[lammps-users] cutoff value delete_atoms overlap > value for pair potential

Dear lammps-users,

I want to create a bicrystal separated by a symmetric tilt grain boundary. In documentation, the delete_atoms command is able to remove atoms that are too close to each other.

However, it’s mentioned that when “overlap” style is used, a pair style with force cutoffs greater than or equal to the desired overlap cutoff between pairs of relevant atom types must be included, even though the pair potential will not be evaluated. I found that for the pair potential file that I use, the cutoff value (0.3 distance unit) is, I think, too small such that there are still several atoms in GB that are too close to each other. As a result, when I try to obtain a relaxed structure, most atoms near the boundary are significantly displaced, making the boundary looks amorphous. However, when I increase the cutoff value (to 1.2 distance unit) and relax the structure again, most atoms near the boundary are not displaced so much and symmetric tilt GB structure is still preserved.

My question is: what would be the physical consequence if I use the cutoff value for “overlap” style in delete_atoms command that is higher than the cutoff of the pair potential?

That concludes my email and many thanks for your help.


The pair potential in this case is not being used to compute
the energy of the system or to run dynamics with. It's
cutoff is simply being used by the neighbor list routine
to create a neighbor list with enough atom pairs in it that
the delete_atoms operation can do its job. As soon
as delete_atoms is used, you can redefine whatever
pair potential you want and a new cutoff, before running
dynamics, etc.

In other words, it doesn't matter what pair potential you
use to do the delete_atoms. E.g. just a LJ is fine.
Just define a cutoff as long (or longer)
than the overlap distance you want to delete with. If you don't do
that then you will get an error, b/c the neighbor list doesn't contain
pairs out to the distance you are asking it to delete.