Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

Barclay, Paul Linford; Zhang, Duan Zhong

doi:10.1016/j.jcp.2021.110238

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Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

Barclay, Paul Linford·Zhang, Duan Zhong

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Abstract

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. Furthermore, 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.

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74 ATOMIC AND MOLECULAR PHYSICS Molecular dynamics deformation non-equilibrium periodic boundary conditions

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Barclay, Paul Linford, Zhang, Duan Zhong. 2021-03-02. Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations. https://doi.org/10.1016/j.jcp.2021.110238

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