class TestConformer(unittest.TestCase):
"""
Contains unit tests of the :class:`Conformer` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.ethylene = Conformer(
E0 = (0.0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(28.03,"amu")),
NonlinearRotor(inertia=([3.41526,16.6498,20.065],"amu*angstrom^2"), symmetry=4),
HarmonicOscillator(frequencies=([828.397,970.652,977.223,1052.93,1233.55,1367.56,1465.09,1672.25,3098.46,3111.7,3165.79,3193.54],"cm^-1")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
)
self.oxygen = Conformer(
E0 = (0.0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(31.99,"amu")),
LinearRotor(inertia=(11.6056,"amu*angstrom^2"), symmetry=2),
HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
],
spinMultiplicity = 3,
opticalIsomers = 1,
)
# The following data is for ethane at the CBS-QB3 level
self.coordinates = numpy.array([
[ 0.0000, 0.0000, 0.0000],
[ -0.0000, -0.0000, 1.0936],
[ 1.0430, -0.0000, -0.3288],
[ -0.4484, 0.9417, -0.3288],
[ -0.7609, -1.2051, -0.5580],
[ -0.7609, -1.2051, -1.6516],
[ -0.3125, -2.1468, -0.2292],
[ -1.8039, -1.2051, -0.2293],
])
self.number = numpy.array([6, 1, 1, 1, 6, 1, 1, 1])
self.mass = numpy.array([12, 1.007825, 1.007825, 1.007825, 12, 1.007825, 1.007825, 1.007825])
self.E0 = -93.5097
self.conformer = Conformer(
E0 = (self.E0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(30.0469,"amu")),
NonlinearRotor(inertia=([6.27071,25.3832,25.3833],"amu*angstrom^2"), symmetry=6),
HarmonicOscillator(frequencies=([818.917,819.479,987.099,1206.76,1207.05,1396,1411.35,1489.73,1489.95,1492.49,1492.66,2995.36,2996.06,3040.77,3041,3065.86,3066.02],"cm^-1")),
HinderedRotor(inertia=(1.56768,"amu*angstrom^2"), symmetry=3, barrier=(2.69401,"kcal/mol"), quantum=False, semiclassical=False),
],
spinMultiplicity = 1,
opticalIsomers = 1,
coordinates = (self.coordinates,"angstrom"),
number = self.number,
mass = (self.mass,"amu"),
)
def test_getPartitionFunction_ethylene(self):
"""
Test the StatMech.getPartitionFunction() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Qexplist = numpy.array([4.05311e+09, 4.19728e+10, 2.82309e+12, 7.51135e+13, 1.16538e+15])
for T, Qexp in zip(Tlist, Qexplist):
Qact = self.ethylene.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-4*Qexp)
def test_getHeatCapacity_ethylene(self):
"""
Test the StatMech.getHeatCapacity() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Cvexplist = numpy.array([5.11186, 7.40447, 11.1659, 13.1221, 14.1617]) * constants.R
for T, Cvexp in zip(Tlist, Cvexplist):
Cvact = self.ethylene.getHeatCapacity(T)
self.assertAlmostEqual(Cvexp, Cvact, 3)
def test_getEnthalpy_ethylene(self):
"""
Test the StatMech.getEnthalpy() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Hexplist = numpy.array([4.23129, 5.04826, 7.27337, 8.93167, 10.1223]) * constants.R * Tlist
for T, Hexp in zip(Tlist, Hexplist):
Hact = self.ethylene.getEnthalpy(T)
self.assertAlmostEqual(Hexp, Hact, delta=1e-4*Hexp)
def test_getEntropy_ethylene(self):
"""
Test the StatMech.getEntropy() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Sexplist = numpy.array([26.3540, 29.5085, 35.9422, 40.8817, 44.8142]) * constants.R
for T, Sexp in zip(Tlist, Sexplist):
Sact = self.ethylene.getEntropy(T)
self.assertAlmostEqual(Sexp, Sact, 3)
def test_getSumOfStates_ethylene(self):
"""
Test the StatMech.getSumOfStates() method for ethylene.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
sumStates = self.ethylene.getSumOfStates(Elist)
densStates = self.ethylene.getDensityOfStates(Elist)
for n in range(10, len(Elist)):
self.assertTrue(0.8 < numpy.sum(densStates[0:n+1]) / sumStates[n] < 1.25, '{0} != {1}'.format(numpy.sum(densStates[0:n+1]), sumStates[n]))
def test_getDensityOfStates_ethylene(self):
