From: Robert H. <ha...@st...> - 2009-05-21 22:35:35
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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-...@no...>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 <ha...@st...> 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 <ha...@st...> > wrote: > >> > >> > >> 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? > >> > >> 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 <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. > >>> > > > >>> > > > >>> > > >>> > > ------------------------------------------------------------------------------ > >>> > > 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 > >>> > > Jmo...@li... > >>> > > 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 > >>> > Jmo...@li... > >>> > 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 > >>> Jmo...@li... > >>> 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 > > Jmo...@li... > > 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 > Jmo...@li... > 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 |