From: Robert H. <ha...@st...> - 2011-09-08 17:03:43
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I guess we are reading the .cell file. Is this a different file? Pieremanuele, how hard would it be to read frequencies from CASTEP files? On Thu, Sep 8, 2011 at 12:01 PM, Robert Hanson <ha...@st...> 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 <kr...@gm...> 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 <kr...@gm... >> > <mailto:kr...@gm...>> 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 <kr...@gm... >> > <mailto:kr...@gm...> >> > > <mailto:kr...@gm... <mailto:kr...@gm...>>> 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 >> > > Jmo...@li... >> > <mailto:Jmo...@li...> >> > > <mailto:Jmo...@li... >> > <mailto:Jmo...@li...>> >> > > 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 >> > > Jmo...@li... >> > <mailto:Jmo...@li...> >> > > 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 >> > Jmo...@li... >> > <mailto:Jmo...@li...> >> > 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 >> > >> > >> > 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 >> > Jmo...@li... >> > 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 >> Jmo...@li... >> 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 > > > 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 |