ACCESS-NRI · anton-seaice · Sep 23, 2025 · Jul 18, 2025 · Jul 23, 2025 · Aug 13, 2025
diff --git a/MOM_input b/MOM_input
@@ -28,20 +28,20 @@ AUTO_MASKTABLE = True           !   [Boolean] default = False
 USE_REGRIDDING = True           !   [Boolean] default = False
                                 ! If True, use the ALE algorithm (regridding/remapping). If False, use the
                                 ! layered isopycnal algorithm.
-THICKNESSDIFFUSE = True         !   [Boolean] default = False
-                                ! If true, isopycnal surfaces are diffused with a Laplacian coefficient of KHTH.
-THICKNESSDIFFUSE_FIRST = True   !   [Boolean] default = False
-                                ! If true, do thickness diffusion or interface height smoothing before dynamics.
-                                ! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
 DT = 1800.0                     !   [s]
                                 ! The (baroclinic) dynamics time step.  The time-step that is actually used will
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
 DT_THERM = 3600.0               !   [s] default = 1800.0
-                                ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
-                                ! an integer multiple of DT and less than the forcing or coupling time-step,
-                                ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
-                                ! multiple of the coupling timestep.  By default DT_THERM is set to DT.
+                                ! The thermodynamic time step. Ideally DT_THERM should be an integer multiple of
+                                ! DT and of DT_TRACER_ADVECT and less than the forcing or coupling time-step.
+                                ! However, if THERMO_SPANS_COUPLING is true, DT_THERM can be an integer multiple
+                                ! of the coupling timestep. By default DT_THERM is set to DT.
+THICKNESSDIFFUSE = True         !   [Boolean] default = False
+                                ! If true, isopycnal surfaces are diffused with a Laplacian coefficient of KHTH.
+THICKNESSDIFFUSE_FIRST = True   !   [Boolean] default = False
+                                ! If true, do thickness diffusion or interface height smoothing before dynamics.
+                                ! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
 HFREEZE = 10.0                  !   [m] default = -1.0
                                 ! If HFREEZE > 0, melt potential will be computed. The actual depth over which
                                 ! melt potential is computed will be min(HFREEZE, OBLD), where OBLD is the
@@ -67,6 +67,12 @@ CHECK_BAD_SURFACE_VALS = True   !   [Boolean] default = False
                                 ! If true, check the surface state for ridiculous values.
 SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
                                 ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
+WRITE_GEOM = 2                  ! default = 1
+                                ! If =0, never write the geometry and vertical grid files. If =1, write the
+                                ! geometry and vertical grid files only for a new simulation. If =2, always
+                                ! write the geometry and vertical grid files. Other values are invalid.
+GEOM_FILE = "access-om3.mom6.geometry.nc" ! default = "ocean_geometry"
+                                ! The file into which to write the ocean geometry.
 
 ! === module MOM_domains ===
 TRIPOLAR_N = True               !   [Boolean] default = False
@@ -147,6 +153,10 @@ USE_IDEAL_AGE_TRACER = True     !   [Boolean] default = False
 
 ! === module ideal_age_example ===
 
+! === module MOM_fixed_initialization ===
+
+! === module MOM_grid_init ===
+
 ! === module MOM_coord_initialization ===
 REGRIDDING_COORDINATE_MODE = "ZSTAR" ! default = "LAYER"
                                 ! Coordinate mode for vertical regridding. Choose among the following
@@ -214,16 +224,8 @@ TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True !   [Boolean] default = False
                                 ! If true, initial conditions are on the model horizontal grid. Extrapolation
                                 ! over missing ocean values is done using an ICE-9 procedure with vertical ALE
                                 ! remapping .
-Z_INIT_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for initialization. See
-                                ! REMAPPING_USE_OM4_SUBCELLS for more details. We recommend setting this option
-                                ! to false.
 
 ! === module MOM_diag_mediator ===
-DIAG_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for diagnostics. See
-                                ! REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting this option to
-                                ! false.
 DIAG_COORD_DEF_Z = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "WOA09"
                                 ! Determines how to specify the coordinate resolution. Valid options are:
                                 !  PARAM       - use the vector-parameter DIAG_COORD_RES_Z
@@ -320,10 +322,6 @@ USE_STORED_SLOPES = True        !   [Boolean] default = False
 KH_RES_SCALE_COEF = 0.4         !   [nondim] default = 1.0
                                 ! A coefficient that determines how KhTh is scaled away if RESOLN_SCALED_... is
                                 ! true, as F = 1 / (1 + (KH_RES_SCALE_COEF*Rd/dx)^KH_RES_FN_POWER).
-EBT_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
-                                ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
-                                ! this option to false.
 
 ! === module MOM_set_visc ===
 CHANNEL_DRAG = True             !   [Boolean] default = False
@@ -472,10 +470,6 @@ MLE_MLD_DECAY_TIME = 3.456E+05  !   [s] default = 0.0
                                 ! MLD.
 
