def characteriseTSinternal(self, mol):
os.chdir((self.workingDir + '/Raw/' + self.procNum))
if (self.lowMeth == 'nwchem'):
mol = tl.setCalc(mol, self.lowString, 'nwchem2', self.lowLev)
self.Reac.get_forces()
else:
mol = tl.setCalc(mol, self.lowString, self.lowMeth, self.lowLev)
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
print("getting vibs")
TSFreqs, zpe = tl.getVibString(viblist, False, True)
print("vibs done " + str(zpe))
imaginaryFreq = tl.getImageFreq(viblist)
vib.clean()
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 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
def getPath(Reac, Prod, gl):
xyzfile3 = open(("IRC3.xyz"), "w")
Path = []
Path.append(Reac.copy())
for i in range(0, 30):
image = Reac.copy()
image = tl.setCalc(image, "DOS/", gl.lowerMethod, gl.lowerLevel)
Path.append(image)
image = Prod.copy()
image = tl.setCalc(image, "DOS/", gl.lowerMethod, gl.lowerLevel)
Path.append(image)
neb1 = NEB(Path, k=1.0, remove_rotation_and_translation=True)
try:
neb1.interpolate('idpp', optimizer="MDMin", k=1.0)
except:
neb1.interpolate()
optimizer = FIRE(neb1)
optimizer.run(fmax=0.07, steps=500)
neb2 = NEB(Path, k=1.0, climb=True, remove_rotation_and_translation=True)
optimizer = FIRE(neb2)
optimizer.run(fmax=0.07, steps=1500)
for i in range(0, len(Path)):
tl.printTraj(xyzfile3, Path[i])
xyzfile3.close()
return Path
def __init__(self, cartesians, species, i, glo):
self.twoStageTS = False
self.tempBiEne = 0
self.energyDictionary = {"".join(species): 0}
self.MiddleSteps = 2
self.spline_ene = []
self.NEBrelax = glo.NEBrelax
self.NEBsteps = glo.NEBsteps
self.eneBaseline = 0.0
self.workingDir = os.getcwd()
self.procNum = str(i)
self.lowString = 'Raw/calcLow' + str(i) + '/'
self.lowLev = glo.lowerLevel
self.lowMeth = glo.lowerMethod
self.highLev = glo.higherLevel
self.highMeth = glo.higherMethod
self.highString = 'Raw/calcHigh' + str(i) + '/'
self.singleString = 'Raw/calcSingle' + str(i) + '/'
self.singleMeth = glo.singleMethod
self.singleLev = glo.singleLevel
self.ReacFreqs = []
self.Reac = Atoms(symbols=species, positions=cartesians)
self.ReacName = tl.getSMILES(self.Reac, False)
self.TS = Atoms(symbols=species, positions=cartesians)
self.TSFreqs = []
self.TS2 = Atoms(symbols=species, positions=cartesians)
self.TS2Freqs = []
self.ProdFreqs = []
self.Prod = Atoms(symbols=species, positions=cartesians)
self.ProdName = tl.getSMILES(self.Prod, False)
self.biProd = Atoms(symbols=species, positions=cartesians)
self.biProdName = tl.getSMILES(self.Prod, False)
self.biProdFreqs = []
self.biReac = Atoms(symbols=species, positions=cartesians)
self.biReacName = tl.getSMILES(self.Reac, False)
self.biReacFreqs = []
self.CombProd = Atoms(symbols=species, positions=cartesians)
self.CombProdFreqs = []
self.CombReac = Atoms(symbols=species, positions=cartesians)
self.is_bimol_prod = False
self.is_bimol_reac = False
self.imaginaryFreq = 0.0
self.imaginaryFreq2 = 0.0
self.barrierlessReaction = False
self.forwardBarrier = 0.0
self.forwardBarrier2 = 0.0
self.reactantEnergy = 0.0
self.productEnergy = 0.0
self.have_reactant = False
self.inc = glo.dynPrintFreq
self.dynPrintStart = glo.dynPrintStart
self.printNEB = glo.printNEB
self.QTS3 = glo.QTS3
self.MidPoint = Atoms(symbols=species, positions=cartesians)
self.checkAltProd = glo.checkAltProd
self.AltProd = Atoms(symbols=species, positions=cartesians)
self.is_IntermediateProd = False
self.TScorrect = False
self.TS2correct = False
self.CombProductEnergy = 0
def newReac(self, path, name, Reac, opt):
if Reac == True:
self.Reac = read(path + '/Reac.xyz')
else:
self.Reac = read(path + '/Prod.xyz')
self.ReacName = name
self.CombReac = self.Reac.copy()
self.TS = self.Reac.copy()
self.TSFreqs = []
self.TS2 = self.Reac.copy()
self.TS2Freqs = []
self.ProdFreqs = []
self.Prod = self.Reac.copy()
self.spline_ene = []
self.ProdName = tl.getSMILES(self.Prod, False)
self.biProd = self.Reac.copy()
self.biProdName = tl.getSMILES(self.Prod, False)
self.biProdFreqs = []
self.CombProd = self.Reac.copy()
self.is_bimol_prod = False
self.is_bimol_reac = False
self.imaginaryFreq = 0.0
self.imaginaryFreq2 = 0.0
self.barrierlessReaction = False
self.forwardBarrier = 0.0
self.forwardBarrier2 = 0.0
self.have_reactant = True
self.is_IntermediateProd = False
self.AltProd = self.Reac.copy()
self.TScorrect = False
self.reactantEnergy = self.Reac.get_potential_energy()
if opt:
self.optReac()
def newReacFromSMILE(self, SMILE, opt=False):
self.ReacName = SMILE
SMILE.replace('____', '.')
SMILE.replace('comp', '.')
