Changing Freesurface post-processing routine to a Sampler

[mbkuhn]

Summary

FreeSurface is designed to find the location of the air-water interface in simulations with vof. This PR converts that capability to a Sampler type, enabling sampling of fields at the interface and native output with AMReX particles.

Pull request type

Please check the type of change introduced:

• Bugfix
• Feature
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no api changes)
• Build related changes
• Documentation content changes
• Other (please describe):

Checklist

The following is included:

• new unit-test(s)
• new regression test(s)
• documentation for new capability

This PR was tested by running:

• the unit tests
  • on GPU
  • on CPU
• the regression tests
  • on GPU
  • on CPU

[mbkuhn]

I plan to change the names of the files from FreeSurface to FreeSurfaceSampler, but that would make it much harder to review. So I'm saving that for last.

[mbkuhn]

Also, I have python scripts to read in the data for every sampler type (ascii, native, and netcdf). I think these should be added to tools, and they'd be set up to read the output from the reg test that I added this sampler too. Thoughts?

Figuring out the layout of any of these types took me some time, and having an example should be helpful.

[mbkuhn]

some evidence it works

[marchdf]

Examples are useful! Maybe better in the documentation? I worry about adding python scripts that could go out of date because we can't test them automatically. We can chat more about that.

[mbkuhn]

Examples are useful! Maybe better in the documentation? I worry about adding python scripts that could go out of date because we can't test them automatically. We can chat more about that.

That's a good idea. I learned that jupyter notebooks can be included in sphinx documentation, so I might try that.

[mbkuhn]

I set up the docs so that they actually run the jupyter notebooks and generate the plots, and the notebooks are displayed in the docs for easy copy-paste.

[mbkuhn]

Here's how the docs look with these changes.

docs_with_notebooks.tar.gz

[mbkuhn]

@jrood-nrel do you think you could take a look at what I'm doing with the docs, namely, changing the conf.py and docs.yml files?

@moprak-nrel do you have time to look over the stuff in the source code?

[jrood-nrel]

conf.py looks fine. I think I would object to committing several binary files here though.

[mbkuhn]

conf.py looks fine. I think I would object to committing several binary files here though.

Thanks for the feedback. I'll talk to Marc about what's the best way to incorporate this stuff.