def testLoadOxygenFromGaussianLog(self):
"""
Uses a Gaussian03 log file for oxygen (O2) to test that its
molecular degrees of freedom can be properly read.
"""
log = GaussianLog(os.path.join(os.path.dirname(__file__), "test", "oxygen.log"))
conformer = log.loadConformer()
E0 = log.loadEnergy()
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, IdealGasTranslation)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, LinearRotor)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, HinderedRotor)]) == 0)
trans = [mode for mode in conformer.modes if isinstance(mode, IdealGasTranslation)][0]
rot = [mode for mode in conformer.modes if isinstance(mode, LinearRotor)][0]
vib = [mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)][0]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 7.11169e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 7.13316e1, delta=1e-4)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.00037e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -150.374756, 4)
self.assertEqual(conformer.spinMultiplicity, 3)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadEthyleneFromGaussianLog_G3(self):
"""
Uses a Gaussian03 log file for ethylene (C2H4) to test that its
molecular degrees of freedom can be properly read.
"""
log = GaussianLog(
os.path.join(os.path.dirname(__file__), 'data', 'ethylene_G3.log'))
conformer = log.loadConformer()
E0 = log.loadEnergy()
self.assertTrue(
len([
mode for mode in conformer.modes
if isinstance(mode, IdealGasTranslation)
]) == 1)
self.assertTrue(
len([
mode for mode in conformer.modes
if isinstance(mode, NonlinearRotor)
]) == 1)
self.assertTrue(
len([
mode for mode in conformer.modes
if isinstance(mode, HarmonicOscillator)
]) == 1)
self.assertTrue(
len([
mode for mode in conformer.modes
if isinstance(mode, HinderedRotor)
]) == 0)
trans = [
mode for mode in conformer.modes
if isinstance(mode, IdealGasTranslation)
][0]
rot = [
mode for mode in conformer.modes
if isinstance(mode, NonlinearRotor)
][0]
vib = [
mode for mode in conformer.modes
if isinstance(mode, HarmonicOscillator)
][0]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist),
5.83338e6,
delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist),
2.53410e3,
delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist),
1.0304e0,
delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -78.562189,
4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadEthyleneFromGaussianLog(self):
"""
Uses a Gaussian03 log file for ethylene (C2H4) to test that its
molecular degrees of freedom can be properly read.
"""
log = GaussianLog(os.path.join(os.path.dirname(__file__), "test", "ethylene.log"))
conformer = log.loadConformer()
E0 = log.loadEnergy()
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, IdealGasTranslation)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, NonlinearRotor)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode, HinderedRotor)]) == 0)
trans = [mode for mode in conformer.modes if isinstance(mode, IdealGasTranslation)][0]
rot = [mode for mode in conformer.modes if isinstance(mode, NonlinearRotor)][0]
vib = [mode for mode in conformer.modes if isinstance(mode, HarmonicOscillator)][0]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 5.83338e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 2.59622e3, delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.0481e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -78.416641, 4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadOxygenFromGaussianLog(self):
"""
Uses a Gaussian03 log file for oxygen (O2) to test that its
molecular degrees of freedom can be properly read.
"""
log = GaussianLog(os.path.join(os.path.dirname(__file__),'data','oxygen.log'))
conformer = log.loadConformer()
E0 = log.loadEnergy()
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode,IdealGasTranslation)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode,LinearRotor)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode,HarmonicOscillator)]) == 1)
self.assertTrue(len([mode for mode in conformer.modes if isinstance(mode,HinderedRotor)]) == 0)
trans = [mode for mode in conformer.modes if isinstance(mode,IdealGasTranslation)][0]
rot = [mode for mode in conformer.modes if isinstance(mode,LinearRotor)][0]
vib = [mode for mode in conformer.modes if isinstance(mode,HarmonicOscillator)][0]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 7.11169e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 7.13316e1, delta=1e-4)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.00037e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -150.3784877, 4)
self.assertEqual(conformer.spinMultiplicity, 3)
self.assertEqual(conformer.opticalIsomers, 1)