A question about NEB in ATK 2008.10

[fangyongxinxi]

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)

[Anders Blom]

It's necessary to set the k-point sampling on the KohnShamMethod, if you want to use it for periodic systems. Use an example for a KohnShamMethod for a normal bulk system (not for NEB) made with the Script Generator as a template, then you will see how to introduce it.