def test_load_number_scans(self):
"""
Ensures proper scan angle found in Gaussian scan job
"""
log = GaussianLog(
os.path.join(self.data_path, 'isobutanolQOOH_scan.log'))
self.assertAlmostEqual(log._load_number_scans(), 36)
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_load_scan_with_freq(self):
"""
Ensures that the length of enegies with hr scans and freq calc is correct
"""
log = GaussianLog(os.path.join(self.data_path, 'hr_scan_with_freq.log'))
self.assertAlmostEqual(log._load_number_scans(), 36)
self.assertAlmostEqual(log._load_scan_angle(), 10.0)
vlist, _ = log.load_scan_energies()
self.assertEqual(len(vlist), 37)
def test_gaussian_log_error_termination(self):
"""
Ensures that error termination gaussian log file raises an logError
"""
file_path = os.path.join(self.data_path, 'error_termination.out')
log = GaussianLog(file_path)
with self.assertRaises(LogError) as log_error:
log.load_conformer()
self.assertTrue(f'The Gaussian job in {file_path} did not converge.' in str(log_error.exception))
def test_check_for_errors(self):
"""
Uses Gaussian log files that had various errors
to test if errors are properly parsed.
"""
with self.assertRaises(LogError):
GaussianLog(os.path.join(self.data_path, 'l913.out'))
with self.assertRaises(LogError):
GaussianLog(os.path.join(self.data_path, 'l9999.out'))
with self.assertRaises(LogError):
GaussianLog(os.path.join(self.data_path, 'error_termination.out'))
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', 'gaussian',
'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(self.data_path, 'gaussian', '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(self.data_path, '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)
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)