Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

DOI10.1016/J.CPC.2015.10.024zbMath1352.65660OpenAlexW2115400927WikidataQ62846539 ScholiaQ62846539MaRDI QIDQ2374010

Toshiyuki Imamura, Yuji Sugita, Jaewoon Jung, Chigusa Kobayashi

Publication date: 14 December 2016

Published in: Computer Physics Communications (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.cpc.2015.10.024

zbMATH Keywords

molecular dynamics (MD) simulationfast Fourier transform (FFT)hybrid (MPI+OpenMP) parallelizationmidpoint cell methodparticle mesh Ewald (PME) calculationvolumetric decomposition

Mathematics Subject Classification ID

Numerical methods for discrete and fast Fourier transforms (65T50) Parallel numerical computation (65Y05)

Related Items (3)

Minimizing Communication in the Multidimensional FFT ⋮ A Flexible Framework for Multidimensional DFTs ⋮ Fast multipole preconditioners for sparse matrices arising from elliptic equations

Uses Software

• PFFT
• 2DECOMP

Cites Work

• Performance of the 3D FFT on the 6D network torus QCDOC parallel supercomputer
• An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations
• A parallel FFT on an MIMD machine
• PFFT: An Extension of FFTW to Massively Parallel Architectures
• P3DFFT: A Framework for Parallel Computations of Fourier Transforms in Three Dimensions
• An Algorithm for the Machine Calculation of Complex Fourier Series
• Scalable parallel FFT for spectral simulations on a Beowulf cluster

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