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pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules
Author(s) -
Heimbach Ingo,
Rhiem Florian,
Beule Fabian,
Knodt David,
Heinen Josef,
Jones Robert O.
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24697
Subject(s) - visualization , merge (version control) , marching cubes , atom (system on chip) , anisotropy , molecular graphics , python (programming language) , spheres , computer science , crystallography , materials science , computer graphics , computational science , physics , molecular physics , chemistry , computer graphics (images) , optics , artificial intelligence , astronomy , information retrieval , embedded system , operating system
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.