def test_load_co_modes_from_qchem_log(self):
"""
Uses a QChem log file for CO to test that its
molecular degrees of freedom can be properly read.
"""
log = QChemLog(
os.path.join(os.path.dirname(__file__), 'data', 'co.out'))
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, NonlinearRotor)
]) == 0)
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)
def testLoadNpropylModesFromQChemLog(self):
"""
Uses a QChem log file for npropyl to test that its
molecular modes can be properly read.
"""
log = QChemLog(
os.path.join(os.path.dirname(__file__), 'data', 'npropyl.out'))
conformer, unscaled_frequencies = log.loadConformer()
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)
def testNumberOfAtomsFromQChemLog(self):
"""
Uses a QChem log files to test that
number of atoms can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
self.assertEqual(log.getNumberOfAtoms(), 10)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
self.assertEqual(log.getNumberOfAtoms(), 2)
def testSpinMultiplicityFromQChemLog(self):
"""
Uses a QChem log file for npropyl to test that its
molecular degrees of freedom can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
conformer, unscaled_frequencies = log.loadConformer()
self.assertEqual(conformer.spinMultiplicity, 2)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
conformer, unscaled_frequencies = log.loadConformer()
self.assertEqual(conformer.spinMultiplicity, 1)
def testLoadNpropylModesFromQChemLog(self):
"""
Uses a QChem log file for npropyl to test that its
molecular modes can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
conformer, unscaled_frequencies = log.loadConformer()
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)
def testLoadVibrationsFromQChemLog(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
conformer, unscaled_frequencies = log.loadConformer()
self.assertEqual(len(conformer.modes[2]._frequencies.getValue()), 24)
self.assertEqual(conformer.modes[2]._frequencies.getValue()[5], 881.79)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
conformer, unscaled_frequencies = log.loadConformer()
self.assertEqual(len(conformer.modes[2]._frequencies.getValue()), 1)
self.assertEqual(conformer.modes[2]._frequencies.getValue(), 2253.16)
def test_energy_from_qchem_log(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'npropyl.out'))
self.assertAlmostEqual(log.load_energy(), -310896203.5432524, delta=1e-5)
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'co.out'))
self.assertAlmostEqual(log.load_energy(), -297402545.0217114, delta=1e-5)
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'CH4_sp_qchem.out'))
self.assertAlmostEqual(log.load_energy(), -106356735.53661588, delta=1e-5)
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_number_of_atoms_from_qchem_log(self):
"""
Uses a QChem log files to test that
number of atoms can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'npropyl.out'))
self.assertEqual(log.get_number_of_atoms(), 10)
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'co.out'))
self.assertEqual(log.get_number_of_atoms(), 2)
def testEnergyFromQChemLog(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
self.assertAlmostEqual(log.loadEnergy(), -310896203.5432524, 1e-5)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
self.assertAlmostEqual(log.loadEnergy(), -297402545.0217114, 1e-5)
def testEnergyFromQChemLog(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
self.assertAlmostEqual(log.loadEnergy(), -310896203.5432524, delta=1e-5)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
self.assertAlmostEqual(log.loadEnergy(), -297402545.0217114, delta=1e-5)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','CH4_sp_qchem.out'))
self.assertAlmostEqual(log.loadEnergy(), -106356735.53661588, delta=1e-5)
def test_spin_multiplicity_from_qchem_log(self):
"""
Uses a QChem log file for npropyl to test that its
molecular degrees of freedom can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'npropyl.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(conformer.spin_multiplicity, 2)
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'co.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(conformer.spin_multiplicity, 1)
def test_load_vibrations_from_qchem_log(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'npropyl.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(len(conformer.modes[2]._frequencies.value), 24)
self.assertEqual(conformer.modes[2]._frequencies.value[5], 881.79)
log = QChemLog(os.path.join(os.path.dirname(__file__), 'data', 'co.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(len(conformer.modes[2]._frequencies.value), 1)
self.assertEqual(conformer.modes[2]._frequencies.value, 2253.16)
def testLoadVibrationsFromQChemLog(self):
"""
Uses a QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','npropyl.out'))
conformer, unscaled_frequencies = log.loadConformer(symfromlog=True)
self.assertEqual(len(conformer.modes[2]._frequencies.getValue()), 24)
self.assertEqual(conformer.modes[2]._frequencies.getValue()[5], 881.79)
log = QChemLog(os.path.join(os.path.dirname(__file__),'data','co.out'))
conformer, unscaled_frequencies = log.loadConformer(symfromlog=True)
self.assertEqual(len(conformer.modes[2]._frequencies.getValue()), 1)
self.assertEqual(conformer.modes[2]._frequencies.getValue(), 2253.16)
def test_rotor_symmetry_determination(self):
"""
Test that the correct symmetry number is determined for rotor potential scans.
"""
path1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_NRotor.out')
path2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_CRotor.out')
scan_log1 = QChemLog(path1)
scan_log2 = QChemLog(path2)
v_list1, angle = scan_log1.load_scan_energies()
v_list2, angle = scan_log2.load_scan_energies()
symmetry1 = determine_rotor_symmetry(energies=v_list1, label='NCC', pivots=[])
symmetry2 = determine_rotor_symmetry(energies=v_list2, label='NCC', pivots=[])
self.assertEqual(symmetry1, 1)
self.assertEqual(symmetry2, 3)