def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusHigh = Arrhenius(
A = (1.39e+16,"cm^3/(mol*s)"),
n = -0.534,
Ea = (2.243,"kJ/mol"),
T0 = (1,"K"),
)
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.lindemann = Lindemann(
arrheniusHigh = self.arrheniusHigh,
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 setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusHigh = Arrhenius(
A=(1.39e+16, "cm^3/(mol*s)"),
n=-0.534,
Ea=(2.243, "kJ/mol"),
T0=(1, "K"),
)
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.lindemann = Lindemann(
arrheniusHigh=self.arrheniusHigh,
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,
)
class TestLindemann(unittest.TestCase):
"""
Contains unit tests of the Lindemann class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusHigh = Arrhenius(
A=(1.39e+16, "cm^3/(mol*s)"),
n=-0.534,
Ea=(2.243, "kJ/mol"),
T0=(1, "K"),
)
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.lindemann = Lindemann(
arrheniusHigh=self.arrheniusHigh,
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_arrheniusHigh(self):
"""
Test that the Lindemann arrheniusHigh property was properly set.
"""
self.assertTrue(self.lindemann.arrheniusHigh is self.arrheniusHigh)
def test_arrheniusLow(self):
"""
Test that the Lindemann arrheniusLow property was properly set.
"""
self.assertTrue(self.lindemann.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the Lindemann Tmin property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the Lindemann Tmax property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the Lindemann Pmin property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Pmin.value_si * 1e-5, self.Pmin,
6)
def test_Pmax(self):
"""
Test that the Lindemann Pmax property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Pmax.value_si * 1e-5, self.Pmax,
6)
def test_comment(self):
"""
Test that the Lindemann comment property was properly set.
"""
self.assertEqual(self.lindemann.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the Lindemann.isPressureDependent() method.
"""
self.assertTrue(self.lindemann.isPressureDependent())
def test_getRateCoefficient(self):
"""
Test the Lindemann.getRateCoefficient() method.
"""
Tlist = numpy.array([300, 500, 1000, 1500])
Plist = numpy.array([1e4, 1e5, 1e6])
Kexp = numpy.array([
[1.38023e+08, 2.45661e+08, 2.66439e+08],
[6.09146e+07, 2.12349e+08, 2.82604e+08],
[4.75671e+06, 4.09594e+07, 1.71441e+08],
[7.03616e+05, 6.85062e+06, 5.42111e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.lindemann.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact,
Kexp[t, p],
delta=1e-4 * Kexp[t, p])
def test_pickle(self):
"""
Test that a Lindemann object can be pickled and unpickled with no loss
of information.
"""
import cPickle
lindemann = cPickle.loads(cPickle.dumps(self.lindemann, -1))
self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value,
lindemann.arrheniusHigh.A.value,
delta=1e0)
self.assertEqual(self.lindemann.arrheniusHigh.A.units,
lindemann.arrheniusHigh.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value,
lindemann.arrheniusHigh.n.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.n.units,
lindemann.arrheniusHigh.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value,
lindemann.arrheniusHigh.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.Ea.units,
lindemann.arrheniusHigh.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value,
lindemann.arrheniusHigh.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.T0.units,
lindemann.arrheniusHigh.T0.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value,
lindemann.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.lindemann.arrheniusLow.A.units,
lindemann.arrheniusLow.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value,
lindemann.arrheniusLow.n.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.n.units,
lindemann.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value,
lindemann.arrheniusLow.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.Ea.units,
lindemann.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value,
lindemann.arrheniusLow.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.T0.units,
lindemann.arrheniusLow.T0.units)
self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value,
4)
self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units)
self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value,
4)
self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units)
self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value,
4)
self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units)
self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value,
4)
self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units)
efficiencies = {}
for mol, eff in self.lindemann.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in lindemann.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.lindemann.comment, lindemann.comment)
def test_repr(self):
"""
Test that a Lindemann object can be reconstructed from its repr()
output with no loss of information.
"""
lindemann = None
exec('lindemann = {0!r}'.format(self.lindemann))
self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value,
lindemann.arrheniusHigh.A.value,
delta=1e0)
self.assertEqual(self.lindemann.arrheniusHigh.A.units,
lindemann.arrheniusHigh.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value,
lindemann.arrheniusHigh.n.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.n.units,
lindemann.arrheniusHigh.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value,
lindemann.arrheniusHigh.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.Ea.units,
lindemann.arrheniusHigh.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value,
lindemann.arrheniusHigh.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.T0.units,
lindemann.arrheniusHigh.T0.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value,
lindemann.arrheniusLow.A.value,
delta=1e0)
self.assertEqual(self.lindemann.arrheniusLow.A.units,
lindemann.arrheniusLow.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value,
lindemann.arrheniusLow.n.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.n.units,
lindemann.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value,
lindemann.arrheniusLow.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.Ea.units,
lindemann.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value,
lindemann.arrheniusLow.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.T0.units,
lindemann.arrheniusLow.T0.units)
self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value,
4)
self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units)
self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value,
4)
self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units)
self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value,
4)
self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units)
self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value,
4)
self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units)
efficiencies = {}
for mol, eff in self.lindemann.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in lindemann.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.lindemann.comment, lindemann.comment)
def test_changeRate(self):
"""
Test the Lindemann.changeRate() method.
