migrate FATES to use the normal BGC call sequence

Externals_CLM.cfg

@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.66.1_api.25.5.0
+repo_url = https://github.com/rgknox/fates
+branch = clm-cbalance
 required = True
 
 [externals_description]

bld/CLMBuildNamelist.pm

@@ -91,11 +91,13 @@ OPTIONS
                                     This toggles off the namelist variable: use_cn
                                 bgc   = Carbon Nitrogen with methane, nitrification, vertical soil C,
                                         CENTURY or MIMICS decomposition
-                                    This toggles on the namelist variables:
+				        This toggles on the namelist variables:
                                           use_cn, use_lch4, use_nitrif_denitrif
-                                fates = FATES/Ecosystem Demography with below ground BGC
-                                    This toggles on the namelist variables:
-                                          use_fates
+				fates = FATES/Ecosystem Demography with below ground BGC
+				        CENTURY or MIMICS decomposition
+                                        This toggles on the namelist variables:
+				        use_fates. use_lch4 and use_nitrif_denitrif are optional
+
                               (Only for CLM4.5/CLM5.0)
      -[no-]chk_res            Also check [do NOT check] to make sure the resolution and
                               land-mask is valid.
@@ -763,26 +765,12 @@ sub setup_cmdl_fates_mode {
           }
        }
 
-      # The following variables may be set by the user and are compatible with use_fates
-      # no need to set defaults, covered in a different routine
-      my @list  = (  "use_lch4" );
-      foreach my $var ( @list ) {
-	  if ( defined($nl->get_value($var))  ) {
-	      $nl_flags->{$var} = $nl->get_value($var);
-	      $val = $nl_flags->{$var};
-	      my $group = $definition->get_group_name($var);
-	      $nl->set_variable_value($group, $var, $val);
-	      if (  ! $definition->is_valid_value( $var, $val ) ) {
-		  my @valid_values   = $definition->get_valid_values( $var );
-		  $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
-	      }
-	  }
-      }
     } else {
        # dis-allow fates specific namelist items with non-fates runs
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
-                      "use_fates_cohort_age_tracking",
-                      "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode","use_fates_tree_damage" );
+                      "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
+		      "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
+		      "fates_parteh_mode","use_fates_tree_damage" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -2979,24 +2967,30 @@ sub setup_logic_supplemental_nitrogen {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) {
-    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
-                'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
-  }
+      # If this is non-fates, non-sp and crop is active
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+		  'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
 
+  } 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'});
+  }
+
   #
   # Error checking for suplnitro
   #
   my $suplnitro = $nl->get_value('suplnitro');
   if ( defined($suplnitro) ) {
     if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
-      $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV is active!");
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV nor FATES is active!");
     }
     if ( ! &value_is_true($nl_flags->{'use_crop'}) && $suplnitro =~ /PROG_CROP_ONLY/i ) {
       $log->fatal_error("supplemental Nitrogen is set to run over prognostic crops, but prognostic crop is NOT active!");
     }
 
     if ( $suplnitro =~ /ALL/i ) {
-      if ( $nl_flags->{'bgc_spinup'} eq "on" ) {
+      if ( $nl_flags->{'bgc_spinup'} eq "on" && $nl_flags->{'bgc_mode'} ne "fates" ) {
         $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" );
       }
     }
@@ -3313,6 +3307,12 @@ sub setup_logic_luna {
                  'use_cn'=>$nl_flags->{'use_cn'} );
   }
   $nl_flags->{'use_luna'} = $nl->get_value('use_luna');
+
+  # LUNA can NOT be on with FATES
+  if ( &value_is_true( $nl_flags->{'use_luna'} ) && &value_is_true( $nl_flags->{'use_fates'} )) {
+     $log->fatal_error("Cannot turn use_luna to true when bgc=fates" );
+  }
+
   my $vcmax_opt= $nl->get_value('vcmax_opt');
   # lnc_opt only applies if luna is on or for vcmax_opt=3/4
   if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) {
@@ -3479,18 +3479,18 @@ sub setup_logic_nitrogen_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   #
-  # Nitrogen deposition for bgc=CN
+  # Nitrogen deposition for bgc=CN or fates
   #
-  if ( $nl_flags->{'bgc_mode'} =~/bgc/ ) {
+  if ( ($nl_flags->{'bgc_mode'} =~/bgc/) ) {   # or  ($nl_flags->{'bgc_mode'} =~/fates/) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'},
                 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'},
-                'use_cn'=>$nl_flags->{'use_cn'},
-                'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
+		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'},
-                'use_cn'=>$nl_flags->{'use_cn'},
-                'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
+		'use_cn'=>$nl_flags->{'use_cn'}, 
+		'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'},
                 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'},
                 'sim_year_range'=>$nl_flags->{'sim_year_range'});
@@ -4220,6 +4220,13 @@ sub setup_logic_fates {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       '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

@@ -146,7 +146,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Supplmental Nitrogen mode -->
 <suplnitro use_cn=".true." >NONE</suplnitro>
-<suplnitro use_fates=".true." >NONE</suplnitro>
+<suplnitro use_fates=".true." >ALL</suplnitro>
 
 <!-- Albedo for glaciers -->
 <albice phys="clm5_1" >0.50,0.30</albice>
@@ -510,6 +510,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_luna phys="clm5_0"  >.true.</use_luna>
 <use_luna phys="clm5_0"  use_fates=".true." >.false.</use_luna>
 <use_luna phys="clm4_5"  >.false.</use_luna>
+<use_luna phys="clm4_5"  use_fates=".true." >.false.</use_luna>
 
