Ngee arctic im4/pft physiology

cime_config/tests.py

@@ -74,6 +74,14 @@
             )
         },
 
+    "e3sm_land_mytests" : {
+        "share" : True,
+        "time"  : "0:45:00",
+        "tests" : (
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-arcticpft_codetest_I1850CNPRDCTCBC",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-arcticpft_onsetgdd_I1850CNPRDCTCBC"
+            )
+        },
 
     "e3sm_land_developer" : {
         "share" : True,
@@ -93,6 +101,8 @@
             "SMS_Ly2_P1x1.1x1_smallvilleIA.IELMCNCROP.elm-per_crop",
             "SMS.r05_r05.IELM.elm-topounit",
             "ERS.ELM_USRDAT.I1850ELM.elm-usrdat",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-arcticpft_codetest_I1850CNPRDCTCBC",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-arcticpft_onsetgdd_I1850CNPRDCTCBC",
             "ERS.f09_f09.IELM.elm-lnd_rof_2way",
             "ERS.r05_r05.IELM.elm-V2_ELM_MOSART_features"
             )

components/elm/bld/namelist_files/namelist_definition.xml

@@ -1801,6 +1801,15 @@ Specifies the method for decomposing CLM grids across processors.
     pflotran file prefix.
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- Namelist options related to plant phenology                                               -->
+<!-- ========================================================================================  -->
+
+<entry id="onset_gdd_extension" type="logical" category="default_settings"
+    group="elm_inparm" valid_values="">
+    Runtime flag to turn on/off stress_deciduous PFT's onset gdd summation end from summer solstice to offset starting.
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- Namelist options related to Variably Saturated Flow Model (VSFM)                          -->
 <!-- ========================================================================================  -->

components/elm/cime_config/testdefs/testmods_dirs/elm/arcticpft_codetest_I1850CNPRDCTCBC/shell_commands

@@ -0,0 +1,12 @@
+./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=1980
+./xmlchange DATM_CLMNCEP_YR_END=2015
+./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
+./xmlchange NTASKS=6
+echo "
+ taxmode = 'cycle','extend','extend'
+">>user_nl_datm

components/elm/cime_config/testdefs/testmods_dirs/elm/arcticpft_codetest_I1850CNPRDCTCBC/user_nl_elm

@@ -0,0 +1,12 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
+!
+! below is a new physioloy file example, from Sulman et al 2021, 
+! by adding a few parameters into default (clm_params_c211124.nc) as following: 
+! (1) pft-level controls of Nfixation by individual plant NPP: Nfix_NPP_c1, Nfix_NPP_c2 
+! (2) MR reduction during dormant seasons: dormant_mr_factor, domant_mr_temp
+! (3) pft-level 'lwtop_ann' for live woody tissue turnover: lwtop_pfts 
+! (4) plant rhizomes added as part of roots for all PFTs incl. graminoids: rhizome_long
+! 
+! but, all with default values (i.e. won't change simualtion results from default)
+! NOTE: have to copy this file here to $DIN_LOC_ROOT/lnd/clm2/paramdata/ in your system.
+ paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c211124arctic.nc'

components/elm/cime_config/testdefs/testmods_dirs/elm/arcticpft_onsetgdd_I1850CNPRDCTCBC/shell_commands

@@ -0,0 +1,16 @@
+./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=1980
+./xmlchange DATM_CLMNCEP_YR_END=2015
+./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
+./xmlchange NTASKS=6
+echo "
+ taxmode = 'cycle','extend','extend'
+">>user_nl_datm
+# a long run of test for onset_gdd summation ending in arctic,
+# but have to xmlchange the following after ./case.setup called
+# ./xmlchange --file env_test.xml STOP_N=200
+# ./xmlchange --file env_test.xml STOP_OPTION=nyears

components/elm/cime_config/testdefs/testmods_dirs/elm/arcticpft_onsetgdd_I1850CNPRDCTCBC/user_nl_elm

