Bugs item #3131614, was opened at 2010-12-07 17:36 Message generated for change (Comment added) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3131614&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: Fixed Priority: 5 Private: No Submitted By: Ben Stein () Assigned to: Bob Hanson (hansonr) Summary: Orbitals not found in NBO output. Initial Comment: The attached NBO files do not seem to be loading into jmol correctly, while the polypeptide from a previous discussion (https://sourceforge.net/tracker/?func=detail&aid=2975200&group_id=23629&atid=379136) works fine. The atom geometry loads fine, but when I attempt to plot an orbital, the following error appears: "script ERROR: no MO basis/coefficient data available for this frame". The only difference I can see is that these NBO plot files have numbers in scientific notation. Jmol 12.0.24 OS X 10.6.5 Thanks, Ben ---------------------------------------------------------------------- >Comment By: Ben Stein () Date: 2010-12-22 21:14 Message: I don't have a whole lot of time right this moment to really give it a thorough testing (holidays and all that), but so far things are looking good. As far as SP functions go, I don't think gennbo supports them (at least not according to the manual), but the gaussian/gamess/etc. specific nbo might. Here is what I've checked so far: Spin restricted loads the NBOs fine, both from the .3x files and .out file. The NBOs that I've checked against other plots seem to match up great. I'll test a few more compounds though, with varying basis sets. Spin unrestricted also loads the NBOs fine, but I can't see how to select between alpha and beta orbitals. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-12-17 04:47 Message: Ben, See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip This needs careful testing. It should: -- load genNBO .out files directly, provided .31, .36 or .37, and.46 are in the directory of the .out file and have the same root name -- load .31 - .37 directly. -- handle UHF well -- display orbitals properly If NBO ever uses SP basis sets ("L") I would like to test that. Bob ---------------------------------------------------------------------- Comment By: Ben Stein () Date: 2010-12-15 18:16 Message: Sorry about that, I had some issues with the file size. It should be OK now. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-12-15 04:05 Message: progress! But no files attached.... ---------------------------------------------------------------------- Comment By: Ben Stein () Date: 2010-12-15 03:53 Message: Thanks very much, it seems to be working great. I'll run through some bigger molecules and check some more. One thing though, spin unrestricted calculations don't seem to be reading in properly, I've attached a simple example. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-12-14 21:38 Message: You must have all the .xx files in the same directory and with the same name as the .out file. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-12-14 21:21 Message: This NBO file has nonstandard order of P orbital ocefficients. I've added capability to read them to Jmol 12.1.26. See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip. Please confirm that the orbitals as calculated are the ones depicted. ---------------------------------------------------------------------- Comment By: Ben Stein () Date: 2010-12-14 17:32 Message: I've just tried to open the nbo output file (ch4nbo.out, with the AONBO keyword present) and I'm getting an unexpected end of file error: script ERROR: Unexpected end of file after line 5: null I parsed the file in python and I don't see and crazy characters in there, so I'm not sure whats going on. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3131614&group_id=23629 ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
