def characteriseTSExt(self, mol, low, path, QTS3):
os.chdir((self.workingDir))
# Higher level optimisation via some external program
if low:
print("looking for TS at lower level")
mol = tl.setCalc(mol, self.lowString, self.lowMeth + 'TS',
self.lowLev)
else:
mol = tl.setCalc(mol, self.highString, self.highMeth + 'TS',
self.highLev)
try:
mol.get_forces()
except:
pass
if not low and self.highMeth == "gauss":
mol, imaginaryFreq, TSFreqs, zpe, rmol, pmol = tl.getGausTSOut(
self.workingDir + '/Raw/calcHigh' + self.procNum, path,
self.highLev, self.CombReac, self.CombProd, mol,
self.is_bimol_reac, QTS3)
os.chdir((self.workingDir))
else:
print("getting TS geom")
if low:
mol = tl.getOptGeom(
self.workingDir + '/Raw/' + 'calcLow' + self.procNum + '/',
'none', self.Reac, self.lowMeth)
else:
mol = tl.getOptGeom(
self.workingDir + '/Raw/' + 'calcLow' + self.procNum + '/',
'none', self.Reac, self.lowMeth)
# Then calculate frequencies
os.chdir((self.workingDir + '/Raw/' + self.procNum))
print("getting TS freqs")
if low:
mol = tl.setCalc(mol, self.lowString, self.lowMeth + 'Freq',
self.lowLev)
else:
mol = tl.setCalc(mol, self.highString, self.highMeth + 'Freq',
self.highLev)
try:
mol.get_forces()
except:
pass
print("reading TS freqs")
if low:
try:
imaginaryFreq, TSFreqs, zpe, rmol, pmol = tl.getTSFreqs(
self.workingDir + '/Raw/' + self.procNum +
'/Raw/calcLow' + self.procNum,
path + '/TSPreDirectImag', self.lowMeth, self.TS)
except:
os.chdir((self.workingDir))
else:
try:
imaginaryFreq, TSFreqs, zpe, rmol, pmol = tl.getTSFreqs(
self.workingDir + '/Raw/' + self.procNum +
'/Raw/calcHigh' + self.procNum, path + '/TSDirectImag',
self.highMeth, self.TS)
except:
os.chdir((self.workingDir))
os.chdir((self.workingDir))
# Finally get single point energy
mol = tl.setCalc(mol, self.singleString, self.singleMeth,
self.singleLev)
print("Getting single point energy for reaction" + str(self.ReacName) +
"_" + str(self.ProdName) + " TS = " +
str(mol.get_potential_energy()) + "zpe = " + str(zpe) +
"reactant energy = " + str(self.reactantEnergy))
energy = mol.get_potential_energy() + zpe
return TSFreqs, imaginaryFreq, zpe, energy, mol, rmol, pmol
def characteriseMinExt(self, mol, high):
# Low level optimisation with BFGS
os.chdir((self.workingDir))
mol = tl.setCalc(mol, self.lowString, self.lowMeth, self.lowLev)
min = BFGS(mol)
try:
min.run(fmax=0.1, steps=100)
except:
min.run(fmax=0.1, steps=100)
if high:
if self.highMeth == "gauss":
mol, freqs, zpe = tl.getGausOut(
self.workingDir + '/Raw/calcHigh' + self.procNum,
self.highLev, mol)
os.chdir((self.workingDir))
else:
# Higher level optimisation via some external program
mol = tl.setCalc(mol, self.highString, self.highMeth + 'Opt',
self.highLev)
try:
mol.get_forces()
except:
pass
mol = tl.getOptGeom(
self.workingDir + '/' + 'Raw/calcHigh' + self.procNum +
'/', 'none', self.Reac, self.highMeth)
# Then calculate frequencies
os.chdir((self.workingDir + '/Raw/' + self.procNum))
mol = tl.setCalc(mol, self.highString, self.highMeth + 'Freq',
self.highLev)
try:
mol.get_forces()
except:
pass
freqs, zpe = self.characteriseFreqInternal(mol)
os.chdir((self.workingDir))
else:
if self.lowMeth == "gauss":
mol, freqs, zpe = tl.getGausOut(
self.workingDir + '/Raw/calcLow' + self.procNum,
self.lowLev, mol)
os.chdir((self.workingDir))
else:
# Higher level optimisation via some external program
mol = tl.setCalc(mol, self.lowString, self.lowMeth + 'Opt',
self.lowLev)
try:
mol.get_forces()
except:
pass
mol = tl.getOptGeom(
self.workingDir + '/Raw/' + 'calcLow' + self.procNum + '/',
'none', self.Reac, self.lowMeth)
# Then calculate frequencies
os.chdir((self.workingDir + '/Raw/' + self.procNum))
mol = tl.setCalc(mol, self.lowString, self.lowMeth + 'Freq',
self.lowLev)
try:
mol.get_forces()
except:
pass
freqs, zpe = tl.getFreqs(mol)
os.chdir((self.workingDir))
# Finally get single point energy
mol = tl.setCalc(mol, self.singleString, self.singleMeth,
self.singleLev)
energy = mol.get_potential_energy() + zpe
return freqs, energy, mol