Proof-of-concept: Modify reaction rates in memory

[ischoegl]

Changes proposed in this pull request

This PR builds on #995 (and will be rebased once #995 is merged, i.e. 80ish commits are not specific to this PR).

• Allow for modifications of rate parameters without having to 'modify' reactions
• Proof-of-concept implemented for ArrheniusRate

Addresses Cantera/enhancements#87.

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

In [1]: import cantera as ct
   ...: rxn = gas.reaction(0)
   ...: rxn
Out[1]: <ElementaryReaction: H2 + O <=> H + OH>

In [2]: gas.forward_rate_constants
Out[2]: 
array([5.19544737e+03, 1.34865000e+07, 2.55079922e+09, 4.25372812e+01,
       5.48180502e+06, 0.00000000e+00, 3.00385071e-09, 3.82748853e+09,
       5.81796100e+17, 1.93894637e+14, 9.91318424e+06])

In [3]: A = rxn.rate.pre_exponential_factor
   ...: A
Out[3]: 38.7

In [4]: rxn.rate.pre_exponential_factor = 2 * A
   ...: gas.reaction(0).rate.pre_exponential_factor
Out[4]: 77.4000015258789

In [5]: gas.forward_rate_constants
Out[5]: 
array([1.03908950e+04, 1.34865000e+07, 2.55079922e+09, 4.25372812e+01,
       5.48180502e+06, 0.00000000e+00, 3.00385071e-09, 3.82748853e+09,
       5.81796100e+17, 1.93894637e+14, 9.91318424e+06])

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

[codecov]

Codecov Report

Merging #1051 (602111b) into main (ec85c24) will decrease coverage by 0.24%.
The diff coverage is 69.41%.

❗ Current head 602111b differs from pull request most recent head 2e73274. Consider uploading reports for the commit 2e73274 to get more accurate results

@@            Coverage Diff             @@
##             main    #1051      +/-   ##
==========================================
- Coverage   65.35%   65.10%   -0.25%     
==========================================
  Files         315      315              
  Lines       45995    45320     -675     
  Branches    19531    19257     -274     
==========================================
- Hits        30060    29507     -553     
+ Misses      13443    13343     -100     
+ Partials     2492     2470      -22     

Impacted Files	Coverage Δ
include/cantera/kinetics/MultiRateBase.h	100.00% <ø> (ø)
include/cantera/kinetics/MultiRate.h	67.79% <51.72%> (-14.23%)	⬇️
src/kinetics/Arrhenius.cpp	90.47% <55.55%> (+0.05%)	⬆️
include/cantera/kinetics/Arrhenius.h	94.36% <60.00%> (-5.64%)	⬇️
include/cantera/kinetics/RxnRates.h	82.84% <75.00%> (ø)
src/kinetics/BulkKinetics.cpp	88.52% <83.33%> (ø)
include/cantera/kinetics/Custom.h	85.71% <100.00%> (ø)
include/cantera/kinetics/Falloff.h	77.98% <100.00%> (ø)
include/cantera/kinetics/ReactionRate.h	90.19% <100.00%> (+3.70%)	⬆️
src/kinetics/GasKinetics.cpp	84.65% <0.00%> (-4.35%)	⬇️
... and 27 more

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[ischoegl]

Setting this back to draft as it will require rebasing due to merge conflicts with #1061

[ischoegl]

As anticipated, the PR now has merge conflicts after #1061 was merged (which curiously don't show up here). I moved 'easy' modifications to #1088, as the rest will likely require some discussion.

[ischoegl]

@speth ... I rebased the PR now that major updates based on #1101 are settling down. At the moment, modifications are only implemented for ArrheniusRate.

[ischoegl]

Closing as this feature is likely premature.