Pierre de Buyl's homepage

Using H5MD in lammps

H5MD is a HDF5 based file format for molecular data. In short, it is binary, portable and self-describing.

In this blog post I present the use of H5MD in the Molecular Dynamics program lammps. I have written a dump style for lammps, i.e. a piece of code to write the particles' coordinates to a file.

As an example, I present a MD simulation of a Lennard-Jones fluid and a short analysis of the resulting H5MD file. The analysis is deliberately concise to outline the H5MD specifics and not the computations.

{% notebook 2014/h5md_lennard_jones.ipynb %}

Comments !

Generated with Pelican. Theme based on MIT-licensed Skeleton.