forked from ReactionMechanismGenerator/RMG-Py
-
Notifications
You must be signed in to change notification settings - Fork 0
/
rmg.py
executable file
·152 lines (126 loc) · 6.25 KB
/
rmg.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2015 Prof. William H. Green ([email protected]),
# Prof. Richard H. West ([email protected]) and the RMG Team ([email protected])
#
# 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__':
# 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
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
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,
'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)