Fast electrostatic force calculation on parallel computer clusters

  • Authors:

  • Amirali Kia;Daejoong Kim;Eric Darve

  • Affiliations:

  • Mechanical Engineering, Stanford University, Mechanics and Computation Division, 496 Lomita Mall, Stanford 94305-4040, United States;Mechanical Engineering, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul 121-742, Republic of Korea;Mechanical Engineering, Stanford University, Mechanics and Computation Division, 496 Lomita Mall, Stanford 94305-4040, United States

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2008

Quantified Score

Hi-index 31.45

Visualization

Abstract

The fast multipole method (FMM) and smooth particle mesh Ewald (SPME) are well known fast algorithms to evaluate long range electrostatic interactions in molecular dynamics and other fields. FMM is a multi-scale method which reduces the computation cost by approximating the potential due to a group of particles at a large distance using few multipole functions. This algorithm scales like O(N) for N particles. SPME algorithm is an O(NlnN) method which is based on an interpolation of the Fourier space part of the Ewald sum and evaluating the resulting convolutions using fast Fourier transform (FFT). Those algorithms suffer from relatively poor efficiency on large parallel machines especially for mid-size problems around hundreds of thousands of atoms. A variation of the FMM, called PWA, based on plane wave expansions is presented in this paper. A new parallelization strategy for PWA, which takes advantage of the specific form of this expansion, is described. Its parallel efficiency is compared with SPME through detail time measurements on two different computer clusters.