def calc_productAndTS(name):
smiles = 'C1' + name + 'C1'
mol = rdkitTools.smiles2plams(smiles)
mol.properties.smiles = smiles
product = dftb(templates.geometry.overlay(settings),
mol,
job_name=name + "_product")
constraint1 = "dist 1 2"
constraint2 = "dist 4 5"
sv1 = startvalue[name[0]]
sv2 = startvalue[name[2]]
# scan input
if name[0] == name[2]:
# symmetric molecule
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 4,
'start': [sv1, sv2],
'stepsize': [0.1, 0.1]
}
}
else:
scan = {
'constraint': constraint1,
'surface': {
'nsteps': 4,
'start': sv1,
'stepsize': 0.1
},
'scan': {
'constraint': constraint2,
'surface': {
'nsteps': 4,
'start': sv2,
'stepsize': 0.1
}
}
}
# PES = gathered (promised) result objects for each point in the scan
PES = PES_scan(dftb,
settings,
product.molecule,
scan,
job_name=name + "_PESscan")
# get the object presenting the molecule with the maximum energy calculated from the scan
apprTS = select_max(PES, 'energy')
# perform the TS optimization using the default TS template
TS = dftb(templates.ts.overlay(settings),
apprTS.molecule,
job_name=name + "_TS")
return product, TS
'start': sv1,
'stepsize': 0.1
},
'scan': {
'constraint': constraint2,
'surface': {
'nsteps': 4,
'start': sv2,
'stepsize': 0.1
}
}
}
# returns a set of results object containing the output of
# each point in the scan
LT = PES_scan(dftb, settings, product, scan)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(LT, 'energy')
# Run the TS optimization, using the default TS template
TS = dftb(templates.ts.overlay(settings), apprTS.molecule)
# Actual execution of the jobs
reactives = [E_reactant, E_product, TS]
E_reactant, E_product, TS = run(gather(*reactives), n_processes=1)
# Retrieve the molecular coordinates
mol = TS.molecule
d1 = bond_distance(mol.atoms[0].coords, mol.atoms[1].coords)
constraint1 = "dist 1 5"
constraint2 = "dist 3 4"
# scan input
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 6,
'start': [2.3, 2.3],
'stepsize': [0.1, 0.1]
}
}
# returns a set of results object containing the output of
# each point in the scan
lt = PES_scan([dftb, adf], settings, cnc, scan)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
appr_hess = dftb(templates.freq.overlay(settings), apprTS.molecule)
t = Settings()
t.specific.adf.geometry.inithess = appr_hess.archive.path
# Run the TS optimization with ADF, using initial hessian from DFTB freq calculation
ts = run(adf(templates.ts.overlay(settings).overlay(t), appr_hess.molecule),
n_processes=1)
# Retrieve the molecular coordinates