Update ocean_BGC tag, add COBALT_input and override to all experiment…

…s, and update NWA12 xml (#48) * add COBALT_input/COBALT_override,and namelists * add COBALT_input/override to exps * Update baselines for NWA12-COBALT * Update NWA xml to include COBALT_input/override * Update ocean_BGC tag * Update NWA12-RT baseline again
NOAA-GFDL · Jun 7, 2024 · 8fb00cd · 8fb00cd
1 parent 89ae908
commit 8fb00cd
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Showing 21 changed files with 80 additions and 9 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -22,10 +22,6 @@
 	path = src/Icepack
 	url = https://github.com/CICE-Consortium/Icepack.git
 	branch = Icepack1.3.3
-[submodule "src/ocean_BGC"]
-	path = src/ocean_BGC
-	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC.git
-	branch = dev/cefi
 [submodule "src/ice_param"]
 	path = src/ice_param
 	url = https://github.com/NOAA-GFDL/ice_param.git
@@ -46,3 +42,7 @@
 	path = src/coupler
 	url = https://github.com/NOAA-GFDL/FMScoupler.git
 	branch = 2024.01.01
+[submodule "src/ocean_BGC"]
+	path = src/ocean_BGC
+	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC.git
+	branch = dev/cefi
diff --git a/exps/NEP10.COBALT/INPUT/COBALT_input b/exps/NEP10.COBALT/INPUT/COBALT_input
@@ -0,0 +1 @@
+do_case2_mod = True
diff --git a/exps/NEP10.COBALT/INPUT/COBALT_override b/exps/NEP10.COBALT/INPUT/COBALT_override
diff --git a/exps/NEP10.COBALT/input.nml_24hr b/exps/NEP10.COBALT/input.nml_24hr
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/NEP10.COBALT/input.nml_24hr_rst b/exps/NEP10.COBALT/input.nml_24hr_rst
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/NEP10.COBALT/input.nml_48hr b/exps/NEP10.COBALT/input.nml_48hr
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/NWA12.COBALT/INPUT/COBALT_input b/exps/NWA12.COBALT/INPUT/COBALT_input
@@ -0,0 +1 @@
+do_case2_mod = True
diff --git a/exps/NWA12.COBALT/INPUT/COBALT_override b/exps/NWA12.COBALT/INPUT/COBALT_override
diff --git a/exps/NWA12.COBALT/driver.sh b/exps/NWA12.COBALT/driver.sh
@@ -59,7 +59,7 @@ mv ocean.stats RESTART_24hrs_rst
 
 # Define the directories containing the files
 DIR1="./RESTART_24hrs_rst"
-DIR2="/gpfs/f5/cefi/proj-shared/github/ci_data/reference/main/NWA12.COBALT/20240531"
+DIR2="/gpfs/f5/cefi/proj-shared/github/ci_data/reference/main/NWA12.COBALT/20240606"
 
 # Define the files to compare
 FILES=("$DIR2"/*.nc)

diff --git a/exps/NWA12.COBALT/input.nml_24hr b/exps/NWA12.COBALT/input.nml_24hr
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/NWA12.COBALT/input.nml_24hr_rst b/exps/NWA12.COBALT/input.nml_24hr_rst
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/NWA12.COBALT/input.nml_48hr b/exps/NWA12.COBALT/input.nml_48hr
@@ -14,6 +14,11 @@
         parameter_filename = 'INPUT/SIS_input','INPUT/SIS_layout','INPUT/SIS_override'
 /
 
+ &cobalt_input_nml
+        parameter_filename = 'INPUT/COBALT_input',
+                             'INPUT/COBALT_override'
+/
+
  &atmos_model_nml
         layout= 1,1
 /

diff --git a/exps/OM4.single_column.COBALT/COBALT_input b/exps/OM4.single_column.COBALT/COBALT_input
diff --git a/exps/OM4.single_column.COBALT/COBALT_override b/exps/OM4.single_column.COBALT/COBALT_override
diff --git a/exps/OM4.single_column.COBALT/diag_table b/exps/OM4.single_column.COBALT/diag_table
@@ -287,10 +287,11 @@ OM4_single_column
  #"generic_cobalt ","wc_vert_int_jfe_iceberg","wc_vert_int_jfe_iceberg",  "ocean_cobalt_fluxes_int","all","mean","none",2
  #"generic_cobalt ","wc_vert_int_jno3_iceberg","wc_vert_int_jno3_iceberg","ocean_cobalt_fluxes_int","all","mean","none",2
  #"generic_cobalt ","wc_vert_int_jpo4_iceberg","wc_vert_int_jpo4_iceberg","ocean_cobalt_fluxes_int","all","mean","none",2
- "generic_cobalt ","wc_vert_int_jprod_n2amx", "wc_vert_int_jprod_n2amx", "ocean_cobalt_fluxes_int","all","mean","none",2
+ #"generic_cobalt ","wc_vert_int_jprod_n2amx", "wc_vert_int_jprod_n2amx", "ocean_cobalt_fluxes_int","all","mean","none",2
+ "generic_cobalt ","wc_vert_int_jnamx", "wc_vert_int_namx", "ocean_cobalt_fluxes_int","all","mean","none",2
  "generic_cobalt ","wc_vert_int_net_phyto_resp", "wc_vert_int_net_phyto_resp", "ocean_cobalt_fluxes_int","all","mean","none",2
  "generic_cobalt ","wc_vert_int_npp",         "wc_vert_int_npp",         "ocean_cobalt_fluxes_int","all","mean","none",2
- "generic_cobalt ","wc_vert_int_chemoautopp", "wc_vert_int_chemoautopp", "ocean_cobalt_fluxes_int","all","mean","none",2
+ #"generic_cobalt ","wc_vert_int_chemoautopp", "wc_vert_int_chemoautopp", "ocean_cobalt_fluxes_int","all","mean","none",2
 #=======================================
 # ocean_cobalt_tracers_month_z
 #=======================================

