Journal Article

Field‐programmable gate array acceleration of the Tersoff potential in LAMMPS

Deng, Quan, Liu, Qiang

2025

Overview

Molecular dynamics simulation is a common method to help humans understand the microscopic world. The traditional general‐purpose high‐performance computing platforms are hindered by low computational and power efficiency, constraining the practical application of large‐scale and long‐time many‐body molecular dynamics simulations. In order to address these problems, a novel molecular dynamics accelerator for the Tersoff potential is designed based on field‐programmable gate array (FPGA) platforms, which enables the acceleration of LAMMPS using FPGAs. Firstly, an on‐the‐fly method is proposed to build neighbor lists and reduce storage usage. Besides, multilevel parallelizations are implemented to enable the accelerator to be flexibly deployed on FPGAs of different scales and achieve good performance. Finally, mathematical models of the accelerator are built, and a method for using the models to determine the optimal‐performance parameters is proposed. Experimental results show that, when tested on the Xilinx Alveo U200, the proposed accelerator achieves a performance of 9.51 ns/day for the Tersoff simulation in a 55,296‐atom system, which is a 2.00×$$ \\times $$ increase in performance when compared to Intel I7‐8700K and 1.70×$$ \\times $$ to NVIDIA Tesla K40c under the same test case. In addition, in terms of computational efficiency and power efficiency, the proposed accelerator achieves improvements of 2.00×$$ \\times $$ and 7.19×$$ \\times $$ compared to Intel I7‐8700K, and 4.33×$$ \\times $$ and 2.11×$$ \\times $$ compared to NVIDIA Titan Xp, respectively. We propose an FPGA‐based molecular dynamics accelerator with customized computing architecture for the Tersoff potential. The designed accelerator achieves good acceleration of the Tersoff potential, showing the potential of extending LAMMPS to FPGAs for high power efficiency and high computational efficiency.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: Algorithms / Computing time / Design optimization / Efficiency / Field programmable gate arrays / field‐programmable gate array / Flexibility / high‐performance computing / Molecular dynamics / Power efficiency / Power management / reconfigurable computing / Semiconductors / Simulation / Tersoff potential / Workloads