def test_load_ethylene_from_gaussian_log_cbsqb3(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(self.data_path, 'ethylene.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), 2.59622e3, delta=1e-2)
self.assertAlmostEqual(vib.get_partition_function(t_list), 1.0481e0, delta=1e-4)
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -78.467452, 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(self.data_path, '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 test_gaussian_energies(self):
"""
test parsing double hydride, MP2, CCSD, CCSD(T) form Gaussian log
"""
log_doublehybrid = GaussianLog(os.path.join(self.data_path, 'B2PLYP.LOG'))
log_mp2 = GaussianLog(os.path.join(self.data_path, 'UMP2_C_ATOM.LOG'))
log_ccsd = GaussianLog(os.path.join(self.data_path, 'UCCSD_C_ATOM.LOG'))
log_ccsdt = GaussianLog(os.path.join(self.data_path, 'UCCSDT_C_ATOM.LOG'))
log_qb3 = GaussianLog(os.path.join(os.path.dirname(os.path.dirname(__file__)),
'../examples/arkane/species/C2H5/', 'ethyl_cbsqb3.log'))
self.assertAlmostEqual(log_doublehybrid.load_energy() / constants.Na / constants.E_h, -0.40217794572194e+02,
delta=1e-6)
self.assertAlmostEqual(log_mp2.load_energy() / constants.Na / constants.E_h, -0.37504683723025e+02,
delta=1e-6)
self.assertAlmostEqual(log_ccsd.load_energy() / constants.Na / constants.E_h, -37.517151426,
delta=1e-6)
self.assertAlmostEqual(log_ccsdt.load_energy() / constants.Na / constants.E_h, -0.37517454469e+02,
delta=1e-6)
self.assertAlmostEqual(log_qb3.load_energy() / constants.Na / constants.E_h, -79.029798,
delta=1e-6)
