MXE: A package for simulating long-term diffusive mass transport phenomena in nanoscale systems

Abstract

We present a package to simulate long-term diffusive mass transport in systems with atomic scale resolution. The implemented framework is based on a non-equilibrium statistical thermo-chemo-mechanical formulation of atomic systems where effective transport rates are computed using a kinematic diffusion law. Our implementation is built as an add-on to the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code, it is compatible with other LAMMPS’ functionalities, and shows a good parallel scalability and efficiency. In applications involving diffusive mass transport, this framework is able to simulate problems of technological interest for exceedingly large time scales using an atomistic description, which are not reachable with the state-of-the-art molecular dynamics techniques. Several examples, involving complex diffusive behavior in materials, are investigated with the framework. We found good qualitative and quantitative comparison with known theories and models, with Monte Carlo methods, as well as with experimental results. Thus, our implementation can be used as a tool to understand diffusive behavior in materials where experimental characterization is difficult to perform. Program summaryProgram Title: MXE packageProgram Files doi:http://dx.doi.org/10.17632/s2mhjb8hyk.1Licensing provisions: GNU GPLv3Programming language: c++Supplementary material: The user manual and examples are provided along with the source code.External routines: MPI, LAMMPS, 12 December 2018 (http://lammps.sandia.gov/)Nature of problem: The simulation of diffusive mass transport in atomistic systems, involving vacancies, interstitials and solute atoms, is often challenging due to the exceedingly large time scale involved in these slow processes. Thus, molecular dynamics, a preferred technique to simulate atomistic systems, is not capable of accessing these long-term diffusive timescale, hindering its application to this kind of phenomena.Solution method: We present an implementation for simulating diffusive mass transport in atomic system. The methodology is based on two main pillars: (i) A non-equilibrium thermodynamic formulation of atomic system (Venturini et al., 2014); and (ii) Fokker–Planck master equation that encompasses the time evolution of the atomic molar fraction field in atomic systems (Ponga and Sun, 2018). The proposed implementation is built as a user package of the popular Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The implementation is flexible and robust, shows good parallel scalability and efficiency, and is compatible with all features available in LAMMPS.Additional comments including restrictions and unusual features: Unique features of the implementation involve the simulation of vacancy, interstitial, solutes and substitutional alloys for exceedingly large time scales.The current implementation in this package is limited to the Embedded Atom Model potentials.