"""
Test the StatMech.getDensityOfStates() method for ethylene.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
densStates = self.ethylene.getDensityOfStates(Elist)
T = 100
Qact = numpy.sum(densStates * numpy.exp(-Elist / constants.R / T))
Qexp = self.ethylene.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-1*Qexp)
def test_getPartitionFunction_oxygen(self):
"""
Test the StatMech.getPartitionFunction() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Qexplist = numpy.array([1.55584e+09, 9.38339e+09, 1.16459e+11, 5.51016e+11, 1.72794e+12])
for T, Qexp in zip(Tlist, Qexplist):
Qact = self.oxygen.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-4*Qexp)
def test_getHeatCapacity_oxygen(self):
"""
Test the StatMech.getHeatCapacity() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Cvexplist = numpy.array([3.52538, 3.70877, 4.14751, 4.32063, 4.39392]) * constants.R
for T, Cvexp in zip(Tlist, Cvexplist):
Cvact = self.oxygen.getHeatCapacity(T)
self.assertAlmostEqual(Cvexp, Cvact, 3)
def test_getEnthalpy_oxygen(self):
"""
Test the StatMech.getEnthalpy() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Hexplist = numpy.array([3.50326, 3.54432, 3.75062, 3.91623, 4.02765]) * constants.R * Tlist
for T, Hexp in zip(Tlist, Hexplist):
Hact = self.oxygen.getEnthalpy(T)
self.assertAlmostEqual(Hexp, Hact, delta=1e-4*Hexp)
def test_getEntropy_oxygen(self):
"""
Test the StatMech.getEntropy() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Sexplist = numpy.array([24.6685, 26.5065, 29.2314, 30.9513, 32.2056]) * constants.R
for T, Sexp in zip(Tlist, Sexplist):
Sact = self.oxygen.getEntropy(T)
self.assertAlmostEqual(Sexp, Sact, 3)
def test_getSumOfStates_oxygen(self):
"""
Test the StatMech.getSumOfStates() method for oxygen.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
sumStates = self.oxygen.getSumOfStates(Elist)
densStates = self.oxygen.getDensityOfStates(Elist)
for n in range(10, len(Elist)):
self.assertTrue(0.8 < numpy.sum(densStates[0:n+1]) / sumStates[n] < 1.25, '{0} != {1}'.format(numpy.sum(densStates[0:n+1]), sumStates[n]))
def test_getDensityOfStates_oxygen(self):
"""
Test the StatMech.getDensityOfStates() method for oxygen.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
densStates = self.oxygen.getDensityOfStates(Elist)
T = 100
Qact = numpy.sum(densStates * numpy.exp(-Elist / constants.R / T))
Qexp = self.oxygen.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-1*Qexp)
def test_getTotalMass(self):
"""
Test the Conformer.getTotalMass() method.
"""
self.assertAlmostEqual(self.conformer.getTotalMass()*constants.Na*1000., numpy.sum(self.mass), 6)
def test_getCenterOfMass(self):
"""
Test the Conformer.getCenterOfMass() method.
"""
cm = self.conformer.getCenterOfMass()
self.assertAlmostEqual(cm[0]*1e10, -0.38045, 4)
self.assertAlmostEqual(cm[1]*1e10, -0.60255, 4)
self.assertAlmostEqual(cm[2]*1e10, -0.27900, 4)
def test_getMomentOfInertiaTensor(self):
"""
Test the Conformer.getMomentOfInertiaTensor() method.
"""
I = self.conformer.getMomentOfInertiaTensor()
self.assertAlmostEqual(I[0,0]*constants.Na*1e23, 20.65968, 4)
self.assertAlmostEqual(I[0,1]*constants.Na*1e23, -7.48115, 4)
self.assertAlmostEqual(I[0,2]*constants.Na*1e23, -3.46416, 4)
self.assertAlmostEqual(I[1,0]*constants.Na*1e23, -7.48115, 4)
self.assertAlmostEqual(I[1,1]*constants.Na*1e23, 13.53472, 4)
self.assertAlmostEqual(I[1,2]*constants.Na*1e23, -5.48630, 4)
self.assertAlmostEqual(I[2,0]*constants.Na*1e23, -3.46416, 4)
self.assertAlmostEqual(I[2,1]*constants.Na*1e23, -5.48630, 4)
self.assertAlmostEqual(I[2,2]*constants.Na*1e23, 22.84296, 4)
def test_getPrincipalMomentsOfInertia(self):
"""
Test the Conformer.getPrincipalMomentsOfInertia() method.
