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Create YAML file outputs in RMG for use in Cantera #2321

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Create YAML file outputs in RMG for use in Cantera #2321

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Commits on Aug 2, 2024

  1. Tweaking Chemkin species list parser for readability. 

    This took me a while to figure out  what was happening.
So I changed variable name, removed a redundant if block,
and added a couple of comments.
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  2. Cleaning up chemkinTest methods for multidentate adsorbate writing. 

    It was fragile, depending on the precise ordering of lines
in the test file.
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  3. Cleaning up and extending a chemkin test mechanism. 

    To enable proper conversion in Cantera (for a future test)
we need some gas phase parts to the chemkin mechanism.
I added two extra types of surface reaction, an adsorption
sticking coefficient, and an associative desorption.
I also tidied up the species names and formatting.
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  4. Updating methods that create in-memory Cantera objects of things. 

    to_cantera for Reaction and Species and some surface kinetics types

squashed commit from Richard:
Should be able to use the to_cantera_kinetics methods.
Not sure about all these nested elifs. I think some are confused.

Co-authored-by:  Nora Khalil <khalil.nor@northeastern.edu>
Co-authored-by:  Richard West <r.west@northeastern.edu>
    @Nora-Khalil @rwest
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  5. Fixing docstrings in surface kinetics.

    @rwest
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  6. Added to_cantera_kinetics for SurfaceArrhenius and StickingCoefficient 

    Nick add cm^5/(mol^2*s) dimensionality

Co-authored-by:  Sevy Harris <harris.se@northeastern.edu>
Co-authored-by:  Nicholas Tietje <tietje.n@northeastern.edu>
    @sevyharris @ntietje1 @rwest
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  7. Adding to_cantera_kinetics for ArrheniusBM class. 

    Cantera now has a BlowersMasel kinetics class.

This requires Cantera > 2.6
As described in
https://cantera.org/dev/python/kinetics.html#cantera.BlowersMaselRate
the API may change suddenly on some versions.
    @rwest
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  8. Testing conversion to Cantera for adsorbed species and reactions. 

    This is in the canteramodelTest. We load a gas/surface mechanism 
saved in chemkin format (updated in prior commit) into both RMG
and into Cantera. We then convert the RMG objects into Cantera objects
and then compare them all - species and reactions.
This mirrors the way the gas phase parts were tested.
Hopefully increases test coverage of the new to_cantera_kinetics methods.
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  9. Save cantera files that were made from chemkin files to a separate fo… 

    …lder.

So they don't over-write the ones that are being written directly.
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  10. Rename yml to yaml_rms, because it was specific to RMS 

    This allows the Cantera yaml writer to live alongside it
    @Nora-Khalil @rwest
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  11. Enable Cantera-YAML writing. 

    Nora did most of the work.
Richard did some cleanup.
Nick fixed species_to_dict function to use correct parameter as rxn species.

Co-authored-by:  Nora Khalil <khalil.nor@northeastern.edu>
Co-authored-by: Richard West <r.west@northeastern.edu>
Co-authored-by:  Nicholas Tietje <tietje.n@northeastern.edu>
    @Nora-Khalil @rwest @ntietje1
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  12. Minor: Fix a Cython declaration in a Reaction method. 

    Although Atom is a subclass of Vertex, it adds an element
attribute. This leads to more efficient Cython code
(and quietens a warning in vscode).
    @rwest
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