From 468da8ccd04c20190f1bfbbacf847b2f04f1251c Mon Sep 17 00:00:00 2001
From: Gustavo Marques <gmarques@ucar.edu>
Date: Wed, 8 Jan 2025 15:29:41 -0700
Subject: [PATCH 1/4] Update tx2_3v2 defaults for beta05

- Added new topographic edits and updated channel list.
- Enabled COMPUTE_MONIN_OBUKHOV = True to improve the OBL seasonal cycle by limiting the OBL depth to no deeper than the Monin-Obukhov depth.
- Updated background mixing parameters:
  - KV = 1.0E-6
  - KD = 1.0E-7
  - PRANDTL_BKGND = 10
- Configured MLE backup settings:
  - Set MLE_FRONT_LENGTH_FROM_FILE = True
  - Updated MLE_FL_FILE to "mle-lf-clim-tx2_3v2_20250108.nc"
- Enabled Leithy parameterization with:
  - USE_LEITHY = True
  - LEITH_BI_CONST = 90.0
  - LEITHY_CK = 1.0 (full backscatter)
  - LEITH_AH = False
---
 param_templates/MOM_input.yaml      | 57 +++++++++++++++++++++++------
 param_templates/json/MOM_input.json | 55 ++++++++++++++++++++--------
 2 files changed, 84 insertions(+), 28 deletions(-)

diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml
index 4eb1503..ddf8652 100644
--- a/param_templates/MOM_input.yaml
+++ b/param_templates/MOM_input.yaml
@@ -558,6 +558,15 @@ Global:
         value:
             $OCN_GRID == "tx2_3v2": "ocean_topo_tx2_3v2_240501.nc"
             $OCN_GRID == "tx0.25v1": "ocean_topog.nc"
+    TOPO_EDITS_FILE:
+        description: |
+            "default = ''
+            The file from which to read a list of i,j,z topography overrides."
+        datatype: string
+        value:
+            $OCN_GRID == "tx2_3v2": "ocean_topo_tx2_3v2_240501.nc"
+            $OCN_GRID == "tx0.25v1": "ocean_topog.nc"
+
     MAXIMUM_DEPTH:
         description: |
             "[m]
@@ -1050,10 +1059,12 @@ Global:
         value:
             $OCN_GRID == "tx0.25v1": 0.01
             $OCN_GRID == "MISOMIP": 0.001
-    LEITH_AH:
+    USE_LEITHY:
         description: |
             "[Boolean] default = False
-            If true, use a biharmonic Leith nonlinear eddy viscosity."
+            If true, use a modified version of the biharmonic Leith nonlinear
+            eddy viscosity. This implementation can include harmonic backscatter
+            when LEITHY_CK > 0."
         datatype: logical
         units: Boolean
         value:
@@ -1066,7 +1077,7 @@ Global:
         datatype: real
         units: nondim
         value:
-            $OCN_GRID == "tx2_3v2": 128.0
+            $OCN_GRID == "tx2_3v2": 90.0
     USE_LAND_MASK_FOR_HVISC:
         description: |
             "[Boolean] default = False
@@ -1500,8 +1511,22 @@ Global:
         datatype: real
         units: m
         value:
-            $OCN_GRID == "tx2_3v2": 1000.0
             $OCN_GRID == "tx0.25v1": 500.0
+    MLE_FRONT_LENGTH_FROM_FILE:
+        description: |
+            "[Boolean] default = False
+            If true, the MLE front-length scale is read from a file."
+        datatype: logical
+        units: Boolean
+        value:
+            $OCN_GRID == "tx2_3v2": True
+    MLE_FL_FILE:
+        description: |
+            "The path to the file containing the MLE
+            front-length scale.."
