def testTransitionState(self):
"""Test loading of transition state input file."""
ts = input.transitionState(
'TS',
os.path.join(self.directory, 'reactions', 'H+C2H4=C2H5', 'TS.py'))
self.assertTrue(isinstance(ts, rmgpy.species.TransitionState))
def test_transition_state(self):
"""
Test loading a transition state from input file-like kew word arguments
"""
label0 = 'TS1'
kwargs = {
'E0': (39.95, 'kcal/mol'),
'spinMultiplicity':
2,
'opticalIsomers':
1,
'frequency': (-1934, 'cm^-1'),
'modes': [
HarmonicOscillator(frequencies=(
[792, 987, 1136, 1142, 1482, 2441, 3096, 3183], 'cm^-1')),
NonlinearRotor(rotationalConstant=([0.928, 0.962,
5.807], "cm^-1"),
symmetry=1,
quantum=False),
IdealGasTranslation(mass=(31.01843, "g/mol"))
]
}
ts0 = transitionState(label0, **kwargs)
self.assertEqual(ts0.label, 'TS1')
self.assertAlmostEqual(ts0.conformer.E0.value_si, 167150.8)
self.assertEqual(ts0.conformer.spin_multiplicity, 2)
self.assertEqual(ts0.conformer.optical_isomers, 1)
self.assertEqual(ts0.frequency.value_si, -1934.0)
self.assertEqual(len(ts0.conformer.modes), 3)
def test_reaction(self):
"""
Test loading a reaction from input file-like kew word arguments
"""
species(label='methoxy',
structure=SMILES('C[O]'),
E0=(9.44, 'kcal/mol'),
modes=[
HarmonicOscillator(frequencies=(
[758, 960, 1106, 1393, 1403, 1518, 2940, 3019, 3065],
'cm^-1')),
NonlinearRotor(rotationalConstant=([0.916, 0.921,
5.251], "cm^-1"),
symmetry=3,
quantum=False),
IdealGasTranslation(mass=(31.01843, "g/mol"))
],
spinMultiplicity=2,
opticalIsomers=1,
molecularWeight=(31.01843, 'amu'),
collisionModel=TransportData(sigma=(3.69e-10, 'm'),
epsilon=(4.0, 'kJ/mol')),
energyTransferModel=SingleExponentialDown(alpha0=(0.956,
'kJ/mol'),
T0=(300, 'K'),
n=0.95))
species(label='formaldehyde',
E0=(28.69, 'kcal/mol'),
molecularWeight=(30.0106, "g/mol"),
collisionModel=TransportData(sigma=(3.69e-10, 'm'),
epsilon=(4.0, 'kJ/mol')),
energyTransferModel=SingleExponentialDown(alpha0=(0.956,
'kJ/mol'),
T0=(300, 'K'),
n=0.95),
spinMultiplicity=1,
opticalIsomers=1,
modes=[
HarmonicOscillator(
frequencies=([1180, 1261, 1529, 1764, 2931, 2999],
'cm^-1')),
NonlinearRotor(rotationalConstant=([
1.15498821005263, 1.3156969584727, 9.45570474524524
], "cm^-1"),
symmetry=2,
quantum=False),
IdealGasTranslation(mass=(30.0106, "g/mol"))
])
species(label='H',
E0=(0.000, 'kcal/mol'),
molecularWeight=(1.00783, "g/mol"),
collisionModel=TransportData(sigma=(3.69e-10, 'm'),
epsilon=(4.0, 'kJ/mol')),
energyTransferModel=SingleExponentialDown(alpha0=(0.956,
'kJ/mol'),
T0=(300, 'K'),
n=0.95),
modes=[IdealGasTranslation(mass=(1.00783, "g/mol"))],
spinMultiplicity=2,
opticalIsomers=1)
transitionState(
label='TS3',
E0=(34.1, 'kcal/mol'),
spinMultiplicity=2,
opticalIsomers=1,
frequency=(-967, 'cm^-1'),
modes=[
HarmonicOscillator(frequencies=(
[466, 581, 1169, 1242, 1499, 1659, 2933, 3000], 'cm^-1')),
NonlinearRotor(rotationalConstant=([0.970, 1.029,
3.717], "cm^-1"),
symmetry=1,
quantum=False),
IdealGasTranslation(mass=(31.01843, "g/mol"))
])
reactants = ['formaldehyde', 'H']
products = ['methoxy']
tunneling = 'Eckart'
rxn = reaction('CH2O+H=Methoxy',
reactants,
products,
'TS3',
tunneling=tunneling)
self.assertEqual(rxn.label, 'CH2O+H=Methoxy')
self.assertEqual(len(rxn.reactants), 2)
self.assertEqual(len(rxn.products), 1)
self.assertAlmostEqual(rxn.reactants[0].conformer.E0.value_si, 0)
self.assertAlmostEqual(rxn.reactants[1].conformer.E0.value_si,
120038.96)
self.assertAlmostEqual(rxn.products[0].conformer.E0.value_si, 39496.96)
self.assertAlmostEqual(rxn.transition_state.conformer.E0.value_si,
142674.4)
self.assertAlmostEqual(rxn.transition_state.frequency.value_si, -967.0)
self.assertIsInstance(rxn.transition_state.tunneling, Eckart)
def testTransitionState(self):
"""Test loading of transition state input file."""
ts = input.transitionState('TS', os.path.join(self.directory, 'reactions', 'H+C2H4=C2H5', 'TS.py'))
self.assertTrue(isinstance(ts, TransitionState))
