[Pw_forum] How to calculate Mean Square Displacement (MSD)
Ari P Seitsonen
Ari.P.Seitsonen at iki.fi
Mon Oct 30 10:37:18 CET 2017
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/Contact
> 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 its
> initial position. If it matters the displacements are too large, maybe
> the timestep is too large if doing molecular dynamics?
> Lorenzo Paulatto - Paris
> Pw_forum mailing list
> Pw_forum at pwscf.org
More information about the users