Fix problems in ThermoPhase and Kinetics classes for the experimental Matlab toolbox

[ssun30]

Changes proposed in this pull request

• Fix known problems in ThermoPhase and Kinetics classes discovered by the new test suite.
• Remove filtered tests when problems are fixed.

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

Partially address Cantera/enhancements#177

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

PR #1496 introduced a test suite to the experimental Matlab interfaces. Currently, 12 out of 26 tests implemented in the test suite for the experimental Matlab interface are marked as filtered since they could not pass. This PR will address these problems so they will pass. Some changes to the Clib may be required as some of these problems are not related to the Matlab side of the interface.

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 #1586 (e213360) into main (de77fa3) will decrease coverage by 0.02%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main    #1586      +/-   ##
==========================================
- Coverage   72.72%   72.70%   -0.02%     
==========================================
  Files         370      370              
  Lines       56286    56298      +12     
  Branches    20369    20375       +6     
==========================================
  Hits        40932    40932              
- Misses      12357    12369      +12     
  Partials     2997     2997              

Files	Coverage Δ
src/clib/ct.cpp	18.87% <0.00%> (-0.23%)	⬇️

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[ssun30]

Sorry I've been busy with class and proposal defense in the past few weeks. I just got some time to go over the PR again. I mentioned to Ray earlier that some methods could not return correct error messages. It turns out these are methods that return certain indices such as thermo_speciesIndex and thermo_elementIndex.

They do not throw exceptions when the returned values are out of bounds (npos). Instead, there are dedicated methods to check whether these indices are out of bounds, for example Phase::checkSpeciesIndex. From my understanding, it was done this way so that three-body reactions (with undefined species 'M') do not cause errors when they are imported. Therefore I've moved the error handling into the Clib layer.

The other remaining issue with the ThermoPhase class in the Matlab interface is that multi-property setters (such as ThermoPhase.TDY may set incorrect values. I couldn't pinpoint the cause just yet and will test it on Thursday.

[speth]

Thanks for these updates, @ssun30. I think this is important progress for the new Matlab toolbox, and I'm glad to see it moving forward. I had just a few suggestions related to the current updates.

[speth]

Thanks, @ssun30! This looks good to me.