[Pw_forum] About the mean square displacement in CP output

Bertrand SITAMTZE siyouber at yahoo.fr
Fri Apr 30 17:15:36 CEST 2010

Dear Antonio,

Thanks very much for responding. To plot MSD(t) I just go through the standard  output file and collect all the calculated MSDs fo each atoms. The time is computed using each "nfi"(the first column of the output file). I will be gratefull if you indicate a postprocessing code.
How to used an oscillating MDS to compute the diffusion coefficient as usually done?

Thanks once again

Laboratory of Material Sciences
Department of Physics
University of Yaounde I-Cameroon

--- En date de : Ven 30.4.10, Antonio Tilocca <uccaati at ucl.ac.uk> a écrit :

De: Antonio Tilocca <uccaati at ucl.ac.uk>
Objet: Re: [Pw_forum] About the mean square displacement in CP output
À: pw_forum at pwscf.org
Date: Vendredi 30 avril 2010, 16h09

Dear Bertrand:

I am not sure I understand how you are extracting the MSD(t) from the CP
trajectory: are you just plotting the final values shown in the standard
output file, or (as it would be recommended) calculating them by
post-processing the trajectory file? In any event, a flat, oscillating
MSD(t), after an initial increase, is exactly what you would
expect for a solid.

Antonio Tilocca

>From siyouber at yahoo.fr  Thu Apr 29 15:09:27 2010
>From: siyouber at yahoo.fr (Bertrand SITAMTZE)
>Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT)
>Subject: [Pw_forum] About the mean square displacement in CP output

>I am running CP dynamic with fixed temperature for a given solid system,
>using cp.x. The microcanonical calculation went very well with a
>conserved energy.Now the energy is still conserved. But my emphasis is on
> the mean
>square displacement(MSD) of atoms. They are calculated and plotted as a
>function of time. At the begining, the dependence seems to be linear at
>after, the MSD seem to oscillate around certain values which can be taken
>as a mean value after a sufficiently long time. My questions are: 1)
>According to the litterature, the dependence at the beginning should be
>quadratic and became linear after a long time. But for condensed system
>a solid it is, the MSD should saturate after a very long time. What is
>happening for my case? 2) The MSD computed with cp.x are tree
>dimensionnal. Please, confirm it or not. 3) In which file should I see
>those MSD are computed?

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