@@ -0,0 +1,16 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
+!
+! below is a new physioloy file example, from Sulman et al 2021, 
+! by adding a few parameters into default (clm_params_c211124.nc) as following: 
+! (1) pft-level controls of Nfixation by individual plant NPP: Nfix_NPP_c1, Nfix_NPP_c2 
+! (2) MR reduction during dormant seasons: dormant_mr_factor, domant_mr_temp
+! (3) pft-level 'lwtop_ann' for live woody tissue turnover: lwtop_pfts 
+! (4) plant rhizomes added as part of roots for all PFTs incl. graminoids: rhizome_long
+! 
+! but, all with default values (i.e. won't change simualtion results from default)
+! NOTE: have to copy this file here to $DIN_LOC_ROOT/lnd/clm2/paramdata/ in your system, if not yet.
+ paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c211124arctic.nc'
+!
+! and also need to turn on a namelist option.
+! use_onset_gdd_ext = .true.
+

components/elm/src/biogeochem/AllocationMod.F90

@@ -832,9 +832,12 @@ subroutine Allocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soilp
                  (f3*(1._r8-f4)*(1._r8+f2))/cpdw
 
          else
-            c_allometry(p) = 1._r8+g1+f1+f1*g1
+            c_allometry(p) = 1._r8+g1+f1+f1*g1+f3+f3*g1  ! B Sulman: Let graminoids allocate rhizomes (all livecroot) using stem_leaf parameter
             n_allometry(p) = 1._r8/cnl + f1/cnfr
+            if(cnlw>0) n_allometry(p) = n_allometry(p) + f3/cnlw ! Rhizomes
             p_allometry(p) = 1._r8/cpl + f1/cpfr
+            if(cplw>0) p_allometry(p) = p_allometry(p) + f3/cplw ! Rhizomes
+
          end if
          plant_ndemand(p) = availc(p)*(n_allometry(p)/c_allometry(p))
          plant_pdemand(p) = availc(p)*(p_allometry(p)/c_allometry(p))
@@ -2589,6 +2592,10 @@ subroutine Allocation3_PlantCNPAlloc (bounds            , &
             cpool_to_livecrootc_storage(p) = nlc * f2 * f3 * f4 * (1._r8 - fcur)
             cpool_to_deadcrootc(p)         = nlc * f2 * f3 * (1._r8 - f4) * fcur
             cpool_to_deadcrootc_storage(p) = nlc * f2 * f3 * (1._r8 - f4) * (1._r8 - fcur)
+         else
+            ! Assume "stem" allocation in graminoids goes to rhizomes which are all live wood (B Sulman)
+            cpool_to_livecrootc(p)         = nlc * f3 * fcur
+            cpool_to_livecrootc_storage(p) = nlc * f3 * (1._r8 - fcur)
          end if
          if (ivt(p) >= npcropmin) then ! skip 2 generic crops
             cpool_to_livestemc(p)          = nlc * f3 * f4 * fcur
@@ -2642,6 +2649,10 @@ subroutine Allocation3_PlantCNPAlloc (bounds            , &
             npool_to_livecrootn_storage(p) = (nlc * f2 * f3 * f4 / cnlw) * (1._r8 - fcur)
             npool_to_deadcrootn(p)         = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * fcur
             npool_to_deadcrootn_storage(p) = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur)
+         elseif (cnlw > 0.0_r8) then
+            ! Assume "stem" allocation in graminoids goes to rhizomes which are all live wood (B Sulman)
+            npool_to_livecrootn(p)         = (nlc * f3 / cnlw ) * fcur
+            npool_to_livecrootn_storage(p) = (nlc * f3 / cnlw ) * (1._r8 - fcur)
          end if
          if (ivt(p) >= npcropmin) then ! skip 2 generic crops
             cng = graincn(ivt(p))
@@ -2686,6 +2697,10 @@ subroutine Allocation3_PlantCNPAlloc (bounds            , &
             ppool_to_livecrootp_storage(p) = (nlc * f2 * f3 * f4 / cplw) * (1._r8 -fcur)
             ppool_to_deadcrootp(p)         = (nlc * f2 * f3 * (1._r8 - f4) / cpdw)* fcur
             ppool_to_deadcrootp_storage(p) = (nlc * f2 * f3 * (1._r8 - f4) / cpdw)* (1._r8 - fcur)
+         elseif (cplw > 0.0_r8) then
+            ! Assume "stem" allocation in graminoids goes to rhizomes which are all live wood (B Sulman)
+            ppool_to_livecrootp(p)         = (nlc * f3 / cplw ) * fcur
+            ppool_to_livecrootp_storage(p) = (nlc * f3 / cplw ) * (1._r8 - fcur)
          end if
          if (ivt(p) >= npcropmin) then ! skip 2 generic crops
             cpg = graincp(ivt(p))
@@ -2711,10 +2726,10 @@ subroutine Allocation3_PlantCNPAlloc (bounds            , &
          ! growth is assigned here.
 
