In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals are extended to allow for the computation between molecules stored across three cells. A general framework for the computation of three-body interactions in linked cells is described, and then used to implement the corresponding traversals. In addition, our analysis is combined with the commonly used cutoff conditions, because they influence the total workload of the computation of interactions. The combinations between traversals and truncation conditions are validated using the well-known Lennard-Jones fluid. Validation case studies are taken from the literature and configured into homogeneous and inhomogeneous scenarios. Finally, strong scalability and performance in terms of molecule updates are measured at node-level.

翻译：本文开发了用于分子动力学中三体相互作用并行计算的算法。尽管文献中已有用于计算对相互作用的遍历方法，但本研究将其扩展至允许计算存储于三个单元间的分子相互作用。文中描述了一种用于链接单元中三体相互作用计算的通用框架，并基于此实现了相应的遍历算法。此外，我们的分析结合了常用的截断条件，因为这些条件会影响相互作用计算的总工作量。通过经典的Lennard-Jones流体对遍历算法与截断条件的组合进行了验证。验证案例研究取自文献，并配置为均匀与非均匀场景。最后，在节点级别测量了分子更新方面的强扩展性与性能表现。