Parallel point defect identification in molecular dynamics simulations without post-processing: A compute and dump style for LAMMPS

Two classes for the molecular dynamics program LAMMPS – one compute style and one dump style – are presented that are designed to identify, count, and output point defects in cascade damage and related molecular dynamics simulations. The calculations are done in parallel across multiple MPI processes, and can be done at the same time as the original simulation. This drastically reduces storage requirements by eliminating the need to post-process every atom in the system. Non-cubic lattices, free surfaces, and large voids can be eliminated from the output by suitable choices of the reference lattice. The classes are derived from LAMMPS’s Dump and Compute classes, and pose no additional overhead to LAMMPS if they are not used.

针对分子动力学程序LAMMPS，本文提出两类工具——一种计算风格（compute style）与一种输出风格（dump style），旨在识别、统计并输出级联损伤及相关分子动力学模拟中的点缺陷。该计算可通过多消息传递接口（MPI）进程并行执行，且可与原始模拟同步进行。此举无需对系统内所有原子进行后处理，可大幅降低存储需求。通过合理选择参考晶格，可在输出中剔除非立方晶格、自由表面与大型空洞。这两类工具均继承自LAMMPS的Dump与Compute类，若未启用则不会为LAMMPS带来额外开销。