def testDetermineQMSoftware(self):
"""
Ensures that determine_qm_software returns a GaussianLog object
"""
log = determine_qm_software(
os.path.join(os.path.dirname(__file__), 'data', 'oxygen.log'))
self.assertIsInstance(log, GaussianLog)
def parse_e_elect(path, zpe_scale_factor=1.):
"""
Parse the zero K energy, E0, from an sp job output file.
"""
if not os.path.isfile(path):
raise InputError('Could not find file {0}'.format(path))
log = determine_qm_software(fullpath=path)
try:
e_elect = log.loadEnergy(zpe_scale_factor) * 0.001 # convert to kJ/mol
except Exception:
logger.warning('Could not read e_elect from {0}'.format(path))
e_elect = None
return e_elect
def get_zpe(path):
"""
Determine the calculated ZPE from a frequency output file"
Args:
path (str): The path to a frequency calculation output file.
Returns:
float: The calculated zero point energy in J/mol.
"""
statmech_log = determine_qm_software(path)
zpe = statmech_log.loadZeroPointEnergy()
return zpe
def parse_e0(path):
"""
Parse the zero K energy, E0, from an sp job output file
"""
if not os.path.isfile(path):
raise InputError('Could not find file {0}'.format(path))
log = determine_qm_software(fullpath=path)
try:
e0 = log.loadEnergy(frequencyScaleFactor=1.) * 0.001 # convert to kJ/mol
except Exception:
logging.warning('Could not read E0 from {0}'.format(path))
e0 = None
return e0
def parse_dipole_moment(path):
"""
Parse the dipole moment in Debye from an opt job output file.
"""
lines = _get_lines_from_file(path)
log = determine_qm_software(path)
dipole_moment = None
if isinstance(log, GaussianLog):
# example:
# Dipole moment (field-independent basis, Debye):
# X= -0.0000 Y= -0.0000 Z= -1.8320 Tot= 1.8320
read = False
for line in lines:
if 'dipole moment' in line.lower() and 'debye' in line.lower():
read = True
elif read:
dipole_moment = float(line.split()[-1])
read = False
elif isinstance(log, QChemLog):
# example:
# Dipole Moment (Debye)
# X 0.0000 Y 0.0000 Z 2.0726
# Tot 2.0726
skip = False
read = False
for line in lines:
if 'dipole moment' in line.lower() and 'debye' in line.lower():
skip = True
elif skip:
skip = False
read = True
elif read:
dipole_moment = float(line.split()[-1])
read = False
elif isinstance(log, MolproLog):
# example:
# Dipole moment /Debye 2.96069859 0.00000000 0.00000000
for line in lines:
if 'dipole moment' in line.lower() and '/debye' in line.lower():
splits = line.split()
dm_x, dm_y, dm_z = float(splits[-3]), float(splits[-2]), float(
splits[-1])
dipole_moment = (dm_x**2 + dm_y**2 + dm_z**2)**0.5
else:
raise ParserError(
'Currently dipole moments can only be parsed from either Gaussian, Molpro, or QChem '
'optimization output files')
if dipole_moment is None:
raise ParserError('Could not parse the dipole moment')
return dipole_moment
def parse_xyz_from_file(path):
"""
Parse xyz coordinated from:
.xyz - XYZ file
.gjf - Gaussian input file
.out or .log - ESS output file (Gaussian, QChem, Molpro)
other - Molpro or QChem input file
"""
lines = _get_lines_from_file(path)
file_extension = os.path.splitext(path)[1]
xyz = None
relevant_lines = list()
if file_extension == '.xyz':
relevant_lines = lines[2:]
elif file_extension == '.gjf':
start_parsing = False
for line in lines:
if start_parsing and line and line != '\n' and line != '\r\n':
relevant_lines.append(line)
elif start_parsing:
break
else:
splits = line.split()
if len(splits) == 2 and all([s.isdigit() for s in splits]):
start_parsing = True
elif 'out' in file_extension or 'log' in file_extension:
log = determine_qm_software(fullpath=path)
coords, number, _ = log.loadGeometry()
xyz = get_xyz_string(coords=coords, numbers=number)
else:
record = False
for line in lines:
if '$end' in line or '}' in line:
break
if record and len(line.split()) == 4:
relevant_lines.append(line)
elif '$molecule' in line:
record = True
elif 'geometry={' in line:
record = True
if not relevant_lines:
raise ParserError(
'Could not parse xyz coordinates from file {0}'.format(path))
if xyz is None and relevant_lines:
xyz = ''.join([line for line in relevant_lines if line])
return standardize_xyz_string(xyz)
def test_determine_qm_software(self):
"""
Ensures that determine_qm_software returns a GaussianLog object
"""
log = determine_qm_software(os.path.join(self.data_path, 'oxygen.log'))
self.assertIsInstance(log, GaussianLog)
def testDetermineQMSoftware(self):
"""
Ensures that determine_qm_software returns a GaussianLog object
"""
log = determine_qm_software(os.path.join(os.path.dirname(__file__),'data','oxygen.log'))
self.assertIsInstance(log,GaussianLog)
