I let you know; I'll get some of my students (if they do what I ask which is not always true) to do something for my group web pages. The "bigger" Wien2k community is only starting to use jmol, but I expect there will be examples and I'll let you know if/when I run across some.
On 5/23/09, Robert Hanson <hans...@stolaf.edu> wrote: > that's what I figured. The key for you is to introduce enough slop in the > loadAtomDataTolerance parameter to get the job done. Since you don't have > the issue of disordered crystals, you can be quite generous there -- 0.5 > Angstroms easily. In other situations people will need to have a much > tighter tolerance. So I set the default to be on the low side -- and the > system will notify you with a warning if no atoms matched the position (a > potential problem) or a debugging message (not a problem) if more than one > did. > > Since I was working on this code anyway, and it seemed like such a neat > solution, I also added the ability to add other parameters as well this way > --- occupation, partialcharge, temperature, and even atom position "xyz". > There are going to be some very good applications of this. Since you already > are making .XYZ files for your vibrations, this should be just about all you > need. > > I'm quite excited to see this avenue of Jmol use developing. Do show us some > cool web pages with jiggling crystals some time. > > Bob > > > > On Sat, May 23, 2009 at 8:05 AM, Laurence Marks <l-ma...@northwestern.edu> > wrote: > > > I did not get back to you yesterday -- proposals. > > > > The difference between the vibration positions in the xyz file and the > > atom positions in SrTiO3.struct is "right", not a concern. More > > explanation than you want. SrTiO3 is only cubic in an average sense at > > room temperature; really it is dynamically fluctuating with soft > > phonons (vibrations) being cubic only in the average structure. The > > xyz file was refined (DFT) in a cubic cell and is non-symmetric, this > > is "right". The other SrTiO3.struct file is symmetry constrained to be > > cubic, which is OK but not quite consistent with the xyz file -- there > > is no need for them to be. More accurately the real (DFT) cell should > > be tetragonal cell. > > > > > > > > > > On 5/23/09, Robert Hanson <hans...@stolaf.edu> wrote: > > > I've changed the tolerance for this and added more functionality. See > > > http://chemapps.stolaf.edu/jmol/docs/#loadproperty > > > > > > Laurence, you will need to do something like: > > > > > > set loadAtomDataTolerance 0.2 > > > > > > because your vib data don't match the struct file data more precisely > than > > > that. > > > > > > Bob > > > > > > > > > > > > > > > On Fri, May 22, 2009 at 2:41 PM, Robert Hanson <hans...@stolaf.edu> > wrote: > > > > > > > OK, Laurence. Check out > > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > > and associated files. The idea is that now anyone can load vibration > > > information from any file format supporting that by just adding the > > > "VIBRATION" keyword to the load command. > > > > > > > > > > > > > > > > The command is: > > > > > > > > load VIBRATION "filename" > > > > > > > > Jmol 11.7.37 introduces the capability to apply vibrational data from > one > > > file to model data in another. Adding VIBRATION to the load command > > > instructs Jmol to load only the vibrational information from a file. The > > > vibrational data are applied to the currently selected set of atoms. > > > > > > > > All standard load parameters are accepted, although many will be > ignored, > > > however whereas the default for a normal LOAD operation is to load all > > > files, the default for LOAD VIBRATION is to read only the first set of > > > vibrational data in a multi-model file. > > > > > > > > For each "atom" position and vector that is read, Jmol applies the > > > vibration to all selected atoms having a unit cell normalized position > > > within loadAtomDataTolerance (default 0.2) Angstroms of the position > read > > > from the file. > > > > > > > > If the file being loaded contains embedded Jmol script commands, those > > > commands will be processed after the application of the vibrational > vectors. > > > > > > > > For example, > > > > > > > > load "myfile.struct" {{5 5 1}} PACKED; select _O; load VIBRATION > > > "vibs.xyz" 3 > > > > > > > > first loads a set of unit cells from myfile.struct, then applies only > to > > > the oxygen atoms the third vibration set found in vibs.xyz. All oxygen > atoms > > > in all unit cells are given vibrational vectors even though the data in > > > vibs.xyz might only be for one unit cell. > > > > > > > > > > > > I'm betting this will serve your purposes nicely. I increased the > default > > > tolerance to 0.2 Angstroms because I noticed that in the file you gave > me > > > the O atom positions were 0.13 Angstrom off from the ones in > SrTiO3.struct. > > > But this is now settable, so you may want to play with that. > > > > > > > > -Bob > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, May 21, 2009 at 6:20 PM, Laurence Marks > <l-ma...@northwestern.edu> > > > wrote: > > > > > > > > > N.B., for the example I sent there may be a slight drift (i.e. > > > > > vibration is not about the center-of-mass). This is due to numerical > > > > > issues in the DFT which I have to work around (later). > > > > > > > > > > On Thu, May 21, 2009 at 6:09 PM, Laurence Marks > > > > > > > > > > > > > > > > > > > > <l-ma...@northwestern.edu> wrote: > > > > > > Works nicely, although that's not the best example because it will > > > > > > only ever load packed! Not a problem. > > > > > > > > > > > > On Thu, May 21, 2009 at 6:01 PM, Laurence Marks > > > > > > <l-ma...@northwestern.edu> wrote: > > > > > >> Actually, SrTiO3 is very strange, goes unstable by very small > amounts > > > > > >> with soft vibrations (phonons). > > > > > >> > > > > > >> Your too quick for me, I'm only just testing that I have the > right > > > jar > > > > > >> for the #jmolsript: at the end of Wien2k, so it may be a bit > before I > > > > > >> respond sensibly to your earlier email! > > > > > >> > > > > > >> On Thu, May 21, 2009 at 5:54 PM, Robert Hanson > <hans...@stolaf.edu> > > > wrote: > > > > > >>> Naive comment: > > > > > >>> > > > > > >>> If the Strontium atoms are the massive ones, wouldn't the > oxygens be > > > the > > > > > >>> ones that move? > > > > > >>> > > > > > >>> -- > > > > > >>> 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. > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > 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. > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > > > 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 > > -- 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
