Bugs item #3017294, was opened at 2010-06-16 15:44 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3017294&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: Graphics Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: g03 MO visualization wrong follow-up Initial Comment: I just now got around to checking out the fixes to the g03 (and other) MO reader. Actually I only checked the g03. There are still problems with the program encountering g orbital information. Enclosed is another edited calculation for Sn, where (like before) I have a diagonal matrix for the MOs, but I put in an anti-diagonal one for the NBOs, so we can check both. In model 2, there are 83 MOs, but only the first 65 show up. The 66th is one with g-orbitals. Not a single NBO one shows up. Note (I did not modify the labeling of the orbitals, so the assignment as to what kind of orbital it is is completely wrong, but that shouldn\'t matter :-). The file was too big to be uploaded, so I made a gzipped tarbal for it. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2010-09-01 10:26 Message: yes, you can assume g+ orbitals are just ignored. May I close this? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-18 07:17 Message: OK, all files pass the JUnit test, which means if they are using the new DF-mapping method in MOReader (Gaussian, Gamess, QChem, GenNBO, WebMO) then all orbital types there are recognized. Jaguar and Psi are also MOReaders, but Psi output doesn't identify MO type, so it's not clear how to remove G/H/I orbitals or determine orbital order, and I don't have example files for Jaguar. Rene, the solution was to not have the all the different readers switching orbital order but instead just pass on to MOCalculation a mapping array. That would be very simple to define for each reader -- right now I'm getting it on the fly, but if we know a reader's order, it would be simpler just to set the array. For now, this seemed the safest and most general. Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-18 06:44 Message: I'll test all examples today. ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2010-06-18 06:28 Message: I just checked the qchem reader for the MOs, and it does have a problem with not recognizing MOs with spherical orbitals (even d). I loaded H2O-B3LYP-631Gd_pure.out from the example data files and get the message: The Resolver thinks Qchem Disabling orbitals of type 4 -- Cannot read orbital order for: D 1 D 2 D 3 D 4 D 5 expecting: DXX DYY DZZ DXY DXZ DYZ atomic orbital order is unrecognized -- skipping reading of MOs. dList=D 1 D 2 D 3 D 4 D 5 I know I had to do some strange stuff way back when I wrote the initial reader for MOs there, but with all the modifications, I am not really sure anymore what is going on :-). René ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-17 15:57 Message: OK, Rene, please check what I just checked in. Should be skipping over G orbitals and reading the spherical NBO AOs in the proper order. Hard to tell. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-17 14:15 Message: hmm, except it might not be incrementing the coefficient pointer properly.... ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-17 14:13 Message: second comment noted -- yes, a message will show up in the Java console to the effect of "Jmol can't recognize this basis function -- ignored" The file readers are passing the G orbitals on -- though not sorting them -- and MOCalculation is just not using them for the visualization. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-06-17 14:11 Message: OK. So, first thing, Jmol is going to ignore G orbitals. Everyone OK with that? I'll look at that file and see what's up. Everything else checkout ok? ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2010-06-16 15:48 Message: Oops. It does show orbitals 102 and above since those don't have any g contribution. Can I conclude that g (or higher) orbitals will just be skipped in the visualization part? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3017294&group_id=23629 ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
