Merge pull request ESCOMP#882 from JessicaNeedham/JessicaNeedham-IO-s…

…izeagemortality Add a new fates dimension to track cohort age.
slevis-lmwg · Mar 26, 2020 · 0d93237 · 0d93237
2 parents 5220caa + cad203f
commit 0d93237
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diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.33.0_api.8.1.0
+tag = sci.1.34.0_api.9.0.0
 required = True
 
 [PTCLM]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -774,7 +774,8 @@ sub setup_cmdl_fates_mode {
       }
     } else {
        # dis-allow fates specific namelist items with non-fates runs
-       my @list  = (  "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", 
+	my @list  = (  "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
+		       "use_fates_cohort_age_tracking", 
                       "use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode" );
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -3897,7 +3898,7 @@ sub setup_logic_fates {
     if ($physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", 
-                       "use_fates_inventory_init", "use_fates_logging","fates_parteh_mode" );
+                       "use_fates_inventory_init", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'} );
         }

diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -2641,6 +2641,7 @@ lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr18
 <!-- ===== FATES DEFAULTS =========== -->
 <use_fates_spitfire            use_fates=".true.">.false.</use_fates_spitfire>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
+<use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
 <use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
 <use_fates_logging             use_fates=".true.">.false.</use_fates_logging>

diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -629,9 +629,14 @@ Toggle to turn on the logging module (only relevant if FATES is being used).
 </entry>
 
 <entry id="use_fates_planthydro" type="logical" category="physics"
-        group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on plant hydraulics (only relevant if FATES is on).
-(use_fates_planthydro=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)
+       group="clm_inparm" valid_values="" value=".false.">
+  Toggle to turn on plant hydraulics (only relevant if FATES is on).
+  (use_fates_planthydro=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)
+</entry>
+
+<entry id="use_fates_cohort_age_tracking" type="logical" category="physics"
+       group="clm_inparm" valid_values="" value=".false.">
+  Toggle to turn on cohort age tracking (only relevant if FATES is on).
 </entry>
 
 <entry id="use_fates_ed_st3" type="logical" category="physics"

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1959,6 +1959,16 @@
       <option name="wallclock">00:40:00</option>
     </options>
   </test>
+  <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruGs" testmods="clm/FatesSizeAgeMort">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="hobart" compiler="nag" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>      
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruGs" testmods="clm/FatesPPhys">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/include_user_mods
@@ -0,0 +1 @@
+../FatesColdDef
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/user_nl_clm
@@ -0,0 +1,3 @@
+hist_empty_htapes = .true.
+use_fates_cohort_age_tracking=.true.
+hist_fincl1       = 'M9_SCPF','M10_SCPF','M10_CAPF','NPLANT_CACLS','NPLANT_CAPF', 'M9_SCLS','M10_SCLS','M10_CACLS'
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
@@ -210,6 +210,7 @@ module clm_varctl
   logical, public            :: use_fates_spitfire = .false.           ! true => use spitfire model
   logical, public            :: use_fates_logging = .false.            ! true => turn on logging module
   logical, public            :: use_fates_planthydro = .false.         ! true => turn on fates hydro
+  logical, public            :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking
   logical, public            :: use_fates_ed_st3   = .false.           ! true => static stand structure
   logical, public            :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology
   logical, public            :: use_fates_inventory_init = .false.     ! true => initialize fates from inventory

diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
@@ -221,11 +221,12 @@ subroutine control_init( )
     namelist /clm_inparm/ fates_paramfile, use_fates,   &
           use_fates_spitfire, use_fates_logging,        &
           use_fates_planthydro, use_fates_ed_st3,       &
+          use_fates_cohort_age_tracking,                &
           use_fates_ed_prescribed_phys,                 &
           use_fates_inventory_init,                     &
           fates_inventory_ctrl_filename,                &
           fates_parteh_mode
-
+    
 
