ctsm5.4.003: Merge post-5.4 to master

.gitmodules

@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/NGEET/fates
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_010
+fxtag = cismwrap_2_2_011
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
@@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.61_add_domain_ne3np4.pg2_1
+fxtag = ccs_config_cesm1.0.66
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git

bld/CLMBuildNamelist.pm

@@ -4501,7 +4501,7 @@ sub setup_logic_cropcal_streams {
        'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}
        );
     if ( &value_is_true($cropcals_rx_adapt) ) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline', 'stream_gdd20_seasons'=>$stream_gdd20_seasons);
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldFileName_gdd20_baseline', 'stream_gdd20_seasons'=>$stream_gdd20_seasons, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'});
     }
   }
 

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -455,9 +455,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <bt_min                   fire_method="li2024crujra" >0.85d00</bt_min>
 <bt_max                   fire_method="li2024crujra" >0.98d00</bt_max>
 <cli_scale                fire_method="li2024crujra" >0.03d00</cli_scale>
-<boreal_peatfire_c        fire_method="li2024crujra" >0.28d-4</boreal_peatfire_c>
+<boreal_peatfire_c        fire_method="li2024crujra" >0.58d-4</boreal_peatfire_c>
 <pot_hmn_ign_counts_alpha fire_method="li2024crujra" >0.010d00</pot_hmn_ign_counts_alpha>
-<non_boreal_peatfire_c    fire_method="li2024crujra" >0.71d-4</non_boreal_peatfire_c>
+<non_boreal_peatfire_c    fire_method="li2024crujra" >0.75d-4</non_boreal_peatfire_c>
 <cropfire_a1              fire_method="li2024crujra" >0.34d00</cropfire_a1>
 <occur_hi_gdp_tree        fire_method="li2024crujra" >0.33d00</occur_hi_gdp_tree>
 <lfuel                    fire_method="li2024crujra" >75.d00</lfuel>
@@ -467,7 +467,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <max_rh30_affecting_fuel  fire_method="li2024crujra" >95.</max_rh30_affecting_fuel>
 <defo_fire_precip_thresh_bet fire_method="li2024crujra" >1.8d00</defo_fire_precip_thresh_bet>
 <defo_fire_precip_thresh_bdt fire_method="li2024crujra" >0.6d00</defo_fire_precip_thresh_bdt>
-<borpeat_fire_soilmoist_denom fire_method="li2024crujra" > 0.35d00</borpeat_fire_soilmoist_denom>
+<borpeat_fire_soilmoist_denom fire_method="li2024crujra" > 0.3d00</borpeat_fire_soilmoist_denom>
 <nonborpeat_fire_precip_denom fire_method="li2024crujra" >6.5d00</nonborpeat_fire_precip_denom>
 
 
@@ -577,7 +577,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <snow_thermal_cond_method phys="clm6_0">Sturm1997</snow_thermal_cond_method>
 
 <snow_thermal_cond_glc_method>Jordan1991</snow_thermal_cond_glc_method>
-<snow_thermal_cond_glc_method phys="clm6_0">Jordan1991</snow_thermal_cond_glc_method>
+<snow_thermal_cond_glc_method phys="clm6_0">Sturm1997</snow_thermal_cond_glc_method>
 
 <snow_thermal_cond_lake_method>Jordan1991</snow_thermal_cond_lake_method>
 <snow_thermal_cond_lake_method phys="clm6_0">Sturm1997</snow_thermal_cond_lake_method>
@@ -622,7 +622,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/clm60_params.ctsm6_li2024.c250822.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c251124.nc</paramfile>
 <paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c250311.nc</paramfile>
 <paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c250311.nc</paramfile>
 
@@ -2280,7 +2280,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <model_year_align_cropcal_cultivar_gdds   >2000</model_year_align_cropcal_cultivar_gdds>
 
 <!-- crop calendars: default maturity requirement files -->
-<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20250809_025305.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
+<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/cultivar_gdds.c251120.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
 <stream_fldfilename_cultivar_gdds cropcals_rx=".true." lnd_tuning_mode="clm4_5_GSWP3v1">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
 <stream_fldfilename_cultivar_gdds cropcals_rx=".true." lnd_tuning_mode="clm5_0_GSWP3v1">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
 <stream_fldfilename_cultivar_gdds cropcals_rx=".true." lnd_tuning_mode="clm6_0_GSWP3v1">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
@@ -2295,7 +2295,10 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <stream_meshfile_cropcal cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>
 <stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
 <stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
-<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false.">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false.">lnd/clm2/cropdata/calendars/processed/gdd20_baseline.c251120.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false." lnd_tuning_mode="clm4_5_GSWP3v1">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false." lnd_tuning_mode="clm5_0_GSWP3v1">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false." lnd_tuning_mode="clm6_0_GSWP3v1">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
 <stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_start>
 <stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_end>

cime_config/config_component.xml

@@ -436,7 +436,7 @@ Caveats:
 
   <entry id="NEONVERSION">
     <type>char</type>
-    <valid_values>v1,v2,v3,latest</valid_values>
+    <valid_values>v1,v2,v3,v4,latest</valid_values>
     <default_value>latest</default_value>
     <group>run_component_ctsm</group>
     <file>env_run.xml</file>

doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst

@@ -354,9 +354,9 @@ The burned area due to peat fires is given as :math:`{A}_{b}`:
 .. math::
    :label: 23.37
 
-   A_{b} = c \ f_{cli,p} f_{peat} (1 - f_{sat} ) A_{g}
+   A_{b} = c \ f_{cli,p} f_{peat} A_{g}
 
