Merge pull request #2365 from wwieder/mimics_NEON_Derecho

Add litterfall fluxes that bypass litter pools, directly contributing to SOM + a few other mimics updates

Author: slevis-lmwg

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -524,9 +524,9 @@ 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/ctsm60_params_nfix.c241119.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params_nfix.c241119.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params_nfix.c241119.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c250311.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>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm

@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_ciso_cwd_hr_params_nfix.c241119.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_ciso_cwd_hr_params.c250311.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm

@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241119.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c250311.nc'

doc/ChangeLog

@@ -1,4 +1,82 @@
 ===============================================================
+Tag name: ctsm5.3.033
+Originator(s): wwieder, slevis (Will Wieder, Sam Levis, UCAR/TSS)
+Date: Wed 19 Mar 2025 02:43:55 PM MDT
+One-line Summary: Add new mimics_fi param = frac of litter inputs bypassing litter pools
+
+Purpose and description of changes
+----------------------------------
+
+ Summary from the PR: removes NPP control on turnover
+                      fixes density dependent control on turnover
+                      adds litterfall fluxes that bypass litter pools, directly contributing to SOM
+
+ This PR also addresses the issue of varying microbial turnover with depth.
+
+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
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2361 MIMICS todo list
+ Fixes #2248 Should microbial turnover vary with depth in MIMICS?
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+ Updated values in the default mimics parameters
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ New parameter files
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: MIMICS
+    - what platforms/compilers: All
+    - nature of change: Larger than roundoff/same climate
+
+ Soil C stocks will change in mimics cases with these code and parameter updates.
+
+ Also, three ciso_cwd_hr tests show diffs because the most recent previous ciso paramfile had roundoff diffs from the rest of the paramfiles for no reason that wwieder and slevis could identify. The new ciso paramfile does not have such diffs.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2365 MIMICS updates
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.032
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Mon 17 Mar 2025 09:49:08 AM MDT

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.033 multiple 03/19/2025 Add new mimics_fi param = frac of litter inputs bypassing litter pools
        ctsm5.3.032   slevis 03/17/2025 Add option to use CRUJRA2024 with clm6 and clm5
        ctsm5.3.031   slevis 03/13/2025 Merge b4b-dev
        ctsm5.3.030 samrabin 03/07/2025 Fix FATES branch runs

src/biogeochem/CNCStateUpdate1Mod.F90

@@ -9,6 +9,7 @@ module CNCStateUpdate1Mod
   use clm_varpar                         , only : ndecomp_cascade_transitions, nlevdecomp
   use clm_time_manager                   , only : get_step_size_real
   use clm_varpar                         , only : i_litr_min, i_litr_max, i_cwd
+  use clm_varpar                         , only : i_met_lit, i_str_lit, i_phys_som, i_chem_som
   use pftconMod                          , only : npcropmin, nc3crop, pftcon
   use abortutils                         , only : endrun
   use decompMod                          , only : bounds_type
@@ -17,7 +18,7 @@ module CNCStateUpdate1Mod
   use CropType                           , only : crop_type
   use CropReprPoolsMod                   , only : nrepr, repr_grain_min, repr_grain_max
   use CropReprPoolsMod                   , only : repr_structure_min, repr_structure_max
-  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn
+  use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, decomp_method, mimics_decomp, use_soil_matrixcn
   use SoilBiogeochemCarbonFluxType       , only : soilbiogeochem_carbonflux_type
   use SoilBiogeochemCarbonStateType      , only : soilbiogeochem_carbonstate_type
   use PatchType                          , only : patch
@@ -170,6 +171,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
     associate(                                                               & 
          ivt                   => patch%itype                                , & ! Input:  [integer  (:)     ]  patch vegetation type                                
 
+         mimics_fi             => pftcon%mimics_fi                         , & ! Input: MIMICS parameter fi
          woody                 => pftcon%woody                             , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
 
          cascade_donor_pool    => decomp_cascade_con%cascade_donor_pool    , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
@@ -206,10 +208,21 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, &
                !
                if (.not. use_soil_matrixcn) then
                   ! phenology and dynamic land cover fluxes
-                  do i = i_litr_min, i_litr_max
-                     cf_soil%decomp_cpools_sourcesink_col(c,j,i) = &
-                          cf_veg%phenology_c_to_litr_c_col(c,j,i) * dt
-                  end do
+                  if (decomp_method == mimics_decomp) then
+                     do i = i_litr_min, i_litr_max  ! in MIMICS these are 1 and 2
+                        cf_soil%decomp_cpools_sourcesink_col(c,j,i) = (1 - mimics_fi(i)) * &
+                           cf_veg%phenology_c_to_litr_c_col(c,j,i) * dt
+                     end do
+                     cf_soil%decomp_cpools_sourcesink_col(c,j,i_phys_som) = mimics_fi(1) * &
+                        cf_veg%phenology_c_to_litr_c_col(c,j,i_met_lit) * dt
+                     cf_soil%decomp_cpools_sourcesink_col(c,j,i_chem_som) = mimics_fi(2) * &
+                        cf_veg%phenology_c_to_litr_c_col(c,j,i_str_lit) * dt
+                  else
+                     do i = i_litr_min, i_litr_max
+                        cf_soil%decomp_cpools_sourcesink_col(c,j,i) = &
+                             cf_veg%phenology_c_to_litr_c_col(c,j,i) * dt
+                     end do
+                  end if
 
