ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
neb = NEB(images, parallel=True)
neb.interpolate()
qn = BFGS(neb)
if rank % (size // 3) == 0:
traj = PickleTrajectory(’neb%d.traj’ % j, ’w’, images[1 + j], master=True)
qn.attach(traj)
qn.run(fmax=0.05)
6.2.11 Diffusion of gold atom on Al(100) surface (constraint)
In this tutorial, we will calculate the energy barrier that was found using the NEB method in the Diffusion of gold
atom on Al(100) surface (NEB) tutorial. Here, we use a siple FixedPlane constraint that forces the Au atom to
relax in the yz-plane only:
from ase.lattice.surface import fcc100, add_adsorbate
from ase.constraints import FixAtoms, FixedPlane
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100(’Al’, size=(2, 2, 3))
add_adsorbate(slab, ’Au’, 1.7, ’hollow’)
slab.center(axis=2, vacuum=4.0)
# Make sure the structure is correct:
#view(slab)
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
#print mask
fixlayers = FixAtoms(mask=mask)
# Constrain the last atom (Au atom) to move only in the yz-plane:
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
# Use EMT potential:
slab.set_calculator(EMT())
# Initial state:
for i in range(5):
qn = QuasiNewton(slab, trajectory=’mep%d.traj’ % i)
qn.run(fmax=0.05)
slab[-1].x += slab.get_cell()[0, 0] / 8
The result can be analysed with the command ag mep?.traj -n -1 (choose Tools → NEB). The barrier is found to
be 0.35 eV - exactly as in the NEB tutorial.
Here is a side-view of the path (unit cell repeated twice):
6.2. ASE 37