Make a CESM workflow

[ashjbarnes]

The aim is to have a single notebook that runs through setting up a regional mom6 case with a data atmosphere within the CESM framework. A CESM specific library of functions will be written that complements the main package, but makes all of the required CESM changes.

Workflow:

1. Set up regional-mom6 forcing data and filesystem as usual
2. Use @alperaltuntas's mom6_bathy tool to create an ESMF grid from the hgrid.nc and bathymetry.nc files generated by regional-mom6
3. Create a CESM case for a generic mom6 only global run.
4. Using the new CESM-regional-mom6 tools, modify the CESM case appropriately. This involves:

• [x] Put all of the configuration files generated by regional-mom6 into SourceMods/scr.mom folder.
• [x] Handle the case of the MOM_layout file. So far this must be copied manually! SourceMods only seems to overwrite files, not introduce new ones
• [x] Add a line to MOM_override to point INPUTDIR to the mom6 input files.
• [x] Handle the fact that MOM6 within CESM doesn't appear to follow subdirectories, and so can't find things in the forcing folder
• [x] Using xmlchange, modify memory to symmetric,
• [x] Using xmlchange modify OCN_NX,OCN_NY according to domain size
• [x] Using xmlchange modify NTASKS_* to 1 for everything but ocean, and set ocean depending on ocean mask
• [x] Using xmlchange modify every MESH except for atmosphere to the newly created ESMF one, as well as the MASK_MESH and MASK_GRID
• [x] Using xmlchange modify RUN_REFDATE and RUN_STARTDATE
• [x] Calculate what the actual minimum depth is based on the minumum levels parameter in regional-mom6. This value needs to go in the MOM_override to ensure that the ocean_geometry file generated by MOM6 matches the mask table that we generate within the ESMF mesh.

Ultimately, these functions will be used with a modified version of Alper's VisualCaseGen. An example notebook will serve as a test case that we can run CI / workflows on, and could also be used to spin up other regional domains.

[ashjbarnes]

A basic version of this has been achieved in the regional-casegen repo. More issues there pertaining to its future development