Merge branch 'njeffery/seaice/updated-icepack-bgc' into master

This version uses a branch of Icepack with BGC enabled
E3SM-Project/Icepack.git branch njeffery/merge-fixes-to-bgc

components/mpas-seaice/bld/build-namelist

@@ -628,12 +628,7 @@ add_default($nl, 'config_recover_tracer_means_check');
 ##################################
 # Namelist group: column_package #
 ##################################
-
-if ($ice_bgc eq 'ice_bgc') {
-        add_default($nl, 'config_column_physics_type', 'val'=>"column_package");
-} else {
-        add_default($nl, 'config_column_physics_type');
-}
+add_default($nl, 'config_column_physics_type');
 add_default($nl, 'config_use_column_shortwave');
 add_default($nl, 'config_use_column_vertical_thermodynamics');
 if ($ice_bgc eq 'ice_bgc') {
@@ -681,6 +676,7 @@ if ($ice_bgc eq 'ice_bgc') {
         add_default($nl, 'config_use_humics', 'val'=>".true.");
         add_default($nl, 'config_use_DON', 'val'=>".true.");
         add_default($nl, 'config_use_iron', 'val'=>".true.");
+        add_default($nl, 'config_couple_biogeochemistry_fields');
 } else {
         add_default($nl, 'config_use_vertical_biochemistry', 'val'=>".false.");
         add_default($nl, 'config_use_vertical_tracers', 'val'=>".false.");
@@ -694,6 +690,7 @@ if ($ice_bgc eq 'ice_bgc') {
         add_default($nl, 'config_use_humics', 'val'=>".false.");
         add_default($nl, 'config_use_DON', 'val'=>".false.");
         add_default($nl, 'config_use_iron', 'val'=>".false.");
+        add_default($nl, 'config_couple_biogeochemistry_fields', 'val'=>".false.");
 }
 add_default($nl, 'config_use_chlorophyll');
 add_default($nl, 'config_use_macromolecules');

components/mpas-seaice/bld/build-namelist-section

@@ -193,6 +193,7 @@ add_default($nl, 'config_use_floe_size_distribution');
 # Namelist group: biogeochemistry #
 ###################################
 
+add_default($nl, 'config_couple_biogeochemistry_fields');
 add_default($nl, 'config_use_brine');
 add_default($nl, 'config_use_vertical_zsalinity');
 add_default($nl, 'config_use_vertical_biochemistry');

components/mpas-seaice/bld/namelist_files/namelist_defaults_mpassi.xml

@@ -215,6 +215,7 @@
 <config_use_floe_size_distribution>false</config_use_floe_size_distribution>
 
 <!-- biogeochemistry -->
+<config_couple_biogeochemistry_fields>false</config_couple_biogeochemistry_fields>
 <config_use_brine>false</config_use_brine>
 <config_use_vertical_zsalinity>false</config_use_vertical_zsalinity>
 <config_use_vertical_biochemistry>false</config_use_vertical_biochemistry>
@@ -343,12 +344,12 @@
 <config_mobility_type_proteins>0.0</config_mobility_type_proteins>
 <config_mobility_type_dissolved_iron>0.0</config_mobility_type_dissolved_iron>
 <config_mobility_type_particulate_iron>0.5</config_mobility_type_particulate_iron>
-<config_mobility_type_black_carbon1>0.0</config_mobility_type_black_carbon1>
-<config_mobility_type_black_carbon2>0.0</config_mobility_type_black_carbon2>
-<config_mobility_type_dust1>0.0</config_mobility_type_dust1>
-<config_mobility_type_dust2>0.0</config_mobility_type_dust2>
-<config_mobility_type_dust3>0.0</config_mobility_type_dust3>
-<config_mobility_type_dust4>0.0</config_mobility_type_dust4>
+<config_mobility_type_black_carbon1>-1.0</config_mobility_type_black_carbon1>
+<config_mobility_type_black_carbon2>-1.0</config_mobility_type_black_carbon2>
+<config_mobility_type_dust1>-1.0</config_mobility_type_dust1>
+<config_mobility_type_dust2>-1.0</config_mobility_type_dust2>
+<config_mobility_type_dust3>-1.0</config_mobility_type_dust3>
+<config_mobility_type_dust4>-1.0</config_mobility_type_dust4>
 <config_ratio_C_to_N_diatoms>7.0</config_ratio_C_to_N_diatoms>
 <config_ratio_C_to_N_small_plankton>7.0</config_ratio_C_to_N_small_plankton>
 <config_ratio_C_to_N_phaeocystis>7.0</config_ratio_C_to_N_phaeocystis>