     ! CLM 5.0 nitrogen flags
     namelist /clm_inparm/ use_flexibleCN, use_luna
@@ -638,6 +639,7 @@ subroutine control_spmd()
     call mpi_bcast (use_fates_spitfire, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_logging, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_ed_st3, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_ed_prescribed_phys,  1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_inventory_init, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -983,6 +985,7 @@ subroutine control_print ()
        write(iulog, *) '    fates_paramfile = ', fates_paramfile
        write(iulog, *) '    fates_parteh_mode = ', fates_parteh_mode
        write(iulog, *) '    use_fates_planthydro = ', use_fates_planthydro
+       write(iulog, *) '    use_fates_cohort_age_tracking = ', use_fates_cohort_age_tracking
        write(iulog, *) '    use_fates_ed_st3 = ',use_fates_ed_st3
        write(iulog, *) '    use_fates_ed_prescribed_phys = ',use_fates_ed_prescribed_phys
        write(iulog, *) '    use_fates_inventory_init = ',use_fates_inventory_init

diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
@@ -22,7 +22,7 @@ module histFileMod
   use PatchType      , only : patch                
   use EDTypesMod     , only : nclmax
   use EDTypesMod     , only : nlevleaf
-  use FatesInterfaceMod , only : nlevsclass, nlevage
+  use FatesInterfaceMod , only : nlevsclass, nlevage, nlevcoage
   use FatesInterfaceMod , only : nlevheight
   use EDTypesMod        , only : nfsc
   use FatesLitterMod    , only : ncwd
@@ -1071,6 +1071,7 @@ subroutine hist_update_hbuf(bounds)
     do t = 1,ntapes
 !$OMP PARALLEL DO PRIVATE (f, num2d, numdims)
        do f = 1,tape(t)%nflds
+
           numdims = tape(t)%hlist(f)%field%numdims
 
           if ( numdims == 1) then   
@@ -1392,6 +1393,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d)
     ! !USES:
     use subgridAveMod   , only : p2g, c2g, l2g, p2l, c2l, p2c
     use decompMod       , only : BOUNDS_LEVEL_PROC
+    use clm_varctl      , only : iulog
     !
     ! !ARGUMENTS:
     integer, intent(in) :: t            ! tape index
@@ -1442,6 +1444,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d)
     no_snow_behavior    =  tape(t)%hlist(f)%field%no_snow_behavior
     hpindex             =  tape(t)%hlist(f)%field%hpindex
 
+
     if (no_snow_behavior /= no_snow_unset) then
        ! For multi-layer snow fields, build a special output variable that handles
        ! missing snow layers appropriately
@@ -1461,6 +1464,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d)
        call hist_set_snow_field_2d(field, clmptr_ra(hpindex)%ptr, no_snow_behavior, type1d, &
             beg1d, end1d)
     else
+
        field => clmptr_ra(hpindex)%ptr(:,1:num2d)
        field_allocated = .false.
     end if
@@ -2066,17 +2070,20 @@ subroutine htape_create (t, histrest)
     call ncd_defdim(lnfid, 'scale_type_string_length', scale_type_strlen, dimid)
     call ncd_defdim( lnfid, 'levdcmp', nlevdecomp_full, dimid)
 
