[CPMD-list] visualization of vibrational modes

[Axel Kohlmeyer]

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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