[CPMD-list] visualization of vibrational modes

[Alexander Isaev]

Dear Yong,

Both Molden and gOpenmol DO work with that output. Nice thing, they are free :)

Sincerely,
Alexandr

 


---------- Original Message ----------------------------------
From: "Yong Zhang" <zhangymall11 at gmail.com>
Date:  Fri, 13 Oct 2006 14:32:01 -0400

>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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>>
>>
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