基于FPGA的分子动力学模拟匹配单元设计

Design of Match Units for Molecular Dynamics Simulations Based on FPGA

摘要:

为减少分子动力学模拟中短程力计算的时间消耗，设计并实现基于现场可编程门阵列的分子动力学模拟匹配单元。理论上，分析了分子动力学模拟中粒子间作用力的物理规律，提出两种满足短程力计算要求的粒子对的筛选方法：偏序法和平面法。技术上，使用新兴的硬件描述语言SpinalHDL，在Xilinx Virtex UltraScale+ HBM VCU128 FPGA板卡上实现了匹配单元。最后，将硬件测试结果与理论结果进行对比，验证了匹配单元可以有效过滤掉对短程力计算没有贡献的粒子对。同时对使用偏序法、平面法和使用直接计算法两种不同情况下的资源消耗进行对比分析，表明使用偏序法、平面法可以节省系统70%的DSP资源。

Abstract:

To reduce the time consumption of rang-limited force calculations in molecular dynamics simulations, a field-programmable gate array-based molecular dynamics simulation matching unit is designed and implemented. Theoretically, the physical laws of inter-particle forces in molecular dynamics simulations are analyzed, and two filtering methods for particle pairs that meet the requirements of rang-limited force calculations are proposed: the partial-order method and the planar method. Technically, the matching unit was implemented on a Xilinx Virtex UltraScale+ HBM VCU128 FPGA board using SpinalHDL, an emerging hardware description language. Finally, the hardware test results are compared with the theoretical results to verify that the matching unit can effectively filter out the particle pairs that do not contribute to the rang-limited force calculation. At the same time, a comparative analysis of the resource consumption of using the partial order method, the plane method and the direct calculation method shows that the use of the partial order method and the plane method can save 70% of the system's DSP resources.