https://github.com/pdebuyl/pyh5md

Read and write H5MD files
https://github.com/pdebuyl/pyh5md

hdf5 molecular-dynamics

Last synced: 4 months ago
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Read and write H5MD files

• Host: GitHub
• URL: https://github.com/pdebuyl/pyh5md
• Owner: pdebuyl
• Created: 2012-12-28T12:45:13.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2017-12-19T15:21:57.000Z (about 7 years ago)
• Last Synced: 2024-09-22T08:47:30.034Z (5 months ago)
• Topics: hdf5, molecular-dynamics
• Language: Python
• Size: 92.8 KB
• Stars: 12
• Watchers: 5
• Forks: 5
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
pyh5md : Read and write H5MD files

==================================

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.

[H5MD]: http://nongnu.org/h5md/

[HDF5]: http://www.hdfgroup.org/HDF5/

[h5py]: http://h5py.org/

pyh5md used to define a complex class structure. Since version 1.0.0.dev1, a light

subclassing of h5py's classes is used instead.

Install

-------

    python setup.py install --user

or

    pip install --user .

installs pyh5md for the current user

Examples

--------

Once pyh5md is installed:

    cd examples

    python random_walk_1d.py

executes an example program that generates the H5MD file `walk_1d.h5`.

Usage

-----

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[:]