size=size,
element="Au",
debug=0,
periodic=(0, 0, 1))
basis = atoms.GetUnitCell()
center = 0.5 * array([basis[0, 0], basis[1, 1], basis[2, 2]]) + array(
[0.1, 0.1, 0.1])
disl = Dislocation(center, atoms.MillerToDirection((1, 1, 0)),
atoms.MillerToDirection((1, 1, 0)) / 2.0)
#atoms = ListOfAtoms(slab)
disl.ApplyTo(atoms)
atoms.SetCalculator(EMT(EMTRasmussenParameters()))
# Constant temperatur dynamics
dyn = Langevin(atoms, 5 * femtosecond, 300 * kB, 0.002)
# Run Common Neighbor Analysis on each n_output timestep, using the
# positions averaged over the last n_avg timesteps, and writing the
# result to the output file.
avg = TimeAveragedPositions(atoms, n_avg, n_output)
dyn.Attach(avg)
cna = RestrictedCNA(avg, verbose=1)
avg.Attach(cna)
# We output and plot the instantaneous positions. Replace atoms with
# avg to output and plot the averaged positions instead.
plotlog = open("plot.log", "w")
