Merge pull request #389 from chrislxj/master

New create_test updates and new output variables
CoLM-SYSU · Feb 27, 2025 · ac7665a · ac7665a
2 parents 3dc58e1 + 8701573
commit ac7665a
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Showing 13 changed files with 529 additions and 194 deletions.
diff --git a/main/BGC/MOD_BGC_CNSummary.F90 b/main/BGC/MOD_BGC_CNSummary.F90
@@ -19,10 +19,11 @@ MODULE MOD_BGC_CNSummary
    USE MOD_Namelist, only: DEF_USE_NITRIF, DEF_USE_DiagMatrix
    USE MOD_Vars_PFTimeInvariants, only: pftclass
    USE MOD_Vars_PFTimeVariables, only:irrig_method_p
+   USE MOD_Vars_TimeInvariants, only: BD_all
    USE MOD_BGC_Vars_TimeVariables, only: &
        totlitc, totsomc, totcwdc, decomp_cpools, decomp_cpools_vr, ctrunc_soil,ctrunc_veg, ctrunc_vr, &
        totlitn, totsomn, totcwdn, decomp_npools, decomp_npools_vr, ntrunc_soil,ntrunc_veg, ntrunc_vr, &
-       totvegc, totvegn, totcolc, totcoln, sminn, sminn_vr, &
+       totvegc, totvegn, totcolc, totcoln, sminn, sminn_vr, totsoiln_vr, &
        leafc, frootc, livestemc, deadstemc, livecrootc, deadcrootc, leafc_storage, frootc_storage, livestemc_storage, &
        deadstemc_storage, livecrootc_storage, deadcrootc_storage, leafc_xfer, frootc_xfer, livestemc_xfer, &
        deadstemc_xfer, livecrootc_xfer, deadcrootc_xfer, xsmrpool, &
@@ -262,16 +263,19 @@ SUBROUTINE soilbiogeochem_nitrogenstate_summary(i,nl_soil,dz_soi,ndecomp_pools)
       totcwdn(i) = 0._r8
       sminn(i)   = 0._r8
       ntrunc_soil(i)  = 0._r8
+      totsoiln_vr(1:nl_soil,i) = 0 ! soil total nitrogen (gN/gsoil * 100%)
 
       DO l = 1, ndecomp_pools
          decomp_npools(l,i) = 0._r8
          DO j = 1, nl_soil
             decomp_npools(l,i) = decomp_npools(l,i) + decomp_npools_vr(j,l,i) * dz_soi(j)
+            totsoiln_vr(j,i)   = totsoiln_vr(j,i) + decomp_npools_vr(j,l,i) / (BD_all(j,i) * 1000) * 100 !(unit %)
          ENDDO
       ENDDO
 
       DO j = 1, nl_soil
          sminn(i) = sminn(i) + sminn_vr(j,i) * dz_soi(j)
+         totsoiln_vr(j,i) = totsoiln_vr(j,i) + sminn_vr(j,i) / (BD_all(j,i) * 1000) * 100 !(unit %)
       ENDDO
 
