ctsm5.4.056: Merge wetlands.n04.ctsm5.4.055 to master

bld/CLMBuildNamelist.pm

@@ -3532,11 +3532,12 @@ sub setup_logic_methane {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'finundation_method',
                 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
     my $finundation_method = remove_leading_and_trailing_quotes($nl->get_value('finundation_method' ));
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ch4finundated',
-             'finundation_method'=>$finundation_method);
-    if ($opts->{'driver'} eq "nuopc" ) {
-        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ch4finundated',
-                    'finundation_method'=>$finundation_method);
+    # prognostic inundation does not require an input stream; other methods do
+    if($finundation_method ne 'h2osfc') {
+	     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ch4finundated',
+		    'finundation_method'=>$finundation_method);
+	     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ch4finundated',
+			'finundation_method'=>$finundation_method);
     }
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_aereoxid_prog',
                 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );

doc/ChangeLog

@@ -1,4 +1,131 @@
 ===============================================================
+Tag name: ctsm5.4.056
+Originator(s): slevis (Samuel Levis,UCAR/TSS,slevis@ucar.edu)
+Date: Wed Sep  9 04:48:03 PM MDT 2026
+One-line Summary: Merge the wetlands branch to master
+
+Purpose and description of changes
+----------------------------------
+
+ The wetlands branch has these tags...
+   branch_tags/wetlands.n01.ctsm5.4.029
+   branch_tags/wetlands.n02.ctsm5.4.029
+   branch_tags/wetlands.n03.ctsm5.4.029
+   branch_tags/wetlands.n03.ctsm5.4.044
+   branch_tags/wetlands.n04.ctsm5.4.044
+   branch_tags/wetlands.n04.ctsm5.4.054 <-- PR #4204 started with this tag, I merged ctsm5.4.055 to it, then I merged to master (explained next)
+   branch_tags/wetlands.n05.ctsm5.4.054
+ We wanted wetlands.n04.ctsm5.4.055 merged to master, and we accomplished this with PR #4204, without merging or tagging anything new in the wetlands branch.
+
+ Main updates coming in with the wetlands branch:
+ 1. Changes to snow-covered fraction and inundated fraction where the two overlap.
+ 2. Changes to the methane parameterization.
+ Best evaluation of updates (1) and (2): https://webext.cgd.ucar.edu/I20TR/ctsm5.4.024_f19_wetlandCH4_151_HIST/ctsm5.4.024_f19_wetlandCH4_151_HIST_1850_2023_vs_ctsm5.4.024_f19_150_HIST_1850_2023/website
+ 3. Changes to phenology to improve high-lat survivability by allowing plants to green up after the summer solstice.
+ Best evaluation of (3): https://github.com/NCAR/LMWG_dev/issues/174
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+[Remove entire section if none of the boxes are checked.]
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[X] clm6_0
+
+[X] clm5_0
+
+[X] ctsm5_0-nwp
+
+Bugs fixed
+----------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ List of PRs available below
+
+Notes of particular relevance for users
+---------------------------------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for users (e.g., need to interpolate initial conditions):
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+
+Changes made to namelist defaults (e.g., changed parameter values):
+
+Changes to the datasets (e.g., streams, surface or initial files):
+
+Changes to the parameter file (output of tools/param_utils/compare_paramfiles):
+
+Changes to documentation:
+ Updating doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst
+ Opened issue for further updates: https://github.com/ESCOMP/CTSM/issues/4205
+
+Contributors:
+ swensosc, wwieder, lifang0209
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+ Updating src/dyn_subgrid/test/dynColumnStateUpdater_test/test_column_state_updater.pf
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK (2 expected fails)
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- PEND (rerunning 3 tests)
+    izumi ------- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ---- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: larger than roundoff, subtly new climate
+
+   If this tag changes climate list the run(s) done to evaluate the new
+   climate. Preferably in https://github.com/NCAR/LMWG_dev (or give details below):
+    - Best evaluation of updates (1) and (2) listed in the changes section above:
+      https://webext.cgd.ucar.edu/I20TR/ctsm5.4.024_f19_wetlandCH4_151_HIST/ctsm5.4.024_f19_wetlandCH4_151_HIST_1850_2023_vs_ctsm5.4.024_f19_150_HIST_1850_2023/website
+    - Best evaluation of update (3):
+      https://github.com/NCAR/LMWG_dev/issues/174
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/3893 from swensosc/wetland_update
+ https://github.com/ESCOMP/ctsm/pull/3934 from wwieder/wetlands_fire
+ https://github.com/ESCOMP/ctsm/pull/3933 from swensosc/wetland_update
+ https://github.com/ESCOMP/ctsm/pull/4091 merge master to wetlands 
+ https://github.com/ESCOMP/ctsm/pull/4108 from swensosc/seasonal_decid_onset
+ https://github.com/ESCOMP/ctsm/pull/4191 merge master to wetlands
+ https://github.com/ESCOMP/ctsm/pull/4204 this master tag ctsm5.4.056
+
+===============================================================
+===============================================================
 Tag name: ctsm5.4.055
 Originator(s): sacks (Bill Sacks)
 Date: Tue Sep  8 16:01:56 MDT 2026

