Initial Condition Extrusion + Chem Examples

[DimAdam-01]

Description

Please include a summary of the changes and the related issue(s) if they exist.
Please also include relevant motivation and context.

IC Extrusion: The workflow for extending Initial Conditions to higher dimensions has been simplified. The updated methodology is now more robust and user-friendly.
Documentation & Examples: To assist users with this new methodology, three new reference examples have been uploaded to the repository (one 1D case and two 2D cases).

Fixes #(issue) [optional]

Type of change

Please delete options that are not relevant.

• A current methodology being more user-friendly

Scope

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

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

• Test 1D Flamelet
• Test 2D Premixed Flame interacting with 2 vortices (From pyro paper)

Flame_Vortex_Interaction.mp4

• Test 2D Premixed Flame with perturbed flame front

Flame_Insta.mp4

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

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 a Rocprof Systems profile using ./mfc.sh run XXXX --gpu -t simulation --rsys --hip-trace, 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

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 42.87%. Comparing base (31c938f) to head (a8126e6).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1109      +/-   ##
==========================================
- Coverage   44.00%   42.87%   -1.13%     
==========================================
  Files          71       71              
  Lines       20293    20607     +314     
  Branches     1982     1993      +11     
==========================================
- Hits         8929     8835      -94     
- Misses      10227    10552     +325     
- Partials     1137     1220      +83     

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