DAFMPB swMATH ID: 40371 Software Authors: Zhang, Bo; Debuhr, Jackson; Niedzielski, Drake; Mayolo, Silvio; Lu, Benzhuo; Sterling, Thomas Description: DASHMM accelerated adaptive fast multipole Poisson-Boltzmann solver on distributed memory architecture. We present DAFMPB (DASHMM-accelerated Adaptive Fast Multipole Poisson-Boltzmann solver) for rapid evaluation of the electrostatic potentials and forces, and total solvation-free energy in biomolecular systems modeled by the linearized Poisson-Boltzmann (LPB) equation. DAFMPB first reformulates the LPB into a boundary integral equation and then discretizes it using the node-patch scheme [33]. It solves the resulting linear system using GMRES, where it adopts the DASHMM library [14] to accelerate the matrix-vector multiplication in each iteration. DASHMM is built on top of a global address space allowing the user of DAFMPB to operate on both shared and distributed memory computers with modification of their code. This paper is a brief summary of the program, including the algorithm, implementation, installation and usage. Homepage: https://arxiv.org/abs/1710.06316 Source Code: https://github.com/zhang416/dafmpb Keywords: Poisson-Boltzmann equation; boundary element method; DASHMM; distributed computing Related Software: tabipb; VCMM; DASHMM; TABI; PyGBe; PBEQ-Solver; PAFMPB; TMSmesh; AFMPB; MIBPB; UHBD; APBS Cited in: 1 Document Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year DASHMM accelerated adaptive fast multipole Poisson-Boltzmann solver on distributed memory architecture. Zbl 07417534Zhang, Bo; Debuhr, Jackson; Niedzielski, Drake; Mayolo, Silvio; Lu, Benzhuo; Sterling, Thomas 2019 all top 5 Cited by 6 Authors 1 Debuhr, Jackson 1 Lu, Benzhuo 1 Mayolo, Silvio 1 Niedzielski, Drake 1 Sterling, Thomas Lawrence 1 Zhang, Bo Cited in 1 Serial 1 Communications in Computational Physics Cited in 3 Fields 1 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Biology and other natural sciences (92-XX) Citations by Year