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 classify_gauss_outputs(gauss_files, only_converged=False):
"""
Classify the gaussian output files into single point ('sp'), frequency
('freq') and scan ('scan')
Args:
gauss_files (list): A list of paths to gaussian output file
Returns:
classified (dict): A dict indicates the files and some properties
"""
classified = {'sp': [], 'freq': [], 'scan': []}
for gauss_file in gauss_files:
options = parse_gauss_options(gauss_file)
job_type = get_gauss_job_type(options)
converged = get_gauss_termination_status(gauss_file)
if job_type in ['opt', 'opt+freq', 'composite']:
if not only_converged or converged:
log = GaussianLog(gauss_file)
energy = log.load_energy() / Na / E_h
ts = 'TS' if 'opt' in options.keys() and 'ts' in options['opt'] else 'nonTS'
classified['sp'].append((gauss_file, converged,
options['method'][0], energy, ts))
if job_type in ['freq', 'opt+freq', 'composite']:
if not only_converged or converged:
freqs = get_gauss_frequencies(gauss_file)
classified['freq'].append((gauss_file, converged,
options['method'][0], freqs))
if job_type == 'scan':
if not only_converged or converged:
scan_info = parse_gauss_scan_info(gauss_file)
classified['scan'].append((gauss_file, converged,
options['method'][0], scan_info))
return classified
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)