @@ sub setup_cmdl_fates_mode {
     } else {
        # 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_cohort_age_tracking","use_fates_inventory_init","use_fates_dbh_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
                       "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
                       "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel",
@@ -4896,7 +4896,7 @@ 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  = (  "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
-                       "use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
+                       "use_fates_inventory_init","use_fates_dbh_init","fates_seeddisp_cadence","fates_history_dimlevel",
                        "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
                        "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                        "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
@@ -4961,6 +4961,10 @@ sub setup_logic_fates {
               }
            }
         }
+        my $var = "use_fates_dbh_init";
+        if ( &value_is_true($nl->get_value($var)) && ( !&value_is_true($nl->get_value("use_fates_nocomp")))) {
+            $log->fatal_error("$var can only be .true. use_fates_nocomp is .true." );
+        }
         # make sure that fates landuse x pft mode has the necessary run mode configurations
         my $var = "use_fates_lupft";
         if ( defined($nl->get_value($var))  ) {

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2715,6 +2715,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <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>
 <use_fates_inventory_init       use_fates=".true.">.false.</use_fates_inventory_init>
+<use_fates_dbh_init             use_fates=".true.">.false.</use_fates_dbh_init>
 <use_fates_sp                   use_fates=".true.">.false.</use_fates_sp>
 <use_fates_lupft                use_fates=".true.">.false.</use_fates_lupft>
 <use_fates_potentialveg         use_fates=".true.">.false.</use_fates_potentialveg>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -881,6 +881,14 @@ Full pathname to the inventory initialization control file.
 (Only relevant if FATES is on).
 </entry>
 
+
+<entry id="use_fates_dbh_init" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Initialize cohorts at coldstart with diameter at breast height instead of density
+(Applies only if use_fates_nocomp=.true.)
+(Only relevant if FATES is on).
+</entry>
+
 <entry id="fates_history_dimlevel" type="integer(2)" category="physics"
        group="clm_inparm" valid_values="0,1,2" >
   Setting for what types of FATES history to be allocate and

cime_config/testdefs/testlist_clm.xml

@@ -4104,6 +4104,14 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="ERS_D_Ld10" grid="f45_f45_mg37" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdNoCompInitDbh">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>

cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/include_user_mods

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

cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/shell_commands

@@ -0,0 +1,10 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates/
+FATESPARAMFILE=$CASEDIR/fates_params_init_dbh.json
+
+cp $FATESDIR/parameter_files/fates_params_default.json $FATESPARAMFILE
+
+$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_recruit_init_seed --values 0.01 --indices all
+
+echo "fates_paramfile = '$FATESPARAMFILE'" >> $CASEDIR/user_nl_clm

cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/user_nl_clm

@@ -0,0 +1 @@
+use_fates_dbh_init = .true.

doc/ChangeLog

@@ -1,4 +1,74 @@
 ===============================================================
+Tag name: ctsm5.4.039
+Originator(s): mvdebolskiy (Matvey Debolskiy, University of Oslo, matvey.debolskiy@geo.uio.no)
+Date: Mon May 11 04:00:00 PR MDT 2026
+One-line Summary: Add FATES namelist option to initialize cohorts with diameter at breast height (DBH)
+
+Purpose and description of changes
+----------------------------------
+
+FATES allows for the ability to initialize seedling by density or DBH.  Prior to this change,
+the user would update the `fates_recruit_init_density` parameter to use a negative value to
+initalize by DBH.  This pull request removes this global switch behavior and creates a namelist
+option for the user.  The FATES parameter file and behavior has been updated to include a new
+parameter for users to set the initial DBH by plant functional type.
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   New namelist option to control FATES:
+      use_fates_dbh_init
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   Sets the default for use_fates_dbh_init to false
+
+Changes to the parameter file (output of tools/param_utils/compare_paramfiles):
+   Adds fates_recruit_init_dbh to the FATES parameter file
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   - Note that this option currently is only applicable with use_fates_nocomp
+
+Changes to tests or testing:
+   Added test module FatesColdNoCompInitDbh
+
+Testing summary:
+----------------
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- TBD
+    izumi ------- OK
+
+  fates tests: (baseline comparison against fates-sci.1.92.4_api.45.0.0-ctsm5.4.037)
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.92.4_api.45.0.0 -> sci.1.92.5_api.46.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+https://github.com/ESCOMP/CTSM/pull/3910
+https://github.com/NGEET/fates/pull/1550
+
+===============================================================
+===============================================================
 Tag name: ctsm5.4.038
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu May  7 03:29:26 PM MDT 2026
@@ -10249,7 +10319,7 @@ Answer changes
 --------------
 
