On Jun 17, 2008, at 7:54 , Bob Hanson wrote: > Michael Sternberg wrote: >> Thank you for the quick fix! I downloaded and tested 11.5.41. >> Scalars with a decimal(!) are recognized as partial charges, and >> "select" and "color" can operate on them. Great! >> > -- right -- I forgot to mention that integer in the 5th field of an > xyz > file are translated as formal charge, not partial charge. I figured > this > would not be an issue, as any program that generates partial charges > will add the decimal even for integers. Correct me if I'm wrong.
> The XYZ reader reads any of the following now: > > Sym x y z > Sym x y z vibX vibY vibZ > Sym x y z FormalCharge(int) > Sym x y z FormalCharge(int) vibX vibY vibZ > Sym x y z PartialCharge(decimal) > Sym x y z PartialCharge(decimal) vibX vibY vibZ > > where Sym is either an element symbol (C, Fe, Si) or an element symbol > preceded by an isotope number (2H, 13C, etc.) > I believe this is sort of a bastardization of the original XMOL > format. > But I agree, it's a great format. This will work fine. Formal charge is a good extension. If a program should use printf %g for the scalar, files can be fixed easily, without concern for white-space or column widths. The opportunity of formal vs. partial charge is too good to pass, ditto for the isotopes. > What a lot of people probably don't realize is that you can even apply > full symmetry (unit cells, symmetry operations) to this file format > simply by adding UNITCELL and SPACEGROUP parameters to the LOAD > command. > In other words, you can "retrofit" simple xyz data to an original > full-symmetry format. That is really a very powerful capability of > Jmol. Thanks for pointing this out. We've been using XYZ mainly as a simple bridging format from in-house codes to viz., and this feature allows recovering unitcells. Regards, Michael ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
