OK, Laurence. Check out
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and associated
files. The idea is that now anyone can load vibration information from any
file format supporting that by just adding the "VIBRATION" keyword to the
load command.
The command is:
load VIBRATION "filename"
Jmol 11.7.37 introduces the capability to apply vibrational data from one
file to model data in another. Adding VIBRATION to the load command
instructs Jmol to load only the vibrational information from a file. The
vibrational data are applied to the currently selected set of atoms.
All standard load parameters are accepted, although many will be ignored,
however whereas the default for a normal LOAD operation is to load all
files, the default for LOAD VIBRATION is to read only the first set of
vibrational data in a multi-model file.
For each "atom" position and vector that is read, Jmol applies the vibration
to all selected atoms having a unit cell normalized position within *
loadAtomDataTolerance* (default 0.2) Angstroms of the position read from the
file.
If the file being loaded contains embedded Jmol script commands, those
commands will be processed after the application of the vibrational vectors.
For example,
*load "myfile.struct" {{5 5 1}} PACKED; select _O; load VIBRATION "vibs.xyz"
3*
first loads a set of unit cells from myfile.struct, then applies only to the
oxygen atoms the third vibration set found in vibs.xyz. All oxygen atoms in
all unit cells are given vibrational vectors even though the data in
vibs.xyz might only be for one unit cell.
I'm betting this will serve your purposes nicely. I increased the default
tolerance to 0.2 Angstroms because I noticed that in the file you gave me
the O atom positions were 0.13 Angstrom off from the ones in SrTiO3.struct.
But this is now settable, so you may want to play with that.
-Bob
On Thu, May 21, 2009 at 6:20 PM, Laurence Marks <l-ma...@northwestern.edu>wrote:
> N.B., for the example I sent there may be a slight drift (i.e.
> vibration is not about the center-of-mass). This is due to numerical
> issues in the DFT which I have to work around (later).
>
> On Thu, May 21, 2009 at 6:09 PM, Laurence Marks
> <l-ma...@northwestern.edu> wrote:
> > Works nicely, although that's not the best example because it will
> > only ever load packed! Not a problem.
> >
> > On Thu, May 21, 2009 at 6:01 PM, Laurence Marks
> > <l-ma...@northwestern.edu> wrote:
> >> Actually, SrTiO3 is very strange, goes unstable by very small amounts
> >> with soft vibrations (phonons).
> >>
> >> Your too quick for me, I'm only just testing that I have the right jar
> >> for the #jmolsript: at the end of Wien2k, so it may be a bit before I
> >> respond sensibly to your earlier email!
> >>
> >> On Thu, May 21, 2009 at 5:54 PM, Robert Hanson <hans...@stolaf.edu>
> wrote:
> >>> Naive comment:
> >>>
> >>> If the Strontium atoms are the massive ones, wouldn't the oxygens be
> the
> >>> ones that move?
> >>>
> >>> --
> >>> 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
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> >>> is a gathering of tech-side developers & brand creativity
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> >>>
> >>
> >>
> >>
> >> --
> >> 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.
> >>
> >
> >
> >
> > --
> > 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.
> >
>
>
>
> --
> 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.
>
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals.
> Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://www.creativitycat.com
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 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
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Group, R/GA, & Big Spaceship. http://www.creativitycat.com
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