Merge branch 'thorntonpe/lnd/IM3_testing_2'(PR #6607)

Change handling for how snow burial of shrubs is calculated, with parameterization for bending of stems. Change the treatment of surface weather downscaling on topounits, so that the downscaling happens when using the coupler bypass code branch. Introduce four new parameters controlling the burial of shrubs by snow into vegetation physiology file. If new parameters are not included on the physiology file the code replaces with default values, which then produce BFB results with code before this PR. The four new parameters are: taper, stocking, bendresist, and vegshape. Development Lead: Rich Fiorella rfiorella@lanl.gov Development Team: Katrina Bennett kbennett@lnl.gov, Cade Trotter ctrotter@lanl.gov, Claire Bachand cbachand@lanl.gov [BFB]
E3SM-Project · Oct 8, 2024 · 4b85dbe · 4b85dbe
2 parents 5130bd1 + 3cb0e38
commit 4b85dbe
Show file tree

Hide file tree

Showing 21 changed files with 1,065 additions and 446 deletions.
diff --git a/cime_config/tests.py b/cime_config/tests.py
@@ -49,6 +49,9 @@
             "ERS.f19_g16.I20TRGSWCNPECACNTBC.elm-eca_f19_g16_I20TRGSWCNPECACNTBC",
             "ERS.f19_g16.I20TRGSWCNPRDCTCBC.elm-ctc_f19_g16_I20TRGSWCNPRDCTCBC",
             "ERS.r05_r05.ICNPRDCTCBC.elm-cbudget",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-snowveg_arctic",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC",
             )
         },
 
@@ -94,8 +97,6 @@
             "SMS.r05_r05.IELM.elm-topounit",
             "ERS.ELM_USRDAT.I1850ELM.elm-usrdat",
             "ERS.r05_r05.IELM.elm-lnd_rof_2way",
-            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC",
-            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC",
             "ERS.r05_r05.IELM.elm-V2_ELM_MOSART_features",
             "ERS.ELM_USRDAT.IELM.elm-surface_water_dynamics"
             )

diff --git a/components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/shell_commands b/components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/shell_commands
@@ -0,0 +1,10 @@
+./xmlchange LND_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange ATM_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange LND_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange ATM_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange DATM_MODE=CLM1PT
+./xmlchange DATM_CLMNCEP_YR_START=2000
+./xmlchange DATM_CLMNCEP_YR_END=2000
+./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
+./xmlchange NTASKS=1
+./xmlchange NTHRDS=1
diff --git a/components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/user_nl_elm b/components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/user_nl_elm
@@ -0,0 +1,8 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
+! this test has a parameter file with four new parameters defined for NGEE Arctic IM3
+! meant to improve snow-vegetation interactions.
+! bendresist -> varies between 0 and 1, represents how much vegetation bends under snow loading
+! vegshape -> suggested value 1 (parabolic), but 2 also used previously (Liston and Heimstra, 2011)
+! taper -> deadstem height/radius ratio, moved from hardcoded in VegStructUpdateMod to pftvarcon
+! stocking -> individual density on landscape (plants/m2), moved from hardcoded in VegStructUpdateMod to pftvarcon
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_ngeea-im3_c240822.nc'
diff --git a/components/elm/src/biogeochem/AllocationMod.F90 b/components/elm/src/biogeochem/AllocationMod.F90
diff --git a/components/elm/src/biogeochem/CNAllocationBetrMod.F90 b/components/elm/src/biogeochem/CNAllocationBetrMod.F90
@@ -26,13 +26,13 @@ module CNAllocationBeTRMod
   use PhotosynthesisType  , only : photosyns_type
   use CropType            , only : crop_type
   use VegetationPropertiesType, only : veg_vp
-  use LandunitType        , only : lun_pp                
+  use LandunitType        , only : lun_pp
   use ColumnType          , only : col_pp
-  use ColumnDataType      , only : col_cf, col_ns, col_nf, col_ps, col_pf  
+  use ColumnDataType      , only : col_cf, col_ns, col_nf, col_ps, col_pf
   use VegetationType      , only : veg_pp
   use VegetationDataType  , only : veg_cs, veg_ns, veg_nf, veg_ps, veg_pf
-  use VegetationDataType  , only : veg_cf, c13_veg_cf, c14_veg_cf  
-  
+  use VegetationDataType  , only : veg_cf, c13_veg_cf, c14_veg_cf
+
   ! bgc interface & pflotran module switches
   use elm_varctl          , only : nu_com
   use SoilStatetype       , only : soilstate_type
@@ -359,7 +359,7 @@ subroutine Allocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soilp
     associate(                                                                                   &
          ivt                          => veg_pp%itype                                             , & ! Input:  [integer  (:) ]  pft vegetation type
 
