title: Analyzing and Driving Cluster Formation in Atomistic Simulations.
abstract: In this paper a set of computational tools for identifying the phases contained in a system composed of atoms or 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.
authors.affiliation: Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast , Belfast BT7 1NN, United Kingdom.
authors.forename: Gareth A
authors.identifier: http://orcid.org/0000-0002-4763-9317
authors.initials: GA
authors.lastname: Tribello
authors.affiliation: Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich , USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland.
authors.forename: Federico
authors.identifier: http://orcid.org/0000-0003-0830-8141
authors.initials: F
authors.lastname: Giberti
authors.affiliation: Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom.
authors.forename: Gabriele C
authors.identifier: http://orcid.org/0000-0002-6156-7399
authors.initials: GC
authors.lastname: Sosso
authors.affiliation: Department of Chemical Engineering, University College London , Torrington Place, London WC1E 7JE, United Kingdom.
authors.forename: Matteo
authors.initials: M
authors.lastname: Salvalaglio
authors.affiliation: Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich , USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello