class TestThirdBody(unittest.TestCase):
"""
Contains unit tests of the ThirdBody class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusLow = Arrhenius(
A=(2.62e+33, "cm^6/(mol^2*s)"),
n=-4.76,
Ea=(10.21, "kJ/mol"),
T0=(1, "K"),
)
self.efficiencies = {
"C": 3,
"C(=O)=O": 2,
"CC": 3,
"O": 6,
"[Ar]": 0.7,
"[C]=O": 1.5,
"[H][H]": 2
}
self.Tmin = 300.
self.Tmax = 2000.
self.Pmin = 0.01
self.Pmax = 100.
self.comment = """H + CH3 -> CH4"""
self.thirdBody = ThirdBody(
arrheniusLow=self.arrheniusLow,
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
efficiencies=self.efficiencies,
comment=self.comment,
)
def test_arrheniusLow(self):
"""
Test that the ThirdBody arrhenius property was properly set.
"""
self.assertTrue(self.thirdBody.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the ThirdBody Tmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the ThirdBody Tmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the ThirdBody Pmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmin.value_si * 1e-5, self.Pmin,
6)
def test_Pmax(self):
"""
Test that the ThirdBody Pmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmax.value_si * 1e-5, self.Pmax,
6)
def test_comment(self):
"""
Test that the ThirdBody comment property was properly set.
"""
self.assertEqual(self.thirdBody.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the ThirdBody.isPressureDependent() method.
"""
self.assertTrue(self.thirdBody.isPressureDependent())
def test_getEffectivePressure(self):
"""
Test the ThirdBody.getEffectivePressure() method.
"""
P = 1.0
# Test that each pure bath gas gives the correct effective pressure
# Create list of species objects
species = [
Species(molecule=[mol])
for mol in self.thirdBody.efficiencies.keys()
]
for mol, eff in self.thirdBody.efficiencies.items():
for spec in species:
if spec.isIsomorphic(mol):
i = species.index(spec)
break
fractions = numpy.zeros(len(species))
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Also test a mixture of bath gases
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
eff = 0
for mol in self.thirdBody.efficiencies.keys():
if species[0].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
if species[1].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Test the same thing, only with a list of species that are Molecule objects
species = [
mol.copy(deep=True) for mol in self.thirdBody.efficiencies.keys()
]
for mol, eff in self.thirdBody.efficiencies.items():
for spec in species:
if spec.isIsomorphic(mol):
i = species.index(spec)
break
fractions = numpy.zeros(len(species))
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Also test a mixture of bath gases
eff = 0
for mol in self.thirdBody.efficiencies.keys():
if species[0].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
if species[1].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Here, test a non-normalized set of fractions (they are still 50% of each)
fractions = numpy.zeros(len(species))
fractions[0] = 0.7
fractions[1] = 0.7
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
def test_getEffectiveColliderEfficiencies(self):
"""
Test the getEffectiveColliderEfficiencies() method
"""
# Create list of molecules
molecules = [
Molecule(SMILES=smiles) for smiles in
["C", "C(=O)=O", "CC", "O", "[Ar]", "[C]=O", "[H][H]"]
]
methodEfficiencies = self.thirdBody.getEffectiveColliderEfficiencies(
molecules)
efficiencies = numpy.array([3, 2, 3, 6, 0.7, 1.5, 2])
numpy.testing.assert_array_almost_equal(efficiencies,
methodEfficiencies)
# Use a smaller list of molecules
molecules = [Molecule(SMILES=smiles) for smiles in ["C", "CC", "[Ar]"]]
methodEfficiencies = self.thirdBody.getEffectiveColliderEfficiencies(
molecules)
efficiencies = numpy.array([3, 3, 0.7])
numpy.testing.assert_array_almost_equal(efficiencies,
methodEfficiencies)
def test_getRateCoefficient(self):
"""
Test the ThirdBody.getRateCoefficient() method.
