ctsm5.4.026: Transfer biophysical variables for output with FATES dimensions

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.89.0_api.43.0.0
+fxtag = sci.1.91.1_api.43.1.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates

cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm

@@ -31,4 +31,7 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
 'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU',
-'FATES_TRANSITION_MATRIX_LULU'
+'FATES_TRANSITION_MATRIX_LULU',
+'FATES_VEGC_LUPF','FATES_NOCOMP_PATCHAREA_LUPF',
+'FATES_TVEG_LU','FATES_TSA_LU','FATES_SWABS_LU','FATES_NETLW_LU',
+'FATES_SHFLUX_LU','FATES_LHFLUX_LU','FATES_GPP_LU'

doc/ChangeLog

@@ -1,4 +1,76 @@
 ===============================================================
+Tag name: ctsm5.4.026
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Wed Mar 18 01:12:09 AM MDT 2026
+One-line Summary: Transfer biophysical variables for output with FATES dimensions
+
+Purpose and description of changes
+----------------------------------
+
+This pull request updates the high frequency wrapper procedure in the interface to pass
+biophysical CLM variables to be output along FATES dimensions. The FATES land use x
+pft dimension is also added to the history module.  The FATES base land use test module
+adds the FATES history noted above to the test output.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+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.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+  - Landuse history variables adding to the base FatesColdLUH2 test module
+
+Contributors: @ckoven
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+  izumi fates tested against `fates-sci.1.89.0_api.43.0.0-ctsm5.4.025`
+  derecho fates tested against `fates-sci.1.91.1_api.43.1.0-ctsm5.4.025`
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, fates only
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+  fates: sci.1.89.0_api.43.0.0 -> sci.1.91.1_api.43.1.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+https://github.com/ESCOMP/CTSM/pull/3760
+https://github.com/NGEET/fates/pull/1536
+
+===============================================================
+===============================================================
 Tag name: ctsm5.4.025
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Mon Mar 16 12:46:16 PM MDT 2026

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.4.026 glemieux 03/18/2026 Transfer biophysical variables for output with FATES dimensions
        ctsm5.4.025     erik 03/16/2026 Merge b4b-dev to master
        ctsm5.4.024     erik 03/11/2026 Update derecho_intel again and a few fixes for it
        ctsm5.4.023 samrabin 03/10/2026 Replace more netCDFs with NaN issues

src/main/clm_driver.F90

@@ -1182,7 +1182,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
           call clm_fates%wrap_update_hifrq_hist(bounds_clump, &
                soilbiogeochem_carbonflux_inst, &
-               soilbiogeochem_carbonstate_inst)
+               soilbiogeochem_carbonstate_inst, &
+               solarabs_inst, energyflux_inst, temperature_inst)
 
 
           if( is_beg_curr_day() ) then

src/main/histFileMod.F90

@@ -2583,6 +2583,7 @@ subroutine htape_create (t, f, histrest)
        call ncd_defdim(lnfid, 'fates_levclscpf', nclmax*nlevsclass*numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levlanduse', n_landuse_cats, dimid)
        call ncd_defdim(lnfid, 'fates_levlulu', n_landuse_cats * n_landuse_cats, dimid)
+       call ncd_defdim(lnfid, 'fates_levlupft', n_landuse_cats * numpft_fates, dimid)
     end if
 
     if ( .not. lhistrest )then
@@ -5811,6 +5812,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        num2d = n_landuse_cats
     case ('fates_levlulu')
        num2d = n_landuse_cats * n_landuse_cats
+    case ('fates_levlupft')
+       num2d = n_landuse_cats * numpft_fates
     case('cft')
        if (cft_size > 0) then
           num2d = cft_size

src/utils/clmfates_interfaceMod.F90

@@ -3067,24 +3067,34 @@ end subroutine WrapUpdateFatesSeedInOut
 
  subroutine wrap_update_hifrq_hist(this, bounds_clump, &
                                    soilbiogeochem_carbonflux_inst,     &
-                                   soilbiogeochem_carbonstate_inst)
+                                   soilbiogeochem_carbonstate_inst,    &
+                                   solarabs_inst, energyflux_inst,     &
+                                   temperature_inst)
 
