name changes (WIP)

bld/CLMBuildNamelist.pm

@@ -3325,12 +3325,12 @@ sub setup_logic_supplemental_nitrogen {
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) {
       # If this is non-fates, non-sp and crop is active
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-		  'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
+                 'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
 
   } elsif ( $nl_flags->{'bgc_mode'} eq "fates" && not &value_is_true( $nl_flags->{'use_fates_sp'})  ) {
       # Or... if its fates but not fates-sp
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-		  'suplnitro', 'fates_parteh_mode'=>$nl->get_value('fates_parteh_mode'));
+                 'suplnitro', 'fates_parteh_mode'=>remove_leading_and_trailing_quotes($nl->get_value('fates_parteh_mode')));
   }
   #
   # Error checking for suplnitro
@@ -3351,15 +3351,15 @@ sub setup_logic_supplemental_nitrogen {
     }
 
     my $parteh_mode = $nl->get_value('fates_parteh_mode');
-    if ( ($parteh_mode == 1) && ($suplnitro !~ /ALL/) ) {
+    if ( ($parteh_mode =~ /carbon_only/i) && ($suplnitro !~ /ALL/i) ) {
       $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
-                        "and fates_parteh_mode is 1, so Nitrogen is not active; " .
+                        "and fates_parteh_mode = $parteh_mode, so Nitrogen is not active; " .
                         "change suplnitro back to ALL");
     }
-    if ( ($parteh_mode == 2) && &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+    if ( ($parteh_mode =~ /carbon_nitrogen/i) && &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
       $log->fatal_error("FATES is on, " .
-                        "FATES-SP is active, but fates_parteh_mode is 2, so Nitrogen is active; " .
-                        "change fates_parteh_mode to 1 or do not use FATES-SP");
+                        "FATES-SP is active, but fates_parteh_mode = $parteh_mode, so Nitrogen is active; " .
+                        "change fates_parteh_mode to carbon_only or do not use FATES-SP");
     }
   }
 }

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2675,7 +2675,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <use_fates_luh                  use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
 <use_fates_luh                  use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
 <use_fates_luh                  use_fates=".true."                                >.false.</use_fates_luh>
-<fates_parteh_mode              use_fates=".true.">1</fates_parteh_mode>
+<fates_parteh_mode              use_fates=".true.">carbon_only</fates_parteh_mode>
 <fates_seeddisp_cadence         use_fates=".true.">0</fates_seeddisp_cadence>
 <use_fates_nocomp               use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
 <use_fates_nocomp               use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
@@ -2687,7 +2687,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 
 <!-- Supplmental Nitrogen mode -->
 <suplnitro >NONE</suplnitro>
-<suplnitro fates_parteh_mode="1" >ALL</suplnitro>
+<suplnitro fates_parteh_mode="carbon_only" >ALL</suplnitro>
 
 <!-- =========================================  -->
 <!-- Defaults for dynamic subgrid               -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -713,8 +713,8 @@ Toggle to turn on the FATES model
 Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
 </entry>
 
-<entry id="fates_parteh_mode" type="integer" category="physics"
-        group="clm_inparm" valid_values="1,2">
+<entry id="fates_parteh_mode" type="char*256" category="physics"
+       group="clm_inparm" valid_values="carbon_only,carbon_nitrogen">
 Switch deciding which nutrient model to use in FATES.
 (Only relevant if FATES is on)
 </entry>

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm

@@ -1,4 +1,4 @@
-fates_parteh_mode = 2
+fates_parteh_mode = 'carbon_nitrogen'
 hist_fincl1       = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
 'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF',
 'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2_synthN/user_nl_clm

