Re: [ESPResSo-users] Periodic boundary condition OIF

[Wink, Markus]

Hi Ivan,

thank you for your answer. The periodicity works if I only use "ks". I  have to 
think about, whether just having the parameter "ks" is enough to represent my 
system. 

But using it, another question arose. Using point-like particles, there is the 
command "part pid print folded_position" to get the folded position. Having a 
look at the OIf implementation, I did not find anything comparable. So if I put 
"oif_object_analyze object-id 0 origin", I don't get the folded position, but 
the position of the origin is out of the simulation box. Of course, it is no 
problem to write a small script calculating the folded positions, but I was 
wondering, if this is already implemented and I just did not find it.

Best wishes,

Markus


-----Ursprüngliche Nachricht-----
Von: Ivan Cimrak [mailto:address@hidden 
Gesendet: Mittwoch, 21. Januar 2015 09:46
An: Wink, Markus
Cc: address@hidden
Betreff: Re: [ESPResSo-users] Periodic boundary condition OIF

Hi Markus,

First, I will give you a simple answer:
If you use streching only (e.g. by "oif_create_template template-id 0 
nodes-file NODES.dat triangles-file TRIANLGES.dat ks 0.05"), then the 
periodicity will work.

Here comes the longer answer:
stretching forces are implemented in a way that the periodicity is used in the 
same way as the original Espresso does. However, the local area, bending, 
global area and volume forces are implemented slightly
different: The coordinates of the particles are first folded before the 
calculation of the forces. This however means that natural periodicity of 
Espresso is broken.

The reason for the folding was that without it it did not work correctly. This 
is an issue that is on our TODO list though.


Ivan




On Tue, Jan 20, 2015 at 4:46 PM, Wink, Markus <address@hidden> wrote:
> Hello everybody,
>
>
>
> if putting point-like particles into a lb-fluid, the periodic boundary 
> condition works just fine. Meaning, that when a particle leaves the 
> simulation box at one end it enters the box at the other end again. In 
> contrast to that, if I use the Object in fluid package, I don’t get 
> that behavior. Every time, the extended object reaches the end of the 
> simulation box, I get the following error message and no further 
> integration steps are
> performed:
>
>
>
> broken: particles sum 3, id 0, partn 2, bond 2346
>
>
>
> I was wondering if the periodic boundary condition is implemented in 
> the oif-package and if: How can I apply/switch on a periodic condition 
> for the extended object?
>
>
>
> Thank you very much 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