Genarris 2.0: A random structure generator for molecular crystals

Published: 6 February 2020| Version 1 | DOI: 10.17632/grx6mz4pjn.1
Contributors:
Rithwik Tom,
Timothy Rose,
Imanuel Bier,
Harriet O’Brien,
Álvaro Vázquez-Mayagoitia,
Noa Marom

Description

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine.

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