Thanks Geoff. Is it specific to NWChem's output? I ask, because Avogadro displays Gaussian-calculated imaginary modes quite well. I believe that Gaussian simply doesn't print the 6 (or 5) rotations and translations.
Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 Fax: 979 845 0158 On 2012-11-09 2:55 PM, Geoffrey Hutchison wrote: > The current default in Avogadro (and Open Babel, which reads the vibrations) > is to ignore the 6 lowest degrees of freedom. This removes rotations and > translations. > > Now, it seems like this might be useful to set as a user-option: “Show > Rotations and Translations” since you sometimes wish to see things like > imaginary frequencies. > > Hope that helps, > -Geoff > > On Nov 9, 2012, at 3:18 PM, Andrew Yeung wrote: > >> Hi all >> >> I posted a question at the NWChem forum >> (http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id644/Do_I_have_an_imaginary_frequency....html), >> and they suggested I get in touch with the Avogadro developers. >> >> In a B3LYP/cc-pvtz frequency calculation, the log file lists: >> >> >> ---------------------------------------------------------------------------- >> Normal Eigenvalue || Projected Derivative Dipole Moments (debye/angs) >> Mode [cm**-1] || [d/dqX] [d/dqY] [d/dqZ] >> ------ ---------- || ------------------ ------------------ >> ----------------- >> 1 -32.993 || 0.001 0.000 -0.009 >> 2 0.000 || -0.001 0.002 0.012 >> 3 0.000 || 0.000 -0.023 0.001 >> 4 0.000 || 0.000 0.009 0.001 >> 5 0.000 || -0.001 -0.003 0.017 >> 6 0.000 || 0.000 0.011 0.001 >> 7 0.000 || 0.006 0.000 -0.074 >> 8 56.848 || 0.000 0.000 0.000 >> 9 77.476 || -0.030 -0.001 0.393 >> 10 116.618 || -0.244 -0.001 -0.019 >> 11 154.375 || 0.000 0.000 0.000 >> 12 250.918 || -0.001 0.387 0.002 >> >> When I try to visualize the file in Avogadro, it does not show me this >> -32.99 cm-1 imaginary vibration. Is this expected behavior? >> >> Thanks and regards. >> >> -- >> Andrew Yeung >> Donald J. Darensbourg Research Group >> Department of Chemistry, Texas A&M University >> 3255 TAMU >> College Station, TX 77843-3255 >> >> Tel: 979 845 4837 >> Fax: 979 845 0158 >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_nov >> _______________________________________________ >> Avogadro-Discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_nov > _______________________________________________ > Avogadro-Discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_nov _______________________________________________ Avogadro-Discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
