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from math import pi, cos, sin
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLengths
from ase.optimize import BFGS
from ase.build import fcc111, add_adsorbate
for wrap in [False, True]:
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO', positions=[(-xpos + 1.2, 0, -zpos),
(-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixBondLengths([[-3, -2], [-3, -1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%d.traj' % wrap)
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
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