class TestSoluteDatabase(TestCase):
def setUp(self):
self.database = SolvationDatabase()
self.database.load(
os.path.join(settings['database.directory'], 'solvation'))
def runTest(self):
pass
def testSoluteLibrary(self):
"Test we can obtain solute parameters from a library"
species = Species(molecule=[
Molecule(SMILES='COC=O')
]) #methyl formate - we know this is in the solute library
libraryData = self.database.getSoluteDataFromLibrary(
species, self.database.libraries['solute'])
self.assertEqual(len(libraryData), 3)
soluteData = self.database.getSoluteData(species)
self.assertTrue(isinstance(soluteData, SoluteData))
S = soluteData.S
self.assertEqual(S, 0.68)
self.assertTrue(soluteData.V is not None)
def testMcGowan(self):
"Test we can calculate and set the McGowan volume for species containing H,C,O,N or S"
self.testCases = [
['CCCCCCCC', 1.2358], #n-octane, in library
['C(CO)O', 0.5078], #ethylene glycol
['CC#N', 0.4042], #acetonitrile
['CCS', 0.5539] #ethanethiol
]
for smiles, volume in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
soluteData.setMcGowanVolume(
species) # even if it was found in library, recalculate
self.assertTrue(
soluteData.V is not None
) # so if it wasn't found in library, we should have calculated it
self.assertAlmostEqual(
soluteData.V, volume
) # the volume is what we expect given the atoms and bonds
def testDiffusivity(self):
"Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity"
species = Species(molecule=[Molecule(SMILES='O')]) # water
soluteData = self.database.getSoluteData(species)
T = 298.
solventViscosity = 0.00089 # water is about 8.9e-4 Pa.s
D = soluteData.getStokesDiffusivity(T, solventViscosity) # m2/s
self.assertAlmostEqual((D * 1e9), 1.3, 1)
# self-diffusivity of water is about 2e-9 m2/s
def testSolventLibrary(self):
"Test we can obtain solvent parameters from a library"
solventData = self.database.getSolventData('water')
self.assertTrue(solventData is not None)
self.assertEqual(solventData.s_h, 2.836)
self.assertRaises(DatabaseError, self.database.getSolventData,
'orange_juice')
def testViscosity(self):
"Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters"
solventData = self.database.getSolventData('water')
self.assertAlmostEqual(solventData.getSolventViscosity(298), 0.0009155)
def testSoluteGeneration(self):
"Test we can estimate Abraham solute parameters correctly using group contributions"
self.testCases = [
[
'1,2-ethanediol', 'C(CO)O', 0.823, 0.685, 0.327, 2.572, 0.693,
None
],
]
for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteDataFromGroups(
Species(molecule=[species.molecule[0]]))
self.assertAlmostEqual(soluteData.S, S, places=2)
self.assertAlmostEqual(soluteData.B, B, places=2)
self.assertAlmostEqual(soluteData.E, E, places=2)
self.assertAlmostEqual(soluteData.L, L, places=2)
self.assertAlmostEqual(soluteData.A, A, places=2)
def testLonePairSoluteGeneration(self):
"Test we can obtain solute parameters via group additivity for a molecule with lone pairs"
molecule = Molecule().fromAdjacencyList("""
CH2_singlet
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmmonia(self):
"Test we can obtain solute parameters via group additivity for ammonia"
molecule = Molecule().fromAdjacencyList("""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmide(self):
"Test that we can obtain solute parameters via group additivity for an amide"
molecule = Molecule().fromAdjacencyList("""
1 N u0 p1 {2,S} {3,S} {4,S}
2 H u0 {1,S}
3 C u0 {1,S} {6,S} {7,S} {8,S}
4 C u0 {1,S} {5,D} {9,S}
5 O u0 p2 {4,D}
6 H u0 {3,S}
7 H u0 {3,S}
8 H u0 {3,S}
9 H u0 {4,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationCO(self):
"Test that we can obtain solute parameters via group additivity for CO."
molecule = Molecule().fromAdjacencyList("""
1 C u0 p1 c-1 {2,T}
2 O u0 p1 c+1 {1,T}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testRadicalandLonePairGeneration(self):
"""
Test we can obtain solute parameters via group additivity for a molecule with both lone
pairs and a radical
"""
molecule = Molecule().fromAdjacencyList("""
[C]OH
multiplicity 2
1 C u1 p1 c0 {2,S}
2 O u0 p2 c0 {1,S} {3,S}
3 H u0 p0 c0 {2,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testCorrectionGeneration(self):
"Test we can estimate solvation thermochemistry."
self.testCases = [
# solventName, soluteName, soluteSMILES, Hsolv, Gsolv
['water', 'acetic acid', 'C(C)(=O)O', -56500, -6700 * 4.184],
[
'water', 'naphthalene', 'C1=CC=CC2=CC=CC=C12', -42800,
-2390 * 4.184
],
['1-octanol', 'octane', 'CCCCCCCC', -40080, -4180 * 4.184],
['1-octanol', 'tetrahydrofuran', 'C1CCOC1', -28320, -3930 * 4.184],
['benzene', 'toluene', 'C1(=CC=CC=C1)C', -37660, -5320 * 4.184],
['benzene', '1,4-dioxane', 'C1COCCO1', -39030, -5210 * 4.184]
]
for solventName, soluteName, smiles, H, G in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
solventData = self.database.getSolventData(solventName)
solvationCorrection = self.database.getSolvationCorrection(
soluteData, solventData)
self.assertAlmostEqual(
solvationCorrection.enthalpy / 10000.,
H / 10000.,
0,
msg=
"Solvation enthalpy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}"
.format(soluteName, solventName, solvationCorrection.enthalpy,
H)) #0 decimal place, in 10kJ.
self.assertAlmostEqual(
solvationCorrection.gibbs / 10000.,
G / 10000.,
0,
msg=
"Solvation Gibbs free energy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}"
.format(soluteName, solventName, solvationCorrection.gibbs, G))
class TestSoluteDatabase(TestCase):
def setUp(self):
self.database = SolvationDatabase()
self.database.load(
os.path.join(settings['database.directory'], 'solvation'))
def tearDown(self):
"""
Reset the database & liquid parameters for solution
"""
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
from rmgpy.rmg.model import Species as DifferentSpecies
DifferentSpecies.solventData = None
DifferentSpecies.solventName = None
DifferentSpecies.solventStructure = None
DifferentSpecies.solventViscosity = None
def runTest(self):
pass
def testSoluteLibrary(self):
"Test we can obtain solute parameters from a library"
species = Species(molecule=[
Molecule(SMILES='COC=O')
]) #methyl formate - we know this is in the solute library
libraryData = self.database.getSoluteDataFromLibrary(
species, self.database.libraries['solute'])
self.assertEqual(len(libraryData), 3)
soluteData = self.database.getSoluteData(species)
self.assertTrue(isinstance(soluteData, SoluteData))
S = soluteData.S
self.assertEqual(S, 0.68)
self.assertTrue(soluteData.V is not None)
def testMcGowan(self):
"Test we can calculate and set the McGowan volume for species containing H,C,O,N or S"
self.testCases = [
['CCCCCCCC', 1.2358], #n-octane, in library
['C(CO)O', 0.5078], #ethylene glycol
['CC#N', 0.4042], #acetonitrile
['CCS', 0.5539] #ethanethiol
]
for smiles, volume in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
soluteData.setMcGowanVolume(
species) # even if it was found in library, recalculate
self.assertTrue(
soluteData.V is not None
) # so if it wasn't found in library, we should have calculated it
self.assertAlmostEqual(
soluteData.V, volume
) # the volume is what we expect given the atoms and bonds
def testDiffusivity(self):
"Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity"
species = Species(molecule=[Molecule(SMILES='O')]) # water
soluteData = self.database.getSoluteData(species)
T = 298.