+        datatype: string
+        value:
+            $OCN_GRID == "tx2_3v2": "mle-lf-clim-tx2_3v2_20250108.nc"
     MLE_MLD_DECAY_TIME:
         description: |
             "[s] default = 0.0
@@ -1585,7 +1610,7 @@ Global:
         datatype: real
         units: m2 s-1
         value:
-            $OCN_GRID == "tx2_3v2": 0.0
+            $OCN_GRID == "tx2_3v2": 1.0E-07
             $OCN_GRID == "tx0.25v1": 1.5E-05
             $OCN_GRID == "MISOMIP": 5.0E-05
             else: 2.0E-05
@@ -1607,7 +1632,7 @@ Global:
         value: # KV/KD:
             $OCN_GRID == "tx0.25v1": = 1.0E-04 / 1.5E-05
             $OCN_GRID == "MISOMIP": = 1.0E-04 / 5.0E-05
-            else: = 1.0E-04 / 2.0E-05
+            else: = 1.0E-06 / 1.0E-07
     KD_MIN:
         description: |
             "[m2 s-1] default = 2.0E-07
@@ -1618,7 +1643,7 @@ Global:
         datatype: real
         units: m2 s-1
         value:
-            $OCN_GRID == "tx2_3v2":  2.0E-07
+            $OCN_GRID == "tx2_3v2":  1.0E-07
             else: 2.0E-06
     INT_TIDE_DECAY_SCALE:
         description: |
@@ -2581,7 +2606,7 @@ Global:
         datatype: string
         value:
             $OCN_GRID == "tx0.25v1": "MOM_channels_global_025"
-            $OCN_GRID == "tx2_3v2":  "MOM_channels_global_tx2_3v2_240501"
+            $OCN_GRID == "tx2_3v2":  "channels_tx2_3v2_250107.txt"
     SMAG_BI_CONST:
         description: |
             "[nondim] default = 0.0
@@ -2720,7 +2745,8 @@ Global:
             The file from which to read a list of i,j,z topography overrides."
         datatype: string
         value:
-            $OCN_GRID == "tx0.25v1": "All_edits.nc"
+            $OCN_GRID == "tx2_3v2": 'topo_edits_tx2_3v2_250107.nc'
+            else: ''
     PARALLEL_RESTARTFILES:
         description: |
             "[Boolean] default = False
@@ -3167,7 +3193,7 @@ Global:
         datatype: real
         units: m2 s-1
         value:
-            $OCN_GRID == "tx2_3v2": 0.0
+            $OCN_GRID == "tx2_3v2": 1.0E-06
             else: 1.0E-04
     KV_BBL_MIN:
         description: |
@@ -3715,6 +3741,13 @@ KPP:
             If True, use Stokes Similarity package.
         datatype: logical
         value:
-            $COMP_WAV == "ww3" and $WAV_GRID in ["wtx2_3v2", "wgx3v7"]: True    
-
+            $COMP_WAV == "ww3" and $WAV_GRID in ["wtx2_3v2", "wgx3v7"]: True
+    COMPUTE_MONIN_OBUKHOV:
+        description: |
+            default = False
+            If True, limit the OBL depth to be no deeper than Monin-Obukhov depth.
+        datatype: logical
+        units: Boolean
+        value:
+            $OCN_GRID == "tx2_3v2": True
 ...
diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json
index 37ca4fb..4328b5a 100644
--- a/param_templates/json/MOM_input.json
+++ b/param_templates/json/MOM_input.json
@@ -426,6 +426,14 @@
             "$OCN_GRID == \"tx0.25v1\"": "ocean_topog.nc"
          }
       },
+      "TOPO_EDITS_FILE": {
+         "description": "\"default =\nThe file from which to read a list of i,j,z topography overrides.\"\n",
+         "datatype": "string",
+         "value": {
+            "$OCN_GRID == \"tx2_3v2\"": "topo_edits_tx2_3v2_250107.nc",
+            "else": ""
+         }
+      },
       "MAXIMUM_DEPTH": {
          "description": "\"[m]\nThe maximum depth of the ocean.\"\n",
          "datatype": "real",
@@ -799,8 +807,8 @@
             "$OCN_GRID == \"MISOMIP\"": 0.001
          }
       },
-      "LEITH_AH": {
-         "description": "\"[Boolean] default = False\nIf true, use a biharmonic Leith nonlinear eddy viscosity.\"\n",
+      "USE_LEITHY": {
+         "description": "\"[Boolean] default = False\nIf true, use a modified version of the biharmonic Leith nonlinear\neddy viscosity. This implementation can include harmonic backscatter\nwhen LEITHY_CK > 0.\"\n",
