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
checkConformerEnergy(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 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
checkConformerEnergy(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 loadScanEnergies(self):
"""
Extract the optimized energies in J/mol from a log file, e.g. the
result of a Gaussian "Scan" quantum chemistry calculation.
"""
optfreq = False
rigidScan = False
# The array of potentials at each scan angle
Vlist = []
# Parse the Gaussian log file, extracting the energies of each
# optimized conformer in the scan
f = open(self.path, 'r')
line = f.readline()
while line != '':
# If the job contains a "freq" then we want to ignore the last energy
if ' freq ' in line:
optfreq = 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:
rigidScan = True
# The lines containing "SCF Done" give the energy at each
# iteration (even the intermediate ones)
if 'SCF Done:' in line:
E = float(line.split()[4])
#rigid scans will only not optimize, so just append every time it finds an energy.
if rigidScan:
Vlist.append(E)
# We want to keep the values of E that come most recently before
# the line containing "Optimization completed", since it refers
# to the optimized geometry
if 'Optimization completed' in line:
Vlist.append(E)
line = f.readline()
# Close file when finished
f.close()
#give warning in case this assumption is not true
if rigidScan == True:
print ' Assuming', os.path.basename(
self.path), 'is the output from a rigid scan...'
Vlist = numpy.array(Vlist, numpy.float64)
# check to see if the scanlog indicates that a one of your reacting species may not be the lowest energy conformer
checkConformerEnergy(Vlist, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to kJ/mol
Vlist -= numpy.min(Vlist)
Vlist *= constants.E_h * constants.Na
if optfreq: 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 = numpy.arange(0.0, 2 * math.pi + 0.00001,
2 * math.pi / (len(Vlist) - 1), numpy.float64)
return Vlist, angle
def loadScanEnergies(self):
"""
Extract the optimized energies in J/mol from a log file, e.g. the
result of a Gaussian "Scan" quantum chemistry calculation.
"""
optfreq = False
rigidScan=False
# The array of potentials at each scan angle
Vlist = []
# Parse the Gaussian log file, extracting the energies of each
# optimized conformer in the scan
f = open(self.path, 'r')
line = f.readline()
while line != '':
# If the job contains a "freq" then we want to ignore the last energy
if ' freq ' in line:
optfreq = 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:
rigidScan=True
# The lines containing "SCF Done" give the energy at each
# iteration (even the intermediate ones)
if 'SCF Done:' in line:
E = float(line.split()[4])
#rigid scans will only not optimize, so just append every time it finds an energy.
if rigidScan:
Vlist.append(E)
# We want to keep the values of E that come most recently before
# the line containing "Optimization completed", since it refers
# to the optimized geometry
if 'Optimization completed' in line:
Vlist.append(E)
line = f.readline()
# Close file when finished
f.close()
#give warning in case this assumption is not true
if rigidScan==True:
print ' Assuming', os.path.basename(self.path), 'is the output from a rigid scan...'
Vlist = numpy.array(Vlist, numpy.float64)
# check to see if the scanlog indicates that a one of your reacting species may not be the lowest energy conformer
checkConformerEnergy(Vlist, self.path)
# Adjust energies to be relative to minimum energy conformer
# Also convert units from Hartree/particle to kJ/mol
Vlist -= numpy.min(Vlist)
Vlist *= constants.E_h * constants.Na
if optfreq: 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 = numpy.arange(0.0, 2*math.pi+0.00001, 2*math.pi/(len(Vlist)-1), numpy.float64)
return Vlist, angle
