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Merge pull request ESCOMP#3910 from mvdebolskiy/add-fates-switch
ctsm5.4.039: add new fates namelist switch for dbh init when nocomp is on
2 parents e1f563b + 4212124 commit f1e0f23

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‎.gitmodules‎

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

‎bld/CLMBuildNamelist.pm‎

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@@ -816,7 +816,7 @@ sub setup_cmdl_fates_mode {
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} else {
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# dis-allow fates specific namelist items with non-fates runs
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my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
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"use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
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"use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_dbh_init","use_fates_fixed_biogeog",
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"use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
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"fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
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"flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel",
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if (&value_is_true( $nl_flags->{'use_fates'}) ) {
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add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
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my @list = ( "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
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"use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
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"use_fates_inventory_init","use_fates_dbh_init","fates_seeddisp_cadence","fates_history_dimlevel",
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"fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
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"use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
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"fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
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}
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}
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}
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my $var = "use_fates_dbh_init";
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if ( &value_is_true($nl->get_value($var)) && ( !&value_is_true($nl->get_value("use_fates_nocomp")))) {
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$log->fatal_error("$var can only be .true. use_fates_nocomp is .true." );
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}
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# make sure that fates landuse x pft mode has the necessary run mode configurations
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my $var = "use_fates_lupft";
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if ( defined($nl->get_value($var)) ) {

‎bld/namelist_files/namelist_defaults_ctsm.xml‎

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@@ -2715,6 +2715,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
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<use_fates_ed_st3 use_fates=".true.">.false.</use_fates_ed_st3>
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<use_fates_ed_prescribed_phys use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
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<use_fates_inventory_init use_fates=".true.">.false.</use_fates_inventory_init>
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<use_fates_dbh_init use_fates=".true.">.false.</use_fates_dbh_init>
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<use_fates_sp use_fates=".true.">.false.</use_fates_sp>
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<use_fates_lupft use_fates=".true.">.false.</use_fates_lupft>
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<use_fates_potentialveg use_fates=".true.">.false.</use_fates_potentialveg>

‎bld/namelist_files/namelist_definition_ctsm.xml‎

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

‎bld/unit_testers/build-namelist_test.pl‎

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@@ -165,7 +165,7 @@ sub cat_and_create_namelistinfile {
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#
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# Figure out number of tests that will run
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#
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my $ntests = 3406;
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my $ntests = 3407;
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if ( defined($opts{'compare'}) ) {
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$ntests += 2061;
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namelst=>"use_fates_sp=T,use_fates_nocomp=F",
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phys=>"clm5_0",
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},
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"useFATESDBHInitWONoComp" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
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namelst=>"use_fates_dbh_init=T,use_fates_nocomp=F",
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phys=>"clm6_0",
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},
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"useFATESSPwithLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan",
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namelst=>"use_fates_sp=T,use_fates_luh=T",
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phys=>"clm5_0",

‎cime_config/testdefs/testlist_clm.xml‎

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

‎cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/include_user_mods‎

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../FatesColdNoComp

‎cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/shell_commands‎

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

‎cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompInitDbh/user_nl_clm‎

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use_fates_dbh_init = .true.

‎doc/ChangeLog‎

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==============================================================
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Tag name: ctsm5.4.039
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Originator(s): mvdebolskiy (Matvey Debolskiy, University of Oslo, matvey.debolskiy@geo.uio.no)
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Date: Thu May 14 01:07:45 PM MDT 2026
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One-line Summary: Add FATES namelist option to initialize cohorts with diameter at breast height (DBH)
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Purpose and description of changes
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----------------------------------
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FATES allows for the ability to initialize seedling by density or DBH. Prior to this change,
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the user would update the `fates_recruit_init_density` parameter to use a negative value to
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initalize by DBH. This pull request removes this global switch behavior and creates a namelist
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option for the user. The FATES parameter file and behavior has been updated to include a new
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parameter for users to set the initial DBH by plant functional type.
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Notes of particular relevance for users
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---------------------------------------
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Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
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New namelist option to control FATES:
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use_fates_dbh_init
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Changes made to namelist defaults (e.g., changed parameter values):
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Sets the default for use_fates_dbh_init to false
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Changes to the parameter file (output of tools/param_utils/compare_paramfiles):
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Adds fates_recruit_init_dbh to the FATES parameter file
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Notes of particular relevance for developers:
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---------------------------------------------
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Caveats for developers (e.g., code that is duplicated that requires double maintenance):
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- Note that this option currently is only applicable with use_fates_nocomp
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Changes to tests or testing:
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Added test module FatesColdNoCompInitDbh
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Testing summary:
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----------------
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build-namelist tests (if CLMBuildNamelist.pm has changed):
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derecho - OK (2 expected fails)
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regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
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derecho ----- OK
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izumi ------- OK
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fates tests: (baseline comparison against fates-sci.1.92.4_api.45.0.0-ctsm5.4.037)
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derecho ----- OK
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izumi ------- OK
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Answer changes
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--------------
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Changes answers relative to baseline: No
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Other details
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-------------
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List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
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fates: sci.1.92.4_api.45.0.0 -> sci.1.92.5_api.46.0.0
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Pull Requests that document the changes (include PR ids):
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(https://github.com/ESCOMP/ctsm/pull)
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https://github.com/ESCOMP/CTSM/pull/3910
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https://github.com/NGEET/fates/pull/1550
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===============================================================
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===============================================================
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Tag name: ctsm5.4.038
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Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)

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