Possibly. But first you will have to promise me you won't make the atom
vibrations be so totally unrealistically large! ;)
So you are using animated gifs there that you produce with something. You
will need to:
1) create a JavaScript function on that page that will be called by the
image map.
2) have access to the G03 log file.
3) decide what you want to have happen in the Jmol window -- will it be the
atoms of the crystal themselves vibrating? Will it be another structure,
simpler and more like the one in the GIF?
4) assign vibration vectors to the atoms in the Jmol crystal and get them
vibrating.
(4) is the tricky part. If you want the crystal atoms to vibrate, I suggest
loading the G03 log file into a second Jmol frame using "load append", then
copy the vibration vectors when needed to the atoms in the first model --
the crystal using something like:
load append "myfile.g03"
display 1.1
{1.1}.vxyz = {2.2}.vxyz.all
vibration on
But you may have to map the atoms differently -- the above assumes the first
atom of the g03 file is the same as the first atom in the CIF file, etc. So
you might need something like:
{atomIndex=0}.vxyz = {atomnoIndex=33}.vxyz
{atomIndex=1}.vxyz = {atomnoIndex=34}.vxyz
etc.
Bob Hanson
On Tue, Oct 6, 2009 at 5:29 PM, Tzontonel <[email protected]>wrote:
> Hi guys,
>
> I have a big question, but first I make a short introduction. My work-page
> is: http://rdrs.uaic.ro/minerals/vib.html
> Scroll down (Raman spectrum and vibrations), when you see the vibration
> jmolapplet (second applet in this page). When you click on the spectral
> line/peak (example: 1087.4 band), a newpopup open with a gif animation. I
> don't want this "method". The big question: it's possible to click on the
> spectra line and then interact with vibration applet (in the same page)? Now
> I use this code on the spectrum photo:
>
> [...]
> <img src="spectra/calcite.jpg" class="vibration_map" alt="Calcite spectra"
> border="0" usemap="#calcite_map">
> <map name="calcite_map">
> <area shape="rect" coords="72,1,92,261"
> href="JavaScript:newPopup1('vibrations/calcite/Translational (Ca,
> CO3).html');" title="Translational (Ca, CO3)" alt="Translational (Ca, CO3)">
> <area shape="rect" coords="167,1,189,261"
> href="JavaScript:newPopup1('vibrations/calcite/V4 Symmetric
> deformation.html');" title="V4 Symmetric deformation" alt="V4 Symmetric
> deformation">
> <area shape="rect" coords="251,1,271,261"
> href="JavaScript:newPopup1('vibrations/calcite/V1 Symmetric
> stretching.html');" title="V1 Symmetric stretching" alt="V1 Symmetric
> stretching">
> <area shape="rect" coords="329,1,349,261"
> href="JavaScript:newPopup1('vibrations/calcite/V3 Asymmetric
> stretching.html');" title="V3 Asymmetric stretching" alt="V3 Asymmetric
> stretching">
> <area shape="rect" coords="398,1,418,261" title="V1+V4" alt="V1+V4">
> </map>
> [...]
>
>
> It's possible to change the href code with a JavaScript command who
> interact with vibration applet. When I press on the area shape, the
> jmolapplet vibration change with respectively frame/vibration.
>
> Note: I use the .log file (Gaussian03w) inside the applet.
>
> stud. Andrei Ionut Apopei
> Department of Geology
>
>
>
> ------------------------------------------------------------------------------
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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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