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from ase.build import add_adsorbate, fcc100
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
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)
slab.set_constraint(FixAtoms(mask=mask))
# Use EMT potential:
slab.calc = EMT()
# Initial state:
qn = QuasiNewton(slab, trajectory='initial.traj')
qn.run(fmax=0.05)
# Final state:
slab[-1].x += slab.get_cell()[0, 0] / 2
qn = QuasiNewton(slab, trajectory='final.traj')
qn.run(fmax=0.05)
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