title: On coarse projective integration for atomic deposition in amorphous systems.
abstract: Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the "equation-free" framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the "lifting" operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO2 using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 220 South 33rd Street, 311A Towne Building, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Claire Y
authors.initials: CY
authors.lastname: Chuang
authors.affiliation: Department of Chemical and Biological Engineering, University of New Mexico, 1 University of New Mexico, MSC01 1120, Albuquerque, New Mexico 87131, USA.
authors.forename: Sang M
authors.initials: SM
authors.lastname: Han
authors.affiliation: Lawrence Livermore National Laboratory, P.O. Box 808, L-367, Livermore, California 94550, USA.
authors.forename: Luis A
authors.initials: LA
authors.lastname: Zepeda-Ruiz
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 220 South 33rd Street, 311A Towne Building, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Talid
authors.initials: T
authors.lastname: Sinno