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)