First pass at getting fates-sp mode to run without soil BGC

Externals.cfg

@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.15
+tag = ccs_config_cesm0.0.30
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,11 +44,11 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.15
+tag = cime6.0.23
 required = True
 
 [cmeps]
-tag = cmeps0.13.47
+tag = cmeps0.13.63
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.10
+tag = share1.0.11
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -84,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_6
+tag = pio2_5_7
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

bld/CLMBuildNamelist.pm

@@ -870,9 +870,14 @@ sub setup_cmdl_bgc {
               'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
   my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( $var ) );
 
-  if ( &value_is_true($nl_flags->{'use_cn'}) ||  &value_is_true($nl_flags->{'use_fates'}))  {
+  if (      &value_is_true($nl_flags->{'use_cn'}) ) {
      if ( $soil_decomp_method eq "None" ) {
-        $log->fatal_error("$var must NOT be None if use_cn or use_fates are on");
+        $log->fatal_error("$var must NOT be None if use_cn is on");
+     }
+  } elsif ( &value_is_true($nl_flags->{'use_fates'}) && (not &value_is_true($nl->get_value('use_fates_sp')))  )  {
+     print  "use_fates_sp = ", $nl_flags->{'use_fates_sp'}, "\n";
+     if ( $soil_decomp_method eq "None" ) {
+        $log->fatal_error("$var must NOT be None if use_fates is on and use_fates_sp is not TRUE");
      }
   } elsif ( $soil_decomp_method ne "None" ) {
      $log->fatal_error("$var must be None if use_cn and use_fates are off");

cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods

@@ -1 +1,2 @@
 ../FatesColdDef
+../../../../usermods_dirs/fates_sp

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -0,0 +1,35 @@
+use_fates_sp = .true.
+soil_decomp_method = 'None'
+use_lch4 = .false.
+fates_spitfire_mode = 0
+hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
+              'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
+              'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
+              'FATES_STOREC_PF', 'FATES_RECRUITMENT_PF', 'FATES_MORTALITY_PF', 'FATES_PATCHAREA_AP', 'FATES_LAI_AP',
+              'FATES_CANOPYAREA_AP', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS', 'FATES_EFFECT_WSPEED',
+              'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',
+              'FATES_FUEL_BULKD', 'FATES_FUEL_EFF_MOIST', 'FATES_FUEL_SAV', 'FATES_FUEL_AMOUNT', 'FATES_FRAGMENTATION_SCALER_SL',
+              'FATES_FUEL_MOISTURE_FC', 'FATES_FUEL_AMOUNT_FC', 'FATES_BURNFRAC_AP', 'FATES_FIRE_INTENSITY_BURNFRAC_AP',
+              '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_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',
+              'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
+              'FATES_GPP_UNDERSTORY', 'FATES_AUTORESP_UNDERSTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
+              'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_UNDERSTORY', 
+              'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ',
+              'FATES_VEGC_ABOVEGROUND_SZ', 'FATES_LAI_CANOPY_SZ', 'FATES_MORTALITY_CANOPY_SZ', 'FATES_NPLANT_USTORY_SZ',
+              'FATES_LAI_USTORY_SZ', 'FATES_NPLANT_SZ', 'FATES_NPLANT_AC', 'FATES_MORTALITY_BACKGROUND_SZ',
+              'FATES_MORTALITY_HYDRAULIC_SZ', 'FATES_MORTALITY_CSTARV_SZ', 'FATES_MORTALITY_IMPACT_SZ',
+              'FATES_MORTALITY_FIRE_SZ', 'FATES_MORTALITY_TERMINATION_SZ', 'FATES_MORTALITY_LOGGING_SZ',
+              'FATES_MORTALITY_FREEZING_SZ', 'FATES_MORTALITY_SENESCENCE_SZ', 'FATES_MORTALITY_AGESCEN_SZ',
+              'FATES_MORTALITY_AGESCEN_AC', 'FATES_MORTALITY_USTORY_SZ', 'FATES_FROOTMAINTAR', 'FATES_CROOTMAINTAR',
+              'FATES_LSTEMMAINTAR', 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
+              'FATES_LITTER_AG_FINE_EL', 'FATES_LITTER_BG_FINE_EL', 'FATES_LITTER_BG_CWD_EL', 'FATES_LITTER_AG_CWD_EL',
+              'FATES_LITTER_CWD_ELDC', 'FATES_LEAF_ALLOC', 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
+              'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC', 'FATES_AUTORESP', 'FATES_GROWTH_RESP',
+              'FATES_LEAFMAINTAR', 'FATES_MAINT_RESP', 'FATES_NPP', 'FATES_NPP_PF',
+              'FATES_c_to_litr_cel_c', 'FATES_c_to_litr_lab_c', 'FATES_c_to_litr_lig_c'

