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Re: [ESPResSo-users] OIF - background_errors

From: Wink, Markus
Subject: Re: [ESPResSo-users] OIF - background_errors
Date: Thu, 10 Apr 2014 09:01:58 +0000

Dear all, 

I have changed the potential to a LJ-potential with the following parameters:

set sig 1
set epsilon 1.5
set shift [expr 0.25*$epsilon]
set cut [expr 1.2246*$sig]
inter 0 10 lennard-jones $epsilon $sig $cut $shift 0.0

Anyway, I get the error message:

broken: particles sum 1, id 0, partn 2, bond 2346

I don't exactly know what that error message means. I guess, that my object 
tears apart (thus the binding between the nodes is not strong enough?). So 
changing the kv, kb and ks parameters for the objects need to be changed. Am I 

Besides that: how do I know what values to choose for the LJ potential to 
simulate the system. Is there any literature you could recommend on how to find 
the right parameters or do you have a hint on how to get them?


Markus Wink

-----Urspr√ľngliche Nachricht-----
Von: address@hidden [mailto:address@hidden Im Auftrag von Iveta Jancigova
Gesendet: Mittwoch, 9. April 2014 09:57
An: address@hidden
Betreff: Re: [ESPResSo-users] OIF - background_errors


it also depends on the size of your object. If it is small, it basically "flows 
with the fluid" and as the fluid flows past the obstacle, so does the object.

However, if your object is large - let's say, half of the object is in the flow 
that goes above the obstacle and the other half in the flow that goes below the 
obstacle, then the object hits the obstacle and the soft-sphere potential is 
not strong enough to prevent particles from entering.

If you send the complete script together with obstacles and the mesh-files you 
are using for your object, we could take a look.


> Message: 1
> Date: Tue, 8 Apr 2014 11:21:12 +0000
> From: "Wink, Markus" <address@hidden>
> To: "address@hidden" <address@hidden>
> Subject: [ESPResSo-users] OIF - background_errors 0
> Message-ID:
>       <address@hidden>
> Content-Type: text/plain; charset="us-ascii"
> Dear ESPResSo-community,
> I have got a question concerning the OIF implementation. In my case I 
> have put an object (a sphere) in a microfluidic channel that has a 
> rhomboid as a barrier inside. I applied a constant force density to 
> achieve a fluid flow. I want to investigate the trajectory of the 
> object inside the channel. As it reaches the rhomboid, the object is 
> deflected by it. Nevertheless, I get an error message after some time 
> the object is in contact with the rhomboid:
> background_errors 0 {063 rhomboid constraint 4 violated by particle 
> 376}
> My interpretation is, that one node of my object (particle 376) tries 
> to enters the rhomboid. That of cause should not be the case.
> The rhomboid was defined by the command:
> constraint rhomboid corner $corX $corY $corZ a $aX $aY $aZ b $bX $bY 
> $bZ c $cX $cY $cZ direction 1 type 10 lbboundary rhomboid corner $corX 
> $corY $corZ a $aX $aY $aZ b $bX $bY $bZ c $cX $cY $cZ direction 1
> The object is defined by:
> oif_add_object object-id 0 template-id 0 origin 125 85 9 part-type 0 
> mass 1
> The object-rhomboid interaction is implemented by:
> inter 0 10 soft-sphere 0.0001 1.2 0.1 0.0
> How can I avoid the error message mentioned above? Is there any 
> mistake in my script? Does it help to lower the time step (so far, I 
> chose time_step 0.1)?
> Thanks for your help?
> Greetings
> Markus Wink

Iveta Jancigova, PhD student
Department of Information Networks
Faculty of Management Science and Informatics University of Zilina
E-mail: address@hidden
Office: B352
Work Phone: +421-41-5134313

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