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Topography generation
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).
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.
The general workflow to generate the topography and the corresponding land/sea masks is the following:
- Interpolate GEBCO data onto model grid.
- Fill cells that have a sea area fraction smaller than some value.
- Remove isolated seas.
- Apply minimum and maximum allowed ocean depths.
- Remove potholes.
- 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.
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.