"""
I, V = self.conformer.getPrincipalMomentsOfInertia()
self.assertAlmostEqual(I[0]*constants.Na*1e23, 6.27074, 4)
self.assertAlmostEqual(I[1]*constants.Na*1e23, 25.38321, 3)
self.assertAlmostEqual(I[2]*constants.Na*1e23, 25.38341, 3)
#print V
# For some reason the axes seem to jump around (positioning and signs change)
# but the absolute values should be the same as we expect
expected = sorted([0.497140,
0.610114,
0.616938,
0.787360,
0.018454,
0.616218,
0.364578,
0.792099,
0.489554])
result = sorted(abs(V).flat)
for i,j in zip(expected, result):
self.assertAlmostEqual(i, j, 4)
return
def test_getInternalReducedMomentOfInertia(self):
"""
Test the Conformer.getInternalReducedMomentOfInertia() method.
"""
I = self.conformer.getInternalReducedMomentOfInertia(pivots=[1,5], top1=[1,2,3,4])
self.assertAlmostEqual(I*constants.Na*1e23, 1.56768, 4)
def test_getNumberDegreesOfFreedom(self):
"""
Test the Conformer.getNumberDegreesOfFreedom() method.
"""
#this is for ethane:
numberDegreesOfFreedom = self.conformer.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 24)
#this is for ethylene:
# It doesn't check aganist 3*Natoms, because Natoms is not declared.
numberDegreesOfFreedom = self.ethylene.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 18)
#this is for CO
# It doesn't check aganist 3*Natoms, because Natoms is not declared.
numberDegreesOfFreedom = self.oxygen.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 6)
class TestConformer(unittest.TestCase):
"""
Contains unit tests of the :class:`Conformer` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.ethylene = Conformer(
E0 = (0.0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(28.03,"amu")),
NonlinearRotor(inertia=([3.41526,16.6498,20.065],"amu*angstrom^2"), symmetry=4),
HarmonicOscillator(frequencies=([828.397,970.652,977.223,1052.93,1233.55,1367.56,1465.09,1672.25,3098.46,3111.7,3165.79,3193.54],"cm^-1")),
],
spinMultiplicity = 1,
opticalIsomers = 1,
)
self.oxygen = Conformer(
E0 = (0.0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(31.99,"amu")),
LinearRotor(inertia=(11.6056,"amu*angstrom^2"), symmetry=2),
HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
],
spinMultiplicity = 3,
opticalIsomers = 1,
)
# The following data is for ethane at the CBS-QB3 level
self.coordinates = numpy.array([
[ 0.0000, 0.0000, 0.0000],
[ -0.0000, -0.0000, 1.0936],
[ 1.0430, -0.0000, -0.3288],
[ -0.4484, 0.9417, -0.3288],
[ -0.7609, -1.2051, -0.5580],
[ -0.7609, -1.2051, -1.6516],
[ -0.3125, -2.1468, -0.2292],
[ -1.8039, -1.2051, -0.2293],
])
self.number = numpy.array([6, 1, 1, 1, 6, 1, 1, 1])
self.mass = numpy.array([12, 1.007825, 1.007825, 1.007825, 12, 1.007825, 1.007825, 1.007825])
self.E0 = -93.5097
self.conformer = Conformer(
E0 = (self.E0,"kJ/mol"),
modes = [
IdealGasTranslation(mass=(30.0469,"amu")),
NonlinearRotor(inertia=([6.27071,25.3832,25.3833],"amu*angstrom^2"), symmetry=6),
HarmonicOscillator(frequencies=([818.917,819.479,987.099,1206.76,1207.05,1396,1411.35,1489.73,1489.95,1492.49,1492.66,2995.36,2996.06,3040.77,3041,3065.86,3066.02],"cm^-1")),
HinderedRotor(inertia=(1.56768,"amu*angstrom^2"), symmetry=3, barrier=(2.69401,"kcal/mol"), quantum=False, semiclassical=False),
],
spinMultiplicity = 1,
opticalIsomers = 1,
coordinates = (self.coordinates,"angstrom"),
number = self.number,
mass = (self.mass,"amu"),
)
def test_getPartitionFunction_ethylene(self):
"""
Test the StatMech.getPartitionFunction() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Qexplist = numpy.array([4.05311e+09, 4.19728e+10, 2.82309e+12, 7.51135e+13, 1.16538e+15])
for T, Qexp in zip(Tlist, Qexplist):
Qact = self.ethylene.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-4*Qexp)
