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]> 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 supercellwith
> 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 <olorieg...@
> 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]
> *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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