Abstract
In this paper, we study the parallelization of a Cartesian grid based treecode algorithm in evaluating electrostatic potentials in a charged particle system. The treecode algorithm uses a far-field Taylor expansion to compute \(\mathcal {O}(N \log {N})\) particle-cluster interactions to replace the \(\mathcal {O}(N^2)\) particle-particle interactions. The treecode algorithm is implemented with MPI based parallelization. We design schemes to optimize the implementation adaptive to the particle location. The numerical results show high parallel efficiency. These optimized schemes are further extended to accelerate GMRES iteration in solving boundary integral Poisson–Boltzmann equation in which the discretized linear algebraic system resembles the interactions of the charged system.
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Chen, J., Geng, W. (2016). Parallel Computing of the Adaptive N-Body Treecode Algorithm for Solving Boundary Integral Poisson-Boltzmann Equation. In: Xie, J., Chen, Z., Douglas, C., Zhang, W., Chen, Y. (eds) High Performance Computing and Applications. HPCA 2015. Lecture Notes in Computer Science(), vol 9576. Springer, Cham. https://doi.org/10.1007/978-3-319-32557-6_8
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DOI: https://doi.org/10.1007/978-3-319-32557-6_8
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