Re: [ESPResSo-users] Particle in Fluid, periodic boundary conditions

[Wink, Markus]

Hi Ulf,

extending the rhomboids as you proposed seems to solve the problem. Now, I 
don’t' see the jumps in the velocity or z-position anymore. Thanks a lot for 
your help. 

So the problem was, that the halo nodes were not correctly marked as boundary 
nodes and that resulted in a wrong hydrodynamic behavior of the fluid? Did I 
get it right? 
Good to know.

KR, Markus


-----Ursprüngliche Nachricht-----
Von: address@hidden [mailto:address@hidden Im Auftrag von Ulf Schiller
Gesendet: Dienstag, 2. Dezember 2014 15:04
An: address@hidden
Betreff: Re: [ESPResSo-users] Particle in Fluid, periodic boundary conditions

Hi Markus,

try the following: make the rhomboids extend from -1 to boxY+1 in the 
y-direction to ensure that the halo nodes are correctly marked as boundary. It 
can be debated whether this is a bug or a feature.

Cheers,
Ulf

On 02/12/14 12:52, Ulf Schiller wrote:
> Hi Markus,
> 
> I tried another thing and replaced the boundaries by plane walls 
> normal to the x and z direction. With that, I do not see any peculiarities.
> This suggests that the issue is related to the more complex boundaries 
> in your system. I'll have a look at your boundaries.tcl tonight.
> 
> Cheers,
> Ulf
> 
> On 01/12/14 17:08, Wink, Markus wrote:
>> Hello everybody,
>>
>>  
>>
>> I performed simulations as Ulf proposed to help to track the problem 
>> down. In detail three different simulations are performed, graphs on 
>> that can be found attached:
>>
>> 1)      I removed the boundaries, putting a particle with an initial
>> velocity v_0y. I can see the exponential decrease of the velocity in 
>> y-direction (as expected). The z-position is pretty stable, 
>> nevertheless I see an (uncorrelated (?)) change of the velocity in z 
>> direction. It seems to be directed towards the –z direction, although 
>> it is very small (of the orders of 1E-24 ), so I guess it is an numerical 
>> artifact (?).
>> Nevertheless I don’t see the jump in the z-position nor in the z-velocity.
>>
>> 2)      A simulation as in 1), in addition the particle has an initial
>> velocity in the +z direction (of the order I got for the lift force). 
>> I still see the exponential decrease in both the z- and y-velocity. 
>> No jumps of the z-position at the boundaries can be found.
>>
>> 3)      The same as simulation 1), but this time with boundaries. I see
>> the migration towards the middle of the channel as expected (notice, 
>> that this time, the initial z-velocity of the particle is set to zero).
>> Neither a jump in the z-velocity nor in the z-position can be seen.
>>
>>  
>>
>> In combination of the first script I posted (which was the same as in 
>> simulation 3 here, but furthermore an external force is exerted to 
>> the
>> fluid) I see the jump in the z-component of the position and the 
>> z-component of the velocity only if there is a combination of 
>> boundaries and an external force acting on the fluid. What is missing 
>> is a simulation with no boundaries and an external force acting on the fluid.
>>
>>  
>>
>> I furthermore played around with the friction coefficient. If I lower 
>> it by three orders of magnitude, I still notice a jump in the 
>> z-component of the velocity, although it is not as steep as before. I 
>> am not sure what this means.
>>
>>  
>>
>> I hope this helps to isolate the problem.
>>
>>  
>>
>> Kind regards
>>
>>  
>>
>> Markus
>>
>>  
>>
>>  
>>
>>  
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Ulf Schiller [mailto:address@hidden
>> Gesendet: Montag, 1. Dezember 2014 16:41
>> An: address@hidden
>> Cc: Joost de Graaf; Wink, Markus
>> Betreff: Re: [ESPResSo-users] Particle in Fluid, periodic boundary 
>> conditions
>>
>>  
>>
>> Hi Joost, Markus, all,
>>
>>  
>>
>> after a quick inspection I can't see any relevant changes to the 
>> coupling on that branch (I've not gone through the CUDA 
>> implementation though). After merging and running the script Markus 
>> provided, I'm afraid the issue persists. I don't have time to track 
>> this down, but according to my experience it is likely to be due to one of 
>> the following:
>>
>> - problem with pos-lattice mapping (less likely since only halo 
>> affected)
>>
>> - halo not up-to-date
>>
>> - forces missing in halo upon redef of fluid momentum
>>
>>  
>>
>> Note that this bug potentially affects any system with particle-fluid 
>> coupling and periodic boundary conditions.
>>
>>  
>>
>> Cheers,
>>
>> Ulf
>>
>>  
>>
>> On 28/11/14 15:27, Joost de Graaf wrote:
>>
>>> Dear Markus,
>>
>>>
>>
>>> Sorry about that. The ENGINE branch on hmenke's git account
>>
>>>
>>
>>> https://github.com/hmenke/espresso/tree/engine
>>
>>>
>>
>>> has a fix for the bug. As I said, I recalled seeing something like 
>>> it,
>>
>>> and at that time we apparently fixed the problem (which I cannot
>>
>>> remember doing). We are still working on one last testcase for the
>>
>>> ENGINE branch, before we have it pulled into the Master, which will
>>
>>> take about a week. Then a lot of the LB bugs should be fixed.
>>
>>>
>>
>>> Kind Regards, Joost
>>
>>>
>>
>>> On 28 November 2014 at 16:24, Joost de Graaf 
>>> <address@hidden
>>
>>> <mailto:address@hidden>> wrote:
>>
>>>
>>
>>>     Dear Markus,
>>
>>>
>>
>>>
>>
>>>
>>
>>>     On 24 November 2014 at 21:24, Joost de Graaf
>>
>>>     <address@hidden <mailto:address@hidden
>> <mailto:address@hidden:address@hidden
>> >>>
>> wrote:
>>
>>>
>>
>>>         Dear Markus,
>>
>>>
>>
>>>         I remember spotting something like this in one of the older
>>
>>>         versions of the master, but I tried to find it and could not
>>
>>>         reproduce the bug with the latest version, which one are you
>> using?
>>
>>>
>>
>>>         KR, Joost
>>
>>>
>>
>>>         On 24 November 2014 at 19:35, Ulf Schiller 
>>> <address@hidden
>>
>>>         <mailto:address@hidden>> wrote:
>>
>>>
>>
>>>             Hi Markus,
>>
>>>
>>
>>>             On 24/11/14 18:12, Wink, Markus wrote:
>>
>>>             > can explain it to me? It seems, that the periodic
>> boundary condition in
>>
>>>             > the LB Fluid doesn’t work. If I remove the fluid I 
>>> don’t
>> see that.
>>
>>>
>>
>>>             Yes, looks like something is at odds with the 
>>> periodicity
>>
>>>             here. Can you
>>
>>>             plot the z-velocity over x-position? That may point 
>>> towards
>>
>>>             what is
>>
>>>             going wrong.
>>
>>>
>>
>>>             Cheers,
>>
>>>             Ulf
>>
>>  
>>
>> --
>>
>> Dr Ulf D Schiller
>>
>> Centre for Computational Science
>>
>> University College London
>>
>> 20 Gordon Street
>>
>> London WC1H 0AJ
>>
>> United Kingdom
>>
>>  
>>
>> Phone: +44 (0)20 7679 5300
>>
>>  
>>
> 
> 


--
Dr Ulf D Schiller
Centre for Computational Science
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom

Phone: +44 (0)20 7679 5300