def main():
args = parseCommandLineArguments()
if args.useOriginalReactions and not args.original:
raise InputError(
'Cannot use original reactions without a previously run RMG job')
maximumIsotopicAtoms = args.maximumIsotopicAtoms[0]
useOriginalReactions = args.useOriginalReactions
inputFile = args.input
outputdir = os.path.abspath(
args.output[0]) if args.output else os.path.abspath('.')
original = os.path.abspath(args.original[0]) if args.original else None
kie = args.kineticIsotopeEffect[0] if args.kineticIsotopeEffect else None
supported_kie_methods = ['simple']
if kie not in supported_kie_methods and kie is not None:
raise InputError(
'The kie input, {0}, is not one of the currently supported methods, {1}'
.format(kie, supported_kie_methods))
initializeLog(logging.INFO, os.path.join(os.getcwd(), 'RMG.log'))
run(inputFile,
outputdir,
original=original,
maximumIsotopicAtoms=maximumIsotopicAtoms,
useOriginalReactions=useOriginalReactions,
kineticIsotopeEffect=kie)
def main():
initializeLog(logging.INFO,'treegen.log')
dbdir = settings['database.directory']
familyName, nprocs = parse_arguments()
database = RMGDatabase()
database.load(
path=dbdir,
thermoLibraries=['Klippenstein_Glarborg2016', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo',
'primaryThermoLibrary', 'primaryNS', 'NitrogenCurran', 'NOx2018', 'FFCM1(-)',
'SulfurLibrary', 'SulfurGlarborgH2S'],
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
kineticsFamilies=[familyName],
kineticsDepositories=['training'],
# frequenciesLibraries = self.statmechLibraries,
depository=False, # Don't bother loading the depository information, as we don't use it
)
family = database.kinetics.families[familyName]
family.cleanTree(database.thermo)
family.generateTree(thermoDatabase=database.thermo, nprocs=min(4, nprocs))
family.checkTree()
family.regularize()
templateRxnMap = family.getReactionMatches(thermoDatabase=database.thermo, removeDegeneracy=True, getReverse=True, fixLabels=True)
family.makeBMRulesFromTemplateRxnMap(templateRxnMap, nprocs=min(6, nprocs))
family.checkTree()
family.save(os.path.join(dbdir,'kinetics','families',familyName))
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 run_simulation(inputFile,
chemkinFile,
dictFile,
diffusionLimited=True,
checkDuplicates=True):
"""
Runs a standalone simulation of RMG. Runs sensitivity analysis if sensitive species are given.
Also runs uncertainty analysis if uncertainty options block is present in input file.
diffusionLimited=True implies that if it is a liquid reactor diffusion limitations will be enforced
otherwise they will not be in a liquid reactor
"""
output_dir = os.path.abspath(os.path.dirname(inputFile))
initializeLog(logging.INFO, os.path.join(output_dir, 'simulate.log'))
rmg = loadRMGJob(inputFile,
chemkinFile,
dictFile,
generateImages=False,
checkDuplicates=checkDuplicates)
start_time = time()
# conduct simulation
simulate(rmg, diffusionLimited)
end_time = time()
time_taken = end_time - start_time
logging.info("Simulation took {0} seconds".format(time_taken))
def main():
# Parse the command-line arguments (requires the argparse module)
# args = parse_command_line_arguments()
# AJ: change path to intended input file
# args = parse_command_line_arguments(["/Users/agnes/Documents/Software/RMG/RMG-Py/examples/rmg/superminimal/input.py"])
args = parse_command_line_arguments(
["./examples/rmg/superminimal/input.py"])
if args.postprocess:
print "Postprocessing the profiler statistics (will be appended to RMG.log)"
else:
# 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
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
logging.info(rmgpy.settings.report())
kwargs = {
'restart': args.restart,
'walltime': args.walltime,
'kineticsdatastore': args.kineticsdatastore
}
if args.profile:
import cProfile
global_vars = {}
local_vars = {
'inputFile': args.file,
'output_dir': args.output_directory,
'kwargs': kwargs,
'RMG': RMG
}
command = """rmg = RMG(inputFile=inputFile, outputDirectory=output_dir); rmg.execute(**kwargs)"""
stats_file = os.path.join(args.output_directory, 'RMG.profile')
print("Running under cProfile")
if not args.postprocess:
# actually run the program!
cProfile.runctx(command, global_vars, local_vars, stats_file)
# postprocess the stats
log_file = os.path.join(args.output_directory, 'RMG.log')
processProfileStats(stats_file, log_file)
makeProfileGraph(stats_file)
else:
rmg = RMG(inputFile=args.file, outputDirectory=args.output_directory)
rmg.execute(**kwargs)
def generate_RMG_model(inputFile, outputDirectory):
"""
Generate the RMG-Py model NOT containing any non-normal isotopomers.
