Re: problem with periodicity

[Jean-Noël Grad]

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