中圖分類號：TP391 文獻(xiàn)標(biāo)志碼：A DOI: 10.16157/j.issn.0258-7998.233897 中文引用格式： 高萍，段曉輝，劉衛(wèi)國，等. 基于國產(chǎn)申威眾核架構(gòu)的二維材料分子動力學(xué)模擬算法優(yōu)化[J]. 電子技術(shù)應(yīng)用，2023，49(12)：1-7. 英文引用格式： Gao Ping，Duan Xiaohui，Liu Weiguo，et al. Optimization of molecular dynamics simulation algorithm for two-dimensional material on Sunway[J]. Application of Electronic Technique，2023，49(12)：1-7.
Optimization of molecular dynamics simulation algorithm for two-dimensional material on Sunway
Gao Ping1，2，Duan Xiaohui2，3，Liu Weiguo2，3，Guo Jiaxu2，Liu Jia1，Wan Wubing1，2， Gan Lin1，2，Yang Guangwen1，2
1.Department of Computer Science and Technology， Tsinghua University， Beijing 100084， China； 2.National Supercomputing Center in Wuxi， Wuxi 214072， China；3. School of Software， Shandong University， Jinan 250101， China；4.College of Computer Science and Technology， Jilin University， Changchun 130012， China
Abstract： Molecular dynamics (MD) simulation is an important tool to explore the microcosmic world, which is widely used in many fields. Two-dimensional materials is an important research direction of MD in the field of materials science, in which the calculation of interlayer interactions is the most time-consuming part. High performance computing is a key technology to improve the simulation efficiency of two-dimensional materials. In this work, the powerful computing power of a new generation of Sunway supercomputer is utilized to improve the MD simulation efficiency of two-dimensional materials. For the interlayer force field, multiple algorithm optimization strategies such as eliminating redundant calculation, multi-core fusion and setting buffer are adopted. It implements thread-level parallelism by software Cache accumulation force, communication between computation processing elements accumulation energy and C++ feature. The hardware and software Cache coordination policy is adopted to improve storage access efficiency. The experimental results show that the overall performance is improved by 155 times, the simulation efficiency is about 2 ns/day, and the weak extension parallel efficiency reaches 92.7%.
Key words : molecular dynamics；high performance computing；LAMMPS；two-dimensional materials；Sunway