"""
Tlist = numpy.array([
300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400,
1500
])
k0list = numpy.array(
[self.lindemann.getRateCoefficient(T, 1e5) for T in Tlist])
self.lindemann.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.lindemann.getRateCoefficient(T, 1e5)
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)
class TestLindemann(unittest.TestCase):
"""
Contains unit tests of the Lindemann class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.arrheniusHigh = Arrhenius(
A = (1.39e+16,"cm^3/(mol*s)"),
n = -0.534,
Ea = (2.243,"kJ/mol"),
T0 = (1,"K"),
)
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.lindemann = Lindemann(
arrheniusHigh = self.arrheniusHigh,
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_arrheniusHigh(self):
"""
Test that the Lindemann arrheniusHigh property was properly set.
"""
self.assertTrue(self.lindemann.arrheniusHigh is self.arrheniusHigh)
def test_arrheniusLow(self):
"""
Test that the Lindemann arrheniusLow property was properly set.
"""
self.assertTrue(self.lindemann.arrheniusLow is self.arrheniusLow)
def test_Tmin(self):
"""
Test that the Lindemann Tmin property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the Lindemann Tmax property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Tmax.value_si, self.Tmax, 6)
def test_Pmin(self):
"""
Test that the Lindemann Pmin property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Pmin.value_si*1e-5, self.Pmin, 6)
def test_Pmax(self):
"""
Test that the Lindemann Pmax property was properly set.
"""
self.assertAlmostEqual(self.lindemann.Pmax.value_si*1e-5, self.Pmax, 6)
def test_comment(self):
"""
Test that the Lindemann comment property was properly set.
"""
self.assertEqual(self.lindemann.comment, self.comment)
def test_isPressureDependent(self):
"""
Test the Lindemann.isPressureDependent() method.
"""
self.assertTrue(self.lindemann.isPressureDependent())
def test_getRateCoefficient(self):
"""
Test the Lindemann.getRateCoefficient() method.
"""
Tlist = numpy.array([300,500,1000,1500])
Plist = numpy.array([1e4,1e5,1e6])
Kexp = numpy.array([
[1.38023e+08, 2.45661e+08, 2.66439e+08],
[6.09146e+07, 2.12349e+08, 2.82604e+08],
[4.75671e+06, 4.09594e+07, 1.71441e+08],
[7.03616e+05, 6.85062e+06, 5.42111e+07],
])
for t in range(Tlist.shape[0]):
for p in range(Plist.shape[0]):
Kact = self.lindemann.getRateCoefficient(Tlist[t], Plist[p])
self.assertAlmostEqual(Kact, Kexp[t,p], delta=1e-4*Kexp[t,p])
def test_pickle(self):
"""
Test that a Lindemann object can be pickled and unpickled with no loss
of information.
"""
import cPickle
lindemann = cPickle.loads(cPickle.dumps(self.lindemann,-1))
self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0)
self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units)
self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4)
self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units)
self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4)
self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units)
self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4)
self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units)
self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4)
self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units)
efficiencies = {}
for mol, eff in self.lindemann.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in lindemann.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.lindemann.comment, lindemann.comment)
def test_repr(self):
"""
Test that a Lindemann object can be reconstructed from its repr()
output with no loss of information.
"""
lindemann = None
exec('lindemann = {0!r}'.format(self.lindemann))
self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0)
self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0)
self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4)
self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units)
self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4)
self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units)
self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4)
self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units)
self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4)
self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units)
self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4)
self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units)
self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4)
self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units)
efficiencies = {}
for mol, eff in self.lindemann.efficiencies.iteritems():
efficiencies[mol.toSMILES()] = eff
pickled_efficiencies = {}
for mol, eff in lindemann.efficiencies.iteritems():
pickled_efficiencies[mol.toSMILES()] = eff
self.assertEqual(efficiencies, pickled_efficiencies)
self.assertEqual(self.lindemann.comment, lindemann.comment)
def test_changeRate(self):
"""
Test the Lindemann.changeRate() method.
"""
Tlist = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500])
k0list = numpy.array([self.lindemann.getRateCoefficient(T,1e5) for T in Tlist])
self.lindemann.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.lindemann.getRateCoefficient(T,1e5)
self.assertAlmostEqual(2*kexp, kact, delta=1e-6*kexp)
