Simple Periodic Boundary Conditions for Molecular Simulation of Uniaxial Flow

TL;DR

This paper introduces a simplified, time-periodic rotating periodic boundary condition method for molecular dynamics simulations of uniaxial and biaxial stretching flows, improving upon previous complex schemes.

Contribution

It presents a new single automorphism remapping PBC approach for USF and BSF that is simpler, time-periodic, and has improved lattice spacing properties.

Findings

The new PBCs are time-periodic up to a rotation matrix.

They outperform previous methods in simplicity and lattice spacing.

Applicable to uniaxial and biaxial stretching flows.

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.