          "datatype": "logical",
          "units": "Boolean",
          "value": {
@@ -812,7 +820,7 @@
          "datatype": "real",
          "units": "nondim",
          "value": {
-            "$OCN_GRID == \"tx2_3v2\"": 128.0
+            "$OCN_GRID == \"tx2_3v2\"": 90.0
          }
       },
       "USE_LAND_MASK_FOR_HVISC": {
@@ -1125,10 +1133,24 @@
          "datatype": "real",
          "units": "m",
          "value": {
-            "$OCN_GRID == \"tx2_3v2\"": 1000.0,
             "$OCN_GRID == \"tx0.25v1\"": 500.0
          }
       },
+      "MLE_FRONT_LENGTH_FROM_FILE": {
+         "description": "\"[Boolean] default = False\nIf true, the MLE front-length scale is read from a file.\"\n",
+         "datatype": "logical",
+         "units": "Boolean",
+         "value": {
+            "$OCN_GRID == \"tx2_3v2\"": true
+         }
+      },
+      "MLE_FL_FILE": {
+         "description": "\"The path to the file containing the MLE\nfront-length scale..\"\n",
+         "datatype": "string",
+         "value": {
+            "$OCN_GRID == \"tx2_3v2\"": "mle-lf-clim-tx2_3v2_20250108.nc"
+         }
+      },
       "MLE_MLD_DECAY_TIME": {
          "description": "\"[s] default = 0.0\nThe time-scale for a running-mean filter applied to the mixed-layer\ndepth used in the MLE restratification parameterization. When\nthe MLD deepens below the current running-mean the running-mean\nis instantaneously set to the current MLD.\"\n",
          "datatype": "real",
@@ -1195,7 +1217,7 @@
          "datatype": "real",
          "units": "m2 s-1",
          "value": {
-            "$OCN_GRID == \"tx2_3v2\"": 0.0,
+            "$OCN_GRID == \"tx2_3v2\"": 1e-07,
             "$OCN_GRID == \"tx0.25v1\"": 1.5e-05,
             "$OCN_GRID == \"MISOMIP\"": 5e-05,
             "else": 2e-05
@@ -1214,7 +1236,7 @@
          "value": {
             "$OCN_GRID == \"tx0.25v1\"": "= 1.0E-04 / 1.5E-05",
             "$OCN_GRID == \"MISOMIP\"": "= 1.0E-04 / 5.0E-05",
-            "else": "= 1.0E-04 / 2.0E-05"
+            "else": "= 1.0E-06 / 1.0E-07"
          }
       },
       "KD_MIN": {
@@ -1222,7 +1244,7 @@
          "datatype": "real",
          "units": "m2 s-1",
          "value": {
-            "$OCN_GRID == \"tx2_3v2\"": 2e-07,
+            "$OCN_GRID == \"tx2_3v2\"": 1e-07,
             "else": 2e-06
          }
       },
@@ -2040,7 +2062,7 @@
          "datatype": "string",
          "value": {
             "$OCN_GRID == \"tx0.25v1\"": "MOM_channels_global_025",
-            "$OCN_GRID == \"tx2_3v2\"": "MOM_channels_global_tx2_3v2_240501"
+            "$OCN_GRID == \"tx2_3v2\"": "channels_tx2_3v2_250107.txt"
          }
       },
       "SMAG_BI_CONST": {
@@ -2153,13 +2175,6 @@
             "$OCN_GRID == \"tx0.25v1\"": true
          }
       },
-      "TOPO_EDITS_FILE": {
-         "description": "\"default =\nThe file from which to read a list of i,j,z topography overrides.\"\n",
-         "datatype": "string",
-         "value": {
-            "$OCN_GRID == \"tx0.25v1\"": "All_edits.nc"
-         }
-      },
       "PARALLEL_RESTARTFILES": {
          "description": "\"[Boolean] default = False\nIf true, each processor writes its own restart file,\notherwise a single restart file is generated\"\n",
          "datatype": "logical",
@@ -2535,7 +2550,7 @@
          "datatype": "real",
          "units": "m2 s-1",
          "value": {
-            "$OCN_GRID == \"tx2_3v2\"": 0.0,
+            "$OCN_GRID == \"tx2_3v2\"": 1e-06,
             "else": 0.0001
          }
       },
@@ -3011,6 +3026,14 @@
          "value": {
             "$COMP_WAV == \"ww3\" and $WAV_GRID in [\"wtx2_3v2\", \"wgx3v7\"]": true
          }
+      },
+      "COMPUTE_MONIN_OBUKHOV": {
+         "description": "default = False\nIf True, limit the OBL depth to be no deeper than Monin-Obukhov depth.\n",
