def main():
"""
Driver function that parses command line arguments and passes them to the execute function.
"""
# Parse the command-line arguments (requires the argparse module)
args = parse_command_line_arguments()
# Initialize the logging system (resets the RMG.log file)
level = logging.INFO
if args.debug:
level = 0
elif args.verbose:
level = logging.DEBUG
elif args.quiet:
level = logging.WARNING
kwargs = {
'restart': args.restart,
'walltime': args.walltime,
'log': level,
'kineticsdatastore': args.kineticsdatastore
}
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
rmg = RMG(inputFile=args.file, outputDirectory=args.output_directory)
# Add output listeners:
rmg.attach(ChemkinWriter(args.output_directory))
rmg.attach(OutputHTMLWriter(args.output_directory))
execute(rmg, **kwargs)
def main():
"""
Driver function that parses command line arguments and passes them to the execute function.
"""
# Parse the command-line arguments (requires the argparse module)
args = parse_command_line_arguments()
# Initialize the logging system (resets the RMG.log file)
level = logging.INFO
if args.debug:
level = 0
elif args.verbose:
level = logging.DEBUG
elif args.quiet:
level = logging.WARNING
kwargs = {
'restart': args.restart,
'walltime': args.walltime,
'log': level,
'kineticsdatastore': args.kineticsdatastore
}
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
rmg = RMG(inputFile=args.file, outputDirectory=args.output_directory)
# Add output listeners:
rmg.attach(ChemkinWriter(args.output_directory))
rmg.attach(OutputHTMLWriter(args.output_directory))
execute(rmg, **kwargs)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import rmgpy.tools.generate_reactions as generate_reactions
from rmgpy.rmg.main import initializeLog, RMG
from rmgpy.chemkin import ChemkinWriter
from rmgpy.rmg.output import OutputHTMLWriter
inputFile = self.input
output_directory = self.getDirname()
rmg = RMG()
# Add output listeners:
rmg.attach(ChemkinWriter(output_directory))
rmg.attach(OutputHTMLWriter(output_directory))
generate_reactions.execute(rmg, inputFile, output_directory)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import rmgpy.tools.generate_reactions as generate_reactions
from rmgpy.rmg.main import initializeLog, RMG
from rmgpy.chemkin import ChemkinWriter
from rmgpy.rmg.output import OutputHTMLWriter
inputFile = self.input
output_directory = self.getDirname()
rmg = RMG()
# Add output listeners:
rmg.attach(ChemkinWriter(output_directory))
rmg.attach(OutputHTMLWriter(output_directory))
generate_reactions.execute(rmg, inputFile, output_directory)
def main():
"""
Driver function that parses command line arguments and passes them to the execute function.
"""
# Parse the command-line arguments (requires the argparse module)
args = parseCommandLineArguments()
# For output and scratch directories, if they are empty strings, set them
# to match the input file location
inputFile = args.file[0]
inputDirectory = os.path.abspath(os.path.dirname(inputFile))
if args.output_directory == "":
args.output_directory = inputDirectory
if args.scratch_directory == "":
args.scratch_directory = inputDirectory
# Initialize the logging system (resets the RMG.log file)
level = logging.INFO
if args.debug:
level = 0
elif args.verbose:
level = logging.DEBUG
elif args.quiet:
level = logging.WARNING
kwargs = {
"scratch_directory": args.scratch_directory,
"restart": args.restart,
"walltime": args.walltime,
"log": level,
}
initializeLog(level, os.path.join(args.output_directory, "RMG.log"))
rmg = RMG(inputFile=inputFile, outputDirectory=args.output_directory)
# Add output listeners:
rmg.attach(ChemkinWriter(args.output_directory))
rmg.attach(OutputHTMLWriter(args.output_directory))
execute(rmg, **kwargs)
def main():
"""
Driver function that parses command line arguments and passes them to the execute function.
"""
# Parse the command-line arguments (requires the argparse module)
args = parseCommandLineArguments()
# For output and scratch directories, if they are empty strings, set them
# to match the input file location
inputFile = args.file[0]
inputDirectory = os.path.abspath(os.path.dirname(inputFile))
if args.output_directory == '':
args.output_directory = inputDirectory
if args.scratch_directory == '':
args.scratch_directory = inputDirectory
# Initialize the logging system (resets the RMG.log file)
level = logging.INFO
if args.debug: level = 0
elif args.verbose: level = logging.DEBUG
elif args.quiet: level = logging.WARNING
kwargs = {
'scratch_directory': args.scratch_directory,
'restart': args.restart,
'walltime': args.walltime,
'log': level,
'kineticsdatastore': args.kineticsdatastore
}
initializeLog(level, os.path.join(args.output_directory,'RMG.log'))
rmg = RMG(inputFile=inputFile, outputDirectory=args.output_directory)
# Add output listeners:
rmg.attach(ChemkinWriter(args.output_directory))
rmg.attach(OutputHTMLWriter(args.output_directory))
execute(rmg, **kwargs)
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
