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from ase.autoneb import AutoNEB
from ase.build import fcc211, add_adsorbate
from ase.constraints import FixAtoms
from ase.neb import NEBTools
from ase.optimize import QuasiNewton
def test_autoneb(asap3):
EMT = asap3.EMT
fmax = 0.02
# Pt atom adsorbed in a hollow site:
slab = fcc211('Pt', size=(3, 2, 2), vacuum=4.0)
add_adsorbate(slab, 'Pt', 0.5, (-0.1, 2.7))
# Fix second and third layers:
slab.set_constraint(FixAtoms(range(6, 12)))
# Use EMT potential:
slab.calc = EMT()
# Initial state:
with QuasiNewton(slab, trajectory='neb000.traj') as qn:
qn.run(fmax=fmax)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
with QuasiNewton(slab, trajectory='neb001.traj') as qn:
qn.run(fmax=fmax)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def attach_calculators(images):
for i in range(len(images)):
images[i].calc = EMT()
autoneb = AutoNEB(attach_calculators,
prefix='neb',
optimizer='BFGS',
n_simul=3,
n_max=7,
fmax=fmax,
k=0.5,
parallel=False,
maxsteps=[50, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert abs(nebtools.get_barrier()[0] - 0.937) < 1e-3
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