-         woody                        => veg_vp%woody                                      , & ! Input:  [real(r8) (:)   ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                        => veg_vp%woody                                      , & ! Input:  [real(r8) (:)   ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          froot_leaf                   => veg_vp%froot_leaf                                 , & ! Input:  [real(r8) (:)   ]  allocation parameter: new fine root C per new leaf C (gC/gC)
          croot_stem                   => veg_vp%croot_stem                                 , & ! Input:  [real(r8) (:)   ]  allocation parameter: new coarse root C per new stem C (gC/gC)
          stem_leaf                    => veg_vp%stem_leaf                                  , & ! Input:  [real(r8) (:)   ]  allocation parameter: new stem c per new leaf C (gC/gC)
@@ -1167,7 +1167,7 @@ subroutine Allocation3_PlantCNPAlloc (bounds            , &
     associate(                                                                                 &
          ivt                          => veg_pp%itype                                           , & ! Input:  [integer  (:) ]  pft vegetation type
 !
-         woody                        => veg_vp%woody                                    , & ! Input:  [real(r8) (:)   ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                        => veg_vp%woody                                    , & ! Input:  [real(r8) (:)   ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          froot_leaf                   => veg_vp%froot_leaf                               , & ! Input:  [real(r8) (:)   ]  allocation parameter: new fine root C per new leaf C (gC/gC)
          croot_stem                   => veg_vp%croot_stem                               , & ! Input:  [real(r8) (:)   ]  allocation parameter: new coarse root C per new stem C (gC/gC)
          stem_leaf                    => veg_vp%stem_leaf                                , & ! Input:  [real(r8) (:)   ]  allocation parameter: new stem c per new leaf C (gC/gC)

diff --git a/components/elm/src/biogeochem/CNGapMortalityBeTRMod.F90 b/components/elm/src/biogeochem/CNGapMortalityBeTRMod.F90
@@ -18,9 +18,9 @@ module CNGapMortalityBeTRMod
   use ColumnType          , only : col_pp
   use ColumnDataType      , only : col_cf, col_nf, col_pf
   use VegetationPropertiesType      , only : veg_vp
-  use VegetationType      , only : veg_pp  
-  use VegetationDataType  , only : veg_cs, veg_cf, veg_ns, veg_nf 
-  use VegetationDataType  , only : veg_ps, veg_pf 
+  use VegetationType      , only : veg_pp
+  use VegetationDataType  , only : veg_cs, veg_cf, veg_ns, veg_nf
+  use VegetationDataType  , only : veg_ps, veg_pf
 
   use PhosphorusFluxType  , only : phosphorusflux_type
   use PhosphorusStateType , only : phosphorusstate_type
@@ -121,7 +121,7 @@ subroutine CNGapMortality (&
     associate(                                                                                              &
          ivt                                 =>    veg_pp%itype                                              , & ! Input:  [integer  (:) ]  pft vegetation type
 
-         woody                               =>    veg_vp%woody                                       & ! Input:  [real(r8) (:) ]  binary flag for woody lifeform
+         woody                               =>    veg_vp%woody                                       & ! Input:  [real(r8) (:) ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          )
 
       ! set the mortality rate based on annual rate

diff --git a/components/elm/src/biogeochem/CNNStateUpdate1BeTRMod.F90 b/components/elm/src/biogeochem/CNNStateUpdate1BeTRMod.F90
@@ -59,7 +59,7 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     associate(                                                                                           &
          ivt                   => veg_pp%itype                                , & ! Input:  [integer  (:)     ]  pft vegetation type
 
