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Re: [ESPResSo] constraints
Re: [ESPResSo] constraints
Tue, 04 Sep 2007 09:05:45 +0200
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in principle I agree that it is worthwile to rethink the way the
constraints are implemented (using the folded coordinates and making the
thing fully periodic, the current constraint does not exacly work
intuitively). However, so far Espresso does not work this way and
changing it just like that makes systems of people crash that have been
(admittedly only sort of ;-) ) working so far.
For the polymer command, which is just for setting up a system, using
the folded positions is even more tricky since it results in a
pseudo-connected macromolecule which is disrupted since half of the
macromolecule may end up in the top half of the box and half ends up in
the bottom half of the box and it is cut by the constraint. And I do not
see how this is different if you put the wall anywhere else in the cell.
Olaf Lenz wrote:
> If you sent a copy of your email to the ESPResSo user's mailing list,
> please write it in English!
> Nils Binz wrote:
> >Ich wollte mal nachfragen, aus welchem Grund du in der
> >in polymer.c die folded-positions der Teilchen ueberpruefst, wir
> hatten hier
> >naemlich folgendes Problem:
> >Eine Wand (constraint) wird ganz an den Rand der Box gesetzt und nun
> wird ein
> >Polymer aufgesetzt. Wenn das Polymer die Wand ueberschreiten wuerde,
> >ueberschreitet es gleichzeitig auch die Box, die folded-positions der
> >kritischen Teilchen sind also auf der gleichen Seite der wall obwohl
> sie die
> >constraint verletzen.
> Probably it is useful to rehearse the discussion on the developers list
> on "Nsquare cellsystem and folded positions": The problem is, that the
> constraints so far used the "internally folded" coordinates to check
> whether a constraint was violated or not. The internally folded
> coordinates depend on the used cellsystem.
> Consequently, the different constraints worked differently for different
> cellsystem, which definitely can not be a good solution.
> In your case of a wall on the border of the system, this had the effect
> that the constraints worked in the way you described: when a particle
> walks over the wall, the constraint was violated. This was, however,
> more or less a bug. The system should behave periodically: when a
> particle is moved over the limits of the box, it is folded, and the
> coordinates have to be evaluated according to the folded position, and
> not according to the absolute position - and even less according to the
> internally folded position.
> Also, think of the strange behaviour of your system: when you put a wall
> directly on the border of the system, particles can get pretty close to
> the border, which means that they effectively interact with the
> particles close to the border on the other side, i.e. you get periodic
> I think the correct solution would be not to put the wall on the border
> of the system, but to leave some safety margin to the border to catch
> the particles that jump over the wall.
> Best regards
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