@Article{CiCP-25-1235,
author = {Bo Zhang, Jackson DeBuhr, Drake Niedzielski, Silvio Mayolo, Benzhuo Lu and Thomas Sterling},
title = {DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture},
journal = {Communications in Computational Physics},
year = {2018},
volume = {25},
number = {4},
pages = {1235--1258},
abstract = {<p style="text-align: justify;">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.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.OA-2018-0098},
url = {http://global-sci.org/intro/article_detail/cicp/12897.html}
}