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rmg.py
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rmg.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2010 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
################################################################################
"""
RMG is an automatic chemical mechanism generator. It is awesomely awesome.
"""
import os.path
import sys
import argparse
import logging
import rmgpy
from rmgpy.rmg.main import RMG, initializeLog, processProfileStats, makeProfileGraph
################################################################################
def parseCommandLineArguments():
"""
Parse the command-line arguments being passed to RMG Py. This uses the
:mod:`argparse` module, which ensures that the command-line arguments are
sensible, parses them, and returns them.
"""
parser = argparse.ArgumentParser(description=
"""
Reaction Mechanism Generator (RMG) is an automatic chemical reaction
mechanism generator that constructs kinetic models composed of
elementary chemical reaction steps using a general understanding of
how molecules react.
""")
parser.add_argument('file', metavar='FILE', type=str, nargs=1,
help='a file describing the job to execute')
# Options for controlling the amount of information printed to the console
# By default a moderate level of information is printed; you can either
# ask for less (quiet), more (verbose), or much more (debug)
group = parser.add_mutually_exclusive_group()
group.add_argument('-q', '--quiet', action='store_true', help='only print warnings and errors')
group.add_argument('-v', '--verbose', action='store_true', help='print more verbose output')
group.add_argument('-d', '--debug', action='store_true', help='print debug information')
# Add options for controlling what directories files are written to
parser.add_argument('-o', '--output-directory', type=str, nargs=1, default='',
metavar='DIR', help='use DIR as output directory')
parser.add_argument('-s', '--scratch-directory', type=str, nargs=1, default='',
metavar='DIR', help='use DIR as scratch directory')
parser.add_argument('-l', '--library-directory', type=str, nargs=1, default='',
metavar='DIR', help='use DIR as library directory')
# Add restart option
parser.add_argument('-r', '--restart', action='store_true', help='restart an incomplete job')
parser.add_argument('-p', '--profile', action='store_true', help='run under cProfile to gather profiling statistics, and postprocess them if job completes')
parser.add_argument('-P', '--postprocess', action='store_true', help='postprocess profiling statistics from previous [failed] run; does not run the simulation')
parser.add_argument('-t', '--walltime', type=str, nargs=1, default='0',
metavar='HH:MM:SS', help='set the maximum execution time')
return parser.parse_args()
################################################################################
if __name__ == '__main__':
""" GUPPY PROFILING DISABLED FOR NOW
# Initialize the memory profiler
# It works best if we do this as the very first thing
# If the memory profiler package is not installed then carry on
try:
from guppy import hpy
hp = hpy()
hp.heap()
except ImportError:
pass
"""
# 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
import os.path
inputDirectory = os.path.abspath(os.path.dirname(args.file[0]))
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())
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)