I let you know; I'll get some of my students (if they do what I ask
which is not always true) to do something for my group web pages. The
"bigger" Wien2k community is only starting to use jmol, but I expect
there will be examples and I'll let you know if/when I run across
some.

On 5/23/09, Robert Hanson <hans...@stolaf.edu> wrote:
> that's what I figured. The key for you is to introduce enough slop in the
> loadAtomDataTolerance parameter to get the job done. Since you don't have
> the issue of disordered crystals, you can be quite generous there -- 0.5
> Angstroms easily. In other situations people will need to have a much
> tighter tolerance. So I set the default to be on the low side -- and the
> system will notify you with a warning if no atoms matched the position (a
> potential problem) or a debugging message (not a problem) if more than one
> did.
>
> Since I was working on this code anyway, and it seemed like such a neat
> solution, I also added the ability to add other parameters as well this way
> --- occupation, partialcharge, temperature, and even atom position "xyz".
> There are going to be some very good applications of this. Since you already
> are making .XYZ files for your vibrations, this should be just about all you
> need.
>
> I'm quite excited to see this avenue of Jmol use developing. Do show us some
> cool web pages with jiggling crystals some time.
>
> Bob
>
>
>
> On Sat, May 23, 2009 at 8:05 AM, Laurence Marks <l-ma...@northwestern.edu>
> wrote:
>
> > I did not get back to you yesterday -- proposals.
> >
> > The difference between the vibration positions in the xyz file and the
> > atom positions in SrTiO3.struct is "right", not a concern. More
> > explanation than you want. SrTiO3 is only cubic in an average sense at
> > room temperature; really it is dynamically fluctuating with soft
> > phonons (vibrations) being cubic only in the average structure. The
> > xyz file was refined (DFT) in a cubic cell and is non-symmetric, this
> > is "right". The other SrTiO3.struct file is symmetry constrained to be
> > cubic, which is OK but not quite consistent with the xyz file -- there
> > is no need for them to be. More accurately the real (DFT) cell should
> > be tetragonal cell.
> >
> >
> >
> >
> > On 5/23/09, Robert Hanson <hans...@stolaf.edu> wrote:
> > > I've changed the tolerance for this and added more functionality. See
> > > http://chemapps.stolaf.edu/jmol/docs/#loadproperty
> > >
> > > Laurence, you will need to do something like:
> > >
> > > set loadAtomDataTolerance 0.2
> > >
> > > because your vib data don't match the struct file data more precisely
> than
> > > that.
> > >
> > > Bob
> > >
> > >
> > >
> > >
> > > On Fri, May 22, 2009 at 2:41 PM, Robert Hanson <hans...@stolaf.edu>
> wrote:
> > >
> > > > 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
> > > 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
> > > > > >>>
> > > > > >>>
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --
> > > > > >> 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
> > > >
> > >
> > >
> > >
> > > --
> > > 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
> 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
> > >
> > >
> >
> >
> > --
> > 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
>
> ------------------------------------------------------------------------------
>  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
>
>


-- 
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.

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