Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces

DOI10.1016/J.CPC.2020.107742MaRDI QIDQ6041590zbMATH OpenOpenAlexFDO

Authors Jiahui Chen, Weihua Geng, Daniel R. Reynolds

Publication date 31 May 2023

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

Full work available at URL https://doi.org/10.1016/j.cpc.2020.107742

zbMATH Keywords

electrostaticsload balancingMPIparallel computingtreecode

Mathematics Subject Classification ID

Boltzmann equations (35Q20) PDEs in connection with optics and electromagnetic theory (35Q60) Series expansions (e.g., Taylor, Lidstone series, but not Fourier series) (41A58) Iterative numerical methods for linear systems (65F10) Parallel numerical computation (65Y05) Numerical algorithms for specific classes of architectures (65Y10) Software, source code, etc. for problems pertaining to optics and electromagnetic theory (78-04) Electro- and magnetostatics (78A30) Motion of charged particles (78A35) Multipole methods applied to problems in optics and electromagnetic theory (78M16) Nuclear physics (81V35) Many-body theory; quantum Hall effect (81V70) Computational methods for problems pertaining to biology (92-08) Developmental biology, pattern formation (92C15)

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Cites work

• A Cartesian treecode for screened Coulomb interactions
• A decomposition of multidimensional point sets with applications to k -nearest-neighbors and n -body potential fields
• A fast algorithm for particle simulations
• A fast directional algorithm for high frequency acoustic scattering in two dimensions
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A modified parallel tree code for \(N\)-body simulation of the large-scale structure of the universe
• A new version of the fast multipole method for screened Coulomb interactions in three dimensions
• A parallel version of the fast multipole method
• A particle method and adaptive treecode for vortex sheet motion in three-dimensional flow
• A treecode algorithm for simulating electron dynamics in a Penning-Malmberg trap
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
• Fast evaluation of multiquadric RBF sums by a Cartesian treecode
• Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• PVFMM: A parallel kernel independent FMM for particle and volume potentials

Cited in

(6)

• A Cartesian treecode for screened Coulomb interactions
• Treecode-accelerated Green iteration for Kohn-Sham density functional theory
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• A parallel adaptive treecode algorithm for evolution of elastically stressed solids
• Treecode algorithms for computing nonbonded particle interactions
• Parallel TREE code for two-component ultracold plasma analysis

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