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Re: [ESPResSo-users] LB Boundary

From: Vincent Ustach
Subject: Re: [ESPResSo-users] LB Boundary
Date: Tue, 20 Aug 2013 12:11:01 -0700

I meant to send this last night! I solved it by only typing lbboundary rhomboid, I was able to get the correct usage in the error message:

usage: lbboundary rhomboid corner <x> <y> <z> a <ax> <ay> <az> b <bx> <by> <bz> c <cx> <cy> <cz> direction {inside|outside} type <t> [penetrable <0|1>] [reflecting <1|2>]
    while executing
"lbboundary rhomboid   "

I missed the line of looking under constraints for syntax. Thanks Georg.



--Vincent Ustach
  University of California, Davis

On Mon, Aug 19, 2013 at 6:02 PM, Vincent Ustach <address@hidden> wrote:
Unfortunately that's not it.

--Vincent Ustach
  University of California, Davis

On Mon, Aug 19, 2013 at 12:35 AM, Georg Rempfer <address@hidden> wrote:
Can you try p instead of pos? I remember having implemented it with p, not pos.

2013/8/19 Vincent Ustach <address@hidden>

I received the following error that leads me to believe there is another parameter besides "pos" that is the head of the "tripod"

Error: Unknown parameter pos in lbboundary rhomboid
    while executing
"lbboundary rhomboid pos 100 100 100 a 100 25 100  b 25 100 100 c 100 100 25 direction -1  "
    (file "rhomb.tcl" line 85)

could it go by some other name? By leaving out pos 100 100 100 I was able to run this simulation. Leaving pos out of the command defaults to the origin as the tripod head.

In the code documentation it does say pos but I am finding problems. This is ver 3.2.0



--Vincent Ustach
  University of California, Davis

On Wed, Jul 17, 2013 at 12:13 AM, Georg Rempfer <address@hidden> wrote:
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.


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

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