Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
DOI10.1016/J.CPC.2015.10.024zbMATH Open1352.65660OpenAlexW2115400927WikidataQ62846539 ScholiaQ62846539MaRDI QIDQ2374010FDOQ2374010
Authors: Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita 
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
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molecular dynamics (MD) simulationfast Fourier transform (FFT)hybrid (MPI+OpenMP) parallelizationmidpoint cell methodparticle mesh Ewald (PME) calculationvolumetric decomposition
Parallel numerical computation (65Y05) Numerical methods for discrete and fast Fourier transforms (65T50)
Cites Work
- P3DFFT: A framework for parallel computations of Fourier transforms in three dimensions
- PFFT: An extension of FFTW to massively parallel architectures
- An Algorithm for the Machine Calculation of Complex Fourier Series
- Scalable parallel FFT for spectral simulations on a Beowulf cluster
- An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations
- Performance of the 3D FFT on the 6D network torus QCDOC parallel supercomputer
- A parallel FFT on an MIMD machine
Cited In (5)
- Minimizing Communication in the Multidimensional FFT
- Parallel three-dimensional nonequispaced fast Fourier transforms and their application to particle simulation
- Fast multipole preconditioners for sparse matrices arising from elliptic equations
- Multi-axis decomposition of density functional program for strong scaling up to 82,944 nodes on the K computer: compactly folded 3D-FFT communicators in the 6D torus network
- A flexible framework for multidimensional DFTs
Uses Software
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