Update netcdf planes for amr levels not coincident with the edge

[marchdf]

Summary

As described in #1380, netcdf format for the boundary planes would not allow for refinement levels to start in the middle of the domain. This PR fixes that.

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

Additional background

Now one can have this with the netcdf format (refinement zone starts partway up the domain):

They look reasonable when isualizing the planes in python:

As usual with these boundary planes, it's the 80/20 rule. the code changes are small but making sure they work... ugh.

Closes #1380

[marchdf]

@rybchuk I've done the testing I could and it looks reasonable. But it being so new and stuff... could be bugs. LMK if you see anything weird happening.

[rybchuk]

You're the man, thanks Marc!!

• I have confirmed that I can write BCs for land-based sims with 1 level of refinement and offshore sims for 2 levels of refinement (with the offshore caveats from Offshore boundary plane failing time tolerance #1342)! The offshore sim starts from a checkpoint.
• I can also read BCs for that offshore sim.

I ran the test cases (attached) out only for ~20 iterations, but the log file is demonstrating healthy behavior. I'll soon be doing much longer i/o simulations and I'll follow up if anything goes awry. It might be a few days before I get to these longer sims, but if you want me to run them before you merge the PR, let me know and I can shuffle my timeline around.

offshore_lev2_write.txt
onshore_lev1_write.txt
offshore_lev2_read_log.txt
offshore_lev2_read.txt

[marchdf]

Excellent news, thanks for checking @rybchuk !