"""
Tlist = numpy.array([300, 500, 1000, 1500])
Plist = numpy.array([1e4, 1e5, 1e6])
Kexp = numpy.array([
[2.83508e+08, 2.83508e+09, 2.83508e+10],
[7.68759e+07, 7.68759e+08, 7.68759e+09],
[4.84353e+06, 4.84353e+07, 4.84353e+08],
[7.05740e+05, 7.05740e+06, 7.05740e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.thirdBody.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact,
Kexp[t, p],
delta=1e-4 * Kexp[t, p])
def test_pickle(self):
"""
Test that a ThirdBody object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
thirdBody = cPickle.loads(cPickle.dumps(self.thirdBody, -1))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value,
thirdBody.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units,
thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value,
thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units,
thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value,
thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units,
thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value,
thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units,
thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value,
4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value,
4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value,
4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value,
4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
efficiencies = {}
for mol, eff in self.thirdBody.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in thirdBody.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_repr(self):
"""
Test that a ThirdBody object can be successfully reconstructed
from its repr() output with no loss of information.
"""
thirdBody = None
exec('thirdBody = {0!r}'.format(self.thirdBody))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value,
thirdBody.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units,
thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value,
thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units,
thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value,
thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units,
thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value,
thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units,
thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value,
4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value,
4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value,
4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value,
4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
efficiencies = {}
for mol, eff in self.thirdBody.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in thirdBody.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_changeRate(self):
"""
Test the ThirdBody.changeRate() method.
"""
Tlist = numpy.array([
300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400,
1500
])
k0list = numpy.array(
[self.thirdBody.getRateCoefficient(T, 1e5) for T in Tlist])
self.thirdBody.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.thirdBody.getRateCoefficient(T, 1e5)
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)
class TestThirdBody(unittest.TestCase):
"""
Contains unit tests of the ThirdBody class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusLow = Arrhenius(
A=(2.62e+33, "cm^6/(mol^2*s)"),
n=-4.76,
Ea=(10.21, "kJ/mol"),
T0=(1, "K"),
)
self.efficiencies = {
"C": 3,
"C(=O)=O": 2,
"CC": 3,
"O": 6,
"[Ar]": 0.7,
"[C]=O": 1.5,
"[H][H]": 2
}
self.Tmin = 300.
self.Tmax = 2000.
self.Pmin = 0.01
self.Pmax = 100.
self.comment = """H + CH3 -> CH4"""
self.thirdBody = ThirdBody(
arrheniusLow=self.arrheniusLow,
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
efficiencies=self.efficiencies,
comment=self.comment,
)
def test_arrheniusLow(self):
"""
Test that the ThirdBody arrhenius property was properly set.
"""
self.assertTrue(self.thirdBody.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the ThirdBody Tmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the ThirdBody Tmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the ThirdBody Pmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmin.value_si * 1e-5, self.Pmin,
6)
def test_Pmax(self):
"""
Test that the ThirdBody Pmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmax.value_si * 1e-5, self.Pmax,
6)
def test_comment(self):
"""
Test that the ThirdBody comment property was properly set.
"""
self.assertEqual(self.thirdBody.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the ThirdBody.isPressureDependent() method.
"""
self.assertTrue(self.thirdBody.isPressureDependent())
def test_getEffectivePressure(self):
"""
Test the ThirdBody.getEffectivePressure() method.
"""
P = 1.0
# Test that each pure bath gas gives the correct effective pressure
species = self.efficiencies.keys()
for spec, eff in self.efficiencies.items():
fractions = numpy.zeros(len(species))
i = species.index(spec)
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertEqual(P * eff, Peff)
# Also test a mixture of bath gases
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
eff = 0.5 * self.efficiencies[species[0]] + 0.5 * self.efficiencies[
species[1]]
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertEqual(P * eff, Peff)
def test_getRateCoefficient(self):
"""
Test the ThirdBody.getRateCoefficient() method.