diff --git a/exps/OM4.single_column.COBALT/driver.sh b/exps/OM4.single_column.COBALT/driver.sh
@@ -10,13 +10,15 @@ echo "Test started:  " `date`
 echo "run 48hrs test ..."
 ln -fs input.nml_48hr input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out1 2>err1
+tail out1
 mv RESTART RESTART_48hrs
 mv ocean.stats* RESTART_48hrs
 
 #
 echo "run 24hrs test ..."
 ln -fs input.nml_24hr input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out2 2>err2
+tail out2
 mv RESTART RESTART_24hrs
 mv ocean.stats* RESTART_24hrs
 
@@ -30,6 +32,7 @@ popd
 echo "run 24hrs rst test ..."
 ln -fs input.nml_24hr_rst input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out3 2>err3
+tail out3
 mv RESTART RESTART_24hrs_rst
 mv ocean.stats* RESTART_24hrs_rst
 

diff --git a/exps/OM4.single_column.COBALT/input.nml_24hr b/exps/OM4.single_column.COBALT/input.nml_24hr
@@ -17,6 +17,12 @@
                              'SIS_layout',
                              'SIS_override' /
 
+ &cobalt_input_nml
+        parameter_filename = 'COBALT_input',
+                             'COBALT_override'
+/
+
+
  &atmos_model_nml
            layout = 1, 1
 /

diff --git a/exps/OM4.single_column.COBALT/input.nml_24hr_rst b/exps/OM4.single_column.COBALT/input.nml_24hr_rst
@@ -17,6 +17,12 @@
                              'SIS_layout',
                              'SIS_override' /
 
+&cobalt_input_nml
+        parameter_filename = 'COBALT_input',
+                             'COBALT_override'
+/
+
+
  &atmos_model_nml
            layout = 1, 1
 /

diff --git a/exps/OM4.single_column.COBALT/input.nml_48hr b/exps/OM4.single_column.COBALT/input.nml_48hr
@@ -17,6 +17,11 @@
                              'SIS_layout',
                              'SIS_override' /
 
+ &cobalt_input_nml
+        parameter_filename = 'COBALT_input',
+                             'COBALT_override'
+/
+
  &atmos_model_nml
            layout = 1, 1
 /

diff --git a/src/ocean_BGC b/src/ocean_BGC
diff --git a/xmls/NWA12/CEFI_NWA12_cobalt.xml b/xmls/NWA12/CEFI_NWA12_cobalt.xml
@@ -208,6 +208,9 @@ frecheck -r layout -p ncrc5.intel22 -x CEFI_NWA12_cobalt.xml CEFI_NWA12_COBALT_V
         do_chksum = .false.
         do_endpoint_chksum = .false.
       </namelist>
+      <namelist name ="cobalt_input_nml">
+        parameter_filename = 'INPUT/COBALT_input','INPUT/COBALT_override'
+      </namelist>
       <namelist name="generic_tracer_nml">
         do_generic_tracer=.true.
         do_generic_abiotic=.false.
@@ -591,6 +594,21 @@ cat > $work/INPUT/MOM_override << MOM_OVERRIDE_EOF
 #override DT_THERM = 1200.0
 #override DT = 400        
 MOM_OVERRIDE_EOF
+
+truncate -s 0 $work/INPUT/COBALT_override
+cat > $work/INPUT/COBALT_override << COBALT_OVERRIDE_EOF
+! Put the contents of your COBALT_override file here.
+! For parameters which are not specified in the COBALT_input file, just set the new value, ex:
+! do_case2_mod = True
+! For parameters which are specified in the COBALT_input file, specify an override, ex:
+!#override do_case2_mod = True
+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		      
+COBALT_INPUT_EOF
         ]]>
       </csh>
     </input>
@@ -661,7 +679,7 @@ MOM_OVERRIDE_EOF
          cd $work
          #Make a directory to trick FRE to pick up and archive in ascii
          mkdir extra.results
-         mv MOM_parameter_doc* SIS_parameter_doc* seaice.stats* ocean.stats* extra.results/
+         mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* seaice.stats* ocean.stats* extra.results/
          cp diag_table extra.results/.
          #When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
          #This causes problems for ferret and python tools for analysis.
+33 −2		.github/workflows/cobalt_ci.yml
+86 −0		generic_tracers/cobalt_param_doc.F90
+1 −9		generic_tracers/cobalt_reg_diag.F90
+0 −6		generic_tracers/cobalt_send_diag.F90
+10 −5		generic_tracers/cobalt_types.F90
+530 −399		generic_tracers/generic_COBALT.F90