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

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 cavit...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 38; no. 6; pp. 389 - 394
Main Authors: Heimbach, Ingo, Rhiem, Florian, Beule, Fabian, Knodt, David, Heinen, Josef, Jones, Robert O.
Format: Journal Article
Language:English
Published: United States Wiley Subscription Services, Inc 05.03.2017
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
volume
and surface area
marching cubes
split and merge
cavity shape
Python
ISSN:0192-8651, 1096-987X, 1096-987X
Online Access:Get full text
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Summary: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.
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.24697