I may have a chance to look at this this weekend, if someone else cannot check it first. Off the top of my head this does sound like it should work, and I don't see how it would break other things. If you get to check this post to the list so that I won't duplicate effort.
Jonathan On Oct 21, 2009, at 7:14 PM, SourceForge.net wrote: > Bugs item #2883616, was opened at 2009-10-21 19:14 > Message generated for change (Tracker Item Submitted) made by adefusco > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2883616&group_id=23629 > > Please note that this message will contain a full copy of the > comment thread, > including the initial issue submission, for this request, > not just the latest update. > Category: File Input/Output > Group: None > Status: Open > Resolution: None > Priority: 5 > Private: No > Submitted By: Albert DeFusco (adefusco) > Assigned to: Miguel (migueljmol) > Summary: GAMESS hssend optimization (with fix) > > Initial Comment: > Optimizations performed with hssend=.true. in the $statpt group will > compute the Hessian and frequencies immediately after optimization > has completed. Currently this output does not display properly. It > is manifest in two ways: > (1) the normal mode displacements are applied starting from the > first model (1.1) which is the input geometry before optimization > (2) the normal mode atomSets are displayed with the starting > geometry not the final. > > I have also attached an optimization (with hssend=.true.) to help > illustrate this bug. In dimer.gamess there are 18 geometry steps. > This means Jmol will identify 20 models for the optimization run. > The first model is the input (COORDINATES (BOHR)). The second model > is NSERCH=0. This is supposed to be identical to the first. The > next 18 models are the optimization steps. The final 18 models are > vibration frequencies. It is these last 18 models to which the > normal mode displacements should be applied, not the first 18, and > the geometry should match model 18. > > I have included an updated GamessReader.java based on revision 11151 > which fixes the two issues above. Three changes were required: > (1) Always clone from the LastModel. This works even without the > optimization (runtyp=hessian). [lines 180-183] > (2) Use getCurrentAtomSetIndex to help find our current position in > atoms[] which includes all atoms from all models. [lines 137-144] > (3) The vector displacements will only be applied to the new cloned > atomSets. [lines 197-199] > It is possible there is a more elegant solution to changes 2 and 3. > > > ---------------------------------------------------------------------- > > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2883616&group_id=23629 > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers 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/facstaff/gutow ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