Returns created RMG object.
"""
initializeLog(logging.INFO, os.path.join(outputDirectory, 'RMG.log'))
# generate mechanism:
rmg = RMG(inputFile = os.path.abspath(inputFile),
outputDirectory = os.path.abspath(outputDirectory))
rmg.execute()
return rmg
def generate_RMG_model(inputFile, outputDirectory):
"""
Generate the RMG-Py model NOT containing any non-normal isotopomers.
Returns created RMG object.
"""
initializeLog(logging.INFO, os.path.join(outputDirectory, 'RMG.log'))
# generate mechanism:
rmg = RMG(inputFile=os.path.abspath(inputFile),
outputDirectory=os.path.abspath(outputDirectory))
rmg.execute()
return rmg
def main():
# Parse the command-line arguments (requires the argparse module)
args = parse_command_line_arguments()
if args.postprocess:
print "Postprocessing the profiler statistics (will be appended to RMG.log)"
else:
# 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
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
logging.info(rmgpy.settings.report())
kwargs = {
'restart': args.restart,
'walltime': args.walltime,
'kineticsdatastore': args.kineticsdatastore
}
if args.profile:
import cProfile
global_vars = {}
local_vars = {
'inputFile': args.file,
'output_dir': args.output_directory,
'kwargs': kwargs,
'RMG': RMG
}
command = """rmg = RMG(inputFile=inputFile, outputDirectory=output_dir); rmg.execute(**kwargs)"""
stats_file = os.path.join(args.output_directory, 'RMG.profile')
print("Running under cProfile")
if not args.postprocess:
# actually run the program!
cProfile.runctx(command, global_vars, local_vars, stats_file)
# postprocess the stats
log_file = os.path.join(args.output_directory, 'RMG.log')
processProfileStats(stats_file, log_file)
makeProfileGraph(stats_file)
else:
rmg = RMG(inputFile=args.file, outputDirectory=args.output_directory)
rmg.execute(**kwargs)
def main():
args = parseCommandLineArguments()
if args.useOriginalReactions and not args.original:
raise InputError('Cannot use original reactions without a previously run RMG job')
maximumIsotopicAtoms = args.maximumIsotopicAtoms[0]
useOriginalReactions = args.useOriginalReactions
inputFile = args.input
outputdir = os.path.abspath(args.output[0]) if args.output else os.path.abspath('.')
original = os.path.abspath(args.original[0]) if args.original else None
kie = args.kineticIsotopeEffect[0] if args.kineticIsotopeEffect else None
supported_kie_methods = ['simple']
if kie not in supported_kie_methods and kie is not None:
raise InputError('The kie input, {0}, is not one of the currently supported methods, {1}'.format(kie,supported_kie_methods))
initializeLog(logging.INFO, os.path.join(os.getcwd(), 'RMG.log'))
run(inputFile, outputdir, original=original,
maximumIsotopicAtoms=maximumIsotopicAtoms,
useOriginalReactions=useOriginalReactions,
kineticIsotopeEffect = kie)
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)
inputDirectory = os.path.abspath(os.path.dirname(inputFile))
if args.output_directory == '':
args.output_directory = inputDirectory
if args.scratch_directory == '':
args.scratch_directory = inputDirectory
if args.postprocess:
print "Postprocessing the profiler statistics (will be appended to RMG.log)"
args.profile = True
else:
# 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
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
logging.info(rmgpy.settings.report())
output_dir = args.output_directory
kwargs = {
'scratch_directory': args.scratch_directory,
'restart': args.restart,
'walltime': args.walltime,
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,
inputDirectory = os.path.abspath(os.path.dirname(inputFile))
if args.output_directory == '':
args.output_directory = inputDirectory
if args.scratch_directory == '':
args.scratch_directory = inputDirectory
if args.postprocess:
print "Postprocessing the profiler statistics (will be appended to RMG.log)"
args.profile = True
else:
# 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
initializeLog(level, os.path.join(args.output_directory, 'RMG.log'))
logging.info(rmgpy.settings.report())
output_dir = args.output_directory
kwargs = {
'scratch_directory': args.scratch_directory,
'restart': args.restart,
'walltime': args.walltime,
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,