I am trying to simulate the movement and clustering of vacancies in a bulk. I create my block, remove some atoms, and then strain. The goal is to then watch the many microvacancies cluster into a larger vacancy as per the paper referenced below. The paper attached used a GCMC swap with metropolis criteria, which appears to be the command fix/atom swap, to swap lattice atoms with vacancies. However, I am not able to get this to work. The command requires 2 atom types, one being the bulk atom. However, as far as I know the second atom cannot be a vacancy.
Is there any way to use this command (or some other command), to allow for vacancy migration during straining? It is tough to visualize as well as seeing the vacancies is difficult.
I confess I haven't read the paper you referenced, but since nobody
else replied yet,...
No. There is no way to use fix atom/swap with vacancies.
You will have to dream up some kind of particle which behaves like a
vacancy, and somehow keep the particle from drifting away from the
1) Perhaps the author is not integrating the equations of motion? In
that case, I imagine you could define a type of particle which simply
exerts no force on it's neighbors at all, and let the system evolve
just using "fix atom/swap" and nothing else. (IE, don't use things
like "fix nvt", or "fix npt")
2) On the other hand, if the particles in the simulation need to be
able to wiggle, then perhaps a particle of the same size which
interacts only sterically (repulsively) with the normal atoms might
also behave in a way that approximates a vacancy. (? As long as you
don't care too much about bulk mechanical properties. Such particles
could definitely make the resulting crystal more stiff than it
otherwise would be.) One way to do that would be to use a
Lennard-Jones interaction and set the cutoff to where the local minima
is located (at sigma*2^(1/6)). Such particles would tend to cluster
together to minimize the their contact with normal atoms (which is
unfavorable compared to contacts between normal atoms). (Since you
are simulating a bulk crystal, I assume you are using periodic
boundary conditions. Otherwise you also have to worry about
preventing particles on the surface from drifting away.)
3) Failing that, you will have to find some way to keep the particles
from drifting away from the vacancy site. Perhaps an external force?
I don't know if this helped at all.
(P.S. Hopefully, you realize that when you use "fix atom_swap" in
LAMMPS, you are not necessarily swapping atoms which are located
nearby in space. But this does not matter unless you care about the
dynamics of the system.)