Fix writing out and testing Concentration.

[ktbolt]

This fixes writing Concentration data and updates the CI test to check those results. #638.

[claude]

Claude Code Review

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 73.41%. Comparing base (ba305f5) to head (c01d717).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #642   +/-   ##
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  Coverage   73.41%   73.41%           
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  Files         269      269           
  Lines       40337    40337           
  Branches     6755     6753    -2     
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  Hits        29612    29612           
  Misses      10482    10482           
  Partials      243      243           

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[kko27]

Approved! I did have two comments.

1. Is there documentation for setting up simulations that involve scalar transport? I did not realize that there was a nuance of creating an Alias output type (to rename temperature as concentration).
2. Where does the reference solution for this test case come from?

[ktbolt]

@kko27 There is some basic documentation for the Precomputed_solution parameter but it does not really explain the scalar transport usage well enough. I think we will add a User Guide section for this.

The reference solution is from rerunning the simulation with the updated solver.xml file.

[zasexton]

looks good to merge

[zasexton]

@kko27 There is some basic documentation for the Precomputed_solution parameter but it does not really explain the scalar transport usage well enough. I think we will add a User Guide section for this.

The reference solution is from rerunning the simulation with the updated solver.xml file.

This is also my bad. Originally I added the Precomputed_solution for any solution field data that is needed by another physics (for example the velocity field of a porous media model in scalar transport). It used to be that the solver required that solution field to be computed in a preceding simulation but, as you can imagine, this ends up being more overhead if you don't expect this to be a two-way coupled problem and the prior solution can be assumed instead of re-computed each time.

[zasexton]

I think the CI failures result from the field Concentration not being defined in the reference solution file, so test_dye_AD fails with ValueError: Field Concentration not in reference result for 1, 3, and 4 processes on both Ubuntu and macOS. These may need to be regenerated.

[ktbolt]

@zasexton Thanks for reminding me about this!

I did add a new reference solution file for test_dye_AD but it seems that it did not get merged correctly.