solventViscosity = 0.00089 # water is about 8.9e-4 Pa.s
D = soluteData.getStokesDiffusivity(T, solventViscosity) # m2/s
self.assertAlmostEqual((D * 1e9), 1.3, 1)
# self-diffusivity of water is about 2e-9 m2/s
def testSolventLibrary(self):
"Test we can obtain solvent parameters from a library"
solventData = self.database.getSolventData('water')
self.assertTrue(solventData is not None)
self.assertEqual(solventData.s_h, 2.836)
self.assertRaises(DatabaseError, self.database.getSolventData,
'orange_juice')
def testViscosity(self):
"Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters"
solventData = self.database.getSolventData('water')
self.assertAlmostEqual(solventData.getSolventViscosity(298), 0.0009155)
def testSoluteGeneration(self):
"Test we can estimate Abraham solute parameters correctly using group contributions"
self.testCases = [
[
'1,2-ethanediol', 'C(CO)O', 0.823, 0.685, 0.327, 2.572, 0.693,
None
],
]
for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteDataFromGroups(
Species(molecule=[species.molecule[0]]))
self.assertAlmostEqual(soluteData.S, S, places=2)
self.assertAlmostEqual(soluteData.B, B, places=2)
self.assertAlmostEqual(soluteData.E, E, places=2)
self.assertAlmostEqual(soluteData.L, L, places=2)
self.assertAlmostEqual(soluteData.A, A, places=2)
def testLonePairSoluteGeneration(self):
"Test we can obtain solute parameters via group additivity for a molecule with lone pairs"
molecule = Molecule().fromAdjacencyList("""
CH2_singlet
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmmonia(self):
"Test we can obtain solute parameters via group additivity for ammonia"
molecule = Molecule().fromAdjacencyList("""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmide(self):
"Test that we can obtain solute parameters via group additivity for an amide"
molecule = Molecule().fromAdjacencyList("""
1 N u0 p1 {2,S} {3,S} {4,S}
2 H u0 {1,S}
3 C u0 {1,S} {6,S} {7,S} {8,S}
4 C u0 {1,S} {5,D} {9,S}
5 O u0 p2 {4,D}
6 H u0 {3,S}
7 H u0 {3,S}
8 H u0 {3,S}
9 H u0 {4,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationCO(self):
"Test that we can obtain solute parameters via group additivity for CO."
molecule = Molecule().fromAdjacencyList("""
1 C u0 p1 c-1 {2,T}
2 O u0 p1 c+1 {1,T}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testRadicalandLonePairGeneration(self):
"""
Test we can obtain solute parameters via group additivity for a molecule with both lone
pairs and a radical
"""
molecule = Molecule().fromAdjacencyList("""
[C]OH
multiplicity 2
1 C u1 p1 c0 {2,S}
2 O u0 p2 c0 {1,S} {3,S}
3 H u0 p0 c0 {2,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testCorrectionGeneration(self):
"Test we can estimate solvation thermochemistry."
self.testCases = [
# solventName, soluteName, soluteSMILES, Hsolv, Gsolv
['water', 'acetic acid', 'C(C)(=O)O', -56500, -6700 * 4.184],
[
'water', 'naphthalene', 'C1=CC=CC2=CC=CC=C12', -42800,
-2390 * 4.184
],
['1-octanol', 'octane', 'CCCCCCCC', -40080, -4180 * 4.184],
['1-octanol', 'tetrahydrofuran', 'C1CCOC1', -28320, -3930 * 4.184],
['benzene', 'toluene', 'C1(=CC=CC=C1)C', -37660, -5320 * 4.184],
['benzene', '1,4-dioxane', 'C1COCCO1', -39030, -5210 * 4.184]
]
for solventName, soluteName, smiles, H, G in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
solventData = self.database.getSolventData(solventName)
solvationCorrection = self.database.getSolvationCorrection(
soluteData, solventData)
self.assertAlmostEqual(
solvationCorrection.enthalpy / 10000.,
H / 10000.,
0,
msg=
"Solvation enthalpy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}"
.format(soluteName, solventName, solvationCorrection.enthalpy,
H)) #0 decimal place, in 10kJ.
self.assertAlmostEqual(
solvationCorrection.gibbs / 10000.,
G / 10000.,
0,
msg=
"Solvation Gibbs free energy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}"
.format(soluteName, solventName, solvationCorrection.gibbs, G))
def testInitialSpecies(self):
" Test we can check whether the solvent is listed as one of the initial species in various scenarios "
# Case 1. when SMILES for solvent is available, the molecular structures of the initial species and the solvent
# are compared to check whether the solvent is in the initial species list
# Case 1-1: the solvent water is not in the initialSpecies list, so it raises Exception
rmg = RMG()
rmg.initialSpecies = []
solute = Species(label='n-octane',
molecule=[Molecule().fromSMILES('C(CCCCC)CC')])
rmg.initialSpecies.append(solute)
rmg.solvent = 'water'
solventStructure = Species().fromSMILES('O')
self.assertRaises(Exception,
self.database.checkSolventinInitialSpecies, rmg,
solventStructure)
# Case 1-2: the solvent is now octane and it is listed as the initialSpecies. Although the string
# names of the solute and the solvent are different, because the solvent SMILES is provided,
# it can identify the 'n-octane' as the solvent
rmg.solvent = 'octane'
solventStructure = Species().fromSMILES('CCCCCCCC')
