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Ewald Summation Based on Nonuniform Fast Fourier Transform
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.ORCID-id: 0000-0001-9783-4535
2006 (engelsk)Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 425, nr 1-3, s. 142-147Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

We present a novel approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations. The method can easily be implemented in existing simulation programs. We report here some results from our implementation, where we utilize widely available libraries, and demonstrate the accuracy, and expected computational complexity of our approach.

sted, utgiver, år, opplag, sider
2006. Vol. 425, nr 1-3, s. 142-147
HSV kategori
Identifikatorer
URN: urn:nbn:se:su:diva-22616DOI: 10.1016/j.cplett.2006.04.106OAI: oai:DiVA.org:su-22616DiVA, id: diva2:189168
Merknad
Part of urn:nbn:se:su:diva-1008Tilgjengelig fra: 2006-05-19 Laget: 2006-05-19 Sist oppdatert: 2022-02-25bibliografisk kontrollert
Inngår i avhandling
1. Algorithms for Molecular Dynamics Simulations
Åpne denne publikasjonen i ny fane eller vindu >>Algorithms for Molecular Dynamics Simulations
2006 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel MD simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed.

A method for performing ab initio MD is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored.

Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared.

Next, a method for treating electrostatic interactions in MD simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform---ENUF for short. The method scales as N log N, where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs.

Finally, an outlook is given and some directions for further developments are suggested.

sted, utgiver, år, opplag, sider
Stockholm: Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, 2006. s. 93
Emneord
molecular dynamics, MD, first principles molecular dynamics, quantum mechanics, liquid water, parallel algorithm, data parallel, MPI, Coulombic interaction, Ewald summation, nonuniform fast Fourier transform, FFT, FFTW, NFFT, ENUF
HSV kategori
Identifikatorer
urn:nbn:se:su:diva-1008 (URN)91-7155-277-4 (ISBN)
Disputas
2006-06-10, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 13:00
Opponent
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Tilgjengelig fra: 2006-05-19 Laget: 2006-05-19bibliografisk kontrollert

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