An algorithm for three-dimensional Voronoi S-network
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...
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Published in | Journal of computational chemistry Vol. 27; no. 14; pp. 1676 - 1692 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
Hoboken
Wiley Subscription Services, Inc., A Wiley Company
15.11.2006
Wiley Subscription Services, Inc |
Subjects | |
Online Access | Get full text |
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Summary: | 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 |
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Bibliography: | ark:/67375/WNG-2494ZPQ6-X istex:236EEC610A31128D370176C0AD01E2CCB6B7B636 Russian Foundation for Fundamental Research - No. 01-03-32903; No. 05-03-32647 INTAS Project - No. 2001-0067 ArticleID:JCC20484 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 0192-8651 1096-987X |
DOI: | 10.1002/jcc.20484 |