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
# Case 2: the solvent SMILES is not provided. In this case, it can identify the species as the
# solvent by looking at the string name.
# Case 2-1: Since 'n-octane and 'octane' are not equal, it raises Exception
solventStructure = None
self.assertRaises(Exception,
self.database.checkSolventinInitialSpecies, rmg,
solventStructure)
# Case 2-2: The label 'n-ocatne' is corrected to 'octane', so it is identified as the solvent
rmg.initialSpecies[0].label = 'octane'
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
def testSolventMolecule(self):
" Test we can give a proper value for the solvent molecular structure when different solvent databases are given "
# solventlibrary.entries['solvent_label'].item should be the instance of Species with the solvent's molecular structure
# if the solvent database contains the solvent SMILES or adjacency list. If not, then item is None
# Case 1: When the solventDatabase does not contain the solvent SMILES, the item attribute is None
solventlibrary = SolventLibrary()
solventlibrary.loadEntry(index=1, label='water', solvent=None)
self.assertTrue(solventlibrary.entries['water'].item is None)
# Case 2: When the solventDatabase contains the correct solvent SMILES, the item attribute is the instance of
# Species with the correct solvent molecular structure
solventlibrary.loadEntry(index=2,
label='octane',
solvent=None,
molecule='CCCCCCCC')
solventSpecies = Species().fromSMILES('C(CCCCC)CC')
self.assertTrue(
solventSpecies.isIsomorphic(solventlibrary.entries['octane'].item))
# Case 3: When the solventDatabase contains the correct solvent adjacency list, the item attribute is the instance of
# the species with the correct solvent molecular structure.
# This will display the SMILES Parse Error message from the external function, but ignore it.
solventlibrary.loadEntry(index=3,
label='ethanol',
solvent=None,
molecule="""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 O u0 p2 c0 {2,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
""")
solventSpecies = Species().fromSMILES('CCO')
self.assertTrue(
solventSpecies.isIsomorphic(
solventlibrary.entries['ethanol'].item))
# Case 4: when the solventDatabase contains incorrect values for the molecule attribute, it raises Exception
# This will display the SMILES Parse Error message from the external function, but ignore it.
self.assertRaises(Exception,
solventlibrary.loadEntry,
index=4,
label='benzene',
solvent=None,
molecule='ring')
class TestSoluteDatabase(TestCase):
def setUp(self):
self.database = SolvationDatabase()
self.database.load(os.path.join(settings['database.directory'], 'solvation'))
def runTest(self):
pass
def testSoluteLibrary(self):
"Test we can obtain solute parameters from a library"
species = Species(molecule=[Molecule(SMILES='COC=O')]) #methyl formate - we know this is in the solute library
libraryData = self.database.getSoluteDataFromLibrary(species, self.database.libraries['solute'])
self.assertEqual(len(libraryData), 3)
soluteData = self.database.getSoluteData(species)
self.assertTrue(isinstance(soluteData, SoluteData))
S = soluteData.S
self.assertEqual(S, 0.68)
self.assertTrue(soluteData.V is not None)
def testMcGowan(self):
"Test we can calculate and set the McGowan volume for species containing H,C,O,N or S"
self.testCases = [
['CCCCCCCC', 1.2358], #n-octane, in library
['C(CO)O', 0.5078], #ethylene glycol
['CC#N', 0.4042], #acetonitrile
['CCS', 0.5539] #ethanethiol
]
for smiles, volume in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
soluteData.setMcGowanVolume(species) # even if it was found in library, recalculate
self.assertTrue(soluteData.V is not None) # so if it wasn't found in library, we should have calculated it
self.assertAlmostEqual(soluteData.V, volume) # the volume is what we expect given the atoms and bonds
def testDiffusivity(self):
"Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity"
species = Species(molecule=[Molecule(SMILES='COC=O')])
soluteData = self.database.getSoluteData(species)
T = 298
solventViscosity = 0.001
D = soluteData.getStokesDiffusivity(T, solventViscosity)
self.assertAlmostEqual((D*1E12), 0.00000979)
def testSolventLibrary(self):
"Test we can obtain solvent parameters from a library"
solventData = self.database.getSolventData('water')
self.assertTrue(solventData is not None)
self.assertEqual(solventData.s_h, 2.836)
self.assertRaises(DatabaseError, self.database.getSolventData, 'orange_juice')
def testViscosity(self):
"Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters"
solventData = self.database.getSolventData('water')
self.assertAlmostEqual(solventData.getSolventViscosity(298), 0.0009155)
def testSoluteGeneration(self):
"Test we can estimate Abraham solute parameters correctly using group contributions"
self.testCases = [
['1,2-ethanediol', 'C(CO)O', 0.823, 0.685, 0.327, 2.572, 0.693, None],
]
for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteDataFromGroups(Species(molecule=[species.molecule[0]]))
self.assertAlmostEqual(soluteData.S, S, places=2)
self.assertAlmostEqual(soluteData.B, B, places=2)
self.assertAlmostEqual(soluteData.E, E, places=2)
self.assertAlmostEqual(soluteData.L, L, places=2)
self.assertAlmostEqual(soluteData.A, A, places=2)
def testLonePairSoluteGeneration(self):
"Test we can obtain solute parameters via group additivity for a molecule with lone pairs"
molecule=Molecule().fromAdjacencyList(
"""
CH2_singlet
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmmonia(self):
"Test we can obtain solute parameters via group additivity for ammonia"
molecule=Molecule().fromAdjacencyList(
"""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmide(self):
"Test that we can obtain solute parameters via group additivity for an amide"
molecule=Molecule().fromAdjacencyList(
"""
1 N u0 p1 {2,S} {3,S} {4,S}
2 H u0 {1,S}
3 C u0 {1,S} {6,S} {7,S} {8,S}
4 C u0 {1,S} {5,D} {9,S}
5 O u0 p2 {4,D}
6 H u0 {3,S}
7 H u0 {3,S}
8 H u0 {3,S}
9 H u0 {4,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testRadicalandLonePairGeneration(self):
"""
Test we can obtain solute parameters via group additivity for a molecule with both lone
pairs and a radical
"""
molecule=Molecule().fromAdjacencyList(
"""
[C]OH
multiplicity 2
1 C u1 p1 c0 {2,S}
2 O u0 p2 c0 {1,S} {3,S}
3 H u0 p0 c0 {2,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testCorrectionGeneration(self):
"Test we can estimate solvation thermochemistry."
self.testCases = [
# solventName, soluteName, soluteSMILES, Hsolv, Gsolv
['water', 'acetic acid', 'C(C)(=O)O', -56500, -6700*4.184],
['water', 'naphthalene', 'C1=CC=CC2=CC=CC=C12', -42800, -2390*4.184],
['1-octanol', 'octane', 'CCCCCCCC', -40080, -4180*4.184],
['1-octanol', 'tetrahydrofuran', 'C1CCOC1', -28320, -3930*4.184],
['benzene', 'toluene', 'C1(=CC=CC=C1)C', -37660, -5320*4.184],
['benzene', '1,4-dioxane', 'C1COCCO1', -39030, -5210*4.184]
]
for solventName, soluteName, smiles, H, G in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
solventData = self.database.getSolventData(solventName)
solvationCorrection = self.database.getSolvationCorrection(soluteData, solventData)
self.assertAlmostEqual(solvationCorrection.enthalpy / 10000., H / 10000., 0, msg="Solvation enthalpy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.enthalpy, H)) #0 decimal place, in 10kJ.
