class TestTransportDatabase(unittest.TestCase):
"""
Contains unit test of the :class: 'TransportDatabase' class
"""
def setUp(self):
"""
a function run before each unit test in this class
"""
self.libraries = ['GRI-Mech', 'PrimaryTransportLibrary']
self.groups = ['ring', 'nonring']
self.libraryOrder = []
path = os.path.join(settings['database.directory'], 'transport')
self.transportdb = TransportDatabase()
self.transportdb.load(path, self.libraries)
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:
molecule=Molecule(SMILES=smiles)
species = Species(molecule=[molecule])
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 testJobackOnBenzeneBonds(self):
"Test Joback doesn't crash on Cb desription of beneze"
adjlist = """
1 C u0 p0 {2,D} {6,S} {7,S}
2 C u0 p0 {1,D} {3,S} {8,S}
3 C u0 p0 {2,S} {4,D} {9,S}
4 C u0 p0 {3,D} {5,S} {10,S}
5 C u0 p0 {4,S} {6,D} {11,S}
6 C u0 p0 {1,S} {5,D} {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}
"""
m = Molecule().fromAdjacencyList(adjlist)
species = Species(molecule=[m])
transportData, blank, blank2 = self.transportdb.getTransportPropertiesViaGroupEstimates(species)
self.assertIsNotNone(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))
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))