components/mpas-seaice/bld/namelist_files/namelist_definition_mpassi.xml

@@ -955,6 +955,14 @@ Default: Defined in namelist_defaults.xml
 
 <!-- biogeochemistry -->
 
+<entry id="config_couple_biogeochemistry_fields" type="logical"
+	category="biogeochemistry" group="biogeochemistry">
+Couple ocean and seaice biogeochemical fields
+
+Valid values: true or false
+Default: Defined in namelist_defaults.xml
+</entry>
+
 <entry id="config_use_brine" type="logical"
 	category="biogeochemistry" group="biogeochemistry">
 Use the brine height tracer

components/mpas-seaice/cime_config/buildnml

@@ -722,6 +722,15 @@ def buildnml(case, caseroot, compname):
             lines.append('    <var name="netCarbonFlux"/>')
             lines.append('    <var name="absoluteCarbonError"/>')
             lines.append('    <var name="relativeCarbonError"/>')
+            lines.append('    <var name="initialBlackCarbon"/>')
+            lines.append('    <var name="finalBlackCarbon"/>')
+            lines.append('    <var name="blackCarbonChange"/>')
+            lines.append('    <var name="blackCarbonChangeFlux"/>')
+            lines.append('    <var name="blackCarbonConsAtmBlackCarbonFlux"/>')
+            lines.append('    <var name="blackCarbonConsOceanBlackCarbonFlux"/>')
+            lines.append('    <var name="netBlackCarbonFlux"/>')
+            lines.append('    <var name="absoluteBlackCarbonError"/>')
+            lines.append('    <var name="relativeBlackCarbonError"/>')
             lines.append('</stream>')
             lines.append('')
             lines.append('<immutable_stream name="conservationCheckRestart"')

components/mpas-seaice/driver/ice_comp_mct.F

@@ -1950,7 +1950,8 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
       config_use_aerosols,              &
       config_use_modal_aerosols,        &
       config_use_zaerosols,             &
-      config_use_column_biogeochemistry
+      config_use_column_biogeochemistry, &
+      config_couple_biogeochemistry_fields
 
    character(len=strKIND), pointer ::   &
       config_column_physics_type,       &
@@ -2070,6 +2071,8 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
       call mpas_pool_get_config(configs, "config_use_aerosols", config_use_aerosols)
       call mpas_pool_get_config(configs, "config_use_modal_aerosols", config_use_modal_aerosols)
       call mpas_pool_get_config(configs, "config_use_column_biogeochemistry", config_use_column_biogeochemistry)
+      call mpas_pool_get_config(configs, "config_couple_biogeochemistry_fields", config_couple_biogeochemistry_fields)
+      call mpas_pool_get_config(configs, "config_use_zaerosols", config_use_zaerosols)
 
       call mpas_pool_get_subpool(block_ptr % structs, 'mesh', meshPool)
       call mpas_pool_get_subpool(block_ptr % structs, 'ocean_coupling', oceanCoupling)
@@ -2108,9 +2111,13 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
          call mpas_pool_get_array(aerosols, "atmosAerosolFlux", atmosAerosolFlux)
       endif
 
