Merge pull request #300 from alperaltuntas/remove_duplicate_params

Remove duplicate parameters in template files

Author: alperaltuntas

.github/workflows/general-ci-tests.yml

@@ -94,6 +94,23 @@ jobs:
       - name: Run the check_default_params script
         run: python tests/check_default_params.py
 
+  # Job to check if duplicate parameters exist in param template files
+  check_duplicate_params:
+    
+    runs-on: ubuntu-latest
+    
+    steps:
+      # Checkout the repo
+      - uses: actions/checkout@v4
+      
+      # Run the test
+      - name: Run the check_duplicate_params script
+        run: |
+          python tests/check_duplicate_params.py param_templates/MOM_input.yaml
+          python tests/check_duplicate_params.py param_templates/input_data_list.yaml
+          python tests/check_duplicate_params.py param_templates/input_nml.yaml
+          python tests/check_duplicate_params.py param_templates/diag_table.yaml
+  
   # Job to run check_input_data_list script
   check_input_data_list:
 

cime_config/buildnml

@@ -399,10 +399,13 @@ def prechecks(case, inst_suffixes):
                 f"Missing rpointer files in rundir. Expected files with pattern {rpointer_pattern}.",
             )
 
-    # check if the restart file is present in rundir
+    # check if the restart file is present in rundir for fresh branch or hybrid runs
     if run_type in ["branch", "hybrid"] and not continue_run and not get_refcase:
-        restart_file = os.path.join(rundir, f'./{run_refcase}.mom6.r.{run_refdate}-{run_reftod}.nc')
-        assert os.path.exists(restart_file), f"Missing restart file {run_refcase}.mom6.r.{run_refdate}-{run_reftod}.nc in rundir."
+        restart_file_pattern = run_refcase + r".mom6.*.r." + run_refdate + "-" + run_reftod + r".*nc$"
+        restart_files = [
+            f for f in os.listdir(rundir) if re.match(restart_file_pattern, f)
+        ]
+        assert len(restart_files) > 0, f"Missing restart file in rundir. Expected file matching pattern {restart_file_pattern}."
 
 def postchecks(case,  MOM_input_final):
     """Performs checks after input files are generated. To be called within prep_input() as a final step."""

param_templates/MOM_input.yaml

@@ -89,13 +89,6 @@ Global:
             $OCN_GRID == "tx2_3v2": 480
             $OCN_GRID == "tx0.25v1": 1080
             $OCN_GRID == "MISOMIP": 40
-    IO_LAYOUT:
-        description: |
-            "default = 0
-            The processor layout to be used, or 0,0 to automatically
-            set the io_layout to be the same as the layout."
-        datatype: string
-        value: 1, 1
     NK:
         description: |
             "[nondim]
@@ -295,7 +288,9 @@ Global:
             "default = WRIGHT_FULL
             EQN_OF_STATE determines which ocean equation of state should be used."
         datatype: string
-        value: "WRIGHT_FULL"
+        value: 
+            $OCN_GRID == "MISOMIP": "LINEAR"
+            else: "WRIGHT_FULL"
     DTFREEZE_DP:
         description: |
             "[deg C Pa-1] default = 0.0
@@ -2946,16 +2941,6 @@ Global:
         units: not defined
         value:
             $OCN_GRID == "MISOMIP": 1.0
-    EQN_OF_STATE:
-        description: |
-            "default = 'WRIGHT'
-            EQN_OF_STATE determines which ocean equation of state
-            should be used.  Currently, the valid choices are
-            'LINEAR', 'UNESCO', and 'WRIGHT'.
-            This is only used if USE_EOS is true."
-        datatype: string
-        value:
-            $OCN_GRID == "MISOMIP": "LINEAR"
     RHO_T0_S0:
         description: |
             "[kg m-3] default = 1000.0
@@ -3148,7 +3133,6 @@ Global:
              target density."
         datatype: logical
         units: Boolean
-        value:
         value:
             $MOM6_VERTICAL_GRID == "hycom1" and $OCN_GRID == "tx2_3v2": True
     ISOMIP_TNUDG:
@@ -3737,8 +3721,8 @@ Global:
             be the same as the layout.
         datatype: list
         value:
-            $OCN_GRID == "tx0.25v1":
-              4, 3
+            $OCN_GRID == "tx0.25v1": 4, 3
+            else: 1, 1
     AUTO_MASKTABLE:
         description: |
             Turn on automatic mask table generation to eliminate land blocks

