[Pw_forum] About the mean square displacement in CP output

[Bertrand SITAMTZE]

Dear Antonio and all users, 

Thanks for responses you have given until now. But I am a bit confused.

Please could sombody tels me how to compute the diffusion coefficient in a solid using Ab-initio Molecular dynamics?


Best regards

 ****************************
Bertrand SITAMTZE YOUMBI
Laboratory of Material Sciences
Department of Physics
University of Yaounde I-Cameroon
***********************************


--- En date de : Lun 3.5.10, 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: Lundi 3 mai 2010, 11h45


Dear Bertrand,

the way you are obtaining the MSD(t) is not the best: in that way, every
time point is only averaged using a single time origin, whereas it is
advisable, for a better statistics, to perform an extended average over a large
number of non-correlated time origins, as described (with examples of
codes) in the Allen-Tildesley book, for instance. However, the trend that
you obtain with your approximate approach is qualitatively correct.

As for your other question, as Sandro has already pointed out, the zero
slope of your (constant) MSD(t) shows the absence of diffusion,
as expected for a solid, on your short observation time.

Antonio Tilocca
UCL


> Message: 2
> Date: Fri, 30 Apr 2010 15:15:36 +0000 (GMT)
> From: Bertrand SITAMTZE <siyouber at yahoo.fr>
> Subject: Re: [Pw_forum] About the mean square displacement in CP
>     output
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <414847.4559.qm at web26504.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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?
>
> ****************************
> Bertrand SITAMTZE YOUMBI
> 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 ?crit?:
>
> De: Antonio Tilocca <uccaati at ucl.ac.uk>
> Objet: Re: [Pw_forum] About the mean square displacement in CP output
> ?: 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
> UCL
>
>
>
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