def test_getHeatCapacity_ethylene(self):
"""
Test the StatMech.getHeatCapacity() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Cvexplist = numpy.array([5.11186, 7.40447, 11.1659, 13.1221, 14.1617]) * constants.R
for T, Cvexp in zip(Tlist, Cvexplist):
Cvact = self.ethylene.getHeatCapacity(T)
self.assertAlmostEqual(Cvexp, Cvact, 3)
def test_getEnthalpy_ethylene(self):
"""
Test the StatMech.getEnthalpy() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Hexplist = numpy.array([4.23129, 5.04826, 7.27337, 8.93167, 10.1223]) * constants.R * Tlist
for T, Hexp in zip(Tlist, Hexplist):
Hact = self.ethylene.getEnthalpy(T)
self.assertAlmostEqual(Hexp, Hact, delta=1e-4*Hexp)
def test_getEntropy_ethylene(self):
"""
Test the StatMech.getEntropy() method for ethylene.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Sexplist = numpy.array([26.3540, 29.5085, 35.9422, 40.8817, 44.8142]) * constants.R
for T, Sexp in zip(Tlist, Sexplist):
Sact = self.ethylene.getEntropy(T)
self.assertAlmostEqual(Sexp, Sact, 3)
def test_getSumOfStates_ethylene(self):
"""
Test the StatMech.getSumOfStates() method for ethylene.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
sumStates = self.ethylene.getSumOfStates(Elist)
densStates = self.ethylene.getDensityOfStates(Elist)
for n in range(10, len(Elist)):
self.assertTrue(0.8 < numpy.sum(densStates[0:n+1]) / sumStates[n] < 1.25, '{0} != {1}'.format(numpy.sum(densStates[0:n+1]), sumStates[n]))
def test_getDensityOfStates_ethylene(self):
"""
Test the StatMech.getDensityOfStates() method for ethylene.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
densStates = self.ethylene.getDensityOfStates(Elist)
T = 100
Qact = numpy.sum(densStates * numpy.exp(-Elist / constants.R / T))
Qexp = self.ethylene.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-1*Qexp)
def test_getPartitionFunction_oxygen(self):
"""
Test the StatMech.getPartitionFunction() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Qexplist = numpy.array([1.55584e+09, 9.38339e+09, 1.16459e+11, 5.51016e+11, 1.72794e+12])
for T, Qexp in zip(Tlist, Qexplist):
Qact = self.oxygen.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-4*Qexp)
def test_getHeatCapacity_oxygen(self):
"""
Test the StatMech.getHeatCapacity() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Cvexplist = numpy.array([3.52538, 3.70877, 4.14751, 4.32063, 4.39392]) * constants.R
for T, Cvexp in zip(Tlist, Cvexplist):
Cvact = self.oxygen.getHeatCapacity(T)
self.assertAlmostEqual(Cvexp, Cvact, 3)
def test_getEnthalpy_oxygen(self):
"""
Test the StatMech.getEnthalpy() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Hexplist = numpy.array([3.50326, 3.54432, 3.75062, 3.91623, 4.02765]) * constants.R * Tlist
for T, Hexp in zip(Tlist, Hexplist):
Hact = self.oxygen.getEnthalpy(T)
self.assertAlmostEqual(Hexp, Hact, delta=1e-4*Hexp)
def test_getEntropy_oxygen(self):
"""
Test the StatMech.getEntropy() method for oxygen.
"""
Tlist = numpy.array([300,500,1000,1500,2000])
Sexplist = numpy.array([24.6685, 26.5065, 29.2314, 30.9513, 32.2056]) * constants.R
for T, Sexp in zip(Tlist, Sexplist):
Sact = self.oxygen.getEntropy(T)
self.assertAlmostEqual(Sexp, Sact, 3)
def test_getSumOfStates_oxygen(self):
"""
Test the StatMech.getSumOfStates() method for oxygen.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
sumStates = self.oxygen.getSumOfStates(Elist)
densStates = self.oxygen.getDensityOfStates(Elist)
for n in range(10, len(Elist)):
self.assertTrue(0.8 < numpy.sum(densStates[0:n+1]) / sumStates[n] < 1.25, '{0} != {1}'.format(numpy.sum(densStates[0:n+1]), sumStates[n]))
def test_getDensityOfStates_oxygen(self):
"""
Test the StatMech.getDensityOfStates() method for oxygen.
