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

• Published in: Journal of computational chemistry 2017-03, Vol.38 (6), p.389-394
• Main Authors: Heimbach, Ingo, Rhiem, Florian, Beule, Fabian, Knodt, David, Heinen, Josef, Jones, Robert O.
• Format: Article
• Language: English
• Subjects: Amorphous materials; and surface area; Anisotropy; Asphericity; Atomic structure; cavity shape; Chemical bonds; Computer simulation; Condensed matter physics; Crystal structure; Crystals; Distribution functions; Exports; High resolution; Holes; Interactive systems; Lattice vacancies; Lattices; marching cubes; Marching cubes algorithms; Mathematical analysis; Molecular structure; Molecules; Python; Routines; split and merge; Unit cell; Visualization; Voids; volume
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.24697

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. © 2016 Wiley Periodicals, Inc. Empty regions (vacancies, cavities, voids) of, for example, a disordered or crystalline material or a molecule, can influence or even dominate its properties. It is, however, difficult to determine—or even define—such empty regions. pyMolDyn is a Python program that calculates and visualizes such regions (for several definitions) and determines important properties, including the cavity centers, volumes, and surface areas, as well as several shape parameters.