EON: Software for long time simulations of atomic scale systems

Samuel T. Chill, Matthew Welborn, Rye Terrell, Liang Zhang, Jean Claude Berthet, Andreas Pedersen, Hannes Jónsson, Graeme Henkelman

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)

Abstract

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Original languageEnglish
Article number055002
JournalModelling and Simulation in Materials Science and Engineering
Volume22
Issue number5
DOIs
Publication statusPublished - 1 Jul 2014

Other keywords

  • accelerated molecular dynamics
  • adaptive kinetic Monte Carlo
  • rare event dynamics
  • saddle points
  • transition state finding

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