Complete the FATES-CLM nitrogen coupling

bld/CLMBuildNamelist.pm

@@ -1706,10 +1706,10 @@ 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);
 
@@ -3330,7 +3330,7 @@ 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
@@ -3349,6 +3349,18 @@ 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/) ) {
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
+                        "and fates_parteh_mode is 1, so Nitrogen is not active; " .
+                        "change suplnitro back to ALL");
+    }
+    if ( ($parteh_mode == 2) && &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");
+    }
   }
 }
 
@@ -4926,14 +4938,6 @@ sub setup_logic_fates {
                     'use_fates_managed_fire'=>$nl->get_value('use_fates_managed_fire'),
                     'use_fates_sp'=>$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

@@ -220,10 +220,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <megan_use_gamma_sm>.false.</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>
@@ -2689,6 +2685,9 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/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/testlist_clm.xml

@@ -3849,7 +3849,27 @@
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment">Exact restart debug test covering Fates CNP nutrients mode.</option>
+      <option name="comment">Exact restart debug test covering Fates CNP nutrients mode (P still prescribed in clm).</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesCruRsGs" testmods="clm/FatesColdPRT2_suplnAll">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment">Exact restart debug test covering Fates CNP nutrients mode with suplnitro set to ALL.</option>
+    </options>
+  </test>
+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesCruRsGs" testmods="clm/FatesColdPRT2_synthN">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment">Exact restart debug test covering Fates CNP nutrients mode with both P and N prescribed to replicate what happened before the CLM-FATES-CN coupling.</option>
     </options>
   </test>
   <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="HIST_DATM%CRUv7_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV_SESP" testmods="clm/FatesColdLandUse">

cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm

@@ -27,7 +27,7 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_DEMOTION_CARBONFLUX', 'FATES_PROMOTION_CARBONFLUX',
 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
-'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
+'FATES_CBALANCE_ERROR', 'FATES_LEAF_ALLOC',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
 'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU',

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands

@@ -1,13 +1,10 @@
 SRCDIR=`./xmlquery SRCROOT --value`
 CASEDIR=`./xmlquery CASEROOT --value`
 FATESDIR=$SRCDIR/src/fates/
-
-FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_np.json
+FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_p.json
 
 cp $FATESDIR/parameter_files/fates_params_default.json $FATESPARAMFILE
 
-$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_cnp_prescribed_nuptake --values 1.0 --indices all
-
-$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_cnp_prescribed_puptake --values 1.0 --indices all
+$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_cnp_prescribed_puptake --values 10.0 --indices all
 
-echo "fates_paramfile = '$FATESPARAMFILE'" >> $CASEDIR/user_nl_clm
+echo "fates_paramfile = '$FATESPARAMFILE'" >> $CASEDIR/user_nl_clm

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2_suplnAll/include_user_mods

@@ -0,0 +1,3 @@
+../nofireemis
+../cn_conly
+../FatesColdPRT2

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2_synthN/include_user_mods

@@ -0,0 +1,3 @@
+../Fates
+../FatesCold
+../FatesSetupParamBuild/

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2_synthN/shell_commands

@@ -0,0 +1,11 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates/
+FATESPARAMFILE=$CASEDIR/fates_params_prt2_prescribed_np.json
+
+cp $FATESDIR/parameter_files/fates_params_default.json $FATESPARAMFILE
+
+$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_cnp_prescribed_puptake --values 10.0 --indices all
+$FATESDIR/tools/modify_fates_paramfile.py --overwrite --fin $FATESPARAMFILE --param fates_cnp_prescribed_nuptake --values 10.0 --indices all
+
+echo "fates_paramfile = '$FATESPARAMFILE'" >> $CASEDIR/user_nl_clm

cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2_synthN/user_nl_clm

@@ -0,0 +1,12 @@
+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',
+'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',
+'FATES_NEFFLUX','FATES_NDEMAND','FATES_NFIX_SYM','FATES_STOREN','FATES_STOREN_TF',
+'FATES_VEGN','FATES_SAPWOODN','FATES_LEAFN','FATES_FROOTN','FATES_REPRON','FATES_VEGN_SZPF',
+'FATES_LEAFN_SZPF','FATES_FROOTN_SZPF','FATES_SAPWOODN_SZPF','FATES_STOREN_SZPF','FATES_STOREN_TF_CANOPY_SZPF',
+'FATES_STOREN_TF_USTORY_SZPF','FATES_REPRON_SZPF','FATES_STOREP','FATES_STOREP_TF','FATES_VEGP','FATES_SAPWOODP',
+'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND',
+'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF',
+'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF',
+'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF'

src/biogeochem/CNDriverMod.F90

@@ -479,7 +479,7 @@ 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

@@ -239,17 +239,14 @@ 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
             else
-               npp = col_lag_npp(c)
+               ! need to put npp in units of gC/m^2/year here first
+               npp = col_lag_npp(c) * secspday * dayspyr
             end if
 
             if (npp /= spval) then
-               ! need to put npp in units of gC/m^2/year here first
-               t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp *(secspday * dayspyr))))/(secspday * dayspyr)  
+               t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp))) / (secspday * dayspyr)
                nfix_to_sminn(c) = max(0._r8,t)
             else
                nfix_to_sminn(c) = 0._r8
@@ -262,14 +259,13 @@ 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
+               ! %ema_npp is Smoothed [gc/m2/yr]
+               npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp
             else 
                npp = cannsum_npp(c)
             end if
 
-            t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp)))/(secspday * dayspyr)
+            t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp))) / (secspday * dayspyr)
             nfix_to_sminn(c) = max(0._r8,t)
          end do
       endif

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_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
   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_cnp, fates_c_only
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -491,12 +492,19 @@ 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)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_cnp .and. use_fates_sp )then
+             write(iulog,*) ' When fates_parteh_mode == fates_cnp,'
+             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.'//&
                    errMsg(sourcefile, __LINE__))
           end if