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
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