@@ -1,4 +1,4 @@
-fates_parteh_mode = 2
+fates_parteh_mode = 'carbon_nitrogen'
 hist_fincl1       = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
 'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF',
 'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',

src/main/clm_varctl.F90

@@ -324,9 +324,16 @@ module clm_varctl
 
   integer, public            :: fates_seeddisp_cadence = iundef         ! 0 => no seed dispersal
                                                                         ! 1, 2, 3 => daily, monthly, or yearly dispersal
-  integer, public            :: fates_parteh_mode = -9                  ! = 1 indicated by fates_c_only is carbon only
-                                                                        ! = 2 indicated by fates_cnp is C+N+P, though clm cannot enable phosphorus yet, so clm needs fates_cnp_prescribed_puptake > 1 (recommended value 10) in the fates paramfile
-                                                                        ! no others enabled
+  character(len=256), public :: fates_parteh_mode = ''                  ! FATES Plant Allocation Reactions and Transport Hypotheses
+                                                                        ! = carbon_only : Cycle carbon in FATES only
+                                                                        ! = carbon_nitrogen: Cycle both carbon and nitrogen
+                                                                        ! in FATES. FATES will cycle phosphorus as well,
+                                                                        ! to do this, FATES will generate synthetic uptake
+                                                                        ! conditions to make sure that phosphorus is saturated
+                                                                        ! in the plant stores
+                                                                        ! so clm needs fates_cnp_prescribed_puptake > 1
+                                                                        ! (recommended value 10) in the fates paramfile
+
   integer, public            :: fates_spitfire_mode = 0                
                                                                         ! 0 for no fire; 1 for constant ignitions;
                                                                         ! > 1 for external data (lightning and/or anthropogenic ignitions)

src/main/clm_varpar.F90

@@ -53,8 +53,16 @@ module clm_varpar
   integer, public, parameter :: mxpft       =  78     ! maximum number of PFT's for any mode;
   integer, public, parameter :: mxsowings   =   1     ! maximum number of crop growing seasons to begin in any year;
   integer, public            :: mxharvests            ! maximum number of crop harvests in any year
-                                                      ! (allows for multiple harvests in a calendar year in case harvest occurs near
+                                                      ! (allows for multiple harvests in a calendar
+                                                      ! year in case harvest occurs near
                                                       ! beginning/end of year);
+
+  ! These strings define the clm-fates coupling, i.e. which chemical species
+  ! are cycled between the two, see corresponding values for fates_parteh_mode:
+  ! bld/namelist_files/namelist_definition_ctsm.xml
+  character(len=256), public, parameter :: clmfates_carbon_only = 'carbon_only'
+  character(len=256), public, parameter :: clmfates_carbon_nitrogen = 'carbon_nitrogen'
+
   ! FIX(RF,032414) might we set some of these automatically from reading pft-physiology?
   integer, public, parameter :: nlayer      =   3     ! number of VIC soil layer --Added by AWang
   integer, public    :: nlayert               ! number of VIC soil layer + 3 lower thermal layers

src/main/controlMod.F90

@@ -20,6 +20,8 @@ module controlMod
   use decompInitMod                    , only: clump_pproc
   use clm_varcon                       , only: h2osno_max
   use clm_varpar                       , only: maxpatch_glc, numrad, nlevsno
+  use clm_varpar                       , only: clmfates_carbon_only
+  use clm_varpar                       , only: clmfates_carbon_nitrogen
   use fileutils                        , only: getavu, relavu, get_filename
   use histFileMod                      , only: max_tapes, max_namlen
   use histFileMod                      , only: hist_empty_htapes, hist_dov2xy, hist_avgflag_pertape, hist_type1d_pertape
@@ -51,7 +53,7 @@ module controlMod
   use CanopyFluxesMod                  , only: CanopyFluxesReadNML
   use shr_drydep_mod                   , only: n_drydep
   use clm_varctl
-  use PRTGenericMod, only : fates_cnp, fates_c_only
+
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -492,19 +494,19 @@ subroutine control_init(dtime)
              use_fates_bgc = .true.
           end if
 