+
     if(use_fates)then
        call ncd_defdim(lnfid, 'fates_levscag', nlevsclass * nlevage, 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_levcacls', nlevcoage, 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_fates, dimid)
+       call ncd_defdim(lnfid, 'fates_levcapf', nlevcoage*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_fates, dimid)
@@ -2500,6 +2507,9 @@ subroutine htape_timeconst(t, mode)
     use FatesInterfaceMod, only : fates_hdim_levsclass
     use FatesInterfaceMod, only : fates_hdim_pfmap_levscpf
     use FatesInterfaceMod, only : fates_hdim_scmap_levscpf
+    use FatesInterfaceMod, only : fates_hdim_levcoage
+    use FatesInterfaceMod, only : fates_hdim_pfmap_levcapf
+    use FatesInterfaceMod, only : fates_hdim_camap_levcapf
     use FatesInterfaceMod, only : fates_hdim_levage
     use FatesInterfaceMod, only : fates_hdim_levheight
     use FatesInterfaceMod, only : fates_hdim_levpft
@@ -2591,6 +2601,12 @@ subroutine htape_timeconst(t, mode)
                   long_name='FATES pft index of the combined pft-size class dimension', units='-', ncid=nfid(t))
              call ncd_defvar(varname='fates_scmap_levscpf',xtype=ncd_int, dim1name='fates_levscpf', &
                   long_name='FATES size index of the combined pft-size class dimension', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_levcacls', xtype=tape(t)%ncprec, dim1name='fates_levcacls', &
+                  long_name='FATES cohort age class lower bound', units='years', ncid=nfid(t))
+             call ncd_defvar(varname='fates_pftmap_levcapf',xtype=ncd_int, dim1name='fates_levcapf', &
+                  long_name='FATES pft index of the combined pft-cohort age class dimension', units='-', ncid=nfid(t))
+             call ncd_defvar(varname='fates_camap_levcapf',xtype=ncd_int, dim1name='fates_levcapf', &
+                  long_name='FATES cohort age index of the combined pft-cohort age dimension', units='-', ncid=nfid(t))
              call ncd_defvar(varname='fates_levage',xtype=tape(t)%ncprec, dim1name='fates_levage', &
                   long_name='FATES patch age (yr)', ncid=nfid(t))
              call ncd_defvar(varname='fates_levheight',xtype=tape(t)%ncprec, dim1name='fates_levheight', &
@@ -2655,8 +2671,11 @@ subroutine htape_timeconst(t, mode)
              call ncd_io(varname='fates_scmap_levscag',data=fates_hdim_scmap_levscag, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_agmap_levscag',data=fates_hdim_agmap_levscag, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levscls',data=fates_hdim_levsclass, ncid=nfid(t), flag='write')
+             call ncd_io(varname='fates_levcacls',data=fates_hdim_levcoage, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_pftmap_levscpf',data=fates_hdim_pfmap_levscpf, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_scmap_levscpf',data=fates_hdim_scmap_levscpf, ncid=nfid(t), flag='write')
+             call ncd_io(varname='fates_pftmap_levcapf',data=fates_hdim_pfmap_levcapf, ncid=nfid(t), flag='write')
+             call ncd_io(varname='fates_camap_levcapf',data=fates_hdim_camap_levcapf, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levage',data=fates_hdim_levage, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levheight',data=fates_hdim_levheight, ncid=nfid(t), flag='write')
              call ncd_io(varname='fates_levpft',data=fates_hdim_levpft, ncid=nfid(t), flag='write')
@@ -4910,6 +4929,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        num2d = nlevdecomp_full
     case ('fates_levscls')
        num2d = nlevsclass
+    case('fates_levcacls')
+       num2d = nlevcoage
     case ('fates_levpft')
        num2d = numpft_fates
     case ('fates_levage')
@@ -4922,6 +4943,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        num2d = ncwd
     case ('fates_levscpf')
        num2d = nlevsclass*numpft_fates
+    case ('fates_levcapf')
+       num2d = nlevcoage*numpft_fates
     case ('fates_levscag')
        num2d = nlevsclass*nlevage
     case ('fates_levscagpf')
@@ -4974,8 +4997,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
     end select
 
     ! History buffer pointer
-
     hpindex = pointer_index()
+
 
     if (present(ptr_lnd)) then
        l_type1d = grlnd
@@ -4991,6 +5014,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        l_type1d = namel
        l_type1d_out = namel
        clmptr_ra(hpindex)%ptr => ptr_lunit
+
        if (present(set_lake)) then
           do l = bounds%begl,bounds%endl
              if (lun%lakpoi(l)) ptr_lunit(l,:) = set_lake
@@ -5056,6 +5080,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out,
        l_type1d = namep
        l_type1d_out = namep
        clmptr_ra(hpindex)%ptr => ptr_patch
+
        if (present(set_lake)) then
           do p = bounds%begp,bounds%endp
              l =patch%landunit(p)

