Maximum volume simplex method for automatic selection and classification of atomic environments and environment descriptor compression
Creators
- 1. Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- 2. National Center for Computational Design and Discovery of Novel Materials (MARVEL), Lausanne, Switzerland
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Description
Fingerprint distances, which measure the similarity of atomic environments, are commonly calculated from atomic environment fingerprint vectors. In this work, we present the simplex method that can perform the inverse operation, i.e., calculating fingerprint vectors from fingerprint distances. The fingerprint vectors found in this way point to the corners of a simplex. For a large dataset of fingerprints, we can find a particular largest simplex, whose dimension gives the effective dimension of the fingerprint vector space. We show that the corners of this simplex correspond to landmark environments that can be used in a fully automatic way to analyze structures. In this way, we can, for instance, detect atoms in grain boundaries or on edges of carbon flakes without any human input about the expected environment. By projecting fingerprints on the largest simplex, we can also obtain fingerprint vectors that are considerably shorter than the original ones but whose information content is not significantly reduced.
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References
Journal reference Parsaeifard, Behnam, et al. "Maximum volume simplex method for automatic selection and classification of atomic environments and environment descriptor compression." The Journal of Chemical Physics 153.21 (2020): 214104., doi: 10.1063/5.0030061
Journal reference (Paper where the data is discussed.) Parsaeifard, Behnam, et al. "Fingerprint-Based Detection of Non-Local Effects in the Electronic Structure of a Simple Single Component Covalent System." Condensed Matter 6.1 (2021): 9., doi: 10.3390/condmat6010009
Journal reference (Paper where the data is discussed.) Parsaeifard, Behnam, et al. "Fingerprint-Based Detection of Non-Local Effects in the Electronic Structure of a Simple Single Component Covalent System." Condensed Matter 6.1 (2021): 9.
Journal reference (Paper where the data is discussed.) Parsaeifard, Behnam, et al. "An assessment of the structural resolution of various fingerprints commonly used in machine learning." Machine Learning: Science and Technology 2.1 (2021): 015018., doi: 10.1088/2632-2153/abb212
Journal reference (Paper where the data is discussed.) Parsaeifard, Behnam, et al. "An assessment of the structural resolution of various fingerprints commonly used in machine learning." Machine Learning: Science and Technology 2.1 (2021): 015018.