The Jmol application probably does have some minor issues there. I'm not
sure if you load vibrational data by script, for example, that the vibration
button works. Most of us use the console. But should that be the case, then
a bug report should be filed so I can get to it.
If you have implemented vibrations in an XYZ file, then that's all you need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file("yyy.xyz")
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript = ""
for (var i = 3; i <= S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm guessing
here
var x = "{" + (S[i])[3][45] + "}"
var v = "{" + (S[i])[48][0] + "}"
myscript = myscript + "x=" + x + ";v=" + v+";{within(-2.5,x)}.vxyz =
v\n"
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks <l-ma...@northwestern.edu>wrote:
> Let me be a bit more specific. I have implemented vibrations using an
> xyz file, but since this does not contain the crystal lattice
> information cell repeats have to be done ahead of time. What I would
> like to do is for a crystal (cif, Wien2k, other) add vibrations
> (probably with a script) and then display these using "standard" tools
> for repeating the unit cell etc, with the vibrations obeying the
> appropriate symmetry and translational operations.
>
> When I attempted to do this it looked like this is not currently
> supported (the vibrations button was inactive) although I might not
> have done it correctly and I don't think I used the console.
>
> N.B., there are some issues with the vibrations having a lower
> symmetry than the unit cell so strictly speaking the cell should have
> P1 symmetry. Walk before run; are vibrations active for crystals.
>
> N.N.B., an alternative would be to be able to add crystalline repeat
> information to an xyz format.
>
> --
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Electron crystallography is the branch of science that uses electron
> scattering to study the structure of matter.
>
>
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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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