Feature Requests item #2974999, was opened at 2010-03-23 13:29 Message generated for change (Comment added) made by ghermitage You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2974999&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: New IO Format Group: None Status: Open Priority: 5 Private: No Submitted By: Granger Hermitage (ghermitage) Assigned to: Nobody/Anonymous (nobody) Summary: accept GenNBO 5 output Initial Comment: Accept GenNBO 5 output as a source of Natural Bond Orbital data. At the moment NBO output appearing in electronic structure system (e.g. Gaussian) output is accepted (provided $NBO AONBO=P $END is given as input to the ESS). Running NBO analysis as GenNBO (standalone rather than embedded in an ESS) can be quite advantageous, for the parameters of the NBO analysis can be changed without rerunning the ESS job which can take hundreds of times longer to run than GenNBO. It would be nice if JMol accepted GenNBO output for NBO visualization. This is not a large change, because the GenNBO output format is the same as for the NBO output appearing in the middle of ESS output. Secondly, this is handy because the GenNBO output derived from any ESS output can be accepted. No modifications are necessary to make use of a new/different ESS as input to GenNBO provided that the ESS outputs the GenNBO input .47 format file format (Jmol doesn't need to know that format). ESSs that don't have NBO 5 as standard (e.g. Gaussian 03+09, ADF) do support .47 format output so GenNBO 5 can be used. It may be possible to take GenNBO output and insert it into ESS output so that it can read by Jmol, but it would be nice if the GenNBO output (typically suffixed .nbo) could be read as is. ---------------------------------------------------------------------- >Comment By: Granger Hermitage (ghermitage) Date: 2010-03-24 02:06 Message: Gaussian 03 and 09 are supplied with NBO 3.1 installed in the ESS. My license for NBO 5 is a single research group license, and can't be installed in the ESSs because they are site wide. If NBO 5 output were appended to the end of ESS output which contained NBO 3.1 output, your code would have to figure out which version of NBO was in use at what part of the output and switch to the right formatting and positioning. The text of headings used for locating data sections could change between NBO 3.1 and NBO 5. I don't think you should deal with NBO 3.1 because it is not for serious use, but it is what is used by default in at least Gaussian 03 and 09. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-03-23 22:38 Message: Make that Gaussian, GAMESS, Jaguar, QChem, and PSI ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-03-23 22:32 Message: The issue is that the NBO output does not list the AO basis functions. So Jmol has no way to know how to build the orbitals. And also I think it doesn't have atom positions. But I think I have a solution. I added a bit of code that allows multiple NBO sections and basically starts over with a new set of orbitals if a second NBO output section is found. So all you should have to do is concatentate the NBO output onto the end of the original ESS output, and you are good to go. This should work with Gaussian, GAMESS, Jaguar, QChem, NWChem, and PSI, because they all access that same code. What do you think? ---------------------------------------------------------------------- Comment By: Granger Hermitage (ghermitage) Date: 2010-03-23 17:11 Message: Zipped small GenNBO 5 output file attached. ---------------------------------------------------------------------- Comment By: Granger Hermitage (ghermitage) Date: 2010-03-23 14:28 Message: Yes, everything you need is in the GenNBO output. There is a 256KB limit for upload? Unzipped, a sample output file is 15MB. ---------------------------------------------------------------------- Comment By: Granger Hermitage (ghermitage) Date: 2010-03-23 14:24 Message: Hmm, won't upload a 3.5MB file - send it to you directly? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-03-23 14:00 Message: note -- we'll need: -atom symbols or atomic numbers -coordinates in Bohr or Angstrom -atomic basis function coefficients are those in the NBO output? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-03-23 13:49 Message: sounds great to me. Send us some output examples of various types. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2974999&group_id=23629 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
