Re: Particle moves out of box size

[Jean-Noël Grad]

Dear Ahmad Reza,

The particle position is stored internally as two vectors: the position 
within the unit cell and the number of periodic images. The second 
vector is on average (0,0,0) and as such, most of the time the folded 
position is equal to the unfolded position. If you have an external 
field, the periodic images vector will increase in the direction of the 
field, and so will system.part[:].pos since it returns the unfolded 
position. You are probably interested in system.part[:].pos_folded:
https://espressomd.github.io/doc/espressomd.html#espressomd.particle_data.ParticleHandle.pos_folded

Please note that the espressomd.cluster_analysis.ClusterStructure 
algorithm did not always fold the coordinates of the center of mass. 
This bug was fixed a few days ago:
https://github.com/espressomd/espresso/pull/4363

Best,
JN

On 2021-10-27 14:52, Ahmad Reza Motezakker wrote:
> Dear EspressoMD users,
>
> I have some polymers made of monomers coupled with fluid in a box with
> periodicity in all directions. After analysis of the positions, I
> realize that the range of positions of some particles are out of box.
> Could you please share with me the possible reason?
>
> Best regards,
>
> Ahmad Reza