-      if (config_use_column_biogeochemistry) then
-         call mpas_pool_get_config(configs, "config_use_zaerosols", config_use_zaerosols)
-         call mpas_pool_get_subpool(block_ptr % structs, 'biogeochemistry', biogeochemistry)
+      call mpas_pool_get_subpool(block_ptr % structs, 'biogeochemistry', biogeochemistry)
+      if (config_use_zaerosols) then
+         call mpas_pool_get_array(biogeochemistry, 'oceanZAerosolConc', oceanZAerosolConc)
+         call mpas_pool_get_array(biogeochemistry, 'atmosBlackCarbonFlux', atmosBlackCarbonFlux)
+         call mpas_pool_get_array(biogeochemistry, 'atmosDustFlux', atmosDustFlux)
+      endif
+      if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
 
          call mpas_pool_get_array(biogeochemistry, 'oceanAlgaeConc', oceanAlgaeConc)
          call mpas_pool_get_array(biogeochemistry, 'oceanDOCConc', oceanDOCConc)
@@ -2124,15 +2131,10 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
          call mpas_pool_get_array(biogeochemistry, 'oceanHumicsConc', oceanHumicsConc)
          call mpas_pool_get_array(biogeochemistry, 'oceanParticulateIronConc', oceanParticulateIronConc)
          call mpas_pool_get_array(biogeochemistry, 'oceanDissolvedIronConc', oceanDissolvedIronConc)
-         call mpas_pool_get_array(biogeochemistry, 'oceanZAerosolConc', oceanZAerosolConc)
          call mpas_pool_get_array(biogeochemistry, 'carbonToNitrogenRatioAlgae', carbonToNitrogenRatioAlgae)
          call mpas_pool_get_array(biogeochemistry, 'carbonToNitrogenRatioDON', carbonToNitrogenRatioDON)
          call mpas_pool_get_array(biogeochemistry, 'DOCPoolFractions', DOCPoolFractions)
 
-         if (config_use_zaerosols) then
-            call mpas_pool_get_array(biogeochemistry, "atmosBlackCarbonFlux", atmosBlackCarbonFlux)
-            call mpas_pool_get_array(biogeochemistry, "atmosDustFlux", atmosDustFlux)
-         endif
       endif
 
       do i = 1, nCellsSolve
@@ -2224,8 +2226,44 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
            endif
         endif
 
+        ! set aerosols, if configured
+        if (config_use_zaerosols) then
+           oceanZAerosolConc(1,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer1, n)
+           oceanZAerosolConc(2,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer2, n)
+           oceanZAerosolConc(3,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer3, n)
+           oceanZAerosolConc(4,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer4, n)
+           oceanZAerosolConc(5,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer5, n)
+           oceanZAerosolConc(6,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer6, n)
+           if (config_use_modal_aerosols) then
+              atmosBlackCarbonFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_bcphodry, n) &
+                                        + x2i_i % rAttr(index_x2i_Faxa_bcphidry, n)
+              atmosBlackCarbonFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_bcphiwet, n)
+              !combine wet and dry dust
+              atmosDustFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet1, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry1, n)
+              atmosDustFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet2, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry2, n)
+              atmosDustFlux(3,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet3, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry3, n)
+              atmosDustFlux(4,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet4, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry4, n)
+           else
+              atmosBlackCarbonFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_bcphodry, n)
+              atmosBlackCarbonFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_bcphidry, n) &
+                                        + x2i_i % rAttr(index_x2i_Faxa_bcphiwet, n)
+              ! combine wet and dry dust
+              atmosDustFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet1, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry1, n)
+              atmosDustFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet2, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry2, n)
+              atmosDustFlux(3,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet3, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry3, n)
+              atmosDustFlux(4,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet4, n) &
+                                 + x2i_i % rAttr(index_x2i_Faxa_dstdry4, n)
+           endif
+        endif
         ! import biogeochemistry fields, if configured
-        if (config_use_column_biogeochemistry) then
+        if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
            oceanAlgaeConc(1,i)           = x2i_i % rAttr(index_x2i_So_algae1, n)
            oceanAlgaeConc(2,i)           = x2i_i % rAttr(index_x2i_So_algae2, n)
            oceanAlgaeConc(3,i)           = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_algae3, n)
@@ -2245,42 +2283,6 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
            oceanParticulateIronConc(2,i) = x2i_i % rAttr(index_x2i_So_fep2, n)
            oceanDissolvedIronConc(1,i)   = x2i_i % rAttr(index_x2i_So_fed1, n)
            oceanDissolvedIronConc(2,i)   = x2i_i % rAttr(index_x2i_So_fed2, n)
-           oceanZAerosolConc(1,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer1, n)
-           oceanZAerosolConc(2,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer2, n)
-           oceanZAerosolConc(3,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer3, n)
-           oceanZAerosolConc(4,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer4, n)
-           oceanZAerosolConc(5,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer5, n)
-           oceanZAerosolConc(6,i)        = 0.0_RKIND !x2i_i % rAttr(index_x2i_So_zaer6, n)
-           ! set aerosols, if configured
-           if (config_use_zaerosols) then
-              if (config_use_modal_aerosols) then
-                 atmosBlackCarbonFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_bcphodry, n) &
-                                           + x2i_i % rAttr(index_x2i_Faxa_bcphidry, n)
-                 atmosBlackCarbonFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_bcphiwet, n)
-                 ! combine wet and dry dust
-                 atmosDustFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet1, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry1, n)
-                 atmosDustFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet2, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry2, n)
-                 atmosDustFlux(3,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet3, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry3, n)
-                 atmosDustFlux(4,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet4, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry4, n)
-              else
-                 atmosBlackCarbonFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_bcphodry, n)
-                 atmosBlackCarbonFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_bcphidry, n) &
-                                           + x2i_i % rAttr(index_x2i_Faxa_bcphiwet, n)
-                 ! combine wet and dry dust
-                 atmosDustFlux(1,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet1, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry1, n)
-                 atmosDustFlux(2,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet2, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry2, n)
-                 atmosDustFlux(3,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet3, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry3, n)
-                 atmosDustFlux(4,i) = x2i_i % rAttr(index_x2i_Faxa_dstwet4, n) &
-                                    + x2i_i % rAttr(index_x2i_Faxa_dstdry4, n)
-              endif
-           endif
         endif
       end do
 
