Hi Jonathan,I took a peek at the gamess file you mentioned and the example of the qchem reader doesn't work completely here.
Since whenever MO information is encountered the orbitals are appended to the orbitals vector (so it keeps adding mutliple sets of orbitals to the same vector). At the end of the readMolecularOrbitals method the existing moData structure is associated with the atomset. Thus this happens for the first and last structure encountered (or any other that triggers the reading of the MO orbitals). So it looks like you have to generate a new moData instance (as I did in qchem), but here you need to reuse the basis set definition (i.e. the shells, and gaussians) from your first structure (since the basis set is not output again) and start over with the build-up a newly created orbitals vector.
Cheers, 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? BobDr. Jonathan H. Gutow Chemistry Department [email protected]UW-Oshkosh Office: 920-424-1326800 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
------------------------------------------------------------------------------ Are you an open source citizen? Join us for the Open Source Bridge conference! Portland, OR, June 17-19. Two days of sessions, one day of unconference: $250. Need another reason to go? 24-hour hacker lounge. Register today! http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org
_______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
