Re: problem with periodicity

[Rudolf Weeber]

Hi Zahra,
On Tue, May 26, 2020 at 06:58:29PM +0430, Zahra Fazli wrote:
> I have just started working with ESPResSo and I have a basic question about
> periodicity. I tied to simulate a simple system of particles interacting
> via WCA interactions and within a box with periodic boundary conditions;
> but I found that particles do not respect periodic boundary condition ( I
> activate periodicity with:  system.periodicity = [1.0, 1.0, 1.0] ).
> I also tried to run one of the samples in espresso source named
> lj_liquid.py  and I encountered the same problem.
> Can anyone help me how to solve this problem with periodic boundary
> conditions?
In what way are periodic boundary condition snot respected?
Did you look at the particle positions via
system.part[0].pos, etc? 
If yes, those do not get folded back into the simulation box. You can use them, 
to find out how far the particle has travelled in total, e.g., for mean square 
displacement.
If you look at the `pos_folded` property under periodic boundary conditions 
instead, it will always be 0<=x<l, where l is the box length.

BTW: system.periodicicity = [True, True True] is preferrable to passing 
floating point values as (such as 1.0) you did.
Fully periodic is also the default.

Maybe, the visualization related samples in the samples folder are of interest, 
as well.

Hope that helps
Regards, Rudolf

--
Dr. Rudolf Weeber
Institute for Computational Physics
Universität Stuttgart
Allmandring 3
70569 Stuttgart
Germany
Phone: +49(0)711/685-67717
Email: address@hidden
http://www.icp.uni-stuttgart.de/~icp/Rudolf_Weeber