       DO l = 1, ndecomp_pools

diff --git a/main/BGC/MOD_BGC_Vars_TimeVariables.F90 b/main/BGC/MOD_BGC_Vars_TimeVariables.F90
@@ -154,6 +154,7 @@ MODULE MOD_BGC_Vars_TimeVariables
    real(r8), allocatable :: decomp_npools_vr         (:,:,:)  ! vertical resolved: soil decomposition (litter, cwd, soil) nitrogen (gN m-3)
    real(r8), allocatable :: decomp_npools            (:,:)    ! soil decomposition (litter, cwd, soil) nitrogen (gN m-2)
    real(r8), allocatable :: decomp_npools_vr_Cap     (:,:,:)  ! vertical resolved: soil decomposition (litter, cwd, soil organic matter) carbon Capacity (gC m-3)
+   real(r8), allocatable :: totsoiln_vr              (:,:)  ! vertical resolved: total soil nitrogen (%: gN/gSoil*100)
    real(r8), allocatable :: ntrunc_vr                (:,:)    ! currently not used
    real(r8), allocatable :: ntrunc_veg               (:)      ! currently not used
    real(r8), allocatable :: ntrunc_soil              (:)      ! currently not used
@@ -462,6 +463,7 @@ SUBROUTINE allocate_BGCTimeVariables
             allocate (decomp_npools_vr             (nl_soil_full,ndecomp_pools,numpatch)) ; decomp_npools_vr  (:,:,:) = spval
             allocate (decomp_npools                (ndecomp_pools,numpatch))              ; decomp_npools       (:,:) = spval
             allocate (decomp_npools_vr_Cap         (nl_soil_full,ndecomp_pools,numpatch)) ; decomp_npools_vr_Cap(:,:,:) = spval
+            allocate (totsoiln_vr                  (nl_soil,numpatch))                    ; totsoiln_vr         (:,:) = spval
             allocate (ntrunc_vr                    (nl_soil,numpatch))                    ; ntrunc_vr           (:,:) = spval
             allocate (ntrunc_veg                   (numpatch))                            ; ntrunc_veg            (:) = spval
             allocate (ntrunc_soil                  (numpatch))                            ; ntrunc_soil           (:) = spval
@@ -756,6 +758,7 @@ SUBROUTINE deallocate_BGCTimeVariables ()
             deallocate (decomp_npools_vr             )
             deallocate (decomp_npools                )
             deallocate (decomp_npools_vr_Cap         )
+            deallocate (totsoiln_vr                  )
             deallocate (ntrunc_vr                    )
             deallocate (ntrunc_veg                   )
             deallocate (ntrunc_soil                  )
@@ -955,7 +958,8 @@ SUBROUTINE WRITE_BGCTimeVariables (file_restart)
       CALL ncio_write_vector (file_restart, 'altmax_lastyear_indx ', 'patch', landpatch, altmax_lastyear_indx )
 
       CALL ncio_write_vector (file_restart, 'decomp_npools_vr     ', 'soil_full', nl_soil_full, 'ndecomp_pools', ndecomp_pools, &
-                                                                     'patch', landpatch,     decomp_npools_vr)
+                                                                     'patch', landpatch,      decomp_npools_vr)
+      CALL ncio_write_vector (file_restart, 'totsoiln_vr          ', 'soil' ,   nl_soil, 'patch', landpatch, totsoiln_vr )
       IF(DEF_USE_DiagMatrix)THEN
          CALL ncio_write_vector (file_restart, 'decomp_npools_vr_Cap ', 'soil_full', nl_soil_full, 'ndecomp_pools', ndecomp_pools, &
                                                                      'patch', landpatch,     decomp_npools_vr_Cap)
@@ -1118,15 +1122,16 @@ SUBROUTINE READ_BGCTimeVariables (file_restart)
       CALL ncio_read_vector (file_restart, 'altmax_lastyear_indx ', landpatch, altmax_lastyear_indx )
 
