def __loadOldReactions(self, path, species):
"""
Load an old-style reaction library from `path`. This algorithm can
handle both the pressure-independent and pressure-dependent reaction
files. If the pressure-dependent file is read, the extra pressure-
dependent kinetics information is ignored unless the kinetics database
is a seed mechanism.
"""
from rmgpy.chemkin import readReactionsBlock
f = open(path, 'r')
reactionList = readReactionsBlock(f, speciesDict=species)
f.close()
return reactionList
def __loadOldReactions(self, path, species):
"""
Load an old-style reaction library from `path`. This algorithm can
handle both the pressure-independent and pressure-dependent reaction
files. If the pressure-dependent file is read, the extra pressure-
dependent kinetics information is ignored unless the kinetics database
is a seed mechanism.
"""
from rmgpy.chemkin import readReactionsBlock
f = open(path, 'r')
reactionList = readReactionsBlock(f, speciesDict=species)
f.close()
return reactionList
def testPDepJob(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.inputFile = self.input_file
self.tst1.outputDirectory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.jobList = []
self.tst1.jobList = self.tst1.loadInputFile(self.tst1.inputFile)
self.tst1.execute()
job = self.tst1.jobList[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimumGrainCount, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.activeJRotor)
self.assertEquals(job.network.pathReactions[0].label,'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.E0_TS.value_si,-24267.2)
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.frequency.value_si,-1679.04)
self.assertEquals(len(job.network.netReactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().fromSMILES('[CH2]C(=O)OO'),
'acetylperoxy': Species().fromSMILES('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = readReactionsBlock(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.getRateCoefficient(1000.0, 1.0), 88.879056605)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.24e-6)
def testPDepJob(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.inputFile = self.input_file
self.tst1.outputDirectory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.jobList = []
self.tst1.jobList = self.tst1.loadInputFile(self.tst1.inputFile)
self.tst1.execute()
job = self.tst1.jobList[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimumGrainCount, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.activeJRotor)
self.assertEquals(job.network.pathReactions[0].label,'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.E0_TS.value_si,-24267.2)
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.frequency.value_si,-1679.04)
self.assertEquals(len(job.network.netReactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().fromSMILES('[CH2]C(=O)OO'),
'acetylperoxy': Species().fromSMILES('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = readReactionsBlock(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.getRateCoefficient(1000.0, 1.0), 88.879056605)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.24e-6)