@@ -2293,7 +2295,7 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
 
         seaSurfaceTemperature(i)  = seaSurfaceTemperature(i) - seaiceFreshWaterFreezingPoint
 
-        if (config_use_column_biogeochemistry) then
+        if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
            ! convert from mmol C/m^3 to mmol N/m^3
            oceanAlgaeConc(1,i)           = oceanAlgaeConc(1,i) / carbonToNitrogenRatioAlgae(1)
            oceanAlgaeConc(2,i)           = oceanAlgaeConc(2,i) / carbonToNitrogenRatioAlgae(2)
@@ -2343,7 +2345,12 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
       call mpas_pool_get_field(aerosols, "atmosAerosolFlux", atmosAerosolFluxField)
    endif
 
-   if (config_use_column_biogeochemistry) then
+   if (config_use_zaerosols) then
+      call mpas_pool_get_field(biogeochemistry, "atmosBlackCarbonFlux", atmosBlackCarbonFluxField)
+      call mpas_pool_get_field(biogeochemistry, "atmosDustFlux", atmosDustFluxField)
+      call mpas_pool_get_field(biogeochemistry, 'oceanZAerosolConc', oceanZAerosolConcField)
+   endif
+   if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
       call mpas_pool_get_subpool(domain % blocklist % structs, 'biogeochemistry', biogeochemistry)
 
       call mpas_pool_get_field(biogeochemistry, 'oceanAlgaeConc', oceanAlgaeConcField)
@@ -2358,11 +2365,6 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
       call mpas_pool_get_field(biogeochemistry, 'oceanHumicsConc', oceanHumicsConcField)
       call mpas_pool_get_field(biogeochemistry, 'oceanParticulateIronConc', oceanParticulateIronConcField)
       call mpas_pool_get_field(biogeochemistry, 'oceanDissolvedIronConc', oceanDissolvedIronConcField)
-      call mpas_pool_get_field(biogeochemistry, 'oceanZAerosolConc', oceanZAerosolConcField)
-      if (config_use_zaerosols) then
-         call mpas_pool_get_field(biogeochemistry, "atmosBlackCarbonFlux", atmosBlackCarbonFluxField)
-         call mpas_pool_get_field(biogeochemistry, "atmosDustFlux", atmosDustFluxField)
-      endif
    endif
 
