标题： 用于高性能分子动力学模拟中三体相互作用的多重时间步进方法 显示英文标题

标题： The Multiple Time-Stepping Method for 3-Body Interactions in High Performance Molecular Dynamics Simulations

摘要： 理解分子系统的复杂行为对于物理学、材料科学和生物学等领域是基础性的。分子动力学（MD）模拟是研究原子级动态的重要工具。本工作专注于提高涉及二体和三体相互作用的MD模拟的效率。传统的二体势能通常无法完全捕捉分子系统的复杂性，因此包含三体相互作用非常重要。然而，这些相互作用属于三次复杂度类，与二体相互作用的二次复杂度相比，计算成本更高，即使应用了截断距离也是如此。提高效率的一种方法是使用r-RESPA多时间步算法来减少三体相互作用的计算次数。在本工作中，我们研究了这种方法，在并行化计算的高性能计算（HPC）方法背景下进行。特别是，我们研究了一种文献中提出的减少通信的分布式内存并行方法，并提出了一种新颖的共享内存并行截断方法，该方法在粒子模拟库AutoPas中实现。结果和方法得到了讨论，为MD模拟效率的潜在提升提供了见解。 显示英文摘要

摘要： Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on improving the efficiency of MD simulations involving two-body and three-body interactions. Traditional two-body potentials often can not fully capture the complexity of molecular systems, making the inclusion of three-body interactions important. However, these interactions are in a cubic complexity class, compared to a quadratic one for two-body interactions, and therefore are computationally expensive, even when a cutoff distance is applied. One way to improve efficiency is to use the r-RESPA multiple time-stepping algorithm to reduce the number of three-body interaction calculations. In this work, we investigate this method in the context of High Performance Computing (HPC) methods that parallelize the calculations. In particular, we investigate a communication-reducing distributed-memory parallel method from literature and present a novel shared-memory parallel cutoff method, implemented in the particle simulation library AutoPas. The results and methods are discussed, providing insights into potential advancements in MD simulation efficiency.