Re: [ESPResSo-users] LB Boundary

[Stefan Kesselheim]

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