else:
raise ValueError('Invalid format for wall time; should be HH:MM:SS.')
except ValueError, e:
raise ValueError('Invalid format for wall time; should be HH:MM:SS.')
# Save initialization time
settings.initializationTime = time.time()
# Set up log (uses stdout and a file)
logging.initialize(options.verbose, os.path.join(settings.outputDirectory,'RMG.log'))
# Log start timestamp
logging.info('RMG execution initiated at ' + time.asctime() + '\n')
# Print out RMG header
logging.logHeader()
# 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)
def execute(inputFile, options):
# Set directories
settings.libraryDirectory = options.libraryDirectory
# Set up log (uses stdout and a file)
logging.initialize(options.verbose, os.path.join(settings.outputDirectory,'RMG.log'))
# Log start timestamp
logging.info('RMG execution initiated at ' + time.asctime() + '\n')
# Print out RMG header
logging.logHeader()
# Read input file
network, Tlist, Plist, grainSize, numGrains, method, model = io.readInputFile(inputFile)
# Shift network such that lowest-energy isomer has a ground state of 0.0
logging.info('Zeroing lowest energy isomer...')
network.shiftToZeroEnergy()
# Determine energy grains
logging.info('Determining energy grains...')
Elist = network.determineEnergyGrains(grainSize, numGrains, max(Tlist))
# Calculate density of states for all isomers in network
logging.info('Calculating densities of states...')
network.calculateDensitiesOfStates(Elist)
# # DEBUG: Plot densities of states
# import pylab
# legend = []
# for isomer in network.isomers:
# if isomer.densStates is not None:
# pylab.semilogy(Elist / 1000.0, isomer.densStates, '-')
# #legend.append(str(isomer))
# pylab.xlabel('Energy (kJ/mol)')
# pylab.ylabel('Density of states (mol/J)')
# #pylab.legend(legend, loc=4)
# pylab.show()
# Determine phenomenological rate coefficients
logging.info('Calculating phenomenological rate coefficients...')
K = network.calculateRateCoefficients(Tlist, Plist, Elist, method)
# Create net reaction objects
network.netReactions = []
index = 0
for i, reactantIsomer in enumerate(network.isomers):
for j, productIsomer in enumerate(network.isomers[0:i]):
netReaction = reaction.PDepReaction(reactantIsomer.species, productIsomer.species, network, None)
netReaction.id = 'netReaction%i' % (index+1)
index += 1
network.netReactions.append(netReaction)
# Fit interpolation model
if model[0].lower() == 'chebyshev':
modelType, degreeT, degreeP = model
chebyshev = kinetics.ChebyshevKinetics()
chebyshev.fitToData(Tlist, Plist, K[:,:,j,i], degreeT, degreeP)
netReaction.kinetics = [chebyshev]
elif model.lower() == 'pdeparrhenius':
pDepArrhenius = kinetics.PDepArrheniusKinetics()
pDepArrhenius.fitToData(Tlist, Plist, K[:,:,j,i])
netReaction.kinetics = [pDepArrhenius]
else:
pass
# Save results to file
logging.info('Saving results...')
outputFile = os.path.join(os.path.dirname(inputFile), 'output.xml')
io.writeOutputFile(outputFile, network, Tlist, Plist, Elist, method, model)
logging.info('')
# Log end timestamp
logging.info('RMG execution terminated at ' + time.asctime())
