[Pw_forum] Mean Square Displacement (MSD) of atoms

[Bertrand SITAMTZE]

Dear Changru

Thank very much for your answer.

The routines in Daan Frenkel and Berend Smit's book is are not suitable for postprocessing the *.pos file. Maybe these could give an idea, but I would like to have a routine that could help in postprocessing the *.pos file.

Secondly, what about the "Means square Displacement" printed every "isave" step in the *.out file? I though one could collect all the printed MSDs in one file to build the total MSD for all ions. Is this correct?

Thank once again for your help


********************************
Bertrand SITAMTZE YOUMBI, PhD
Laboratory of Material Sciences
University of Yaounde I-Cameroon
*****************************

--- En date de : Lun 17.1.11, Changru Ma <crma at sissa.it> a écrit :

De: Changru Ma <crma at sissa.it>
Objet: Re: [Pw_forum] Mean Square Displacement (MSD) of atoms
À: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Lundi 17 janvier 2011, 23h15

Dear Bertrand,
Positions of each ions during the dynamics will be written in $outdir/prefix.pos every iprint steps. They are sorted by specie, and converted to real a.u. coordinates.
You have to write a code yourself to calculate the MSD. Understanding molecular simulation: from algorithms to applications by Daan Frenkel and Berend Smit page 91 and page 95 might be helpful.
Best wishes,Changru
On 17 Jan, 2011, at 18:06, Bertrand SITAMTZE wrote:
Dear all,

I have performed ab-initio Molecular Dynamics within the CP code and I would like to collect the MSD of each ions during the dynamics.

Please could somebody tell me how to proceed from QE output?

Thanks very much for your answers

********************************
Bertrand SITAMTZE YOUMBI, PhD
Laboratory of Material Sciences
University of Yaounde I-Cameroon
*****************************







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---
Changru Ma
SISSA & Theory at Elettra group
email: crma at sissa.it
tel: +39 040 375 8713 (Elettra)
      +39 040 378 7870 (SISSA)
http://www.sissa.it/~crma
---



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