Merge pull request ESCOMP#766 from rgknox/rgknox-parteh-api-v2

interface changes for fates-parteh (nutrients)

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.27.1_api.7.3.0
+tag = sci.1.30.0_api.8.0.0
 required = True
 
 [PTCLM]

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -3,9 +3,11 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_spitfire= .true.
-hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
+hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN_ELEM','LITTER_OUT_ELEM',
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF',
-   'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN'
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF',
+   'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN',
+   'LITTER_FINES_AG_ELEM','LITTER_FINES_BG_ELEM','LITTER_CWD_AG_ELEM','LITTER_CWD_BG_ELEM',
+   'SEED_BANK'

cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm

@@ -27,4 +27,6 @@ hist_fincl1       = 'NCL_BY_AGE','NPATCH_BY_AGE','BIOMASS_BY_AGE','NPP_BY_AGE','
                     'NPP_LEAF_UNDERSTORY_SCLS','NPP_FROOT_UNDERSTORY_SCLS','NPP_BSW_UNDERSTORY_SCLS',
                     'NPP_BDEAD_UNDERSTORY_SCLS','NPP_BSEED_UNDERSTORY_SCLS','NPP_STORE_UNDERSTORY_SCLS','RDARK_UNDERSTORY_SCLS',
                     'LIVESTEM_MR_UNDERSTORY_SCLS','LIVECROOT_MR_UNDERSTORY_SCLS','FROOT_MR_UNDERSTORY_SCLS','RESP_G_UNDERSTORY_SCLS',
-                    'RESP_M_UNDERSTORY_SCLS'
+                    'RESP_M_UNDERSTORY_SCLS','LITTER_IN_ELEM','LITTER_OUT_ELEM','SEED_BANK_ELEM','SEEDS_IN_LOCAL_ELEM','SEEDS_IN_EXTERN_ELEM',
+		    'SEED_GERM_ELEM','SEED_DECAY','CBALANCE_ERROR_FATES','ERROR_FATES','LITTER_FINES_AG_ELEM','LITTER_FINES_BG_ELEM','LITTER_CWD_BG_ELEM',
+		    'LITTER_CWD_AG_ELEM','LITTER_CWD'

cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm

@@ -6,5 +6,5 @@ hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT'
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF',
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF',
    'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN'

cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm

@@ -2,4 +2,4 @@ hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT'
    'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
    'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT',
-   'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC'
+   'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR'

src/main/histFileMod.F90

@@ -24,8 +24,10 @@ module histFileMod
   use EDTypesMod     , only : nlevleaf
   use FatesInterfaceMod , only : nlevsclass, nlevage
   use FatesInterfaceMod , only : nlevheight
-  use EDTypesMod     , only : nfsc, ncwd
-  use FatesInterfaceMod , only : numpft_ed => numpft
+  use EDTypesMod        , only : nfsc
+  use FatesLitterMod    , only : ncwd
+  use EDTypesMod        , only : num_elements_fates => num_elements
+  use FatesInterfaceMod , only : numpft_fates => numpft
   use ncdio_pio 
 
   !
@@ -191,6 +193,9 @@ module histFileMod
      integer :: beg1d_out                      ! on-node 1d hbuf pointer start index
      integer :: end1d_out                      ! on-node 1d hbuf pointer end index
      integer :: num1d_out                      ! size of hbuf first dimension (all nodes)
+     integer :: numdims                        ! the actual number of dimensions, this allows
+                                               ! for 2D arrays, where the second dimension is allowed
+                                               ! to be 1
      integer :: num2d                          ! size of hbuf second dimension (e.g. number of vertical levels)
      integer :: hpindex                        ! history pointer index 
      character(len=scale_type_strlen) :: p2c_scale_type       ! scale factor when averaging patch to column
@@ -306,7 +311,7 @@ subroutine hist_printflds()
   end subroutine hist_printflds
 