       CALL ncio_read_vector (file_restart, 'decomp_npools_vr     ',   nl_soil_full, ndecomp_pools, landpatch, decomp_npools_vr)
+      CALL ncio_read_vector (file_restart, 'totsoiln_vr          ',   nl_soil, landpatch, totsoiln_vr, defval = 1._r8)
       IF(DEF_USE_DiagMatrix)THEN
-         CALL ncio_read_vector (file_restart, 'decomp_npools_vr_Cap ',   nl_soil_full, ndecomp_pools, landpatch, decomp_npools_vr_Cap, defval = 1._r8)
+         CALL ncio_read_vector (file_restart, 'decomp_npools_vr_Cap ',nl_soil_full, ndecomp_pools, landpatch, decomp_npools_vr_Cap, defval = 1._r8)
       ENDIF
-      CALL ncio_read_vector (file_restart, 'ntrunc_vr            ',   nl_soil, landpatch, ntrunc_vr            )
-      CALL ncio_read_vector (file_restart, 'ntrunc_veg           ', landpatch, ntrunc_veg           )
-      CALL ncio_read_vector (file_restart, 'ntrunc_soil          ', landpatch, ntrunc_soil          )
-      CALL ncio_read_vector (file_restart, 'sminn_vr             ',   nl_soil, landpatch, sminn_vr             )
-      CALL ncio_read_vector (file_restart, 'smin_no3_vr          ',   nl_soil, landpatch, smin_no3_vr          )
-      CALL ncio_read_vector (file_restart, 'smin_nh4_vr          ',   nl_soil, landpatch, smin_nh4_vr          )
+      CALL ncio_read_vector (file_restart, 'ntrunc_vr            ',   nl_soil, landpatch, ntrunc_vr  )
+      CALL ncio_read_vector (file_restart, 'ntrunc_veg           ', landpatch, ntrunc_veg            )
+      CALL ncio_read_vector (file_restart, 'ntrunc_soil          ', landpatch, ntrunc_soil           )
+      CALL ncio_read_vector (file_restart, 'sminn_vr             ',   nl_soil, landpatch, sminn_vr   )
+      CALL ncio_read_vector (file_restart, 'smin_no3_vr          ',   nl_soil, landpatch, smin_no3_vr)
+      CALL ncio_read_vector (file_restart, 'smin_nh4_vr          ',   nl_soil, landpatch, smin_nh4_vr)
 
       IF(DEF_USE_NITRIF)THEN
          CALL ncio_read_vector (file_restart, 'tCONC_O2_UNSAT       ',   nl_soil, landpatch, tconc_o2_unsat         )
@@ -1379,8 +1384,9 @@ SUBROUTINE check_BGCTimeVariables ()
 
       CALL check_vector_data ('decomp_npools_vr         ', decomp_npools_vr         )
       CALL check_vector_data ('decomp_npools            ', decomp_npools            )
+      CALL check_vector_data ('totsoiln_vr              ', totsoiln_vr              )
       IF(DEF_USE_DiagMatrix)THEN
-         CALL check_vector_data ('decomp_npools_vr_Cap',decomp_npools_vr_Cap)
+         CALL check_vector_data ('decomp_npools_vr_Cap  ',decomp_npools_vr_Cap      )
       ENDIF
       CALL check_vector_data ('ntrunc_vr                ', ntrunc_vr                )
       CALL check_vector_data ('ntrunc_veg               ', ntrunc_veg               )
@@ -1391,8 +1397,8 @@ SUBROUTINE check_BGCTimeVariables ()
       CALL check_vector_data ('smin_nh4_vr              ', smin_nh4_vr              )
 
       IF(DEF_USE_NITRIF)THEN
-         CALL check_vector_data ('tCONC_O2_UNSAT           ', tconc_o2_unsat )
-         CALL check_vector_data ('tO2_DECOMP_DEPTH_UNSAT   ', to2_decomp_depth_unsat   )
+         CALL check_vector_data ('tCONC_O2_UNSAT           ', tconc_o2_unsat        )
+         CALL check_vector_data ('tO2_DECOMP_DEPTH_UNSAT   ', to2_decomp_depth_unsat)
       ENDIF
 
       CALL check_vector_data ('sminn                    ', sminn                    )

diff --git a/main/MOD_Hist.F90 b/main/MOD_Hist.F90
@@ -1088,6 +1088,46 @@ SUBROUTINE hist_out (idate, deltim, itstamp, etstamp, ptstamp, &
              a_fpi, file_hist, 'f_fpi', itime_in_file, sumarea, filter, &
              'fraction of immobalization','unitless')
 
