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from ase.build import add_adsorbate, fcc100
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms, FixedPlane
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:
# from ase.visualize import view
# 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.calc = EMT()
for i in range(5):
qn = QuasiNewton(slab, trajectory='mep%d.traj' % i)
qn.run(fmax=0.05)
# Move gold atom along x-axis:
slab[-1].x += slab.get_cell()[0, 0] / 8
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