self.Reac = tl.getMolFromSmile(SMILE)
self.CombReac = self.Reac.copy()
self.TS = self.Reac.copy()
self.TSFreqs = []
self.TS2 = self.Reac.copy()
self.TS2Freqs = []
self.ProdFreqs = []
self.spline_ene = []
self.Prod = self.Reac.copy()
self.ProdName = tl.getSMILES(self.Prod, False)
self.biProd = self.Reac.copy()
self.biProdName = tl.getSMILES(self.Prod, False)
self.biProdFreqs = []
self.CombProd = self.Reac.copy()
self.is_bimol_prod = False
self.is_bimol_reac = False
self.imaginaryFreq = 0.0
self.imaginaryFreq2 = 0.0
self.barrierlessReaction = False
self.forwardBarrier = 0.0
self.forwardBarrier2 = 0.0
self.have_reactant = True
self.is_IntermediateProd = False
self.AltProd = self.Reac.copy()
self.TScorrect = False
if opt:
self.optReac()
def optReac(self):
print('minimising')
self.is_bimol_reac = False
self.CombReac = tl.setCalc(self.CombReac, self.lowString, self.lowMeth,
self.lowLev)
self.ReacName = tl.getSMILES(self.CombReac, True, True)
FullName = self.ReacName.split('____', 1)
path = (self.workingDir + '/Raw/calcHigh' + self.procNum)
try:
self.CombReac._calc.close()
except:
pass
if len(FullName) > 1:
self.is_bimol_reac = True
self.ReacName = FullName[0].strip('\n\t')
self.biReacName = FullName[1].strip('\n\t')
self.Reac = tl.getMolFromSmile(self.ReacName)
self.biReac = tl.getMolFromSmile(self.biReacName)
else:
self.Reac = self.CombReac
self.Reac = tl.setCalc(self.Reac, self.highString, self.highMeth,
self.highLev)
try:
self.Reac._calc.minimise_stable(path, self.Reac)
except:
self.Reac = tl.setCalc(self.Reac, self.lowString, self.lowMeth,
self.lowLev)
self.Reac._calc.minimise_stable(path, self.Reac)
try:
self.ReacFreqs, zpe = self.Reac._calc.read_vibs()
except:
self.ReacFreqs, zpe = self.characteriseFreqInternal(self.Reac)
self.Reac = tl.setCalc(self.Reac, self.singleString, self.singleMeth,
self.singleLev)
self.reactantEnergy = self.Reac.get_potential_energy() + zpe
try:
self.Reac._calc.close()
except:
pass
if self.is_bimol_reac == True:
self.biReac = tl.setCalc(self.biReac, self.highString,
self.highMeth, self.highLev)
try:
self.biReac._calc.minimise_stable(path, self.biReac)
except:
self.biReac = tl.setCalc(self.biReac, self.lowString,
self.lowMeth, self.lowLev)
self.biReac._calc.minimise_stable(path, self.biReac)
try:
self.biReacFreqs, zpe = self.biReac._calc.read_vibs()
except:
self.biReacFreqs, zpe = self.characteriseFreqInternal(
self.biReac)
self.biReac = tl.setCalc(self.biReac, self.singleString,
self.singleMeth, self.singleLev)
self.reactantEnergy += (self.biReac.get_potential_energy() + zpe)
try:
self.biReac._calc.close()
except:
pass
def characteriseTSFreqInternal(self, mol):
os.chdir((self.workingDir + '/' + '/Raw/' + self.procNum))
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
freqs, zpe = tl.getVibString(viblist, False, True)
vib.clean()
os.chdir((self.workingDir))
imaginaryFreq = tl.getImageFreq(viblist)
return freqs, zpe, imaginaryFreq
def re_init(self, path):
self.TS = read(path + '/Reac.xyz')
self.TSFreqs = []
self.TS2 = read(path + '/Reac.xyz')
self.TS2Freqs = []
self.ProdFreqs = []
self.spline_ene = []
self.Prod = read(path + '/Reac.xyz')
self.ProdName = tl.getSMILES(self.Prod, False).strip('\n\t')
self.biProd = read(path + '/Reac.xyz')
self.biProdName = tl.getSMILES(self.Prod, False).strip('\n\t')
self.biProdFreqs = []
self.CombProd = read(path + '/Reac.xyz')
self.is_bimol_prod = False
self.imaginaryFreq = 0.0
self.imaginaryFreq2 = 0.0
self.barrierlessReaction = False
self.forwardBarrier = 0.0
self.forwardBarrier2 = 0.0
self.productEnergy = 0.0
self.TScorrect = False
def refineTSpoint(self, MolList, TrajStart):
iMol = MolList[TrajStart - 100].copy()
iMol = tl.setCalc(iMol, self.lowString, self.lowMeth, self.lowLev)
startName = tl.getSMILES(iMol, True)
startName = startName.split('____')
if len(startName) > 1:
startName = startName[0]
# Look for change in optimised geometry along reaction path
point = 0
for i in range(TrajStart - 99, TrajStart + 100):
iMol = MolList[i].copy()
iMol = tl.setCalc(iMol, self.lowString, self.lowMeth, self.lowLev)
Name = tl.getSMILES(iMol, True)
FullName = Name.split('____')
if len(FullName) > 1:
FullName = FullName[0]
if FullName != self.startName and FullName != self.ReacName:
point = i
return point
return TrajStart
def optTSpoint(self, trans, path, MolList, TrajStart, idx):
self.TS = MolList[TrajStart].copy()
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
c = FixAtoms(trans)
self.TS.set_constraint(c)
min = BFGS(self.TS)
min.run(fmax=0.05, steps=50)
os.mkdir(path + '/Data/')
write(path + '/Data/TSGuess.xyz', self.TS)
TSGuess = self.TS.copy()
del self.TS.constraints
if self.biReac or self.biProd:
QTS3 = False
else:
QTS3 = True
if (self.twoStageTS):
try:
self.TSFreqs, self.imaginaryFreq, zpe, energy, self.TS, rmol, pmol = self.characteriseTSExt(
self.TS, True, path, QTS3)
except:
pass
try:
self.TSFreqs, self.imaginaryFreq, zpe, energy, self.TS, rmol, pmol = self.characteriseTSExt(
self.TS, False, path, QTS3)
except:
try:
print(
"High Level TS opt for TS1 failed looking at lower level")
self.TSFreqs, self.imaginaryFreq, zpe, energy, self.TS, rmol, pmol = self.characteriseTSExt(
self.TS, True, path, QTS3)
except:
pass
try:
self.TScorrect = self.compareRandP(rmol, pmol)
except:
self.TScorrect = False
self.TS = TSGuess
self.TSFreqs, self.imaginaryFreq, zpe, energy = self.characteriseTSinternal(
self.TS)
write(path + '/TS1.xyz', self.TS)
self.forwardBarrier = energy
if (self.forwardBarrier < self.reactantEnergy
and self.forwardBarrier < self.productEnergy):
self.barrierlessReaction = True
def re_init_bi(self, cartesians, species):
self.Reac = Atoms(symbols=species, positions=cartesians)
self.CombReac = self.Reac.copy()
self.TS = Atoms(symbols=species, positions=cartesians)
self.TSFreqs = []
self.spline_ene = []
self.TS2 = Atoms(symbols=species, positions=cartesians)
self.TS2Freqs = []
self.ProdFreqs = []
self.Prod = Atoms(symbols=species, positions=cartesians)
self.ProdName = tl.getSMILES(self.Prod, False)
