Sorry, I missed the 2x2x2 supercell business -- just adapt the lattice {i j
k} and SUPERCELL parameters to suit:
load ..... {1 1 1} supercell {2 2 2}
would be one 2x2x2 supercell.
load ..... {2 2 1} supercell {2 2 2}
would be four such supercells.
Bob
On Mon, Nov 28, 2011 at 10:20 PM, Robert Hanson <[email protected]> wrote:
>
>
> On Mon, Nov 28, 2011 at 9:14 PM, krishna Mohan Grangadhran Prasanna <
> [email protected]> wrote:
>
>> Dear Jmol-users,
>>
>> Am a newbie user of Jmol. Since I deal with extended systems in general,
>> I wish to visualize these systems with Jmol (version 12.0).
>> Suppose if I have XYZ information of atoms and Lattice Vectors (ie.
>> Cartesian components of the L.V.), can I use Jmol to plot super-cell and/or
>> its periodic repetitions?
>>
>
> yes and yes
>
>
>>
>> For example, if I have the below data, (like vasp’s POSCAR format), How
>> can I use Jmol to visualize a 2x2x2 cell? Do I really want to use
>> Jmol-script?
>>
>> rather than what?
>
>
>> Lattice Vectors [u v w] =
>>
>> 4.36130393 -2.518 0.0
>> 4.36130393 2.518 0.0
>> 0.0 0.0 16.0540126
>>
>> Geometry =
>> Cu .00000000 .00000000 -.02858610
>> Cu 2.18065197 1.25900000 -.02858610
>> Cu 2.18065197 -1.25900000 -.02858610
>> Cu 4.36130393 .00000000 -.02858610
>> Cu 1.45376813 .0000000 -2.05580070
>> Cu 3.63442009 1.2590000 -2.05580070
>> Cu 3.63442009 -1.2590000 -2.05580070
>> Cu 5.81507206 .0000000 -2.05580070
>> Cu 2.90753593 .00000000 -4.08264189
>> Cu 5.08818789 1.25900000 -4.08264189
>> Cu 5.08818789 -1.25900000 -4.08264189
>> Cu 7.26883986 .00000000 -4.08264189
>> C -.00134965 .00000000 3.50000000
>> H .51772049 -.89768008 3.86520453
>> H -1.03852359 .00000000 3.86458322
>> H .51772049 .89768008 3.86520453
>> H -.00021200 .00000000 2.39768919
>>
>>
> What is the actual source of the data? It doesn't look like POSCAR data to
> me. Sure would be easier just to read the VASP output if you have that.
>
> But if you can preprocess that data a bit, it should be no problem. With
> Jmol 12.3.8 (see
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip -- which I
> just uploaded) you can do this using the new ZMATRIX option (I know, this
> is not a Z-Matrix, but the option allows for Gaussian Z-Matrix format,
> which includes simple Cartesian input as well:
>
> load data 'model'
> #ZMATRIX
>
> Cu .00000000 .00000000 -.02858610
> Cu 2.18065197 1.25900000 -.02858610
> Cu 2.18065197 -1.25900000 -.02858610
> Cu 4.36130393 .00000000 -.02858610
> Cu 1.45376813 .0000000 -2.05580070
> Cu 3.63442009 1.2590000 -2.05580070
> Cu 3.63442009 -1.2590000 -2.05580070
> Cu 5.81507206 .0000000 -2.05580070
> Cu 2.90753593 .00000000 -4.08264189
> Cu 5.08818789 1.25900000 -4.08264189
> Cu 5.08818789 -1.25900000 -4.08264189
> Cu 7.26883986 .00000000 -4.08264189
> C -.00134965 .00000000 3.50000000
> H .51772049 -.89768008 3.86520453
> H -1.03852359 .00000000 3.86458322
> H .51772049 .89768008 3.86520453
> H -.00021200 .00000000 2.39768919
> end 'model' {2 2 1} supercell {3 1 1} spacegroup "P1" unitcell [
>
> 4.36130393 -2.518 0.0
> 4.36130393 2.518 0.0
> 0.0 0.0 16.0540126
> ]
>
> Bob Hanson
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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