self.assertAlmostEqual(solvationCorrection.gibbs / 10000., G / 10000., 0, msg="Solvation Gibbs free energy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.gibbs, G))
class TestDiffusionLimited(unittest.TestCase):
"""
Contains unit tests of the DiffusionLimited class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
octyl_pri = Species(
label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.772759, 0.093255, -5.84447e-05, 1.8557e-08,
-2.37127e-12, -3926.9, 37.6131
],
Tmin=(298, 'K'),
Tmax=(1390, 'K')),
NASAPolynomial(coeffs=[
25.051, 0.036948, -1.25765e-05, 1.94628e-09, -1.12669e-13,
-13330.1, -102.557
],
Tmin=(1390, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(577.856, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="[CH2]CCCCCCC")])
octyl_sec = Species(
label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.304233, 0.0880077, -4.90743e-05, 1.21858e-08,
-8.87773e-13, -5237.93, 36.6583
],
Tmin=(298, 'K'),
Tmax=(1383, 'K')),
NASAPolynomial(coeffs=[
24.9044, 0.0366394, -1.2385e-05, 1.90835e-09, -1.10161e-13,
-14713.5, -101.345
],
Tmin=(1383, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(577.856, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="CC[CH]CCCCC")])
ethane = Species(label="",
thermo=ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000,
1500], 'K'),
Cpdata=([
10.294, 12.643, 14.933, 16.932, 20.033,
22.438, 26.281
], 'cal/(mol*K)'),
H298=(12.549, 'kcal/mol'),
S298=(52.379, 'cal/(mol*K)'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(133.032, 'J/(mol*K)'),
comment="""Thermo library: CH"""),
molecule=[Molecule(SMILES="C=C")])
decyl = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-1.31358, 0.117973, -7.51843e-05, 2.43331e-08,
-3.17523e-12, -9689.68, 43.501
],
Tmin=(298, 'K'),
Tmax=(1390, 'K')),
NASAPolynomial(coeffs=[
31.5697, 0.0455818, -1.54995e-05, 2.39711e-09,
-1.3871e-13, -21573.8, -134.709
],
Tmin=(1390, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(719.202, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")])
acetone = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.75568, 0.0264934, -6.55661e-05,
1.94971e-07, -1.82059e-10, -27905.3, 9.0162
],
Tmin=(10, 'K'),
Tmax=(422.477, 'K')),
NASAPolynomial(coeffs=[
0.701289, 0.0344988, -1.9736e-05,
5.48052e-09, -5.92612e-13, -27460.6, 23.329
],
Tmin=(422.477, 'K'),
Tmax=(3000, 'K'))
],
Tmin=(10, 'K'),
Tmax=(3000, 'K'),
E0=(-232.025, 'kJ/mol'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(232.805, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)C")])
peracetic_acid = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.81786, 0.016419, 3.32204e-05,
-8.98403e-08, 6.63474e-11, -42057.8,
9.65245
],
Tmin=(10, 'K'),
Tmax=(354.579, 'K')),
NASAPolynomial(coeffs=[
2.75993, 0.0283534, -1.72659e-05,
5.08158e-09, -5.77773e-13, -41982.8,
13.6595
],
Tmin=(354.579, 'K'),
Tmax=(3000, 'K'))
],
Tmin=(10, 'K'),
Tmax=(3000, 'K'),
E0=(-349.698, 'kJ/mol'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(199.547, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)OO")])
acetic_acid = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.97665, 0.00159915, 8.5542e-05,
-1.76486e-07, 1.20201e-10, -53911.5,
8.99309
],
Tmin=(10, 'K'),
Tmax=(375.616, 'K')),
NASAPolynomial(coeffs=[
1.57088, 0.0272146, -1.67357e-05,
5.01453e-09, -5.82273e-13, -53730.7,
18.2442
],
Tmin=(375.616, 'K'),
Tmax=(3000, 'K'))
],
Tmin=(10, 'K'),
Tmax=(3000, 'K'),
E0=(-448.245, 'kJ/mol'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(182.918, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)O")])
criegee = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.23876, 0.0679583, -3.35611e-05,
7.91519e-10, 3.13038e-12, -77986, 13.6438
],
Tmin=(10, 'K'),
Tmax=(1053.46, 'K')),
NASAPolynomial(coeffs=[
9.84525, 0.0536795, -2.86165e-05,
7.39945e-09, -7.48482e-13, -79977.6, -21.4187
],
Tmin=(1053.46, 'K'),
Tmax=(3000, 'K'))
],
Tmin=(10, 'K'),
Tmax=(3000, 'K'),
E0=(-648.47, 'kJ/mol'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(457.296, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)OOC(C)(O)C")])
self.database = SolvationDatabase()
self.database.load(
os.path.join(settings['database.directory'], 'solvation'))
self.solvent = 'octane'
diffusionLimiter.enable(self.database.getSolventData(self.solvent),
self.database)
self.T = 298
self.uni_reaction = Reaction(reactants=[octyl_pri],
products=[octyl_sec])
self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'),
n=0,
Ea=(0, 'kJ/mol'))
self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane],
products=[decyl])
self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22,
'cm^3/molecule/s'),
n=0,
Ea=(0, 'kJ/mol'))
self.tri_bi_reaction = Reaction(
reactants=[acetone, peracetic_acid, acetic_acid],
products=[criegee, acetic_acid])
self.tri_bi_reaction.kinetics = Arrhenius(A=(1.07543e-11,
'cm^6/(mol^2*s)'),
n=5.47295,
Ea=(-38.5379, 'kJ/mol'))
self.intrinsic_rates = {
self.uni_reaction:
self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.bi_uni_reaction:
self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.tri_bi_reaction:
self.tri_bi_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
}
def tearDown(self):
diffusionLimiter.disable()
def testGetEffectiveRateUnimolecular(self):
"""
Tests that the effective rate is the same as the intrinsic rate for
unimiolecular reactions.
