def get_atoms():
# 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)
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))
# Use EMT potential:
slab.set_calculator(EMT())
# Initial state:
qn = QuasiNewton(slab, logfile=None)
qn.run(fmax=0.05)
initial = slab.copy()
# Final state:
slab[-1].x += slab.get_cell()[0, 0] / 2
qn = QuasiNewton(slab, logfile=None)
qn.run(fmax=0.05)
final = slab.copy()
# Setup a NEB calculation
constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial])
images = [initial]
for i in range(3):
image = initial.copy()
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images, parallel=mpi.parallel)
neb.interpolate()
def set_calculator(calc):
i = 0
for image in neb.images[1:-1]:
if not mpi.parallel or mpi.rank // (mpi.size // 3) == i:
image.set_calculator(calc)
i += 1
neb.set_calculator = set_calculator
return neb
from ase_ext.io import PickleTrajectory
from ase_ext.neb import NEB
from ase_ext.calculators.lj import LennardJones
from ase_ext.optimize import QuasiNewton
print([a.get_potential_energy() for a in PickleTrajectory('H.traj')])
images = [PickleTrajectory('H.traj')[-1]]
for i in range(4):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images)
neb.interpolate()
for image in images:
image.set_calculator(LennardJones())
for a in neb.images:
print(a.positions[-1], a.get_potential_energy())
dyn = QuasiNewton(neb, trajectory='mep.traj')
print(dyn.run(fmax=0.01, steps=25))
for a in neb.images:
print(a.positions[-1], a.get_potential_energy())
initial = Atoms('Cu',
positions=[(0, 0, 0)],
cell=(d, d, 1.0),
pbc=(True, True, False))
initial *= (2, 2, 1) # 2x2 (100) surface-cell
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.0
initial += Atom('Ag', (d / 2, d / 2, h0))
if 0:
view(initial)
# Make band:
images = [initial.copy() for i in range(6)]
neb = NEB(images, climb=True)
# Set constraints and calculator:
constraint = FixAtoms(list(range(len(initial) - 1)))
for image in images:
image.set_calculator(EMT())
image.set_constraint(constraint)
# Displace last image:
images[-1].positions[-1] += (d, 0, 0)
#images[-1].positions[-1] += (d, d, 0)
# Relax height of Ag atom for initial and final states:
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.01)
dyn2 = QuasiNewton(images[-1])
print(Z[0] - Z[1])
print(Z[1] - Z[2])
print(Z[2] - Z[3])
b = 1.2
h = 2.0
slab += Atom('C', (d, 2 * y / 3, h))
slab += Atom('O', (3 * d / 2, y / 3, h))
traj = PickleTrajectory('initial.traj', 'w', slab)
dyn = QuasiNewton(slab)
dyn.attach(traj.write)
dyn.run(fmax=0.05)
#view(slab)
# Make band:
images = [slab.copy() for i in range(6)]
neb = NEB(images, climb=True)
# Set constraints and calculator:
for image in images:
image.set_calculator(EMT())
image.set_constraint(constraint)
# Displace last image:
images[-1].positions[-1] = (2 * d, 2 * y / 3, h)
traj = PickleTrajectory('final.traj', 'w', images[-1])
dyn = QuasiNewton(images[-1])
dyn.attach(traj.write)
dyn.run(fmax=0.05)
# Interpolate positions between initial and final states:
neb.interpolate()
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.2373
initial += Atom('Pt', (10.96, 11.074, h0))
initial += Atom('Pt', (13.7, 11.074, h0))
initial += Atom('Pt', (9.59, 8.701, h0))
initial += Atom('Pt', (12.33, 8.701, h0))
initial += Atom('Pt', (15.07, 8.701, h0))
initial += Atom('Pt', (10.96, 6.328, h0))
initial += Atom('Pt', (13.7, 6.328, h0))
if 0:
view(initial)
# Make band:
images = [initial.copy() for i in range(7)]
neb = NEB(images)
# Set constraints and calculator:
indices = np.compress(initial.positions[:, 2] < -5.0,
list(range(len(initial))))
constraint = FixAtoms(indices)
for image in images:
image.set_calculator(ASAP())
image.constraints.append(constraint)
# Displace last image:
for i in range(1, 8, 1):
images[-1].positions[-i] += (d / 2, -h1 / 3, 0)
write('initial.traj', images[0])
# Relax height of Ag atom for initial and final states: