better species naming for cantera models

[goldmanm]

To the best of my knowledge, cantera does not have the restrictive species naming guidelines that chemkin has. When generating a cantera model, we can apply more descriptive names (like their SMILES) than would be possible with chemkin.

We currently create the cantera input file by converting from the chemkin input file with ck2cti. Getting better naming would require generating the input file directly from RMG.

@alongd, you wrote the cantera conversion for RMG, do you have thoughts on this?

[alongd]

I'm not familiar with the naming convention on Cantera; if it's really that flexible, this could be a nice feature.

[goldmanm]

I wrote up this notebook which provides the species, thermo and reaction blocks to input into a cti file so analysis can be conducted in cantera with SMILES as the species names.

This is kind of a first step to getting better naming for the species in cantera modules.

[goldmanm]

I found a way to rename species from an RMG run and place them into a cantera input file.

I also commonly use this method, which renames all species based on SMILES and ensures they don't overlap. This requires the soln2cti and test_mechanism_from_solution.py which is in PR 451 in cantera. You can just put it in the same directory

def make_string_labels_independent(species):
    """
    This method reads in species labels and makes sure none of them conflict
    If a conflict occurs, the second occurance will have '-2' added
    """
    
    labels = set()
    for spec in species:
        duplicate_index = 1
        potential_label = spec.label
        while potential_label in labels:
            duplicate_index += 1
            potential_label = spec.label + '-{}'.format(duplicate_index)
        spec.label = potential_label
        labels.add(potential_label)

# use the method
species, reactions = loadChemkinFile(chemkinPath, speciesDictPath, readComments = False, useChemkinNames=False)
make_string_labels_independent(species)

#convert to cantera objects
ct_species = [spec.toCantera(useChemkinIdentifier = False) for spec in species]
# since this can return a rxn or list of reactions, this allows to make a list based on the returned type
ct_reactions = []
for rxn in reactions:
    ct_rxn = rxn.toCantera(useChemkinIdentifier = False)
    if isinstance(ct_rxn, list):
        ct_reactions.extend(ct_rxn)
    else:
        ct_reactions.append(ct_rxn)

gas = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
                  species=ct_species, reactions=ct_reactions)
# make cantera input file
new_file = soln2cti.write(gas)
# move the file to new location
os.rename(new_file, os.path.join(mainPath,'cantera_new_names.cti'))

[mjohnson541]

should this issue be closed @goldmanm?

[JacksonBurns]

This issue is no longer relevant - we have switched to Cantera 2.6 in #2288 and this function is gone. Closing as stale.