"""
effective_rate = diffusionLimiter.getEffectiveRate(
self.uni_reaction, self.T)
self.assertEqual(effective_rate,
self.intrinsic_rates[self.uni_reaction])
def testGetEffectiveRate2to1(self):
"""
Tests that the effective rate is limited in the forward direction for
a 2 -> 1 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(
self.bi_uni_reaction, self.T)
self.assertTrue(
effective_rate < self.intrinsic_rates[self.bi_uni_reaction])
self.assertTrue(
effective_rate >= 0.2 * self.intrinsic_rates[self.bi_uni_reaction])
def testGetEffectiveRate3to2(self):
"""
Tests that the effective rate is limited for a 3 -> 2 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(
self.tri_bi_reaction, self.T)
self.assertTrue(
effective_rate < self.intrinsic_rates[self.tri_bi_reaction])
self.assertTrue(
effective_rate >= 0.2 * self.intrinsic_rates[self.tri_bi_reaction])
class TestSoluteDatabase(TestCase):
def setUp(self):
self.database = SolvationDatabase()
self.database.load(os.path.join(settings['database.directory'], 'solvation'))
def runTest(self):
pass
def testSoluteLibrary(self):
"Test we can obtain solute parameters from a library"
species = Species(molecule=[Molecule(SMILES='COC=O')]) #methyl formate - we know this is in the solute library
libraryData = self.database.getSoluteDataFromLibrary(species, self.database.libraries['solute'])
self.assertEqual(len(libraryData), 3)
soluteData = self.database.getSoluteData(species)
self.assertTrue(isinstance(soluteData, SoluteData))
S = soluteData.S
self.assertEqual(S, 0.68)
self.assertTrue(soluteData.V is not None)
def testMcGowan(self):
"Test we can calculate and set the McGowan volume for species containing H,C,O,N or S"
self.testCases = [
['CCCCCCCC', 1.2358], #n-octane, in library
['C(CO)O', 0.5078], #ethylene glycol
['CC#N', 0.4042], #acetonitrile
['CCS', 0.5539] #ethanethiol
]
for smiles, volume in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
soluteData.setMcGowanVolume(species) # even if it was found in library, recalculate
self.assertTrue(soluteData.V is not None) # so if it wasn't found in library, we should have calculated it
self.assertAlmostEqual(soluteData.V, volume) # the volume is what we expect given the atoms and bonds
def testDiffusivity(self):
"Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity"
species = Species(molecule=[Molecule(SMILES='O')]) # water
soluteData = self.database.getSoluteData(species)
T = 298.
solventViscosity = 0.00089 # water is about 8.9e-4 Pa.s
D = soluteData.getStokesDiffusivity(T, solventViscosity) # m2/s
self.assertAlmostEqual((D * 1e9), 1.3, 1)
# self-diffusivity of water is about 2e-9 m2/s
def testSolventLibrary(self):
"Test we can obtain solvent parameters from a library"
solventData = self.database.getSolventData('water')
self.assertTrue(solventData is not None)
self.assertEqual(solventData.s_h, 2.836)
self.assertRaises(DatabaseError, self.database.getSolventData, 'orange_juice')
def testViscosity(self):
"Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters"
solventData = self.database.getSolventData('water')
self.assertAlmostEqual(solventData.getSolventViscosity(298), 0.0009155)
def testSoluteGeneration(self):
"Test we can estimate Abraham solute parameters correctly using group contributions"
self.testCases = [
['1,2-ethanediol', 'C(CO)O', 0.823, 0.685, 0.327, 2.572, 0.693, None],
]
for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteDataFromGroups(Species(molecule=[species.molecule[0]]))
self.assertAlmostEqual(soluteData.S, S, places=2)
self.assertAlmostEqual(soluteData.B, B, places=2)
self.assertAlmostEqual(soluteData.E, E, places=2)
self.assertAlmostEqual(soluteData.L, L, places=2)
self.assertAlmostEqual(soluteData.A, A, places=2)
def testLonePairSoluteGeneration(self):
"Test we can obtain solute parameters via group additivity for a molecule with lone pairs"
molecule=Molecule().fromAdjacencyList(
"""
CH2_singlet
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmmonia(self):
"Test we can obtain solute parameters via group additivity for ammonia"
molecule=Molecule().fromAdjacencyList(
"""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationAmide(self):
"Test that we can obtain solute parameters via group additivity for an amide"
molecule=Molecule().fromAdjacencyList(
"""
1 N u0 p1 {2,S} {3,S} {4,S}
2 H u0 {1,S}
3 C u0 {1,S} {6,S} {7,S} {8,S}
4 C u0 {1,S} {5,D} {9,S}
5 O u0 p2 {4,D}
6 H u0 {3,S}
7 H u0 {3,S}
8 H u0 {3,S}
9 H u0 {4,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testSoluteDataGenerationCO(self):
"Test that we can obtain solute parameters via group additivity for CO."
molecule=Molecule().fromAdjacencyList(
"""
1 C u0 p1 c-1 {2,T}
2 O u0 p1 c+1 {1,T}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testRadicalandLonePairGeneration(self):
"""
Test we can obtain solute parameters via group additivity for a molecule with both lone
pairs and a radical
"""
molecule=Molecule().fromAdjacencyList(
"""
[C]OH
multiplicity 2
1 C u1 p1 c0 {2,S}
2 O u0 p2 c0 {1,S} {3,S}
3 H u0 p0 c0 {2,S}
""")
species = Species(molecule=[molecule])
soluteData = self.database.getSoluteDataFromGroups(species)
self.assertTrue(soluteData is not None)
def testCorrectionGeneration(self):
"Test we can estimate solvation thermochemistry."
self.testCases = [
# solventName, soluteName, soluteSMILES, Hsolv, Gsolv
['water', 'acetic acid', 'C(C)(=O)O', -56500, -6700*4.184],
['water', 'naphthalene', 'C1=CC=CC2=CC=CC=C12', -42800, -2390*4.184],
['1-octanol', 'octane', 'CCCCCCCC', -40080, -4180*4.184],
['1-octanol', 'tetrahydrofuran', 'C1CCOC1', -28320, -3930*4.184],
['benzene', 'toluene', 'C1(=CC=CC=C1)C', -37660, -5320*4.184],
['benzene', '1,4-dioxane', 'C1COCCO1', -39030, -5210*4.184]
]
for solventName, soluteName, smiles, H, G in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
solventData = self.database.getSolventData(solventName)
solvationCorrection = self.database.getSolvationCorrection(soluteData, solventData)
self.assertAlmostEqual(solvationCorrection.enthalpy / 10000., H / 10000., 0, msg="Solvation enthalpy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.enthalpy, H)) #0 decimal place, in 10kJ.