-         woody                 => veg_vp%woody                         , & ! Input:  [real(r8) (:)     ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                 => veg_vp%woody                         , & ! Input:  [real(r8) (:)     ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
 
          cascade_donor_pool    => decomp_cascade_con%cascade_donor_pool    , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
          cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input:  [integer  (:)     ]  which pool is C added to for a given decomposition step

diff --git a/components/elm/src/biogeochem/CNPhenologyBeTRMod.F90 b/components/elm/src/biogeochem/CNPhenologyBeTRMod.F90
@@ -525,7 +525,7 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
          prev_dayl                           =>    grc_pp%prev_dayl                                         , & ! Input:  [real(r8)  (:)   ]  daylength from previous time step (s)
 
          season_decid                        =>    veg_vp%season_decid                               , & ! Input:  [real(r8)  (:)   ]  binary flag for seasonal-deciduous leaf habit (0 or 1)
-         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:)   ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:)   ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
 
          t_soisno                            =>    col_es%t_soisno                         , & ! Input:  [real(r8)  (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
 
@@ -875,7 +875,7 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
          dayl                                =>    grc_pp%dayl                                              , & ! Input:  [real(r8)  (:)   ]  daylength (s)
 
          leaf_long                           =>    veg_vp%leaf_long                                  , & ! Input:  [real(r8)  (:)   ]  leaf longevity (yrs)
-         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:)   ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:)   ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          stress_decid                        =>    veg_vp%stress_decid                               , & ! Input:  [real(r8)  (:)   ]  binary flag for stress-deciduous leaf habit (0 or 1)
 
          soilpsi                             =>    soilstate_vars%soilpsi_col                            , & ! Input:  [real(r8)  (:,:) ]  soil water potential in each soil layer (MPa)
@@ -2295,7 +2295,7 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, &
     associate(                                                                                             &
          ivt                                 =>    veg_pp%itype                                             , & ! Input:  [integer   (:) ]  pft vegetation type
 
-         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:) ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                               =>    veg_vp%woody                                      , & ! Input:  [real(r8)  (:) ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
 
          onset_flag                          =>    cnstate_vars%onset_flag_patch                           , & ! Input:  [real(r8)  (:) ]  onset flag
          onset_counter                       =>    cnstate_vars%onset_counter_patch                        , & ! Input:  [real(r8)  (:) ]  onset days counter
@@ -2880,7 +2880,7 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
     associate(                                                                             &
          ivt                      =>    veg_pp%itype                                        , & ! Input:  [integer  (:) ]  pft vegetation type
 
-         woody                    =>    veg_vp%woody                                 , & ! Input:  [real(r8) (:) ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                    =>    veg_vp%woody                                 , & ! Input:  [real(r8) (:) ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          livewdcn                 =>    veg_vp%livewdcn                              , & ! Input:  [real(r8) (:) ]  live wood (phloem and ray parenchyma) C:N (gC/gN)
          deadwdcn                 =>    veg_vp%deadwdcn                              , & ! Input:  [real(r8) (:) ]  dead wood (xylem and heartwood) C:N (gC/gN)
 

diff --git a/components/elm/src/biogeochem/CarbonStateUpdate1Mod.F90 b/components/elm/src/biogeochem/CarbonStateUpdate1Mod.F90
@@ -200,7 +200,7 @@ subroutine CarbonStateUpdate1(bounds, &
 
     associate(                                                                                 &
          ivt                   =>    veg_pp%itype                               , & ! Input:  [integer  (:)     ]  pft vegetation type
-         woody                 =>    veg_vp%woody                               , & ! Input:  [real(r8) (:)     ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                 =>    veg_vp%woody                               , & ! Input:  [real(r8) (:)     ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          cascade_donor_pool    =>    decomp_cascade_con%cascade_donor_pool      , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
          cascade_receiver_pool =>    decomp_cascade_con%cascade_receiver_pool   , & ! Input:  [integer  (:)     ]  which pool is C added to for a given decomposition step
          harvdate              =>    crop_vars%harvdate_patch                     & ! Input:  [integer  (:)     ]  harvest date

diff --git a/components/elm/src/biogeochem/GrowthRespMod.F90 b/components/elm/src/biogeochem/GrowthRespMod.F90
@@ -51,7 +51,7 @@ subroutine GrowthResp(num_soilp, filter_soilp)
     associate(                                                                      &
          ivt                           =>    veg_pp%itype                         , & ! Input:  [integer (:)]  pft vegetation type
 
