title: pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules.
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. © 2016 Wiley Periodicals, Inc.
authors.affiliation: PGI/JCNS-TA, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: Ingo
authors.initials: I
authors.lastname: Heimbach
authors.affiliation: PGI/JCNS-TA, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Rhiem
authors.affiliation: PGI/JCNS-TA, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Beule
authors.affiliation: PGI/JCNS-TA, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Knodt
authors.affiliation: PGI/JCNS-TA, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: Josef
authors.initials: J
authors.lastname: Heinen
authors.affiliation: Peter Grünberg Institut PGI-1, Forschungszentrum Jülich, D-52425, Jülich, Germany.
authors.forename: Robert O
authors.identifier: 0000-0003-1167-4812
authors.initials: RO
authors.lastname: Jones
keywords: Python; and surface area; cavity shape; marching cubes; split and merge; volume