Re: [Jmol-users] Change vibration scale from xyz embedded script

[Robert H. <ha...@st...>]

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/
>> >      >     _______________________________________________
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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 <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