An algorithm for three-dimensional Voronoi S-network

• Published in: Journal of computational chemistry Vol. 27; no. 14; pp. 1676 - 1692
• Main Authors: Medvedev, N. N., Voloshin, V. P., Luchnikov, V. A., Gavrilova, M. L.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 15.11.2006; Wiley Subscription Services, Inc
• Subjects: additively-weighted Voronoi diagram; algorithm; Algorithms; Biochemistry; Computer based modeling; computer models of molecular systems; Computer Simulation; Delaunay simplex; Geometry; Models, Chemical; Molecular structure; polydisperse packings; Spheres; structure; voids
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.20484

The paper presents an algorithm for calculating the three‐dimensional Voronoi–Delaunay tessellation for an ensemble of spheres of different radii (additively‐weighted Voronoi diagram). Data structure and output of the algorithm is oriented toward the exploration of the voids between the spheres. The main geometric construct that we develop is the Voronoi S‐network (the network of vertices and edges of the Voronoi regions determined in relation to the surfaces of the spheres). General scheme of the algorithm and the key points of its realization are discussed. The principle of the algorithm is that for each determined site of the network we find its neighbor sites. Thus, starting from a known site of the network, we sequentially find the whole network. The starting site of the network is easily determined based on certain considerations. Geometric properties of ensembles of spheres of different radii are discussed, the conditions of applicability and limitations of the algorithm are indicated. The algorithm is capable of working with a wide variety of physical models, which may be represented as sets of spheres, including computer models of complex molecular systems. Emphasis was placed on the issue of increasing the efficiency of algorithm to work with large models (tens of thousands of atoms). It was demonstrated that the experimental CPU time increases linearly with the number of atoms in the system, O(n). © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006