     ! Arguments
     class(hlm_fates_interface_type), intent(inout)    :: this
     type(bounds_type), intent(in)                     :: bounds_clump
     type(soilbiogeochem_carbonflux_type), intent(in)  :: soilbiogeochem_carbonflux_inst
     type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst
+    type(solarabs_type),                   intent(in) :: solarabs_inst
+    type(energyflux_type),                 intent(in) :: energyflux_inst
+    type(temperature_type),                intent(in) :: temperature_inst
 
     ! locals
     real(r8) :: dtime
-    integer  :: s, c, nc
+    integer  :: s, c, nc, ifp, p
 
     call t_startf('fates_wrap_update_hifrq_hist')
 
     associate(&
         hr            => soilbiogeochem_carbonflux_inst%hr_col,       & ! (gC/m2/s) total heterotrophic respiration
         totsomc       => soilbiogeochem_carbonstate_inst%totsomc_col, & ! (gC/m2) total soil organic matter carbon
-        totlitc       => soilbiogeochem_carbonstate_inst%totlitc_col)   ! (gC/m2) total litter carbon in BGC pools
+        totlitc       => soilbiogeochem_carbonstate_inst%totlitc_col, & ! (gC/m2) total litter carbon in BGC pools
+        eflx_lh_tot   => energyflux_inst%eflx_lh_tot_patch, &    ! (W/m2) latent heat flux
+        eflx_sh_tot   => energyflux_inst%eflx_sh_tot_patch, &    ! (W/m2) sensible heat flux
+        fsa_patch     => solarabs_inst%fsa_patch, &              ! (W/m2) absorbed solar flux
+        eflx_lwrad_net=> energyflux_inst%eflx_lwrad_net_patch, & ! (W/m2) net longwave radiative flux
+        t_ref2m       => temperature_inst%t_ref2m_patch)            ! (K) 2-m air temperature
 
       nc = bounds_clump%clump_index
 
@@ -3105,6 +3115,21 @@ subroutine wrap_update_hifrq_hist(this, bounds_clump, &
          end do
       end if
 
+
+      ! Summarize biophysical variables that we want to output on FATES dimensions
+      ! Note that we pass in the bareground patch values here by starting the ifp
+      ! do loop from zero
+      do s = 1, this%fates(nc)%nsites
+         c = this%f2hmap(nc)%fcolumn(s)
+         do ifp = 0, this%fates(nc)%sites(s)%youngest_patch%patchno
+            p = ifp + col%patchi(c)
+            this%fates(nc)%bc_in(s)%lhflux_pa(ifp) = eflx_lh_tot(p)
+            this%fates(nc)%bc_in(s)%shflux_pa(ifp) = eflx_sh_tot(p)
+            this%fates(nc)%bc_in(s)%swabs_pa(ifp)  = fsa_patch(p)
+            this%fates(nc)%bc_in(s)%t2m_pa(ifp)    = t_ref2m(p)
+         end do
+      end do
+
       dtime = get_step_size_real()
 
       ! Update history variables that track these variables
@@ -3348,7 +3373,7 @@ subroutine init_history_io(this,bounds_proc)
    use FatesIOVariableKindMod, only : site_height_r8, site_elem_r8, site_elpft_r8
    use FatesIOVariableKindMod, only : site_elcwd_r8, site_elage_r8, site_agefuel_r8
    use FatesIOVariableKindMod, only : site_cdpf_r8, site_cdsc_r8, site_clscpf_r8
-   use FatesIOVariableKindMod, only : site_landuse_r8, site_lulu_r8
+   use FatesIOVariableKindMod, only : site_landuse_r8, site_lulu_r8, site_lupft_r8
    use FatesIODimensionsMod, only : fates_bounds_type
 
 
@@ -3454,7 +3479,7 @@ subroutine init_history_io(this,bounds_proc)
              site_scagpft_r8, site_agepft_r8, site_elem_r8, site_elpft_r8, &
              site_elcwd_r8, site_elage_r8, site_agefuel_r8, &
              site_cdsc_r8, site_cdpf_r8, &
-             site_landuse_r8, site_lulu_r8)
+             site_landuse_r8, site_lulu_r8, site_lupft_r8)
 
 
            d_index = fates_hist%dim_kinds(dk_index)%dim2_index
@@ -3808,6 +3833,9 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
 
    fates%lulu_begin = 1
    fates%lulu_end   = n_landuse_cats * n_landuse_cats
+
+   fates%lupft_begin = 1
+   fates%lupft_end = n_landuse_cats * numpft_fates
 
    call t_stopf('fates_hlm2fatesbnds')