"""
Tlist = numpy.array([300, 500, 1000, 1500])
Plist = numpy.array([1e4, 1e5, 1e6])
Kexp = numpy.array([
[2.83508e+08, 2.83508e+09, 2.83508e+10],
[7.68759e+07, 7.68759e+08, 7.68759e+09],
[4.84353e+06, 4.84353e+07, 4.84353e+08],
[7.05740e+05, 7.05740e+06, 7.05740e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.thirdBody.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact,
Kexp[t, p],
delta=1e-4 * Kexp[t, p])
def test_pickle(self):
"""
Test that a ThirdBody object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
thirdBody = cPickle.loads(cPickle.dumps(self.thirdBody, -1))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value,
thirdBody.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units,
thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value,
thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units,
thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value,
thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units,
thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value,
thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units,
thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value,
4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value,
4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value,
4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value,
4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
self.assertEqual(self.thirdBody.efficiencies, thirdBody.efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_repr(self):
"""
Test that a ThirdBody object can be successfully reconstructed
from its repr() output with no loss of information.
"""
thirdBody = None
exec('thirdBody = {0!r}'.format(self.thirdBody))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value,
thirdBody.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units,
thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value,
thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units,
thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value,
thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units,
thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value,
thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units,
thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value,
4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value,
4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value,
4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value,
4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
self.assertEqual(self.thirdBody.efficiencies, thirdBody.efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_changeRate(self):
"""
Test the ThirdBody.changeRate() method.
"""
Tlist = numpy.array([
300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400,
1500
])
k0list = numpy.array(
[self.thirdBody.getRateCoefficient(T, 1e5) for T in Tlist])
self.thirdBody.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.thirdBody.getRateCoefficient(T, 1e5)
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)
class TestThirdBody(unittest.TestCase):
"""
Contains unit tests of the ThirdBody class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusLow = Arrhenius(
A = (2.62e+33,"cm^6/(mol^2*s)"),
n = -4.76,
Ea = (10.21,"kJ/mol"),
T0 = (1,"K"),
)
self.efficiencies = {"C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2}
self.Tmin = 300.
self.Tmax = 2000.
self.Pmin = 0.01
self.Pmax = 100.
self.comment = """H + CH3 -> CH4"""
self.thirdBody = ThirdBody(
arrheniusLow = self.arrheniusLow,
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
Pmin = (self.Pmin,"bar"),
Pmax = (self.Pmax,"bar"),
efficiencies = self.efficiencies,
comment = self.comment,
)
def test_arrheniusLow(self):
"""
Test that the ThirdBody arrhenius property was properly set.
"""
self.assertTrue(self.thirdBody.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the ThirdBody Tmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the ThirdBody Tmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the ThirdBody Pmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmin.value_si*1e-5, self.Pmin, 6)
def test_Pmax(self):
"""
Test that the ThirdBody Pmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmax.value_si*1e-5, self.Pmax, 6)
def test_comment(self):
"""
Test that the ThirdBody comment property was properly set.
"""
self.assertEqual(self.thirdBody.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the ThirdBody.isPressureDependent() method.
"""
self.assertTrue(self.thirdBody.isPressureDependent())
def test_getEffectivePressure(self):
"""
Test the ThirdBody.getEffectivePressure() method.
"""
P = 1.0
# Test that each pure bath gas gives the correct effective pressure
# Create list of species objects
species = [Species(molecule=[mol]) for mol in self.thirdBody.efficiencies.keys()]
for mol, eff in self.thirdBody.efficiencies.items():
for spec in species:
if spec.isIsomorphic(mol):
i = species.index(spec)
break
fractions = numpy.zeros(len(species))
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Also test a mixture of bath gases
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
eff = 0
for mol in self.thirdBody.efficiencies.keys():
if species[0].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
if species[1].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Test the same thing, only with a list of species that are Molecule objects
species = [mol.copy(deep=True) for mol in self.thirdBody.efficiencies.keys()]
for mol, eff in self.thirdBody.efficiencies.items():
for spec in species:
if spec.isIsomorphic(mol):
i = species.index(spec)
break
fractions = numpy.zeros(len(species))
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Also test a mixture of bath gases
eff = 0
for mol in self.thirdBody.efficiencies.keys():
if species[0].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
if species[1].isIsomorphic(mol):
eff += 0.5 * self.thirdBody.efficiencies[mol]
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
# Here, test a non-normalized set of fractions (they are still 50% of each)
fractions = numpy.zeros(len(species))
fractions[0] = 0.7
fractions[1] = 0.7
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertAlmostEqual(P * eff, Peff)
def test_getEffectiveColliderEfficiencies(self):
"""
Test the getEffectiveColliderEfficiencies() method
"""
# Create list of molecules
molecules = [Molecule(SMILES=smiles) for smiles in ["C", "C(=O)=O", "CC", "O", "[Ar]", "[C]=O", "[H][H]"]]
methodEfficiencies = self.thirdBody.getEffectiveColliderEfficiencies(molecules)
efficiencies = numpy.array([3, 2, 3, 6, 0.7, 1.5, 2])
numpy.testing.assert_array_almost_equal(efficiencies, methodEfficiencies)
# Use a smaller list of molecules
molecules = [Molecule(SMILES=smiles) for smiles in ["C", "CC", "[Ar]"]]
methodEfficiencies = self.thirdBody.getEffectiveColliderEfficiencies(molecules)
efficiencies = numpy.array([3, 3, 0.7])
numpy.testing.assert_array_almost_equal(efficiencies, methodEfficiencies)
def test_getRateCoefficient(self):
"""
Test the ThirdBody.getRateCoefficient() method.