-         woody                         =>    veg_vp%woody                         , & ! Input:  [real(r8) (:)]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                         =>    veg_vp%woody                         , & ! Input:  [real(r8) (:)]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
 
          cpool_to_leafc                =>    veg_cf%cpool_to_leafc                , & ! Input:  [real(r8) (:)]
          cpool_to_leafc_storage        =>    veg_cf%cpool_to_leafc_storage        , & ! Input:  [real(r8) (:)]
@@ -98,7 +98,7 @@ subroutine GrowthResp(num_soilp, filter_soilp)
          )
 
       ! Loop through patches
-      ! start pft loop 
+      ! start pft loop
       do fp = 1,num_soilp
 
         p = filter_soilp(fp)

diff --git a/components/elm/src/biogeochem/MaintenanceRespMod.F90 b/components/elm/src/biogeochem/MaintenanceRespMod.F90
@@ -70,7 +70,7 @@ subroutine readMaintenanceRespParams ( ncid )
      call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
      if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__))
      br_mr_Inst = tempr
-     
+
    end subroutine readMaintenanceRespParams
 
   !-----------------------------------------------------------------------
@@ -107,7 +107,7 @@ subroutine MaintenanceResp(bounds, &
 
     associate(                                                        &
          ivt            =>    veg_pp%itype                             , & ! Input:  [integer  (:)   ]  patch vegetation type
-         woody          =>    veg_vp%woody                      , & ! Input:  [real(r8) (:)   ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody          =>    veg_vp%woody                      , & ! Input:  [real(r8) (:)   ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
          br_xr          =>    veg_vp%br_xr                      , & ! Input:  [real(r8) (:)   ]  base rate for excess respiration
          frac_veg_nosno =>    canopystate_vars%frac_veg_nosno_patch , & ! Input:  [integer  (:)   ]  fraction of vegetation not covered by snow (0 OR 1) [-]
          laisun         =>    canopystate_vars%laisun_patch         , & ! Input:  [real(r8) (:)   ]  sunlit projected leaf area index
@@ -160,7 +160,7 @@ subroutine MaintenanceResp(bounds, &
             ! calculate temperature corrections for each soil layer, for use in
             ! estimating fine root maintenance respiration with depth
             tcsoi(c,j) = Q10**((t_soisno(c,j)-SHR_CONST_TKFRZ - 20.0_r8)/10.0_r8)
-        
+
          end do
       end do
 

diff --git a/components/elm/src/biogeochem/NitrogenStateUpdate1Mod.F90 b/components/elm/src/biogeochem/NitrogenStateUpdate1Mod.F90
@@ -130,7 +130,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
     associate(                                                                                           &
          ivt                   => veg_pp%itype                                , & ! Input:  [integer  (:)     ]  pft vegetation type
 
-         woody                 => veg_vp%woody                         , & ! Input:  [real(r8) (:)     ]  binary flag for woody lifeform (1=woody, 0=not woody)
+         woody                 => veg_vp%woody                         , & ! Input:  [real(r8) (:)     ]  woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
 
          cascade_donor_pool    => decomp_cascade_con%cascade_donor_pool    , & ! Input:  [integer  (:)     ]  which pool is C taken from for a given decomposition step
          cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input:  [integer  (:)     ]  which pool is C added to for a given decomposition step
@@ -147,7 +147,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
          do j = 1, nlevdecomp
             do fc = 1,num_soilc
                c = filter_soilc(fc)
-               
+
                ! N deposition and fixation (put all into NH4 pool)
                col_ns%smin_nh4_vr(c,j) = col_ns%smin_nh4_vr(c,j) + col_nf%ndep_to_sminn(c)*dt * ndep_prof(c,j)
                col_ns%smin_nh4_vr(c,j) = col_ns%smin_nh4_vr(c,j) + col_nf%nfix_to_sminn(c)*dt * nfixation_prof(c,j)
@@ -219,7 +219,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
                end do
             end if
          end do
-         
+
          do j = 1, nlevdecomp
             ! column loop
             do fc = 1,num_soilc
@@ -254,8 +254,8 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
 
             end do ! end of column loop
          end do
-         
-      endif  !end if is_active_betr_bgc 
+
+      endif  !end if is_active_betr_bgc
 
       ! forest fertilization
       call get_curr_date(kyr, kmo, kda, mcsec)