Re: [ESPResSo-users] LB Boundary

[Vincent Ustach]

Georg,

Thanks for your advice. I realize now that rhomboid will not work because of the structure I want to make. Do attachments work on this listserve? See attached for the picture of walls made of particles. The membrane is the squares with the square pyramid cut out. The pore is the pyramidal cut out shape. The square in the bottom of the figure is to prevent particles from going from source to sink through the periodic boundary.

I was thinking the rhomboid shape is a 2-D four sided shape, not a 3-D shape. Fundamentally I misunderstood the idea that a node must be inside or outside the boundary and all the lbboundaries are 3-D.

Stefan,

Thanks for your continued help. I will look for this command that will help apply the particle geometry to lbnode boundaries. According to the UG "set" is not supported with lbnode.

the code
lbnode 15 15 15 set boundary 1
 

gives the error
unknown feature "boundary" of lbnode x y z set
    while executing

"lbnode 15 15 15 set boundary 1 "

Otherwise I am going to start work on the developer's side to allow individual boundary nodes to be set.

Cheers,

Vincent

--Vincent Ustach
  University of California, Davis

On Wed, Jul 17, 2013 at 12:53 AM, Stefan Kesselheim <address@hidden> wrote:

Hi Vincent, hi Georg, hi Mailing list,
one little remark. Vincent, you have made your geometry with particles already? Then it should be possible to just mark all lbnodes "inside" as wall nodes. There should be command similar to lbnode set boundary…
The lbboundaries do nothing but evaluating for every boundary which node is inside and which one is not.
One thing however comes to my mind: We collect the forces on every lb boundary in every step. The forces acting on nodes which are set independently of lbboundaries probably accidentally are collected in lbboundary 0.
This is of course undesired, but I did not think about that when implementing it. Not having lbboundary 0 might lead to crashes.
It might make sense to define an "nonexistent" lbboundary (e.g. a sphere at coordinates much larger than the box_l) as lbboundary 0. This is a workaround, and I hope I can clean that up soon.
Cheers
Stefan

On Jul 17, 2013, at 9:22 AM, Georg Rempfer <address@hidden> wrote:

> Hello Vincent,
>
> another hint: the lbfluid grid's origin is located at (agrid/2,
> agrid/2, agrid/2). So to create a cubic boundary that contains the
> lbnode at (x+agrid/2, y+agrid/2, z+agrid/2) use pos = (x, y, z) and a
> = (agrid, 0 , 0), b = (0, agrid, 0), and c = (0, 0, agrid), where x,
> y, and z are integers ranging from 0 to box_l - 1 (in the respective
> direction).
>
> Greetings,
> Georg
>
> 2013/7/17 Georg Rempfer <address@hidden>:
>> Hello Vincent,
>>
>> the pos argument is used to define any of the corners and the
>> arguments a, b, and c are meant to define three edges adjacent to the
>> corner given by pos. You can imagine this as a tripod consisting of
>> three vectors (a,b, and c) originating at pos. In other terms, pos
>> gives the coordinates of one of the corners and a, b, and c give the
>> difference vectors of three neighboring corners and pos.
>>
>> I remember we recently used lbboundaries in that fashion to do a
>> similar thing. A minor problem that occurred was that with the
>> creation of every individual boundary, the whole boundary grid got
>> reinitialized, which made the initialization very slow when we used
>> hundreds of boundaries. I am not sure that this is going to happen for
>> you as well, as it might have been caused by code not present in the
>> current master / release versions. If it does happen, please just
>> notify us using this mailing list. This should be easy to fix.
>>
>> Greetings,
>> Georg
>>
>> 2013/7/17 Vincent Ustach <address@hidden>:
>>> Hello all,
>>>
>>> I have a complex geometry made of walls of particles with LJ and coulomb
>>> potentials to simulate roughness and charge, respectively.
>>>
>>> These simulate a thin membrane with a pore. The pore shape is square
>>> pyramidal.
>>>
>>> I also need hydrodynamic boundaries and I believe some of these can be
>>> modeled using several "lbboundary rhomboid" constraints that will follow the
>>> shape of the walls of particles. If not, I will look into augmenting the C
>>> code to allow for flagging of individual boundaries.
>>>
>>> My question is regarding the shape args of the lbboundary rhomboid. If "pos
>>> [3]" is the coordinates of one corner, are a and b and c the other three
>>> corners?
>>>
>>> Thanks,
>>>
>>> --Vincent Ustach

Screen shot 2013-07-17 at 7.28.45 PM.png
Description: PNG image