Create new script to set cullCell

[sbrus89]

Currently, the cullCell variable is being set in the base_mesh step inside inject_bathymetry.py (#176). This PR puts this functionality in a new script, so it doesn't affect the global_ocean mesh creation.

closes #176

[xylar]

@sbrus89, I think the new script didn't get git added. Could you do that?

[sbrus89]

@xylar, I just added it.

[xylar]

Thanks @sbrus89. This looks like exactly what's needed.

[xylar]

@mark-petersen and @pwolfram, I know your availability is limited right now. Please make it a priority to review this (maybe just by inspection). I will make sure @sbrus89 and I test this carefully on the major test cases that use this script before it gets merged to ocean/develop.

[sbrus89]

This should remove this from the global_ocean workflow. From here, we can just add it back to the cases (i.e. Delaware Bay) where it is needed later on.

[mark-petersen]

Approved by visual inspection. I agree this is what we want, so adding cull cells must be explicitly called. I see that you are not adding a call to inject_cullCell anywhere, which is fine. You are making the user add it by hand.

[xylar]

@mark-petersen,

I see that you are not adding a call to inject_cullCell anywhere, which is fine. You are making the user add it by hand.

We believe that the Delaware Bay test case may need to call this new script but no current test cases need that capability.

[xylar]

Thanks for the reviews while you're on travel! Much appreciated!

[xylar]

@pwolfram, I'm going to merge this PR and #180 into ocean/develop tomorrow morning. If you would like to give feedback, please do so before then.

[mark-petersen]

Yes, please merge those two into ocean/develop today when you are ready. These are a small number of COMPASS changes, and we can do an E3SM PR for these and the added atmospheric forcing, which also has associated COMPASS changes. We are trying to keep E3SM PRs in small chunks of MPAS changes, but I think this group is reasonable.

@xylar, @matthewhoffman and @jonbob, if you guys have time today, please proceed. I'm busy during the day, but could otherwise do it soon.

1. merge Create new script to set cullCell #179 and Make coastal refined meshes produced with JGSAW BFB between runs #180 into ocean/develop
2. single merge of ocean/develop into e3sm/develop (no PR required)
3. E3SM PR with updated mpas-source to head of e3sm/develop. This only adds Time Varying Atmospheric Forcing #123, Create new script to set cullCell #179, Make coastal refined meshes produced with JGSAW BFB between runs #180.

You can use this text for the PR description:
This pull request adds capability for stand-alone MPAS-Ocean to include time varying wind and pressure forcing. The added code is not called during E3SM simulations. Also adds associated COMPASS files for testing.
bfb

and first comment, mention testing here:
#123 (comment)

[pwolfram]

Approved via visual inspection; we'll just add this in later when needed.

Thanks @sbrus89 and @xylar

[xylar]

Testing

I tested the nightly regression suite on badger with GNU and this branch is bit-for-bit identical to the current ocean/develop