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

[Felix Höfling]

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?
>
>   trajectory
>    \-- 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?
>
> Peter

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:
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

Kind regards,

Felix