Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

PL Barclay and DZ Zhang, JOURNAL OF COMPUTATIONAL PHYSICS, 435, 110238 (2021).

DOI: 10.1016/j.jcp.2021.110238

A generalization of the Lees-Edwards periodic boundary conditions (gLE- PBC) for molecular dynamics (MD) simulations is developed to allow for arbitrary deformations to be applied to the domain. The gLE-PBC domain remains a rectangular cuboid regardless of the applied deformation in contrast with the Lagrangian-rhomboid periodic boundary conditions (LR- PBC) where the domain deforms according to the applied deformation. The kinematics of gLE-PBC are validated against pure shear. The gLE-PBC method for interacting systems is then validated against the LR-PBC method and analytical solutions for a solid under isotropic compression, one-dimensional shearing, three-dimensional extension and shearing and for a liquid under Couette flow. Bulk physical properties extracted from the gLE-PBC simulations agree well with values calculated from equilibrium MD simulations. Three dimensional shearing and a deformation with a full velocity gradient matrix are also simulated, showing the range of problems gLE-PBC can explore. (C) 2021 Elsevier Inc. All rights reserved.

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