This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann(AFMPB)solver.We introduce and discuss the following components in order:the Poi...This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann(AFMPB)solver.We introduce and discuss the following components in order:the Poisson-Boltzmann model,boundary integral equation reformulation,surface mesh generation,the nodepatch discretization approach,Krylov iterative methods,the new version of fast multipole methods(FMMs),and a dynamic prioritization technique for scheduling parallel operations.For each component,we also remark on feasible approaches for further improvements in efficiency,accuracy and applicability of the AFMPB solver to largescale long-time molecular dynamics simulations.The potential of the solver is demonstrated with preliminary numerical results.展开更多
基金supported by NSF,DOE,HHMI,and NIH(B.Z./X.S./N.P.:NSF 0905164,B.Z./J.H.:NSF 0811130 and NSF 0905473,J.A.M.:NSF MCB1020765 and NIH GM31749)the NSF Center of Theoretical Biological Physics(CTBP)partially funded by the Chinese Academy of Sciences,the State Key Laboratory of Scientific/Engineering Computing,and the China NSF(NSFC1097218).
文摘This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann(AFMPB)solver.We introduce and discuss the following components in order:the Poisson-Boltzmann model,boundary integral equation reformulation,surface mesh generation,the nodepatch discretization approach,Krylov iterative methods,the new version of fast multipole methods(FMMs),and a dynamic prioritization technique for scheduling parallel operations.For each component,we also remark on feasible approaches for further improvements in efficiency,accuracy and applicability of the AFMPB solver to largescale long-time molecular dynamics simulations.The potential of the solver is demonstrated with preliminary numerical results.
