Merge pull request #1874 from rgknox/fates_v2nutr_compatability

compatabiilty with FATES v2 nutrient API

Author: ekluzek

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.59.7_api.24.1.0
+tag = sci.1.61.0_api.25.0.0
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -492,7 +492,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.24.0.0_12pft_c220608.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221128.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -15,7 +15,7 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_FUEL_AMOUNT', 'FATES_LITTER_IN', 'FATES_LITTER_OUT',
 'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_STOREC', 'FATES_VEGC',
 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
-'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
+'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
 'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
 'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',

cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm

@@ -70,4 +70,4 @@ hist_fincl1       = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF',
 'FATES_CROOTMAINTAR_USTORY_SZ', 'FATES_FROOTMAINTAR_USTORY_SZ',
 'FATES_GROWAR_USTORY_SZ', 'FATES_MAINTAR_USTORY_SZ', 'FATES_VEGC_SZPF',
 'FATES_LEAFC_SZPF', 'FATES_FROOTC_SZPF', 'FATES_SAPWOODC_SZPF',
-'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF', 'FATES_CEFFLUX_SZPF'
+'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF'

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm

@@ -1 +1,12 @@
-fates_parteh_mode = 2
+fates_parteh_mode = 2
+hist_fincl1       = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
+'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF',
+'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',
+'FATES_NEFFLUX','FATES_NDEMAND','FATES_NFIX_SYM','FATES_STOREN','FATES_STOREN_TF',
+'FATES_VEGN','FATES_SAPWOODN','FATES_LEAFN','FATES_FROOTN','FATES_REPRON','FATES_VEGN_SZPF',
+'FATES_LEAFN_SZPF','FATES_FROOTN_SZPF','FATES_SAPWOODN_SZPF','FATES_STOREN_SZPF','FATES_STOREN_TF_CANOPY_SZPF',
+'FATES_STOREN_TF_USTORY_SZPF','FATES_REPRON_SZPF','FATES_STOREP','FATES_STOREP_TF','FATES_VEGP','FATES_SAPWOODP',
+'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND',
+'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF',
+'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF',
+'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF'

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -18,7 +18,7 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FA
               'FATES_FUEL_AMOUNT_AP', 'FATES_FUEL_BURNT_BURNFRAC_FC', 'FATES_LITTER_IN', 'FATES_LITTER_OUT', 'FATES_SEED_BANK',
               'FATES_SEEDS_IN', 'FATES_LITTER_IN_EL', 'FATES_LITTER_OUT_EL', 'FATES_SEED_BANK_EL', 'FATES_SEEDS_IN_LOCAL_EL',
               'FATES_SEEDS_IN_EXTERN_EL', 'FATES_SEED_GERM_EL', 'FATES_SEED_DECAY_EL', 'FATES_STOREC', 'FATES_VEGC',
-              'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 
+              'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 
               'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
               'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S',
               'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',

doc/ChangeLog

@@ -1,4 +1,81 @@
 ===============================================================
+Tag name: ctsm5.1.dev115
+Originator(s): rgknox (Ryan Knox)
+Date: Fri Dec  2 15:45:32 MST 2022
+One-line Summary: API compatability with FATES V2 nutrient dynamics
+
+Purpose and description of changes
+----------------------------------
+
+This set of changes allows CTSM to continue API compatability with changes to the FATES API. FATES has updated its nutrient dynamics routine, and required a modification to the test environment, some minor updates to variable dimensions in the history, and a call to a new FATES history routine.  Implicitly, the updating of the FATES tag introduces new content in the FATES model since the last API update (mostly bug fixes).
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+
+The changes here will only affect FATES simulations. Any FATES simulation will be affected. Carbon-only FATES simulations will not have qualitatively different results since the last API update (but will have bit-for-bit differences). Nutrient enabled FATES simulations (not fully coupled to CLM, only via prognosed plant N,P boundaries), and FATES-Hydro simulations (bug fix) will be different.
+
+Bugs fixed or introduced
+------------------------
+
+See the descriptions in FATES tags between sci.1.57.4_api.24.0.0 to sci.1.60.0_api.25.0.0 for details on FATES changes in this tag.
+
+CTSM issues fixed (include CTSM Issue #): None
+
+Externals issues fixed (include issue #): None
+
+Known bugs introduced in this tag (include issue #): None
+
+Known bugs found since the previous tag (include issue #): None
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+This set of changes comes with an updated FATES parameter file. This includes format changes only. No changes to variable values were introduced. Format changes are relegated to new parameters and/or name changes only.  These changes are encapsulated in: fates/parameter_files/archive/apichange_24.2to25.xml
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Nothing of note regarding changes for developers.
+
+Changes to tests or testing:  New history variables were added to the FATES PRT2 user_nl_clm.
+
+
+Testing summary:
+----------------
+
+regular
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- nominal: /glade/scratch/rgknox/tests_1201-121507ch
+    izumi ------- nominal: /scratch/cluster/rgknox/tests_1201-122133iz
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    cheyenne ---- nominal against ctsm5.1_dev112 /glade/scratch/rgknox/tests_1130-082657ch
+    izumi ------- NA
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: FATES answers changed relative to base. Explanation already provided (nutrient and hydro changes are qualitative).
+
+
+Other details
+-------------
+
+FATES external was updated.
+
+Pull Requests that document the changes (include PR ids):
+
+https://github.com/ESCOMP/CTSM/pull/1874
+https://github.com/NGEET/fates/pull/880
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev114
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh
 Date: Sat Nov 19 18:11:15 MST 2022

