Merge branch 'njeffery/seaice/update-icepack-bgc-v3-indices' into nex…

…t (PR #6457)

Adds icepack BGC

Updates the version of icepack to one that includes sea ice BGC

Tested in ocean-sea ice BGC active simulations.

[NML]
[non-BFB] only for tests with biogeochemistry and/or sea ice aerosols
          active

cime_config/config_grids.xml

@@ -626,6 +626,16 @@
       <mask>IcoswISC30E3r5</mask>
     </model_grid>
 
+    <model_grid alias="TL319_r05_IcoswISC30E3r5" compset="(DATM|XATM|SATM)">
+      <grid name="atm">TL319</grid>
+      <grid name="lnd">r05</grid>
+      <grid name="ocnice">IcoswISC30E3r5</grid>
+      <grid name="rof">r05</grid>
+      <grid name="glc">null</grid>
+      <grid name="wav">null</grid>
+      <mask>IcoswISC30E3r5</mask>
+    </model_grid>
+
     <model_grid alias="TL319_IcosXISC30E3r7" compset="(DATM|XATM|SATM)">
       <grid name="atm">TL319</grid>
       <grid name="lnd">TL319</grid>

components/mpas-seaice/bld/build-namelist

@@ -681,6 +681,7 @@ 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($nl, 'config_use_vertical_tracers', 'val'=>".false.");
@@ -694,11 +695,14 @@ if ($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');
 add_default($nl, 'config_use_modal_aerosols');
 add_default($nl, 'config_use_zaerosols');
+add_default($nl, 'config_use_atm_dust_file');
+add_default($nl, 'config_use_iron_solubility_file');
 add_default($nl, 'config_skeletal_bgc_flux_type');
 add_default($nl, 'config_scale_initial_vertical_bgc');
 add_default($nl, 'config_biogrid_bottom_molecular_sublayer');

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');
@@ -212,6 +213,8 @@ add_default($nl, 'config_use_DON');
 add_default($nl, 'config_use_iron');
 add_default($nl, 'config_use_modal_aerosols');
 add_default($nl, 'config_use_zaerosols');
+add_default($nl, 'config_use_atm_dust_file');
+add_default($nl, 'config_use_iron_solubility_file');
 add_default($nl, 'config_skeletal_bgc_flux_type');
 add_default($nl, 'config_scale_initial_vertical_bgc');
 add_default($nl, 'config_biogrid_bottom_molecular_sublayer');

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

@@ -221,6 +221,7 @@
 <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>
@@ -240,6 +241,8 @@
 <config_use_iron>false</config_use_iron>
 <config_use_modal_aerosols>false</config_use_modal_aerosols>
 <config_use_zaerosols>false</config_use_zaerosols>
+<config_use_atm_dust_file>false</config_use_atm_dust_file>
+<config_use_iron_solubility_file>false</config_use_iron_solubility_file>
 <config_skeletal_bgc_flux_type>'Jin2006'</config_skeletal_bgc_flux_type>
 <config_scale_initial_vertical_bgc>false</config_scale_initial_vertical_bgc>
 <config_biogrid_bottom_molecular_sublayer>0.006</config_biogrid_bottom_molecular_sublayer>
@@ -349,12 +352,12 @@
 <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
@@ -1107,6 +1115,22 @@ Valid values: true or false
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_use_atm_dust_file" type="logical"
+	category="biogeochemistry" group="biogeochemistry">
+Read atmospheric dust fluxes from a file
+
+Valid values: true or false
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_use_iron_solubility_file" type="logical"
+	category="biogeochemistry" group="biogeochemistry">
+Read atmospheric dust-iron solubility from a file
+
+Valid values: true or false
+Default: Defined in namelist_defaults.xml
+</entry>
+
 <entry id="config_skeletal_bgc_flux_type" type="char*1024"
 	category="biogeochemistry" group="biogeochemistry">
 Determines the ocean-ice fluxes of biogeochemistry for the bottom1-layer model: in Jin2006, the piston velocity is a function of ice growth/melt rate, in default, the piston velocity is constant

components/mpas-seaice/cime_config/buildnml

@@ -72,6 +72,7 @@ def buildnml(case, caseroot, compname):
     decomp_prefix = ''
     data_iceberg_file = ''
     points_file = ''
+    dust_iron_file = ''
 
     if ice_grid == 'oEC60to30v3':
         decomp_date = '230424'
@@ -300,6 +301,7 @@ def buildnml(case, caseroot, compname):
         decomp_date = '20231120'
         decomp_prefix = 'partitions/mpas-seaice.graph.info.'
         data_iceberg_file = 'Iceberg_Climatology_Merino.IcoswISC30E3r5.20231120.nc'
+        dust_iron_file = 'ecoForcingSurfaceMonthly+WetDryDustSolFrac.IcoswISC30E3r5.20240511.nc'
         if ice_ic_mode == 'spunup':
             if iceberg_mode == 'data':
                 grid_date = '20240207'
@@ -357,6 +359,8 @@ def buildnml(case, caseroot, compname):
             input_list.write("points = {}/ice/mpas-seaice/{}/{}\n".format(din_loc_root, ice_mask, points_file))
         if iceberg_mode == 'data':
             input_list.write("data_iceberg = {}/ice/mpas-seaice/{}/{}\n".format(din_loc_root, ice_mask, data_iceberg_file))
+        if dust_iron_file != '':
+            input_list.write("dust_iron = {}/ocn/mpas-o/{}/{}\n".format(din_loc_root, ice_mask, dust_iron_file))
 
     #--------------------------------------------------------------------
     # Invoke mpas build-namelist - output will go in $CASEBUILD/mpassiconf
@@ -602,10 +606,19 @@ def buildnml(case, caseroot, compname):
             lines.append('<immutable_stream name="ISPOLDailyWOAForcing"')
             lines.append('                  type="input"')
             lines.append('                  io_type="{}"'.format(ice_pio_typename))
-            lines.append('                  filename_template="{}/ice/mpas-cice/general/ISPOLDailyWOAForcing_10132022.nc"')
+            lines.append('                  filename_template="{}/ice/mpas-cice/general/ISPOLDailyWOAForcing_10132022.nc"'.format(din_loc_root))
             lines.append('                  filename_interval="none"')
             lines.append('                  input_interval="none" />')
             lines.append('')
+            if dust_iron_file != '':
+                lines.append('<immutable_stream name="DustIronMonthlyForcing"')
+                lines.append('                  type="input"')
+                lines.append('                  io_type="{}"'.format(ice_pio_typename))
+                lines.append('                  filename_template="{}/ocn/mpas-o/{}/{}"'.format(din_loc_root, ice_mask, dust_iron_file))
+                lines.append('                  filename_interval="none"')
+                lines.append('                  input_interval="none" />')
+                lines.append('')
+
             lines.append('<immutable_stream name="abort_contents"')
             lines.append('                  type="none"')
             lines.append('                  filename_template="abort_variables.nc" />')
@@ -748,6 +761,15 @@ 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"')