self.biProd = Atoms(symbols=species, positions=cartesians)
self.biProdName = tl.getSMILES(self.Prod, False)
self.biProdFreqs = []
self.CombProd = Atoms(symbols=species, positions=cartesians)
self.is_bimol_prod = False
self.imaginaryFreq = 0.0
self.imaginaryFreq2 = 0.0
self.barrierlessReaction = False
self.forwardBarrier = 0.0
self.forwardBarrier2 = 0.0
self.productEnergy = 0.0
self.TScorrect = False
self.optReac()
def quickOptProd(self, cart, alt):
self.is_bimol_prod = False
if alt == True:
self.CombProd = self.AltProd.copy()
else:
self.CombProd.set_positions(cart)
try:
self.CombProd._calc.close()
except:
pass
path = (self.workingDir + '/Raw/calcHigh' + self.procNum)
self.CombProd = tl.setCalc(self.CombProd, self.lowString, self.lowMeth,
self.lowLev)
self.ProdName = tl.getSMILES(self.CombProd, True, partialOpt=True)
FullName = self.ProdName.split('____', 1)
if len(FullName) > 1:
self.is_bimol_prod = True
self.ProdName = FullName[0].strip('\n\t')
self.biProdName = FullName[1].strip('\n\t')
self.Prod = tl.getMolFromSmile(self.ProdName)
self.biProd = tl.getMolFromSmile(self.biProdName)
else:
self.Prod = self.CombProd
self.ProdName = tl.getSMILES(self.Prod, False, partialOpt=False)
def compareRandP(self, rmol, pmol):
# Check if TS links reac and prod
rmol = tl.setCalc(rmol, self.lowString, self.lowMeth, self.lowLev)
Name = tl.getSMILES(rmol, False).strip('\n\t')
FullName = Name.split('____')
try:
rmol._calc.close()
except:
pass
pmol = tl.setCalc(pmol, self.lowString, self.lowMeth, self.lowLev)
min = BFGS(pmol)
Name2 = tl.getSMILES(pmol, False).strip('\n\t')
FullName2 = Name2.split('____')
if ((FullName == self.ReacName and FullName2 == self.ProdName) or
(FullName2[0] == self.ReacName and FullName[0] == self.ProdName)):
TScorrect = True
else:
TScorrect = False
print('TS1 try does not connect reactants and products')
try:
pmol._calc.close()
except:
pass
return TScorrect
def runTrajectory(self):
# Create specific directory
fails = 0
self.Mol =tl.setCalc(self.Mol, 'Traj_' + str(self.procNum), self.method, self.level)
coords = self.Mol.get_positions()
reac_smile = tl.getSMILES(self.Mol,True)
self.Mol.set_positions(coords)
workingDir = os.getcwd()
newpath = workingDir + '/Raw/traj' + str(self.procNum)
print("making directory " + newpath)
if not os.path.exists(newpath):
os.makedirs(newpath)
os.chdir(newpath)
file_name = str(newpath + "/totaltraj.xyz")
if os.path.isfile(file_name):
expand = 1
while True:
expand += 1
new_file_name = file_name.split(".xyz")[0] + str(expand) + ".xyz"
if os.path.isfile(new_file_name):
continue
else:
file_name = new_file_name
break
namefile = open((file_name), "a")
self.numberOfSteps = 0
consistantChange = 0
#Multiple stepsizes
self.smallStep = self.timeStep
timeStep = self.timeStep
eneBXDon = False
eBounded= False
comBounded = False
print("getting first forces")
try:
self.forces = self.Mol.get_forces()
except:
try:
self.forces = self.Mol.get_forces()
except:
print("forces error")
self.forces = np.zeros(len(self.forces.shape))
#Get MDintegrator type
if self.MDIntegrator == 'VelocityVerlet':
mdInt = ChemDyME.MDIntegrator.VelocityVerlet(self.forces, self.velocity, self.Mol)
elif self.MDIntegrator == 'Langevin':
mdInt = ChemDyME.MDIntegrator.Langevin(units.kB * self.LangTemp, self.LangFric, self.forces, self.velocity, self.Mol,timeStep)
# Then set up reaction criteria or connectivity map
con = ChemDyME.Connectivity.NunezMartinez(self.Mol)
# Then set up various BXD procedures
if self.comBXD or self.biMolecular:
self.comBXD = True
if self.mixedTimestep == True:
mdInt.reset(self.timeStep * 10)
comBxd = ChemDyME.BXDconstraint.COM(self.Mol, 0, self.minCOM, hitLimit = 100000, activeS = self.fragIdx, runType="fixed")
if self.eneBXD:
eneBXD = ChemDyME.BXDconstraint.Energy(self.Mol, -10000, 10000, hitLimit = 1, adapMax = self.adaptiveSteps, runType="adaptive")
# Run MD trajectory for specified number of steps
for i in range(0,self.mdSteps):
t = process_time()
try:
self.ene = self.Mol.get_potential_energy()
except:
pass
# Update the COM seperation and check whether it is bounded
if self.comBXD:
comBxd.update(self.Mol)
comBounded = comBxd.inversion
if self.comBXD and eneBXDon and i % self.printFreq == 0:
print("Ene = " + str(eneBXD.s[0]) + ' S = ' + str(comBxd.s[0]) + ' step = ' + str(i) + ' process = ' + str(self.procNum) + ' time = ' + str(process_time()-t) + ' temperature = ' + str(self.Mol.get_temperature()))
elif self.comBXD and i % self.printFreq == 0 :
print("Ene = " + "NA" + ' S = ' + str(comBxd.s[0]) + ' step = ' + str(i) + ' process = ' + str(self.procNum) + ' time = ' + str(process_time()-t) + ' temperature = ' + str(self.Mol.get_temperature()))
elif eneBXDon and i % self.printFreq == 0:
print("Ene = " + str(self.Mol.get_potential_energy()) + ' box = ' + str(eneBXD.box) + ' step = ' + str(i) + ' process = ' + str(self.procNum) + ' time = ' + str(process_time()-t) + ' temperature = ' + str(self.Mol.get_temperature()) + ' Etot ' + str(self.Mol.get_potential_energy() + self.Mol.get_kinetic_energy()))
if i % self.printFreq == 0 and self.geom_print is True:
tl.printTraj(namefile, self.Mol.copy())
# Now check whether to turn BXDE on
if self.comBXD:
if (self.biMolecular or self.comBXD) and comBxd.s[0] < self.minCOM and eneBXDon == False:
if self.mixedTimestep == True:
mdInt.reset(self.timeStep)
eneBXDon = False
elif self.eneBXD and self.ReactionCountDown == 0:
eneBXDon = True
if eneBXDon == True:
eneBXD.update(self.Mol)
eBounded = eneBXD.inversion
if comBounded is True and self.ReactionCountDown == 0:
self.Mol.set_positions(mdInt.old_positions)
com_del_phi = comBxd.del_constraint(self.Mol)
if comBxd.stuck == True and comBxd.s[0] < self.minCOM:
comBxd.stuckFix()
if eBounded:
self.Mol.set_positions(mdInt.old_positions)
try:
e_del_phi = eneBXD.del_constraint(self.Mol)
except:
pass
# Perform inversion if required
if eBounded is True and comBounded is True:
mdInt.constrain2(e_del_phi, com_del_phi)
elif eBounded is False and comBounded is True:
mdInt.constrain(com_del_phi)
