Bugs item #3016142, was opened at 2010-06-14 15:51 Message generated for change (Comment added) made by rkanters You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3016142&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? Initial Comment: Hi, We noticed some strange orbitals in the visualization of some NBO results when we used Sn with an effective core potential and f and g orbitals. I wasn't sure whether the high order orbitals would be causing a problem, so in order to try to hunt down the problem, I had the student just calculate a single point Sn4+ run with the same basis set. Since we still got linear combinations of our AOs in there, I decided to modify the AOs it calculated by editing the log file myself. I made the AO matrix a unit matrix, so I could see each atomic orbital. I also truncated the log file a bit so it wouldn't be too large. In the attached case model 2 has MOs. If you look at mo 25 (a D 0) one, it looks similar in shape as the mo 26 ( D+1) one just rotated from the x to y axis. To me they look like the X2 and Y2 orbitals and not the spherical ones. Another hint is that mo 25 and mo 30 are both supposed to be D 0 orbitals, but they have different shapes all together, which could result form indexing based on the 5 spherical d orbitals in an array that is set up for the 6 cartesians. ---------------------------------------------------------------------- >Comment By: Rene Kanters (rkanters) Date: 2010-06-15 07:53 Message: Sorry about all the updates on this issue, but I just found another possible set of problems with these large basis sets and the g03 reader. 1) when the basis set is read from a checkpoint file, the reader doesn't find the expected line for determining whether it is a spherical basis set, since we get something like Basis read from chk: Sn_PMe_MDF_NBO_JMolView.chk (5D, 7F) in the file. Testing for " Basis read" and being smarter about finding the () section could help that. 2) I am also not sure what the reader/visualization does when it encounters g orbitals. If it were to skip them, things may be fine as long as the orbitals of interest do not have much g character. This second part has me worried about the other readers (like qchem, because I had to do some tricky stuff way back when I worked on that) that should be able to interpret MOs as well. ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2010-06-15 06:20 Message: I forgot to add that this bug is in the latest development version as well (I just synchronized this morning 12.0.RC19_dev), but that in release 11.8.RC5 the AOs show indeed the spherical ones for MOs 25-29 (and not the 6 cartesian ones version 12 shows for MOs 25-30). I would use the older version, but reading the NBO analysis output throws an error for that one. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3016142&group_id=23629 ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
