Simple Periodic Boundary Conditions for Molecular Simulation of Uniaxial Flow

Abstract

We present rotating periodic boundary conditions (PBCs) for the simulation of nonequilibrium molecular dynamics (NEMD) under uniaxial stretching flow (USF) or biaxial stretching flow (BSF). Such nonequilibrium flows need specialized PBCs since the simulation box deforms with the background flow. The technique builds on previous models using one or lattice remappings, and is simpler than the PBCs developed for the general three dimensional flow. For general three dimensional flows, Dobson \cite{Dobson} and Hunt \cite{Hunt} proposed schemes which are not time-periodic since they use more than one automorphism remapping. This paper presents a single automorphism remapping PBCs for USF and BSF which is time periodic up to a rotation matrix and has a better minimum lattice spacing properties.