[Pw_forum] Mean Square Displacement (MSD) of atoms

[Changru Ma]

Dear Bertrand,

The mean square displacement of atoms in a simulation can be easily
computed by its definition

MSD = < (r(t) - r(0)) ** 2.0 >

Be careful when you compute r(t) - r(0), as Giovanni La Penna mentioned.
You's better post process .pos to .xsf by cppp.x first and then calculate
MSD from .xsf file.

"Mean square Displacement" printed every isave step in the output file is
the mean square displacement of each ionic specie. It's calculated in
Modules/ions_base.f90, subroutine ions_displacement(). What you want is
"to collect the MSD of each ions during the dynamics". So you have to
calculate it yourself.

Best wishes,
Changru

> 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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-- 
Changru Ma, PhD Student
SISSA and Theory at Elettra Group
email: crma at sissa.it


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