Reaction Mechanism Simulator YAML File Generation #1629
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Codecov Report
@@ Coverage Diff @@
## master #1629 +/- ##
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- Coverage 41.47% 41.37% -0.11%
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Files 176 177 +1
Lines 29314 29455 +141
Branches 6035 6059 +24
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+ Hits 12158 12186 +28
- Misses 16303 16417 +114
+ Partials 853 852 -1
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rmgpy/yml.py
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| from rmgpy.kinetics.arrhenius import * | ||
| from rmgpy.kinetics.falloff import * | ||
| from rmgpy.kinetics.chebyshev import * | ||
| from rmgpy.data.solvation import * |
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Can you replace all of the * imports with explicit ones?
rmgpy/yml.py
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| from rmgpy.data.solvation import * | ||
| from rmgpy.util import makeOutputSubdirectory | ||
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| def convertchemkin2yml(chemkinpath,spcdictpath=None,output="chem.rms"): |
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Can you add spaces to after all commas in this file, in accordance with PEP-8?
rmgpy/yml.py
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| return D | ||
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| def getradicals(spc): | ||
| if spc.molecule[0].toSMILES() == "[O][O]": |
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What is the purpose of this function? Can you not use Molecule.getRadicalCount?
Also, why does oxygen need to be special cased? Could you add a comment explaining?
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I think this is faster since the multiplicities are known.
This is typically used for analyzing radical production in RMS and it's very useful to treat O2 as a stable molecule when you're looking at bulk radical production/loss
rmgpy/yml.py
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| elif obj is None: | ||
| return None | ||
| else: | ||
| raise ValueError |
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Add a message to this error?
rmgpy/yml.py
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| D["kinetics"] = obj2dict(obj.kinetics,spcs) | ||
| D["type"] = "ElementaryReaction" | ||
| D["radicalchange"] = sum([getradicals(x) for x in obj.products]) - sum([getradicals(x) for x in obj.reactants]) | ||
| elif isinstance(obj,Arrhenius): |
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Is support for the surface kinetics types necessary? I assume not now, since RMG doesn't have surface reactors?
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I've added them in, RMS can read the catalysis output files properly yet, but it will be able to in the future.
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| def getMechDict(spcs, rxns, solvent='solvent', solventData=None): | ||
| D = dict() | ||
| D["Units"] = dict() |
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Does ["Units"] ever get updated anywhere else in the code? Does the YAML format for RMS/Cantera assume that an empty dictionary for units defaults to something?
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It defaults to SI units for everything, unless units are specified for individual floats
rmgpy/yml.py
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| def getMechDict(spcs, rxns, solvent='solvent', solventData=None): | ||
| D = dict() | ||
| D["Units"] = dict() | ||
| D["Reactions"] = [] |
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This line is not needed right? Further down you have D["Reactions"] = [obj2dict(x, spcs) for x in rxns], which will overwrite this line and also return an empty list if there are no reactions.
rmgpy/yml.py
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| D["type"] = "Species" | ||
| D["smiles"] = obj.molecule[0].toSMILES() | ||
| D["thermo"] = obj2dict(obj.thermo, spcs) | ||
| if D["smiles"] == "[O][O]": |
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You defined the getradicals function above, so use this to get rid of the if-else statement here.
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Should be ready to merge now |
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I agree, feel free to merge this as soon as the tests pass (assuming they do). |
Adds generation of .rms YAML files for use in ReactionMechanismSimulator.