Re: [ESPResSo-users] Periodic boundary condition OIF

[Ivan Cimrak]

Hi Markus,

You are right, the "oif_object_analyze object-id 0 origin" command
returns the same as would do the command "part pid print pos". It just
averages positions of all object's particles. These positions are
obtained by "part pid print pos".

With regards,
Ivan

On Wed, Jan 21, 2015 at 3:22 PM, Wink, Markus
<address@hidden> wrote:
> 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



-- 
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