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Re: [ESPResSo-users] Object in Fluid

From: Ivan Cimrak
Subject: Re: [ESPResSo-users] Object in Fluid
Date: Wed, 16 Jul 2014 22:55:50 +0200

Dear Markus,

The error message you have obtained indeed means that the bond of the
object tears apart. The reason for this is that you have too strong
soft_sphere potential. Your forces due to f_body are approximately

On the other hand, soft_sphere potential is given by V(r)=a/(r^n), the
forces due to soft_sphere are thus F(r)=dV/dr=a*n/(r^{n+1}).
Now your soft_sphere potential starts to act at the distance 0.1 from
the obstacle (your cut-off was 0.1) but this means that the particles
immediately get the force of
1.0*1.2/(0.1^2.2) = 190.18  which is way too large. The system gets
shock and then it blows apart.

I would suggest to set soft_sphere much lower, say e.g. a = 0.0005 (or
even smaller). This results to force 0.0005*1.2/(0.1^2.2)=0.095 which
is acceptable. I have tried this setting with smaller channel (for
faster computations) and it worked.

Best regards,


On Wed, Jul 16, 2014 at 8:28 AM, Wink, Markus
<address@hidden> wrote:
> Dear all,
> attached you will find pictures of the starting configuration and the 
> configuration, when the simulation stops with the error message (actually 
> Espresso is not cancelled, but no further integration step will be performed).
> Looking forward to your answers.
> Greetings
> Markus
> -----Ursprüngliche Nachricht-----
> Von: Andrew Jewett [mailto:address@hidden
> Gesendet: Dienstag, 15. Juli 2014 17:59
> An: Wink, Markus
> Cc: address@hidden
> Betreff: Re: [ESPResSo-users] Object in Fluid
> Pictures can be helpful.
> What does the system look like (at nearby times)?
> Cheers
> Andrew
> On Tue, Jul 15, 2014 at 11:31 AM, Wink, Markus <address@hidden> wrote:
>> Dear all,
>> I tried to simulate the movement of a particle past an obstacle inside
>> a microfluidic channel using the oif method. At the moment I am facing
>> the problem, that, when the particle gets near the object, the
>> simulation stops and prints out the error message:
>> “broken: particles sum 2, id 0, partn 2, bond 2346”
>> I am not exactly sure, what that error message means. I guess, that
>> the bond of the object tears apart, so I could change the parameters of the 
>> bond.
>> Does anyone have a clue? For the potential between the particle and
>> the obstacle, I have chosen a soft sphere potential.
>> The files are attached.
>> Thanks a lot for your help.
>> Greetings
>> Markus

Ivan Cimrak
FRI Zilinska Univerzita v Ziline
personal web:
cell-in-fluid group:

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