Fix chemistry‑related bugs

[DimAdam-01]

Description

1. Integrate the new Pyrometheus branch to calculate transport coefficients,
   resolve the issue that prevented multi‑rank execution when using non‑hardcoded initial conditions;
   and fix minor bugs in both the inline Riemann solver and the HLL Riemann solver.

Type of change

• Bug fix (non-breaking change which fixes an issue)

Scope

• This PR comprises a set of related changes with a common goal

How Has This Been Tested?

• Test A: 1D_reactive_shocktube
  Run the 1D shocktube reaction case, compared the result and they had the exact match,

Test Configuration:

• What computers and compilers did you use to test this:

Run on Delta and Delta AI ( A100 and GH GPUs), as well as on my personal laptop

Checklist

• I have added comments for the new code
• I added Doxygen docstrings to the new code
• I have made corresponding changes to the documentation (docs/)
• I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
• I have added example cases in examples/ that demonstrate my new feature performing as expected.
  They run to completion and demonstrate "interesting physics"
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

If your code changes any code source files (anything in src/simulation)

To make sure the code is performing as expected on GPU devices, I have:

• Checked that the code compiles using NVHPC compilers
• Checked that the code compiles using CRAY compilers
• Ran the code on either V100, A100, or H100 GPUs and ensured the new feature performed as expected (the GPU results match the CPU results)
• Ran the code on MI200+ GPUs and ensure the new features performed as expected (the GPU results match the CPU results)
• Enclosed the new feature via nvtx ranges so that they can be identified in profiles
• Ran a Nsight Systems profile using ./mfc.sh run XXXX --gpu -t simulation --nsys, and have attached the output file (.nsys-rep) and plain text results to this PR
• Ran an Omniperf profile using ./mfc.sh run XXXX --gpu -t simulation --omniperf, and have attached the output file and plain text results to this PR.
• Ran my code using various numbers of different GPUs (1, 2, and 8, for example) in parallel and made sure that the results scale similarly to what happens if you run without the new code/feature

[sbryngelson]

has the code that automatically turns a 1D case into an extrapolated 2D one been put into MFC? @DimAdam-01

[DimAdam-01]

I consider it a distinct feature that I intended to add separately, but I can include it in this pull request. @sbryngelson

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 43.16%. Comparing base (40164cf) to head (209dd94).

Files with missing lines	Patch %	Lines
src/common/m_chemistry.fpp	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #829   +/-   ##
=======================================
  Coverage   43.15%   43.16%           
=======================================
  Files          68       68           
  Lines       20262    20263    +1     
  Branches     2424     2424           
=======================================
+ Hits         8745     8746    +1     
  Misses      10054    10054           
  Partials     1463     1463           

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[sbryngelson]

you can't make master MFC use your fork of pyrometheus....

[DimAdam-01]

The original version encountered build errors on Frontier, so I introduced a few modifications to verify whether it would compile successfully there, and it did.

[sbryngelson]

then we need to create a PR for the Pyrometheus fix first

[DimAdam-01]

Yes, I’m speaking with Esteban at the moment.