          gresp_storage = cpool_to_leafc_storage(p) + cpool_to_frootc_storage(p)
-         if (woody(ivt(p)) == 1._r8) then
+         gresp_storage = gresp_storage + cpool_to_livecrootc_storage(p) !Graminoid rhizomes (B Sulman)
+         if (woody(ivt(p)) >= 1.0_r8) then
             gresp_storage = gresp_storage + cpool_to_livestemc_storage(p)
             gresp_storage = gresp_storage + cpool_to_deadstemc_storage(p)
-            gresp_storage = gresp_storage + cpool_to_livecrootc_storage(p)
             gresp_storage = gresp_storage + cpool_to_deadcrootc_storage(p)
          end if
          if (ivt(p) >= npcropmin) then ! skip 2 generic crops

components/elm/src/biogeochem/CarbonIsoFluxMod.F90

@@ -131,6 +131,11 @@ subroutine CarbonIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
            isoveg_cf%livecrootc_to_deadcrootc      , veg_cf%livecrootc_to_deadcrootc, &
            isoveg_cs%livecrootc                   , veg_cs%livecrootc, &
            num_soilp                                            , filter_soilp, 1._r8, 0, isotope)
+
+      call CarbonIsoFluxCalc(&
+           isoveg_cf%livecrootc_to_litter      , veg_cf%livecrootc_to_litter, &
+           isoveg_cs%livecrootc                   , veg_cs%livecrootc, &
+           num_soilp                                            , filter_soilp, 1._r8, 0, isotope)
 
       call CarbonIsoFluxCalc(&
            isoveg_cf%leaf_curmr                    , veg_cf%leaf_curmr, &
@@ -937,9 +942,11 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, &
 
          leaf_prof                 =>    cnstate_vars%leaf_prof_patch                  , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of leaves
          froot_prof                =>    cnstate_vars%froot_prof_patch                 , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of fine roots
+         croot_prof                =>    cnstate_vars%croot_prof_patch                 , & ! Input:  [real(r8) (:,:) ]  (1/m) profile of coarse roots                     
 
          leafc_to_litter           =>    veg_cf%leafc_to_litter         , & ! Input:  [real(r8) (:)   ]
          frootc_to_litter          =>    veg_cf%frootc_to_litter        , & ! Input:  [real(r8) (:)   ]
+         livecrootc_to_litter          =>    veg_cf%livecrootc_to_litter        , & ! Input:  [real(r8) (:)   ]                                                    
          phenology_c_to_litr_met_c =>    col_cf%phenology_c_to_litr_met_c , & ! InOut:  [real(r8) (:,:) ]  C fluxes associated with phenology (litterfall and crop) to litter metabolic pool (gC/m3/s)
          phenology_c_to_litr_cel_c =>    col_cf%phenology_c_to_litr_cel_c , & ! InOut:  [real(r8) (:,:) ]  C fluxes associated with phenology (litterfall and crop) to litter cellulose pool (gC/m3/s)
          phenology_c_to_litr_lig_c =>    col_cf%phenology_c_to_litr_lig_c   & ! InOut:  [real(r8) (:,:) ]  C fluxes associated with phenology (litterfall and crop) to litter lignin pool (gC/m3/s)
@@ -968,6 +975,14 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, &
                           + frootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j)
                      phenology_c_to_litr_lig_c(c,j) = phenology_c_to_litr_lig_c(c,j) &
                           + frootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j)
+
+                     ! nonwoody rhizome litter carbon fluxes
+                     phenology_c_to_litr_met_c(c,j) = phenology_c_to_litr_met_c(c,j) &
+                          + livecrootc_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * croot_prof(p,j)
+                     phenology_c_to_litr_cel_c(c,j) = phenology_c_to_litr_cel_c(c,j) &
+                          + livecrootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * croot_prof(p,j)
+                     phenology_c_to_litr_lig_c(c,j) = phenology_c_to_litr_lig_c(c,j) &
+                          + livecrootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * croot_prof(p,j)
                   end if
                end if