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Re: Position folding issue
From: |
Jean-Noël Grad |
Subject: |
Re: Position folding issue |
Date: |
Tue, 18 Jun 2024 17:54:50 +0200 |
User-agent: |
Mozilla Thunderbird |
Hi,
Thank you for bringing our attention to this issue. This is indeed a
bug, and it affects many releases of ESPResSo. We have opened a ticket
(https://github.com/espressomd/espresso/issues/4940) and will look into
this. This is a challenging bug, because it depends on the Verlet lists
bookkeeping, and the solution will most likely be different for each
ESPResSo version.
Best,
JN
On 6/4/24 21:23, Yuan, Xin wrote:
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