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Robocrystallographer: automated crystal structure text descriptions and analysis

MRS Communications volume 9, pages 874–881 (2019)Cite this article

Abstract

Our ability to describe crystal structure features is of crucial importance when attempting to understand structure–property relationships in the solid state. In this paper, the authors introduce robocrystallographer, an open-source toolkit for analyzing crystal structures. This package combines new and existing open-source analysis tools to provide structural information, including the local coordination and polyhedral type, polyhedral connectivity, octahedral tilt angles, component-dimensionality, and molecule-within-crystal and fuzzy prototype identification. Using this information, robocrystallographer can generate text-based descriptions of crystal structures that resemble descriptions written by human crystallographers. The authors use robocrystallographer to investigate the dimensionalities of all compounds in the Materials Project database and highlight its potential in machine learning studies.

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Acknowledgments

The authors acknowledge many useful discussions with Matt Horton regarding structure dimensionality. The authors additionally acknowledge Matt Horton for his work on the StructureGraph and BondedStructure components of pymatgen and for parsing the AFLOW prototype library. The authors acknowledge Evan Spotte-Smith for his work on the MoleculeGraph functionality in pymatgen. The authors acknowledge useful discussions with Leigh Weston regarding materials science text mining. The authors acknowledge Donny Winston for facilitating the calculation of robocrystallographer on all structures in the Materials Project database. The authors acknowledge useful conversations with Alex Dunn regarding machine learning model optimization. This work was intellectually led and funded by the U.S. Department of Energy (DOE) Basic Energy Sciences (BES) program—the Materials Project—under Grant No. KC23MP. Lawrence Berkeley National Laboratory is funded by the DOE under award DE-AC02-05CH11231.

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Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, Energy Technologies Area, 1 Cyclotron Road, Berkeley, CA, 94720, USA

    Alex M. Ganose & Anubhav Jain

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  1. Alex M. Ganose
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  2. Anubhav Jain
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Correspondence to Anubhav Jain.

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The supplementary material for this article can be found at https://doi.org/10.1557/mrc.2019.94.

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Ganose, A.M., Jain, A. Robocrystallographer: automated crystal structure text descriptions and analysis. MRS Communications 9, 874–881 (2019). https://doi.org/10.1557/mrc.2019.94

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