znh5md 0.1.0

High Performance Interface for H5MD Trajectories

ZnH5MD - High Performance Interface for H5MD Trajectories

ZnH5MD allows easy access to simulation results from H5MD trajectories.

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)
# ['box', '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.

import znh5md
import ase

atoms: list[ase.Atoms]

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

db.add(znh5md.io.AtomsReader(atoms))

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