[CPMD-list] visualization of VIB1.log and VIB2.log in MOLEKEL and MOLDEN

[Axel Kohlmeyer]

On Tue, 30 Jan 2007, Martin Konopka wrote:

MK> Dear CPMD community,

dear martin,

MK> There looks to be the following visualization feature in MOLEKEL
MK> when VIB1.log (produced by CPMD VIBRATIONAL ANALYSIS) is read in:

please note that those files are more or less just a quick hack
and most of the contents were added simply to please molden
upon reading and are not computed (just look at the sources). 
do not expect them to be complete.

for implementation details, you better contact holger langer 
in bochum, who wrote it. 

it would certainly beneficial if somebody would put in the effort
and make those outputs more complete. e.g., adds code that computes
intensities or fills in other properties that you can compute with
both gaussian and cpmd, so that one can use all the tools that are
able to read (fake) gaussian log files.

cheers,
   axel.

MK> 
MK> Oscillation amplitudes of light atoms are artificially suppressed
MK> compared to heavier atoms.
MK> 
MK> I noticed this feature when comparing visualization of a mode
MK> from VIB1.log  and  visualization of the same mode using my own
MK> multiple .xyz file prepared from data in VIBEIGVEC according to
MK> 
MK> r_i = req_i + somefactor * eigvec_i / sqrt(mass_i) * sin(omega t) .
MK> 
MK> (which should be the true trajectory of the mode).
MK> 
MK> To visualize the true trajectory, the numbers in VIB1.log would
MK> have to be eigvec_i / sqrt(mass_i).
MK> However there are only eigvec_i written there.
MK> 
MK> Another thing which convinced me was changing atomic number (Z)
MK> in VIB1.log. It impacts only colors etc but not amplitudes
MK> of the vibrations.
MK> 
MK> The same problem is most likely with VIB2.log .
MK> And not only when visualized in MOLEKEL but MOLDEN also.
MK> 
MK> Is this artificial modification of the oscillation amplitudes
MK> done by purpose for nicer visualization?
MK> (For if one visualizes the true trajectory in a system with
MK> both light atoms like H and heavy ones like Cu, oscillations
MK> of H atoms then look somehow funny - very large.)
MK> 
MK> Thanks and best regards
MK> Martin.
MK> 
MK> 
MK> ------------------------------------------------------------------------
MK> Dr. Martin Konopka             http://www.ccms.elf.stuba.sk/konopka.html
MK> Department of Physics, CCMS                      tel: +421 (0)2 60291714
MK> Slovak University of Technology (FEI STU)        fax: +421 (0)2 65411483
MK> Ilkovicova 3, 812 19 Bratislava, Slovakia
MK> ------------------------------------------------------------------------
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MK> 

-- 
=======================================================================
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
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