"""
Elist = numpy.arange(0, 5000*11.96, 2*11.96)
densStates = self.oxygen.getDensityOfStates(Elist)
T = 100
Qact = numpy.sum(densStates * numpy.exp(-Elist / constants.R / T))
Qexp = self.oxygen.getPartitionFunction(T)
self.assertAlmostEqual(Qexp, Qact, delta=1e-1*Qexp)
def test_getTotalMass(self):
"""
Test the Conformer.getTotalMass() method.
"""
self.assertAlmostEqual(self.conformer.getTotalMass()*constants.Na*1000., numpy.sum(self.mass), 6)
def test_getCenterOfMass(self):
"""
Test the Conformer.getCenterOfMass() method.
"""
cm = self.conformer.getCenterOfMass()
self.assertAlmostEqual(cm[0]*1e10, -0.38045, 4)
self.assertAlmostEqual(cm[1]*1e10, -0.60255, 4)
self.assertAlmostEqual(cm[2]*1e10, -0.27900, 4)
def test_getMomentOfInertiaTensor(self):
"""
Test the Conformer.getMomentOfInertiaTensor() method.
"""
I = self.conformer.getMomentOfInertiaTensor()
self.assertAlmostEqual(I[0,0]*constants.Na*1e23, 20.65968, 4)
self.assertAlmostEqual(I[0,1]*constants.Na*1e23, -7.48115, 4)
self.assertAlmostEqual(I[0,2]*constants.Na*1e23, -3.46416, 4)
self.assertAlmostEqual(I[1,0]*constants.Na*1e23, -7.48115, 4)
self.assertAlmostEqual(I[1,1]*constants.Na*1e23, 13.53472, 4)
self.assertAlmostEqual(I[1,2]*constants.Na*1e23, -5.48630, 4)
self.assertAlmostEqual(I[2,0]*constants.Na*1e23, -3.46416, 4)
self.assertAlmostEqual(I[2,1]*constants.Na*1e23, -5.48630, 4)
self.assertAlmostEqual(I[2,2]*constants.Na*1e23, 22.84296, 4)
def test_getPrincipalMomentsOfInertia(self):
"""
Test the Conformer.getPrincipalMomentsOfInertia() method.
"""
I, V = self.conformer.getPrincipalMomentsOfInertia()
self.assertAlmostEqual(I[0]*constants.Na*1e23, 6.27074, 4)
self.assertAlmostEqual(I[1]*constants.Na*1e23, 25.38321, 3)
self.assertAlmostEqual(I[2]*constants.Na*1e23, 25.38341, 3)
#print V
# For some reason the axes seem to jump around (positioning and signs change)
# but the absolute values should be the same as we expect
expected = sorted([0.497140,
0.610114,
0.616938,
0.787360,
0.018454,
0.616218,
0.364578,
0.792099,
0.489554])
result = sorted(abs(V).flat)
for i,j in zip(expected, result):
self.assertAlmostEqual(i, j, 4)
return # now because the following often fails:
self.assertAlmostEqual(V[0,0], 0.497140, 4)
self.assertAlmostEqual(V[0,1], -0.610114, 4)
self.assertAlmostEqual(V[0,2], -0.616938, 4)
self.assertAlmostEqual(V[1,0], 0.787360, 4)
self.assertAlmostEqual(V[1,1], 0.018454, 4)
self.assertAlmostEqual(V[1,2], 0.616218, 4)
self.assertAlmostEqual(V[2,0], 0.364578, 4)
self.assertAlmostEqual(V[2,1], 0.792099, 4)
self.assertAlmostEqual(V[2,2], -0.489554, 4)
def test_getInternalReducedMomentOfInertia(self):
"""
Test the Conformer.getInternalReducedMomentOfInertia() method.