self.assertAlmostEqual(solvationCorrection.gibbs / 10000., G / 10000., 0, msg="Solvation Gibbs free energy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.gibbs, G))
def testInitialSpecies(self):
" Test we can check whether the solvent is listed as one of the initial species in various scenarios "
# Case 1. when SMILES for solvent is available, the molecular structures of the initial species and the solvent
# are compared to check whether the solvent is in the initial species list
# Case 1-1: the solvent water is not in the initialSpecies list, so it raises Exception
rmg=RMG()
rmg.initialSpecies = []
solute = Species(label='n-octane', molecule=[Molecule().fromSMILES('C(CCCCC)CC')])
rmg.initialSpecies.append(solute)
rmg.solvent = 'water'
solventStructure = Species().fromSMILES('O')
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 1-2: the solvent is now octane and it is listed as the initialSpecies. Although the string
# names of the solute and the solvent are different, because the solvent SMILES is provided,
# it can identify the 'n-octane' as the solvent
rmg.solvent = 'octane'
solventStructure = Species().fromSMILES('CCCCCCCC')
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
# Case 2: the solvent SMILES is not provided. In this case, it can identify the species as the
# solvent by looking at the string name.
# Case 2-1: Since 'n-octane and 'octane' are not equal, it raises Exception
solventStructure = None
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 2-2: The label 'n-ocatne' is corrected to 'octane', so it is identified as the solvent
rmg.initialSpecies[0].label = 'octane'
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
def testSolventMolecule(self):
" Test we can give a proper value for the solvent molecular structure when different solvent databases are given "
# solventlibrary.entries['solvent_label'].item should be the instance of Species with the solvent's molecular structure
# if the solvent database contains the solvent SMILES or adjacency list. If not, then item is None
# Case 1: When the solventDatabase does not contain the solvent SMILES, the item attribute is None
solventlibrary = SolventLibrary()
solventlibrary.loadEntry(index=1, label='water', solvent=None)
self.assertTrue(solventlibrary.entries['water'].item is None)
# Case 2: When the solventDatabase contains the correct solvent SMILES, the item attribute is the instance of
# Species with the correct solvent molecular structure
solventlibrary.loadEntry(index=2, label='octane', solvent=None, molecule='CCCCCCCC')
solventSpecies = Species().fromSMILES('C(CCCCC)CC')
self.assertTrue(solventSpecies.isIsomorphic(solventlibrary.entries['octane'].item))
# Case 3: When the solventDatabase contains the correct solvent adjacency list, the item attribute is the instance of
# the species with the correct solvent molecular structure.
# This will display the SMILES Parse Error message from the external function, but ignore it.
solventlibrary.loadEntry(index=3, label='ethanol', solvent=None, molecule=
"""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 O u0 p2 c0 {2,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
""")
solventSpecies = Species().fromSMILES('CCO')
self.assertTrue(solventSpecies.isIsomorphic(solventlibrary.entries['ethanol'].item))
# Case 4: when the solventDatabase contains incorrect values for the molecule attribute, it raises Exception
# This will display the SMILES Parse Error message from the external function, but ignore it.
self.assertRaises(Exception, solventlibrary.loadEntry, index=4, label='benzene', solvent=None, molecule='ring')
class TestDiffusionLimited(unittest.TestCase):
"""
Contains unit tests of the DiffusionLimited class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
octyl_pri = Species(
label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.772759, 0.093255, -5.84447e-05, 1.8557e-08,
-2.37127e-12, -3926.9, 37.6131
],
Tmin=(298, 'K'),
Tmax=(1390, 'K')),
NASAPolynomial(coeffs=[
25.051, 0.036948, -1.25765e-05, 1.94628e-09, -1.12669e-13,
-13330.1, -102.557
],
Tmin=(1390, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(577.856, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="[CH2]CCCCCCC")])
octyl_sec = Species(
label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.304233, 0.0880077, -4.90743e-05, 1.21858e-08,
-8.87773e-13, -5237.93, 36.6583
],
Tmin=(298, 'K'),
Tmax=(1383, 'K')),
NASAPolynomial(coeffs=[
24.9044, 0.0366394, -1.2385e-05, 1.90835e-09, -1.10161e-13,
-14713.5, -101.345
],
Tmin=(1383, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(577.856, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="CC[CH]CCCCC")])
ethane = Species(label="",
thermo=ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000,
1500], 'K'),
Cpdata=([
10.294, 12.643, 14.933, 16.932, 20.033,
22.438, 26.281
], 'cal/(mol*K)'),
H298=(12.549, 'kcal/mol'),
S298=(52.379, 'cal/(mol*K)'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(133.032, 'J/(mol*K)'),
comment="""Thermo library: CH"""),
molecule=[Molecule(SMILES="C=C")])
decyl = Species(label="",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-1.31358, 0.117973, -7.51843e-05, 2.43331e-08,
-3.17523e-12, -9689.68, 43.501
],
Tmin=(298, 'K'),
Tmax=(1390, 'K')),
NASAPolynomial(coeffs=[
31.5697, 0.0455818, -1.54995e-05, 2.39711e-09,
-1.3871e-13, -21573.8, -134.709
],
Tmin=(1390, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(298, 'K'),
Tmax=(5000, 'K'),
Cp0=(33.2579, 'J/(mol*K)'),
CpInf=(719.202, 'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""),
molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")])
self.database = SolvationDatabase()
self.database.load(
os.path.join(settings['database.directory'], 'solvation'))
self.solvent = 'octane'
diffusionLimiter.enable(self.database.getSolventData(self.solvent),
self.database)
self.T = 298
self.uni_reaction = Reaction(reactants=[octyl_pri],
products=[octyl_sec])
self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'),
n=0,
Ea=(0, 'kJ/mol'))
self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane],
products=[decyl])
self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22,
'cm^3/molecule/s'),
n=0,
Ea=(0, 'kJ/mol'))
self.intrinsic_rates = {
self.uni_reaction:
self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.bi_uni_reaction:
self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
}
def tearDown(self):
diffusionLimiter.disable()
def testGetEffectiveRateUnimolecular(self):
"""
Tests that the effective rate is the same as the intrinsic rate for
unimiolecular reactions.
