Add WithFluxes to IsRefined check

[pdmullen]

PR Summary

The fluxes associated with a field marked Metadata::WithFluxes must undergo flux correction with mesh refinement. Parthenon cannot currently enroll custom PR ops on those fluxes if the associated field is marked Metadata::WithFluxes, but not Metadata::Independent, Metadata::FillGhost, or Metadata::ForceRemeshComm.

This PR simply adds WithFluxes to the IsRefined check to circumvent this issue. Technically, this is a bit slimy, because in the example above, the field itself does not undergo any custom-ops, only its associated fluxes, nevertheless, this appears to be the most expedient solution, and IsRefined should not actually be used when packing relevant fields needed for a particular refinement op (please check me on this one, though: https://github.com/search?q=repo%3Aparthenon-hpc-lab%2Fparthenon+isrefined&type=code). If this is too dirty, please feel free to shoot down this PR.

PR Checklist

• Code passes cpplint
• New features are documented.
• Adds a test for any bugs fixed. Adds tests for new features.
• Code is formatted
• Changes are summarized in CHANGELOG.md
• Change is breaking (API, behavior, ...)
  • Change is additionally added to CHANGELOG.md in the breaking section
  • PR is marked as breaking
  • Short summary API changes at the top of the PR (plus optionally with an automated update/fix script)
• CI has been triggered on Darwin for performance regression tests.
• Docs build
• (@lanl.gov employees) Update copyright on changed files

[Yurlungur]

So as a sanity check, I just went through and reminded myself how the bvals stuff works here. For the most part, metadata is used. the ForEachBoundary loop checks for Metadata::FillGhost and Metadata::Flux and does not use IsRefined.

IsRefined is used to help build the map from refinement functions to variables. I think this is needed regardless, so this is all fine. I would like to maybe rename IsRefined though, given we're now changing the meaning... or at least add a comment above the function explaining.

[pdmullen]

So as a sanity check, I just went through and reminded myself how the bvals stuff works here. For the most part, metadata is used. the ForEachBoundary loop checks for Metadata::FillGhost and Metadata::Flux and does not use IsRefined.

IsRefined is used to help build the map from refinement functions to variables. I think this is needed regardless, so this is all fine. I would like to maybe rename IsRefined though, given we're now changing the meaning... or at least add a comment above the function explaining.

Thanks for the sanity check. I had also come to the same conclusion. I agree with your comment regarding renaming IsRefined. d7c771cd7c771c renames IsRefined -> HasRefinementOps.