   !-----------------------------------------------------------------------
-  subroutine masterlist_addfld (fname, type1d, type1d_out, &
+  subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, &
         type2d, num2d, units, avgflag, long_name, hpindex, &
         p2c_scale_type, c2l_scale_type, l2g_scale_type, &
         no_snow_behavior)
@@ -322,6 +327,7 @@ subroutine masterlist_addfld (fname, type1d, type1d_out, &
     !
     ! !ARGUMENTS:
     character(len=*), intent(in)  :: fname            ! field name
+    integer         , intent(in)  :: numdims          ! number of dimensions
     character(len=*), intent(in)  :: type1d           ! 1d data type
     character(len=*), intent(in)  :: type1d_out       ! 1d output type
     character(len=*), intent(in)  :: type2d           ! 2d output type
@@ -400,6 +406,7 @@ subroutine masterlist_addfld (fname, type1d, type1d_out, &
     masterlist(f)%field%type1d         = type1d
     masterlist(f)%field%type1d_out     = type1d_out
     masterlist(f)%field%type2d         = type2d
+    masterlist(f)%field%numdims        = numdims
     masterlist(f)%field%num2d          = num2d
     masterlist(f)%field%hpindex        = hpindex
     masterlist(f)%field%p2c_scale_type = p2c_scale_type
@@ -1054,17 +1061,20 @@ subroutine hist_update_hbuf(bounds)
     integer :: t                   ! tape index
     integer :: f                   ! field index
     integer :: num2d               ! size of second dimension (e.g. number of vertical levels)
+    integer :: numdims             ! number of dimensions
     character(len=*),parameter :: subname = 'hist_update_hbuf'
     character(len=hist_dim_name_length) :: type2d     ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)"]
     !-----------------------------------------------------------------------
 
     do t = 1,ntapes
 !$OMP PARALLEL DO PRIVATE (f, num2d)
        do f = 1,tape(t)%nflds
-          num2d = tape(t)%hlist(f)%field%num2d
-          if ( num2d == 1) then   
+          numdims = tape(t)%hlist(f)%field%numdims
+
+          if ( numdims == 1) then   
              call hist_update_hbuf_field_1d (t, f, bounds)
           else
+             num2d = tape(t)%hlist(f)%field%num2d
              call hist_update_hbuf_field_2d (t, f, bounds, num2d)
           end if
        end do
@@ -2056,18 +2066,22 @@ subroutine htape_create (t, histrest)
 
     if(use_fates)then
        call ncd_defdim(lnfid, 'fates_levscag', nlevsclass * nlevage, dimid)
-       call ncd_defdim(lnfid, 'fates_levscagpf', nlevsclass * nlevage * numpft_ed, dimid)
-       call ncd_defdim(lnfid, 'fates_levagepft', nlevage * numpft_ed, dimid)
+       call ncd_defdim(lnfid, 'fates_levscagpf', nlevsclass * nlevage * numpft_fates, dimid)
+       call ncd_defdim(lnfid, 'fates_levagepft', nlevage * numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levscls', nlevsclass, dimid)
-       call ncd_defdim(lnfid, 'fates_levpft', numpft_ed, dimid)
+       call ncd_defdim(lnfid, 'fates_levpft', numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levage', nlevage, dimid)
        call ncd_defdim(lnfid, 'fates_levheight', nlevheight, dimid)
        call ncd_defdim(lnfid, 'fates_levfuel', nfsc, dimid)
        call ncd_defdim(lnfid, 'fates_levcwdsc', ncwd, dimid)
-       call ncd_defdim(lnfid, 'fates_levscpf', nlevsclass*numpft_ed, dimid)
+       call ncd_defdim(lnfid, 'fates_levscpf', nlevsclass*numpft_fates, dimid)
        call ncd_defdim(lnfid, 'fates_levcan', nclmax, dimid)
        call ncd_defdim(lnfid, 'fates_levcnlf', nlevleaf * nclmax, dimid)
-       call ncd_defdim(lnfid, 'fates_levcnlfpf', nlevleaf * nclmax * numpft_ed, dimid)
+       call ncd_defdim(lnfid, 'fates_levcnlfpf', nlevleaf * nclmax * numpft_fates, dimid)
+       call ncd_defdim(lnfid, 'fates_levelem', num_elements_fates, dimid)
+       call ncd_defdim(lnfid, 'fates_levelpft', num_elements_fates * numpft_fates, dimid)
+       call ncd_defdim(lnfid, 'fates_levelcwd', num_elements_fates * ncwd, dimid)
+       call ncd_defdim(lnfid, 'fates_levelage', num_elements_fates * nlevage, dimid)
     end if
 