    call mpas_dmpar_exch_halo_field(seaSurfaceTemperatureField)
@@ -2393,8 +2395,12 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
    if (config_use_aerosols) then
       call mpas_dmpar_exch_halo_field(atmosAerosolFluxField)
    endif
-
-   if (config_use_column_biogeochemistry) then
+   if (config_use_zaerosols) then
+      call mpas_dmpar_exch_halo_field(atmosBlackCarbonFluxField)
+      call mpas_dmpar_exch_halo_field(atmosDustFluxField)
+      call mpas_dmpar_exch_halo_field(oceanZAerosolConcField)
+   endif
+   if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
       call mpas_dmpar_exch_halo_field(oceanAlgaeConcField)
       call mpas_dmpar_exch_halo_field(oceanDOCConcField)
       call mpas_dmpar_exch_halo_field(oceanDICConcField)
@@ -2407,11 +2413,6 @@ subroutine ice_import_mct(x2i_i, errorCode)!{{{
       call mpas_dmpar_exch_halo_field(oceanHumicsConcField)
       call mpas_dmpar_exch_halo_field(oceanParticulateIronConcField)
       call mpas_dmpar_exch_halo_field(oceanDissolvedIronConcField)
-      call mpas_dmpar_exch_halo_field(oceanZAerosolConcField)
-      if (config_use_zaerosols) then
-         call mpas_dmpar_exch_halo_field(atmosBlackCarbonFluxField)
-         call mpas_dmpar_exch_halo_field(atmosDustFluxField)
-      endif
    endif
 
 ! REVISION HISTORY:
@@ -2486,6 +2487,7 @@ subroutine ice_export_mct(i2x_i, errorCode)   !{{{
       config_rotate_cartesian_grid,      &
       config_use_topo_meltponds,         &
       config_use_column_biogeochemistry, &
+      config_couple_biogeochemistry_fields, &
       config_use_column_shortwave,       &
       config_use_data_icebergs
 
@@ -2558,6 +2560,7 @@ subroutine ice_export_mct(i2x_i, errorCode)   !{{{
       call MPAS_pool_get_config(configs, "config_rotate_cartesian_grid", config_rotate_cartesian_grid)
       call MPAS_pool_get_config(configs, "config_use_topo_meltponds", config_use_topo_meltponds)
       call MPAS_pool_get_config(configs, "config_use_column_biogeochemistry", config_use_column_biogeochemistry)
+      call mpas_pool_get_config(configs, "config_couple_biogeochemistry_fields", config_couple_biogeochemistry_fields)
       call MPAS_pool_get_config(configs, "config_use_column_shortwave", config_use_column_shortwave)
       call MPAS_pool_get_config(configs, "config_use_data_icebergs", config_use_data_icebergs)
 
@@ -2620,7 +2623,7 @@ subroutine ice_export_mct(i2x_i, errorCode)   !{{{
          call MPAS_pool_get_array(icebergFluxes, "bergLatentHeatFlux", bergLatentHeatFlux)
       endif
 
-      if (config_use_column_biogeochemistry) then
+      if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
          call mpas_pool_get_subpool(block_ptr % structs, 'biogeochemistry', biogeochemistry)
 
          call mpas_pool_get_array(biogeochemistry, 'oceanAlgaeFlux', oceanAlgaeFlux)
@@ -2741,7 +2744,7 @@ subroutine ice_export_mct(i2x_i, errorCode)   !{{{
             i2x_i % rAttr(index_i2x_Fioi_tauy ,n) = tauyo
 
             ! export biogeochemistry fields, if configured
-            if (config_use_column_biogeochemistry) then
+            if (config_use_column_biogeochemistry .and. config_couple_biogeochemistry_fields) then
                ! convert from mmol N/m^3 to mmol C/m^3
                i2x_i % rAttr(index_i2x_Fioi_algae1,n) = oceanAlgaeFlux(1,i) * carbonToNitrogenRatioAlgae(1)
                i2x_i % rAttr(index_i2x_Fioi_algae2,n) = oceanAlgaeFlux(2,i) * carbonToNitrogenRatioAlgae(2)