                   ! NOTE(wjs, 2017-01-02) This used to be set to a non-zero value, but the
                   ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every

src/biogeochem/CNNStateUpdate1Mod.F90

@@ -12,8 +12,9 @@ module CNNStateUpdate1Mod
   use clm_time_manager                , only : get_step_size_real
   use clm_varpar                      , only : nlevdecomp
   use clm_varpar                      , only : i_litr_min, i_litr_max, i_cwd
+  use clm_varpar                      , only : i_met_lit, i_str_lit, i_phys_som, i_chem_som
   use clm_varctl                      , only : iulog, use_nitrif_denitrif
-  use SoilBiogeochemDecompCascadeConType, only : use_soil_matrixcn
+  use SoilBiogeochemDecompCascadeConType, only : decomp_method, mimics_decomp, use_soil_matrixcn
   use CNSharedParamsMod               , only : use_matrixcn
   use clm_varcon                      , only : nitrif_n2o_loss_frac
   use pftconMod                       , only : npcropmin, pftcon
@@ -129,6 +130,7 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     associate(                                                                   & 
          ivt                   => patch%itype                                    , & ! Input:  [integer  (:)     ]  patch vegetation type                                
 
+         mimics_fi             => pftcon%mimics_fi                             , & ! Input:  MIMICS parameter fi
          woody                 => pftcon%woody                                 , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
 
          nf_veg                => cnveg_nitrogenflux_inst                      , & ! Input:
@@ -163,10 +165,21 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
             ! State update without the matrix solution
             !
             if (.not. use_soil_matrixcn) then ! to be consistent with C
-               do i = i_litr_min, i_litr_max
-                  nf_soil%decomp_npools_sourcesink_col(c,j,i) = &
-                     nf_veg%phenology_n_to_litr_n_col(c,j,i) * dt
-               end do
+               if (decomp_method == mimics_decomp) then
+                  do i = i_litr_min, i_litr_max  ! in MIMICS these are 1 and 2
+                     nf_soil%decomp_npools_sourcesink_col(c,j,i) = (1 - mimics_fi(i)) * &
+                        nf_veg%phenology_n_to_litr_n_col(c,j,i) * dt
+                  end do
+                  nf_soil%decomp_npools_sourcesink_col(c,j,i_phys_som) = mimics_fi(1) * &
+                     nf_veg%phenology_n_to_litr_n_col(c,j,i_met_lit) * dt
+                  nf_soil%decomp_npools_sourcesink_col(c,j,i_chem_som) = mimics_fi(2) * &
+                     nf_veg%phenology_n_to_litr_n_col(c,j,i_str_lit) * dt
+               else
+                  do i = i_litr_min, i_litr_max
+                     nf_soil%decomp_npools_sourcesink_col(c,j,i) = &
+                        nf_veg%phenology_n_to_litr_n_col(c,j,i) * dt
+                  end do
+               end if
 
                ! NOTE(wjs, 2017-01-02) This used to be set to a non-zero value, but the
                ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every

src/main/clm_varpar.F90

@@ -82,6 +82,9 @@ module clm_varpar
   integer, public            :: i_litr_min    = -9    ! min index of litter pools; overwritten in SoilBiogeochemDecompCascade*Mod
   integer, public            :: i_litr_max    = -9    ! max index of litter pools; overwritten in SoilBiogeochemDecompCascade*Mod
   integer, public            :: i_met_lit     = -9    ! index of metabolic litter pool; overwritten in SoilBiogeochemDecompCascade*Mod
+  integer, public            :: i_str_lit     = -9    ! index of structural litter pool; overwritten in SoilBiogeochemDecompCascade*Mod
+  integer, public            :: i_phys_som    = -9    ! index of physically protected Soil Organic Matter (SOM); overwritten in SoilBiogeochemDecompCascade*Mod
+  integer, public            :: i_chem_som    = -9    ! index of chemically protected Soil Organic Matter (SOM); overwritten in SoilBiogeochemDecompCascade*Mod
   integer, public            :: i_cop_mic     = -9    ! index of copiotrophic microbial pool; overwritten in SoilBiogeochemDecompCascade*Mod
   integer, public            :: i_oli_mic     = -9    ! index of oligotrophic microbial pool; overwritten in SoilBiogeochemDecompCascade*Mod
   integer, public            :: i_cwd         = -9    ! index of cwd pool; overwritten in SoilBiogeochemDecompCascade*Mod

src/main/pftconMod.F90

@@ -165,6 +165,9 @@ module pftconMod
      real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
      real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
 