elif eBounded is True and comBounded is False:
mdInt.constrain(e_del_phi)
timeStep = self.smallStep
else:
self.numberOfSteps += 1
timeStep = self.timeStep
mdInt.md_step_pos(self.forces, timeStep, self.Mol)
if eBounded and eneBXD.boxList[eneBXD.box].lower.hit( self.Mol.get_potential_energy(), 'down'):
ene = self.Mol.get_potential_energy()
self.Mol.set_positions(mdInt.old_positions)
mdInt.current_positions = mdInt.old_positions
ene1 = self.Mol.get_potential_energy()
hit1 = eneBXD.boxList[eneBXD.box].lower.hit(ene1, 'down')
mdInt.constrained = True
mdInt.md_step_pos(self.forces, timeStep*0.0000001, self.Mol)
ene2 = self.Mol.get_potential_energy()
hit2 = eneBXD.boxList[eneBXD.box].lower.hit(ene2, 'down')
try:
self.forces = self.Mol.get_forces()
except:
try:
self.forces = self.Mol.get_forces()
except:
print("forces error")
self.forces = np.zeros(len(self.forces.shape))
mdInt.md_step_vel(self.forces, timeStep, self.Mol)
self.MolList.append(self.Mol.copy())
# Update connectivity map to check for reaction
con.update(self.Mol)
if con.criteriaMet is True:
if consistantChange == 0:
self.TSpoint = i
self.TSgeom = self.Mol.copy()
consistantChange = self.consistantWindow
elif consistantChange > 0:
if consistantChange == 1:
self.ReactionCountDown = self.window
eneBXDon = False
consistantChange -= 2
else:
consistantChange -= 1
else:
if consistantChange > 0:
consistantChange = 0
con.criteriaMet = False
if not self.ReactionCountDown == 0:
self.ReactionCountDown -= 1
if self.ReactionCountDown == 1:
awrite('temp.xyz', self.Mol)
coords = self.Mol.get_positions()
min = BFGS(self.Mol)
min.run(fmax=0.1, steps=5)
con2 = ChemDyME.Connectivity.NunezMartinez(self.Mol)
pmol_name = tl.getSMILES(self.Mol,False)
self.Mol.set_positions(coords)
if not np.array_equal(con.C,con2.C):
self.ReactionCountDown = 0
self.productGeom = self.Mol.get_positions()
os.chdir(workingDir)
break
elif fails < 5:
self.ReactionCountDown = self.window
fails +=1
else:
fails = 0
self.ReactionCountDown = 0
consistantChange = 0
while eneBXD.boxList[eneBXD.box].lower.hit( self.Mol.get_potential_energy(), 'down'):
eneBXD.box -=1
try:
self.Mol._calc.close()
except:
pass
namefile.close()
os.chdir(workingDir)
def TempBiEne(self, tempBi):
tempBi = tl.setCalc(tempBi, self.singleString, self.singleMeth,
self.singleLev)
ene = tempBi.get_potential_energy()
return ene
def optNEB(self, trans, path, changePoints, mols):
# Open files for saving IRCdata
xyzfile3 = open((path + "/IRC3.xyz"), "w")
MEP = open((path + "/MEP.txt"), "w")
imagesTemp1 = []
index = changePoints[0] - 100
molTemp = mols[index].copy()
imagesTemp1.append(molTemp.copy())
for i in range(0, 100):
imagesTemp1.append(mols[changePoints[0] - 100].copy())
try:
imagesTemp1.append(mols[changePoints[-1] + 300])
except:
imagesTemp1.append(self.CombProd.copy())
neb1 = NEB(imagesTemp1, k=1.0, remove_rotation_and_translation=True)
try:
neb1.interpolate('idpp')
except:
neb1.interpolate()
for i in range(0, len(imagesTemp1)):
try:
imagesTemp1[i] = tl.setCalc(imagesTemp1[i], self.lowString,
self.lowMeth, self.lowLev)
for i in range(0, len(trans)):
c = FixAtoms(trans)
imagesTemp1[i].set_constraint(c)
min = BFGS(imagesTemp1[i])
min.run(fmax=0.005, steps=40)
del imagesTemp1[i].constraints
except:
pass
optimizer = FIRE(neb1)
try:
optimizer.run(fmax=0.07, steps=300)
except:
pass
print("passed seccond neb")
neb1_2 = NEB(imagesTemp1, k=0.01, remove_rotation_and_translation=True)
try:
optimizer.run(fmax=0.07, steps=200)
except:
pass
neb2 = NEB(imagesTemp1,
climb=True,
remove_rotation_and_translation=True)
try:
optimizer.run(fmax=0.07, steps=200)
except:
pass
for i in range(0, len(imagesTemp1)):
tl.printTraj(xyzfile3, imagesTemp1[i])
print("NEB printed")
xyzfile3.close()
point = 0
maxEne = -50000000
try:
for i in range(0, len(imagesTemp1)):
MEP.write(
str(i) + ' ' + str(imagesTemp1[i].get_potential_energy()) +
'\n')
if imagesTemp1[i].get_potential_energy() > maxEne and i > 5:
point = i
maxEne = imagesTemp1[i].get_potential_energy()
self.TS2 = imagesTemp1[point]
except:
point = 0
print("TS Climb part")
write(path + '/TSClimbGuess.xyz', self.TS2)
try:
self.TS2Freqs, self.imaginaryFreq2, zpe, energy, self.TS2, rmol, pmol = self.characteriseTSExt(
self.TS2, False, path, self.QTS3)
except:
self.TS2Freqs, self.imaginaryFreq2, zpe, energy, self.TS2, rmol, pmol = self.characteriseTSExt(
self.TS2, True, path, self.QTS3)
self.TScorrect = self.compareRandP(rmol, pmol)
self.forwardBarrier2 = energy + zpe
def optDynPath(self, trans, path, MolList, changePoints):
# Open files for saving IRCdata
xyzfile = open((path + "/Data/dynPath.xyz"), "w")
MEP = open((path + "/Data/MEP.txt"), "w")
orriginal = open((path + "/Data/orriginalPath.txt"), "w")
dyn = open((path + "/Data/traj.xyz"), "w")
dynList = []
end = int(changePoints + self.dynPrintStart)
length = int(len(MolList))
if end < length:
endFrame = end
else:
endFrame = length
for i in range(int(changePoints - self.dynPrintStart), int(endFrame),
self.inc):
iMol = MolList[i].copy()
tl.printTraj(dyn, iMol)
iMol = tl.setCalc(iMol, self.lowString, self.lowMeth, self.lowLev)
orriginal.write(
str(i) + ' ' + str(iMol.get_potential_energy()) + '\n')
c = FixAtoms(trans)
iMol.set_constraint(c)
min = BFGS(iMol)
try:
min.run(fmax=0.1, steps=150)
except:
min.run(fmax=0.1, steps=1)
del iMol.constraints
tl.printTraj(xyzfile, iMol)
dynList.append(iMol.copy())
maxEne = -50000
point = 0
for i in range(0, len(dynList)):
dynList[i] = tl.setCalc(dynList[i], self.lowString, self.lowMeth,
self.lowLev)
MEP.write(
str(i) + ' ' + str(dynList[i].get_potential_energy()) + '\n')
if dynList[i].get_potential_energy() > maxEne:
point = i
maxEne = dynList[i].get_potential_energy()
self.TS2 = dynList[point]
TS2Guess = self.TS2.copy()
write(path + '/Data/TS2guess.xyz', self.TS2)
try:
self.TS2Freqs, self.imaginaryFreq2, zpe, energy, self.TS2, rmol, pmol = self.characteriseTSExt(
self.TS2, True, path, self.QTS3)
except:
try:
self.TS2Freqs, self.imaginaryFreq2, zpe, energy, self.TS2, rmol, pmol = self.characteriseTSExt(
