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Re: [ESPResSo-users] Object in Fluid

From: Wink, Markus
Subject: Re: [ESPResSo-users] Object in Fluid
Date: Tue, 22 Jul 2014 11:47:53 +0000

Dear Ivan, 

thanks for your help and for the nice video! I tried your script (with the 
configurations you chose, i. e. smaller channel for faster computation) and it 
worked fine. But still, I have some problems which I have no idea how to 

1) I tried a script with my geometry (which was bigger than yours) and 
different parameters for a:  a = 1, a = 0.1, a = 0.01, a = 0.0005, a= 0.00005, 
a= 0.000005. Still, I get the same error message, telling me, that my particle 
tears apart. This is quite strange, since at least for the configuration with 
the smallest a, the force acting on the particle by the obstacle is in the 
order of magnitude of the fluidic force.

2) I played a bit around with your script and changed a few parameter. There 
was some peculiarity occurring:
        - I changed the size of the particle, to get a ratio of particle size / 
channel width, which is in my case interesting. Changing the size of the 
particle by the "stretch 0.1 0.1 0.1" command, I got an error message before 
the first integration step was taken:
        "bending_force.h, calc_bending_force: Angle approaches 0 or 2*Pi
        Background_errors 0 {063 rhomboid constraint 0 violated by particle 
So it seems, that the size of the object plays an important role for the 
stability of the simulation. I don't really understand, where the problem comes 
from, maybe you have an idea. And probably you also have an idea for my first 
question, why still the particle tears apart when reaching the obstacle, 
although I have changed the factor a to a very low value.

Greetings and thanks a lot,


Markus Wink
Fraunhofer ICT-IMM
Doktorand Abteilung Mikrofluidik und Analytik / Microfluidics and Analytics 
Carl-Zeiss-Straße 18-20, 55129 Mainz, Germany
Phone +49 6131 990-396 / Fax +49 6131 990-205 
address@hidden /

-----Ursprüngliche Nachricht-----
Von: Ivan Cimrak [mailto:address@hidden 
Gesendet: Donnerstag, 17. Juli 2014 13:11
An: Wink, Markus
Cc: Andrew Jewett; address@hidden
Betreff: Re: AW: [ESPResSo-users] Object in Fluid

Dear Markus,

I put the scripts in the attachment. I just ran the simulation once again, and 
you can see the result on the video

soft_sphere was activated with parameters inter 0 10 soft-sphere 0.0005 1.2 0.1 

Maybe, when you used too weak soft_sphere (your parameter was 10^(-6) whereas 
mine was 10^(-4)), what happend was that the particles entered the boundary. 
But in that case you would have gotten different error message.

Markus, keep me please informed whether you can resolve this issue.


Dňa 17.7.2014 9:58 Wink, Markus wrote / napísal(a):
> Dear Ivan,
> thanks for your advice. I have tried to lower the factor a as you proposed. I 
> used a = 5*10^-6 , corresponding to a force of f = 9.5*10^-4.
> But still, the particle tears apart. Strange.
> If you still got the script, which you ran and which worked, would you be so 
> kind to send it to me, so I can check, if I made another stupid mistake?
> Greetings and thanks a lot!
> Markus
> -----Ursprüngliche Nachricht-----
> Von: Ivan Cimrak [mailto:address@hidden
> Gesendet: Mittwoch, 16. Juli 2014 22:56
> An: Wink, Markus
> Cc: Andrew Jewett; address@hidden
> Betreff: Re: [ESPResSo-users] Object in Fluid
> 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,
> Ivan
> 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:

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

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