On Thu, May 21, 2009 at 8:59 AM, Laurence Marks <[email protected]>wrote:
> I managed to load TiO.struct and set the vibrations for the Ti, and it
> is there for all equivalent sites so this works fine. (The button at
> the top is fine; the right-mouse click does not show vibrations as an
> option.)
>
> However, I could not find a way to alter the number of unit cells
> being shown without reloading the structure; is there a way of doing
> this?
>
No. These are determined in the loading code and no where else. What people
do sometimes is load more than you need, then only DISPLAY the ones you
want.
>
> The alternative is to use embedded jmol scripting either in an xyz
> file (to set the cell so, maybe {1 1 1} PACKED or similar will be
> understood) or in a cif. I'll try this.
>
Embedded scripts are run after loading, not before. It's an interesting idea
to provide some sort of load functionality within the file, but to date we
don't have that.
>
> N.B., does a "jmolscript:" get embedded in a { } (i.e. C)?
>
There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{ }
sets off math. { } sets off either coordinates or selection, depending upon
the context. What is "C"?
>
> On 5/21/09, Robert Hanson <[email protected]> wrote:
> > The Jmol application probably does have some minor issues there. I'm not
> > sure if you load vibrational data by script, for example, that the
> vibration
> > button works. Most of us use the console. But should that be the case,
> then
> > a bug report should be filed so I can get to it.
> >
> > If you have implemented vibrations in an XYZ file, then that's all you
> need.
> > Just write a little Jmol script that
> >
> > 1) loads the Wien2k or other file with full symmetry
> > 2) reads that xyz file into a variable using vibdata = file("yyy.xyz")
> > 3) changes that to Jmol script format and runs it.
> >
> >
> > I think this is a few lines of Jmol script:
> >
> > function applyVibData(filename)
> > var vibdata = load(filename)
> > var S = vibdata.split()
> > var myscript = ""
> > for (var i = 3; i <= S.size; i=i+1)
> > var line = S[i]
> > # change the numbers below to match your file format -- I'm guessing
> > here
> > var x = "{" + (S[i])[3][45] + "}"
> > var v = "{" + (S[i])[48][0] + "}"
> > myscript = myscript + "x=" + x + ";v=" + v+";{within(-2.5,x)}.vxyz
> =
> > v\n"
> > end for
> > script inline @myscript
> > end function
> >
> >
> >
> > Bob
> >
> >
> >
> > On Thu, May 21, 2009 at 7:11 AM, Laurence Marks <
> [email protected]>
> > wrote:
> > >
> > > Let me be a bit more specific. I have implemented vibrations using an
> > > xyz file, but since this does not contain the crystal lattice
> > > information cell repeats have to be done ahead of time. What I would
> > > like to do is for a crystal (cif, Wien2k, other) add vibrations
> > > (probably with a script) and then display these using "standard" tools
> > > for repeating the unit cell etc, with the vibrations obeying the
> > > appropriate symmetry and translational operations.
> > >
> > > When I attempted to do this it looked like this is not currently
> > > supported (the vibrations button was inactive) although I might not
> > > have done it correctly and I don't think I used the console.
> > >
> > > N.B., there are some issues with the vibrations having a lower
> > > symmetry than the unit cell so strictly speaking the cell should have
> > > P1 symmetry. Walk before run; are vibrations active for crystals.
> > >
> > > N.N.B., an alternative would be to be able to add crystalline repeat
> > > information to an xyz format.
> > >
> > > --
> > > 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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> >
> >
> > --
> > 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
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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.
>
>
> ------------------------------------------------------------------------------
> 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
> [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
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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iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
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