+         "datatype": "logical",
+         "units": "Boolean",
+         "value": {
+            "$OCN_GRID == \"tx2_3v2\"": true
+         }
       }
    }
 }
\ No newline at end of file

From 7211c30815a326d931b2d9333a83682fcc2596a8 Mon Sep 17 00:00:00 2001
From: Gustavo Marques <gmarques@ucar.edu>
Date: Thu, 9 Jan 2025 08:00:29 -0700
Subject: [PATCH 2/4] Add input files to the data list

---
 param_templates/input_data_list.yaml      | 5 ++++-
 param_templates/json/input_data_list.json | 6 +++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/param_templates/input_data_list.yaml b/param_templates/input_data_list.yaml
index ea1c7e3..ed1fec4 100644
--- a/param_templates/input_data_list.yaml
+++ b/param_templates/input_data_list.yaml
@@ -18,6 +18,7 @@ mom.input_data_list:
         $OCN_GRID == "tx2_3v2":  "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/ocean_topog.nc"
     TOPO_EDITS_FILE:
+        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/All_edits.nc"
     TEMP_SALT_Z_INIT_FILE:
         $OCN_GRID in ["tx2_3v2", "tx0.25v1"]:
@@ -34,7 +35,7 @@ mom.input_data_list:
         $OCN_GRID == "tx2_3v2": "${INPUTDIR}/energy_new_tx2_3_conserve_230415_cdf5.nc"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/tidal_amplitude.v20140616.nc"
     CHANNEL_LIST_FILE:
-        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/MOM_channels_global_tx2_3v2_240501"
+        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/channels_tx2_3v2_250107.txt"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/MOM_channels_global_025"
     GEOTHERMAL_FILE:
         $OCN_GRID == "tx2_3v2": "${INPUTDIR}/geothermal_davies2013_tx2_3_20240318_cdf5.nc"
@@ -42,6 +43,8 @@ mom.input_data_list:
     CHL_FILE:
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/seawifs-clim-1997-2010.1440x1080.v20180328.nc"
         $OCN_GRID == "tx2_3v2": "${INPUTDIR}/seawifs-clim-1997-2010-tx2_3v2.230416.nc"
+    MLE_FL_FILE:
+        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/mle-lf-clim-tx2_3v2_20250108.nc"
     CFC_BC_FILE: "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/cfc_atm_20230310.nc"
     DIAG_COORD_DEF_RHO2:
         $OCN_GRID == "tx2_3v2":  "${INPUTDIR}/ocean_rho2_190917.nc"
diff --git a/param_templates/json/input_data_list.json b/param_templates/json/input_data_list.json
index 5a116b2..f26ca0b 100644
--- a/param_templates/json/input_data_list.json
+++ b/param_templates/json/input_data_list.json
@@ -22,6 +22,7 @@
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/ocean_topog.nc"
       },
       "TOPO_EDITS_FILE": {
+         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc",
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/All_edits.nc"
       },
       "TEMP_SALT_Z_INIT_FILE": {
@@ -43,7 +44,7 @@
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/tidal_amplitude.v20140616.nc"
       },
       "CHANNEL_LIST_FILE": {
-         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/MOM_channels_global_tx2_3v2_240501",
+         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/channels_tx2_3v2_250107.txt",
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/MOM_channels_global_025"
       },
       "GEOTHERMAL_FILE": {
@@ -54,6 +55,9 @@
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/seawifs-clim-1997-2010.1440x1080.v20180328.nc",
          "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/seawifs-clim-1997-2010-tx2_3v2.230416.nc"
       },
+      "MLE_FL_FILE": {
+         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/mle-lf-clim-tx2_3v2_20250108.nc"
+      },
       "CFC_BC_FILE": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/cfc_atm_20230310.nc",
       "DIAG_COORD_DEF_RHO2": {
          "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/ocean_rho2_190917.nc"

