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. Paolo On Mon, Oct 30, 2017 at 10:37 AM, Ari P Seitsonen <[email protected]> wrote: > > 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, > > apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*= > -=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / [email protected] / 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). >> >> Nic >> >> Sent from a tiny keyboard... Contact info: http://theossrv1.epfl.ch/Main/ >> Contact >> >> On 30 Oct 2017, at 10:13, Lorenzo Paulatto <[email protected]> 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? >> >> cheers >> >> -- >> Lorenzo Paulatto - Paris >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > -- 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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