Dear Robert, Robert Hanson wrote:
I guess we are reading the .cell file. Is this a different file?
The .cell file is an input file. As far as I know Jmol can not read any CASTEP output files (unless you care to contradict me!).
The main output file - the .castep file - does not include any eigenvector information from a phonon calculation, so while you could read the frequencies, that would not help with animation. The full phonon data file has suffix ".phonon" and is designed to be more easily machine readable. A small example is attached, along with my conversion to xyz. However my scripts does more - including generating a supercell to display phonons at commensurate q/=0 wavevectors. It would be rather neat if JMol could do all of that directly.
There are also trajectory files for MD and geometry optimtimisation, again which we currently convert to xyz, and electron density files, which we convert to Gaussian CUBE. I'm very happy to discuss and help with extensions to read these formats. Keith
Pieremanuele, how hard would it be to read frequencies from CASTEP files? On Thu, Sep 8, 2011 at 12:01 PM, Robert Hanson <[email protected] <mailto:[email protected]>> wrote: oooh. Tell me all about it! We have a CASTEP output reader -- are we not getting frequencies there? On Thu, Sep 8, 2011 at 11:35 AM, Keith Refson <[email protected] <mailto:[email protected]>> wrote: Dear Robert, Yes, that has fixed it. Thanks very much for the very rapid response. Just to let you know the context, I am developing scripts to animate the phonon vibrations from CASTEP output. This works by translating into an xyz file, which seems by far the most convenient way of inputting phonon data into JMol. Keith Refson Robert Hanson wrote: > Good. I think I fixed it. See > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > > > On Thu, Sep 8, 2011 at 10:01 AM, Keith Refson <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> wrote: > > This is with Jmol 12.2.2RC5 run as a stand alone application under > Linux. > > Robert Hanson wrote: > > I don't know. Works for me. What version? > > > > > > On Thu, Sep 8, 2011 at 7:10 AM, Keith Refson <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > > <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> wrote: > > > > 2 > > Mode 1, 1026.29 1/cm jmolscript: {load "" {1 1 1} PACKED > unitcell > > {2.573336 2.573336 2.573336 60.000000 60.000000 60.000000}; > vibration > > scale 0; vibration on} > > B 0.0000 0.0000 0.0000 0.0927 0.2005 -0.0564 > > N 1.2867 0.7429 0.5253 -0.0719 -0.1555 0.0438 > > > > > > (note the "vibration scale 0") still produces a vibration > with a scale > > which is clearly non-zero. > > > > > > Is it possible that you are seeing this specifically with the > > application (not the applet) and specifically for the first model > you load? > > Yes, and yes. A second load of the xyz file into the same jmol session > does honour the "vibration scale" command. > > Keith > > > > > > > Keith > > > > > ------------------------------------------------------------------------------ > > Doing More with Less: The Next Generation Virtual Desktop > > What are the key obstacles that have prevented many mid-market > > businesses > > from deploying virtual desktops? How do next-generation virtual > > desktops > > provide companies an easier-to-deploy, easier-to-manage and more > > affordable > > virtual desktop > model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > > _______________________________________________ > > Jmol-users mailing list > > [email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > > <mailto:[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > > > -- > > 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 <tel:507-786-3107> <tel:507-786-3107 <tel: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 > > > > > > > ------------------------------------------------------------------------------ > > Doing More with Less: The Next Generation Virtual Desktop > > What are the key obstacles that have prevented many mid-market > businesses > > from deploying virtual desktops? How do next-generation virtual > desktops > > provide companies an easier-to-deploy, easier-to-manage and more > affordable > > virtual desktop > model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > > > > > > > > _______________________________________________ > > Jmol-users mailing list > > [email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > Doing More with Less: The Next Generation Virtual Desktop > What are the key obstacles that have prevented many mid-market > businesses > from deploying virtual desktops? How do next-generation virtual > desktops > provide companies an easier-to-deploy, easier-to-manage and more > affordable > virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > _______________________________________________ > Jmol-users mailing list > [email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > 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 <tel: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 > > > ------------------------------------------------------------------------------ > Doing More with Less: The Next Generation Virtual Desktop > What are the key obstacles that have prevented many mid-market businesses > from deploying virtual desktops? How do next-generation virtual desktops > provide companies an easier-to-deploy, easier-to-manage and more affordable > virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > > > > _______________________________________________ > Jmol-users mailing list > [email protected] <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ Jmol-users mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 <tel: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 ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
BN-phon.xyz
Description: application/wine-extension-xyz
BEGIN header
Number of ions 2
Number of branches 6
Number of wavevectors 1
Frequencies in cm-1
IR intensities in (D/A)**2/amu
Unit cell vectors (A)
0.000000 1.819623 1.819623
1.819623 0.000000 1.819623
1.819623 1.819623 0.000000
Fractional Co-ordinates
1 0.000000 0.000000 0.000000 B 10.811000
2 0.250000 0.250000 0.250000 N 14.006740
END header
q-pt= 1 0.000000 0.000000 0.000000 1.000000 1.000000
0.000000 0.000000
1 58.268188 0.0000000
2 58.268188 0.0000000
3 58.292484 0.0000000
4 1026.286406 13.9270643
5 1026.286406 13.9270643
6 1262.072445 13.9271267
Phonon Eigenvectors
Mode Ion X Y
Z
1 1 -0.188759409143 0.000000000000 0.344150676582 0.000000000000
-0.532910085817 0.000000000000
1 2 -0.213788416373 0.000000000000 0.389784162147 0.000000000000
-0.603572578624 0.000000000000
2 1 -0.506371267280 0.000000000000 -0.416656077168 0.000000000000
-0.089715190073 0.000000000000
2 2 -0.573514781701 0.000000000000 -0.471903590472 0.000000000000
-0.101611191184 0.000000000000
3 1 0.381712598768 0.000000000000 -0.381712598812 0.000000000000
-0.381712598730 0.000000000000
3 2 0.433161430960 0.000000000000 -0.433161431010 0.000000000000
-0.433161430917 0.000000000000
4 1 0.431092607594 0.000000000000 -0.160735361462 0.000000000000
0.591827969056 0.000000000000
4 2 -0.380622988260 0.000000000000 0.141917473232 0.000000000000
-0.522540461492 0.000000000000
5 1 0.434492641457 0.000000000000 0.590583470288 0.000000000000
-0.156090828832 0.000000000000
5 2 -0.383624967478 0.000000000000 -0.521441660837 0.000000000000
0.137816693359 0.000000000000
6 1 0.433161430963 0.000000000000 -0.433161430963 0.000000000000
-0.433161430963 0.000000000000
6 2 -0.381712598770 0.000000000000 0.381712598770 0.000000000000
0.381712598770 0.000000000000
------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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