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# fmt: off
from pathlib import Path
import pytest
from ase import Atoms
from ase.build import add_adsorbate, fcc211
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.mep import AutoNEB, NEBTools
from ase.optimize import BFGS, QuasiNewton
@pytest.mark.optimize()
def test_autoneb(asap3, testdir):
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
@pytest.mark.optimize()
def test_Au2Ag(testdir):
def attach_calculators(images):
for i in range(len(images)):
images[i].calc = EMT()
d = 4
initial = Atoms('Au2Ag',
positions=((-d, 0, 0), (-d / 2, 0, 0), (d, 0, 0)))
middle = initial.copy()
middle[1].position[0] = 0
final = initial.copy()
final[1].position[0] += d
attach_calculators([initial, middle, final])
for i, image in enumerate([initial, middle, final]):
image.set_constraint(FixAtoms([0, 2]))
fmax = 0.05
for i, image in enumerate([initial, final]):
opt = QuasiNewton(image)
opt.run(fmax=fmax)
middle.get_forces()
prefix = Path('subdir') / 'neb'
prefix.parent.mkdir()
for i, image in enumerate([initial, middle, final]):
image.write(f'{prefix}00{i}.traj')
autoneb = AutoNEB(attach_calculators,
prefix=prefix,
optimizer=QuasiNewton,
n_simul=1,
n_max=5,
fmax=fmax,
k=0.5,
parallel=False,
maxsteps=[20, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert nebtools.get_barrier()[0] == pytest.approx(4.185, 1e-3)
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