[Pw_forum] How to calculate Mean Square Displacement (MSD)
p.giannozzi at gmail.com
Mon Oct 30 11:02:06 CET 2017
It's a long story and I am not sure I know the end of it. In Car-Parrinello
MD, by the way, the conserved quantity is the centre of mass of nuclei AND
electrons, not of nuclei alone.
About MSD: to compute a diffusion coefficient, one should follow the
diffusing object even outside the supercell, in principle. Not sure that
the code prints atoms where they are, though: maybe it refolds everything
into the supercell.
On Mon, Oct 30, 2017 at 10:37 AM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
> Dear All,
> Yes, never fold back when studying the real mean-square displacement;
> like Nicola wrote, your results would depend on the size of the box.
> One issue to consider is whether one should remove the centre-of-mass
> motion, as there is always such in DFT-based simulations (finite basis
> set/grid in the exchange-correlation term, finite convergence toward
> self-consistency, ...), unless it is removed manually (I do not know if QE
> does it automatically). I tend to do it - sometimes the whole set of atoms
> or molecules has travelled a long distance in a single direction. Then
> there is also the question if the temperature during the simulation is
> correct, or whether one should remove the centre-of-mass velocity also at
> each step... Again, I do not know if QE handles this - can some one confirm
> what is done (CPV, PW)?
> Greetings from Sunny Paris,
> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
> On Mon, 30 Oct 2017, Marzari Nicola wrote:
>> You need to be able to follow genuine diffusion - eg a liquid, a
>> superionic, a fast interstitial...
>> If you fold, your msd will always tend to a constant (rather than eg a
>> straight line with finite slope, as a function of time).
>> Sent from a tiny keyboard... Contact info: http://theossrv1.epfl.ch/Main/
>> On 30 Oct 2017, at 10:13, Lorenzo Paulatto <paulatz at gmail.com> wrote:
>> On 30/10/17 10:09, Marzari Nicola wrote:
>> ?? For MSD you should not fold back.
>> Re-reading the question i think you are right. But I also think
>> that it
>> should not matter, i.e. that each atom should always stay close to
>> initial position. If it matters the displacements are too large,
>> the timestep is too large if doing molecular dynamics?
>> Lorenzo Paulatto - Paris
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>> Pw_forum at pwscf.org
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Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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