Identification of structure in condensed matter with the topological cluster classification

Abstract

We describe the topological cluster classification (TCC) algorithm. The TCC detects local structures with bond topologies similar to isolated clusters which minimise the potential energy for a number of monatomic and binary simple liquids with $m\le 13$ particles. We detail a modified Voronoi bond detection method that optimizes the cluster detection. The method to identify each cluster is outlined, and a test example of Lennard-Jones liquid and crystal phases is considered and critically examined.

28 pages, 28 figures

References in corpus (9)

• Accurate determination of crystal structures based on averaged local bond order parameters
• Understanding fragility in supercooled Lennard-Jones mixtures. I. Locally preferred structures
• Identification of long-lived clusters and their link to slow dynamics in a model glass former
• Lifetimes and Lengthscales of Structural Motifs in a Model Glassformer
• Simulation of Cu-Mg metallic glass: Thermodynamics and Structure
• The effect of attractions on the local structure of liquids and colloidal fluids
• The effect of inter-cluster interactions on the structure of colloidal clusters
• Local structure of Liquid-Vapour Interfaces
• Topological Classification of Clusters in Condensed Phases

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