H5MD: a structured, efficient, and portable file format for molecular data
| Autor: | Peter H. Colberg, Pierre de Buyl, Felix Höfling |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Scheme (programming language)
Database Data hierarchy Computer science FOS: Physical sciences General Physics and Astronomy Experimental data computer.file_format Computational Physics (physics.comp-ph) Hierarchical Data Format Condensed Matter - Soft Condensed Matter computer.software_genre File format Software portability Hardware and Architecture Data file Data_FILES Soft Condensed Matter (cond-mat.soft) computer Physics - Computational Physics computer.programming_language Data compression |
| Popis: | 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. 11 pages, software "pyh5md" present in submission |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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