+     ! MIMICS
+     real(r8), allocatable :: mimics_fi(:)
+
      !  crop
 
      ! These arrays give information about the merge of unused crop types to the types CLM
@@ -504,6 +507,7 @@ subroutine InitAllocate (this)
     allocate( this%taper         (0:mxpft) )
     allocate( this%rstem_per_dbh (0:mxpft) )
     allocate( this%wood_density  (0:mxpft) )
+    allocate( this%mimics_fi(2) )
     allocate( this%crit_onset_gdd_sf (0:mxpft) )
     allocate( this%ndays_on      (0:mxpft) )
 
@@ -1095,6 +1099,9 @@ subroutine InitRead(this)
     !
     ! clm 5 nitrogen variables
     !
+    call ncd_io('mimics_fi',this%mimics_fi, 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
     if (use_flexibleCN) then
        call ncd_io('i_vcad', this%i_vcad, 'read', ncid, readvar=readv) 
        if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) 
@@ -1132,6 +1139,7 @@ subroutine InitRead(this)
        if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
        call ncd_io('wood_density',this%wood_density, 'read', ncid, readvar=readv)
        if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
     else
        this%dbh = 0.0_r8
        this%fbw = 0.0_r8
@@ -1594,6 +1602,7 @@ subroutine Clean(this)
     deallocate( this%rstem_per_dbh)
     deallocate( this%wood_density)
     deallocate( this%taper)
+    deallocate( this%mimics_fi)
     deallocate( this%crit_onset_gdd_sf)
     deallocate( this%ndays_on)
   end subroutine Clean

src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90

@@ -10,7 +10,7 @@ module SoilBiogeochemDecompCascadeMIMICSMod
   use shr_const_mod                      , only : SHR_CONST_TKFRZ
   use shr_log_mod                        , only : errMsg => shr_log_errMsg
   use clm_varpar                         , only : nlevdecomp, ndecomp_pools_max
-  use clm_varpar                         , only : i_met_lit, i_cop_mic, i_oli_mic, i_cwd
+  use clm_varpar                         , only : i_phys_som, i_chem_som, i_str_lit, i_met_lit, i_cop_mic, i_oli_mic, i_cwd
   use clm_varpar                         , only : i_litr_min, i_litr_max, i_cwdl2
   use clm_varctl                         , only : iulog, spinup_state, anoxia, use_lch4, use_fates
   use clm_varcon                         , only : zsoi
@@ -48,10 +48,7 @@ module SoilBiogeochemDecompCascadeMIMICSMod
   real(r8), private, allocatable :: fphys_m1(:,:)
   real(r8), private, allocatable :: fphys_m2(:,:)
   real(r8), private, allocatable :: p_scalar(:,:)
-  integer, private :: i_phys_som  ! index of physically protected Soil Organic Matter (SOM)
-  integer, private :: i_chem_som  ! index of chemically protected SOM
   integer, private :: i_avl_som  ! index of available (aka active) SOM
-  integer, private :: i_str_lit  ! index of structural litter pool
   integer, private :: i_l1m1  ! indices of transitions, eg l1m1: litter 1 -> first microbial pool
   integer, private :: i_l1m2
   integer, private :: i_l2m1
@@ -1293,14 +1290,14 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
             decomp_k(c,j,i_chem_som) = (term_1 + term_2) * w_d_o_scalars
 
             ! Currently, mimics_densdep = 1 so as to have no effect
-            decomp_k(c,j,i_cop_mic) = tau_m1 * &
-                   m1_conc**(mimics_densdep - 1.0_r8) * w_d_o_scalars
+            decomp_k(c,j,i_cop_mic) = tau_m1 * m1_conc**(mimics_densdep) 
+ 
             favl = min(1.0_r8, max(0.0_r8, 1.0_r8 - fphys_m1(c,j) - fchem_m1))
             pathfrac_decomp_cascade(c,j,i_m1s1) = favl
             pathfrac_decomp_cascade(c,j,i_m1s2) = fchem_m1
 
-            decomp_k(c,j,i_oli_mic) = tau_m2 * &
-                   m2_conc**(mimics_densdep - 1.0_r8) * w_d_o_scalars
+            decomp_k(c,j,i_oli_mic) = tau_m2 * m2_conc**(mimics_densdep)
+
             favl = min(1.0_r8, max(0.0_r8, 1.0_r8 - fphys_m2(c,j) - fchem_m2))
             pathfrac_decomp_cascade(c,j,i_m2s1) = favl
             pathfrac_decomp_cascade(c,j,i_m2s2) = fchem_m2