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

From: Pierre de Buyl
Subject: Re: [h5md-user] Periodic and non-periodic boundary conditions
Date: Wed, 29 May 2013 10:17:04 +0200
User-agent: Mutt/1.5.21 (2010-09-15)

On Mon, May 06, 2013 at 11:18:15AM -0400, Peter Colberg wrote:
> 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

For now, we should not take into account all kind of boundary conditions. The
purpose, for now, is to identify correctly the geometry.

Merging this issue with the box image vectors, what could be done is the
  - Have "image" as an optional dataset in a trajectory.
  - The presence of image implies periodicity.
  - Partial periodicity is handled by having the image vectors equal 0 in the
    corresponding dimension.

This is simple and does not encumber the specification too much. A shear rate
attribute should be regarded as optional and implementation dependent anyway so
I am against considering it in the specs. It does not prevent any software to
add it either in /parameters or even as an additional attribute or time
dependent dataset for a given trajectory group.



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