 ! === module MOM_diagnostics ===
-INTWAVE_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
-                                ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
-                                ! this option to false.
 
 ! === module MOM_diabatic_driver ===
 ! The following parameters are used for diabatic processes.
@@ -598,10 +592,6 @@ USE_HORIZONTAL_BOUNDARY_DIFFUSION = True !   [Boolean] default = False
 HBD_LINEAR_TRANSITION = True    !   [Boolean] default = False
                                 ! If True, apply a linear transition at the base/top of the boundary.
                                 ! The flux will be fully applied at k=k_min and zero at k=k_max.
-HBD_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for horizontal boundary
-                                ! diffusion. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
-                                ! this option to false.
 
 ! === module MOM_sum_output ===
 

diff --git a/README.md b/README.md
@@ -1,17 +1,3 @@
-# MOM6-CICE6 1 deg JRA55-do IAF ACCESS-OM3 configuration
-
-**WARNING: This configuration is still under development and should not be used for production.**
-
 See [`main` branch
-README](https://github.com/COSIMA/MOM6-CICE6/blob/main/README.md) for usage
-information.
-
-## Features
-
-- data atmosphere (DATM) = JRA55-do v1-4, IAF 1958-2018
-- data runoff (DROF) = JRA55-do v1-4, IAF 1958-2018
-- tripolar grid
-
-## Requirements
-
-This configuration requires [Payu](https://github.com/payu-org/payu) > v1.1.3 to run.
+README](https://github.com/ACCESS-NRI/access-om3-configs/blob/main/README.md) for usage
+information.
diff --git a/config.yaml b/config.yaml
@@ -1,13 +1,25 @@
-# PBS configuration
+# Payu configuration
 
 # If submitting to a different project to your default, uncomment line below 
 # and change project code as appropriate; also set shortpath below
 # project: x77
-
 # Force payu to always find, and save, files in this scratch project directory
-# (you may need to add the corresponding PBS -l storage flag in sync_data.sh)
 # shortpath: /scratch/v45
 
+# Using payu sync is recommend to copy data from ephemeral scratch space to 
+# longer term storage
+sync:
+    enable: False # set path below and change to true
+    path: null # Set to location on /g/data (e.g. /g/data/PROJECT/USER/EXPERIMENT)
+    restart: True
+
+#Model software version
+modules:
+    use:
+        - /g/data/vk83/modules
+    load:
+        - access-om3/2025.08.001
+
 queue: normal
 ncpus: 240
 jobfs: 10GB
@@ -17,7 +29,6 @@ walltime: 02:00:00
 jobname: 100km_jra55do_iaf
 
 model: access-om3
-
 exe: access-om3-MOM6-CICE6
 input:
     - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.100km/2024.01.25/access-om2-100km-ESMFmesh.nc
@@ -37,15 +48,15 @@ collate: false
 runlog: false
 metadata: 
     enable: false
+manifest:
+  reproduce:
+    exe: false
+    inputs: false
 
 userscripts:
     archive: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/archive.sh
 
-modules:
-    use:
-        - /g/data/vk83/modules
-    load:
-        - access-om3/2025.05.001
-        - nco/5.0.5
+postscript: -v PROJECT,SCRIPTS_DIR=/g/data/vk83/apps/om3-scripts -lstorage=${PBS_NCI_STORAGE}+gdata/xp65 /g/data/vk83/apps/om3-scripts/payu_config/postscript.sh
 
-payu_minimum_version: 1.1.6
+restart_freq: 1YS
+payu_minimum_version: 1.1.7
diff --git a/diagnostic_profiles/README b/diagnostic_profiles/README
diff --git a/diagnostic_profiles/README.md b/diagnostic_profiles/README.md
@@ -0,0 +1,17 @@
+### Preset `diag_table` files for MOM6 diagnostic requests
+
+The `diag_table_<preset>` files in this directory are generated from the corresponding 
+`diag_table_source/diag_table_<preset>_source.yaml` files using the `make_diag_table.py` script.
+To create and use a custom diag_table:
+
+1. Copy a `diag_table_<preset>_source.yaml` file to a new file named `diag_table_source.yaml`
+2. Make the required modifications to the new `diag_table_source.yaml`
+3. In the directory containing your new `diag_table_source.yaml` file, run:
+   ```
+   module use /g/data/vk83/modules
+   module load payu
+   python /g/data/vk83/apps/make_diag_table/make_diag_table.py
+   ```
+   This will produce a new diagnostic table `diag_table` based on `diag_table_source.yaml`.
+5. Place the new `diag_table` file in the `diagnostic_profiles` directory, and provide an informative name.
+6. Modify the `<control_directory>/diag_table` symlink to point to the new diagnostic table.