[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ESPResSo-users] Particle in Fluid, periodic boundary conditions
From: |
Ulf Schiller |
Subject: |
Re: [ESPResSo-users] Particle in Fluid, periodic boundary conditions |
Date: |
Tue, 02 Dec 2014 16:32:48 +0000 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.2.0 |
Hi Markus,
glad to hear that it's working now. And yes, you're right, the walls
were partly permeable at the periodic boundary. As far as I can see,
only LB populations are ever communicated to halo regions, so
everything else has to be taken care of explicitly - this is also why
ghost particles need to be coupled to the fluid, for example.
Cheers,
Ulf
On 02/12/14 14:58, Wink, Markus wrote:
> 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
>
--
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
Re: [ESPResSo-users] Particle in Fluid, periodic boundary conditions, Joost de Graaf, 2014/12/01