Topography generation

Introduction

The supported ACCESS-OM3 configurations use a topography based on the GEBCO2022 global topography dataset. This dataset has a resolution of 15 arc-second (i.e., 1/240 deg = 460m at equator and finer zonally nearer the poles).

domain-tools

The workflow describe below uses different tools that perform specific tasks, like removing seas or generating the land/sea mask. One can find these tools and the instructions to install them here: https://github.com/COSIMA/domain-tools.

General workflow

The general workflow to generate the topography and the corresponding land/sea masks is the following:

1. Interpolate GEBCO data onto model grid.
2. Fill cells that have a sea area fraction smaller than some value.
3. Remove isolated seas.
4. Apply minimum and maximum allowed ocean depths.
5. Remove potholes.
6. Generate the land mask from the topography.

This workflow assumes one already has created the horizontal super-grid to be used and that the model uses a C-grid. It is also very likely that some tweaks to the workflow, like manually editing some parts of the topography, will be necessary to obtain an acceptable result.

Example script

The following is a commented PBS script implementing the above workflow:

#!/usr/bin/env sh
#PBS -P v45
#PBS -q normal
#PBS -l walltime=4:00:00,mem=4GB
#PBS -l wd
#PBS -lstorage=gdata/hh5+gdata/ik11

module use /g/data/ik11/spack/modules
module load domain-tools

set -x
set -e

cp -L --preserve=timestamps /g/data/ik11/inputs/access-om2/input_20200530/mom_025deg/ocean_hgrid.nc .
cp -L --preserve=timestamps /g/data/ik11/inputs/access-om2/input_20200530/mom_025deg/ocean_vgrid.nc .
ln -sf /g/data/ik11/inputs/GEBCO_2022/GEBCO_2022.nc

# Interpolate topography on horizontal grid:
topogtools gen_topo -i GEBCO_2022.nc -o topog_new.nc --hgrid ocean_hgrid.nc --tripolar --longitude-offset -100

# Fill cells that have a sea area fraction smaller than 0.5:
topogtools fill_fraction -i topog_new.nc -o topog_new_fillfraction.nc  --fraction 0.5

# Remove seas:
topogtools deseas -i topog_new_fillfraction.nc -o topog_new_fillfraction_deseas.nc

# Set maximum/minimum depth
topogtools min_max_depth -i topog_new_fillfraction_deseas.nc -o topog_new_fillfraction_deseas_mindepth.nc --level 4

# Fix and check for non-advective cells
topogtools fix_nonadvective -i topog_new_fillfraction_deseas_mindepth.nc -o topog_new_fillfraction_deseas_mindepth_fixnonadvective.nc --potholes
topogtools check_nonadvective -i topog_new_fillfraction_deseas_mindepth_fixnonadvective.nc --potholes

# Create land/sea mask
cp topog_new_fillfraction_deseas_mindepth_fixnonadvective.nc topog.nc
topogtools mask -i topog.nc -o ocean_mask.nc

A more detailed description of the syntax of each command can be found here.