"""
I = self.conformer.getInternalReducedMomentOfInertia(pivots=[1,5], top1=[1,2,3,4])
self.assertAlmostEqual(I*constants.Na*1e23, 1.56768, 4)
def test_getNumberDegreesOfFreedom(self):
"""
Test the Conformer.getNumberDegreesOfFreedom() method.
"""
#this is for ethane:
numberDegreesOfFreedom = self.conformer.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 24)
#this is for ethylene:
# It doesn't check aganist 3*Natoms, because Natoms is not declared.
numberDegreesOfFreedom = self.ethylene.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 18)
#this is for CO
# It doesn't check aganist 3*Natoms, because Natoms is not declared.
numberDegreesOfFreedom = self.oxygen.getNumberDegreesOfFreedom()
self.assertEqual(numberDegreesOfFreedom, 6)
def get_thermo(optfreq_log, optfreq_level, energy_level, energy_log=None,
mol=None, bacs=None, soc=False,
infer_symmetry=False, infer_chirality=False, unique_id='0', scr_dir='SCRATCH'):
q = QChem(logfile=optfreq_log)
symbols, coords = q.get_geometry()
inertia = q.get_moments_of_inertia()
freqs = q.get_frequencies()
zpe = q.get_zpe()
if energy_log is None:
e0 = q.get_energy()
multiplicity = q.get_multiplicity()
else:
m = Molpro(logfile=energy_log)
e0 = m.get_energy()
multiplicity = m.get_multiplicity()
# Infer connections only if not given explicitly
if mol is None:
mol = geo_to_rmg_mol((symbols, coords)) # Does not contain bond orders
# Try to infer point group to calculate symmetry number and chirality
symmetry = optical_isomers = 1
point_group = None
if infer_symmetry or infer_chirality:
qmdata = QMData(
groundStateDegeneracy=multiplicity, # Only needed to check if valid QMData
numberOfAtoms=len(symbols),
atomicNumbers=[atomic_symbol_dict[sym] for sym in symbols],
atomCoords=(coords, 'angstrom'),
energy=(e0 * 627.5095, 'kcal/mol') # Only needed to avoid error
)
settings = type("", (), dict(symmetryPath='symmetry', scratchDirectory=scr_dir))() # Creates anonymous class
pgc = PointGroupCalculator(settings, unique_id, qmdata)
point_group = pgc.calculate()
if point_group is not None:
if infer_symmetry:
symmetry = point_group.symmetryNumber
if infer_chirality and point_group.chiral:
optical_isomers = 2
# Translational mode
mass = mol.getMolecularWeight()
translation = IdealGasTranslation(mass=(mass, 'kg/mol'))
# Rotational mode
if isinstance(inertia, list): # Nonlinear
rotation = NonlinearRotor(inertia=(inertia, 'amu*angstrom^2'), symmetry=symmetry)
else:
rotation = LinearRotor(inertia=(inertia, 'amu*angstrom^2'), symmetry=symmetry)
# Vibrational mode
freq_scale_factor = freq_scale_factors.get(optfreq_level, 1.0)
freqs = [f * freq_scale_factor for f in freqs]
vibration = HarmonicOscillator(frequencies=(freqs, 'cm^-1'))
# Bring energy to gas phase reference state
e0 *= constants.E_h * constants.Na
zpe *= constants.E_h * constants.Na * freq_scale_factor
for sym in symbols:
if soc:
e0 -= (atom_energies[energy_level][sym] - atom_socs[sym]) * constants.E_h * constants.Na
else:
e0 -= atom_energies[energy_level][sym] * constants.E_h * constants.Na
e0 += (h0expt[sym] - h298corr[sym]) * 4184.0
if bacs is not None:
e0 -= get_bac_correction(mol, **bacs) * 4184.0
# Group modes into Conformer object
modes = [translation, rotation, vibration]
conformer = Conformer(modes=modes, spinMultiplicity=multiplicity, opticalIsomers=optical_isomers)
# Calculate heat of formation, entropy of formation, and heat capacities
conformer.E0 = (e0 + zpe, 'J/mol')
hf298 = conformer.getEnthalpy(298.0) + conformer.E0.value_si
s298 = conformer.getEntropy(298.0)
Tlist = [300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0]
cp = np.zeros(len(Tlist))
for i, T in enumerate(Tlist):
cp[i] = conformer.getHeatCapacity(T)
# Return in kcal/mol and cal/mol/K
return hf298/4184.0, s298/4.184, cp/4.184