"""
effective_rate = diffusionLimiter.getEffectiveRate(
self.uni_reaction, self.T)
self.assertEqual(effective_rate,
self.intrinsic_rates[self.uni_reaction])
def testGetEffectiveRate2to1(self):
"""
Tests that the effective rate is limited in the forward direction for
a 2 -> 1 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(
self.bi_uni_reaction, self.T)
self.assertTrue(
effective_rate < self.intrinsic_rates[self.bi_uni_reaction])
self.assertTrue(
effective_rate >= 0.2 * self.intrinsic_rates[self.bi_uni_reaction])
class TestDiffusionLimited(unittest.TestCase):
"""
Contains unit tests of the DiffusionLimited class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
octyl_pri = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-0.772759,0.093255,-5.84447e-05,1.8557e-08,-2.37127e-12,-3926.9,37.6131], Tmin=(298,'K'), Tmax=(1390,'K')),
NASAPolynomial(coeffs=[25.051,0.036948,-1.25765e-05,1.94628e-09,-1.12669e-13,-13330.1,-102.557], Tmin=(1390,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCC")])
octyl_sec = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-0.304233,0.0880077,-4.90743e-05,1.21858e-08,-8.87773e-13,-5237.93,36.6583], Tmin=(298,'K'), Tmax=(1383,'K')),
NASAPolynomial(coeffs=[24.9044,0.0366394,-1.2385e-05,1.90835e-09,-1.10161e-13,-14713.5,-101.345], Tmin=(1383,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="CC[CH]CCCCC")])
ethane = Species(label="", thermo=ThermoData(
Tdata=([300,400,500,600,800,1000,1500],'K'), Cpdata=([10.294,12.643,14.933,16.932,20.033,22.438,26.281],'cal/(mol*K)'), H298=(12.549,'kcal/mol'), S298=(52.379,'cal/(mol*K)'),
Cp0=(33.2579,'J/(mol*K)'), CpInf=(133.032,'J/(mol*K)'), comment="""Thermo library: CH"""),
molecule=[Molecule(SMILES="C=C")])
decyl = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-1.31358,0.117973,-7.51843e-05,2.43331e-08,-3.17523e-12,-9689.68,43.501], Tmin=(298,'K'), Tmax=(1390,'K')),
NASAPolynomial(coeffs=[31.5697,0.0455818,-1.54995e-05,2.39711e-09,-1.3871e-13,-21573.8,-134.709], Tmin=(1390,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(719.202,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")])
acetone = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs = [3.75568, 0.0264934, -6.55661e-05, 1.94971e-07, -1.82059e-10, -27905.3, 9.0162], Tmin = (10, 'K'), Tmax = (422.477, 'K')),
NASAPolynomial(coeffs = [0.701289, 0.0344988, -1.9736e-05, 5.48052e-09, -5.92612e-13, -27460.6, 23.329],Tmin = (422.477, 'K'),Tmax = (3000, 'K'))
],
Tmin = (10, 'K'), Tmax = (3000, 'K'), E0 = (-232.025, 'kJ/mol'), Cp0 = (33.2579, 'J/(mol*K)'), CpInf = (232.805, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)C")])
peracetic_acid = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs = [3.81786, 0.016419, 3.32204e-05, -8.98403e-08, 6.63474e-11, -42057.8, 9.65245], Tmin = (10, 'K'), Tmax = (354.579, 'K')),
NASAPolynomial(coeffs = [2.75993, 0.0283534, -1.72659e-05, 5.08158e-09, -5.77773e-13, -41982.8, 13.6595], Tmin = (354.579, 'K'), Tmax = (3000, 'K'))
],
Tmin = (10, 'K'), Tmax = (3000, 'K'), E0 = (-349.698, 'kJ/mol'),Cp0 = (33.2579, 'J/(mol*K)'), CpInf = (199.547, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)OO")])
acetic_acid = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs = [3.97665, 0.00159915, 8.5542e-05, -1.76486e-07, 1.20201e-10, -53911.5, 8.99309], Tmin = (10, 'K'), Tmax = (375.616, 'K')),
NASAPolynomial(coeffs = [1.57088, 0.0272146, -1.67357e-05, 5.01453e-09, -5.82273e-13, -53730.7, 18.2442], Tmin = (375.616, 'K'), Tmax = (3000, 'K'))
],
Tmin = (10, 'K'), Tmax = (3000, 'K'), E0 = (-448.245, 'kJ/mol'), Cp0 = (33.2579, 'J/(mol*K)'), CpInf = (182.918, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)O")])
criegee = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs = [3.23876, 0.0679583, -3.35611e-05, 7.91519e-10, 3.13038e-12, -77986, 13.6438], Tmin = (10, 'K'), Tmax = (1053.46, 'K')),
NASAPolynomial(coeffs = [9.84525, 0.0536795, -2.86165e-05, 7.39945e-09, -7.48482e-13, -79977.6, -21.4187], Tmin = (1053.46, 'K'), Tmax = (3000, 'K'))
],
Tmin = (10, 'K'), Tmax = (3000, 'K'), E0 = (-648.47, 'kJ/mol'),Cp0 = (33.2579, 'J/(mol*K)'), CpInf = (457.296, 'J/(mol*K)')),
molecule=[Molecule(SMILES="CC(=O)OOC(C)(O)C")])
self.database = SolvationDatabase()
self.database.load(os.path.join(settings['database.directory'], 'solvation'))
self.solvent = 'octane'
diffusionLimiter.enable(self.database.getSolventData(self.solvent), self.database)
self.T = 298
self.uni_reaction = Reaction(reactants=[octyl_pri], products=[octyl_sec])
self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'), n=0, Ea=(0,'kJ/mol'))
self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane], products=[decyl])
self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22, 'cm^3/molecule/s'), n=0, Ea=(0,'kJ/mol'))
self.tri_bi_reaction = Reaction(reactants=[acetone, peracetic_acid, acetic_acid],
products=[criegee, acetic_acid])
self.tri_bi_reaction.kinetics = Arrhenius(A=(1.07543e-11, 'cm^6/(mol^2*s)'), n=5.47295, Ea=(-38.5379, 'kJ/mol'))
self.intrinsic_rates = {
self.uni_reaction: self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.bi_uni_reaction: self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.tri_bi_reaction: self.tri_bi_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
}
def tearDown(self):
diffusionLimiter.disable()
def testGetEffectiveRateUnimolecular(self):
"""
Tests that the effective rate is the same as the intrinsic rate for
unimiolecular reactions.
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.uni_reaction, self.T)
self.assertEqual(effective_rate, self.intrinsic_rates[self.uni_reaction])
def testGetEffectiveRate2to1(self):
"""
Tests that the effective rate is limited in the forward direction for
a 2 -> 1 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.bi_uni_reaction, self.T)
self.assertTrue(effective_rate < self.intrinsic_rates[self.bi_uni_reaction])
self.assertTrue(effective_rate >= 0.2 * self.intrinsic_rates[self.bi_uni_reaction])
def testGetEffectiveRate3to2(self):
"""
Tests that the effective rate is limited for a 3 -> 2 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.tri_bi_reaction, self.T)
self.assertTrue(effective_rate < self.intrinsic_rates[self.tri_bi_reaction])
self.assertTrue(effective_rate >= 0.2 * self.intrinsic_rates[self.tri_bi_reaction])
class TestDiffusionLimited(unittest.TestCase):
"""
Contains unit tests of the DiffusionLimited class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
octyl_pri = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-0.772759,0.093255,-5.84447e-05,1.8557e-08,-2.37127e-12,-3926.9,37.6131], Tmin=(298,'K'), Tmax=(1390,'K')),
NASAPolynomial(coeffs=[25.051,0.036948,-1.25765e-05,1.94628e-09,-1.12669e-13,-13330.1,-102.557], Tmin=(1390,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCC")])
octyl_sec = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-0.304233,0.0880077,-4.90743e-05,1.21858e-08,-8.87773e-13,-5237.93,36.6583], Tmin=(298,'K'), Tmax=(1383,'K')),
NASAPolynomial(coeffs=[24.9044,0.0366394,-1.2385e-05,1.90835e-09,-1.10161e-13,-14713.5,-101.345], Tmin=(1383,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="CC[CH]CCCCC")])
ethane = Species(label="", thermo=ThermoData(
Tdata=([300,400,500,600,800,1000,1500],'K'), Cpdata=([10.294,12.643,14.933,16.932,20.033,22.438,26.281],'cal/(mol*K)'), H298=(12.549,'kcal/mol'), S298=(52.379,'cal/(mol*K)'),
Cp0=(33.2579,'J/(mol*K)'), CpInf=(133.032,'J/(mol*K)'), comment="""Thermo library: CH"""),
molecule=[Molecule(SMILES="C=C")])
decyl = Species(label="", thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[-1.31358,0.117973,-7.51843e-05,2.43331e-08,-3.17523e-12,-9689.68,43.501], Tmin=(298,'K'), Tmax=(1390,'K')),
NASAPolynomial(coeffs=[31.5697,0.0455818,-1.54995e-05,2.39711e-09,-1.3871e-13,-21573.8,-134.709], Tmin=(1390,'K'), Tmax=(5000,'K'))
],
Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(719.202,'J/(mol*K)'),
comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")])
self.database = SolvationDatabase()
self.database.load(os.path.join(settings['database.directory'], 'solvation'))
self.solvent = 'octane'
diffusionLimiter.enable(self.database.getSolventData(self.solvent), self.database)
self.T = 298
self.uni_reaction = Reaction(reactants=[octyl_pri], products=[octyl_sec])
self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'), n=0, Ea=(0,'kJ/mol'))
self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane], products=[decyl])
self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22, 'cm^3/molecule/s'), n=0, Ea=(0,'kJ/mol'))
self.intrinsic_rates = {
self.uni_reaction: self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
self.bi_uni_reaction: self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5),
}
def tearDown(self):
diffusionLimiter.disable()
def testGetEffectiveRateUnimolecular(self):
"""
Tests that the effective rate is the same as the intrinsic rate for
unimiolecular reactions.
