def setUp(self): """setUp gets called before each test""" from rmg import constants, log import rmg.cantera_loader import ctml_writer as cti constants.scratchDirectory = os.path.join(self.testfolder,'temp') if os.path.isdir(constants.scratchDirectory): shutil.rmtree(constants.scratchDirectory) os.makedirs(constants.scratchDirectory) if cti._species: reload(cti) if rmg.cantera_loader._species: reload(rmg.cantera_loader) log.initialize(verbose=20, fstr='RMG.log')
sys.path.append('../source')
import rmg.thermo as thermo
import rmg.species as species
import rmg.structure as structure
from rmg.structure import Structure
propane = structure.Structure(SMILES='CCC')
propane.updateAtomTypes()
GAthermoData = species.getThermoData(propane,thermoClass=thermo.ThermoGAData)
WilhoitData = thermo.convertGAtoWilhoit(GAthermoData, atoms=11, rotors=2, linear=False)
NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData)
"""
test1 = "for T in range(600,1100,100):\n\tGAthermoData.getEnthalpy(T)"
test2 = "for T in range(600,1100,100):\n\tWilhoitData.getEnthalpy(T)"
test3 = "for T in range(600,1100,100):\n\tNASAthermoData.getEnthalpy(T)"
print "****"
print "Timing getEnthalpy:"
t = Timer(test1,startup)
times = t.repeat(repeat=5,number=1000)
print " ThermoGAData took %.3f milliseconds (%s)"%(min(times), times)
t = Timer(test2,startup)
times = t.repeat(repeat=3,number=1000)
print " ThermoWilhoitData took %.3f milliseconds (%s)"%(min(times), times)
t = Timer(test3,startup)
times = t.repeat(repeat=3,number=1000)
print " ThermoNASAData took %.3f milliseconds (%s)"%(min(times), times)
print "****\n\nContinuing with tests..."
# Show debug messages (as databases are loading)
logging.initialize(10,'RMG.log')
unittest.main( testRunner = unittest.TextTestRunner(verbosity=2) )
for product in reaction.products: if product0.isIsomorphic(product): match = True self.assertTrue(match) for kin0 in reaction0.kinetics: match = False for kin in reaction.kinetics: if kin0.equals(kin): match = True self.assertTrue(match) self.assertTrue(reaction0.family.label == reaction.family.label) self.assertTrue(reaction0.atomLabels.keys() == reaction.atomLabels.keys()) self.assertTrue(reaction0.multiplier == reaction.multiplier) self.assertTrue(reaction0.bestKinetics == reaction.bestKinetics) #self.assertTrue(reaction0.reverse == reaction.reverse) ################################################################################ if __name__ == '__main__': # Show debug messages as databases are loading log.initialize(10, 'RMG.log') # Load databases databasePath = '../data/RMG_database' loadThermoDatabases(databasePath) loadKineticsDatabases(databasePath, only_families=['R_Recombination']) # Show info messages during tests log.initialize(20, 'RMG.log') # Conduct tests unittest.main( testRunner = unittest.TextTestRunner(verbosity=2) )
elif len(data) == 2:
settings.wallTime = int(data[-1]) + 60 * int(data[-2])
elif len(data) == 3:
settings.wallTime = int(data[-1]) + 60 * int(data[-2]) + 3600 * int(data[-3])
elif len(data) == 4:
settings.wallTime = int(data[-1]) + 60 * int(data[-2]) + 3600 * int(data[-3]) + 86400 * int(data[-4])
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)
for atomType, count in localAtomTypeCount.iteritems():
logging.info( '\t%i instances of %s' % (count, atomType) )
logging.info( '' )
# Print the totals
logging.info( 'Totals:' )
for atomType, count in totalAtomTypeCount.iteritems():
logging.info( '\t%i instances of %s' % (count, atomType) )
################################################################################
if __name__ == '__main__':
import math
# Show debug messages (as databases are loading)
logging.initialize(10,'database.log')
# Load databases
databasePath = '../data/RMG_database'
# loadThermoDatabases(databasePath)
loadKineticsDatabases(databasePath,only_families=['H_Abstraction'])
# findCatchallNodes()
fit_groups()
# fit_groups(['H abstraction'])
# graph = fit_groups()
# write_xml()
# for node in graph.get_node_list():
# node.set_style('filled')
# node.set_fontcolor('#FFFFFFFF')
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())
structure4.fromAdjacencyList('''
1 *1 H 0 {2,S}
2 *2 H 0 {1,S}
''')
C6H10, isNew = makeNewSpecies(structure1)
H, isNew = makeNewSpecies(structure2)
C6H9, isNew = makeNewSpecies(structure3)
H2, isNew = makeNewSpecies(structure4)
reaction1, isNew = makeNewReaction([C6H9, H2], [C6H10, H], \
[C6H9.structure[0], H2.structure[0]], \
[C6H10.structure[0], H.structure[0]], \
None)
"""
test1 = "reaction1, isNew = makeNewReaction([C6H9, H2], [C6H10, H], [C6H9.structure[0], H2.structure[0]], [C6H10.structure[0], H.structure[0]], None)"
print "Timing makeNewReaction:"
t = Timer(test1,startup)
# times = t.repeat(repeat=1,number=10000)
# print " Test1 took %.3f microseconds (%s)"%(min(times)*1000/10, [tt*1000/10 for tt in times])
print "**************"
# run a certain check without catching errors (turn on PDB debugger first)
import rmg.log as logging
logging.initialize(5,'reactiontest.log')
#import pdb
ReactionSetCheck('test12Cycloaddition').debug()
# now run all the unit tests
unittest.main( testRunner = unittest.TextTestRunner(verbosity=2) )
