def test_get_t1_diagnostic(self):
"""
Ensure molpro can retrieve the T1 diagnostic from CCSD calculations
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'ethylene_f12_dz.out'))
t1_diagnostic = log.get_T1_diagnostic()
self.assertAlmostEqual(t1_diagnostic, 0.01152184)
def testLoadHOSIFromMolpro_log(self):
"""
Uses a molpro log file for HOSI to test that its
molecular degrees of freedom can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'HOSI_ccsd_t1.out'))
conformer, unscaled_frequencies = log.loadConformer(spinMultiplicity=1)
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]
t_list = numpy.array([298.15], numpy.float64)
self.assertAlmostEqual(trans.getPartitionFunction(t_list), 9.175364e7, delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(t_list), 1.00005557e5, delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(t_list), 1.9734989e0, delta=1e-4)
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -768.275662, 4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)
def test_load_non_f12_e0(self):
"""
Load E0 for CCSD(T) (without F12) from a molpro output file
"""
molpro_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'TS_CCSD(T)_no_F12_sp_molpro.out'))
e0 = molpro_log.loadEnergy()
self.assertAlmostEqual(e0, -301585968.58196217, places=7)
def test_load_hosi_from_molpro_log(self):
"""
Uses a molpro log file for HOSI to test that its
molecular degrees of freedom can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'HOSI_ccsd_t1.out'))
conformer, unscaled_frequencies = log.load_conformer(spin_multiplicity=1)
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), 9.175364e7, delta=1e1)
self.assertAlmostEqual(rot.get_partition_function(t_list), 1.00005557e5, delta=1e-2)
self.assertAlmostEqual(vib.get_partition_function(t_list), 1.9734989e0, delta=1e-4)
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -768.275662, 4)
self.assertEqual(conformer.spin_multiplicity, 1)
self.assertEqual(conformer.optical_isomers, 1)
def test_load_negative_frequency(self):
"""
Load an imaginary frequency from a molpro output file
"""
freq_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'molpro_TS.out'))
imaginary_freq = freq_log.load_negative_frequency()
self.assertEqual(imaginary_freq, -1997.98)
def test_load_non_f12_e0(self):
"""
Load E0 for CCSD(T) (without F12) from a molpro output file
"""
molpro_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'TS_CCSD(T)_no_F12_sp_molpro.out'))
e0 = molpro_log.load_energy()
self.assertAlmostEqual(e0, -301585968.58196217, places=7)
def testLoadRadFromMolproLog_F12(self):
"""
Uses a Molpro log file for OH (C2H4) to test that radical
energy can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'OH_f12.out'))
e0 = log.loadEnergy()
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -75.663696424380, 5)
def testLoadQzFromMolproLog_F12(self):
"""
Uses a Molpro log file for ethylene_qz (C2H4) to test that F12b
energy can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'ethylene_f12_qz.out'))
e0 = log.loadEnergy()
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -78.472682755635, 5)
def test_load_mrci_e0(self):
"""
Load the MRCI and MRCI+Davidson energies from a molpro output file
"""
mrci_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'molpro_mrci.out'))
mrciq_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'molpro_mrci+q.out'))
mrci_e0 = mrci_log.loadEnergy()
mrciq_e0 = mrciq_log.loadEnergy()
self.assertAlmostEqual(mrci_e0, -293217091.0381712, places=7)
self.assertAlmostEqual(mrciq_e0, -293284017.3925107, places=7)
def test_load_rad_from_molpro_log_f12(self):
"""
Uses a Molpro log file for OH (C2H4) to test that radical
energy can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'OH_f12.out'))
e0 = log.load_energy()
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -75.663696424380, 5)
def test_load_qz_from_molpro_log_f12(self):
"""
Uses a Molpro log file for ethylene_qz (C2H4) to test that F12b
energy can be properly read.
"""
log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'ethylene_f12_qz.out'))
e0 = log.load_energy()
self.assertAlmostEqual(e0 / constants.Na / constants.E_h, -78.472682755635, 5)
def testLoadDzFromMolproLog_F12(self):
"""
Uses a Molpro log file for ethylene_dz (C2H4) to test that F12a
energy can be properly read.
"""
log=MolproLog(os.path.join(os.path.dirname(__file__),'data','ethylene_f12_dz.out'))
E0=log.loadEnergy()
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -78.474353559604, 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_load_mrci_e0(self):
"""
Load the MRCI and MRCI+Davidson energies from a molpro output file
"""
mrci_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'molpro_mrci.out'))
mrciq_log = MolproLog(os.path.join(os.path.dirname(__file__), 'data', 'molpro_mrci+q.out'))
mrci_e0 = mrci_log.load_energy()
mrciq_e0 = mrciq_log.load_energy()
self.assertAlmostEqual(mrci_e0, -293217091.0381712, places=7)
self.assertAlmostEqual(mrciq_e0, -293284017.3925107, places=7)
def testLoadHOSIFromMolpro_log(self):
"""
Uses a molpro log file for HOSI to test that its
molecular degrees of freedom can be properly read.
"""
log = MolproLog(
os.path.join(os.path.dirname(__file__), 'data',
'HOSI_ccsd_t1.out'))
conformer = log.loadConformer(symfromlog=True, spinMultiplicity=1)
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),
9.175364e7,
delta=1e1)
self.assertAlmostEqual(rot.getPartitionFunction(Tlist),
1.00005557e5,
delta=1e-2)
self.assertAlmostEqual(vib.getPartitionFunction(Tlist),
1.9734989e0,
delta=1e-4)
self.assertAlmostEqual(E0 / constants.Na / constants.E_h, -768.275662,
4)
self.assertEqual(conformer.spinMultiplicity, 1)
self.assertEqual(conformer.opticalIsomers, 1)