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.4.056 multiple 09/10/2026 Merge the wetlands branch to master
        ctsm5.4.055    sacks 09/08/2026 Add temporal smoothing of DYNBAL conservation correction fluxes
        ctsm5.4.054     erik 08/31/2026 Update submodules to the latest needed for cesm3_0_alpha10a
        ctsm5.4.053   oleson 08/18/2026 Resolve problems with running PLUMBER2 sites

doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst

@@ -412,7 +412,9 @@ and the associated nitrogen fluxes are:
 
 where :math:`{f}_{stor,xfer}` is the fraction of current storage pool moved into the transfer pool for display over the incipient onset period. This fraction is set to 0.5, based on the observation that seasonal deciduous trees are capable of replacing their canopies from storage reserves in the event of a severe early-season disturbance such as frost damage or defoliation due to insect herbivory.
 
-If the onset criteria are not met before the summer solstice, then :math:`{GDD}_{sum}` is set to 0.0 and the growing-degree-day accumulation will not start again until the following winter solstice. This mechanism prevents the initiation of very short growing seasons late in the summer in cold climates. The onset counter is decremented on each time step after initiation of the onset period, until it reaches zero, signaling the end of the onset period:
+The *min_critical_daylength_onset* parameter specifies a daylength below which onset may not occur.  If the onset criterion (:math:`{GDD}_{sum} > {GDD}_{sum\_crit}`) is not attained before the daylength becomes less than this parameter in autumn, then :math:`{GDD}_{sum}` is set to 0 and the growing-degree-day accumulation will not start again until the following winter solstice. In cold climates, this mechanism ensures that if the onset criteria are not met, the accumulation does not continue into the following year.
+
+The onset counter is decremented on each time step after initiation of the onset period, until it reaches zero, signaling the end of the onset period:
 
