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

Published: 04-09-2019| Version 1 | DOI: 10.17632/p39kb4fshj.1
Karl D. Hammond


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.