def test_species(self):
"""Test loading of species input file."""
spec = input.species(
'C2H4', os.path.join(self.directory, 'species', 'C2H4',
'ethene.py'))
self.assertTrue(isinstance(spec, Species))
self.assertEqual(len(spec.molecule), 0)
def test_species_atomic_nasa_polynomial(self):
"""
Test loading a atom with NASA polynomials
"""
label0 = "H(1)"
kwargs = {
"structure":
SMILES('[H]'),
"thermo":
NASA(polynomials=[
NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683],
Tmin=(200, 'K'),
Tmax=(1000, 'K')),
NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683],
Tmin=(1000, 'K'),
Tmax=(6000, 'K'))
],
Tmin=(200, 'K'),
Tmax=(6000, 'K'),
comment="""Thermo library: FFCM1(-)"""),
"energyTransferModel":
SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'),
T0=(300, 'K'),
n=0.85)
}
spc0 = species(label0, **kwargs)
self.assertEqual(spc0.label, label0)
self.assertEqual(spc0.smiles, '[H]')
self.assertTrue(spc0.has_statmech())
self.assertEqual(spc0.thermo, kwargs['thermo'])
def test_species_polyatomic_nasa_polynomial(self):
"""
Test loading a species with NASA polynomials
"""
label0 = "benzyl"
kwargs = {
"structure":
SMILES('[c]1ccccc1'),
"thermo":
NASA(polynomials=[
NASAPolynomial(coeffs=[
2.78632, 0.00784632, 7.97887e-05, -1.11617e-07,
4.39429e-11, 39695, 11.5114
],
Tmin=(100, 'K'),
Tmax=(943.73, 'K')),
NASAPolynomial(coeffs=[
13.2455, 0.0115667, -2.49996e-06, 4.66496e-10,
-4.12376e-14, 35581.1, -49.6793
],
Tmin=(943.73, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""Thermo library: Fulvene_H + radical(CbJ)"""),
"energyTransferModel":
SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'),
T0=(300, 'K'),
n=0.85)
}
spc0 = species(label0, **kwargs)
self.assertEqual(spc0.label, label0)
self.assertTrue(spc0.has_statmech())
self.assertEqual(spc0.thermo, kwargs['thermo'])
def test_species(self):
"""
Test loading a species from input file-like kew word arguments
"""
label0 = 'CH2O'
kwargs = {
'E0': (28.69, 'kcal/mol'),
'structure':
SMILES('C=O'),
'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")),
]
}
spc0 = species(label0, **kwargs)
self.assertEqual(spc0.label, 'CH2O')
self.assertEqual(spc0.smiles, 'C=O')
self.assertAlmostEqual(spc0.conformer.E0.value_si, 120038.96)
self.assertEqual(spc0.conformer.spin_multiplicity, 1)
self.assertEqual(spc0.conformer.optical_isomers, 1)
self.assertEqual(len(spc0.conformer.modes), 3)
self.assertIsInstance(spc0.transport_data, TransportData)
self.assertIsInstance(spc0.energy_transfer_model,
SingleExponentialDown)
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 testSpecies(self):
"""Test loading of species input file."""
spec = input.species('C2H4', os.path.join(self.directory, 'species', 'C2H4', 'ethene.py'))
self.assertTrue(isinstance(spec, Species))
self.assertEqual(len(spec.molecule), 0)