 .. math::
    :label: t_onset_decrement

src/biogeochem/CNFireLi2024Mod.F90

@@ -217,7 +217,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          lgdp_col           => cnveg_state_inst%lgdp_col                       , & ! Output: [real(r8) (:)     ]  gdp limitation factor for nfire
          lgdp1_col          => cnveg_state_inst%lgdp1_col                      , & ! Output: [real(r8) (:)     ]  gdp limitation factor for baf per fire
          lpop_col           => cnveg_state_inst%lpop_col                       , & ! Output: [real(r8) (:)     ]  pop limitation factor for baf per fire
-         lfwt               => cnveg_state_inst%lfwt_col                       , & ! Output: [real(r8) (:)     ]  fractional coverage of non-crop and non-bare-soil Patches
+         tgswt              => cnveg_state_inst%tgswt_grc                      , & ! Output: [real(r8) (:)     ]  gridcell fractional coverage of tree, grass and shrub PFTs (0-1)
          trotr1_col         => cnveg_state_inst%trotr1_col                     , & ! Output: [real(r8) (:)     ]  patch weight of BET on the column (0-1)
          trotr2_col         => cnveg_state_inst%trotr2_col                     , & ! Output: [real(r8) (:)     ]  patch weight of BDT on the column (0-1)
          dtrotr_col         => cnveg_state_inst%dtrotr_col                     , & ! Output: [real(r8) (:)     ]  decreased frac. coverage of BET+BDT on grid for dt
@@ -288,24 +288,26 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
         return
      end if
      !
-     ! Calculate fraction of crop (cropf_col) and non-crop and non-bare-soil
-     ! vegetation (lfwt) in vegetated column
+     ! Calculate fraction of crop in vegetation column (cropf_col)
+     ! and fraction of tree, grass, and shrub in grid cell (tgswt)
      !
      do fc = 1,num_soilc
         c = filter_soilc(fc)
+        g = col%gridcell(c)
         cropf_col(c) = 0._r8
-        lfwt(c)      = 0._r8
+        tgswt(g)     = 0._r8
      end do
      do fp = 1, num_soilp
         p = filter_soilp(fp)
         c = patch%column(p)
+        g = col%gridcell(c)
         ! For crop veg types
         if( patch%itype(p) > nc4_grass )then
            cropf_col(c) = cropf_col(c) + patch%wtcol(p)
         end if
-        ! Exclude crops and bare soil
+        ! For tree, grass, and shrub
         if (patch%itype(p) <= nc4_grass .and. patch%itype(p) >= ndllf_evr_tmp_tree) then
-           lfwt(c) = lfwt(c) + patch%wtgcell(p)
+           tgswt(g) = tgswt(g) + patch%wtgcell(p)
         end if
      end do
      !
@@ -543,8 +545,9 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
      do fc = 1, num_soilc
         c = filter_soilc(fc)
         g= col%gridcell(c)
+        tgswt(g) = max(0._r8, min(1._r8, tgswt(g)))
         if(grc%latdeg(g) < cnfire_const%borealat )then
-            if ((trotr1_col(c)+trotr2_col(c))*col%wtgcell(c)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
+            if ((trotr1_col(c)+trotr2_col(c))*tgswt(g)<=0.8_r8.and.trotr1_col(c)+trotr2_col(c)>0.0_r8) then
                baf_peatf(c) = non_boreal_peatfire_c/secsphr*max(0._r8, &
                      min(1._r8,(1._r8-prec30_col(c)*secspday/nonborpeat_fire_precip_denom)))*peatf_lf(c)
             else
@@ -609,12 +612,12 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
               ig = (lh+this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
                    cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
                    cnfire_params%ignition_efficiency)*(1._r8-fs)* &
-                   (lfwt(c)**0.5)
+                   (tgswt(g)**0.5)
            else
               ig = this%forc_lnfm(g)/(5.16_r8+2.16_r8* &
                    cos(SHR_CONST_PI/180._r8*3*min(60._r8,abs(grc%latdeg(g)))))* &
                    cnfire_params%ignition_efficiency*(1._r8-fs)*  &
-                   (lfwt(c)**0.5)
+                   (tgswt(g)**0.5)
            end if
 
            ! Reduce burnability at high elevations
@@ -627,7 +630,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
            nfire(c) = ig/secsphr*fb*fire_m*lgdp_col(c) * topoi  !fire counts/km2/sec
            Lb_lf    = 1._r8+10._r8*(1._r8-EXP(-0.06_r8*forc_wind(g)))
            spread_m = fire_m**0.5_r8
-           fd_col(c) = (lfwt(c)*lgdp1_col(c)*lpop_col(c))**0.5_r8 * fd_col(c)
+           fd_col(c) = (tgswt(g)*lgdp1_col(c)*lpop_col(c))**0.5_r8 * fd_col(c)
            farea_burned(c) = min(1._r8,(cnfire_const%g0*spread_m*fsr_col(c)* &
                 fd_col(c)/1000._r8)**2*nfire(c)*SHR_CONST_PI*Lb_lf+ &
                 baf_crop(c)+baf_peatf(c))  ! fraction (0-1) per sec

