espressomd-users
[Top][All Lists]
Advanced

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Position folding issue


From: Jean-Noël Grad
Subject: Re: Position folding issue
Date: Wed, 19 Jun 2024 20:34:26 +0200
User-agent: Mozilla Thunderbird

Hi again,

Could you please check if applying the attached patch with the command `git apply patch.diff` in the top-level ESPResSo folder, and rebuilding ESPResSo, fixes your trajectories? You should get the correct image numbers in the hdf5 output files, and also in the values returned by p.image_box. Both features were actually broken.

Best,
JN

On 6/18/24 17:54, Jean-Noël Grad wrote:
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

Attachment: patch.diff
Description: Text Data


reply via email to

[Prev in Thread] Current Thread [Next in Thread]