self.TS2, False, path, self.QTS3)
except:
pass
try:
self.TS2correct = self.compareRandP(rmol, pmol)
except:
print("TS2 does not connect products")
self.TS2correct = False
self.TS2 = TS2Guess
self.TS2Freqs, self.imaginaryFreq2, zpe, energy = self.characteriseTSinternal(
self.TS2)
write(path + '/TS2.xyz', self.TS2)
self.forwardBarrier2 = energy
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
def optTS(self, trans, path, MolList, TrajStart):
raw_path = (self.workingDir + '/Raw/calcHigh' + self.procNum)
self.TS = MolList[TrajStart].copy()
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
c = FixAtoms(trans)
self.TS.set_constraint(c)
min = BFGS(self.TS)
min.run(fmax=0.05, steps=50)
os.mkdir(path + '/Data/')
write(path + '/Data/TSGuess.xyz', self.TS)
TSGuess = self.TS.copy()
del self.TS.constraints
self.TS, rmol, pmol, irc_for, irc_rev = self.TS._calc.minimise_ts(
raw_path, self.TS)
try:
self.TScorrect = self.compareRandP(rmol, pmol)
except:
self.TScorrect = False
try:
self.TS._calc.close()
except:
pass
try:
inc = -10
while self.TScorrect == False and inc <= 10:
self.TS = MolList[TrajStart - inc].copy()
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
c = FixAtoms(trans)
self.TS.set_constraint(c)
min = BFGS(self.TS)
min.run(fmax=0.05, steps=50)
write(path + '/Data/TSGuess.xyz', self.TS)
TSGuess = self.TS.copy()
del self.TS.constraints
self.TS, rmol, pmol, irc_for, irc_rev = self.TS._calc.minimise_ts(
raw_path, self.TS)
try:
self.TScorrect = self.compareRandP(rmol, pmol)
except:
self.TScorrect = False
inc += 1
try:
self.TS._calc.close()
except:
pass
except:
pass
if self.TScorrect:
irc_ene = []
irc_rev.reverse()
irc = irc_rev + irc_for
for i in irc:
i = tl.setCalc(i, self.lowString, self.lowMeth, self.lowLev)
irc_ene.append(i.get_potential_energy())
try:
i._calc.close()
except:
pass
write(path + '/Data/IRC.xyz', irc)
write(path + '/TS1.xyz', self.TS)
self.TS = tl.setCalc(self.TS, self.highString, self.highMeth,
self.highLev)
try:
self.TScorrect = self.TS._calc.minimise_ts_only(
self.TS, self.CombReac, self.CombProd)
copyfile(str(self.highString) + 'gaussian.log', path + '/G1.log')
except:
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
try:
self.TSFreqs, zpe, self.imaginaryFreq, self.TScorrect = self.TS._calc.read_ts_vibs(
)
except:
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
self.TSFreqs, zpe, self.imaginaryFreq = self.characteriseTSFreqInternal(
self.TS)
try:
self.TS._calc.close()
except:
pass
self.TS = tl.setCalc(self.TS, self.singleString, self.singleMeth,
self.singleLev)
try:
self.forwardBarrier = self.TS.get_potential_energy() + zpe
self.TS._calc.close()
except:
pass
self.TS = tl.setCalc(self.TS, self.lowString, self.lowMeth,
self.lowLev)
spline = self.TS._calc.minimise_bspline(raw_path, self.CombReac,
self.CombProd)
try:
self.TS._calc.close()
except:
pass
spline_ene = []
try:
self.TS._calc.close()
except:
pass
try:
for sp in spline:
sp = tl.setCalc(sp, self.lowString, self.lowMeth, self.lowLev)
spline_ene.append(float(sp.get_potential_energy()))
try:
sp._calc.close()
except:
pass
max_value = max(spline_ene)
ind = spline_ene.index(max_value)
write(path + '/Data/TS2.xyz', spline[ind])
self.TS2 = spline[ind].copy()
write(path + '/Data/spline.xyz', spline)
with open(path + '/Data/spline_ene.txt', 'w') as f:
for sp in spline_ene:
f.write(str(sp) + "\n")
f.close()
self.spline = spline_ene
self.TS2 = tl.setCalc(self.TS2, self.lowString, self.lowMeth,
self.lowLev)
self.TS2, rmol, pmol, irc_for, irc_rev = self.TS2._calc.minimise_ts(
raw_path, self.TS2)
self.TS2 = tl.setCalc(self.TS2, self.highString, self.highMeth,
self.highLev)
try:
self.TS2correct = self.TS2._calc.minimise_ts_only(
self.TS, self.CombReac, self.CombProd)
copyfile(
str(self.highString) + 'gaussian.log', path + '/G2.log')
except:
self.TS2 = tl.setCalc(self.TS2, self.lowString, self.lowMeth,
self.lowLev)
try:
self.TS2Freqs, zpe, self.imaginaryFreq2, self.TS2correct = self.TS2._calc.read_ts_vibs(
)
except:
self.TS2 = tl.setCalc(self.TS2, self.lowString, self.lowMeth,
self.lowLev)
self.TS2Freqs, zpe, self.imaginaryFreq2 = self.characteriseTSFreqInternal(
self.TS2)
try:
self.TS2._calc.close()
except:
pass
self.TS2 = tl.setCalc(self.TS2, self.singleString, self.singleMeth,
self.singleLev)
try:
self.forwardBarrier2 = self.TS2.get_potential_energy() + zpe
self.TS2._calc.close()
except:
pass
except:
self.TS2correct = False
write(path + '/TS2.xyz', self.TS2)
if (self.forwardBarrier <= self.reactantEnergy
or self.forwardBarrier <= self.productEnergy):
self.barrierlessReaction = True
if self.TScorrect == False and self.TS2correct == True:
self.TS = self.TS2
self.forwardBarrier = self.forwardBarrier2
self.imaginaryFreq = self.imaginaryFreq2
self.TSFreqs = self.TS2Freqs
def runGenBXD(self, Reac, Prod, maxHits, adapMax, pathType, path, bonds, decSteps, histogramBins, pathLength, fixToPath, pathDistCutOff, epsilon):
self.iterations = 0
keepGoing = True
workingDir = os.getcwd()
file = open("geo.xyz","w")
sfile = open("plotData.txt", "w")
#Get MDintegrator type
if self.MDIntegrator == 'VelocityVerlet':
mdInt = ChemDyME.MDIntegrator.VelocityVerlet(self.forces, self.velocity, self.Mol)
elif self.MDIntegrator == 'Langevin':
mdInt = ChemDyME.MDIntegrator.Langevin(units.kB * self.LangTemp, self.LangFric, self.forces, self.velocity, self.Mol, self.timeStep)
#Check whether a list of bounds is present? If so read adaptive boundaries from previous run
BXD = ChemDyME.BXDconstraint.genBXD(self.Mol, Reac, Prod, adapMax = adapMax, activeS = bonds, path = path, pathType = pathType, decorrelationSteps = decSteps, runType = 'adaptive', hitLimit = 1, hist = histogramBins, endDistance=pathLength, fixToPath=fixToPath, pathDistCutOff=pathDistCutOff, epsilon=epsilon )
#Check whether a list of bounds is present? If so read adaptive boundaries from previous run
if os.path.isfile("BXDbounds.txt"):
BXD.readExisitingBoundaries("BXDbounds.txt")
BXD.reset("fixed", maxHits)
else:
BXDfile = open("BXDbounds.txt", "w")
