<div dir="ltr"><div><div>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. <br><br></div>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.<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 30, 2017 at 10:37 AM, Ari P Seitsonen <span dir="ltr"><<a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Dear All,<br>
<br>
Yes, never fold back when studying the real mean-square displacement; like Nicola wrote, your results would depend on the size of the box.<br>
<br>
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)?<br>
<br>
Greetings from Sunny Paris,<br>
<br>
apsi<br>
<br>
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Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Supérieure (ENS), Département de Chimie, Paris<br>
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<br>
<br>
On Mon, 30 Oct 2017, Marzari Nicola wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
You need to be able to follow genuine diffusion - eg a liquid, a superionic, a fast interstitial...<br>
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).<br>
<br>
Nic<br>
<br>
Sent from a tiny keyboard... Contact info: <a href="http://theossrv1.epfl.ch/Main/Contact" rel="noreferrer" target="_blank">http://theossrv1.epfl.ch/Main/<wbr>Contact</a><br>
<br>
On 30 Oct 2017, at 10:13, Lorenzo Paulatto <<a href="mailto:paulatz@gmail.com" target="_blank">paulatz@gmail.com</a>> wrote:<br>
<br>
<br>
On 30/10/17 10:09, Marzari Nicola wrote:<br>
?? For MSD you should not fold back.<br>
<br>
<br>
Re-reading the question i think you are right. But I also think that it<br>
should not matter, i.e. that each atom should always stay close to its<br>
initial position. If it matters the displacements are too large, maybe<br>
the timestep is too large if doing molecular dynamics?<br>
<br>
cheers<br>
<br>
--<br>
Lorenzo Paulatto - Paris<br>
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