Genarris 2.0: A random structure generator for molecular crystals

Published: 6 Feb 2020 | Version 1 | DOI: 10.17632/grx6mz4pjn.1
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Description of this data

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.

Experiment data files

This data is associated with the following publication:

Genarris 2.0: A random structure generator for molecular crystals

Published in: Computer Physics Communications

Latest version

  • Version 1

    2020-02-06

    Published: 2020-02-06

    DOI: 10.17632/grx6mz4pjn.1

    Cite this dataset

    Tom, Rithwik; Rose, Timothy; Bier, Imanuel; O’Brien, Harriet; Vázquez-Mayagoitia, Álvaro; Marom, Noa (2020), “Genarris 2.0: A random structure generator for molecular crystals”, Mendeley Data, v1 http://dx.doi.org/10.17632/grx6mz4pjn.1

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Computational Physics, Crystal

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The files associated with this dataset are licensed under a BSD 3-Clause ("Revised") License licence.

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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice,this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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