Update ReactorSurface / generalize ReactorBase

[ischoegl]

Changes proposed in this pull request

This PR pulls in suggestions from #1788, while trying to avoid unnecessary churn.

• ReactorSurface is now a specialization of ReactorBase
• Propagate changes to all APIs (Python, CLib and MATLAB)
• Clarify ambiguous definitions that may apply in non-physical or undefined contexts (e.g., setting volume on a Reservoir)
• Adopt some fixes from Remove constrains of using PlasmaPhase for 0D reactor and fix the species lock #1860 that touch the same lines

Changes are made in anticipation of the experimental CLib zeroD interface per Cantera/enhancements#220; other references are Cantera/enhancements#202 and Cantera/enhancements#61.

The resulting inheritance diagram is:

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

Closes Cantera/enhancements#213

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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

Attention: Patch coverage is 51.42857% with 51 lines in your changes missing coverage. Please review.

Project coverage is 74.34%. Comparing base (3f2057c) to head (ebdd610).

Files with missing lines	Patch %	Lines
src/zeroD/ReactorSurface.cpp	45.71%	15 Missing and 4 partials ⚠️
include/cantera/zeroD/ReactorSurface.h	18.18%	9 Missing ⚠️
include/cantera/zeroD/ReactorBase.h	11.11%	8 Missing ⚠️
...faces/matlab_experimental/Reactor/ReactorSurface.m	0.00%	5 Missing ⚠️
src/clib/ctreactor.cpp	0.00%	3 Missing ⚠️
src/zeroD/Reactor.cpp	76.92%	1 Missing and 2 partials ⚠️
src/zeroD/ReactorBase.cpp	66.66%	2 Missing ⚠️
include/cantera/zeroD/Reservoir.h	0.00%	1 Missing ⚠️
src/zeroD/ReactorFactory.cpp	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1864      +/-   ##
==========================================
- Coverage   74.36%   74.34%   -0.02%     
==========================================
  Files         443      443              
  Lines       55407    55391      -16     
  Branches     9105     9109       +4     
==========================================
- Hits        41201    41181      -20     
- Misses      11108    11111       +3     
- Partials     3098     3099       +1     

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[ischoegl]

@speth ... I decided to revise this PR once more as I was unsatisfied with the previous version. At this point, the name of the base class remains ReactorBase (my preference ReactorNode would create too much churn). In addition, I disabled undefined operations, where associated properties remain zero if queried from ReactorBase (examples: volume for Reservoir or ReactorSurface is zero as the ReactorBase::setInitialVolume now requires an override to be implemented; similarly, ReactorSurface cannot add inlets/outlets, etc.).

[ischoegl]

Rebased after merge of #1665.

[speth]

Thanks, @ischoegl for moving ahead with this approach. I'm not sure I fully agree with my previous suggestion to have ReactorSurface derive from ReactorBase, but at least this is not too invasive, and I think there is a route to eventually resolving some of the oddities that this introduces. I had just a few suggestions before we merge this.

[ischoegl]

Thanks, @speth ... I addressed both comments, so this PR should be ready for a merge.

Regarding oddities: yes, I am aware of some. For ReactorSurface, a lot of the details depend on how we resolve Cantera/enhancements#202.