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pyMolDyn: Identification, structure, and properties of cavities in condensed matter and molecules

Ingo Heimbach
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

Florian Rhiem
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

Fabian Beule
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

David Knodt
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

Josef Heinen
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

Robert O. Jones
PGI-1 and PGI/JCNS-TA, Forschungszentrum Jülich, D-52425 Jülich, Germany

Video: https://pgi-jcns.fz-juelich.de/pub/media/pymoldyn\_algorithms.mp4

Abstract

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos.

Keywords

Cavity shape, volume, and surface area; Python; marching cubes; split and merge

Bibtex entry

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