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[ESPResSo-users] Periodic box, bonds and mpi

From: Aleksei Kabedev
Subject: [ESPResSo-users] Periodic box, bonds and mpi
Date: Fri, 10 Oct 2014 00:50:58 +0100

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.

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.

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.

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

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


Kind regards,
Aleksei Kabedev

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