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

[Ulf Schiller]

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