# Get forces from designated potential
try:
self.forces = self.Mol.get_forces()
except:
print('forces error')
# Run MD trajectory for specified number of steps
while keepGoing:
t = process_time()
bxdt = process_time()
BXD.update(self.Mol)
bxdte = process_time()
eBounded = BXD.inversion
if eBounded:
self.Mol.set_positions(mdInt.oldPos)
bxd_del_phi = BXD.del_constraint(self.Mol)
if self.MDIntegrator == 'VelocityVerlet' and not eBounded:
print('S ' + str(BXD.s[2]) + ' box ' + str(BXD.box) + ' time ' + str(process_time()-t) + ' Etot ' + str(self.Mol.get_potential_energy() + self.Mol.get_kinetic_energy()))
elif self.iterations % self.printFreq == 0 and not eBounded:
print('pathNode = ' +str(BXD.pathNode) + ' distFromPath = ' + str(BXD.distanceToPath) + ' project = ' +str(BXD.s[2]) + ' S ' + str(BXD.s[0]) + " hits " + str(BXD.boxList[BXD.box].upper.hits) + ' ' + str(BXD.boxList[BXD.box].lower.hits) + " points in box " + str(len(BXD.boxList[BXD.box].data)) + ' box ' + str(BXD.box) + ' time ' + str(process_time()-t) + ' temperature ' + str(self.Mol.get_temperature()))
if self.iterations % (self.printFreq/100) == 0:
sfile.write('S \t=\t' + str(BXD.s[0]) + '\tbox\t=\t' + str(BXD.box) + " hits " + str(BXD.boxList[BXD.box].upper.hits) + ' ' + str(BXD.boxList[BXD.box].lower.hits) + "\n")
sfile.flush()
# Perform inversion if required
if eBounded is True:
mdInt.constrain(bxd_del_phi)
mdpt = process_time()
mdInt.mdStepPos(self.forces, self.timeStep, self.Mol)
mdpte = process_time()
# Get forces from designated potential
ft = process_time()
try:
self.forces = self.Mol.get_forces()
except:
print('forces error')
fte = process_time()
mdvt = process_time()
mdInt.mdStepVel(self.forces, self.timeStep, self.Mol)
mdvte = process_time()
self.numberOfSteps += 1
if self.iterations % self.printFreq == 0:
tl.printTraj(file,self.Mol)
self.iterations += 1
#print( "Forces time = " + str(fte - ft) + " BXDtime = " + str(bxdte - bxdt) + " MDP time = " + str(mdpte - mdpt) + "MDV time = " + str(mdvte - mdvt))
#check if one full run is complete, if so stop the adaptive search
if BXD.completeRuns == 1:
keepGoing = False
#Check whether inital run and adaptive box placement run, save boundaries and rest all bxd boundaries ready for convergence
if BXD.runType == "adaptive":
# reset all box data other than boundary positions and prepare to run full BXD
# print boundaries to file
keepGoing = True
BXD.printBounds(BXDfile)
BXD.reset("fixed", maxHits)
file.close()
# Rerun BXD with new adaptively set bounds to converge box to box statistics
# Get forces and energy from designated potential
try:
self.forces = self.Mol.get_forces()
except:
print('forces error')
while keepGoing:
t = process_time()
BXD.update(self.Mol)
eBounded = BXD.inversion
if eBounded:
self.Mol.set_positions(mdInt.oldPos)
eBounded = BXD.inversion
if self.MDIntegrator == 'VelocityVerlet' and self.iterations % self.printFreq == 0:
print('S ' + str(BXD.s[2]) + ' box ' + str(BXD.box) + ' time ' + str(process_time()-t) + ' Epot ' + str(self.Mol.get_potential_energy() + self.Mol.get_kinetic_energy()))
elif self.iterations % self.printFreq == 0:
print('pathNode = ' +str(BXD.pathNode) + ' project = ' +str(BXD.s[2]) + ' S ' + str(BXD.s[0]) + " hits " + str(BXD.boxList[BXD.box].upper.hits) + ' ' + str(BXD.boxList[BXD.box].lower.hits) + " points in box " + str(len(BXD.boxList[BXD.box].data)) + ' box ' + str(BXD.box) + ' time ' + str(process_time()-t) + ' temperature ' + str(self.Mol.get_temperature()))
# Perform inversion if required
if eBounded is True:
mdInt.constrain(BXD.del_phi)
mdInt.mdStepPos(self.forces, self.timeStep, self.Mol)
# Get forces from designated potential
try:
self.forces = self.Mol.get_forces()
except:
print('forces error')
mdInt.mdStepVel(self.forces, self.timeStep, self.Mol)
self.numberOfSteps += 1
if BXD.completeRuns == 1:
keepGoing = False
#Look for exsisting results files from previous runs and open a new results file numbered sequentially from those that exsist already
i = 0
while(os.path.isfile("BXDprofile" + str(i) + ".txt")):
i += 1
BXDprofile = open("BXDprofile" + str(i) + ".txt", "w")
BXDrawData = open("BXDrawData" + str(i) + ".txt", "w")
BXDlowRes = open("BXDlowResProfile" + str(i) + ".txt" , "w")
BXD.gatherData(BXDprofile, BXDrawData, self.LangTemp, BXDlowRes)
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 run(gl):
#Read reactant definition
if gl.StartType == 'file':
Reac = read(gl.Start)
elif gl.StartType == 'Smile':
Reac = tl.getMolFromSmile(gl.Start)
#Read product definition
if gl.EndType == 'file':
Prod = read(gl.End)
elif gl.EndType == 'Smile':
Prod = tl.getMolFromSmile(gl.End)
#Set calculatiors
#Reac = tl.setCalc(Reac,"DOS/", gl.trajMethod, gl.atomTypes)
if gl.trajMethod == "openMM":
Reac = tl.setCalc(Reac, "GenBXD/", gl.trajMethod, gl)
else:
Reac = tl.setCalc(Reac, "GenBXD/", gl.trajMethod, gl.trajLevel)
Prod = tl.setCalc(Prod, "GenBXD/", gl.trajMethod, gl.trajLevel)
# Partially minimise both reactant and product
if gl.GenBXDrelax:
min = BFGS(Reac)
try:
min.run(fmax=0.1, steps=20)
except:
min.run(fmax=0.1, steps=20)
min2 = BFGS(Prod)
try:
min2.run(fmax=0.1, steps=20)
except:
min2.run(fmax=0.1, steps=20)
# Get important interatomic distances
if gl.CollectiveVarType == "changedBonds":
cbs = ct.getChangedBonds2(Reac, Prod)
elif gl.CollectiveVarType == "all":
cbs = ct.getChangedBonds2(Reac, Prod)
elif gl.CollectiveVarType == "specified":
cbs = gl.CollectiveVar
elif gl.CollectiveVarType == "file":
cbs = gl.principalCoordinates
#Get path to project along
distPath = []
totalPathLength = 0
if gl.PathType == 'curve' or gl.PathType == 'gates':
if gl.PathFile == 'none':
Path = getPath(Reac, Prod, gl)
else:
Path = read(gl.PathFile, index=('::' + str(gl.pathStride)))
distPath.append((ct.getDistMatrix(Path[0], cbs)[0], 0))
for i in range(1, len(Path)):
l = np.linalg.norm(
ct.getDistMatrix(Path[i], cbs)[0] -
ct.getDistMatrix(Path[i - 1], cbs)[0])
totalPathLength += l
distPath.append((ct.getDistMatrix(Path[i],
