Computing Lennard-Jones Potentials and Forces with Reconfigurable Hardware.

Abstract

Abstract — Technological advances have made FPGAs an attractive platform for the acceleration of complex scientific applications. These applications demand high performance and highprecision floating point arithmetic. In this paper, we present a design for calculating the Lennard-Jones potential and force as is done in molecular dynamics simulations. This architecture employs IEEE 754 double precision floating point units, including a square root unit developed for this kernel. The design presented is a modular, very deeply pipelined architecture that exploits the fine-grained parallelism of the calculations. With the Xilinx Virtex-II Pro as a target device, an implementation using two pipelines operating in parallel achieves 3.9 GFLOPS. Index Terms — molecular dynamics, square root, supercomputing I.