yaml2ck: Check if third body is in species list

[corykinney]

Changes proposed in this pull request

This pull request adds a check in yaml2ck for third body efficiencies for species that might not be present in the ct.Solution object due to the skip-undeclared-third-bodies: true flag.

Closes #1683

Using the provided example from the issue referenced:

phases:
- name: test
  thermo: ideal-gas
  elements: [O, H, C, Ar]
  species:
  - gri30.yaml/species: all
  kinetics: gas
  skip-undeclared-elements: true
  skip-undeclared-third-bodies: true
  reactions:
  - gri30.yaml/reactions: declared-species
  transport: mixture-averaged
  state: {T: 300.0, P: 1 atm}

The outputted Chemkin file from python -m cantera.yaml2ck test.yaml --overwrite before the change:

H + O2 + M <=> HO2 + M           2.8000000000000005e+18 -0.86 0.0
AR/0.000E+00/ C2H6/1.500E+00/ CO/7.500E-01/ CO2/1.500E+00/ H2O/0.000E+00/ N2/0.000E+00/ O2/0.000E+00/

versus after the change:

H + O2 + M <=> HO2 + M           2.8000000000000005e+18 -0.86 0.0
AR/0.000E+00/ C2H6/1.500E+00/ CO/7.500E-01/ CO2/1.500E+00/ H2O/0.000E+00/ O2/0.000E+00/

The N2 efficiency is omitted from the list as desired.

Feedback

An example file still needs to be added with a corresponding test case, but before doing so, I wanted to solicit feedback on potential edge cases. What behavior would be expected if no explicit third body species are present in the mechanism? Are there any other possible cases that need to be accounted for proactively?

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

[speth]

Thanks, @corykinney. I think this looks like a clean fix. Could you please add a test to test_convert.py verifying that this works as intended?

[speth]

What behavior would be expected if no explicit third body species are present in the mechanism?

I didn't try it, but I think your patch would add a blank line to the output. I don't see a problem with that.

[corykinney]

@speth I implemented your suggestions and added the necessary test case. It should be good to go, but let me know if I missed anything in the test.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.69%. Comparing base (d37a76b) to head (39816e4).
Report is 19 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1696      +/-   ##
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- Coverage   75.69%   75.69%   -0.01%     
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  Files         443      443              
  Lines       60975    60971       -4     
  Branches     9551     9552       +1     
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- Hits        46158    46154       -4     
  Misses      11786    11786              
  Partials     3031     3031              

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[speth]

Thanks, @corykinney! This looks good to me.