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CPHYSICS
2006

Collision-free spatial hash functions for structural analysis of billion-vertex chemical bond networks

9 years 11 months ago
Collision-free spatial hash functions for structural analysis of billion-vertex chemical bond networks
State-of-the-art molecular dynamics (MD) simulations generate massive datasets involving billion-vertex chemical bond networks, which makes data mining based on graph algorithms such as K-ring analysis a challenge. This paper proposes an algorithm to improve the efficiency of ring analysis of large graphs, exploiting properties of K-rings and spatial correlations of vertices in the graph. The algorithm uses dual-tree expansion (DTE) and spatial hash-function tagging (SHAFT) to optimize computation and memory access. Numerical tests show nearly perfect linear scaling of the algorithm. Also a parallel implementation of the DTE + SHAFT algorithm achieves high scalability. The algorithm has been successfully employed to analyze large MD simulations involving up to 500 million atoms.
Cheng Zhang, Bhupesh Bansal, Paulo S. Branicio, Ra
Added 11 Dec 2010
Updated 11 Dec 2010
Type Journal
Year 2006
Where CPHYSICS
Authors Cheng Zhang, Bhupesh Bansal, Paulo S. Branicio, Rajiv K. Kalia, Aiichiro Nakano, Ashish Sharma, Priya Vashishta
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