From ef5a6b8e438f28f66e457c2dc3a16acf5df2b8b8 Mon Sep 17 00:00:00 2001
From: Gustavo Marques <gmarques@ucar.edu>
Date: Thu, 9 Jan 2025 08:04:19 -0700
Subject: [PATCH 3/4] Add missing input files to the data list

---
 param_templates/input_data_list.yaml      | 2 +-
 param_templates/json/input_data_list.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/param_templates/input_data_list.yaml b/param_templates/input_data_list.yaml
index ed1fec4..a97c2d8 100644
--- a/param_templates/input_data_list.yaml
+++ b/param_templates/input_data_list.yaml
@@ -18,7 +18,7 @@ mom.input_data_list:
         $OCN_GRID == "tx2_3v2":  "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/ocean_topog.nc"
     TOPO_EDITS_FILE:
-        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc"
+        $OCN_GRID == "tx2_3v2": "${INPUTDIR}/topo_edits_tx2_3v2_250107.nc"
         $OCN_GRID == "tx0.25v1": "${INPUTDIR}/All_edits.nc"
     TEMP_SALT_Z_INIT_FILE:
         $OCN_GRID in ["tx2_3v2", "tx0.25v1"]:
diff --git a/param_templates/json/input_data_list.json b/param_templates/json/input_data_list.json
index f26ca0b..30b4f1f 100644
--- a/param_templates/json/input_data_list.json
+++ b/param_templates/json/input_data_list.json
@@ -22,7 +22,7 @@
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/ocean_topog.nc"
       },
       "TOPO_EDITS_FILE": {
-         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/ocean_topo_tx2_3v2_240501.nc",
+         "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/topo_edits_tx2_3v2_250107.nc",
          "$OCN_GRID == \"tx0.25v1\"": "${INPUTDIR}/All_edits.nc"
       },
       "TEMP_SALT_Z_INIT_FILE": {

From 2619750d05a3cb5e92bca523f5300867b21bb5cc Mon Sep 17 00:00:00 2001
From: Gustavo Marques <gmarques@ucar.edu>
Date: Thu, 9 Jan 2025 08:51:57 -0700
Subject: [PATCH 4/4] Remove duplication (TOPO_EDITS_FILE)

---
 param_templates/MOM_input.yaml      | 13 ++-----------
 param_templates/json/MOM_input.json |  4 ++--
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml
index 1fec7db..bbcd56b 100644
--- a/param_templates/MOM_input.yaml
+++ b/param_templates/MOM_input.yaml
@@ -566,9 +566,8 @@ Global:
             The file from which to read a list of i,j,z topography overrides."
         datatype: string
         value:
-            $OCN_GRID == "tx2_3v2": "ocean_topo_tx2_3v2_240501.nc"
-            $OCN_GRID == "tx0.25v1": "ocean_topog.nc"
-
+            $OCN_GRID == "tx2_3v2": "topo_edits_tx2_3v2_250107.nc"
+            $OCN_GRID == "tx0.25v1": "All_edits.nc"
     MAXIMUM_DEPTH:
         description: |
             "[m]
@@ -2722,14 +2721,6 @@ Global:
         value:
             $OCN_GRID == "tx2_3v2": True
             $OCN_GRID == "tx0.25v1": True
-    TOPO_EDITS_FILE:
-        description: |
-            "default =
-            The file from which to read a list of i,j,z topography overrides."
-        datatype: string
-        value:
-            $OCN_GRID == "tx2_3v2": 'topo_edits_tx2_3v2_250107.nc'
-            else: ''
     PARALLEL_RESTARTFILES:
         description: |
             "[Boolean] default = False
diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json
index 90af4a5..83a101e 100644
--- a/param_templates/json/MOM_input.json
+++ b/param_templates/json/MOM_input.json
@@ -430,11 +430,11 @@
          }
       },
       "TOPO_EDITS_FILE": {
-         "description": "\"default =\nThe file from which to read a list of i,j,z topography overrides.\"\n",
+         "description": "\"default = ''\nThe file from which to read a list of i,j,z topography overrides.\"\n",
          "datatype": "string",
          "value": {
             "$OCN_GRID == \"tx2_3v2\"": "topo_edits_tx2_3v2_250107.nc",
-            "else": ""
+            "$OCN_GRID == \"tx0.25v1\"": "All_edits.nc"
          }
       },
       "MAXIMUM_DEPTH": {