cbs)[0], totalPathLength))
elif gl.PathType == 'linear':
distPath = ct.getDistMatrix(Prod, cbs)[0] - ct.getDistMatrix(
Reac, cbs)[0]
if gl.PathType == 'curve' or gl.PathType == 'gates':
pathFile = open('reducedPath.txt', 'w')
for p in distPath:
pathFile.write('s = ' + str(p[0]) + '\n')
pathFile.close()
# initialise then run trajectory
t = ChemDyME.Trajectory.Trajectory(Reac, gl, os.getcwd(), 0, False)
t.runGenBXD(Reac, Prod, gl.maxHits, gl.maxAdapSteps, gl.PathType, distPath,
cbs, gl.decorrelationSteps, gl.histogramBins, totalPathLength,
gl.fixToPath, gl.pathDistCutOff, gl.epsilon)
def optProd(self, cart, alt):
print('optimising product')
self.is_bimol_prod = False
if alt == True:
self.CombProd = self.AltProd.copy()
else:
self.CombProd.set_positions(cart)
try:
self.CombProd._calc.close()
except:
pass
path = (self.workingDir + '/Raw/calcHigh' + self.procNum)
self.CombProd = tl.setCalc(self.CombProd, self.lowString, self.lowMeth,
self.lowLev)
self.ProdName = tl.getSMILES(self.CombProd, True, partialOpt=True)
FullName = self.ProdName.split('____', 1)
if len(FullName) > 1:
self.is_bimol_prod = True
self.ProdName = FullName[0].strip('\n\t')
self.biProdName = FullName[1].strip('\n\t')
self.Prod = tl.getMolFromSmile(self.ProdName)
self.biProd = tl.getMolFromSmile(self.biProdName)
else:
self.Prod = self.CombProd
try:
self.Prod = tl.setCalc(self.Prod, self.highString, self.highMeth,
self.highLev)
self.Prod._calc.minimise_stable(path, self.Prod)
except:
self.Prod = tl.setCalc(self.Prod, self.lowString, self.lowMeth,
self.lowLev)
self.Prod._calc.minimise_stable(path, self.Prod)
try:
self.ProdFreqs, zpe = self.Prod._calc.read_vibs()
except:
self.ProdFreqs, zpe = self.characteriseFreqInternal(self.Prod)
self.ProdName = tl.getSMILES(self.Prod, False, partialOpt=False)
self.Prod = tl.setCalc(self.Prod, self.singleString, self.singleMeth,
self.singleLev)
self.productEnergy = self.Prod.get_potential_energy() + zpe
try:
self.Prod._calc.close()
except:
pass
if self.is_bimol_prod == True:
try:
self.biProd = tl.setCalc(self.biProd, self.highString,
self.highMeth, self.highLev)
self.biProd._calc.minimise_stable(path, self.biProd)
except:
self.biProd = tl.setCalc(self.biProd, self.lowString,
self.lowMeth, self.lowLev)
self.biProd._calc.minimise_stable(path, self.biProd)
try:
self.biProdFreqs, zpe = self.biProd._calc.read_vibs()
except:
self.biProdFreqs, zpe = self.characteriseFreqInternal(
self.biProd)
self.biProd = tl.setCalc(self.biProd, self.singleString,
self.singleMeth, self.singleLev)
self.biProdName = tl.getSMILES(self.biProd,
False,
partialOpt=False)
self.productEnergy += (self.biProd.get_potential_energy() + zpe)
try:
self.biProd._calc.close()
except:
pass
try:
try:
self.CombProd = tl.setCalc(self.CombProd, self.highString,
self.highMeth, self.highLev)
self.CombProd._calc.minimise_stable(path, self.CombProd)
except:
self.CombProd = tl.setCalc(self.CombProd, self.lowString,
self.lowMeth, self.lowLev)
self.CombProd._calc.minimise_stable(path, self.CombProd)
try:
self.CombProdFreqs, zpe = self.CombProd._calc.read_vibs()
except:
self.CombProdFreqs, zpe = self.characteriseFreqInternal(
self.CombProd)
self.CombProd = tl.setCalc(self.CombProd, self.singleString,
self.singleMeth, self.singleLev)
self.CombProdName = tl.getSMILES(self.CombProd,
False,
partialOpt=False)
self.CombProductEnergy = (
self.CombProd.get_potential_energy() + zpe)
try:
self.CombProd._calc.close()
except:
pass
except:
pass
def get_additional_lines(self, ts, p):
string1 = "Prod\n\n0 " + str(self.parameters['mult']) + "\n"
xyz1 = tl.convertMolToGauss(p)
string2 = "TS\n\n0 " + str(self.parameters['mult']) + "\n"
xyz2 = tl.convertMolToGauss(ts)
return string1 + xyz1 + string2 + xyz2
def __init__(self, path):
self.pathStride = 1
self.fixToPath = False
self.pathDistCutOff = False
self.BiList = []
self.full_geom_print = False
mpath = path + '/inp.txt'
self.InitialBi = False
self.mixedTimestep = False
self.RunType = "MechGen"
self.printNEB = False
self.checkAltProd = False
self.eneBXD = False
self.comBXD = False
self.printDynPath = False
self.printNEB = False
self.maxAdapSteps = 0
self.eneBoxes = 0
self.grainSize = 0
self.numberOfBoxes = 10
self.dynPrintFreq = 5
self.dynPrintStart = 100
self.ReactIters = 1
self.NEBrelax = False
self.GenBXDrelax = False
self.NEBsteps = 3
self.printFreq = 10
self.QTS3 = False
# BXD defaults
self.decorrelationSteps = 10
self.histogramBins = 1
self.epsilon = 0.95
self.principalCoordinates = []
# Open Input
inp = open(mpath, "r")
geom = open(mpath,"r").readlines()
self.printString = ""
#Generate empty list to hold mm3 types if required
self.atomTypes = []
self.MMfile = 'test.pdb'
words = geom[1].split()
# Check if the first word is Atoms, if so the starting molecule is specified in the input file
if words[0] == "Atoms":
self.numberOfAtoms = int(words[2])
size = self.numberOfAtoms
self.species = np.zeros(size, dtype='str')
self.cartesians = np.zeros((size,3), dtype='float')
self.masses = np.zeros((size), dtype='float')
for i in range(3,size+3):
# Get index for species and cartesian arrays
j = i - 3
words = geom[i].split()
self.species[j] = words[0]
self.cartesians[j][0] = float(words[1])
self.cartesians[j][1] = float(words[2])
self.cartesians[j][2] = float(words[3])
for i in range (0,size):
if self.species[i] == 'C':
self.masses[i] = 12.0107
if self.species[i] == 'O':
self.masses[i] = 15.9994
if self.species[i] == 'H':
self.masses[i] = 1.00794
if self.species[i] == 'N':
self.masses[i] = 12.0107
self.StartType = "specified"
# Loop over lines
for line in inp:
#GenBXD input;
#Start type is the starting reactant unless specified in already. StartType is a SMILES string or file path to be read in
if re.search("Start", line):
self.StartType = str(line.split()[2])
self.Start = str(line.split()[3])
# End type specifies the target product for the GenBXD run
if re.search("End", line):
self.EndType = str(line.split()[2])
self.End = str(line.split()[3])
if re.search("MMfile", line):
self.MMfile = str(line.split()[2])
