def _setup_images_global():
N_intermediate = 3
N_cell = 2
initial = bulk('Cu', cubic=True)
initial *= N_cell
# place vacancy near centre of cell
D, D_len = get_distances(np.diag(initial.cell) / 2,
initial.positions,
initial.cell, initial.pbc)
vac_index = D_len.argmin()
vac_pos = initial.positions[vac_index]
del initial[vac_index]
# identify two opposing nearest neighbours of the vacancy
D, D_len = get_distances(vac_pos,
initial.positions,
initial.cell, initial.pbc)
D = D[0, :]
D_len = D_len[0, :]
nn_mask = np.abs(D_len - D_len.min()) < 1e-8
i1 = nn_mask.nonzero()[0][0]
i2 = ((D + D[i1])**2).sum(axis=1).argmin()
print(f'vac_index={vac_index} i1={i1} i2={i2} '
f'distance={initial.get_distance(i1, i2, mic=True)}')
final = initial.copy()
final.positions[i1] = vac_pos
initial.calc = calc()
final.calc = calc()
qn = ODE12r(initial)
qn.run(fmax=1e-3)
qn = ODE12r(final)
qn.run(fmax=1e-3)
images = [initial]
for image in range(N_intermediate):
image = initial.copy()
image.calc = calc()
images.append(image)
images.append(final)
neb = NEB(images)
neb.interpolate()
return neb.images, i1, i2
def _ref_vacancy_global(_setup_images_global):
# use distance from moving atom to one of its neighbours as reaction coord
# relax intermediate image to the saddle point using a bondlength constraint
images, i1, i2 = _setup_images_global
initial, saddle, final = (images[0].copy(), images[2].copy(),
images[4].copy())
initial.calc = calc()
saddle.calc = calc()
final.calc = calc()
saddle.set_constraint(FixBondLength(i1, i2))
opt = ODE12r(saddle)
opt.run(fmax=1e-2)
nebtools = NEBTools([initial, saddle, final])
Ef_ref, dE_ref = nebtools.get_barrier(fit=False)
print('REF:', Ef_ref, dE_ref)
return Ef_ref, dE_ref, saddle