src/biogeochem/CNPhenologyMod.F90

@@ -1289,10 +1289,17 @@ function SeasonalDecidOnset( onset_gdd, onset_gddflag, soilt, soila10, t_a5min,
     ! Test to turn off growing degree-day sum, if on.
     ! This test resets the growing degree day sum if it gets past
     ! the summer solstice without reaching the threshold value.
-    ! In that case, it will take until the next winter solstice
-    ! before the growing degree-day summation starts again.
-
-    if (onset_gddflag == 1._r8 .and. ws_flag == 0._r8) then
+    ! After the summer solstice, a daylength criterion is used
+    ! to trigger the reset: if daylength is less than  the
+    ! parameter value, gdd is reset.  This criterion was added to
+    ! allow for situations in the high latitudes when using only
+    ! the summer solstice as a trigger caused some vegetation to never
+    ! achieve onset.
+    ! If the conditional is met, it will take until the next winter 
+    ! solstice before the growing degree-day summation starts again.
+
+    if (onset_gddflag == 1._r8 .and. ws_flag == 0._r8.and. &
+         dayl<min_critical_daylength_onset) then
         onset_gddflag = 0._r8
         onset_gdd = 0._r8
     end if
@@ -1312,18 +1319,19 @@ function SeasonalDecidOnset( onset_gdd, onset_gddflag, soilt, soila10, t_a5min,
        ! shrub, C3 arctic grass)
        if (onset_gdd > crit_onset_gdd .and.  season_decid_temperate == 1) then
            do_onset = .true.
-        ! Note: The check "dayl>min_critical_daylength_onset" in the if
-        ! statement was added because for some coastal
-        ! points the other triggers could allow onset in January/February
-        ! which isn't sustainable and is a degenerate case. To prevent this
-        ! condition was added, but now the other conditions aren't triggered
-        ! until much later so it's value just needs to be high enough to prevent
-        ! the degenerate case of happening too early, and low enough that it
-        ! doesn't restrict onset. As such the value of this parameter shouldn't
-        ! matter for reasonable values between the two degenerate cases.
+           ! Note: The "dayl>min_critical_daylength_onset" criterion
+           ! was added because for some coastal points, onset was triggered 
+           ! too early (e.g January/February).  This criterion ensures that 
+           ! onset does not occur too early, and at the same time (because the
+           ! criterion is symmetric about the solstices), it does not allow
+           ! onset when the day length becomes less than
+           ! min_critical_daylength_onset after the summer solstice.
+           ! The value of min_critical_daylength_onset needs to be high
+           ! enough to prevent onset happening too early, and low enough
+           ! that it doesn't restrict onset.
         else if (season_decid_temperate == 0 .and.  onset_gddflag == 1.0_r8 .and. &
                 soila10 > SHR_CONST_TKFRZ .and. &
-                t_a5min > SHR_CONST_TKFRZ .and. ws_flag==1.0_r8 .and. &
+                t_a5min > SHR_CONST_TKFRZ .and. &
                 dayl>min_critical_daylength_onset .and. &
                 snow_5day<params_inst%snow5d_thresh_for_onset) then
            do_onset = .true.

src/biogeochem/CNVegStateType.F90

@@ -12,6 +12,7 @@ module CNVegStateType
   use landunit_varcon, only : istsoil, istcrop
   use LandunitType   , only : lun
   use ColumnType     , only : col
+  use GridcellType   , only : grc
   use PatchType      , only : patch
   use AnnualFluxDribbler, only : annual_flux_dribbler_type, annual_flux_dribbler_patch
   use dynSubgridControlMod, only : get_for_testing_allow_non_annual_changes
@@ -84,6 +85,7 @@ module CNVegStateType
      real(r8) , pointer :: fbac1_col                   (:)     ! col burned area out of conversion region due to land use fire (/sec)
      real(r8) , pointer :: wtlf_col                    (:)     ! col fractional coverage of non-crop Patches (0-1)
      real(r8) , pointer :: lfwt_col                    (:)     ! col fractional coverage of non-crop and non-bare-soil Patches (0-1)
+     real(r8) , pointer :: tgswt_grc                   (:)     ! gridcell fractional coverage of tree, grass, and shrub PFTs (0-1)
      real(r8) , pointer :: farea_burned_col            (:)     ! col fractional area burned (/sec)
 
      real(r8), pointer :: dormant_flag_patch           (:)     ! patch dormancy flag
@@ -164,15 +166,18 @@ subroutine InitAllocate(this, bounds, alloc_full_veg)
     ! !LOCAL VARIABLES:
     integer :: begp, endp
     integer :: begc, endc
+    integer :: begg, endg
     logical :: allows_non_annual_delta
     !------------------------------------------------------------------------
 
     if(alloc_full_veg)then
        begp = bounds%begp; endp= bounds%endp
        begc = bounds%begc; endc= bounds%endc
+       begg = bounds%begg; endg= bounds%endg
     else
        begp = 0;endp = 0
        begc = 0;endc = 0
+       begg = 0;endg = 0
     end if
 
 
@@ -268,6 +273,9 @@ subroutine InitAllocate(this, bounds, alloc_full_veg)
     allocate(this%fbac1_col           (begc:endc))                   ; this%fbac1_col           (:)   = nan
     allocate(this%wtlf_col            (begc:endc))                   ; this%wtlf_col            (:)   = nan
     allocate(this%lfwt_col            (begc:endc))                   ; this%lfwt_col            (:)   = nan
+
+    allocate(this%tgswt_grc           (begg:endg))                   ; this%tgswt_grc           (:)   = nan
+
     allocate(this%farea_burned_col    (begc:endc))                   ; this%farea_burned_col    (:)   = nan
 
     allocate(this%dormant_flag_patch          (begp:endp)) ;    this%dormant_flag_patch          (:) = nan