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 testLoadEthyleneFromGaussianLog_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.loadConformer()
E0 = log.loadEnergy()
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]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist),
5.83338e6,
delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist),
2.53410e3,
delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist),
1.0304e0,
delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -78.562189,
4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadOxygenFromGaussianLog(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 = log.loadConformer(symfromlog=True)
E0 = log.loadEnergy()
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]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 7.11169e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 7.13316e1, delta=1e-4)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.00037e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -150.3784877, 4)
self.assertEqual(conformer.spinMultiplicity, 3)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadOxygenFromGaussianLog(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.loadConformer()
E0 = log.loadEnergy()
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]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 7.11169e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 7.13316e1, delta=1e-4)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.00037e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -150.3784877, 4)
self.assertEqual(conformer.spinMultiplicity, 3)
self.assertEqual(conformer.opticalIsomers, 1)
def testLoadEthyleneFromGaussianLog_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(os.path.dirname(__file__),'data','ethylene.log'))
conformer, unscaled_frequencies = log.loadConformer()
E0 = log.loadEnergy()
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]
Tlist = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(Tlist), 5.83338e6, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist), 2.59622e3, delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist), 1.0481e0, delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -78.467452, 4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)
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(os.path.dirname(__file__), 'data', '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(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().fromSMILES('CCO')
log = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'ethylene.log'))
spc.conformer = log.loadConformer()[0]
coords, numbers, masses = log.loadGeometry()
spc.conformer.coordinates = coords, 'angstroms'
spc.conformer.number = numbers
spc.conformer.mass = masses, 'amu'
cls.thermo_job = ThermoJob(species=spc, thermoClass='NASA')
def determine_qm_software(fullpath):
"""
Given a path to the log file of a QM software, determine whether it is Gaussian, Molpro, or QChem
"""
with open(fullpath, 'r') as f:
line = f.readline()
software_log = None
while line != '':
if 'gaussian' in line.lower():
f.close()
software_log = GaussianLog(fullpath)
break
elif 'qchem' in line.lower():
f.close()
software_log = QChemLog(fullpath)
break
elif 'molpro' in line.lower():
f.close()
software_log = MolproLog(fullpath)
break
line = f.readline()
else:
raise InputError(
'File at {0} could not be identified as a Gaussian, '
'QChem or Molpro log file.'.format(fullpath))
return software_log
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 testLoadSymmetryAndOptics(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_optical_isomers_and_symmetry_number()
self.assertEqual(optical,1)
self.assertEqual(symmetry,2)
conf = log.loadConformer()[0]
self.assertEqual(conf.opticalIsomers, 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 testLoadSymmetryAndOptics(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_optical_isomers_and_symmetry_number()
self.assertEqual(optical, 1)
self.assertEqual(symmetry, 2)
conf = log.loadConformer()[0]
self.assertEqual(conf.opticalIsomers, 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)