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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 12:00:27 +0200
User-agent: Mozilla/5.0 (Windows NT 6.2; WOW64; rv:24.0) Gecko/20100101 Thunderbird/24.6.0

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 0.00156.

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,


Dňa 15.7.2014 17:31 Wink, Markus wrote / napísal(a):

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.





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

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