make_OM3_025deg_topo

Makes 0.25-degree (25km) topog.nc MOM6 global bathymetry file for ACCESS-OM3-25km, based on the GEBCO 2024 dataset.

The workflow gen_topo.sh contains many steps, and stores intermediate files in topography_intermediate_output so you can check the result of each step. Key stages in the processing are:

• Interpolate GEBCO onto the model grid, setting each cell's altitude to the mean of the GEBCO data within it and setting cells that contain more than 50% land in GEBCO to 100% land in the model (this rule of thumb gives acceptable results in most places but requires some specific fixes to ensure important straits, sills, etc. are well represented).
• Create two global topographies, one (topog_new_fillfraction_edited_deseas.nc) with a coastline suitable for a C-grid (i.e. with 1-cell-wide channels) and another (topog_new_fillfraction_B_edited_fixnonadvective_deseas.nc) with a coastline suitable for both a B-grid and C-grid (i.e. all 1-cell-wide channels are closed off or widened to at least 2 cells); these are identical apart from coastal points and any embayments/channels that are cut off by closing 1-cell-wide channels in the B-grid version.
• These are then merged with combine_by_mask.py using the mask B_mask.nc such the B-grid version is used in regions prone to sea ice and the C-grid version everywhere else. This allows the use of B-grid CICE6 with C-grid MOM6 without ice piling up in narrow channels and inlets.
• Further processing and edits to generate the final topog.nc.
• Generation of associated .nc files based on and consistent with topog.nc.

Workflow Overview

1. Download to Gadi

   This repository contains submodules, so clone with

   git clone --recursive https://github.com/ACCESS-NRI/make_OM3_025deg_topo.git
   cd make_OM3_025deg_topo

2. (optional) Regenerate B-grid mask

   B_mask.nc can be updated with make_B_mask.ipynb if needed

   • run make_B_mask.ipynb on ARE and check it looks like what you want
   • move ~/B_mask.nc to topog generation directory so it can be used in workflow
   • run finalise_B_mask.sh to embed its provenance

3. Generate Topography Use ./gen_topo.sh to generate the topography and associated files. For 0.25-degree (25km) resolution or finer, this will require submission via qsub.

   • add gdata for your project & working directory to the #PBS -l storage= line in gen_topo.sh
   • check/adjust INPUT_HGRID, INPUT_VGRID and INPUT_GEBCO in both gen_topo.sh and finalise.sh
   • submit the script:

   qsub gen_topo.sh

4. Check the output files look OK

   • See whether the final topography topog.nc and associated .nc files look OK. Look carefully for any missing marginal seas, and channels that are too wide or narrow/closed. If there's a problem, you can identify where it arose by inspecting the intermediate outputs in topography_intermediate_output.
   • Run non-advective.ipynb on ARE to see the B-grid changes in the polar coastlines, and check there are no seas/bays without B-grid advective connection to the ocean in topography_intermediate_output/topog_new_fillfraction_B_edited_fixnonadvective_deseas.nc.

5. Fix problems (if any)

   Since all outputs are generated from topog.nc, problems in any of the outputs can generally be fixed by altering the edits applied as part of generating topog.nc in the workflow. There are two files containing lists of edits, which are applied by editTopo.py in gen_topo.sh:

   • edit_025deg_topog.txt is applied twice, once to the precursor to the B- and C-grid files which are later merged, and then again to the merged file.
   • edit_025deg_topog_Bgrid.txt is applied only to the B-grid file prior to merging but after the first application of edit_025deg_topog.txt. This should apply fixes that are suitable for a global B-grid, e.g. to open the Bosphorus so the Black Sea is retained.
   • Run bathymetry-tools/editTopo.py on the appropriate intermediate files to generate new lists of edits which can be appended (with explanatory comments) to edit_025deg_topog.txt or edit_025deg_topog_Bgrid.txt to make them part of the workflow.
   • Return to step 3 to check that the updated workflow does what you want.

6. Finalise Output Files

   Once the output files meet your satisfaction, commit and push the changes, then run finalise.sh to add the git commit hash as metadata in the output .nc files for provenance.

Note on Dependencies

This workflow relies on the xp65 conda environments for running the scripts and generating the outputs. As long as you are a member of the xp65 project, this conda environment is loaded as part of the scripts.