param_templates/input_data_list.yaml

@@ -28,9 +28,6 @@ mom.input_data_list:
         $OCN_GRID in ["tx2_3v2", "tx0.25v1"]:
             $INIT_LAYERS_FROM_Z_FILE == "True":
                 "${INPUTDIR}/${TEMP_SALT_Z_INIT_FILE}"
-    MAX_LAYER_THICKNESS_CONFIG:
-        $MOM6_VERTICAL_GRID == "hycom1" and $OCN_GRID in ["tx2_3v2"]:
-                  "${DIN_LOC_ROOT}/ocn/mom/tx2_3v2/dz_max-2025-09-12.nc"
     SURFACE_PRESSURE_FILE:
         $OCN_GRID == "MISOMIP": "${INPUTDIR}/MISOMIP_181108.nc"
     SALT_RESTORE_FILE:

param_templates/json/MOM_input.json

@@ -43,13 +43,6 @@
             "$OCN_GRID == \"MISOMIP\"": 40
          }
       },
-      "IO_LAYOUT": {
-         "description": "The processor layout to be used, or 0,0 to automatically set the io_layout to\nbe the same as the layout.\n",
-         "datatype": "list",
-         "value": {
-            "$OCN_GRID == \"tx0.25v1\"": "4, 3"
-         }
-      },
       "NK": {
          "description": "\"[nondim]\nThe number of model layers.\"\n",
          "datatype": "integer",
@@ -200,10 +193,11 @@
          }
       },
       "EQN_OF_STATE": {
-         "description": "\"default = 'WRIGHT'\nEQN_OF_STATE determines which ocean equation of state\nshould be used.  Currently, the valid choices are\n'LINEAR', 'UNESCO', and 'WRIGHT'.\nThis is only used if USE_EOS is true.\"\n",
+         "description": "\"default = WRIGHT_FULL\nEQN_OF_STATE determines which ocean equation of state should be used.\"\n",
          "datatype": "string",
          "value": {
-            "$OCN_GRID == \"MISOMIP\"": "LINEAR"
+            "$OCN_GRID == \"MISOMIP\"": "LINEAR",
+            "else": "WRIGHT_FULL"
          }
       },
       "DTFREEZE_DP": {
@@ -3028,6 +3022,14 @@
             "$COMP_WAV == \"ww3\" and $MOM6_WW3_CPL_METHOD == \"most\"": "0.04, 0.11, 0.33"
          }
       },
+      "IO_LAYOUT": {
+         "description": "The processor layout to be used, or 0,0 to automatically set the io_layout to\nbe the same as the layout.\n",
+         "datatype": "list",
+         "value": {
+            "$OCN_GRID == \"tx0.25v1\"": "4, 3",
+            "else": "1, 1"
+         }
+      },
       "AUTO_MASKTABLE": {
          "description": "Turn on automatic mask table generation to eliminate land blocks\n",
          "datatype": "list",

param_templates/json/input_data_list.json

@@ -15,7 +15,7 @@
          "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/lev-2025-09-12.nc"
       },
       "MAX_LAYER_THICKNESS_CONFIG": {
-         "$MOM6_VERTICAL_GRID == \"hycom1\" and $OCN_GRID in [\"tx2_3v2\"]": "${DIN_LOC_ROOT}/ocn/mom/tx2_3v2/dz_max-2025-09-12.nc"
+         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/dz_max-2025-09-12.nc"
       },
       "DIAG_COORD_DEF_Z": {
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/interpolate_zgrid_40L.nc"