+         CALL write_history_variable_2d ( DEF_hist_vars%totvegc, &
+             a_totvegc, file_hist, 'f_totvegc', itime_in_file, sumarea, filter, &
+             'total vegetation carbon','gC m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totlitc, &
+             a_totlitc, file_hist, 'f_totlitc', itime_in_file, sumarea, filter, &
+             'total litter carbon','gC m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totsomc, &
+             a_totsomc, file_hist, 'f_totsomc', itime_in_file, sumarea, filter, &
+             'total soil organic carbon','gC m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totcwdc, &
+             a_totcwdc, file_hist, 'f_totcwdc', itime_in_file, sumarea, filter, &
+             'total coarse woody debris carbon','gC m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totcolc, &
+             a_totcolc, file_hist, 'f_totcolc', itime_in_file, sumarea, filter, &
+             'total ecosystem carbon','gC m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totvegn, &
+             a_totvegn, file_hist, 'f_totvegn', itime_in_file, sumarea, filter, &
+             'total vegetation nitrogen','gN m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totlitn, &
+             a_totlitn, file_hist, 'f_totlitn', itime_in_file, sumarea, filter, &
+             'total litter nitrogen','gN m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totsomn, &
+             a_totsomn, file_hist, 'f_totsomn', itime_in_file, sumarea, filter, &
+             'total soil organic nitrogen','gN m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totcwdn, &
+             a_totcwdn, file_hist, 'f_totcwdn', itime_in_file, sumarea, filter, &
+             'total coarse woody debris nitrogen','gN m-2')
+
+         CALL write_history_variable_2d ( DEF_hist_vars%totcoln, &
+             a_totcoln, file_hist, 'f_totcoln', itime_in_file, sumarea, filter, &
+             'total ecosystem nitrogen','gN m-2')
+
          ! autotrophic respiration
          CALL write_history_variable_2d ( DEF_hist_vars%ar , &
              a_ar, file_hist, 'f_ar', itime_in_file, sumarea, filter, &
@@ -1464,6 +1504,11 @@ SUBROUTINE hist_out (idate, deltim, itstamp, etstamp, ptstamp, &
             a_sminn_vr, file_hist, 'f_sminn_vr', itime_in_file, 'soil', 1, nl_soil, &
             sumarea, filter,'mineral nitrogen density in soil layers','gN/m3')
 
+         ! total nitrogen percentage in soil layers
+         CALL write_history_variable_3d ( DEF_hist_vars%totsoiln_vr, &
+            a_totsoiln_vr, file_hist, 'f_totsoiln_vr', itime_in_file, 'soil', 1, nl_soil, &
+            sumarea, filter,'Total nitrogen in soil layers, percentage of total soil nitrogen mass in total soil mass','%')
+
          ! bulk density in soil layers
          CALL write_history_variable_3d ( DEF_hist_vars%BD_all, &
             a_BD_all, file_hist, 'f_BD_all', itime_in_file, 'soil', 1, nl_soil, &

