output = self._load_scan_specs('S', get_after_letter_spec=True)
return int(output[0][0])
def load_negative_frequency(self):
"""
Return the negative frequency from a transition state frequency
calculation in cm^-1.
"""
frequency = None
frequencies = []
with open(self.path, 'r') as f:
line = f.readline()
while line != '':
# Read vibrational frequencies
if 'Frequencies --' in line:
frequencies.extend(line.split()[2:])
line = f.readline()
frequencies = [float(freq) for freq in frequencies]
frequencies.sort()
try:
frequency = [freq for freq in frequencies if freq < 0][0]
except IndexError:
raise LogError(
f'Unable to find imaginary frequency in Gaussian output file {self.path}'
)
return frequency
register_ess_adapter("GaussianLog", GaussianLog)
while line != '':
# Read vibrational modes
if 'Mode Eigenvalue(AU) Frequency(cm-1)' in line:
line = f.readline()
# example:
# 'Mode Eigenvalue(AU) Frequency(cm-1) Intensity(km/mol) Vib.Temp(K) ZPE(AU) ...'
# ' 1 0.0331810528 170.5666870932i 52.2294230772 245.3982965841 0.0003885795 ...'
frequency = -1 * float(line.split()[2][:-1]) # remove 'i'
break
f.readline()
if frequency is None:
raise LogError(
f'Unable to find imaginary frequency in TeraChem output file {self.path}.'
)
return frequency
def load_scan_pivot_atoms(self):
"""Not implemented for TeraChem"""
raise NotImplementedError(
'The load_scan_pivot_atoms method is not implemented for TeraChem Logs'
)
def load_scan_frozen_atoms(self):
"""Not implemented for TeraChem"""
raise NotImplementedError(
'The load_scan_frozen_atoms method is not implemented for TeraChem Logs'
)
register_ess_adapter("TeraChemLog", TeraChemLog)
angle = np.arange(0.0, 2 * math.pi + 0.00001, 2 * math.pi / (len(v_list) - 1), np.float64)
return v_list, angle
def load_negative_frequency(self):
"""
Return the imaginary frequency from a transition state frequency
calculation in cm^-1.
"""
frequency = 0
with open(self.path, 'r') as f:
for line in f:
# Read imaginary frequency
if ' Frequency:' in line:
frequency = float((line.split()[1]))
break
# Make sure the frequency is imaginary:
if frequency < 0:
return frequency
else:
raise LogError('Unable to find imaginary frequency in QChem output file {0}.'.format(self.path))
def load_scan_pivot_atoms(self):
"""Not implemented for QChem"""
raise NotImplementedError('The load_scan_pivot_atoms method is not implemented for QChem Logs')
def load_scan_frozen_atoms(self):
"""Not implemented for QChem"""
raise NotImplementedError('The load_scan_frozen_atoms method is not implemented for QChem Logs')
register_ess_adapter("QChemLog", QChemLog)
def get_D1_diagnostic(self):
"""
Returns the D1 diagnostic from output log.
If multiple occurrences exist, returns the last occurrence
"""
with open(self.path) as f:
log = f.readlines()
for line in reversed(log):
if 'D1 diagnostic: ' in line:
items = line.split()
return float(items[-1])
raise LogError(
'Unable to find D1 diagnostic in energy file: {0}'.format(
self.path))
def load_scan_pivot_atoms(self):
"""Not implemented for Molpro"""
raise NotImplementedError(
'The load_scan_pivot_atoms method is not implemented for Molpro Logs'
)
def load_scan_frozen_atoms(self):
"""Not implemented for Molpro"""
raise NotImplementedError(
'The load_scan_frozen_atoms method is not implemented for Molpro Logs'
)
register_ess_adapter("MolproLog", MolproLog)
def load_scan_pivot_atoms(self):
"""Not implemented for Orca"""
raise NotImplementedError(
'The load_scan_pivot_atoms method is not implemented for Orca Logs'
)
def load_scan_frozen_atoms(self):
"""Not implemented for Orca"""
raise NotImplementedError(
'The load_scan_frozen_atoms method is not implemented for Orca Logs'
)
def get_T1_diagnostic(self):
"""
Returns the T1 diagnostic from output log.
If multiple occurrences exist, returns the last occurrence
"""
with open(self.path) as f:
log = f.readlines()
for line in reversed(log):
if 'T1 diagnostic ' in line:
items = line.split()
return float(items[-1])
raise LogError(
'Unable to find T1 diagnostic in energy file: {}'.format(
self.path))
register_ess_adapter("OrcaLog", OrcaLog)