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Re: [ESPResSo-users] lbfluid+virtual particles issue

From: Joost de Graaf
Subject: Re: [ESPResSo-users] lbfluid+virtual particles issue
Date: Mon, 30 Nov 2015 09:37:47 +0000

All valid observations, to which I want to add one more. Make sure there is no virtual bead directly on top of you center of mass (non-virtual) bead, as that will also cause these type of errors.

Best, Joost

On 30 November 2015 at 07:45, Kai Szuttor <address@hidden> wrote:

i have also encountered such a "force was nan" error when i simulated a
rigid virtual sites raspberry model. Are there other particles than your
raspberry model in the system and do you use the mass feature? If so it
can happen that the fluctuations on some LB nodes are too large because
of the particle coupling. Then if the mass of your raspberry model is
too small it may happen that you get negative LB populations on a LB
node and you will get an infinite force back from the fluid-particle


On Sun, Nov 29, 2015 at 06:38:02PM -0800, Andrew Jewett wrote:
> On Sun, Nov 29, 2015 at 6:11 PM, Aleksei Kabedev
> <address@hidden> wrote:
> > "background_errors 0 {999 force on particle was NAN.} {999 force on particle
> > was NAN.} {999 force on particle was NAN.} {999 force on particle was NAN.}
> > {999 force on particle was NAN.} {999 force on particle was NAN.} "
> This looks like a generic numerical explosion, and my post to the list
> is a generic response.  (Forgive that.  If you tried the suggestions
> below, and they did not help, then post again.)
> This kind of error could occur for many reasons.  But the most common
> reason is that, at some moment, two atoms are too close together.
> (You say it only happens when real and virtual atoms are too far
> apart.  See below.)
> Generally speaking, to solve this kind of problem, use some
> combination of these strategies:
> -visualize the system.
>   Be sure to check periodic boundary conditions (see below).
> -Try running the simulation with a much smaller timestep.
> -Simplify the system by removing molecules or molecule types.
> Keep simplifying until the error goes away.  That will help you locate
> the problem.  (It helps to do this using a small system.)
>  (For example, get rid of your "rasberrry" molecules, and see if the
> error goes away.  If not, then try building a smaller system with
> fewer LJ particles.  if you have any torsion/dihedral interactions,
> get rid of them.  If you have any charges, set them to zero, etc...)
> > during the integration cycle.
> How long does the simulation run before you get this error?
> (Does this happen during the first verlet iteration.
> Or does the simulation run for a short while and then crash?)
> > It happens if the distance between the central
> > particle and the virtual ones is greater than ~2,
> Not sure what to make of that.
> But be sure to check periodic boundary conditions to rule out the
> possibility that you don't have two particles too close together.
> (In other words, if the boundary box is too small, it possible that
> the atoms in different unit-cells are overlapping.  If you only look
> at one copy of the unit cell, you might not see this problem.  If you
> use VMD, you can test this by selecting the
> "Graphics"->"Representations" menu option, clicking on the "Periodic"
> tab, and click on the +x, -x, +y, -y, +z, -z boxes.  I am not familiar
> with other visualization programs.)
> > whereas the parameters of
> > the flow look as follows
> > lbfluid density 1.0 viscosity 0.5 agrid 1.0 tau 0.02 friction 10.0 ext_force
> > 0.001 0.0 0.0;
> > thermostat lb=1.0
> > timestep=0.01
> > Probably some of you have faced this problem before.
> > Any help in these matters would be greatly appreciated.
> > Thanks!
> Don't know if that helped.
> Good luck.
> > Kind regards,
> > Aleksei Kabedev

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