Departmental Papers (CBE)

Document Type

Journal Article

Date of this Version

November 2004


A new approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into “active” regions centered about each minority species, in which regular molecular dynamics is performed. The number, size and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method (EAM) potential for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.


Postprint version. Published in Journal of Chemical Physics, Volume 121, Issue 18, 8 November 2004, pages 8699-8710.
Publisher URL:


molecular dynamics, simulations, crystalline solids, aggregation, silicon, copper, diffusion, vacancies, vacancy clusters



Date Posted: 19 October 2004

This document has been peer reviewed.