 Changes answers relative to baseline:
-
+ sb
   Summarize any changes to answers, i.e.,
     - what code configurations: FATES mode
     - what platforms/compilers: ALL

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.4.039 glemieux 05/11/2026 Add FATES namelist option to initialize cohorts with diameter at breast height (DBH)
        ctsm5.4.038   slevis 05/07/2026 Merge b4b-dev to master
        ctsm5.4.037 multiple 05/04/2026 Fix for FATES year-boundary restart issue
        ctsm5.4.036 multiple 04/27/2026 Complete the FATES-CLM nitrogen coupling

src/main/clm_varctl.F90

@@ -357,6 +357,7 @@ module clm_varctl
   logical, public            :: use_fates_ed_st3   = .false.            ! true => static stand structure
   logical, public            :: use_fates_ed_prescribed_phys = .false.  ! true => prescribed physiology
   logical, public            :: use_fates_inventory_init = .false.      ! true => initialize fates from inventory
+  logical, public            :: use_fates_dbh_init = .false.            ! true => initialize cohorts with dbh instead of density (nocomp only)
   logical, public            :: use_fates_fixed_biogeog = .false.       ! true => use fixed biogeography mode
   logical, public            :: use_fates_nocomp = .false.              ! true => use no comopetition mode
   logical, public            :: use_fates_daylength_factor = .false.    ! true => enable fates to use host land model daylength factor

src/main/controlMod.F90

@@ -239,6 +239,7 @@ subroutine control_init(dtime)
           use_fates_cohort_age_tracking,                &
           use_fates_ed_prescribed_phys,                 &
           use_fates_inventory_init,                     &
+          use_fates_dbh_init,                           &
           use_fates_fixed_biogeog,                      &
           use_fates_nocomp,                             &
           use_fates_sp,                                 &
@@ -845,6 +846,7 @@ subroutine control_spmd()
     call mpi_bcast (use_fates_ed_st3, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_ed_prescribed_phys,  1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_inventory_init, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_dbh_init, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_fixed_biogeog, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -1266,6 +1268,7 @@ subroutine control_print ()
        write(iulog, *) '    use_fates_ed_st3 = ',use_fates_ed_st3
        write(iulog, *) '    use_fates_ed_prescribed_phys = ',use_fates_ed_prescribed_phys
        write(iulog, *) '    use_fates_inventory_init = ',use_fates_inventory_init
+       write(iulog, *) '    use_fates_dbh_init = ',use_fates_dbh_init
        write(iulog, *) '    use_fates_fixed_biogeog = ', use_fates_fixed_biogeog
        write(iulog, *) '    use_fates_nocomp = ', use_fates_nocomp
        write(iulog, *) '    use_fates_sp = ', use_fates_sp

src/utils/clmfates_interfaceMod.F90

@@ -68,6 +68,7 @@ module CLMFatesInterfaceMod
    use clm_varctl        , only : fates_radiation_model
    use clm_varctl        , only : fates_electron_transport_model
    use clm_varctl        , only : use_fates_inventory_init
+   use clm_varctl        , only : use_fates_dbh_init
    use clm_varctl        , only : use_fates_fixed_biogeog
    use clm_varctl        , only : use_fates_nocomp
    use clm_varctl        , only : use_fates_sp
@@ -430,6 +431,7 @@ subroutine CLMFatesGlobals2()
      integer                                        :: pass_ed_prescribed_phys
      integer                                        :: pass_planthydro
      integer                                        :: pass_inventory_init
+     integer                                        :: pass_dbh_init
      integer                                        :: pass_is_restart
      integer                                        :: pass_cohort_age_tracking
      integer                                        :: pass_tree_damage
@@ -674,6 +676,12 @@ subroutine CLMFatesGlobals2()
 
         call set_fates_ctrlparms('inventory_ctrl_file',cval=fates_inventory_ctrl_filename)
 
+        if(use_fates_dbh_init) then
+           pass_dbh_init = 1
+        else
+           pass_dbh_init = 0
+        end if
+        call set_fates_ctrlparms('use_dbh_init',ival=pass_dbh_init)
 
         ! Check through FATES parameters to see if all have been set
         call set_fates_ctrlparms('check_allset')