Position folding issue

[Yuan, Xin]

Hello,

I have noticed an issue with position folding under periodic boundary conditions. When a particle moves from the original simulation box to the next mirror image, the image number does not increment until the particle is at a distance  (~0.01) away from the boundary. This leads to an issue where the particle's unfolded position would be incorrect if calculated from folded position and image number when the particle is very close to the boundary. This appears to be especially relevant when recording trajectory in H5MD format, as only the folded positions and image numbers are recorded in an H5MD file, and there is no way to extract correct unfolded position from an H5MD file for such particles. I have attached a Jupyter notebook file to illustrate this issue, which was tested on a WSL Ubuntu environment set up according to the instructions in the online documentation as well as other conda environments. Is this a software bug or something I was not doing correctly? Thanks for any help!

Regards,

Xin Yuan

position_folding_error.ipynb
Description: position_folding_error.ipynb