Change search
ReferencesLink to record
Permanent link

Direct link
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.
Show others and affiliations
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
Identifiers
URN: urn:nbn:se:kth:diva-180961DOI: 10.1002/jcc.24250ISI: 000367385000007PubMedID: 26584145OAI: oai:DiVA.org:kth-180961DiVA: diva2:898841
Note

QC 20160129

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

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Wang, Yong-Lei
By organisation
Machine Design (Dept.)Applied Physical Chemistry
In the same journal
Journal of Computational Chemistry
Chemical Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 14 hits
ReferencesLink to record
Permanent link

Direct link