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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
Author(s) -
Yang ShengChun,
Wang YongLei,
Jiao GuiSheng,
Qian HuJun,
Lu ZhongYuan
Publication year - 2016
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24250
Subject(s) - computation , fast fourier transform , cuda , ewald summation , computer science , algorithm , reciprocal , reciprocal lattice , space (punctuation) , computational science , fourier transform , mathematics , parallel computing , physics , mathematical analysis , optics , molecular dynamics , linguistics , philosophy , quantum mechanics , diffraction , operating system
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. © 2015 Wiley Periodicals, Inc.