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Title: On Coarse Projective Integration for Atomic Deposition in Amorphous Systems

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales 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 gradients 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 SiO 2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO 2 using only a few measures of the island size distribution. In conclusion, 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:
 [1] ; ORCiD logo [2] ;  [3] ;  [1]
  1. Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Chemical and Biomolecular Engineering
  2. Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Chemical and Biological Engineering
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Report Number(s):
LLNL-JRNL-694123
Journal ID: ISSN 0021-9606; JCPSA6
Grant/Contract Number:
AC52-07NA27344; DMR-0907365; DMR-0907112; DMR-140059; CMMI-1068841; CMMI-1068970
Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 143; Journal Issue: 13; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; coarse projective integration; atomic deposition; multiscale simulation; island nucleation and growth; molecular dynamics; germanium; amorphous substrates
OSTI Identifier:
1341998

Chuang, Claire Y., Han, Sang M., Zepeda-Ruiz, Luis A., and Sinno, Talid. On Coarse Projective Integration for Atomic Deposition in Amorphous Systems. United States: N. p., Web. doi:10.1063/1.4931991.
Chuang, Claire Y., Han, Sang M., Zepeda-Ruiz, Luis A., & Sinno, Talid. On Coarse Projective Integration for Atomic Deposition in Amorphous Systems. United States. doi:10.1063/1.4931991.
Chuang, Claire Y., Han, Sang M., Zepeda-Ruiz, Luis A., and Sinno, Talid. 2015. "On Coarse Projective Integration for Atomic Deposition in Amorphous Systems". United States. doi:10.1063/1.4931991. https://www.osti.gov/servlets/purl/1341998.
@article{osti_1341998,
title = {On Coarse Projective Integration for Atomic Deposition in Amorphous Systems},
author = {Chuang, Claire Y. and Han, Sang M. and Zepeda-Ruiz, Luis A. and Sinno, Talid},
abstractNote = {Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales 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 gradients 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. In conclusion, 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.},
doi = {10.1063/1.4931991},
journal = {Journal of Chemical Physics},
number = 13,
volume = 143,
place = {United States},
year = {2015},
month = {10}
}