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Re: [ESPResSo] wall normal & box simulation (basic questions)

From: Axel Arnold
Subject: Re: [ESPResSo] wall normal & box simulation (basic questions)
Date: Mon, 22 Jun 2009 11:30:11 +0200
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On Friday 19 June 2009 18:38, Salvador Herrera Velarde wrote:
> Dear All,
> I think that my problems with the wall normal constraints come also from my
> misunderstanding of the primary simulation box in ESPResS
>  In the user's mail list I found that the primary simulation box is not
> centered at (0,0,0) . So the origin of the simulation box is in one of the
> corners?  That means, that I can't place a wall normal constraint at
> negative distances, right?


Yes, (0,0,0) is one of the corners of the simulation box, the opposite corner 
is then (box_l[0], box_l[1], box_l[2]). Nevertheless, that does not mean that 
a wall cannot be placed at negative distances; as I said, the position of the 
wall is measured along its normal from (0,0,0). If the normal is (0,0,-1), 
then all walls with positive distances d correspond to walls at z=-d, which 
are outside the box. Therefore, you obviously need to specify negative 
distances, namely between -box_l[2] and 0 in this example.

> Besides, If I put the particles inside the simulation box in a lattice
> considering that is centered at (0,0,0) ( see below),  is it this wrong in

No, that is fine. After all, the simulation box is periodic, and this simply 
means that all particle coordinates are folded up for distance calculations. 
The only difference will be that the unfolded coordinates are of course still 
centered around (0,0,0).

However, when you use constraints and have periodic boundary conditions in all 
directions, you need to leave a sufficient gap between the walls and the 
periodic box, since a) the constraints act on the folded coordinates and b) 
particles would still interaction with the periodically folded images, even 
if there is a wall inbetween. In the script parts that you sent last time, 
however, I think that was correct.


Dr. Axel Arnold 
Fraunhofer SCAI
Schloss Birlinghoven, 53754 Sankt Augustin, Germany
Tel: +49 2241 14 2575

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