A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid

  • Authors:

  • Ásdís Helgadóttir;Frédéric Gibou

  • Affiliations:

  • Mechanical Engineering Department, University of California, Santa Barbara, CA 93106, United States;Mechanical Engineering Department, University of California, Santa Barbara, CA 93106, United States and Computer Science Department, University of California, Santa Barbara, CA 93106, United State ...

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2011

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Abstract

We introduce a second-order solver for the Poisson-Boltzmann equation in arbitrary geometry in two and three spatial dimensions. The method differs from existing methods solving the Poisson-Boltzmann equation in the two following ways: first, non-graded Quadtree (in two spatial dimensions) and Octree (in three spatial dimensions) grid structures are used; Second, Neumann or Robin boundary conditions are enforced at the irregular domain's boundary. The irregular domain is described implicitly and the grid needs not to conform to the domain's boundary, which makes grid generation straightforward and robust. The linear system is symmetric, positive definite in the case where the grid is uniform, nonsymmetric otherwise. In this case, the resulting matrix is an M-matrix, thus the linear system is invertible. Convergence examples are given in both two and three spatial dimensions and demonstrate that the solution is second-order accurate and that Quadtree/Octree grid structures save a significant amount of computational power at no sacrifice in accuracy.