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

From: Felix Höfling
Subject: Re: [h5md-user] Periodic and non-periodic boundary conditions
Date: Mon, 06 May 2013 15:40:41 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 06.05.2013, 14:11 Uhr, schrieb Peter Colberg <address@hidden>:

Hi all,

How should we store the boundary conditions of a cuboid/triclinic box?

   \-- group1
        \-- box
             +-- type
             +-- periodic

The periodic boundary conditions could be attached to the “box” group
as a D-dimensional attribute “periodic” of integer type, where each
element indicates whether the dimension is periodic (non-zero value)
or non-periodic (zero). Note that HDF5 does not support booleans [1].

[1] http://www.hdfgroup.org/hdf5-quest.html#bool

Does this scheme cover all possible boundary conditions in your simulations?


Hi Peter,

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:

Alternatively, I found a brief summary in Chapter 4.7 of this work:

Kind regards,


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