ZnH5MD - High Performance Interface for H5MD Trajectories

ZnH5MD allows easy access to simulation results from H5MD trajectories. It provides a Python interface and can convert existing data to H5MD files as well as export to other formats.

pip install znh5md["dask"]

Example

In the following example we investigate an H5MD dump from LAMMPS with 1000 atoms and 201 configurations:

import znh5md

traj = znh5md.DaskH5MD("file.h5", time_chunk_size=500, species_chunk_size=100)

print(traj.file.time_dependent_groups)
# ['edges', 'force', 'image', 'position', 'species', 'velocity']

print(traj.force)
# DaskDataSet(value=dask.array<array, shape=(201, 1000, 3), ...)

print(traj.velocity.slice_by_species(species=1))
# DaskDataSet(value=dask.array<reshape, shape=(201, 500, 3), ...)

print(traj.position.value)
# dask.array<array, shape=(201, 1000, 3), dtype=float64, chunksize=(100, 500, 3), ...>

# You can iterate through the data
for item in traj.position.batch(size=27, axis=0):
    for x in item.batch(size=17, axis=1):
        print(x.value.compute())

ASE Atoms

You can use ZnH5MD to store ASE Atoms objects in the H5MD format.

ZnH5MD does not support all features of ASE Atoms objects. It s important to note that unsupported parts are silently ignored and no error is raised.

The ASEH5MD interface will not provide any time and step information.

If you have a list of Atoms with different PBC values, you can use znh5md.io.AtomsReader(atoms, use_pbc_group=True). This will create a pbc group in box/ that also contains step and time. This is not an official H5MD specification so it can cause issues with other tools. If you don't specify this, the pbc of the first atoms in the list will be applied.

import znh5md
import ase

atoms: list[ase.Atoms]

db = znh5md.io.DataWriter(filename="db.h5")

db.add(znh5md.io.AtomsReader(atoms)) # or znh5md.io.ChemfilesReader

data = znh5md.ASEH5MD("db.h5")
data.get_atoms_list() == atoms

CLI

ZnH5MD provides a small set of CLI tools:

• znh5md view <file.h5> to view the File using ase.visualize
• znh5md export <file.h5> <file.xyz> to export the file to .xyz or any other supported file format
• znh5md convert <file.xyz> <file.h5> to save a file.xyz as file.h5 in the H5MD standard.

More examples

A complete documentation is still work in progress. In the meantime, I can recommend looking at the tests, especially test_znh5md.py to learn more about slicing and batching.