Turn on PHA_MLD_CALC and associated runtime parameters to allow MOM6 …

…to calculate a photoacclimation MLD (#85)

* Update BGC tag

* Update MOM6 tag to have new mom6 mld interface

* Update model configs to reflect new interface changes

* Update MOM6 tag again

* Update FMS and coupler to 2024.03, also update xmls

* update ci build driver

* Revert "Update MOM6 tag again"

This reverts commit a5d4615.

* Revert "update ci build driver"

This reverts commit 3f172ee.

* Revert "Update FMS and coupler to 2024.03, also update xmls"

This reverts commit c8c77ff.

* added scale_burial option in COBALT_input

* Changed FRE STEM name

* Created new diag_table to preserve old diag_table

exps/NEP10.COBALT/INPUT/MOM_override

@@ -13,3 +13,9 @@
 #override MLE%MLD_DECAYING_TFILTER = 2.592E+06
 #override MLE%MIN_WSTAR2 = 1.0E-09
 #override MLE_USE_PBL_MLD = True
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03
+#override HREF_FOR_MLD = 10.0 
+#override DIAG_MLD_DENSITY_DIFF = 0.03

exps/NWA12.COBALT/INPUT/MOM_override

@@ -12,3 +12,9 @@
 #override REMAP_AUXILIARY_VARS = True
 #override DIABATIC_FIRST = False
 #override EQN_OF_STATE = "WRIGHT_FULL"
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03
+#override HREF_FOR_MLD = 10.0 
+#override DIAG_MLD_DENSITY_DIFF = 0.03

exps/OM4.single_column.COBALT/MOM_override

@@ -37,3 +37,10 @@
 #override DO_GEOTHERMAL = True 
 #override GEOTHERMAL_SCALE = 0.0
 #override GENERIC_TRACER_IC_FILE = "MOM_IC.nc"
+!MOM6 photo_acc MLD
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03
+#override HREF_FOR_MLD = 10.0 
+#override DIAG_MLD_DENSITY_DIFF = 0.03

xmls/NWA12/CEFI_NWA12_cobalt.xml

@@ -52,7 +52,7 @@ frecheck -r layout -p ncrc6.intel23 -x CEFI_NWA12_cobalt.xml CEFI_NWA12_COBALT_V
   <property name="MOM6_GIT_FIX" value="main"/> <!-- Trying new branch with bug fix for bgc obc index -->
 
   <!-- customize as needed -->
-  <property name="FRE_STEM" value="fre/cefi/NWA/2024_08"/>
+  <property name="FRE_STEM" value="fre/cefi/NWA/2024_09"/>
 
   <!-- Please make sure to change your group, such as b, f, g, m, o... -->
   <property name="NCRC_GROUP" value="ira-cefi"/>
@@ -557,7 +557,7 @@ $baseDate
       </diagTable>
       <dataFile label="diagTable" target="INPUT/" chksum="" size="" timestamp="">
         <dataSource site="ncrc">./diag_tables/diag_table_COBALT_2023-04</dataSource>
-        <dataSource site="ncrc">./diag_tables/diag_table_MOM6_2023-03</dataSource>
+        <dataSource site="ncrc">./diag_tables/diag_table_MOM6_2024-09</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table.SIS</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table_COBALT_neus</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table_MOM6_neus</dataSource>
@@ -591,6 +591,12 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
 #override REMAP_AUXILIARY_VARS = True
 #override DIABATIC_FIRST = False
 #override EQN_OF_STATE = "WRIGHT_FULL"
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03
+#override HREF_FOR_MLD = 10.0 
+#override DIAG_MLD_DENSITY_DIFF = 0.03    
 MOM_OVERRIDE_EOF
 
 truncate -s 0 $work/INPUT/COBALT_override
@@ -605,7 +611,10 @@ COBALT_OVERRIDE_EOF
 truncate -s 0 $work/INPUT/COBALT_input
 cat > $work/INPUT/COBALT_input << COBALT_INPUT_EOF
 ! Put the contents of your COBALT_input file here
-do_case2_mod = True		      
+do_case2_mod = True
+scale_burial = 1.0
+z_burial = 20.0
+z_denit = 20.0
 COBALT_INPUT_EOF
         ]]>
       </csh>

xmls/NWA12/CEFI_NWA12_cobalt_fms2_yaml.xml

@@ -52,7 +52,7 @@ frecheck -r layout -p ncrc6.intel23 -x CEFI_NWA12_cobalt_fms2_yaml.xml CEFI_NWA1
   <property name="MOM6_GIT_FIX" value="main"/> <!-- Trying new branch with bug fix for bgc obc index -->
 
   <!-- customize as needed -->
-  <property name="FRE_STEM" value="fre/cefi/NWA/2024_08_FMS2"/>
+  <property name="FRE_STEM" value="fre/cefi/NWA/2024_09_FMS2"/>
 
   <!-- Please make sure to change your group, such as b, f, g, m, o... -->
   <property name="NCRC_GROUP" value="ira-cefi"/>
@@ -557,7 +557,7 @@ $baseDate
       </diagTable>
       <dataFile label="diagTable" target="INPUT/" chksum="" size="" timestamp="">
         <dataSource site="ncrc">./diag_tables/diag_table_COBALT_2023-04</dataSource>
-        <dataSource site="ncrc">./diag_tables/diag_table_MOM6_2023-03</dataSource>
+        <dataSource site="ncrc">./diag_tables/diag_table_MOM6_2024-09</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table.SIS</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table_COBALT_neus</dataSource>
         <dataSource site="ncrc">./diag_tables/diag_table_MOM6_neus</dataSource>
@@ -591,6 +591,12 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
 #override REMAP_AUXILIARY_VARS = True
 #override DIABATIC_FIRST = False
 #override EQN_OF_STATE = "WRIGHT_FULL"
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03
+#override HREF_FOR_MLD = 10.0 
+#override DIAG_MLD_DENSITY_DIFF = 0.03
 MOM_OVERRIDE_EOF
 
 truncate -s 0 $work/INPUT/COBALT_override
@@ -606,6 +612,9 @@ truncate -s 0 $work/INPUT/COBALT_input
 cat > $work/INPUT/COBALT_input << COBALT_INPUT_EOF
 ! Put the contents of your COBALT_input file here
 do_case2_mod = True
+scale_burial = 1.0
+z_burial = 20.0
+z_denit = 20.0
 COBALT_INPUT_EOF
 
 #hack to test yaml diag_table, convert the diag_table to yaml format