Periodic boundary conditions effects on atomic dynamics analysis

When analyzing the collective behavior of an atomic system modeled using molecular dynamics, the fact that the atomic trajectories under study were calculated under periodic boundary conditions (PBC) is often ignored. This results to artificial effects on the analysis results. We propose a method for determining the minimum size of a simulated cell with a negligible fraction of such artifacts. The method employs an extraction of a subcell with no artificial correlations between the atoms it contains. The technique is illustrated by calculations of the dynamic structure factor (DSF) of an atomic ensemble. Simulations were made for a metal (aluminum), semiconductor (silicon), and insulator (lithium fluoride). We demonstrate that the DSFs of these materials and DSF-based scattering cross-sections are almost not affected by artificial correlations starting from the threshold of similar to 15000 atoms in the simulation cell. We also reveal a problem with the vibrational analysis based on ab-initio molecular dynamics. (C) 2022 Elsevier B.V. All rights reserved.