Complete the FATES-CLM nitrogen coupling

bld/CLMBuildNamelist.pm

@@ -1687,10 +1687,10 @@ sub process_namelist_inline_logic {
   }
   setup_logic_cnmatrix($opts,  $nl_flags, $definition, $defaults, $nl, $envxml_ref);
   setup_logic_spinup($opts,  $nl_flags, $definition, $defaults, $nl);
-  setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_fates($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);
 
@@ -3303,7 +3303,7 @@ sub setup_logic_supplemental_nitrogen {
   } 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, $nl,
-		  'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'});
+		  'suplnitro', 'fates_parteh_mode'=>$nl->get_value('fates_parteh_mode'));
   }
   #
   # Error checking for suplnitro
@@ -3322,6 +3322,18 @@ sub setup_logic_supplemental_nitrogen {
         $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" );
       }
     }
+
+    my $parteh_mode = $nl->get_value('fates_parteh_mode');
+    if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
+                        "and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active. " .
+                        "Change suplnitro back to ALL");
+    }
+    if ( ($parteh_mode == 2) &&  ($suplnitro !~ /NONE/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to NONE, FATES is on, " .
+                        "and FATES-SP is not active, but fates_parteh_mode is 2, so Nitrogen is active; " .
+                        "change suplnitro back to NONE");
+    }
   }
 }
 
@@ -4787,14 +4799,6 @@ sub setup_logic_fates {
                     'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
                     'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
 
-        my $suplnitro = $nl->get_value('suplnitro');
-        my $parteh_mode = $nl->get_value('fates_parteh_mode');
-        if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
-          $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
-                            "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" .
-                            "Change suplnitro back to ALL");
-        }
-
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
         #

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -156,10 +156,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <megan_use_gamma_sm>.true.</megan_use_gamma_sm>
 <megan_min_gamma_sm>0.0d00</megan_min_gamma_sm>
 
-<!-- Supplmental Nitrogen mode -->
-<suplnitro use_cn=".true." >NONE</suplnitro>
-<suplnitro use_fates=".true." >ALL</suplnitro>
-
 <!-- Albedo for glaciers -->
 <albice               >0.50,0.30</albice>
 <albice phys="clm4_5" >0.60,0.40</albice>
@@ -2467,6 +2463,9 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <use_fates_fixed_biogeog        use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
 <fates_history_dimlevel         use_fates=".true.">2,2</fates_history_dimlevel>
 
+<!-- Supplmental Nitrogen mode -->
+<suplnitro >NONE</suplnitro>
+<suplnitro fates_parteh_mode="1" >ALL</suplnitro>
 
 <!-- =========================================  -->
 <!-- Defaults for dynamic subgrid               -->

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands

@@ -1,11 +1,9 @@
 SRCDIR=`./xmlquery SRCROOT --value`
 CASEDIR=`./xmlquery CASEROOT --value`
 FATESDIR=$SRCDIR/src/fates/
-FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_np.nc
+FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_p.nc
 
 ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
 
-$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_cnp_prescribed_nuptake --val 1.0 --allpfts
-
 $FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_cnp_prescribed_puptake --val 1.0 --allpfts
 

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm

@@ -1,4 +1,4 @@
-fates_paramfile = '$CASEROOT/fates_params_prt2_prescribed_np.nc'
+fates_paramfile = '$CASEROOT/fates_params_prt2_prescribed_p.nc'
 fates_parteh_mode = 2
 hist_fincl1       = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
 'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF',

src/biogeochem/CNDriverMod.F90

@@ -478,7 +478,7 @@ subroutine CNDriverNoLeaching(bounds,
                                      cnveg_carbonflux_inst,cnveg_nitrogenstate_inst,cnveg_nitrogenflux_inst,   &
                                      soilbiogeochem_carbonflux_inst,&
                                      soilbiogeochem_state_inst,soilbiogeochem_nitrogenstate_inst,              &
-                                     soilbiogeochem_nitrogenflux_inst,canopystate_inst)
+                                     soilbiogeochem_nitrogenflux_inst,canopystate_inst, clm_fates)
      call t_stopf('soilbiogeochemcompetition')
 
