def generate_isotope_model(output_directory,
rmg0,
isotopes,
use_original_reactions=False,
kinetic_isotope_effect=None):
"""
Replace the core species of the rmg model with the parameter list
of species.
Generate all reactions between new list of core species.
Returns created RMG object.
"""
logging.debug("isotope: called generateIsotopeModel")
rmg = RMG(input_file=rmg0.input_file, output_directory=output_directory)
rmg.attach(ChemkinWriter(output_directory))
logging.info("isotope: making the isotope model for with all species")
initialize_isotope_model(rmg, isotopes)
if use_original_reactions:
logging.info("isotope: finding reactions from the original reactions")
rxns = generate_isotope_reactions(rmg0.reaction_model.core.reactions,
isotopes)
rmg.reaction_model.process_new_reactions(rxns, new_species=[])
else:
logging.info("isotope: enlarging the isotope model")
rmg.reaction_model.enlarge(react_edge=True,
unimolecular_react=rmg.unimolecular_react,
bimolecular_react=rmg.bimolecular_react)
logging.info("isotope: clustering reactions")
clusters = cluster(rmg.reaction_model.core.reactions)
logging.info(
'isotope: fixing the directions of every reaction to a standard')
for isotopomerRxnList in clusters:
ensure_reaction_direction(isotopomerRxnList)
consistent = True
logging.info("isotope: checking symmetry is consistent among isotopomers")
for species_list in cluster(rmg.reaction_model.core.species):
if not ensure_correct_symmetry(species_list):
logging.info("isotopomers of {} with index {} may have wrong "
"symmetry".format(species_list[0],
species_list[0].index))
consistent = False
logging.info(
"isotope: checking that reaction degeneracy is consistent among isotopomers"
)
for rxn_list in clusters:
if not ensure_correct_degeneracies(rxn_list):
logging.info("isotopomers of {} with index {} may have incorrect "
"degeneracy.".format(rxn_list[0], rxn_list[0].index))
consistent = False
if not consistent:
logging.warning(
"isotope: non-consistent degeneracy and/or symmetry was detected. This may lead to "
"unrealistic deviations in enrichment. check log for more details")
if kinetic_isotope_effect:
logging.info(
'isotope: modifying reaction rates using kinetic isotope effect '
'method "{0}"'.format(kinetic_isotope_effect))
if kinetic_isotope_effect == 'simple':
apply_kinetic_isotope_effect_simple(clusters,
rmg.database.kinetics)
else:
logging.warning(
'isotope: kinetic isotope effect {0} is not supported. '
'skipping adding kinetic isotope effects.')
else:
logging.info(
'isotope: not adding kinetic isotope effects since no method was supplied.'
)
logging.info("isotope: saving files")
rmg.save_everything()
rmg.finish()
return rmg
def generate_isotope_model(outputDirectory, rmg0, isotopes, useOriginalReactions = False,
kineticIsotopeEffect = None):
"""
Replace the core species of the rmg model with the parameter list
of species.
Generate all reactions between new list of core species.
Returns created RMG object.
"""
logging.debug("isotope: called generateIsotopeModel")
rmg = RMG(inputFile=rmg0.inputFile, outputDirectory=outputDirectory)
rmg.attach(ChemkinWriter(outputDirectory))
logging.info("isotope: making the isotope model for with all species")
initialize_isotope_model(rmg, isotopes)
if useOriginalReactions:
logging.info("isotope: finding reactions from the original reactions")
rxns = generate_isotope_reactions(rmg0.reactionModel.core.reactions, isotopes)
rmg.reactionModel.processNewReactions(rxns,newSpecies=[])
else:
logging.info("isotope: enlarging the isotope model")
rmg.reactionModel.enlarge(reactEdge=True,
unimolecularReact=rmg.unimolecularReact,
bimolecularReact=rmg.bimolecularReact)
logging.info("isotope: clustering reactions")
clusters = cluster(rmg.reactionModel.core.reactions)
logging.info('isotope: fixing the directions of every reaction to a standard')
for isotopomerRxnList in clusters:
ensure_reaction_direction(isotopomerRxnList)
consistent = True
logging.info("isotope: checking symmetry is consistent among isotopomers")
for species_list in cluster(rmg.reactionModel.core.species):
if not ensure_correct_symmetry(species_list):
logging.info("isotopomers of {} with index {} may have wrong symmetry".format(species_list[0], species_list[0].index))
consistent = False
logging.info("isotope: checking that reaction degeneracy is consistent among isotopomers")
for rxn_list in clusters:
if not ensure_correct_degeneracies(rxn_list):
logging.info("isotopomers of {} with index {} may have incorrect degeneracy.".format(rxn_list[0], rxn_list[0].index))
consistent = False
if not consistent:
logging.warning("isotope: non-consistent degeneracy and/or symmetry was detected. This may lead to unrealistic deviations in enrichment. check log for more details")
if kineticIsotopeEffect:
logging.info('isotope: modifying reaction rates using kinetic isotope effect method "{0}"'.format(kineticIsotopeEffect))
if kineticIsotopeEffect == 'simple':
apply_kinetic_isotope_effect_simple(clusters,rmg.database.kinetics)
else:
logging.warning('isotope: kinetic isotope effect {0} is not supported. skipping adding kinetic isotope effects.')
else:
logging.info('isotope: not adding kinetic isotope effects since no method was supplied.')
logging.info("isotope: saving files")
rmg.saveEverything()
rmg.finish()
return rmg
