Re: [ESPResSo-users] Object in Fluid

[Wink, Markus]

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: http://www.kst.fri.uniza.sk/~icimrak/
cell-in-fluid group: http://cell-in-fluid.fri.uniza.sk