def main(dictionary):
database = TransportDatabase()
database.load(path=os.path.join(settings['database.directory'],
'transport'),
libraries=None)
speciesDict = loadSpeciesDictionary(dictionary)
path = 'tran.dat'
with open(path, 'w') as f:
f.write("! {0:15} {1:8} {2:9} {3:9} {4:9} {5:9} {6:9} {7:9}\n".format(
'Species', 'Shape', 'LJ-depth', 'LJ-diam', 'DiplMom', 'Polzblty',
'RotRelaxNum', 'Data'))
f.write("! {0:15} {1:8} {2:9} {3:9} {4:9} {5:9} {6:9} {7:9}\n".format(
'Name', 'Index', 'epsilon/k_B', 'sigma', 'mu', 'alpha', 'Zrot',
'Source'))
for label, spec in speciesDict.iteritems():
transportDataList = database.getAllTransportProperties(spec)
for transportData, _, _ in transportDataList:
if (not transportData):
missingData = True
else:
missingData = False
if missingData:
f.write('! {0:19s} {1!r}\n'.format(label, transportData))
else:
f.write(
'{0:19} {1:d} {2:9.3f} {3:9.3f} {4:9.3f} {5:9.3f} {6:9.3f} ! {7:s}\n'
.format(
label,
transportData.shapeIndex,
transportData.epsilon.value_si / constants.R,
transportData.sigma.value_si * 1e10,
(transportData.dipoleMoment.value_si *
constants.c *
1e21 if transportData.dipoleMoment else 0),
(transportData.polarizability.value_si *
1e30 if transportData.polarizability else 0),
(transportData.rotrelaxcollnum
if transportData.rotrelaxcollnum else 0),
transportData.comment,
))
class TestTransportDatabase(unittest.TestCase):
"""
Contains unit tests of the :class:`TransportDatabase` class.
"""
@classmethod
def setUpClass(self):
"""A function that is run ONCE before all unit tests in this class."""
self.database = TransportDatabase()
self.database.load(os.path.join(settings['database.directory'], 'transport'),
['GRI-Mech', 'PrimaryTransportLibrary'])
self.speciesList = [
Species().fromSMILES('C'),
Species().fromSMILES('CCCC'),
Species().fromSMILES('O'),
Species().fromSMILES('[CH3]'),
Species().fromSMILES('[OH]'),
Species().fromSMILES('c1ccccc1'),
]
def testJoback(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().fromSMILES(smiles)
transportData, blank, blank2 = self.database.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)
@work_in_progress
def testJobackOnBenzeneBonds(self):
"""Test Joback doesn't crash on Cb desription of benzene"""
species = Species().fromAdjacencyList("""
1 C u0 p0 {2,B} {6,B} {7,S}
2 C u0 p0 {1,B} {3,B} {8,S}
3 C u0 p0 {2,B} {4,B} {9,S}
4 C u0 p0 {3,B} {5,B} {10,S}
5 C u0 p0 {4,B} {6,B} {11,S}
6 C u0 p0 {1,B} {5,B} {12,S}
7 H u0 p0 {1,S}
8 H u0 p0 {2,S}
9 H u0 p0 {3,S}
10 H u0 p0 {4,S}
11 H u0 p0 {5,S}
12 H u0 p0 {6,S}
""")
transportData, blank, blank2 = self.database.getTransportPropertiesViaGroupEstimates(species)
self.assertIsNotNone(transportData)
def testGetTransportProperties(self):
"""Test that we can retrieve best transport properties for a species."""
for species in self.speciesList:
transport = self.database.getTransportProperties(species)
self.assertIsNotNone(transport)
self.assertTrue(isinstance(transport, tuple))
self.assertTrue(isinstance(transport[0], TransportData))
def testGetAllTransportProperties(self):
"""Test that we can retrieve transport properties from all sources for a species.
Used for transport search on website."""
for species in self.speciesList:
transport = self.database.getAllTransportProperties(species)
self.assertIsNotNone(transport)
for result in transport:
self.assertTrue(isinstance(result, tuple))
self.assertTrue(isinstance(result[0], TransportData))
class TestTransportDatabase(unittest.TestCase):
"""
Contains unit tests of the :class:`TransportDatabase` class.
"""
@classmethod
def setUpClass(self):
"""A function that is run ONCE before all unit tests in this class."""
self.database = TransportDatabase()
self.database.load(
os.path.join(settings['database.directory'], 'transport'),
['GRI-Mech', 'PrimaryTransportLibrary'])
self.speciesList = [
Species().fromSMILES('C'),
Species().fromSMILES('CCCC'),
Species().fromSMILES('O'),
Species().fromSMILES('[CH3]'),
Species().fromSMILES('[OH]'),
Species().fromSMILES('c1ccccc1'),
]
def testJoback(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().fromSMILES(smiles)
transportData, blank, blank2 = self.database.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)
@work_in_progress
def testJobackOnBenzeneBonds(self):
"""Test Joback doesn't crash on Cb desription of benzene"""
species = Species().fromAdjacencyList("""
1 C u0 p0 {2,B} {6,B} {7,S}
2 C u0 p0 {1,B} {3,B} {8,S}
3 C u0 p0 {2,B} {4,B} {9,S}
4 C u0 p0 {3,B} {5,B} {10,S}
5 C u0 p0 {4,B} {6,B} {11,S}
6 C u0 p0 {1,B} {5,B} {12,S}
7 H u0 p0 {1,S}
8 H u0 p0 {2,S}
9 H u0 p0 {3,S}
10 H u0 p0 {4,S}
11 H u0 p0 {5,S}
12 H u0 p0 {6,S}
""")
transportData, blank, blank2 = self.database.getTransportPropertiesViaGroupEstimates(
species)
self.assertIsNotNone(transportData)
def testGetTransportProperties(self):
"""Test that we can retrieve best transport properties for a species."""
for species in self.speciesList:
transport = self.database.getTransportProperties(species)
self.assertIsNotNone(transport)
self.assertTrue(isinstance(transport, tuple))
self.assertTrue(isinstance(transport[0], TransportData))
def testGetAllTransportProperties(self):
"""Test that we can retrieve transport properties from all sources for a species.
Used for transport search on website."""
for species in self.speciesList:
transport = self.database.getAllTransportProperties(species)
self.assertIsNotNone(transport)
for result in transport:
self.assertTrue(isinstance(result, tuple))
self.assertTrue(isinstance(result[0], TransportData))
