Incorporating the LMR-R mixture rule into Cantera for the first time

[pjsingal]

Changes proposed in this pull request

• LinearBurkeRate.cpp and LinearBurkeRate.h allow for vastly improved consideration of the mixture-dependent aspect of the rate constants for complex-forming ("pressure-dependent") reactions, using the new reduced-pressure linear mixture rule (LMR-R)

• This code builds, runs, and produces results that have been validated and peer-reviewed

• LMR-R can handle three different representations of the pressure-dependent aspect of complex-forming reactions: Troe, PLOG, and Chebyshev

• LMR-R calculates the mixture-dependent aspect using temperature-dependent third-body efficiencies that have been supplied by the user for at least one collider - these parameters can be provided in either relative or absolute terms, as long as the user's choice is consistent for all colliders in a given reaction

• Description of the theory and instructions for YAML implementation have been added to rate-constants.md and reactions.rst, respectively

• Three new Python examples have been added: jet_stirred_reactor.py, shock_tube.py, flame_speed.py

• The Python examples employ a mechanism containing linear-Burke reactions, ammonia-CO-H2-Alzueta-2023.yaml, which is being added to Cantera/cantera-example-data via a separate PR

• Unit tests have been added, along with the linearBurke-test.yaml mechanism, stored in Cantera/Cantera/test/data

Checklist

[x] The pull request includes a clear description of this code change
[x] Commit messages have short titles and reference relevant issues
[x] Build passes (scons build & scons test) and unit tests address code coverage
[x] Style & formatting of contributed code follows contributing guidelines
[x] The pull request is ready for review

[codecov]

Codecov Report

Attention: Patch coverage is 51.17188% with 125 lines in your changes missing coverage. Please review.

Project coverage is 73.10%. Comparing base (1dd756a) to head (d367a49).
Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
src/kinetics/LinearBurkeRate.cpp	49.15%	102 Missing and 18 partials ⚠️
include/cantera/kinetics/LinearBurkeRate.h	69.23%	4 Missing ⚠️
interfaces/cython/cantera/reaction.pyx	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1710      +/-   ##
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- Coverage   73.23%   73.10%   -0.13%     
==========================================
  Files         381      383       +2     
  Lines       54378    54632     +254     
  Branches     9066     9106      +40     
==========================================
+ Hits        39822    39937     +115     
- Misses      11583    11694     +111     
- Partials     2973     3001      +28     

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[ischoegl]

Thanks for this contribution, @pjsingal! I have a couple of basic recommendations that mostly pertain to formatting. The example data should likely move to the new example_data repository, but it is not urgent at the moment. You may also want to think about adding unit tests.

[speth]

Thanks for the continued work on this, @pjsingal. I would suggest that the first priority at this point is to add some unit tests. I would recommend getting those into place before making any of the other changes that I've suggested below, so you can be sure that making those changes doesn't introduce any regressions.

[speth]

You should be able to get the constructor from input_data working by following the example of the other rate types. This is just a Python data structure containing the same information as the YAML input.

I think you can just remove the rates kwarg -- I'm guessing that's just leftover from copying from the PlogRate implementation.

[pjsingal]

I attempted to follow these instructions, and now have a very bare-bones version of it. However, I could use more advice re: what needs to be added now.

[speth]

Thanks for the updates here, @pjsingal, I think we're getting fairly close.

Could you please temporarily remove the commit that updates the example_data submodule? In that case, the jobs that build the docs and run the examples will fail, but at least all the others should run. Once we finalize the input file format and can merge the PR from the example_data repo, then we can update the submodule commit.

[speth]

Thanks for all the updates, @pjsingal. I think this is good to go. I simplified the commit history and pushed one last commit that just adjusts some minor formatting issues in the code and docs.