Re: [Jmol-users] Vibrations

[Laurence M. <L-...@no...>]

I found an example on a web page on how to use jmolscript in a cif
(probably should be documented better). Works fine for a cif file
although it's technically wrong; the symmetry operations should be
applied to the vibrations. I'll play around with adding vibrations to
a cif file, and making an xyz file understand translational symmetry
(probably some property, a clue with shorten my hunting.)

On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
<L-...@no...> 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?
>
> 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.
>
> N.B., does a "jmolscript:" get embedded in a { } (i.e. C)?
>
> On 5/21/09, Robert Hanson <ha...@st...> 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-...@no...>
>> 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
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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.