Vorotis: Software for Voronoi tessellation analysis using the polyhedron code

K Nishio, COMPUTER PHYSICS COMMUNICATIONS, 278, 108418 (2022).

DOI: 10.1016/j.cpc.2022.108418

The atoms in disordered structures such as liquids and glasses are arranged in a complex manner. Their atomic arrangements are often studied using the Voronoi tessellation method. This method divides the space containing atoms into regions called Voronoi polyhedra. Each polyhedron contains one atom. From the structure of the polyhedron, we can know the bond network, or the topology, of the cluster composed of the atoms in the polyhedron and its neighbors. Thus, the topological order can be characterized by identifying the most dominant Voronoi polyhedron. For this purpose, the Voronoi index has long been used. However, it does not specify how polygons are arranged in the polyhedron. Therefore, polyhedra with different graph structures can have the same index. This problem can lead to failure in characterizing the topological order. In addition, the Voronoi index does not tell anything about the chemical arrangement, namely how different types of atoms are arranged in the cluster. To characterize both of the topological and chemical order of disordered structures, a polyhedron- naming system called the polyhedron code has been developed and implemented in the Vorotis software. This paper presents the essential features of Vorotis.

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