-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 14 October 2004 23:36, Miguel wrote: > > Op Monday 11 October 2004 12:40, schreef Miguel: > >> Rene wrote: > >> >> I looked at the same Gaussian 03 output with v9 and v10. > >> >> With V9 I could see the geometry optimization results AND the > >> >> vibrational results at the end. I completely lost that with the 10 > >> >> version... > >> > >> I don't know what the 'geometry optimization' is. Please explain > > > > Quantum Mechanics (QM) software (e.g. Gaussian, Mopac and many more) can > > do > > a search for the most stable (i.e. with lowest energy) compound... often, > > for > > such searched the start structure, all intermediate and end structures > > are given... I think people look at this to see how effective the search > > was... > > Anyway, this animation does show you a bit where the energy barriers are > > in the structure/energy 'landscape'... > > OK > > Q: So, are you saying that Rene wants to see an 'animation' that is made > up of all the intermediate stages from his input to the most stable > compound?
Yes, I think so... that's also what v9 does, though it shows the input structure (first frame) by default, I think... > > This langscape is the polydimensional space where the energy is plotted > > versus > > some coordinate... the simplest is the 'time' in the search, but Rene > > also mentioned that he would be very interested in seeing such a plot for > > internal coordinates, e.g. a bond length in the structure... > > > > An example. Say we have the structure H-H, but the starting structure is > > not > > 'optimal', i.e. the bond length is slightly longer than the equilibrium > > bond > > length, and hence, the QM energy is not minimal... the geometry > > optimization > > would then, e.g. using steepest decent, search in coordinate space for > > more > > energy stable structures... which would mean, the search would go towards > > the equilibrium distance... > > > >> >> I was hoping to use the Gaussian03 reader as a starting point to do > >> > >> the > >> > >> >> NWChem reader, but it looks like a lot of functionality that I liked > >> >> has been lost.... > >> > >> If v9 better meets your needs then you should keep using it. > > > > But if you start coding... it would be better to code on v10, because > > Miguel > > and I stopped active development of v9, which is the last released > > version of the 'b6' branch in CVS... (So, to get the source of v9, so a > > cvs checkout > > like cvs -r b6 -d Jmol-b6 co Jmol, or so... see CVS help). This allowed > > us to fully focus on v10. > > > >> The main focus of the v10 release was to make a replacement for Chime. > >> There was some collateral damage in the process, in large part because I > >> don't understand a lot of the energy/vibration stuff. > >> > >> Other than the UI control panels, I doubt if any of the *lost* > >> functionality is more than a few days' worth of work. > > > > Very likely... e.g. going to frame 10 of the vibrations would be the > > script > > command 'frame 10'... it only needs to get linked to some GUI element... > > > > (Though a fully script-based GUI, would require a script command to > > retrieve > > the number of vibrations... is that available?) > > > >> > The Gaussian03 reader should be able to read the vibrations, and > >> > >> thought > >> > >> > it did the energy optimization too... Miguel? > >> > >> Don't know ... what is this? > > > > If the Gaussian file has something like "# bla/bla opt" > > on the first line (or second?), it means a geometry optimization... such > > files will have more than one geometries in the file, and the current v10 > > reader might very well just take the first (starting structure), or last > > (the > > optimized structure)... > > I think that Jmol takes the last (optimized) structure Excellent... if you pick only one, it should pick that one... > > The gaussian reader of v9, read all structures as > > frames, so that people could browse through the structures created during > > the search for the most energy stable geometry... > > Q: So, how do these 'intermediate' energy states relate to the vectors > associated with the frequencies? Don't the vibrational vectors all apply > to the most stable geometry? That depends... all files I've seen, but I'm not an expert in this field, have only frequencies for the optimized structure... (Peter said in another email that freqs for all intermediate structures is principally possible, but very unlikely...) So, it's more or less a two step process: 1. do the geometry/energy optimization -> leads to input structure + intermediate structures + optimized structure 2. calc the freqs of the optimized structure Egon - -- [EMAIL PROTECTED] - --------------------------------------- CDK: http://cdk.sf.net/ JChemPaint: http://jchempaint.sf.net/ Jmol: http://www.jmol.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBb4sGd9R8I9Yza6YRApMSAJ4riL9PEP0wWNTqz2QwCR0z3tf6aACguqKJ zdy0ZL4hT4wqaxhkaJsC9Ng= =qTgL -----END PGP SIGNATURE----- ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
