Thanks. The overlapping problem is gone, but the resulting system have
incorrect number of atoms. I got 2783 atoms when using select cell=555. The
structure looks perfect but the number of atoms is not. For my system of
CuAlO2. I got 726 Al atoms, 726 Cu atoms and 1331 O atoms (instead of 726 *2 =
1452 ).
Any help resolving this would be appreciated.
FYI: I use the following commands;
load "filename.cif" {555 555 0} supercell {11 11 2}
select cell=555
write XYZ "output.xyz"
Suleiman.
________________________________
From: Robert Hanson [[email protected]]
Sent: Thursday, November 01, 2012 12:10 PM
To: [email protected]; Oloriegbe, Suleiman
Subject: Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for
Molecular Dynamics
You would first select the atoms you want. For example,
select cell=555
On Thu, Nov 1, 2012 at 11:59 AM, Oloriegbe, Suleiman
<[email protected]<mailto:[email protected]>> wrote:
Thanks Bob,
I didn't get your e-mail despite configuring jmol to allow me receive mails
from the list. I was able to copy your response from the mail list website (see
below). I eventually use;
load "filename.cif" {555 555 0} supercell { 8 8 2 } and got a supercell with
small box encompassing some of the atoms which appears to be fine with some
other noisy residual atoms outside box. When I wrote out the XYZ file, all
atoms appears in the output file.
Is there any command that help print out atoms only in the small box of
interest?
Suleiman.
{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]<http://missouri.edu>
> 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.
"It is better to light a candle than to curse the darkness."
...Eleanor Roosevelt
________________________________
From: Oloriegbe, Suleiman
Sent: Thursday, November 01, 2012 8:51 AM
To: [email protected]<mailto:[email protected]>
Subject: Generating Periodic Boundary Structure in Jmol for Molecular Dynamics
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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