-where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents the effect of climate on the burned area; :math:`f_{peat}` is the fractional coverage of peatland in the grid cell; and :math:`f_{sat}` is the fraction of the grid cell with a water table at the surface or higher. :math:`c` = 0.17 :math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and :math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires are derived using an inverse method, by matching simulations to earlier studies: about 2.4 Mha peatland was burned over Indonesia in 1997 (:ref:`Page et al. 2002 <Pageetal2002>`) and the average burned area of peat fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 (:ref:`Turetsky et al. 2004 <Turetskyetal2004>`).
+where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents the effect of climate on the burned area; and :math:`f_{peat}` is the fractional coverage of peatland in the grid cell. :math:`c` = 0.17 :math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and :math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires are derived using an inverse method, by matching simulations to earlier studies: about 2.4 Mha peatland was burned over Indonesia in 1997 (:ref:`Page et al. 2002 <Pageetal2002>`) and the average burned area of peat fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 (:ref:`Turetsky et al. 2004 <Turetskyetal2004>`).
 
 For tropical peat fires, :math:`f_{cli,p}` is set as a function of long-term precipitation :math:`P_{60d}` :
 

python/ctsm/site_and_regional/tower_arg_parse.py

@@ -195,7 +195,7 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         dest="user_version",
         required=False,
         type=str,
-        choices=["v1", "v2", "v3"],
+        choices=["v1", "v2", "v3", "v4"],
     )
 
     parser.add_argument(

src/biogeochem/CNFireLi2024Mod.F90

@@ -187,7 +187,6 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          rswf_min           => pftcon%rswf_min                                 , & ! Input:
          rswf_max           => pftcon%rswf_max                                 , & ! Input:
          btran2             => this%cnfire_base_type%btran2_patch              , & ! Input:  [real(r8) (:)     ]  root zone soil wetness
-         fsat               => saturated_excess_runoff_inst%fsat_col           , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface
          wf2                => waterdiagnosticbulk_inst%wf2_col                , & ! Input:  [real(r8) (:)     ]  soil water as frac. of whc for top 0.17 m
 
          is_cwd             => decomp_cascade_con%is_cwd                       , & ! Input:  [logical  (:)     ]  TRUE => pool is a cwd pool
@@ -517,10 +516,6 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         g = col%gridcell(c)
 
         ! For crop
-        ! cropf_col(c) * col%wtgcell(c) > 0.1_r8 is added because fires are rare in
-        ! gridcells with limited cropland coverage based on GFED5. Also, this helps to 
-        ! avoid abm (crop fire peak month) regridding error from 0.05 degree to lower resolution
-        ! The condition could be removed if CLM supports the use of mode in abm inputs regridding
         if( forc_t(c)  >=  SHR_CONST_TKFRZ .and. patch%itype(p)  >  nc4_grass .and.  &
              kmo == abm_lf(c) .and. &
              burndate(p) >= 999 .and. patch%wtcol(p)  >  0._r8 )then ! catch  crop burn time
@@ -556,8 +551,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
             end if
         else
            baf_peatf(c) = boreal_peatfire_c/secsphr*exp(-SHR_CONST_PI*(max(wf2(c),0._r8)/borpeat_fire_soilmoist_denom))* &
-                max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)* &
-                (1._r8-fsat(c))
+                max(0._r8,min(1._r8,(tsoi17(c)-SHR_CONST_TKFRZ)/10._r8))*peatf_lf(c)
         end if
      end do
      !

src/biogeophys/CanopyFluxesMod.F90

@@ -437,6 +437,8 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
     real(r8), parameter :: k_cyl_area = 1.0_r8         !departure from cylindrical area
     real(r8), parameter :: k_internal = 0.0_r8         !self-absorbtion of leaf/stem longwave
     real(r8), parameter :: min_stem_diameter = 0.05_r8 !minimum stem diameter for which to calculate stem interactions
+    real(r8), parameter :: min_lai    = 0.1_r8         !minimum elai threshold to add esai to sa_leaf calculation
+                                                       !value is arbitrary but has been effective in avoiding RRTMGP errors in CESM3 development simulations
 
     integer :: dummy_to_make_pgi_happy
     !------------------------------------------------------------------------------
@@ -745,15 +747,26 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
             ! adjust for departure of cylindrical stem model
             sa_stem(p) = k_cyl_area * sa_stem(p)
 
-            !
             ! only calculate separate leaf/stem heat capacity for trees
-            ! and shrubs if dbh is greater than some minimum value
-            ! (set surface area for stem, and fraction absorbed by stem to zero)
+            ! and shrubs if dbh is greater than some minimum value.
+            ! otherwise, set surface area for stem and fraction absorbed by stem to zero,
+            ! and add esai to sa_leaf.
             if(.not.(is_tree(patch%itype(p)) .or. is_shrub(patch%itype(p))) &
                  .or. dbh(p) < min_stem_diameter) then
                frac_rad_abs_by_stem(p) = 0.0_r8
                sa_stem(p) = 0.0_r8
                sa_leaf(p) = sa_leaf(p) + esai(p)
+            else
+               ! Add esai to sa_leaf if elai is less than threshold.
+               ! Intended to avoid small sa_leaf which leads to small leaf conductance
+               ! and high leaf temperature. This in turn can lead to unrealistically
+               ! high surface temperatures passed to the atmospheric model (The RRTMGP
+               ! component in particular, which returns an error and stops the model
+               ! if the surface temperature is greater than 355K).
+               ! See https://github.com/ESCOMP/CTSM/issues/3589 for more info.
+               if(elai(p) < min_lai) then
+                  sa_leaf(p) = sa_leaf(p) + esai(p)
+               endif
             endif
 
             ! if using Satellite Phenology mode, calculate leaf and stem biomass