diff --git a/main/MOD_Vars_1DAccFluxes.F90 b/main/MOD_Vars_1DAccFluxes.F90
@@ -172,6 +172,16 @@ MODULE MOD_Vars_1DAccFluxes
    real(r8), allocatable :: a_hr                 (:)
    real(r8), allocatable :: a_fpg                (:)
    real(r8), allocatable :: a_fpi                (:)
+   real(r8), allocatable :: a_totvegc            (:)
+   real(r8), allocatable :: a_totlitc            (:)
+   real(r8), allocatable :: a_totcwdc            (:)
+   real(r8), allocatable :: a_totsomc            (:)
+   real(r8), allocatable :: a_totcolc            (:)
+   real(r8), allocatable :: a_totvegn            (:)
+   real(r8), allocatable :: a_totlitn            (:)
+   real(r8), allocatable :: a_totcwdn            (:)
+   real(r8), allocatable :: a_totsomn            (:)
+   real(r8), allocatable :: a_totcoln            (:)
    real(r8), allocatable :: a_gpp_enftemp        (:) !1
    real(r8), allocatable :: a_gpp_enfboreal      (:) !2
    real(r8), allocatable :: a_gpp_dnfboreal      (:) !3
@@ -323,6 +333,7 @@ MODULE MOD_Vars_1DAccFluxes
    real(r8), allocatable :: a_soil2n_vr   (:,:)
    real(r8), allocatable :: a_soil3n_vr   (:,:)
    real(r8), allocatable :: a_cwdn_vr     (:,:)
+   real(r8), allocatable :: a_totsoiln_vr (:,:)
    real(r8), allocatable :: a_litr1cCap_vr(:,:)
    real(r8), allocatable :: a_litr2cCap_vr(:,:)
    real(r8), allocatable :: a_litr3cCap_vr(:,:)
@@ -566,6 +577,16 @@ SUBROUTINE allocate_acc_fluxes
             allocate (a_hr                 (numpatch))
             allocate (a_fpg                (numpatch))
             allocate (a_fpi                (numpatch))
+            allocate (a_totvegc            (numpatch))
+            allocate (a_totlitc            (numpatch))
+            allocate (a_totcwdc            (numpatch))
+            allocate (a_totsomc            (numpatch))
+            allocate (a_totcolc            (numpatch))
+            allocate (a_totvegn            (numpatch))
+            allocate (a_totlitn            (numpatch))
+            allocate (a_totcwdn            (numpatch))
+            allocate (a_totsomn            (numpatch))
+            allocate (a_totcoln            (numpatch))
             allocate (a_gpp_enftemp        (numpatch)) !1
             allocate (a_gpp_enfboreal      (numpatch)) !2
             allocate (a_gpp_dnfboreal      (numpatch)) !3
@@ -719,6 +740,7 @@ SUBROUTINE allocate_acc_fluxes
             allocate (a_soil2n_vr   (1:nl_soil,       numpatch))
             allocate (a_soil3n_vr   (1:nl_soil,       numpatch))
             allocate (a_cwdn_vr     (1:nl_soil,       numpatch))
+            allocate (a_totsoiln_vr (1:nl_soil,       numpatch))
             allocate (a_sminn_vr    (1:nl_soil,       numpatch))
             allocate (decomp_vr_tmp (1:nl_soil,       numpatch))
 
@@ -962,6 +984,16 @@ SUBROUTINE deallocate_acc_fluxes ()
             deallocate (a_hr                 )
             deallocate (a_fpg                )
             deallocate (a_fpi                )
+            deallocate (a_totvegc            )
+            deallocate (a_totlitc            )
+            deallocate (a_totcwdc            )
+            deallocate (a_totsomc            )
+            deallocate (a_totcolc            )
+            deallocate (a_totvegn            )
+            deallocate (a_totlitn            )
+            deallocate (a_totcwdn            )
+            deallocate (a_totsomn            )
+            deallocate (a_totcoln            )
             deallocate (a_gpp_enftemp        ) !1
             deallocate (a_gpp_enfboreal      ) !2
             deallocate (a_gpp_dnfboreal      ) !3
@@ -1115,6 +1147,7 @@ SUBROUTINE deallocate_acc_fluxes ()
             deallocate (a_soil2n_vr   )
             deallocate (a_soil3n_vr   )
             deallocate (a_cwdn_vr     )
+            deallocate (a_totsoiln_vr )
             deallocate (a_sminn_vr    )
             deallocate (decomp_vr_tmp )
             deallocate (a_litr1cCap_vr)
@@ -1359,6 +1392,16 @@ SUBROUTINE FLUSH_acc_fluxes ()
             a_hr                 (:) = spval
             a_fpg                (:) = spval
             a_fpi                (:) = spval
+            a_totvegc            (:) = spval
+            a_totlitc            (:) = spval
+            a_totcwdc            (:) = spval
+            a_totsomc            (:) = spval
+            a_totcolc            (:) = spval
+            a_totvegn            (:) = spval
+            a_totlitn            (:) = spval
+            a_totcwdn            (:) = spval
+            a_totsomn            (:) = spval
+            a_totcoln            (:) = spval
             a_gpp_enftemp        (:) = spval
             a_gpp_enfboreal      (:) = spval
             a_gpp_dnfboreal      (:) = spval
@@ -1508,6 +1551,7 @@ SUBROUTINE FLUSH_acc_fluxes ()
             a_soil2n_vr    (:,:) = spval
             a_soil3n_vr    (:,:) = spval
             a_cwdn_vr      (:,:) = spval
+            a_totsoiln_vr  (:,:) = spval
 
