[CPMD-list] visualization of vibrational modes

[Yong Zhang]

Neither Gview98 nor Gview03 works with the faked gaussian output. :-(



On 10/13/06, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:
>
> On Thu, 12 Oct 2006, Yiming Zhang wrote:
>
> YZ> Dear CPMD community,
> YZ>
> YZ> I am wondering if there is a good way to visualize the vibrational
> modes
> YZ> calculated by CPMD.
>
> the most convenient way is currently the output of
> 'faked' gaussian 98 output file(s). see manual.
>
> YZ> For example, rearrange the VIBEIGVEC vectors so that VMD or GaussView
> can
> YZ> read and show the cartoons.
>
> i don't know how well the 'fake gaussian' output works with gaussview,
> but with VMD it will not fly. vmd does not read or store this
> information currently. there is a very new plugin that can ready
> gaussian log files, but so far it is not very forgiving and
> the GAUSS output of cpmd has never been tested with it. an
> alternative way is to do the projections directly and create
> animations from it. please find attached a hacked version of
> the xvibs code that i picked up somewhere on the web ages ago
> and rodolphe vuilleumier's cp2xvibs. both updated to compile and
> run with current compilers.
>
> YZ> If there isn't, any suggestions or comments for writing such a code
> are
> YZ> appreciated.
>
> there are currently plans to expand the functionality in VMD
> so it can handle eigenvectors directly (also from PCA or essential
> dynamics), but it is difficult to predict, when this will be
> available (somebody has to program it...).
>
> best regards,
>
>     axel.
>
> ps.: alessandro, can you put this in the contrib section
> of www.cpmd.org as well? thanks.
>
> YZ>
> YZ> Thanks,
> YZ> Yiming Zhang
> YZ>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>
>
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