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Re: Espressomd-users Digest, Vol 156, Issue 3


From: Xin Yuan
Subject: Re: Espressomd-users Digest, Vol 156, Issue 3
Date: Sat, 22 Jun 2024 02:45:11 -0500

Hello,

After applying the patch, both the p.image_box values and hdf5 output file appear to be corrected. Thanks for the speedy resolution!

Regards,
Xin Yuan

On Thu, Jun 20, 2024 at 11:03 AM <espressomd-users-request@nongnu.org> wrote:
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Today's Topics:

   1. Re: Position folding issue (Jean-Noël Grad)


----------------------------------------------------------------------

Message: 1
Date: Wed, 19 Jun 2024 20:34:26 +0200
From: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>
To: espressomd-users@nongnu.org
Subject: Re: Position folding issue
Message-ID:
        <7f01083a-b722-45bb-863b-7680bd3bbe99@icp.uni-stuttgart.de" target="_blank">7f01083a-b722-45bb-863b-7680bd3bbe99@icp.uni-stuttgart.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

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://urldefense.com/v3/__https://github.com/espressomd/espresso/issues/4940__;!!LkSTlj0I!BbAqyuS1U-JE4-ijzNLGQn38PWSsAKn5HpKt2eqzcpyX7w62vqQmrGsEotDYaW1Er0dgCKfbG1vjDiyrwbSfxdfjVn4$ ) 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
>
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