     if ( .not. lhistrest )then
@@ -2502,6 +2516,15 @@ subroutine htape_timeconst(t, mode)
     use FatesInterfaceMod, only : fates_hdim_canmap_levcnlfpf
     use FatesInterfaceMod, only : fates_hdim_lfmap_levcnlfpf
     use FatesInterfaceMod, only : fates_hdim_pftmap_levcnlfpf
+    use FatesInterfaceMod, only : fates_hdim_levelem
+    use FatesInterfaceMod, only : fates_hdim_elmap_levelpft
+    use FatesInterfaceMod, only : fates_hdim_pftmap_levelpft
+    use FatesInterfaceMod, only : fates_hdim_elmap_levelcwd
+    use FatesInterfaceMod, only : fates_hdim_cwdmap_levelcwd
+    use FatesInterfaceMod, only : fates_hdim_elmap_levelage
+    use FatesInterfaceMod, only : fates_hdim_agemap_levelage
+
+
     !
     ! !ARGUMENTS:
     integer, intent(in) :: t              ! tape index
@@ -2598,6 +2621,20 @@ subroutine htape_timeconst(t, mode)
                    long_name='FATES pft map into patch age x pft', units='-', ncid=nfid(t))
              call ncd_defvar(varname='fates_agmap_levagepft', xtype=ncd_int, dim1name='fates_levagepft', &
                    long_name='FATES age-class map into patch age x pft', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_levelem',xtype=ncd_int, dim1name='fates_levelem', &
+                   long_name='FATES element (C,N,P,...) identifier', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_elmap_levelpft', xtype=ncd_int, dim1name='fates_levelpft', &
+                   long_name='FATES element map into element x pft   ', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_pftmap_levelpft', xtype=ncd_int, dim1name='fates_levelpft', &
+                   long_name='FATES pft map into element x pft', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_elmap_levelcwd', xtype=ncd_int, dim1name='fates_levelcwd', &
+                   long_name='FATES element map into element x cwd', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_cwdmap_levelcwd', xtype=ncd_int, dim1name='fates_levelcwd', &
+                   long_name='FATES cwd map into element x cwd', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_elmap_levelage', xtype=ncd_int, dim1name='fates_levelage', &
+                   long_name='FATES element map into age x pft', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_agemap_levelage', xtype=ncd_int, dim1name='fates_levelage', &
+                   long_name='FATES element map into age x pft', units='-', ncid=nfid(t))
 
           end if
 
@@ -2633,7 +2670,14 @@ subroutine htape_timeconst(t, mode)
              call ncd_io(varname='fates_agmap_levscagpft',data=fates_hdim_agmap_levscagpft, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_pftmap_levscagpft',data=fates_hdim_pftmap_levscagpft, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_pftmap_levagepft',data=fates_hdim_pftmap_levagepft, ncid=nfid(t), flag='write')
-             call ncd_io(varname='fates_agmap_levagepft',data=fates_hdim_agmap_levagepft, ncid=nfid(t), flag='write')             
+             call ncd_io(varname='fates_agmap_levagepft',data=fates_hdim_agmap_levagepft, ncid=nfid(t), flag='write')
+             call ncd_io(varname='fates_levelem',data=fates_hdim_levelem, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_elmap_levelpft',data=fates_hdim_elmap_levelpft, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_pftmap_levelpft',data=fates_hdim_pftmap_levelpft, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_elmap_levelcwd',data=fates_hdim_elmap_levelcwd, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_cwdmap_levelcwd',data=fates_hdim_cwdmap_levelcwd, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_elmap_levelage',data=fates_hdim_elmap_levelage, ncid=nfid(t),flag='write')
+             call ncd_io(varname='fates_agemap_levelage',data=fates_hdim_agemap_levelage, ncid=nfid(t),flag='write')
           end if
 
        endif
@@ -2879,6 +2923,7 @@ subroutine hfields_write(t, mode)
     integer :: num2d                     ! hbuf second dimension size
     integer :: nt                        ! time index
     integer :: ier                       ! error status
+    integer :: numdims                   ! number of dimensions
     character(len=avgflag_strlen) :: avgflag  ! time averaging flag
     character(len=max_chars) :: long_name! long name
     character(len=max_chars) :: units    ! units
@@ -2922,6 +2967,7 @@ subroutine hfields_write(t, mode)
        end1d_out  = tape(t)%hlist(f)%field%end1d_out
        num1d_out  = tape(t)%hlist(f)%field%num1d_out
        type2d     = tape(t)%hlist(f)%field%type2d
+       numdims    = tape(t)%hlist(f)%field%numdims
        num2d      = tape(t)%hlist(f)%field%num2d
        nt         = tape(t)%ntimes
 
