Re: [Jmol-users] Generating Periodic Boundary Structure in Jmol for Molecular Dynamics

[Oloriegbe, S. <olo...@mi...>]

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 [ha...@st...]
Sent: Thursday, November 01, 2012 12:10 PM
To: jmo...@li...; 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 <olo...@mi...<mailto:olo...@mi...>> 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 <olo...@mi...<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: jmo...@li...<mailto:jmo...@li...>
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
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