Title: H5MD: A structured, efficient, and portable file format for molecular data
Authors: de Buyl, Pierre ×
Colberg, Peter H.
Höfling, Felix #
Issue Date: Feb-2014
Publisher: North-Holland Pub. Co.
Series Title: Computer Physics Communications vol:185 pages:1546-1553
Abstract: We propose a new file format named “H5MD” for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD files are HDF5 (Hierarchical Data Format) files with a specific hierarchy and naming scheme. Thus, H5MD inherits many benefits of HDF5, e.g., structured layout of multi-dimensional datasets, data compression, fast and parallel I/O, and portability across many programming languages and hardware platforms. H5MD files are self-contained, and foster the reproducibility of scientific data and the interchange of data between researchers using different simulation programs and analysis software. In addition, the H5MD specification can serve for other kinds of data (e.g. experimental data) and is extensible to supplemental data, or may be part of an enclosing file structure.
ISSN: 0010-4655
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Polymer Chemistry and Materials
× corresponding author
# (joint) last author

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