"""
Tlist = numpy.array([300,500,1000,1500])
Plist = numpy.array([1e4,1e5,1e6])
Kexp = numpy.array([
[2.83508e+08, 2.83508e+09, 2.83508e+10],
[7.68759e+07, 7.68759e+08, 7.68759e+09],
[4.84353e+06, 4.84353e+07, 4.84353e+08],
[7.05740e+05, 7.05740e+06, 7.05740e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.thirdBody.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact, Kexp[t,p], delta=1e-4*Kexp[t,p])
def test_pickle(self):
"""
Test that a ThirdBody object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
thirdBody = cPickle.loads(cPickle.dumps(self.thirdBody,-1))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value, thirdBody.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units, thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value, thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units, thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value, thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units, thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value, thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units, thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value, 4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value, 4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value, 4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value, 4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
efficiencies = {}
for mol, eff in self.thirdBody.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in thirdBody.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_repr(self):
"""
Test that a ThirdBody object can be successfully reconstructed
from its repr() output with no loss of information.
"""
thirdBody = None
exec('thirdBody = {0!r}'.format(self.thirdBody))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value, thirdBody.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units, thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value, thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units, thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value, thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units, thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value, thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units, thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value, 4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value, 4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value, 4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value, 4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
efficiencies = {}
for mol, eff in self.thirdBody.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in thirdBody.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_changeRate(self):
"""
Test the ThirdBody.changeRate() method.
"""
Tlist = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500])
k0list = numpy.array([self.thirdBody.getRateCoefficient(T,1e5) for T in Tlist])
self.thirdBody.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.thirdBody.getRateCoefficient(T,1e5)
self.assertAlmostEqual(2*kexp, kact, delta=1e-6*kexp)
class TestThirdBody(unittest.TestCase):
"""
Contains unit tests of the ThirdBody class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusLow = Arrhenius(
A = (2.62e+33,"cm^6/(mol^2*s)"),
n = -4.76,
Ea = (10.21,"kJ/mol"),
T0 = (1,"K"),
)
self.efficiencies = {"C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2}
self.Tmin = 300.
self.Tmax = 2000.
self.Pmin = 0.01
self.Pmax = 100.
self.comment = """H + CH3 -> CH4"""
self.thirdBody = ThirdBody(
arrheniusLow = self.arrheniusLow,
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
Pmin = (self.Pmin,"bar"),
Pmax = (self.Pmax,"bar"),
efficiencies = self.efficiencies,
comment = self.comment,
)
def test_arrheniusLow(self):
"""
Test that the ThirdBody arrhenius property was properly set.
"""
self.assertTrue(self.thirdBody.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the ThirdBody Tmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the ThirdBody Tmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the ThirdBody Pmin property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmin.value_si*1e-5, self.Pmin, 6)
def test_Pmax(self):
"""
Test that the ThirdBody Pmax property was properly set.
"""
self.assertAlmostEqual(self.thirdBody.Pmax.value_si*1e-5, self.Pmax, 6)
def test_comment(self):
"""
Test that the ThirdBody comment property was properly set.