-          if (fates_parteh_mode == fates_c_only .and. suplnitro == suplnNon)then
-             write(iulog,*) ' When fates_parteh_mode == fates_c_only,'
+          if (trim(fates_parteh_mode) == trim(clmfates_carbon_only) .and. suplnitro == suplnNon)then
+             write(iulog,*) ' When fates_parteh_mode == carbon_only,'
              write(iulog,*) '  you must have supplemental nitrogen turned on, there will be'
              write(iulog,*) '  no nitrogen dynamics with the plants, and therefore no'
              write(iulog,*) '  meaningful limitations to nitrogen.'
-             call endrun(msg=' ERROR: fates_parteh_mode=fates_c_only must have suplnitro set to suplnAll.'//&
+             call endrun(msg=' ERROR: fates_parteh_mode=carbon_only must have suplnitro set to suplnAll.'//&
                    errMsg(sourcefile, __LINE__))
           end if
-          if (fates_parteh_mode == fates_cnp .and. use_fates_sp )then
-             write(iulog,*) ' When fates_parteh_mode == fates_cnp,'
+          if (trim(fates_parteh_mode) == trim(clmfates_carbon_nitrogen) .and. use_fates_sp )then
+             write(iulog,*) ' When fates_parteh_mode == carbon_nirogen,'
              write(iulog,*) '  you must have use_fates_bgc and not use_fates_sp.'
-             write(iulog,*) ' When you have use_fates_sp, then fates_parteh_mode should equal fates_c_only.'
-             call endrun(msg=' ERROR: fates_parteh_mode=fates_cnp and use_fates_sp are inconsistent.'//&
+             write(iulog,*) ' When you have use_fates_sp, then fates_parteh_mode should equal carbon_only.'
+             call endrun(msg=' ERROR: fates_parteh_mode=carbon_nitrogen and use_fates_sp are inconsistent.'//&
                    errMsg(sourcefile, __LINE__))
           end if
 
@@ -856,7 +858,7 @@ subroutine control_spmd()
     call mpi_bcast (flandusepftdat, len(flandusepftdat) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (use_fates_managed_fire, 1, MPI_LOGICAL, 0, mpicom, ier)
 
-    call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier)
+    call mpi_bcast (fates_parteh_mode, len(fates_parteh_mode), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fates_seeddisp_cadence, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (fates_history_dimlevel, 2, MPI_INTEGER, 0, mpicom, ier)
 

src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

@@ -176,8 +176,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
                                          soilbiogeochem_nitrogenflux_inst,canopystate_inst, clm_fates)
     !
     ! !USES:
-    use PRTGenericMod, only : fates_cnp
     use clm_varctl       , only: fates_parteh_mode, allocate_carbon_only, iulog
+    use clm_varpar       , only: clmfates_carbon_only,clmfates_carbon_nitrogen
     use clm_varpar       , only: nlevdecomp, ndecomp_cascade_transitions
     use clm_varpar       , only: i_cop_mic, i_oli_mic
     use clm_varcon       , only: nitrif_n2o_loss_frac
@@ -345,7 +345,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
                do j = 1, nlevdecomp
                   plant_ndemand_vr(c,j) = 0._r8
 
-                  if (fates_parteh_mode == fates_cnp) then
+                  if (trim(fates_parteh_mode) == trim(clmfates_carbon_nitrogen)) then
                      do f = 1, n_pcomp
                         ft = clm_fates%fates(ci)%bc_out(s)%ft_index(f)
 
@@ -612,7 +612,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
                do j = 1, nlevdecomp
                   plant_ndemand_vr(c,j) = 0._r8
 
-                  if (fates_parteh_mode == fates_cnp) then
+                  if (trim(fates_parteh_mode) == trim(clmfates_carbon_nitrogen))then
                      do f = 1, n_pcomp
                         ft = clm_fates%fates(ci)%bc_out(s)%ft_index(f)
 
