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HDF5 and H5MD
Posted by Mihails Milehins
HDF5 is a binary file format and a software library for management of large and complex data sets. The development of the library was initiated in 1987 at the National Centre for Supercomputing Applications at the University of Illinois at Urbana-Champaign. Currently, the software library is supported and developed by the not-for-profit company HDF Group.
The software library provides high-level APIs written in C, C++, Fortran 90 and Java. HDF5 includes utilities for data slicing, data compression and parallel I/O. Bindings to HDF5 are available for Mathematica, MATLAB, Python and other engineering and scientific software.
HDF5 has a long history of applications in CFD and other fields of science. For example,
- HDF5 file format was adopted as the default data storage mechanism by the CFD general notation system (an international standard for CFD data).
- John Hokins Turbulence Databeses distribute the data in the HDF5 file format.
- HDF5 is one of the data formats that is used by NASA Earth Science Data Systems.
HDF5 is distributed under the terms of an open source license.
H5MD is a file format specification for efficient and portable storage of molecular data. The specification was developed in an attempt to simplify the exchange of data between different analysis and simulation software.
The description of the file format was published in the journal Computer Physics Communications in 2014 . Currently, the specification of H5MD is maintained in the form of an open source project at a git repository. Software utilities for management of H5MD are available in the form of C and Python libraries.
 de Buyl P, Colberg PH, Höfling F. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications. 2014 Jun;185(6):1546–53.