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 main():
# Parse the command-line arguments (requires the argparse module)
args = parse_command_line_arguments()
if args.postprocess:
logging.info(
"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
initialize_log(level, os.path.join(args.output_directory, 'RMG.log'))
logging.info(rmgpy.settings.report())
kwargs = {
'restart': args.restart,
'walltime': args.walltime,
'maxproc': args.maxproc,
'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(input_file=inputFile, output_directory=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')
process_profile_stats(stats_file, log_file)
make_profile_graph(stats_file)
else:
rmg = RMG(input_file=args.file, output_directory=args.output_directory)
rmg.execute(**kwargs)
def generate_rmg_model(input_file, output_directory):
"""
Generate the RMG-Py model NOT containing any non-normal isotopomers.
Returns created RMG object.
"""
initialize_log(logging.INFO, os.path.join(output_directory, 'RMG.log'))
# generate mechanism:
rmg = RMG(input_file=os.path.abspath(input_file),
output_directory=os.path.abspath(output_directory))
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)
'walltime': args.walltime,
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,
'output_dir': output_dir,
'kwargs': kwargs,
'RMG': RMG
}
command = """rmg = RMG(); rmg.execute(inputFile, output_dir, **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()
rmg.execute(inputFile, output_dir, **kwargs)
'restart': args.restart,
'walltime': args.walltime,
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,
'output_dir': output_dir,
'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=inputFile, outputDirectory=output_dir)
rmg.execute(**kwargs)
'walltime': args.walltime,
'kineticsdatastore': args.kineticsdatastore
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,
'output_dir': output_dir,
'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=inputFile, outputDirectory=output_dir)
rmg.execute(**kwargs)
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())
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {'args': args, 'RMG': RMG}
command = """rmg = RMG(); rmg.execute(args)"""
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()
rmg.execute(args)
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"))
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {"args": args, "RMG": RMG}
command = """rmg = RMG(); rmg.execute(args)"""
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()
rmg.execute(args)
'walltime': args.walltime,
}
if args.profile:
import cProfile, sys, pstats, os
global_vars = {}
local_vars = {
'inputFile': inputFile,
'output_dir': output_dir,
'kwargs': kwargs,
'RMG': RMG
}
command = """rmg = RMG(); rmg.execute(inputFile, output_dir, **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()
rmg.execute(inputFile, output_dir, **kwargs)