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
@@ -47,6 +47,7 @@ module CLMFatesInterfaceMod
    use clm_varctl        , only : fates_parteh_mode
    use clm_varctl        , only : use_fates_spitfire
    use clm_varctl        , only : use_fates_planthydro
+   use clm_varctl        , only : use_fates_cohort_age_tracking
    use clm_varctl        , only : use_fates_ed_st3
    use clm_varctl        , only : use_fates_ed_prescribed_phys
    use clm_varctl        , only : use_fates_logging
@@ -244,6 +245,7 @@ subroutine init(this, bounds_proc )
       integer                                        :: pass_ed_prescribed_phys
       integer                                        :: pass_logging
       integer                                        :: pass_planthydro
+      integer                                        :: pass_cohort_age_tracking
       integer                                        :: pass_inventory_init
       integer                                        :: pass_is_restart
       integer                                        :: nc        ! thread index
@@ -339,6 +341,13 @@ subroutine init(this, bounds_proc )
       end if
       call set_fates_ctrlparms('use_planthydro',ival=pass_planthydro)
 
+      if(use_fates_cohort_age_tracking) then
+         pass_cohort_age_tracking = 1
+      else
+         pass_cohort_age_tracking = 0
+      end if
+      call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
+
       if(use_fates_logging) then
          pass_logging = 1
       else
@@ -1946,6 +1955,7 @@ subroutine init_history_io(this,bounds_proc)
    use FatesIOVariableKindMod, only : patch_r8, patch_ground_r8, patch_size_pft_r8
    use FatesIOVariableKindMod, only : site_r8, site_ground_r8, site_size_pft_r8
    use FatesIOVariableKindMod, only : site_size_r8, site_pft_r8, site_age_r8
+   use FatesIOVariableKindMod, only : site_coage_r8, site_coage_pft_r8
    use FatesIOVariableKindMod, only : site_fuel_r8, site_cwdsc_r8, site_scag_r8
    use FatesIOVariableKindMod, only : site_scagpft_r8, site_agepft_r8
    use FatesIOVariableKindMod, only : site_can_r8, site_cnlf_r8, site_cnlfpft_r8
@@ -2081,12 +2091,15 @@ subroutine init_history_io(this,bounds_proc)
                               ptr_patch=this%fates_hist%hvars(ivar)%r82d,    & 
                               default=trim(vdefault))
 
+
         case(site_ground_r8, site_size_pft_r8, site_size_r8, site_pft_r8, &
-             site_age_r8, site_height_r8, site_fuel_r8, site_cwdsc_r8, &
+             site_age_r8, site_height_r8, site_coage_r8,site_coage_pft_r8, &
+             site_fuel_r8, site_cwdsc_r8, &
              site_can_r8,site_cnlf_r8, site_cnlfpft_r8, site_scag_r8, & 
              site_scagpft_r8, site_agepft_r8, site_elem_r8, site_elpft_r8, &
              site_elcwd_r8, site_elage_r8)
 
+
            d_index = this%fates_hist%dim_kinds(dk_index)%dim2_index
            dim2name = this%fates_hist%dim_bounds(d_index)%name
            call hist_addfld2d(fname=trim(vname),units=trim(vunits),         &
@@ -2102,6 +2115,7 @@ subroutine init_history_io(this,bounds_proc)
         end select
 
       end associate
+
    end do
  end subroutine init_history_io
 
@@ -2335,7 +2349,7 @@ end subroutine wrap_hydraulics_drive
  subroutine hlm_bounds_to_fates_bounds(hlm, fates)
 
    use FatesIODimensionsMod, only : fates_bounds_type
-   use FatesInterfaceMod, only : nlevsclass, nlevage
+   use FatesInterfaceMod, only : nlevsclass, nlevage, nlevcoage
    use FatesInterfaceMod, only : nlevheight
    use EDtypesMod,        only : nfsc
    use FatesLitterMod,    only : ncwd
@@ -2366,6 +2380,12 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates)
    fates%size_class_begin = 1
    fates%size_class_end = nlevsclass
 
+   fates%coagepf_class_begin = 1
+   fates%coagepf_class_end = nlevcoage * numpft_fates
+
+   fates%coage_class_begin = 1
+   fates%coage_class_end = nlevcoage
+
    fates%pft_class_begin = 1
    fates%pft_class_end = numpft_fates