Fixes Omega ssh calculation

[vanroekel]

The current SSH calculation is designed for stacked shallow water only and was causing issues (such as NaNs in the barotropic channel case) in current tests. The SSH calculation is moved to the VertCoord class and computed alongside ZMid and ZInterface

Checklist

• Linting
  • Pre-commit run locally
• Building
  • CMake build does not produce any new warnings from changes in this PR
• Testing
  • Add a comment to the PR titled Testing with the following:
    • Which machines CTest unit tests
      have been run on and indicate that are all passing.
    • The Polaris omega_pr test suite
      has passed, using the Polaris e3sm_submodules/Omega baseline
    • Document machine(s), compiler(s), and the build path(s) used for -p for both the baseline (Polaris e3sm_submodules/Omega) and the PR build
    • Indicate "All tests passed" or document failing tests
    • Document testing used to verify the changes including any tests that are added/modified/impacted.

resolves #321
resolves #332

[xylar]

Shouldn't this be the following?

Suggested change

	if (KLyr == 0) {
	if (KLyr == KMin) {

[vanroekel]

Oh yes, definitely. I'll fix that

[vanroekel]

Testing
Currently have tested the cases in the related issues.

Barotropic channel

With omega/develop layer thickness at the 10th step in the top layer are

array([nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan])

with this PR

array([33.32555911, 33.32555911, 33.32555911, 33.32555911, 33.32555911,
       33.32555911, 33.32555911, 33.32555911, 33.32555911, 33.32555911,
       33.34110755, 33.34110755, 33.34110755, 33.34110755, 33.34110755,
       33.34110755, 33.34110755, 33.34110755, 33.34110755, 33.34110755,
       33.34110755, 33.34110755, 33.34110755, 33.34110755, 33.34110755,
       33.34110755, 33.34110755, 33.34110755, 33.34110755, 33.34110755,
       33.32555911, 33.32555911, 33.32555911, 33.32555911, 33.32555911,
       33.32555911, 33.32555911, 33.32555911, 33.32555911, 33.32555911])

In the single column test case, also confirmed that when using pseudoThickness in the input file from polaris the ZMid and ZInterface values look as expected and SshCell is 0 as expected.

Currently running the omega_pr suite on perlmutter. Will update when finished.

[vanroekel]

A note that this PR breaks the manufactured solution tests b/c it provides geometric thickness. This would need the Polaris addition of PseudoThickness and renaming in Omega, or alternatively we could add a bit of code to Omega to convert to pseudothickness if layerthickness is provided. Any thoughts on how to proceed?

[cbegeman]

@vanroekel This draft PR converts geometric thickness to pseudo-thickness in the initial condition E3SM-Project/polaris#460. I have also planned to include in this PR a conversion from pseudo-thickness to geometric thickness in the reading of model output. Would this address the issue you're seeing?

[vanroekel]

@vanroekel This draft PR converts geometric thickness to pseudo-thickness in the initial condition E3SM-Project/polaris#460. I have also planned to include in this PR a conversion from pseudo-thickness to geometric thickness in the reading of model output. Would this address the issue you're seeing?

So in the processing of test results it would convert back? That would be excellent. I do think for the planar manufactured solutions we'd need to provide a temperature / salinity for the pseudo thickness, but if we did I think that + your PR would address things.

[cbegeman]

So in the processing of test results it would convert back? That would be excellent. I do think for the planar manufactured solutions we'd need to provide a temperature / salinity for the pseudo thickness, but if we did I think that + your PR would address things.

Exactly. I'll check in with you about the development timing so that this PR doesn't get held up.