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Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non-uniform fast fourier transform
KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.). KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
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2016 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 3, 378-387 p.Article in journal (Refereed) PublishedText
Abstract [en]

We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new algorithm is developed for NFFT for the evaluations of electrostatic interaction energies and forces. Both real-space and reciprocal-space computations are further accelerated by using graphical processing units (GPU) with CUDA technology. Especially, the use of CUNFFT (NFFT based on CUDA) very much reduces the reciprocal-space computation. In order to reach the best performance of this method, we propose a procedure for the selection of optimal parameters with controlled accuracies. With the choice of suitable parameters, we show that our method is a good alternative to the standard Ewald method with the same computational precision but a dramatically higher computational efficiency.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2016. Vol. 37, no 3, 378-387 p.
Keyword [en]
electrostatic interaction calculation, ewald summation, GPU, non-uniform FFT
National Category
Chemical Sciences
URN: urn:nbn:se:kth:diva-180961DOI: 10.1002/jcc.24250ISI: 000367385000007PubMedID: 26584145OAI: diva2:898841

QC 20160129

Available from: 2016-01-29 Created: 2016-01-26 Last updated: 2016-01-29Bibliographically approved

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Wang, Yong-Lei
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Machine Design (Dept.)Applied Physical Chemistry
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