{1 1 1} indicates you want a packed cell, which duplicates atoms on faces.
try {555 555 0} instead and see if that helps.
On Thu, Nov 1, 2012 at 8:51 AM, Oloriegbe, Suleiman <[email protected]
> wrote:
> 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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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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