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
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