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(self.data_path, '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 test_check_for_errors(self):
"""
Uses a QChem log file that reached to maximum number of optimization cycles
to test if errors are properly parsed.
"""
with self.assertRaises(LogError):
QChemLog(os.path.join(self.data_path, 'formyl_azide.out'))
def test_energy_from_qchem_log(self):
"""
Uses QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(self.data_path, 'npropyl.out'))
self.assertAlmostEqual(log.load_energy(),
-310896203.5432524,
delta=1e-7)
log = QChemLog(os.path.join(self.data_path, 'co.out'))
self.assertAlmostEqual(log.load_energy(),
-297402545.0217114,
delta=1e-7)
log = QChemLog(os.path.join(self.data_path, 'CH4_sp.out'))
self.assertAlmostEqual(log.load_energy(),
-106356735.53661588,
delta=1e-7)
def test_zero_point_energy_from_qchem_log(self):
"""
Uses QChem log files to test that
zero point energies can be properly read.
"""
log = QChemLog(os.path.join(self.data_path, 'npropyl.out'))
self.assertAlmostEqual(log.load_zero_point_energy(),
228785.304,
delta=1e-3)
log = QChemLog(os.path.join(self.data_path, 'co.out'))
self.assertAlmostEqual(log.load_zero_point_energy(),
13476.664,
delta=1e-3)
log = QChemLog(os.path.join(self.data_path, 'formyl_azide.out'),
check_for_errors=False)
self.assertAlmostEqual(log.load_zero_point_energy(),
83014.744,
delta=1e-3)
def test_number_of_atoms_from_qchem_log(self):
"""
Uses QChem log files to test that
number of atoms can be properly read.
"""
log = QChemLog(os.path.join(self.data_path, 'npropyl.out'))
self.assertEqual(log.get_number_of_atoms(), 10)
log = QChemLog(os.path.join(self.data_path, 'co.out'))
self.assertEqual(log.get_number_of_atoms(), 2)
def test_spin_multiplicity_from_qchem_log(self):
"""
Uses QChem log files to test that
molecular degrees of freedom can be properly read.
"""
log = QChemLog(os.path.join(self.data_path, 'npropyl.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(conformer.spin_multiplicity, 2)
log = QChemLog(os.path.join(self.data_path, 'co.out'))
conformer, unscaled_frequencies = log.load_conformer()
self.assertEqual(conformer.spin_multiplicity, 1)
def test_load_vibrations_from_qchem_log(self):
"""
Uses QChem log files to test that
molecular energies can be properly read.
"""
log = QChemLog(os.path.join(self.data_path, '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(self.data_path, '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 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)
