Free/Libre software for H5MD files
==================================

This is a list of [free software](https://www.gnu.org/philosophy/free-sw.html)
for use with H5MD files.

Reading and writing H5MD files
------------------------------

The [HDF5 library](http://www.hdfgroup.org/HDF5/) provides interfaces
for C, Fortran, C++, and Java.

[HDF5 for Python](http://www.h5py.org/) provides a Pythonic interface to the
HDF5 binary data format.

[h5xx](https://github.com/h5md/h5xx) is a thin C++ wrapper to ease reading and
writing of HDF5 files.

[fortran_h5md](https://github.com/pdebuyl/fortran_h5md) is a Fortran module to
facilitate the writing of H5MD files.

[pyh5md](https://github.com/pdebuyl/pyh5md) is a Python module that facilitate
reading and writing H5MD files.

[ch5md](https://github.com/pdebuyl/ch5md) is a set of C routines to read and
write H5MD files.

Simulation
----------

[HAL's MD package](http://halmd.org/) is a high-precision molecular dynamics
package for the large-scale simulation of simple and complex liquids.

[ESPResSo](http://espressomd.org/) is a highly versatile software package for
scientific molecular dynamics simulations of coarse-grained atomistic or
bead-spring models for soft matter research.

[ESPResSo++](http://www.espresso-pp.de/) is a software package for the scientific simulation and 
analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research.

[LAMMPS](https://lammps.sandia.gov) is a classical molecular dynamics code with
a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular
Massively Parallel Simulator. See command [dump h5md](https://lammps.sandia.gov/doc/dump_h5md.html).


Analysis and plotting
---------------------

[h5md-tools](https://github.com/fhoefling/h5md-tools) is a tool set for
analysing, plotting, and manipulating data of molecular simulations stored
in the H5MD file format.

[MDAnalysis](https://www.mdanalysis.org) is a Python library for analysing
trajectories from molecular simulations, including the H5MD file format. Version
2.0.0 features parallel I/O using MPI, see [Jakupovic \& Beckstein,
2021](http://conference.scipy.org/proceedings/scipy2021/edis_jakupovic.html).

[VMD-h5mdplugin](https://github.com/jonaslandsgesell/VMD-h5mdplugin.git)
is a H5MD file reader plugin for the molecular visualization program
[VMD](http://www.ks.uiuc.edu/Research/vmd/).

[VOTCA](http://www.votca.org/) is an analysis package for molecular dynamics
data that focuses on systematic coarse-graining and microscopic charge transport.