I want to do ENB calculation by ATK 2008.10, and I make a py file ( copy the format of c2h6 example in ATK 2008.10 ), the structure is periodic . When I run this script, it shows:
NLPolicyError: This instance of KohnSham Method can only be apply to a MoleculeConfiguration
Terminated Abnormally
so, could you give example scripts about how to do NEB with the structures of periodic structure and two-probes structure.
Thanks.
my scripts:
from ATK.KohnSham import *
super_cell = [[4, 0, 0],
[0, 4, 0],
[0, 0, 4]]*Angstrom
elements = [Hydrogen, Hydrogen, Hydrogen]
coordinates = [[ 0. , 0. , 0. ],
[ 0. , 0. , 0.80000001],
[ 0. , 1.20000005, 0. ]]*Angstrom
rt_params = runtimeParameters(verbosity_level = 2)
mesh = electronDensityParameters(mesh_cutoff = 20*Rydberg)
basis = basisSetParameters (type = SingleZetaPolarized)
dft_method = KohnShamMethod(
basis_set_parameters = basis,
electron_density_parameters = mesh
)
# Import NEB routines
from NLExamples import NEB
from NLExamples import KohnShamSimulation
from NLExamples import MDMin
# Collect simulations
simulations = []
for n in range(20):
# each configuration must be a unique class instance,
# so it is neccesary to include the following lines:
mol = PeriodicAtomConfiguration(
super_cell,
elements,
cartesian_coordinates=coordinates
)
sim = KohnShamSimulation(mol,dft_method,rt_params)
simulations.append(sim)
# Define elements and unit cell coordinates
elements = [Hydrogen, Hydrogen, Hydrogen]
coordinates = [[ 0. , 0. , 0. ],
[ 0. , 0. , 1.20000005],
[ 0. , 0.8, 0. ]]*Angstrom # here we change the coordinate os the atoms in the box h2-h3
# Add the final configuration to simulations
mol = PeriodicAtomConfiguration(
super_cell,
elements,
cartesian_coordinates=coordinates
)
sim = KohnShamSimulation(mol,dft_method,rt_params)
simulations.append(sim)
# Setup the NEB simulation
neb = NEB(simulations,linearpath=True,prefix='H3')
# Setup and run MD simulation for NEB
dyn = MDMin(neb,dt=0.05,prefix='H3')
dyn.run(20)
