Copyright 2012-2017 Pierre de Buyl and contributors
License: BSD
pyh5md is a library to read and write easily H5MD files. H5MD is a file format specification based on HDF5 to store molecular data. pyh5md is built on top of h5py, the HDF5 for Python library by Andrew Colette.
pyh5md used to define a complex class structure. Since version 1.0.0.dev1, a light subclassing of h5py's classes is used instead.
python setup.py install --user
or
pip install --user .
installs pyh5md for the current user
Once pyh5md is installed:
cd examples
python random_walk_1d.py
executes an example program that generates the H5MD file walk_1d.h5.
To write data to a particles group named "atoms", with a fixed set of positions:
from pyh5md import File, element
kwargs = {'creator': 'pyh5md README example',
'author': 'Pierre de Buyl',
}
with File('new_file.h5', 'w', **kwargs) as f:
g = f.particles_group('atoms')
g.create_box(dimension=3, boundary=['none']*3)
element(g, 'position', store='fixed', data=np.random.random(size=(32, 3)))
To read data from a H5MD file created with, for instance, LAMMPS:
from pyh5md import File, element
with File('dump_3d.h5', 'r') as f:
g = f.particles_group('all')
box_edges = element(g, 'box/edges').value[0]
position = element(g, 'position').value[:]
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