def test_load_ethylene_from_gaussian_log_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, unscaled_frequencies = log.load_conformer()
e0 = log.load_energy()
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]
t_list = np.array([298.15], np.float64)
self.assertAlmostEqual(trans.get_partition_function(t_list),
5.83338e6,
delta=1e1)
self.assertAlmostEqual(rot.get_partition_function(t_list),
2.53410e3,
delta=1e-2)
self.assertAlmostEqual(vib.get_partition_function(t_list),
1.0304e0,
delta=1e-4)
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -78.562189,
4)
self.assertEqual(conformer.spin_multiplicity, 1)
self.assertEqual(conformer.optical_isomers, 1)
def test_load_oxygen_from_gaussian_log(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, unscaled_frequencies = log.load_conformer()
e0 = log.load_energy()
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]
t_list = np.array([298.15], np.float64)
self.assertAlmostEqual(trans.get_partition_function(t_list),
7.11169e6,
delta=1e1)
self.assertAlmostEqual(rot.get_partition_function(t_list),
7.13316e1,
delta=1e-4)
self.assertAlmostEqual(vib.get_partition_function(t_list),
1.00037e0,
delta=1e-4)
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -150.3784877,
4)
self.assertEqual(conformer.spin_multiplicity, 3)
self.assertEqual(conformer.optical_isomers, 1)
def setUp(cls):
"""A method that is run before each unit test in this class"""
spc = Species().from_smiles('CCO')
log = GaussianLog(
os.path.join(os.path.dirname(__file__), 'data', 'ethylene.log'))
spc.conformer = log.load_conformer()[0]
coords, numbers, masses = log.load_geometry()
spc.conformer.coordinates = coords, 'angstroms'
spc.conformer.number = numbers
spc.conformer.mass = masses, 'amu'
cls.thermo_job = ThermoJob(species=spc, thermo_class='NASA')
def test_get_str_xyz(self):
"""Test generating an xyz string from the species.conformer object"""
log = GaussianLog(
os.path.join(os.path.dirname(__file__), 'data', 'ethylene_G3.log'))
conformer = log.load_conformer()[0]
coords, number, mass = log.load_geometry()
conformer.coordinates, conformer.number, conformer.mass = (
coords, "angstroms"), number, (mass, "amu")
spc1 = Species(smiles='C=C')
spc1.conformer = conformer
xyz_str = get_str_xyz(spc1)
expected_xyz_str = """C 0.00545100 0.00000000 0.00339700
H 0.00118700 0.00000000 1.08823200
H 0.97742900 0.00000000 -0.47841600
C -1.12745800 0.00000000 -0.70256500
H -1.12319800 0.00000000 -1.78740100
H -2.09943900 0.00000000 -0.22075700"""
self.assertEqual(xyz_str, expected_xyz_str)
def test_load_symmetry_and_optics(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'))
optical, symmetry, _ = log.get_symmetry_properties()
self.assertEqual(optical, 1)
self.assertEqual(symmetry, 2)
conf = log.load_conformer()[0]
self.assertEqual(conf.optical_isomers, 1)
found_rotor = False
for mode in conf.modes:
if isinstance(mode, LinearRotor):
self.assertEqual(mode.symmetry, 2)
found_rotor = True
self.assertTrue(found_rotor)