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

[Martin Konopka]

Dear CPMD community,

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

Oscillation amplitudes of light atoms are artificially suppressed
compared to heavier atoms.

I noticed this feature when comparing visualization of a mode
from VIB1.log  and  visualization of the same mode using my own
multiple .xyz file prepared from data in VIBEIGVEC according to

r_i = req_i + somefactor * eigvec_i / sqrt(mass_i) * sin(omega t) .

(which should be the true trajectory of the mode).

To visualize the true trajectory, the numbers in VIB1.log would
have to be eigvec_i / sqrt(mass_i).
However there are only eigvec_i written there.

Another thing which convinced me was changing atomic number (Z)
in VIB1.log. It impacts only colors etc but not amplitudes
of the vibrations.

The same problem is most likely with VIB2.log .
And not only when visualized in MOLEKEL but MOLDEN also.

Is this artificial modification of the oscillation amplitudes
done by purpose for nicer visualization?
(For if one visualizes the true trajectory in a system with
both light atoms like H and heavy ones like Cu, oscillations
of H atoms then look somehow funny - very large.)

Thanks and best regards
Martin.


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Dr. Martin Konopka             http://www.ccms.elf.stuba.sk/konopka.html
Department of Physics, CCMS                      tel: +421 (0)2 60291714
Slovak University of Technology (FEI STU)        fax: +421 (0)2 65411483
Ilkovicova 3, 812 19 Bratislava, Slovakia
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