VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 09 2010 - 05:26:13 CST

> I have a few questions for you guys:
>
> 1) Is this procedure right? I mean: it is actually the phonon DOS what I get after the script is run?

yes.

> 2) I made the calculation setting k_max = 3000 cm^-1, and I got 90 frequency points. Is there any way to increase the number of wavenumber values without changing k_max? I am asking this because I calculated the integral below the DOS curve and I found it not to be normalized to 1.

the integral is normalized to 1.0, that is part of the process.
the only way to have more frequency points is to write out
velocities more frequently. the number of output frequencies
are selected based on what is possible with the spacing
provided from the input.

> 3) Is there any way to do the same thing directly from the LAMMPS trajectory file (i.e., a file which contains positions AND velocities of all the particles of the system)?

yes. if you use a recent version of VMD (you may need a alpha/beta version,
i don't remember exactly when i added this), the velocities will be
read in, too.

cheers,
     axel.

> Thanks a lot!
>
> Juanjo Melendez
> Associate Professor
> Department of Physics
> University of Extremadura
> Avda. de Elvas, s/n 06006 Badajoz (Spain)
> email: melendez_at_unex.es
> phone: +34 924 28 96 55
> fax: +34 924 28 96 51 

--
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.