src/biogeochem/CNCStateUpdate1Mod.F90

@@ -20,7 +20,7 @@ module CNCStateUpdate1Mod
   use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
   use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
   use PatchType                          , only : patch
-  use clm_varctl                         , only : use_fates, use_cn, iulog
+  use clm_varctl                         , only : use_fates, use_cn, iulog, use_fates_sp
   !
   implicit none
   private
@@ -200,7 +200,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8
             end do
          end do
-      else  !use_fates
+      else if ( .not. use_fates_sp ) then !use_fates
          ! here add all fates litterfall and CWD breakdown to litter fluxes
          do j = 1,nlevdecomp
             do fc = 1,num_soilc
@@ -215,29 +215,31 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
          end do
       endif
 
-      ! litter and SOM HR fluxes
-      do k = 1, ndecomp_cascade_transitions
-         do j = 1,nlevdecomp
-            do fc = 1,num_soilc
-               c = filter_soilc(fc)
-               cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
-                    cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
-                    - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
-            end do
-         end do
-      end do
-      do k = 1, ndecomp_cascade_transitions
-         if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
+      if ( .not. use_fates_sp ) then !use_fates
+         ! litter and SOM HR fluxes
+         do k = 1, ndecomp_cascade_transitions
             do j = 1,nlevdecomp
                do fc = 1,num_soilc
                   c = filter_soilc(fc)
-                  cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
-                       cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
-                       + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt
+                  cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = &
+                       cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) &
+                       - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt
                end do
             end do
-         end if
-      end do
+         end do
+         do k = 1, ndecomp_cascade_transitions
+            if ( cascade_receiver_pool(k) /= 0 ) then  ! skip terminal transitions
+               do j = 1,nlevdecomp
+                  do fc = 1,num_soilc
+                     c = filter_soilc(fc)
+                     cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = &
+                          cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) &
+                          + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt
+                  end do
+               end do
+            end if
+         end do
+      end if
 
       if (.not. use_fates) then    
         do fp = 1,num_soilp

src/biogeochem/EDBGCDynMod.F90

@@ -10,7 +10,7 @@ module EDBGCDynMod
   use perf_mod                        , only : t_startf, t_stopf
   use shr_log_mod                     , only : errMsg => shr_log_errMsg
   use abortutils                      , only : endrun
-  use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, century_decomp, decomp_method
+  use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, mimics_decomp, century_decomp, decomp_method
   use CNVegCarbonStateType	      , only : cnveg_carbonstate_type
   use CNVegCarbonFluxType	      , only : cnveg_carbonflux_type
   use SoilBiogeochemStateType         , only : soilbiogeochem_state_type
@@ -29,6 +29,7 @@ module EDBGCDynMod
   use ch4Mod                          , only : ch4_type
   use CLMFatesInterfaceMod            , only : hlm_fates_interface_type
 
+  implicit none
 
   ! public :: EDBGCDynInit         ! BGC dynamics: initialization
   public :: EDBGCDyn             ! BGC Dynamics
@@ -139,21 +140,23 @@ subroutine EDBGCDyn(bounds,                                                    &
     ! zero the column-level C and N fluxes
     ! --------------------------------------------------
 
-    call t_startf('BGCZero')
+    if ( decomp_method /= no_soil_decomp )then
+       call t_startf('SoilBGCZero')
 
-    call soilbiogeochem_carbonflux_inst%SetValues( &
-         num_soilc, filter_soilc, 0._r8)
-    if ( use_c13 ) then
-       call c13_soilbiogeochem_carbonflux_inst%SetValues( &
-            num_soilc, filter_soilc, 0._r8)
-    end if
-    if ( use_c14 ) then
-       call c14_soilbiogeochem_carbonflux_inst%SetValues( &
+       call soilbiogeochem_carbonflux_inst%SetValues( &
             num_soilc, filter_soilc, 0._r8)
+       if ( use_c13 ) then
+          call c13_soilbiogeochem_carbonflux_inst%SetValues( &
+               num_soilc, filter_soilc, 0._r8)
+       end if
+       if ( use_c14 ) then
+          call c14_soilbiogeochem_carbonflux_inst%SetValues( &
+               num_soilc, filter_soilc, 0._r8)
+       end if
+
+       call t_stopf('SoilBGCZero')
     end if
 