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev115   rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics
     ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes
     ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements
     ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests

src/main/histFileMod.F90

@@ -2468,6 +2468,7 @@ subroutine htape_create (t, histrest)
        call ncd_defdim(lnfid, 'fates_levelcwd', num_elements_fates * ncwd, dimid)
        call ncd_defdim(lnfid, 'fates_levelage', num_elements_fates * nlevage, dimid)
        call ncd_defdim(lnfid, 'fates_levagefuel', nlevage * nfsc, dimid)
+       call ncd_defdim(lnfid, 'fates_levclscpf', nclmax*nlevsclass*numpft_fates, dimid)
     end if
 
     if ( .not. lhistrest )then
@@ -5512,6 +5513,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        num2d = num_elements_fates*nlevage
     case ('fates_levagefuel')
        num2d = nlevage*nfsc
+    case('fates_levclscpf')
+       num2d = nclmax * nclmax * numpft_fates
     case('cft')
        if (cft_size > 0) then
           num2d = cft_size

src/utils/clmfates_interfaceMod.F90

@@ -1014,6 +1014,7 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       ! ---------------------------------------------------------------------------------
       call fates_hist%flush_hvars(nc,upfreq_in=1)
 
+      call fates_hist%flush_hvars(nc,upfreq_in=5)
 
       ! ---------------------------------------------------------------------------------
       ! Part II: Call the FATES model now that input boundary conditions have been
@@ -1088,7 +1089,8 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
       ! ---------------------------------------------------------------------------------
       call fates_hist%update_history_dyn( nc,                    &
                                           this%fates(nc)%nsites, &
-                                          this%fates(nc)%sites)
+                                          this%fates(nc)%sites,  &
+                                          this%fates(nc)%bc_in)
 
       if (masterproc) then
          write(iulog, *) 'clm: leaving fates model', bounds_clump%begg, &
@@ -1659,12 +1661,13 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, &
                ! ------------------------------------------------------------------------
                call fates_hist%flush_hvars(nc,upfreq_in=1)
                do s = 1,this%fates(nc)%nsites
-                  call fates_hist%zero_site_hvars(this%fates(nc)%sites(s),     &
+                  call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
                      upfreq_in=1)
                end do
-               call fates_hist%update_history_dyn( nc, &
-                                                   this%fates(nc)%nsites,                 &
-                                                   this%fates(nc)%sites)
+               call fates_hist%update_history_dyn( nc,                     &
+                                                   this%fates(nc)%nsites,  &
+                                                   this%fates(nc)%sites,   &
+                                                   this%fates(nc)%bc_in)
 
 
             end if
@@ -1831,12 +1834,13 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
            ! ------------------------------------------------------------------------
             call fates_hist%flush_hvars(nc,upfreq_in=1)
             do s = 1,this%fates(nc)%nsites
-               call fates_hist%zero_site_hvars(this%fates(nc)%sites(s),        &
+               call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
                   upfreq_in=1)
             end do
-            call fates_hist%update_history_dyn( nc, &
-                this%fates(nc)%nsites,                 &
-                this%fates(nc)%sites)
+            call fates_hist%update_history_dyn( nc,                     &
+                this%fates(nc)%nsites,                                  &
+                this%fates(nc)%sites,                                   &
+                this%fates(nc)%bc_in) 
 
 
 
@@ -2745,7 +2749,7 @@ subroutine init_history_io(this,bounds_proc)
    use FatesIOVariableKindMod, only : site_can_r8, site_cnlf_r8, site_cnlfpft_r8
    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
+   use FatesIOVariableKindMod, only : site_cdpf_r8, site_cdsc_r8, site_clscpf_r8
    use FatesIODimensionsMod, only : fates_bounds_type
 
 
@@ -2844,7 +2848,7 @@ subroutine init_history_io(this,bounds_proc)
 
         case(site_soil_r8, site_size_pft_r8, site_size_r8, site_pft_r8, &
              site_age_r8, site_height_r8, site_coage_r8,site_coage_pft_r8, &
-             site_fuel_r8, site_cwdsc_r8, &
+             site_fuel_r8, site_cwdsc_r8, site_clscpf_r8, &
              site_can_r8,site_cnlf_r8, site_cnlfpft_r8, site_scag_r8, &
              site_scagpft_r8, site_agepft_r8, site_elem_r8, site_elpft_r8, &
              site_elcwd_r8, site_elage_r8, site_agefuel_r8, &
@@ -3227,6 +3231,10 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
 
    fates%cdam_begin = 1
    fates%cdam_end = nlevdamage
+
+   fates%clscpf_begin = 1
+   fates%clscpf_end = numpft_fates * nlevsclass * nclmax
+   
 
    call t_stopf('fates_hlm2fatesbnds')