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.uni_reaction, self.T)
self.assertEqual(effective_rate, self.intrinsic_rates[self.uni_reaction])
def testGetEffectiveRate2to1(self):
"""
Tests that the effective rate is limited in the forward direction for
a 2 -> 1 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.bi_uni_reaction, self.T)
self.assertTrue(effective_rate < self.intrinsic_rates[self.bi_uni_reaction])
self.assertTrue(effective_rate >= 0.2 * self.intrinsic_rates[self.bi_uni_reaction])
class TestSoluteDatabase(TestCase):
def setUp(self):
self.database = SolvationDatabase()
self.database.load(os.path.join(settings['database.directory'], 'solvation'))
def runTest(self):
pass
def testSoluteLibrary(self):
"Test we can obtain solute parameters from a library"
species = Species(molecule=[Molecule(SMILES='COC=O')]) #methyl formate - we know this is in the solute library
libraryData = self.database.getSoluteDataFromLibrary(species, self.database.libraries['solute'])
self.assertEqual(len(libraryData), 3)
soluteData = self.database.getSoluteData(species)
self.assertTrue(isinstance(soluteData, SoluteData))
S = soluteData.S
self.assertEqual(S, 0.68)
self.assertTrue(soluteData.V is not None)
def testMcGowan(self):
"Test we can calculate and set the McGowan volume for species containing H,C,O,N or S"
self.testCases = [
['CCCCCCCC', 1.2358], #n-octane, in library
['C(CO)O', 0.5078], #ethylene glycol
['CC#N', 0.4042], #acetonitrile
['CCS', 0.5539] #ethanethiol
]
for smiles, volume in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
soluteData.setMcGowanVolume(species) # even if it was found in library, recalculate
self.assertTrue(soluteData.V is not None) # so if it wasn't found in library, we should have calculated it
self.assertAlmostEqual(soluteData.V, volume) # the volume is what we expect given the atoms and bonds
def testDiffusivity(self):
"Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity"
species = Species(molecule=[Molecule(SMILES='COC=O')])
soluteData = self.database.getSoluteData(species)
T = 298
solventViscosity = 0.001
D = soluteData.getStokesDiffusivity(T, solventViscosity)
self.assertAlmostEqual((D*1E12), 0.00000979)
def testSolventLibrary(self):
"Test we can obtain solvent parameters from a library"
solventData = self.database.getSolventData('water')
self.assertTrue(solventData is not None)
self.assertEqual(solventData.s_h, 2.836)
self.assertRaises(DatabaseError, self.database.getSolventData, 'orange_juice')
def testViscosity(self):
"Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters"
solventData = self.database.getSolventData('water')
self.assertAlmostEqual(solventData.getSolventViscosity(298), 0.0009155)
def testSoluteGeneration(self):
"Test we can estimate Abraham solute parameters correctly using group contributions"
self.testCases = [
# from RMG-Java test runs by RWest (mostly in agreement with Jalan et. al. supplementary data)
['1,2-ethanediol', 'C(CO)O', 0.823, 0.685, 0.327, 2.572, 0.693, None],
# a nitrogen case
#['acetonitrile', 'CC#N', 0.9, 0.33, 0.237, 1.739, 0.04, None],
# a sulfur case
#['ethanethiol', 'CCS', 0.35, 0.24, 0.392, 2.173, 0, None]
]
for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteDataFromGroups(Species(molecule=[species.molecule[0]]))
self.assertAlmostEqual(soluteData.S, S, places=2)
self.assertAlmostEqual(soluteData.B, B, places=2)
self.assertAlmostEqual(soluteData.E, E, places=2)
self.assertAlmostEqual(soluteData.L, L, places=2)
self.assertAlmostEqual(soluteData.A, A, places=2)
def testCorrectionGeneration(self):
"Test we can estimate solvation thermochemistry."
self.testCases = [
# solventName, soluteName, soluteSMILES, Hsolv, Gsolv
['water', 'acetic acid', 'C(C)(=O)O', -56500, -6700*4.184],
['water', 'naphthalene', 'C1=CC=CC2=CC=CC=C12', -42800, -2390*4.184],
['1-octanol', 'octane', 'CCCCCCCC', -40080, -4180*4.184],
['1-octanol', 'tetrahydrofuran', 'C1CCOC1', -28320, -3930*4.184],
['benzene', 'toluene', 'C1(=CC=CC=C1)C', -37660, -5320*4.184],
['benzene', '1,4-dioxane', 'C1COCCO1', -39030, -5210*4.184]
]
for solventName, soluteName, smiles, H, G in self.testCases:
species = Species(molecule=[Molecule(SMILES=smiles)])
soluteData = self.database.getSoluteData(species)
solventData = self.database.getSolventData(solventName)
solvationCorrection = self.database.getSolvationCorrection(soluteData, solventData)
self.assertAlmostEqual(solvationCorrection.enthalpy / 10000., H / 10000., 0, msg="Solvation enthalpy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.enthalpy, H)) #0 decimal place, in 10kJ.
self.assertAlmostEqual(solvationCorrection.gibbs / 10000., G / 10000., 0, msg="Solvation Gibbs free energy discrepancy ({2:.0f}!={3:.0f}) for {0} in {1}".format(soluteName, solventName, solvationCorrection.gibbs, G))