Tom, you are in luck!
Just add a Jmol LOAD command as the comment in the XYZ file:
12
jmolscript: load "" {1 2 1} spacegroup "x,y,z;x,y,1-z" unitcell {6.0 6.0 5.0
90 90 90}
C 1.38480 0.00000 0.00000 1.0 1.38480 0.00000 0.00000
C -1.38480 -0.00000 0.00000 0.9 -1.38480 -0.00000 0.00000
C 0.69240 1.19927 0.00000 0.3 0.69240 1.19927 0.00000
C 0.69240 -1.19927 0.00000 -0.3 0.69240 -1.19927 0.00000
C -0.69240 -1.19927 0.00000 0.3 -0.69240 -1.19927 0.00000
C -0.69240 1.19927 0.00000 0.6 -0.69240 1.19927 0.00000
H 1.22858 2.12797 0.00000 0.4 1.22858 2.12797 0.00000
H 1.22858 -2.12797 0.00000 0.5 1.22858 -2.12797 0.00000
H -1.22858 -2.12797 0.00000 0.6 -1.22858 -2.12797 0.00000
H -1.22858 2.12797 0.00000 0.8 -1.22858 2.12797 0.00000
H -2.45717 -0.00000 0.00000 0.0 -2.45717 -0.00000 0.00000
H 2.45717 0.00000 0.00000 -1.3 2.45717 0.00000 0.00000
That fourth column is the partial charge. The last three columns are bogus
vibrations -- you won't need those.
Here "jmolScript:" indicates an embedded command, and
LOAD "" {1 2 1} spacegroup ... unitcell ...
tells Jmol to reload the file with that set of load parameters.
All coordinates are considered Cartesian -- don't use unit coordinates here.
Bob
On Mon, Oct 26, 2009 at 4:36 PM, Thomas Manz <[email protected]> wrote:
> Hi,
>
> I want to store partial atomic charges for periodic structures
> and load them into jmol for visualization purposes. Does anyone know
> the simplest file format to accomplish this?
>
> I know that partial atomic charges can be stored in an xyz file format.
> Does anyone know whether periodic lattice vectors can also be
> placed in an xyz file format and loaded into jmol.
> If so, does anyone know where I could obtain a sample file of a
> periodic structure in xzy format that can be read by jmol?
>
> Sincere thanks,
>
> -Tom M.
>
>
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--
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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