@@ -1094,7 +1094,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
                s = clm_fates%f2hmap(ci)%hsites(c)
                n_pcomp = clm_fates%fates(ci)%bc_out(s)%num_plant_comps
 
-               ! if fates_parteh_mode /= fates_cnp then plant_ndemand = 0 and this if-statement gets skipped
+               ! if fates_parteh_mode /= clmfates_carbon_nitrogen then
+               ! plant_ndemand = 0 and this if-statement gets skipped
                if ( plant_ndemand(c) > tiny(plant_ndemand(c)) ) then
                   do f = 1, n_pcomp
                      ft = clm_fates%fates(ci)%bc_out(s)%ft_index(f)

src/utils/clmfates_interfaceMod.F90

@@ -46,7 +46,7 @@ module CLMFatesInterfaceMod
    use CNProductsMod     , only : cn_products_type
    use clm_varctl        , only : iulog
    use clm_varctl        , only : fates_parteh_mode
-   use PRTGenericMod     , only : fates_cnp
+   use PRTGenericMod     , only : carbon_only,carbon_nitrogen_phosphorus
    use clm_varctl        , only : use_fates
    use clm_varctl        , only : fates_spitfire_mode
    use clm_varctl        , only : use_fates_managed_fire
@@ -93,6 +93,8 @@ module CLMFatesInterfaceMod
    use clm_varpar        , only : nlevdecomp
    use clm_varpar        , only : nlevdecomp_full
    use clm_varpar        , only : nlevsoi
+   use clm_varpar        , only : clmfates_carbon_only
+   use clm_varpar        , only : clmfates_carbon_nitrogen
    use PhotosynthesisMod , only : photosyns_type
    use atm2lndType       , only : atm2lnd_type
    use SurfaceAlbedoType , only : surfalb_type
@@ -314,6 +316,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches)
      integer             :: pass_use_sp
      integer             :: pass_masterproc
      integer             :: pass_use_luh2
+     integer             :: pass_parteh_mode
      logical             :: verbose_output
 
      call t_startf('fates_globals1')
@@ -364,8 +367,24 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches)
         end if
         call set_fates_ctrlparms('use_luh2',ival=pass_use_luh2)
 
-
-        call set_fates_ctrlparms('parteh_mode',ival=fates_parteh_mode)
+        if(trim(fates_parteh_mode)==trim(clmfates_carbon_only))then
+           pass_parteh_mode = carbon_only
+        elseif(trim(fates_parteh_mode)==trim(clmfates_carbon_nitrogen))then
+           ! FATES has NO carbon_nitrogen mode. It cycles
+           ! either carbon alone, or carbon with both nutrients
+           ! If we want to couple nitrogen, we tell FATES
+           ! to use synthetic uptake conditions for phosphorus, which
+           ! most likely will be ample so that P stores in plants
+           ! are saturated and non-limiting
+           pass_parteh_mode = carbon_nitrogen_phosphorus
+        else
+           write(iulog,*) 'FATES coupling mode must be either'
+           write(iulog,*) trim(clmfates_carbon_only),' or '
+           write(iulog,*) trim(clmfates_carbon_nitrogen)
+           write(iulog,*) 'you specified: ',trim(fates_parteh_mode)
+           call endrun(msg=errMsg(sourcefile, __LINE__))
+        end if
+        call set_fates_ctrlparms('parteh_mode',ival=pass_parteh_mode)
 
      end if
 
@@ -2809,7 +2828,7 @@ subroutine wrap_WoodProducts(this, bounds_clump, num_soilc, filter_soilc, &
            this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod100c
 
       ! If N cycling is on
-      if (fates_parteh_mode == fates_cnp) then
+      if ( trim(fates_parteh_mode)==trim(clmfates_carbon_nitrogen) ) then
 
          n_products_inst%hrv_deadstem_to_prod10_grc(g) = &
               n_products_inst%hrv_deadstem_to_prod10_grc(g) + &