[ESPResSo] FW: constraints ; interactions

[Guillaume Larsen]

Dear Floh,

Thank you very much for your reply.

According to your suggestions, I slightly changed the way particles and polymers are placed in the box.
Previously I already imposed polymers and particles to be placed at a distance limit from the walls, but appeared to be too small. I have increased this limit and it now it works like a charm.
Note that, I changed the built-in polymer function to impose each monomer to be placed at a certain distance away from the walls (not only the first bead like it is implemented originally).
This way, polymers are placed at once with every beads away from the walls.

However, It works only for the 12-6LJ potential, but still doesn't work for the generic 9-3LJ potential... Seems to be related to the choice of potential parameters.

Regards,

Guillaume



> Date: Tue, 26 Oct 2010 11:58:53 +0200
> From: address@hidden
> To: address@hidden
> CC: address@hidden
> Subject: Re: [ESPResSo] constraints ; interactions
>
> Dear Guillaume,
>
> I never experienced your segmentation fault (maybe a particle is put
> exactly onto a constraint?), neither your "bond type unknown". Maybe for
> the latter, you have to check if your system is set up correctly or
> maybe send the relevant parts of your script.
>
> But of course I have often seen the "bond broken" message. :o) In
> general, I can tell you that systems with constraints (especially very
> dense systems) have to be dealt with very carefully. The most common
> problem stems from doing the warmup like for unconstrained systems with
> a "force capped lennard jones" potential. The problem with this method
> is, that ALL LJ-potentials are capped, including the constraint
> potential, which is very likely to be Lennard-Jones, too. So the
> particles can actually violate the constraints and afterwards experience
> very high forces.
>
> The solution for me was, to do two more things manually:
> 1. Place the particles in the box manually per TCL random generator.
> This lets you choose the region you place them in easily and you can
> leave a small gap between your particle region and the constraint.
> 2. The warmup. For me it turned out to be the most clever way to put
> particles in the box and slowly grow the LJ-sigma from a very small
> (significantly smaller than the analye_mindist smallest particles
> distance) value to the size I want my particles to have. That way, you
> can warm up your system without giving the particles the chance to
> violate your constraints. I also slowly grow the timestep during my
> warmup, starting with a small value.
>
> This might already solve your problems, hopefully.
>
> Greetings and I hope I could help,
>
> Floh
> (Stuttgart)
>
> Am 26.10.10 11:17, schrieb Guillaume Larsen:
> > Dear all,
> >
> > I am implementing cell constraints with associated LJ and Tunable slip
> > interactions. For information, the system is composed of 3 different
> > types of polymers plus 1 type of particle.
> > When I choose the standard 12-6 LJ potential, I get "segmentation fault"
> > error at the beginning of the integration. Instead, if I choose a
> > generic LJ potential (like 9-3LJ with appropriate parameters), I get the
> > following message: background_errors 0 {082 add_bonded_force: bond type
> > of atom 1 unknown} and also 1 bond broken between particles error
> > message. I precise that the warm-up stage is processed correctly.
> > Basically, the whole definition of the system - particles, polymer,
> > thermostat, particles/polymers interactions... - works fine for an
> > analysis without the use of cell constraints.
> > Does anybody have a clue about the meaning of errors I get?
> >
> > Thank you very much in advance,
> >
> > Guillaume Larsen
> >
> >
> >
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