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())
logging.info('')
# Consider stopping gracefully if the next iteration might take us
# past the wall time
if settings.wallTime > 0 and len(execTime) > 1:
t = execTime[-1]
dt = execTime[-1] - execTime[-2]
if t + 2 * dt > settings.wallTime:
logging.info('MODEL GENERATION TERMINATED')
logging.info('')
logging.info('There is not enough time to complete the next iteration before the wall time is reached.')
logging.info('The output model may be incomplete.')
logging.info('')
logging.info('The current model core has %s species and %s reactions' % (len(reactionModel.core.species), len(reactionModel.core.reactions)))
logging.info('The current 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)
return
# 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('')
logging.info('RMG execution terminated at ' + time.asctime())
################################################################################