Hi Peter,
I might have misunderstood what exactly happens or seems to be going on.
Maybe I was confused by the first sentence in your error description:
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.
Well, of course, since there’s nothing wrong with that.
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.
So would I. But of course you can be found in different periodic copies in
the UNFOLDED coordinates and still have a small true distance.
Apparently, minimum image convention is used also in the calculation of bond distances, which makes no sense in the unfolded coordinates.
I’m not sure whether this sentence is meant as a deduction from the previous
one, or whether this is an independent observation. But I’d agree it'd be odd
to calculate bond distance while also applying minimum image, if you have
the unfolded coordinates available. It just seems unnecessary. (Even though
of course not wrong.)
Concerning your second email:
in UNFOLDED coordinates, it should never happen that any bond length is longer than box_l/2.
Yes. Unless, of course, the bond broke ;-)
Therefore, if it is necessary to apply the minimum image convention for bonds, it should be seen as an error.
It should not be necessary. But I’d not call it an error. It’s superfluous work.
Espresso applies the minimum image convention, and lets this error silently pass.
So maybe I still don’t understand what you mean by error. For bonds the bare
distance and the minimum image distance should aways be the same. If not,
the bond is broken.
Best,
Markus
-- Dr. Markus Deserno ++1-412-268-4401 (office)Professor of Physics ++1-412-681-0648 (fax)Carnegie Mellon University ++1-412-268-8367 (Theresa Gabrielli)5000 Forbes Avenue www.cmu.edu/biolphys/deserno/
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
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
-- Dr. Markus Deserno ++1-412-268-4401 (office)Professor of Physics ++1-412-681-0648 (fax)Carnegie Mellon University ++1-412-268-8367 (Theresa Gabrielli)5000 Forbes Avenue www.cmu.edu/biolphys/deserno/
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
Tel. +420221951029
Fax +420224919752
--
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
Tel. +420221951029
Fax +420224919752
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