"""
self.assertEqual(self.thirdBody.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the ThirdBody.isPressureDependent() method.
"""
self.assertTrue(self.thirdBody.isPressureDependent())
def test_getEffectivePressure(self):
"""
Test the ThirdBody.getEffectivePressure() method.
"""
P = 1.0
# Test that each pure bath gas gives the correct effective pressure
species = self.efficiencies.keys()
for spec, eff in self.efficiencies.items():
fractions = numpy.zeros(len(species))
i = species.index(spec)
fractions[i] = 1.0
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertEqual(P * eff, Peff)
# Also test a mixture of bath gases
fractions = numpy.zeros(len(species))
fractions[0] = 0.5
fractions[1] = 0.5
eff = 0.5 * self.efficiencies[species[0]] + 0.5 * self.efficiencies[species[1]]
Peff = self.thirdBody.getEffectivePressure(P, species, fractions)
self.assertEqual(P * eff, Peff)
def test_getRateCoefficient(self):
"""
Test the ThirdBody.getRateCoefficient() method.
"""
Tlist = numpy.array([300,500,1000,1500])
Plist = numpy.array([1e4,1e5,1e6])
Kexp = numpy.array([
[2.83508e+08, 2.83508e+09, 2.83508e+10],
[7.68759e+07, 7.68759e+08, 7.68759e+09],
[4.84353e+06, 4.84353e+07, 4.84353e+08],
[7.05740e+05, 7.05740e+06, 7.05740e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.thirdBody.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact, Kexp[t,p], delta=1e-4*Kexp[t,p])
def test_pickle(self):
"""
Test that a ThirdBody object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
thirdBody = cPickle.loads(cPickle.dumps(self.thirdBody))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value, thirdBody.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units, thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value, thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units, thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value, thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units, thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value, thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units, thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value, 4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value, 4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value, 4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value, 4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
self.assertEqual(self.thirdBody.efficiencies, thirdBody.efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_repr(self):
"""
Test that a ThirdBody object can be successfully reconstructed
from its repr() output with no loss of information.
"""
thirdBody = None
exec('thirdBody = {0!r}'.format(self.thirdBody))
self.assertAlmostEqual(self.thirdBody.arrheniusLow.A.value, thirdBody.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.thirdBody.arrheniusLow.A.units, thirdBody.arrheniusLow.A.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.n.value, thirdBody.arrheniusLow.n.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.n.units, thirdBody.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.Ea.value, thirdBody.arrheniusLow.Ea.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.Ea.units, thirdBody.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.thirdBody.arrheniusLow.T0.value, thirdBody.arrheniusLow.T0.value, 4)
self.assertEqual(self.thirdBody.arrheniusLow.T0.units, thirdBody.arrheniusLow.T0.units)
self.assertAlmostEqual(self.thirdBody.Tmin.value, thirdBody.Tmin.value, 4)
self.assertEqual(self.thirdBody.Tmin.units, thirdBody.Tmin.units)
self.assertAlmostEqual(self.thirdBody.Tmax.value, thirdBody.Tmax.value, 4)
self.assertEqual(self.thirdBody.Tmax.units, thirdBody.Tmax.units)
self.assertAlmostEqual(self.thirdBody.Pmin.value, thirdBody.Pmin.value, 4)
self.assertEqual(self.thirdBody.Pmin.units, thirdBody.Pmin.units)
self.assertAlmostEqual(self.thirdBody.Pmax.value, thirdBody.Pmax.value, 4)
self.assertEqual(self.thirdBody.Pmax.units, thirdBody.Pmax.units)
self.assertEqual(self.thirdBody.efficiencies, thirdBody.efficiencies)
self.assertEqual(self.thirdBody.comment, thirdBody.comment)
def test_changeRate(self):
"""
Test the ThirdBody.changeRate() method.
"""
Tlist = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500])
k0list = numpy.array([self.thirdBody.getRateCoefficient(T,1e5) for T in Tlist])
self.thirdBody.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.thirdBody.getRateCoefficient(T,1e5)
self.assertAlmostEqual(2*kexp, kact, delta=1e-6*kexp)