custom coords

[Yurlungur]

PR Summary

This PR is designed to support codes like Phoebus, Artemis, and Assail downstream that uses coordinates that are not the uniform cartesian coordinate system. It lets you tag a mesh variable as a coordinates array. To do say, make your variable a node-centered 3-vector and add the Metadata::CoordinatesVec MetadataFlag to it. Then fill this variable with the x, y, and z coordinates of your nodes as appropriate.

If you do this, the variable will automatically be output in dumps and restarts and the xdmf file will will record this field as your coordinates per meshblock. Tested in parthenon-mhd.

This is also ready for downstream testing and review in downstream codes. Depends on #1019 . I haven't fully cleaned up formatting/linting/docs yet.

PR Checklist

• [x] Code passes cpplint
• [x] New features are documented.
• [ ] Adds a test for any bugs fixed. Adds tests for new features.
• [x] Code is formatted
• [x] 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.
• [x] Docs build
• [x] (@lanl.gov employees) Update copyright on changed files

[Yurlungur]

Now documented. This is completely ready for review. No tests, as I don't want us to add Visit or Paraview to our CI, but tested by hand with Visit and Paraview.

[Yurlungur]

Thanks @pgrete I'll make these changes and submit a tirival PR to fix