Re: a bug or a feature?

Hi Markus,

I am afraid that you may have misplaced one "NOT" in your reply. If you say "for bonds it never seems to make sense to not first apply it", why would you call it a feature if Espresso does something that does not make sense?

Perhaps I did not make one thing clear: in UNFOLDED coordinates, it should never happen that any bond length is longer than box_l/2. Therefore, if it is necessary to apply the minimum image convention for bonds, it should be seen as an error. In the current implementation, Espresso applies the minimum image convention, and lets this error silently pass.

Can anyone give an example when bond_length > box_l/2 is not an error? If yes, then I fully agree that it should be seen as a feature.

With regards,

Peter

On Fri, Apr 16, 2021 at 3:51 PM Markus Deserno <deserno@andrew.cmu.edu> wrote:

Folks,

I cannot conceive of a single instance where I wanted to know a
bond distance but would NOT want the minimum image convention
applied. Note that I specifically said “BOND DISTANCE”. there are
many situations where I care about a DISTANCE and I do NOT
want the minimum image convention. But for bonds it never seems
to make sense to not first apply it.

So I’d be inclined to call it a "feature”.

Best,
Markus

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On Apr 16, 2021, at 6:46 AM, Peter Košovan <peter.kosovan@natur.cuni.cz> wrote:

Dear Espresso developers,

Today, we noticed an unexpected behaviour of Espresso, that I would consider a bug, but it might also be a feature. Before submitting a bug report, I want to ask your opinion.

In brief: if two particles connected by a bond but they are found in different periodic copies of the simulation box, then Espresso runs without any error or warning. Since particles are internally represented in unfolded coordinates, I would expect to get a "bond broken" error if the (unfolded) distance is greater than box_l/2. Apparently, minimum image convention is used also in the calculation of bond distances, which makes no sense in the unfolded coordinates.

If we agree that such behaviour is undesired, I will submit a bug report and a minimal working example.

With regards,

Peter

--
Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
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From:	Peter Košovan
Subject:	Re: a bug or a feature?
Date:	Fri, 16 Apr 2021 16:14:06 +0200