 <!-- Flexible CN options -->
 <MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>

bld/unit_testers/build-namelist_test.pl

@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1975;
+my $ntests = 1978;
 if ( defined($opts{'compare'}) ) {
    $ntests += 1344;
 }
@@ -984,6 +984,21 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_1",
                                    },
+     "useFATESWluna"             =>{ options=>"--bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"use_luna=TRUE",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
+     "useFATESWfun"              =>{ options=>"--bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"use_fun=TRUE",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
+     "useFATESWOsuplnitro"       =>{ options=>"--bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"suplnitro='NONE'",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
      "FireNoneButBGCfireon"    =>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"fire_method='li2021gswpfrc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

src/biogeochem/CNAnnualUpdateMod.F90

@@ -10,6 +10,7 @@ module CNAnnualUpdateMod
   use CNvegStateType      , only : cnveg_state_type
   use PatchType           , only : patch
   use filterColMod        , only : filter_col_type, col_filter_from_filter_and_logical_array
+  use ColumnType          , only : col
   !
   implicit none
   private
@@ -21,7 +22,7 @@ module CNAnnualUpdateMod
 contains
 
   !-----------------------------------------------------------------------
-  subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
+  subroutine CNAnnualUpdate(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, &
        cnveg_state_inst, cnveg_carbonflux_inst)
     !
     ! !DESCRIPTION:
@@ -34,10 +35,10 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi
     !
     ! !ARGUMENTS:
     type(bounds_type)           , intent(in)    :: bounds  
-    integer                     , intent(in)    :: num_soilc         ! number of soil columns in filter
-    integer                     , intent(in)    :: filter_soilc(:)   ! filter for soil columns
-    integer                     , intent(in)    :: num_soilp         ! number of soil patches in filter
-    integer                     , intent(in)    :: filter_soilp(:)   ! filter for soil patches
+    integer                     , intent(in)    :: num_bgc_soilc         ! number of bgc soil columns in filter
+    integer                     , intent(in)    :: filter_bgc_soilc(:)   ! filter for bgc soil columns
+    integer                     , intent(in)    :: num_bgc_vegp         ! number of bgc veg patches in filter
+    integer                     , intent(in)    :: filter_bgc_vegp(:)   ! filter for bgc veg patches
     type(cnveg_state_type)      , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst
     !
@@ -53,22 +54,25 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi
     dt = get_step_size_real()
     secspyear = get_curr_days_per_year() * secspday
 
-    do fc = 1,num_soilc
-       c = filter_soilc(fc)
-       cnveg_state_inst%annsum_counter_col(c) = cnveg_state_inst%annsum_counter_col(c) + dt
-       if (cnveg_state_inst%annsum_counter_col(c) >= secspyear) then
-          end_of_year(c) = .true.
-          cnveg_state_inst%annsum_counter_col(c) = 0._r8
-       else
-          end_of_year(c) = .false.
+    do fc = 1,num_bgc_soilc
+       c = filter_bgc_soilc(fc)
+       if(.not.col%is_fates(c))then
+          cnveg_state_inst%annsum_counter_col(c) = cnveg_state_inst%annsum_counter_col(c) + dt
+          if (cnveg_state_inst%annsum_counter_col(c) >= secspyear) then
+             end_of_year(c) = .true.
+             cnveg_state_inst%annsum_counter_col(c) = 0._r8
+          else
+             end_of_year(c) = .false.
+          end if
        end if
     end do
+
 
-    do fp = 1,num_soilp
-       p = filter_soilp(fp)
+    do fp = 1,num_bgc_vegp
+       p = filter_bgc_vegp(fp)
        c = patch%column(p)
 
-       if (end_of_year(c)) then
+       if (end_of_year(c) .and. .not.col%is_fates(c)) then
 
           ! update annual plant ndemand accumulator
           cnveg_state_inst%annsum_potential_gpp_patch(p)  = cnveg_state_inst%tempsum_potential_gpp_patch(p)
@@ -94,20 +98,22 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi
     end do
 
     ! Get column-level averages, just for the columns that have reached their personal end-of-year
-    filter_endofyear_c = col_filter_from_filter_and_logical_array( &
-         bounds = bounds, &
-         num_orig = num_soilc, &
-         filter_orig = filter_soilc, &
-         logical_col = end_of_year(bounds%begc:bounds%endc))
-
-    call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, &
-         cnveg_carbonflux_inst%annsum_npp_patch(bounds%begp:bounds%endp), &
-         cnveg_carbonflux_inst%annsum_npp_col(bounds%begc:bounds%endc))
-
-    call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, &
-         cnveg_state_inst%annavg_t2m_patch(bounds%begp:bounds%endp), &
-         cnveg_state_inst%annavg_t2m_col(bounds%begc:bounds%endc))
-
+    if(num_bgc_vegp>0)then
+       filter_endofyear_c = col_filter_from_filter_and_logical_array( &
+            bounds = bounds, &
+            num_orig = num_bgc_soilc, &
+            filter_orig = filter_bgc_soilc, &
+            logical_col = end_of_year(bounds%begc:bounds%endc))
+
+       call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, &
+            cnveg_carbonflux_inst%annsum_npp_patch(bounds%begp:bounds%endp), &
+            cnveg_carbonflux_inst%annsum_npp_col(bounds%begc:bounds%endc))
+
+       call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, &
+            cnveg_state_inst%annavg_t2m_patch(bounds%begp:bounds%endp), &
+            cnveg_state_inst%annavg_t2m_col(bounds%begc:bounds%endc))
+    end if
+
  end subroutine CNAnnualUpdate
 
 end module CNAnnualUpdateMod