-    call t_stopf('BGCZero')
-
     ! --------------------------------------------------
     ! Nitrogen Deposition, Fixation and Respiration
     ! --------------------------------------------------
@@ -187,16 +190,17 @@ subroutine EDBGCDyn(bounds,                                                    &
             soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst)
     end if
 
-    ! calculate potential decomp rates and total immobilization demand (previously inlined in CNDecompAlloc)
-    call SoilBiogeochemPotential (bounds, num_soilc, filter_soilc,                                                    &
-         soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,                  &
-         soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst,                                         &
-         cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & 
-         p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
-         p_decomp_cn_gain=p_decomp_cn_gain(begc:endc,1:nlevdecomp,1:ndecomp_pools), &
-         pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
-         p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions))
-
+    if ( decomp_method /= no_soil_decomp )then
+       ! calculate potential decomp rates and total immobilization demand (previously inlined in CNDecompAlloc)
+       call SoilBiogeochemPotential (bounds, num_soilc, filter_soilc,                                                    &
+            soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,                  &
+            soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst,                                         &
+            cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & 
+            p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
+            p_decomp_cn_gain=p_decomp_cn_gain(begc:endc,1:nlevdecomp,1:ndecomp_pools), &
+            pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
+            p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions))
+    end if
 
     !--------------------------------------------
     ! Resolve the competition between plants and soil heterotrophs 
@@ -212,17 +216,18 @@ subroutine EDBGCDyn(bounds,                                                    &
     ! Calculation of actual immobilization and decomp rates, following
     ! resolution of plant/heterotroph  competition for mineral N (previously inlined in CNDecompAllocation in CNDecompMod)
 
-    call t_startf('SoilBiogeochemDecomp')
+    if ( decomp_method /= no_soil_decomp )then
+       call t_startf('SoilBiogeochemDecomp')
 
-    call SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc,                                                       &
-         soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,                  &
-         soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst,                                         &
-         cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools),                       & 
-         p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
-         pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
-         p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions))
+       call SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc,                                                       &
+            soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,                  &
+            soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst,                                         &
+            cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools),                       & 
+            p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
+            pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), &
+            p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions))
 
-    call t_stopf('SoilBiogeochemDecomp')
+       call t_stopf('SoilBiogeochemDecomp')
 
 
     !--------------------------------------------
@@ -243,16 +248,17 @@ subroutine EDBGCDyn(bounds,                                                    &
     ! Calculate vertical mixing of soil and litter pools
     !--------------------------------------------
 
-    call t_startf('SoilBiogeochemLittVertTransp')
+       call t_startf('SoilBiogeochemLittVertTransp')
 
-    call SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc,            &
-         active_layer_inst, soilbiogeochem_state_inst,                            &
-         soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,         &
-         c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, &
-         c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, &
-         soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
+       call SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc,            &
+            active_layer_inst, soilbiogeochem_state_inst,                            &
+            soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst,         &
+            c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, &
+            c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, &
+            soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst)
 
-    call t_stopf('SoilBiogeochemLittVertTransp')
+       call t_stopf('SoilBiogeochemLittVertTransp')
+    end if
 
     end associate
 

src/main/clm_driver.F90

@@ -81,6 +81,7 @@ module clm_driver
   use clm_instMod
   use EDBGCDynMod            , only : EDBGCDyn, EDBGCDynSummary
   use SoilMoistureStreamMod  , only : PrescribedSoilMoistureInterp, PrescribedSoilMoistureAdvance
+  use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, decomp_method
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -1090,14 +1091,16 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
                active_layer_inst, atm2lnd_inst, water_inst%waterfluxbulk_inst,                     &
                canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst)
 
-          call EDBGCDynSummary(bounds_clump,                                             &
-                filter(nc)%num_soilc, filter(nc)%soilc,                                  &
-                filter(nc)%num_soilp, filter(nc)%soilp,                                  &
-                soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst,         &
-                c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, &
-                c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, &
-                soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst,     &
-                nc)
+          if ( decomp_method /= no_soil_decomp )then
+             call EDBGCDynSummary(bounds_clump,                                             &
+                   filter(nc)%num_soilc, filter(nc)%soilc,                                  &
+                   filter(nc)%num_soilp, filter(nc)%soilp,                                  &
+                   soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst,         &
+                   c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, &
+                   c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, &
+                   soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst,     &
+                   nc)
+          end if
 
           call clm_fates%wrap_update_hifrq_hist(bounds_clump, &
                soilbiogeochem_carbonflux_inst, &