def __init__(
self,
groundStateDegeneracy=-1,
numberOfAtoms=None,
stericEnergy=None,
molecularMass=None,
energy=0,
atomicNumbers=None,
rotationalConstants=None,
atomCoords=None,
frequencies=None,
source=None,
):
#: Electronic ground state degeneracy in RMG taken as number of radicals +1
self.groundStateDegeneracy = groundStateDegeneracy
self.numberOfAtoms = numberOfAtoms #: Number of atoms.
self.stericEnergy = Energy(stericEnergy)
self.molecularMass = Mass(molecularMass)
self.energy = Energy(energy)
self.atomicNumbers = atomicNumbers
self.rotationalConstants = Frequency(rotationalConstants)
self.atomCoords = Length(atomCoords)
self.frequencies = Frequency(frequencies)
self.source = source
self.testValid()
def testJoback(self):
#values calculate from joback's estimations
self.testCases = [
[
'acetone', 'CC(=O)C',
Length(5.36421, 'angstroms'),
Energy(3.20446, 'kJ/mol'),
"Epsilon & sigma estimated with Tc=500.53 K, Pc=47.11 bar (from Joback method)"
],
[
'cyclopenta-1,2-diene', 'C1=C=CCC1', None, None, None
], # not sure what to expect, we just want to make sure it doesn't crash
['benzene', 'c1ccccc1', None, None, None],
]
for name, smiles, sigma, epsilon, comment in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
transportData, blank, blank2 = self.transportdb.getTransportPropertiesViaGroupEstimates(
species)
# check Joback worked.
# If we don't know what to expect, don't check (just make sure we didn't crash)
if comment:
self.assertTrue(transportData.comment == comment)
if sigma:
self.assertAlmostEqual(transportData.sigma.value_si * 1e10,
sigma.value_si * 1e10, 4)
if epsilon:
self.assertAlmostEqual(transportData.epsilon.value_si,
epsilon.value_si, 1)
def test_joback(self):
"""Test transport property estimation via Joback groups."""
self.testCases = [
[
'acetone', 'CC(=O)C',
Length(5.36421, 'angstroms'),
Energy(3.20446, 'kJ/mol'),
"Epsilon & sigma estimated with Tc=500.53 K, Pc=47.11 bar (from Joback method)"
],
[
'cyclopenta-1,2-diene', 'C1=C=CCC1', None, None, None
], # not sure what to expect, we just want to make sure it doesn't crash
['benzene', 'c1ccccc1', None, None, None],
]
# values calculate from joback's estimations
for name, smiles, sigma, epsilon, comment in self.testCases:
species = Species().from_smiles(smiles)
transport_data, blank, blank2 = self.database.get_transport_properties_via_group_estimates(
species)
# check Joback worked.
# If we don't know what to expect, don't check (just make sure we didn't crash)
if comment:
self.assertTrue(transport_data.comment == comment)
if sigma:
self.assertAlmostEqual(transport_data.sigma.value_si * 1e10,
sigma.value_si * 1e10, 4)
if epsilon:
self.assertAlmostEqual(transport_data.epsilon.value_si,
epsilon.value_si, 1)
def __init__(self, shapeIndex=None, epsilon=None, sigma=None, dipoleMoment=None, polarizability=None,
rotrelaxcollnum=None, comment=''):
self.shapeIndex = shapeIndex
try:
self.epsilon = Energy(epsilon)
except quantity.QuantityError:
self.epsilon = quantity.Temperature(epsilon)
self.epsilon.value_si *= constants.R
self.epsilon.units = 'kJ/mol'
self.sigma = Length(sigma)
self.dipoleMoment = DipoleMoment(dipoleMoment)
self.polarizability = Volume(polarizability)
self.rotrelaxcollnum = rotrelaxcollnum
self.comment = comment
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.shapeIndex = 1
self.epsilon = Energy(2.104, 'kJ/mol')
self.sigma = Length(3.402, 'angstroms')
self.dipoleMoment = DipoleMoment(1.000, 'C*m')
self.polarizability = Volume(0.134, 'angstroms^3')
self.rotrelaxcollnum = 0.000
self.comment = 'test'
self.transport = TransportData(
shapeIndex=self.shapeIndex,
epsilon=self.epsilon,
sigma=self.sigma,
dipoleMoment=self.dipoleMoment,
polarizability=self.polarizability,
rotrelaxcollnum=self.rotrelaxcollnum,
comment=self.comment,
)