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Keywords
(11)
Data Mining
Graph Algorithm
Hash Function
massive datasets
Md Simulation
Memory Access
Molecular Dynamic Simulation
Molecular Dynamic
Parallel Implementation
Spatial Correlation
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Collisionfree spatial hash functions for structural analysis of billionvertex chemical bond networks
Collisionfree spatial hash functions for structural analysis of billionvertex chemical bond networks,10.1016/j.cpc.2006.06.001,Computer Physics Comm
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Collisionfree spatial hash functions for structural analysis of billionvertex chemical bond networks
(
Citations: 3
)
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Cheng Zhang
,
Bhupesh Bansal
,
Paulo S. Branicio
,
Rajiv K. Kalia
,
Aiichiro Nakano
,
Ashish Sharma
,
Priya Vashishta
Stateoftheart molecular dynamics (MD) simulations generate
massive datasets
involving billionvertex chemical bond networks, which makes
data mining
based on graph algorithms such as Kring analysis a challenge. This paper proposes an algorithm to improve the efficiency of ring analysis of large graphs, exploiting properties of Krings and spatial correlations of vertices in the graph. The algorithm uses dualtree expansion (DTE) and spatial hashfunction 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.
Journal:
Computer Physics Communications
, vol. 175, no. 5, pp. 339347, 2006
DOI:
10.1016/j.cpc.2006.06.001
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References
(6)
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(
Citations: 105
)
Luc De Raedt
,
Stefan Kramer
Conference:
International Joint Conference on Artificial Intelligence  IJCAI
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CacheOblivious Algorithms
(
Citations: 409
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Matteo Frigo
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Conference:
IEEE Symposium on Foundations of Computer Science  FOCS
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(
Citations: 41
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Erik D. Demaine
Published in 2002.
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(
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,
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Published in 2001.
Computer physics communications
(
Citations: 361
)
Unknown
Journal:
Computer Physics Communications
, vol. 95, no. 1, pp. IFCIFC, 1996
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Citations
(3)
Atomistic visualization: Space–time multiresolution integration of data analysis and rendering
(
Citations: 1
)
Dipesh Bhattarai
,
Bijaya B. Karki
Journal:
Journal of Molecular Graphics & Modelling  J MOL GRAPH MODEL
, vol. 27, no. 8, pp. 951968, 2009
De Novo Ultrascale Atomistic Simulations On HighEnd Parallel Supercomputers
(
Citations: 8
)
Aiichiro Nakano
,
Rajiv K. Kalia
,
Kenichi Nomura
,
Ashish Sharma
,
Priya Vashishta
,
Fuyuki Shimojo
,
Adri C. T. Van Duin
,
William A. Goddard
,
Rupak Biswas
,
Deepak Srivastava
,
Lin H. Yang
Journal:
International Journal of High Performance Computing Applications  IJHPCA
, vol. 22, no. 1, pp. 113128, 2008
Atomistic damage mechanisms during hypervelocity projectile impact on AlN: A largescale parallel molecular dynamics simulation study
(
Citations: 2
)
Paulo S. Branicio
,
Rajiv K. Kalia
,
Aiichiro Nakano
,
Priya Vashishta
,
Fuyuki Shimojo
,
Jose P. Rino
Journal:
Journal of The Mechanics and Physics of Solids  J MECH PHYS SOLIDS
, vol. 56, no. 5, pp. 19551988, 2008