you want
jmolscript: {within(-0.1, atomno=1)}.vxy=...
there to pick up all unit cells.
OK, I have set it up so that
#jmolscript: .....
will be read at the end of wien2k files. So, for example,
#jmolscript: load "" {1 1 1} PACKED
at the end of the file automatically loads a fully packed unit cell, even
just with
load "t.struct"
On Thu, May 21, 2009 at 4:03 PM, Laurence Marks <l-ma...@northwestern.edu>wrote:
> I was thinking about asking you to add the jmolscript protocol to
> Wien2k; anything after the final symmetry element matrices is ignored,
> so could go there. (There is no slack before.)
>
> It looks like if I add (via code) a set of lines
> #jmolscript: {atomno=1}.vxy=...
> #jmolscript: {atomno=2}.vxy=...
>
> This will work so long as I reduce to P1. Fortunately I have the code
> to reduce to debugged, so this is not hard (albeit not elegant). This
> will enable loading with different numbers of cells and everything
> should work....
>
> N.B. For your earlier email, "C" is "c" (as in gcc). It looks as
> though #jmolscript: is a single line command, which is OK; I thought
> it might be possible to have multiple lines with the "C" delinearator.
>
> On Thu, May 21, 2009 at 3:40 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> > 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
> >
> >
>
>
>
> --
> 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
