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Re: [h5md-user] Periodic and non-periodic boundary conditions

From: Peter Colberg
Subject: Re: [h5md-user] Periodic and non-periodic boundary conditions
Date: Mon, 6 May 2013 11:18:15 -0400
User-agent: Mutt/1.5.21 (2010-09-15)

On Mon, May 06, 2013 at 03:40:41PM +0200, Felix Höfling wrote:
> We should also have sheared systems in mind, namely boxes with
> Lees-Edwards boundary conditions or the SLLOD algorithm, which are
> very common methods in non-equilibrium simulations of fluids. If I
> understand the methods right, the image vector changes with time and
> is not anymore an integer multiple of the edge length. Nevertheless,
> I think this would fit into our present scheme for the box
> specification, but would require an additional d-dimensional
> attribute "shear_rate".
> As a modification to your suggestion, I would call the attribute
> "boundary" and give it string values for each direction, e.g.
> "fixed", "periodic", ...
> You may find a short summary on the above methods here:
> Chapter 6.3 in the Book by Evans and Morriss:
> http://rsc.anu.edu.au/~evans/evansmorrissbook.php
> Alternatively, I found a brief summary in Chapter 4.7 of this work:
> http://www.swinburne.edu.au/ict/research/cms/documents/disertations/jgChap4.pdf

Let's start with an initial choice of "nonperiodic" and "periodic".

(See variable-length string array attribute [1] for implementation hint.)

LAMMPS has a non-periodic “shrink-wrapped” boundary condition [2],
where the walls follow the extent of all particles. These boundaries
are not "fixed", but still "nonperiodic".

[1] http://www.hdfgroup.org/ftp/HDF5/examples/misc-examples/attrvstr.c
[2] http://lammps.sandia.gov/doc/boundary.html


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