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
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