Re: problem with periodicity

[Zahra Fazli]

Dear Rudolf, dear Jean-Noël,

Thanks for your useful comments. The problem solved when I printed folded particle positions.

Best,

Zahra

On Tue, May 26, 2020 at 7:33 PM Jean-Noël Grad <address@hidden> wrote:

Dear Zahra,

ESPResSo stores internally unfolded positions. If you print the value of
system.part[:].pos or the result of observable
espressomd.observables.ParticlePositions, you'll see these unfolded
particle positions increasing beyond the box boundaries. If you print
system.part[:].pos_folded, you'll see that positions return to zero when
a particle crosses the box boundaries. You can check it visually with
samples/visualization_ljliquid.py.

The value system.periodicity = [1.0, 1.0, 1.0] is correct (in recent
versions of espresso, you can simply provide [1, 1, 1] or [True, True,
True] instead of floating-point values).

Best,
JN

On 5/26/20 4:28 PM, Zahra Fazli wrote:
> Dear espressomd users,
>
> 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?
>
> Best,
> Zahra