     ! distribute the available N between the competing patches  on the basis of 

src/biogeochem/CNNDynamicsMod.F90

@@ -239,10 +239,7 @@ subroutine CNNFixation(num_soilc, filter_soilc, &
             if(col%is_fates(c))then
                s = clm_fates%f2hmap(clump_index)%hsites(c)
                ! %ema_npp is Smoothed [gc/m2/yr]
-               !npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp/(dayspyr*secspday)
-               ! FATES N cycling is not yet active, so runs are supplemented anyway
-               ! this will be added when FATES N cycling is completed.
-               npp = 0._r8
+               npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp / (dayspyr * secspday)
             else
                npp = col_lag_npp(c)
             end if
@@ -262,9 +259,7 @@ subroutine CNNFixation(num_soilc, filter_soilc, &
 
             if(col%is_fates(c))then
                s = clm_fates%f2hmap(clump_index)%hsites(c)
-               !npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp 
-               ! See above regarding FATES and N fixation
-               npp = 0._r8
+               npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp
             else 
                npp = cannsum_npp(c)
             end if

src/main/clm_varctl.F90

@@ -324,8 +324,8 @@ 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 => carbon only
-                                                                        ! 2 => C+N+P (not enabled yet)
+  integer, public            :: fates_parteh_mode = -9                  ! = 1 indicated by fates_c_only is carbon only
+                                                                        ! = 2 indicated by fates_cn is C+N (P not enabled)
                                                                         ! no others enabled
   integer, public            :: fates_spitfire_mode = 0                
                                                                         ! 0 for no fire; 1 for constant ignitions;

src/main/controlMod.F90

@@ -42,7 +42,7 @@ module controlMod
   use CNSharedParamsMod                , only: use_fun, use_matrixcn
   use CIsoAtmTimeseriesMod             , only: use_c14_bombspike, atm_c14_filename, use_c13_timeseries, atm_c13_filename
   use SoilBiogeochemDecompCascadeConType, only : use_soil_matrixcn
-  use SoilBiogeochemCompetitionMod     , only: suplnitro, suplnNon
+  use SoilBiogeochemCompetitionMod     , only: suplnitro, suplnNon, suplnAll
   use SoilBiogeochemLittVertTranspMod  , only: som_adv_flux, max_depth_cryoturb
   use SoilBiogeochemVerticalProfileMod , only: surfprof_exp
   use SoilBiogeochemNitrifDenitrifMod  , only: no_frozen_nitrif_denitrif
@@ -51,6 +51,7 @@ module controlMod
   use CanopyFluxesMod                  , only: CanopyFluxesReadNML
   use shr_drydep_mod                   , only: n_drydep
   use clm_varctl
+  use PRTGenericMod, only : fates_cn, fates_c_only
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -490,12 +491,18 @@ subroutine control_init(dtime)
              use_fates_bgc = .true.
           end if
 
-          if (fates_parteh_mode == 1 .and. suplnitro == suplnNon .and. use_fates_bgc )then
-             write(iulog,*) ' When FATES with fates_parteh_mode == 1 (ie carbon only mode),'
+          if (fates_parteh_mode == fates_c_only .and. suplnitro == suplnNon .and. use_fates_bgc )then
+             write(iulog,*) ' When fates_parteh_mode == fates_c_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=1 must have suplnitro set to suplnAll.'//&
+             call endrun(msg=' ERROR: fates_parteh_mode=fates_c_only must have suplnitro set to suplnAll.'//&
+                   errMsg(sourcefile, __LINE__))
+          end if
+          if (fates_parteh_mode == fates_cn .and. suplnitro == suplnAll .and. use_fates_bgc )then
+             write(iulog,*) ' When fates_parteh_mode == fates_cn,'
+             write(iulog,*) '  you must have supplemental nitrogen turned off.'
+             call endrun(msg=' ERROR: fates_parteh_mode=fates_cn must have suplnitro set to suplnNon.'//&
                    errMsg(sourcefile, __LINE__))
           end if