Abstract
The accelerated growth rate of repository entries in crystallographic databases makes it arduous to identify and classify their prototype structures. The open-source AFLOW-XtalFinder package was developed to solve this problem. It symbolically maps structures into standard designations following the AFLOW Prototype Encyclopedia and calculates the internal degrees of freedom consistent with the International Tables for Crystallography. To ensure uniqueness, structures are analyzed and compared via symmetry, local atomic geometries, and crystal mapping techniques, simultaneously grouping them by similarity. The software (i) distinguishes distinct crystal prototypes and atom decorations, (ii) determines equivalent spin configurations, (iii) reveals compounds with similar properties, and (iv) guides the discovery of unexplored materials. The operations are accessible through a Python module ready for workflows, and through command line syntax. All the 4+ million compounds in the AFLOW.org repositories are mapped to their ideal prototype, allowing users to search database entries via symbolic structure-type. Furthermore, 15,000 unique structures — sorted by prevalence — are extracted from the AFLOW-ICSD catalog to serve as future prototypes in the Encyclopedia.
Highlights
Scientists have been struggling for decades to identify prototypes (e.g. Strukturbericht series[1] and Pearson’s Handbook2) and duplicates in crystallographic databases; and to label structures in a concise way to recognize structuretypes
Prototype structures are generally classified in terms of their symmetry characteristics
Accurate prototype detection relies on robust symmetry analyses
Summary
Scientists have been struggling for decades to identify prototypes (e.g. Strukturbericht series[1] and Pearson’s Handbook2) and duplicates in crystallographic databases; and to label structures in a concise way to recognize (and enable searching by) structuretypes. Determination of unique crystallographic structures is obfuscated by (i) unit cell representations and (ii) origin choices. While standard forms exist — such as Niggli[7] and Minkowski[8] unit cells — the conversion procedures are highly sensitive to numerical tolerance values and can cast similar structures into differing descriptions[9,10]. The lack of commensurate representations impedes the search for prototypes and inhibits mappings between similar crystals and their corresponding properties. To overcome non-standard descriptions, crystal comparison tools have been developed to identify similar structures. Programs such as Structure Matcher[11], XTALCOMP10, SPAP12, CMPZ13, CRYCOM9, STRUCTURE-TIDY14, and COMPSTRU15 are available with varying objectives related to structure comparison.
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