HDF5 and H5MD

HDF5

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 MathematicaMATLAB, Python and other engineering and scientific software.

HDF5 has a long history of applications in CFD and other fields of science. For example,

HDF5 is distributed under the terms of an open source license.

H5MD

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 [1]. 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.

Software packages for integration with H5MD are available for several molecular dynamics programs, including LAMMPS and VMD.

External Links

 

 

 

 

 

 

References

[1] 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.

Latest Blog Posts

Recent Publications

R Pillai, JD Berry, DJE Harvie, MR Davidson (2017) Electrophoretically mediated partial coalescence of a charged microdropChemical Engineering Science, 169: 273-283. (access here)

JF Xie, BY Cao (2017) Fast nanofluidics by travelling surface wavesMicrofluidics and Nanofluidics, 21: 111 (access here)

AP Gaylard, A Kabanovs, J Jilesen, K Kirwan, DA Lockerby (2017) Simulation of rear surface contamination for a simple bluff bodyJournal of Wind Engineering and Industrial Aerodynamics, 165: 13-22. (full paper here)