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Analyzing and Driving Cluster Formation in Atomistic Simulations

Tribello, GA; Giberti, F; Sosso, GC; Salvalaglio, M; Parrinello, M; (2017) Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation , 13 (3) pp. 1317-1327. 10.1021/acs.jctc.6b01073. Green open access

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Abstract

In this paper a new method for identifying the phases contained in a system composed of atoms/molecules is introduced. The method is rooted in graph theory and combines atom centered symmetry functions, adjacency matrices and clustering algorithms to identify regions of space where the properties of the system constituents can be considered uniform. We show how this method can be used to define collective variables and how these collective variables can be used to enhance the sampling of nucleation events. We then show how this method can be used to analyze simulations of crystal nucleation and growth by using it to analyze simulations of the nucleation of the molecular crystal urea and simulations of nucleation in a semiconducting alloy. The semiconducting alloy example we discuss is particular challenging as multiple nucleation centers are formed. We show, however, that our algorithm is able to detect the grain boundaries in the resulting polycrystal.

Type: Article
Title: Analyzing and Driving Cluster Formation in Atomistic Simulations
Open access status: An open access version is available from UCL Discovery
DOI: 10.1021/acs.jctc.6b01073
Publisher version: http://doi.org/10.1021/acs.jctc.6b01073
Language: English
Additional information: Copyright © 2017 American Chemical Society. This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Chemical Engineering
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/1538753
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