def loadScanEnergies(self):
"""
Extract the optimized energies in J/mol from a QChem log file, e.g. the
result of a QChem "PES Scan" quantum chemistry calculation.
"""
Vlist = []
angle = []
read = False
with open(self.path, 'r') as f:
for line in f:
if '-----------------' in line:
read = False
if read:
values = [float(item) for item in line.split()]
angle.append(values[0])
Vlist.append(values[1])
if 'Summary of potential scan:' in line:
logging.info('found a sucessfully completed QChem Job')
read = True
elif 'SCF failed to converge' in line:
raise InputError('QChem Job did not sucessfully complete: SCF failed to converge')
logging.info(' Assuming {0} is the output from a QChem PES scan...'.format(os.path.basename(self.path)))
Vlist = numpy.array(Vlist, numpy.float64)
# check to see if the scanlog indicates that one of your reacting species may not be the lowest energy conformer
check_conformer_energy(Vlist, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to J/mol
Vlist -= numpy.min(Vlist)
Vlist *= constants.E_h * constants.Na
angle = numpy.arange(0.0, 2*math.pi+0.00001, 2*math.pi/(len(Vlist)-1), numpy.float64)
return Vlist, angle
def load_scan_energies(self):
"""
Extract the optimized energies in J/mol from a log file, e.g. the
result of a Gaussian "Scan" quantum chemistry calculation.
"""
opt_freq = False
rigid_scan = False
vlist = [] # The array of potentials at each scan angle
# Parse the Gaussian log file, extracting the energies of each
# optimized conformer in the scan
with open(self.path, 'r') as f:
line = f.readline()
while line != '':
# If the job contains a "freq" then we want to ignore the last energy
if ' Freq' in line and ' Geom=' in line:
opt_freq = True
# if # scan is keyword instead of # opt, then this is a rigid scan job
# and parsing the energies is done a little differently
if '# scan' in line:
rigid_scan = True
# The lines containing "SCF Done" give the energy at each
# iteration (even the intermediate ones)
if 'SCF Done:' in line:
energy = float(line.split()[4])
# rigid scans will only not optimize, so just append every time it finds an energy.
if rigid_scan:
vlist.append(energy)
# We want to keep the values of energy that come most recently before
# the line containing "Optimization completed", since it refers
# to the optimized geometry
if 'Optimization completed' in line:
vlist.append(energy)
line = f.readline()
# give warning in case this assumption is not true
if rigid_scan:
print(' Assuming', os.path.basename(self.path), 'is the output from a rigid scan...')
vlist = np.array(vlist, np.float64)
# check to see if the scanlog indicates that a one of your reacting species may not be
# the lowest energy conformer
check_conformer_energy(vlist, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to J/mol
vlist -= np.min(vlist)
vlist *= constants.E_h * constants.Na
if opt_freq:
vlist = vlist[:-1]
# Determine the set of dihedral angles corresponding to the loaded energies
# This assumes that you start at 0.0, finish at 360.0, and take
# constant step sizes in between
angle = np.arange(0.0, 2 * math.pi + 0.00001, 2 * math.pi / (len(vlist) - 1), np.float64)
return vlist, angle
def load_scan_energies(self):
"""
Extract the optimized energies in J/mol from a TeraChem torsional scan log file.
"""
v_list = list()
with open(self.path, 'r') as f:
lines = f.readlines()
v_index, expected_num_of_points = 0, 0
for line in lines:
if 'Scan Cycle' in line:
# example: '-=#=- Scan Cycle 5/37 -=#=-'
v_index += 1
if not expected_num_of_points:
expected_num_of_points = int(
line.split()[3].split('/')[1])
if 'Optimized Energy:' in line:
# example: '-=#=- Optimized Energy: -155.0315243910 a.u.'
v = float(line.split()[3])
if len(v_list) == v_index - 1:
# append this point, it is in order
v_list.append(v)
elif len(v_list) < v_index - 1:
# seems like points in this scan are missing... add None's instead,
# later they'll be removed along with the corresponding angles
v_list.extend([None] * (v_index - 1 - len(v_list)))
else:
# we added more points that we should have, something is wrong with the log file or this method
raise LogError(
f'Could not parse scan energies from {self.path}')
logging.info(
' Assuming {0} is the output from a TeraChem PES scan...'.format(
os.path.basename(self.path)))
v_list = np.array(v_list, np.float64)
# check to see if the scanlog indicates that one of the reacting species may not be the lowest energy conformer
check_conformer_energy(v_list, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to J/mol
v_list -= np.min(v_list)
v_list *= constants.E_h * constants.Na
angles = np.arange(0.0, 2 * math.pi + 0.00001,
2 * math.pi / (len(v_list) - 1), np.float64)
# remove None's:
indices_to_pop = [
v_list.index[entry] for entry in v_list if entry is None
]
for i in reversed(indices_to_pop):
v_list.pop(i)
angles.pop(i)
if v_index != expected_num_of_points:
raise LogError(
f'Expected to find {expected_num_of_points} scan points in TeraChem scan log file '
f'{self.path}, but found: {v_index}')
return v_list, angles
def loadScanEnergies(self):
"""
Extract the optimized energies in J/mol from a Qchem log file, e.g. the
result of a Qchem "PES Scan" quantum chemistry calculation.
"""
Vlist = []
angle = []
f = open(self.path, 'r')
line = f.readline()
while line != '':
if 'Summary of potential scan:' in line:
line = f.readline()
print 'found a sucessfully completed Qchem Job'
while '-----------------' not in line:
# print len(line.split())
# Vlist.append(float(line.split()[1]))
values = [float(item) for item in line.split()]
angle.append(values[0])
Vlist.append(values[1])
# Read the next line in the file
line = f.readline()
line = f.readline()
if 'SCF failed to converge' in line:
print 'Qchem Job did not sucessfully complete: SCF failed to converge'
break
# Close file when finished
print ' Assuming', os.path.basename(self.path), 'is the output from a Qchem PES scan...'
f.close()
Vlist = numpy.array(Vlist, numpy.float64)
# check to see if the scanlog indicates that one of your reacting species may not be the lowest energy conformer
check_conformer_energy(Vlist, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to J/mol
Vlist -= numpy.min(Vlist)
Vlist *= constants.E_h * constants.Na
angle = numpy.arange(0.0, 2*math.pi+0.00001, 2*math.pi/(len(Vlist)-1), numpy.float64)
return Vlist, angle
