Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions

Feng Nan Hwang, Shang Rong Cai, Yun Long Shao, Jong Shinn Wu

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

We investigate fully parallel Newton-Krylov-Schwarz (NKS) algorithms for solving the large sparse nonlinear systems of equations arising from the finite element discretization of the three-dimensional Poisson-Boltzmann equation (PBE), which is often used to describe the colloidal phenomena of an electric double layer around charged objects in colloidal and interfacial science. The NKS algorithm employs an inexact Newton method with backtracking (INB) as the nonlinear solver in conjunction with a Krylov subspace method as the linear solver for the corresponding Jacobian system. An overlapping Schwarz method as a preconditioner to accelerate the convergence of the linear solver. Two test cases including two isolated charged particles and two colloidal particles in a cylindrical pore are used as benchmark problems to validate the correctness of our parallel NKS-based PBE solver. In addition, a truly three-dimensional case, which models the interaction between two charged spherical particles within a rough charged micro-capillary, is simulated to demonstrate the applicability of our PBE solver to handle a problem with complex geometry. Finally, based on the result obtained from a PC cluster of parallel machines, we show numerically that NKS is quite suitable for the numerical simulation of interaction between colloidal particles, since NKS is robust in the sense that INB is able to converge within a small number of iterations regardless of the geometry, the mesh size, the number of processors. With help of an additive preconditioned Krylov subspace method NKS achieves parallel efficiency of 71% or better on up to a hundred processors for a 3D problem with 5 million unknowns.

Original languageEnglish
Pages (from-to)1529-1537
Number of pages9
JournalComputer Physics Communications
Volume181
Issue number9
DOIs
StatePublished - Sep 2010

Keywords

  • Colloidal particles
  • Finite element
  • Inexact Newton
  • Overlapping Schwarz preconditioning
  • Parallel processing
  • Poisson-Boltzmann equation

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