Journal Article10.1021/ACS.JCIM.8B00501
An Efficient Lossless Compression Algorithm for Trajectories of Atom Positions and Volumetric Data
Martin Brehm,Martin Thomas +1 more
17
TL;DR: The newly developed and highly efficient lossless compression algorithm for trajectories of atom positions and volumetric data and the BQB file format, which is very robust, flexible, and efficient, is introduced.
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Abstract: We present our newly developed and highly efficient lossless compression algorithm for trajectories of atom positions and volumetric data. The algorithm is designed as a two-step approach. In the first step, efficient polynomial extrapolation schemes reduce the information entropy of the data by exploiting both spatial and temporal continuity. The second step processes the data by a series of transformations (Burrows–Wheeler, move-to-front, run length encoding) and finally compresses the stream with multitable canonical Huffman coding. Our approach reaches a compression ratio of around 15:1 for typical position trajectories in the XYZ format. For volumetric data trajectories in Gaussian Cube format (such as electron density), even a compression ratio of around 35:1 is yielded, which is by far the smallest size of all formats compared here. At the same time, compression and decompression are still reasonably fast for everyday use. The precision of the data can be selected by the user. For storage of the co...
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Citations
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Fast parallel algorithms for short-range molecular dynamics
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- 01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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