make_OM3_topo

Makes resolution-specific topog.nc MOM6 global bathymetry files for ACCESS-OM3 topography workflows based on the GEBCO 2024 dataset. The current workflow supports both 25km and 100km grids.

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).
• Produce a global topography (topog_new_fillfraction_edited_deseas.nc) with a coastline suitable for a C-grid (i.e. with 1-cell-wide channels).
• (optional, USE_BGRID_MERGE=true) Also create a second topography (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); this is identical to the C-grid version apart from coastal points and any embayments/channels that are cut off by closing 1-cell-wide channels. It is 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. This step is off by default — set USE_BGRID_MERGE=true to enable it (see step 3 below).
• 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_topo
   cd make_om3_topo

2. (optional) Regenerate B-grid mask

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

   • run make_B_mask_xxkm.ipynb on ARE and check it looks like what you want
   • move ~/B_mask_xxkm.nc to topog generation directory so it can be used in workflow
   • run finalise_B_mask.sh to embed its provenance. A positional argument specifying the resolution is required:

 ./finalise_B_mask.sh 25km
 ./finalise_B_mask.sh 100km

3. Generate Topography Use ./gen_topo.sh to generate the topography and associated files. The script selects the 25km or 100km workflow from a single case block.

   • add gdata for your project & working directory to the #PBS -l storage= line in gen_topo.sh
   • check/adjust the per-resolution configuration block in gen_topo.sh and finalise.sh
   • for smaller cases such as 100km you can run with a positional argument; for 25km submit with qsub using RESOLUTION:

   ./gen_topo.sh 100km
   qsub -v RESOLUTION=25km -P $PROJECT gen_topo.sh

   • the B-grid merge steps (using B_mask.nc and edit_*_topog_Bgrid.txt, see step 5) are off by default. To enable them, set USE_BGRID_MERGE=true:

   USE_BGRID_MERGE=true ./gen_topo.sh 100km
   qsub -v RESOLUTION=25km,USE_BGRID_MERGE=true -P $PROJECT gen_topo.sh

   • after generating the topography, this will then generate most other masks, forcing and remapping files needed by OM3

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 resolution-specific files containing lists of edits, which are applied by editTopo.py in gen_topo.sh:

   • edit_025deg_topog.txt is always applied, to the C-grid topography. If USE_BGRID_MERGE=true, it is applied a second time to the merged file.
   • edit_025deg_topog_Bgrid.txt is only used when USE_BGRID_MERGE=true; it is applied 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.
   • For the 100 km workflow, the same procedure is used, but with the corresponding edit files edit_100km_topog.txt and edit_100km_topog_Bgrid.txt.
   • Run bathymetry-tools/editTopo.py on the appropriate intermediate files to generate new lists of edits which can be appended (with explanatory comments) to the relevant edit file for your chosen resolution.
   • 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, to commit and push the changes run finalise.sh. This adds the git commit hash as metadata in the output .nc files for provenance. This then triggers creation of the other input/forcing files which depends on the grid and bathymetry, including ESMF mesh files, tidal and wombatlite forcings. A positional argument specifying the resolution is required:

 ./finalise.sh 25km
 ./finalise.sh 100km

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. There's is data loaded from the av17, ik11 and xp65 projects.