Proof-of-Concept: Eliminate reaction specializations

[ischoegl]

Changes proposed in this pull request

Remove remaining specializations per Cantera/enhancements#142

• Create ThreeBodyArrheniusRate specialization for three-body-Arrhenius
• Eliminate ThreeBodyReaction in C++ and Python
• 🚧

Once fully implemented, this PR will allow for a deprecation of ReactionFactory.

If applicable, fill in the issue number this pull request is fixing

Closes Cantera/enhancements#142, closes Cantera/enhancements#133, interferes with #1143

If applicable, provide an example illustrating new features this pull request is introducing

Checklist

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

Thoughts

Due to the introduction of BulkRate.h, this PR has some minor conflicts with #1217

[codecov]

Codecov Report

Merging #1219 (c93ea76) into main (719275e) will decrease coverage by 0.17%.
The diff coverage is 32.38%.

❗ Current head c93ea76 differs from pull request most recent head 8ecc5da. Consider uploading reports for the commit 8ecc5da to get more accurate results

@@            Coverage Diff             @@
##             main    #1219      +/-   ##
==========================================
- Coverage   65.43%   65.26%   -0.18%     
==========================================
  Files         320      322       +2     
  Lines       46249    46368     +119     
  Branches    19657    19724      +67     
==========================================
- Hits        30265    30264       -1     
- Misses      13454    13568     +114     
- Partials     2530     2536       +6     

Impacted Files	Coverage Δ
include/cantera/kinetics/Reaction.h	100.00% <ø> (ø)
include/cantera/kinetics/ReactionData.h	87.27% <0.00%> (-1.62%)	⬇️
src/kinetics/BulkRate.cpp	0.00% <0.00%> (ø)
src/kinetics/BulkKinetics.cpp	84.84% <14.28%> (-3.96%)	⬇️
include/cantera/kinetics/BulkRate.h	14.63% <14.63%> (ø)
src/kinetics/Reaction.cpp	77.85% <30.13%> (-3.39%)	⬇️
include/cantera/kinetics/Arrhenius.h	81.91% <47.82%> (-0.56%)	⬇️
src/kinetics/ReactionRateFactory.cpp	91.93% <50.00%> (-2.90%)	⬇️
src/kinetics/Custom.cpp	77.77% <66.66%> (-5.56%)	⬇️
include/cantera/kinetics/Custom.h	50.00% <100.00%> (-35.72%)	⬇️
... and 8 more

📣 Codecov can now indicate which changes are the most critical in Pull Requests. Learn more

[ischoegl]

@speth ... I was (mostly) successful replacing ThreeBodyReaction, but the current approach does have an estimated 15% speed penalty (note that at the moment, effective three-body concentrations are calculated twice, but disabling updateFromStruct in the ThreeBodyRate<> template is not the culprit). The existing approach of handling third body colliders outside of ReactionRate is simply faster, which means that the separation of BulkRate<> and ThreeBodyRate<> templates that this PR tested is not worth pursuing.

While I will not have the bandwidth at the moment to go back and work out a hybrid approach where an updated ThirdBody object gains the ability to parse (which I believe is what is necessary), much of the machinery to catch three-body reactions is worked out. I believe the feature is overall worth implementing, as it will eliminate ReactionFactory and allow for some significant simplifications along the way.