Bugs item #3413444, was opened at 2011-09-23 16:17 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3413444&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: Fixed Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Bob Hanson (hansonr) Summary: MOs not showing for molden file Initial Comment: Hi, I just, after a long time, updated the Jmol source with the repository and for one reason or another a molden file that works properly (after forcing it to consider it as a molden file since the header has ' [Molden Format]' with Jmol Version: 12.0.49 2011-07-30 15:57, does not show the molecular orbitals. I traced the interpretation of the file and it seems to me that it still indeed reads the orbitals and all, but doesn't display them. A test with the Jmol-datafiles molden sample water_novib.molden show that for that one I am able to show orbitals, so I am completely confused here. I was hoping to change if (leader.startsWith(recordTag)) (line 452 in Resolver.java) to if (leader.trim().startsWith(recordTag)) so that leading spaces in the header would get ignored (and hoping that that would not break any other readers). I'll try to attach the gzipped archive of the file to this report. Thanks, René ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2011-09-25 10:33 Message: Yes, that's the same then as Gaussian, so we are good there. So far we only support S-F. ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2011-09-24 15:02 Message: Hi Bob, The sample file I attached was for a multi-configuration calculation so occupancy doesn't make much sense. Columbus just put 2's for every one of them. I just checked in a molden formatted file with the s, p and d orbitals for an atom so one can see the order in which Jmol visualizes them. The order according to the molden website (http://www.cmbi.ru.nl/molden/molden_format.html) is The following order of D, F en G functions is expected: 5D: D 0, D+1, D-1, D+2, D-2 6D: xx, yy, zz, xy, xz, yz 7F: F 0, F+1, F-1, F+2, F-2, F+3, F-3 10F: xxx, yyy, zzz, xyy, xxy, xxz, xzz, yzz, yyz, xyz 9G: G 0, G+1, G-1, G+2, G-2, G+3, G-3, G+4, G-4 15G: xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy, xxyy xxzz yyzz xxyz yyxz zzxy which, I think (not sure) is indeed what Jmol does. It really is up to the computational package to indeed use that ordering as well :-). Thanks, René ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-09-24 13:09 Message: Rene, can you check on the order of coefficients for 5D and 7F for Molden? Or at least confirm that various orbitals using those appear correctly. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-09-24 13:01 Message: I've modified the Resolver and also enabled reading of the [5D] [7F] records in MoldenReader. Although I think there may be a bug in Molden -- it's reporting all occupancies = 1. Why would that be? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3413444&group_id=23629 ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
