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Generating MOM6 Initial Conditions Using WOA23 dataset

This guide outlines the steps to generate conservative temperature and salinity fields for MOM6 using World Ocean Atlas 2023 (WOA23) data, suitable for ACCESS-OM3 simulations.

Repository and Requirements

Clone the repository that includes all necessary tools and submodules:

git clone --recursive https://github.com/ACCESS-NRI/initial_conditions_access-om3.git
cd initial_conditions_access-om3

A recursive clone is needed because this repository includes Nic Hannah’s ocean-ic code as a submodule, used to interpolate WOA23 data onto MOM6 3D grids.

Step 1: (Optional) Regenerate Temperature & Salinity from Raw WOA23

Use this step only if you want to regenerate T/S fields from a different version of World Ocean Atlas dataset.

./inte.csh

The inte.csh script processes World Ocean Atlas 2023 (WOA23) data to create consistent monthly temperature and salinity fields suitable for generating MOM6 initial conditions.

Purpose

By default, WOA23 provides: - Full-depth annual mean data (XX = 00) - Monthly data (XX = 01–12) only for the upper 1500 m - Seasonal data (XX = 13–16) covering full depth

To use full-depth data with monthly resolution, inte.csh reconstructs it by combining seasonal deep data with monthly shallow data. The WOA23 dataset is based on oceanographic observations collected over the period 1955 to 2022.

What the Script Does

  1. Extract salinity (s_an) from seasonal full-depth data and expand it to monthly resolution.
  2. Use ncks --mk_rec time to add an unlimited time dimension to make the NetCDF files record-aware.
  3. Rename the salinity variable from s_an to practical_salinity for compatibility with the processing pipeline.
  4. Run setup_WOA_initial_conditions.py to combine monthly upper ocean and seasonal lower ocean data, then convert WOA23 in-situ temperature to conservative temperature.

The processed monthly files are output to: 

/g/data/ik11/inputs/access-om3/woa23/monthly

💡 You only need to run this script if you're updating or modifying the WOA23 dataset. Otherwise, skip this step and proceed directly to regridding using make_initial_conditions.sh.

Step 2: Regrid to MOM6 Grid

Use the regridding script to interpolate WOA23 temperature and salinity to your MOM6 model grid.

cd initial_conditions_WOA/
qsub -v VGRID="<path_to_vgrid_file>",HGRID="<path_to_hgrid_file>",INPUT_DIR="<path_to_input_directory>",OUTPUT_DIR="<path_to_output_directory>" -P $PROJECT make_initial_conditions.sh

Replace the variables with your grid and directory paths: - VGRID: MOM6 vertical grid file - HGRID: MOM6 horizontal grid file - INPUT_DIR: Directory with processed WOA23 monthly files - OUTPUT_DIR: Where regridded output will be saved

> Note: This code is not parallelized and may take approximately 24 hours to run for the 25km (0.25°) resolution grid.

Step 3: Finalize & Tag Metadata

Once satisfied with the output, run:

./finalise.sh -o /g/data/ik11/inputs/access-om3/woa23/025/

This: - Commits any changes with git - Adds Git metadata to the NetCDF metadata

Notes

  • Make sure to adjust paths in inte.csh if you change the WOA23 dataset.
  • You can repeat Step 2 to generate initial conditions for any resolution. Step 1 is agnostic of the model resolution as the data is on the WOA23 grid.