             a_litr1cCap_vr (:,:) = spval
             a_litr2cCap_vr (:,:) = spval
@@ -1844,6 +1888,16 @@ SUBROUTINE accumulate_fluxes
             CALL acc1d (decomp_hr          , a_hr                  )
             CALL acc1d (fpg                , a_fpg                 )
             CALL acc1d (fpi                , a_fpi                 )
+            CALL acc1d (totvegc            , a_totvegc             )
+            CALL acc1d (totlitc            , a_totlitc             )
+            CALL acc1d (totcwdc            , a_totcwdc             )
+            CALL acc1d (totsomc            , a_totsomc             )
+            CALL acc1d (totcolc            , a_totcolc             )
+            CALL acc1d (totvegn            , a_totvegn             )
+            CALL acc1d (totlitn            , a_totlitn             )
+            CALL acc1d (totcwdn            , a_totcwdn             )
+            CALL acc1d (totsomn            , a_totsomn             )
+            CALL acc1d (totcoln            , a_totcoln             )
             CALL acc1d (gpp_enftemp        , a_gpp_enftemp         )
             CALL acc1d (gpp_enfboreal      , a_gpp_enfboreal       )
             CALL acc1d (gpp_dnfboreal      , a_gpp_dnfboreal       )
@@ -2077,6 +2131,7 @@ SUBROUTINE accumulate_fluxes
                ENDDO
             ENDDO
             CALL acc2d (decomp_vr_tmp, a_cwdn_vr     )
+            CALL acc2d (totsoiln_vr  , a_totsoiln_vr )
 
             DO i = 1, numpatch
                DO j = 1, nl_soil

diff --git a/run/scripts/SummaryTest.bash b/run/scripts/SummaryTest.bash
@@ -34,9 +34,11 @@ SummaryTest()
    fi
 
 TestCaseLists=$2
+TestType=$4
 nfile=`cat $TestCaseLists|wc -l`
-for CaseName in `awk '{print $1}' $TestCaseLists`
+for ListCase in `awk '{print $1}' $TestCaseLists`
 do
+   CaseName=${TestType}_${ListCase}
    echo $CaseName
    for Var in $Varlist
    do
@@ -79,12 +81,13 @@ done
 }
 
 
-while getopts ":hn:f:i:" options ;
+while getopts ":hn:f:i:t:" options ;
 do
     case $options in
       n) TestName="$OPTARG" ;;
       f) TestCaseList="$OPTARG"  ;;
       i) Varlist="$OPTARG" ;;
+      t) TestType="$OPTARG" ;;
       h) Help; exit;;
       *) echo "invalid option: $@";exit ;;
     esac
@@ -102,6 +105,18 @@ else
    fi
 fi
 
+if [ -z "${TestType}" ]; then
+   echo
+   echo Error: TestType '(-t)' is missing
+   exit
+else
+   case $TestType in
+      SMS);;
+      RES);;
+      *)echo Error: TestType $TestType is invalid
+   esac
+fi
+
 if [ -z "$Varlist" ];then
    Varlist="All"
 else
@@ -111,8 +126,10 @@ else
       Submit_Mksrfdata);;
       Submit_Mkinidata);;
       Submit_Case);;
+      Submit_Restart);;
+      RestartMatch);;
       *) echo "invalid Var option: $Varlist"; exit;;
    esac
 fi
 
-SummaryTest $TestName $TestCaseList $Varlist
+SummaryTest $TestName $TestCaseList $Varlist $TestType