Feature Requests item #2378189, was opened at 2008-12-02 10:15 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2378189&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: Interface Improvements Group: None Status: Open Priority: 5 Private: No Submitted By: Albert DeFusco (adefusco) Assigned to: Nobody/Anonymous (nobody) Summary: Proposed changes to GAMESS-US Reader Initial Comment: Hi there, I am a postdoc with Mark Gordon at Ames Lab and I have been hacking into Jmol recently with the goal of improving its ability to understand output from several methods. Below you will find changes I have made based on the released 11.6 source. I had started using the most recent SVN trunk, but there were some issues regarding antialiasing on the MAC that turned me away. --Additions-- GamessUSReader.java: Can now read EFP1 water molecules for FRAGNAME=[H2ODFT/H2ORHF]. These potentials are currently available in GAMESS. EFP2 potentials are not yet part of the release. This works for any number of EFP molecules and also for optimizations. There are more complete comments in the source. --Changes-- GamessReader.java and GamessUSReader.java I have built support for reading several more types of orbitals (closed shell only). This required changes to GamessReader.java that allow for orbital reading where energy, occupation or symmetry are not present. The changes I made allow for continuous addition of orbitals to the present model. This means that in a single-point run where the "initial guess vectors" are printed along with an RHF (or anything else) for N orbitals, the first N orbitals will be the guess and N+1 to 2N orbitals will be the optimized RHF orbitals. For an MCSCF calculation one may have up to three sets of orbitals (initial guess, MCSCF natural orbitals, MCSCF optimized orbitals). I have left it so that the user would have to be aware of what order the orbitals appear the figure out the mo number to display the desired orbital. (This may not work as expected in all cases.) While I have not tested all possible calculation types, there are some comments about keywords for which the changes work. MoldenReader.java: There were some MOLPRO-generated files that perhaps did not adhere strictly to the documented (albeit vague) standard on the MOLDEN website. I have included several output files which may help understand these changes. The files I want to include are too big to be uploaded here and are available at my website: http://homepage.mac.com/albertdefusco/gamess.tar.bz2 The file is 968 KB. I have had no prior experience with Java and apologize for the flagrant errors I have probably made. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-12-02 18:32 Message: First, let me say I'm very happy your group is looking at this. Thanks very much for contributing your expertise. Jmol 11.6 is closed to new features, but I've adapted your code and checked it in as 11.7.16_dev. Please try that. Don't know what the "antialiasing on the MAC" that could be a problem -- we have a lot of Mac users, and this problem would be important to resolve if it exists. In any case, I did do some substantial re-writing there, so please check it over and let me know if it's in error. It did read the MOs and H2O from the water uracil file. There were problems reading the GUGA file with the header setting as shown, so please take a good look at that. Also, since there are multiple molecular orbital types, what do you suggest in terms of reading only the ones that would be of particular interest. Perhaps we need a "filter" for this? Bob Hanson ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2378189&group_id=23629 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
