Could anyone on the list help me with getting rid of overlapping atoms on
edges, boundaries and corners after generating a superstructure from jmol
through a CIF file. The XYZ file would be use as input in Molecular dynamics
program LAMMPS.
I use load "filename.CIF" {1 1 1} supercell {8 8 2}. There are 8 atoms per unit
cell, so I expect a total of
8* 8 * 8 * 2 = 1024 atoms, but I got 1171 atoms instead.
I took the painstaking method of removing the overlapping atoms visually, but
such approach can be plague with errors, so any help doing it automatically
using a script would be appreciated.
BTW. I read most of the Jmol documentation and non of the commands seems to
help.
Suleiman.
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