Hi Jonathan, The way I understand it (and it has been a little while since I messed with this), is that the setMOData function associates the moData hashtable argument (that contains the basis set and orbital information) with an atomset. I have been looking at qchem data with multiple models each with their own orbitals without a problem. The thing to remember is to make sure to create a new moData hashtable whenever a new model needs one (as I did in the qchem reader whenever I encounter the definition of the basis to be used. (To be sure, I null the moData the moment a new structure is encountered).
I just added a qchem output file to the Jmol-datafiles that has orbitals for each of the optimization steps for optimizing water. I hope this helps. René On Jun 19, 2009, at 9:12 AM, Jonathan Gutow wrote: > Bob and René, > The issue is that orbitals are stored in the orbitals vector which > is associated with the AtomSetCollection rather than with each > AtomSet. Thus when there is a different set of MOs associated with > different AtomSets they are simply appended in order to the orbitals > for the AtomSetCollection. This means that for any given AtomSet > Jmol gives you the list of all orbitals. Glancing through the code > for readers other than GAMESS, I think the problem is the same. > However, I don't have any example data sets from other programs that > have orbitals associated with more than one of the models. > My preference would be to have an orbitals vector associated with > each AtomSet. > > I have put a number of new example files in the gamess directory in > the Jmol-datafiles directory in SVN. A small example file that shows > the problem is HCl_geom_DZV+Diff+CCSD(T).log. Actually, this problem > shows up in all standard GAMESS geometry optimization runs as by > default the initial guess orbitals and the optimized orbitals for the > final geometry are included in the .log file. In this file the > initial guess orbitals associated with the first geometry are 1 - 56 > as loaded by Jmol. The optimized orbitals that go with the final > geometry are numbered 57 +, the way Jmol presently loads them. In > this particular file the initial guess orbitals are listed after the > heading "EIGENVECTORS" and the final geometry MOs are after the > heading "MOLECULAR ORBITALS". > > Let me know what you think and thanks for the suggestions and help. > > Jonathan > On Jun 18, 2009, at 4:19 PM, Robert Hanson wrote: > >> Jonathan, can you send me the GAMESS file and explain exactly what >> it should be doing? >> >> Bob >> > > Dr. Jonathan H. Gutow > Chemistry Department [email protected] > UW-Oshkosh Office: > 920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
