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Re: [ESPResSo-users] Periodic box, bonds and mpi

From: Axel Arnold
Subject: Re: [ESPResSo-users] Periodic box, bonds and mpi
Date: Fri, 10 Oct 2014 10:16:24 +0200
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On 10.10.14 01:50, Aleksei Kabedev wrote:
Dear all,

Could you please have a look at an issue I am dealing with at the moment?

I am trying to solve a problem with the error
"background_errors 2 {079 bond broken between particles 14773, 14775 and 14776 (particles not stored on the same node)} " ocurring.

What that in practice means is that those three particles moved apart more than a processor domain. There has to be in addition an error about broken pair bonds, otherwise, you simply forgot to bind those particles by pair bonds.

I have two brushes of linear polymers attached to the opposite walls of channel. The box is 20*20*100 (the coated surfaces are in the further planes). The length of polymers is about 20 units. If I use flow without fluctuations it seems to be alright(even when chains are significantly inclined), but in case I use thermostat lb 1.0 it gives me an error. I decreased both timestep and tau to really small numbers, capped the forces, but there is still something wrong with it. By the way, I think that capping isn't working in this case for some reason. But I've never used it before, probably did something wrong.

Capping only helps if the problem are strongly overlapping particles. And with LB, you cannot simply reduce the time step, because if you don't reduce the mesh at the same time, you crank up the sound speed and break LB.

I suppose that I could be an issue with the periodic boundary conditions. I don't really understand how does the transferring work for the harmonic bonds if one of the parts from the ending border  (say, with initial coordinates 19.5 1.0 20.0), which is on the second node, is replaced to the beginning (0.5 1.0 20.0) because of the flow, which is on the first.

Don't worry, that is taken care of. Basically, a border shell of particles is exchanged between processors, where the shell is wide enough for any two particles bonded by pair bonds. So, as long as you have pair bonds for the both arms of your angular bond, the particles need to be on the same CPU, if the pair bonds are intact.

Here are the parameters I use, probably I use some of them improperly.

lbboundary wall dist 1.0 normal 0 0 1
lbboundary wall dist [expr -$h + 1] normal 0 0 -1

thermostat lb 1.0

setmd time_step 0.0005
lbfluid  density 1.0 viscosity 5.0 agrid 1.0 tau 0.001 friction 20.0 ext_force $mag 0.0 0.0

Hmm, agrid 1.0 with tau 0.001 is a bit bold, apart from that the magnitude of the external force is important.

set scale 0.6
inter forcecap individual
inter 1 1 lennard-jones 1.0 $scale [expr $scale*$ljr_cut] 1.0 0.0 $scale
inter 0 1 lennard-jones 1.0 $scale [expr $scale*$ljr_cut] 1.0 0.0 $scale
inter 1 2 lennard-jones 1.0 $scale [expr $scale*$ljr_cut] 1.0 0.0 $scale

Now that doesn't work. Effectively, you have particles of diameter scale, and linearly extrapolate the LJ potential below 0.6. However, there it is already pretty steep, so that capping barely helps. You should start at 1.1*0.6 and slowly and gradually reduce to about 0.9*0.6.


JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

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