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
