def execute(inputFile, options):
"""
Generate a reaction model for the set of reaction systems specified in an
input file at location `inputFile`. Output and temporary files will be
placed in the directories `outputDir` and `scratchDir`, respectively; if
either of these are empty strings, the corresponding files will be placed
in the same directory as the input file. The `libraryDir` parameter can be
used to specify additional directories to search for RMG databases. The
`verbose` parameter is an integer specifying the amount of log text seen
at the console; the levels correspond to those of the :data:`logging` module.
"""
# Set directories
settings.outputDirectory = options.outputDirectory
settings.scratchDirectory = options.scratchDirectory
settings.libraryDirectory = options.libraryDirectory
# Save initialization time
settings.initializationTime = time.time()
# Set up log (uses stdout and a file)
initializeLog(options.verbose)
# Log start timestamp
logging.info('RMG execution initiated at ' + time.asctime() + '\n')
# Print out RMG header
printRMGHeader()
# Make output subdirectories
plotDir = os.path.join(settings.outputDirectory, 'plot')
if os.path.exists(plotDir):
for f in os.listdir(plotDir):
os.remove(plotDir + '/' + f)
os.rmdir(plotDir)
os.mkdir(plotDir)
specDir = os.path.join(settings.outputDirectory, 'species')
if os.path.exists(specDir):
for f in os.listdir(specDir):
os.remove(specDir + '/' + f)
os.rmdir(specDir)
os.mkdir(specDir)
# Read input file
reactionModel, coreSpecies, reactionSystems = io.readInputFile(inputFile)
# Initialize reaction model
if options.restart:
import cPickle
logging.info('Loading previous restart file...')
f = open(os.path.join(settings.outputDirectory,'restart.pkl'), 'rb')
species.speciesList = cPickle.load(f)
species.speciesCounter = cPickle.load(f)
reaction.reactionList = cPickle.load(f)
reactionModel = cPickle.load(f)
reactionSystems = cPickle.load(f)
f.close()
options.restart = False # have already restarted
else:
reactionModel.initialize(coreSpecies)
# RMG execution statistics
coreSpeciesCount = []
coreReactionCount = []
edgeSpeciesCount = []
edgeReactionCount = []
execTime = []
restartSize = []
memoryUse = []
# Main RMG loop
done = False
while not done:
done = True
speciesToAdd = []
for index, reactionSystem in enumerate(reactionSystems):
# Conduct simulation
logging.info('Conducting simulation of reaction system %s...' % (index+1))
t, y, dydt, valid, spec = reactionSystem.simulate(reactionModel)
# Postprocess results
logging.info('Saving simulation results for reaction system %s...' % (index+1))
reactionSystem.postprocess(reactionModel, t, y, dydt, str(index+1))
# If simulation is invalid, note which species should be added to
# the core
if not valid:
speciesToAdd.append(spec)
done = False
# Add the notes species to the core
speciesToAdd = list(set(speciesToAdd))
for spec in speciesToAdd:
reactionModel.enlarge(spec)
# Save the restart file
import cPickle
logging.info('Saving restart file...')
f = open(os.path.join(settings.outputDirectory,'restart.pkl'), 'wb')
cPickle.dump(species.speciesList, f)
cPickle.dump(species.speciesCounter, f)
cPickle.dump(reaction.reactionList, f)
cPickle.dump(reactionModel, f)
cPickle.dump(reactionSystems, f)
f.close()
if not done:
logging.info('Updating RMG execution statistics...')
# Update RMG execution statistics
coreSpeciesCount.append(len(reactionModel.core.species))
coreReactionCount.append(len(reactionModel.core.reactions))
edgeSpeciesCount.append(len(reactionModel.edge.species))
edgeReactionCount.append(len(reactionModel.edge.reactions))
execTime.append(time.time() - settings.initializationTime)
from guppy import hpy
hp = hpy()
memoryUse.append(hp.heap().size / 1.0e6)
logging.debug('Execution time: %s s' % (execTime[-1]))
logging.debug('Memory used: %s MB' % (memoryUse[-1]))
restartSize.append(os.path.getsize(os.path.join(settings.outputDirectory,'restart.pkl')) / 1.0e6)
generateExecutionPlots(execTime, coreSpeciesCount, coreReactionCount, edgeSpeciesCount, edgeReactionCount, memoryUse, restartSize)
logging.info('')
# Write output file
logging.info('MODEL GENERATION COMPLETED')
logging.info('')
logging.info('The final model core has %s species and %s reactions' % (len(reactionModel.core.species), len(reactionModel.core.reactions)))
logging.info('The final model edge has %s species and %s reactions' % (len(reactionModel.edge.species), len(reactionModel.edge.reactions)))
io.writeOutputFile(os.path.join(settings.outputDirectory,'output.xml'), reactionModel, reactionSystems)
# Log end timestamp
logging.info('RMG execution terminated at ' + time.asctime())
plotDir = os.path.join(settings.outputDirectory, 'plot')
if os.path.exists(plotDir):
for f in os.listdir(plotDir):
os.remove(plotDir + '/' + f)
os.rmdir(plotDir)
os.mkdir(plotDir)
specDir = os.path.join(settings.outputDirectory, 'species')
if os.path.exists(specDir):
for f in os.listdir(specDir):
os.remove(specDir + '/' + f)
os.rmdir(specDir)
os.mkdir(specDir)
# Read input file
reactionModel, coreSpecies, reactionSystems = io.readInputFile(inputFile)
# Initialize reaction model
if options.restart:
import gzip
import cPickle
import ctml_writer
logging.info('Loading previous restart file...')
f = gzip.GzipFile(os.path.join(settings.outputDirectory,'restart.pkl'), 'rb')
species.speciesList, species.speciesCounter, reaction.reactionList, \
reactionModel, reactionSystems = cPickle.load(f)
f.close()
# Cantera stuff
reload(ctml_writer) # ensure new empty ctml_writer._species and ._reactions lists
for reactor in reactionSystems:
# initialise the ctml_writer thing