@@ -2954,7 +3000,7 @@ subroutine hfields_write(t, mode)
           endif
 
           if (dim2name == 'undefined') then
-             if (num2d == 1) then
+             if (numdims == 1) then
                 call ncd_defvar(ncid=nfid(t), varname=varname, xtype=tape(t)%ncprec, &
                      dim1name=dim1name, dim2name='time', &
                      long_name=long_name, units=units, cell_method=avgstr, &
@@ -2966,7 +3012,7 @@ subroutine hfields_write(t, mode)
                      missing_value=spval, fill_value=spval)
              end if
           else
-             if (num2d == 1) then
+             if (numdims == 1) then
                 call ncd_defvar(ncid=nfid(t), varname=varname, xtype=tape(t)%ncprec, &
                      dim1name=dim1name, dim2name=dim2name, dim3name='time', &
                      long_name=long_name, units=units, cell_method=avgstr, &
@@ -2987,7 +3033,7 @@ subroutine hfields_write(t, mode)
 
           ! Allocate dynamic memory
 
-          if (num2d == 1) then
+          if (numdims == 1) then
              allocate(hist1do(beg1d_out:end1d_out), stat=ier)
              if (ier /= 0) then
                 write(iulog,*) trim(subname),' ERROR: allocation'
@@ -2998,7 +3044,7 @@ subroutine hfields_write(t, mode)
 
           ! Write history output.  Always output land and ocean runoff on xy grid.
 
-          if (num2d == 1) then
+          if (numdims == 1) then
              call ncd_io(flag='write', varname=varname, &
                   dim1name=type1d_out, data=hist1do, ncid=nfid(t), nt=nt)
           else
@@ -3009,7 +3055,7 @@ subroutine hfields_write(t, mode)
 
           ! Deallocate dynamic memory
 
-          if (num2d == 1) then
+          if (numdims == 1) then
              deallocate(hist1do)
           end if
 
@@ -4667,10 +4713,11 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, &
 
     ! Add field to masterlist
 
-    call masterlist_addfld (fname=trim(fname), type1d=l_type1d, type1d_out=l_type1d_out, &
-         type2d='unset', num2d=1, &
-         units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, &
-         p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, l2g_scale_type=scale_type_l2g)
+    call masterlist_addfld (fname=trim(fname), numdims=1, type1d=l_type1d, & 
+          type1d_out=l_type1d_out, type2d='unset', num2d=1, &
+          units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, &
+          p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & 
+          l2g_scale_type=scale_type_l2g)
 
     l_default = 'active'
     if (present(default)) then
@@ -4786,7 +4833,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     case ('fates_levscls')
        num2d = nlevsclass
     case ('fates_levpft')
-       num2d = numpft_ed
+       num2d = numpft_fates
     case ('fates_levage')
        num2d = nlevage
     case ('fates_levheight')
@@ -4796,23 +4843,31 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     case ('fates_levcwdsc')
        num2d = ncwd
     case ('fates_levscpf')
-       num2d = nlevsclass*numpft_ed
+       num2d = nlevsclass*numpft_fates
     case ('fates_levscag')
        num2d = nlevsclass*nlevage
     case ('fates_levscagpf')
-       num2d = nlevsclass*nlevage*numpft_ed
+       num2d = nlevsclass*nlevage*numpft_fates
     case ('fates_levagepft')
-       num2d = nlevage*numpft_ed
+       num2d = nlevage*numpft_fates
     case ('fates_levcan')
        num2d = nclmax
     case ('fates_levcnlf')
        num2d = nlevleaf * nclmax
     case ('fates_levcnlfpf')
-       num2d = nlevleaf * nclmax * numpft_ed
+       num2d = nlevleaf * nclmax * numpft_fates
     case ('ltype')
        num2d = max_lunit
     case ('natpft')
        num2d = natpft_size
+    case ('fates_levelem')
+       num2d = num_elements_fates
+    case ('fates_levelpft')
+       num2d = num_elements_fates*numpft_fates
+    case ('fates_levelcwd')
+       num2d = num_elements_fates*ncwd
+    case ('fates_levelage')
+       num2d = num_elements_fates*nlevage
     case('cft')
        if (cft_size > 0) then
           num2d = cft_size
@@ -4974,12 +5029,12 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
 
     ! Add field to masterlist
 
-    call masterlist_addfld (fname=trim(fname), type1d=l_type1d, type1d_out=l_type1d_out, &
-         type2d=type2d, num2d=num2d, &
-         units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, &
-         p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, l2g_scale_type=scale_type_l2g, &
-         no_snow_behavior=no_snow_behavior)
-
+    call masterlist_addfld (fname=trim(fname), numdims=2, type1d=l_type1d, & 
+          type1d_out=l_type1d_out, type2d=type2d, num2d=num2d, &
+          units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, &
+          p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & 
+          l2g_scale_type=scale_type_l2g, no_snow_behavior=no_snow_behavior)
+    
     l_default = 'active'
     if (present(default)) then
        l_default = default