Published October 28, 2022 | Version 1.1.0
Software Open

Vorotis

  • 1. National Institute of Advanced Industrial Science and Technology (AIST)

Description

1. Official paper

Software for Voronoi tessellation analysis using the polyhedron code, Comput. Phys. Commun. 278 (2022) 108418.

 

2. Overview

Vorotis is software for performing Voronoi tessellation analysis of the atomic structure of materials [1]. It consists of Fortran programs, a Csh script, and Python scripts. The novelty of Vorotis lies in its function to encode Voronoi polyhedra using the polyhedron code (p3 code) [2-5]. The p3 code not only solves the degeneracy problem of the Voronoi index but also makes it possible to characterize the chemi-topological order of multi-component systems. As another distinguished feature, Vorotis has a function to identify crystalline atoms by the local translational order parameter developed in Ref. [6].

 

3. Version 1.1.0 release note

The function to compute the p3 codewords of bipyramidal and tetrahedral clusters has been added [5].

 

4. Q&A

See Discussions at Vorotis GitHub site.

 

[Q1] What is the unit of the cutoff distance and atomic radii?

The unit of the cutoff distance and atomic radii is the same as the unit of the atomic coordinates from which the Voronoi tessellation is made. For example, in the case of examples/04_binary, a Voronoi tessellation is made from the atomic coordinates given in config.txt. The cutoff distance and atomic radii are defined in settings.txt.  Although the unit of the atomic coordinates is not specified, if you assume that it is nm, then the unit of the cutoff distance and atomic radii is nm. If you assume that the atomic coordinates are expressed in Å, then the cutoff distance and atomic radii are expressed in Å.

 

[Q2] What is color in Vorotis?

One of the distinguished features of Vorotis is its ability to represent how different types of atoms are arranged in clusters. To this end, the user assigns a character called color to each atom type. For example, consider an icosahedral cluster composed of a central Cu atom and 12 Zr atoms surrounding the Cu atom. If one assigns C and Z to Cu and Zr atoms, respectively, the cluster is represented by @512;CZ13.

 

5. References

[1] K. Nishio, Vorotis: Software for Voronoi tessellation analysis using the polyhedron code, Comput. Phys. Commun. 278 (2022) 108418.

[2] K. Nishio, T. Miyazaki, How to describe disordered structures, Sci. Rep. 6 (2016) 23455.

[3] K. Nishio, T. Miyazaki, Describing polyhedral tilings and higher dimensional polytopes by sequence of their two-dimensional components, Sci. Rep. 7 (2017) 40269.

[4] K. Nishio, T. Miyazaki, Notation for chemical arrangements in alloys, Phys. Rev. Research 2 (2020) 023193.

[5] K. Nishio, Cluster classification by chemi-topology, Comput. Phys. Commun. 286 (2023) 108659.

[6] K. Nishio, A. K. A. Lu, Can every substance exist as an amorphous solid?, J. Non-Cryst. Solids 576 (2022) 121254.

 

 

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