Ah, but what you can do is this:
Within the file have the embedded command:
jmolscript: load "" { 1 1 1 } packed
This says "reload me with those parameters". Now, the problem might be that
the wien2k reader does not have that enabled. You would have to decide where
you would find room for that, and then we would have to augment the reader
to look for it. How much slack does this file format have?
On Thu, May 21, 2009 at 3:23 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
> On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
> <l-ma...@northwestern.edu>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 <hans...@stolaf.edu> 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 <
>> l-ma...@northwestern.edu>
>> > 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.
>> > >
>> > >
>> >
>> ------------------------------------------------------------------------------
>> > > 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.
>>
>>
>> ------------------------------------------------------------------------------
>> 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
