skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Towards the reliable calculation of residence time for off-lattice kinetic Monte Carlo simulations

Publication Date:
Sponsoring Org.:
OSTI Identifier:
Grant/Contract Number:
FG02-97ER25308; CMMI-1332789
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Modelling and Simulation in Materials Science and Engineering
Additional Journal Information:
Journal Volume: 24; Journal Issue: 6; Related Information: CHORUS Timestamp: 2016-08-06 03:19:17; Journal ID: ISSN 0965-0393
IOP Publishing
Country of Publication:
United Kingdom

Citation Formats

Alexander, Kathleen C., and Schuh, Christopher A.. Towards the reliable calculation of residence time for off-lattice kinetic Monte Carlo simulations. United Kingdom: N. p., 2016. Web. doi:10.1088/0965-0393/24/6/065014.
Alexander, Kathleen C., & Schuh, Christopher A.. Towards the reliable calculation of residence time for off-lattice kinetic Monte Carlo simulations. United Kingdom. doi:10.1088/0965-0393/24/6/065014.
Alexander, Kathleen C., and Schuh, Christopher A.. Fri . "Towards the reliable calculation of residence time for off-lattice kinetic Monte Carlo simulations". United Kingdom. doi:10.1088/0965-0393/24/6/065014.
title = {Towards the reliable calculation of residence time for off-lattice kinetic Monte Carlo simulations},
author = {Alexander, Kathleen C. and Schuh, Christopher A.},
abstractNote = {},
doi = {10.1088/0965-0393/24/6/065014},
journal = {Modelling and Simulation in Materials Science and Engineering},
number = 6,
volume = 24,
place = {United Kingdom},
year = {Fri Aug 05 00:00:00 EDT 2016},
month = {Fri Aug 05 00:00:00 EDT 2016}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1088/0965-0393/24/6/065014

Citation Metrics:
Cited by: 3works
Citation information provided by
Web of Science

Save / Share:
  • The first off-lattice Monte Carlo kinetics model of interstellar dust grain surface chemistry is presented. The positions of all surface particles are determined explicitly, according to the local potential minima resulting from the pair-wise interactions of contiguous atoms and molecules, rather than by a pre-defined lattice structure. The model is capable of simulating chemical kinetics on any arbitrary dust grain morphology, as determined by the user-defined positions of each individual dust grain atom. A simple method is devised for the determination of the most likely diffusion pathways and their associated energy barriers for surface species. The model is applied tomore » a small, idealized dust grain, adopting various gas densities and using a small chemical network. Hydrogen and oxygen atoms accrete onto the grain to produce H{sub 2}O, H{sub 2}, O{sub 2}, and H{sub 2}O{sub 2}. The off-lattice method allows the ice structure to evolve freely; the ice mantle porosity is found to be dependent on the gas density, which controls the accretion rate. A gas density of 2 × 10{sup 4} cm{sup –3}, appropriate for dark interstellar clouds, is found to produce a fairly smooth and non-porous ice mantle. At all densities, H{sub 2} molecules formed on the grains collect within the crevices that divide nodules of ice and within micropores (whose extreme inward curvature produces strong local potential minima). The larger pores produced in the high-density models are not typically filled with H{sub 2}. Direct deposition of water molecules onto the grain indicates that amorphous ices formed in this way may be significantly more porous than interstellar ices that are formed by surface chemistry.« less
  • Point-defect-mediated diffusion processes are investigated in strained SiGe alloys using kinetic lattice Monte Carlo *KLMC* simulation technique. The KLMC simulator incorporates an augmented lattice domain and includes defect structures, atomistic hopping mechanisms, and the stress dependence of transition rates obtained from density functional theory calculation results. Vacancy-mediated interdiffusion in strained SiGe alloys is analyzed, and the stress effect caused by the induced strain of germanium is quantified separately from that due to germanium-vacancy binding. The results indicate that both effects have substantial impact on interdiffusion. © 2010 American Vacuum Society.
  • Within the last decade molecular dynamics simulations of displacement cascades have revealed that glissile clusters of self-interstitial crowdions are formed directly in cascades and that they migrate one-dimensionally along close-packed directions with extremely low activation energies. Occasionally, under various conditions, a crowdion cluster can change its Burgers vector and glide along a different close-packed direction. The recently developed Production Bias Model (PBM) of microstructure evolution under irradiation has been structured to specifically take into account the unique properties of the vacancy and interstitial clusters produced in the cascades. Atomic-scale kinetic Monte Carlo (KMC) simulations have played a useful role inmore » understanding the defect reaction kinetics of one-dimensionally migrating crowdion clusters as a function of the frequency of direction changes. This has made it possible to incorporate the migration properties of crowdion clusters and changes in reaction kinetics into the PBM. In the present paper we utilize similar KMC simulations to investigate the significant role crowdion clusters can play in the formation and stability of void lattices. The creation of stable void lattices, starting from a random distribution of voids, is simulated by a KMC model in which vacancies migrate three-dimensionally and SIA clusters migrate one-dimensionally, interrupted by directional changes. The necessity of both one-dimensional migration and Burgers vectors changes of SIA clusters for the production of stable void lattices is demonstrated, and the effects of the frequency of Burgers vector changes are described.« less
  • In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-“coupled”- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that themore » new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz–Kalos–Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB source code.« less