# PathType defines the prgress along Traj. It is either simpleDistance (distance from boundary), distance (cumulative version of simple distance)
# linear (projection onto linear path between start and end) or curve (projection onto some trajectory or path)
if re.search("PathType", line):
self.PathType = str(line.split()[2])
if self.PathType == 'curve' or self.PathType == 'gates':
self.PathFile = str(line.split()[3])
# Determines the collective variables for GenBXD
if re.search("CollectiveVarType", line):
self.CollectiveVarType = str(line.split()[2])
if self.CollectiveVarType == 'specified':
uVar = line.split()[3]
uVar = uVar.replace("n","\n")
c = StringIO(uVar)
self.CollectiveVar = np.loadtxt(c, delimiter=',')
elif self.CollectiveVarType == 'file':
i = 4
while i < len(line.split()):
array = self.readPrincipalComponents(line.split()[i], line.split()[3])
self.principalCoordinates.append(array)
i+=1
elif self.CollectiveVarType != 'changedBonds':
self.CollectiveVarTraj = str(line.split()[3])
if re.search("RunType", line):
self.RunType = str(line.split()[2])
if re.search("NEBrelax", line):
self.NEBrelax = True
if re.search("printNEB", line):
self.printNEB = True
if re.search("printDynPath", line):
self.printDynPath = True
self.dynPrintFreq = int(line.split()[1])
self.dynPrintStart = int(line.split()[2])
if re.search("QTS3", line):
self.QTS3 = True
if re.search("checkAltProd", line):
self.checkAltProd = True
if re.search("NEBsteps", line):
self.NEBsteps = int(line.split()[2])
if re.search("name", line):
self.dirName = line.split()[2]
if re.search("cores", line):
self.cores =int(line.split()[2])
if re.search("ReactionIterations", line):
self.ReactIters =int(line.split()[2])
if re.search("trajectoryMethod1", line):
self.trajMethod1 = line.split()[2]
self.trajLevel1 = line.split()[3]
self.trajMethod2 = self.trajMethod1
self.trajLevel2 = self.trajLevel1
if re.search("trajectoryMethod2", line):
self.trajMethod2 = line.split()[2]
self.trajLevel2 = line.split()[3]
if re.search("lowLevel", line):
self.lowerMethod = line.split()[2]
self.lowerLevel = line.split()[3]
if re.search("highLevel", line):
self.higherMethod = line.split()[2]
self.higherLevel = line.split()[3]
if re.search("singleLevel", line):
self.singleMethod = line.split()[2]
self.singleLevel = line.split()[3]
if re.search("TrajectoryInitialTemp", line):
self.trajInitT = int(line.split()[2])
if re.search("MDIntegrator", line):
self.MDIntegrator = line.split()[2]
if re.search("mdSteps", line):
self.mdSteps = int(line.split()[2])
if re.search("printFreq", line):
self.printFreq = int(line.split()[2])
if re.search("timeStep", line):
self.timeStep = float(line.split()[2])
if re.search("endOnReaction", line):
self.endOnReaction = bool(line.split()[2])
if re.search("reactionWindow", line):
self.reactionWindow = int(line.split()[2])
if re.search("BiReactant", line):
self.InitialBi = True
if re.search("LangFriction", line):
self.LFric = float(line.split()[2])
if re.search("full_geom_print", line):
self.full_geom_print = True
if re.search("LangTemperature", line):
self.LTemp = float(line.split()[2])
if re.search("BiList", line):
BiListStrings = [str(line.split()[2])]
for x in BiListStrings:
self.BiList.append(tl.getMolFromSmile(x))
if re.search("BiRate", line):
self.BiRates = [str(line.split()[2])]
if re.search("BiTemp", line):
self.BiTemp = float(line.split()[2])
# BXD input
if re.search("eneBXD", line):
if (line.split()[2]) == 'True':
self.eneBXD = True
if (line.split()[2])== 'False':
self.eneBXD = False
if self.eneBXD is True:
if re.search("eneUpper", line):
self.eneUpper = float(line.split()[2])
if re.search("eneLower", line):
self.eneLower = float(line.split()[2])
if re.search("eneAdaptive", line):
if (line.split()[2]) == 'True':
self.eneAdaptive = True
if (line.split()[2])== 'False':
self.eneAdaptive = False
if re.search("eneMax", line):
self.eneMax = float(line.split()[2])
if re.search('eneEvents', line):
self.eneEvents = int(line.split()[2])
if re.search('eneBoxes', line):
self.eneBoxes = int(line.split()[2])
if re.search('decorrelationSteps', line):
self.decorrelationSteps = int(line.split()[2])
if re.search('histogramLevel', line):
self.epsilon = float(line.split()[2])
if re.search('histogramBins', line):
self.histogramBins = int(line.split()[2])
if re.search('fixToPath', line):
self.fixToPath = True
if re.search('pathStride', line):
self.pathStride = int(line.split()[2])
if re.search('pathDistCutOff', line):
uVar = line.split()[2]
if ',' in uVar:
c = StringIO(uVar)
self.pathDistCutOff = np.loadtxt(c, delimiter=',')
else:
self.pathDistCutOff= np.empty(1000)
self.pathDistCutOff.fill(float(uVar))
if re.search("maxHits",line):
self.maxHits = int(line.split()[2])
if re.search("runsThrough",line):
self.runsThrough = int(line.split()[2])
if re.search("adaptiveSteps",line):
self.maxAdapSteps = int(line.split()[2])
if re.search("grainSize",line):
self.grainSize = int(line.split()[2])
if re.search("numberOfBoxes",line):
self.numberOfBoxes = int(line.split()[2])
if re.search("comBXD", line):
if (line.split()[2]) == 'True':
self.comBXD = True
if (line.split()[2])== 'False':
self.comBXD = False
if self.comBXD is True or self.InitialBi is True:
if re.search("minCOM", line):
self.minCOM = float(line.split()[2])
if re.search("fragment_indices", line):
self.fragIndices = [int(line.split()[2]),int(line.split()[3])]
# Geometry opt
if re.search("GeomPot", line):
self.GeomPot1 = line.split()[2]
# Single point ene
if re.search("singlePoint", line):
self.singlePoint = line.split()[2]
# Master Equation
if re.search("maxSimulationTime", line):
self.maxSimulationTime = float(line.split()[2])
if re.search("equilThreshold", line):
self.equilThreshold = int(line.split()[2])
# Look for mm3 types
if re.search("AtomTypes", line):
self.atomTypes = line.split()[2]
self.atomTypes = self.atomTypes.split(",")
for i in range (0,len(self.atomTypes)):
self.atomTypes[i] = float(self.atomTypes[i])
self.trajMethod = self.trajMethod1
self.trajLevel = self.trajLevel1