Abstract
BackgroundDisordered compounds are crucially important for fundamental science and industrial applications. Yet most available methods to explore solid-state material properties require ideal periodicity, which, strictly speaking, does not exist in this type of materials. The supercell approximation is a way to imply periodicity to disordered systems while preserving “disordered” properties at the local level. Although this approach is very common, most of the reported research still uses supercells that are constructed “by hand” and ad-hoc.ResultsThis paper describes a software named supercell, which has been designed to facilitate the construction of structural models for the description of vacancy or substitution defects in otherwise periodically-ordered (crystalline) materials. The presented software allows to apply the supercell approximation systematically with an all-in-one implementation of algorithms for structure manipulation, supercell generation, permutations of atoms and vacancies, charge balancing, detecting symmetry-equivalent structures, Coulomb energy calculations and sampling output configurations. The mathematical and physical backgrounds of the program are presented, along with an explanation of the main algorithms and relevant technical details of their implementation. Practical applications of the program to different types of solid-state materials are given to illustrate some of its potential fields of application. Comparisons of the various algorithms implemented within supercell with similar solutions are presented where possible.ConclusionsThe all-in-one approach to process point disordered structures, powerful command line interface, excellent performance, flexibility and GNU GPL license make the supercell program a versatile set of tools for disordered structures manipulations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0129-3) contains supplementary material, which is available to authorized users.
Highlights
Disordered compounds are crucially important for fundamental science and industrial applications
Okhotnikov et al J Cheminform (2016) 8:17 sites. Because they do not rely on long-range atomic periodicity, local spectroscopies such as solid-state nuclear magnetic resonance (NMR) [4], Raman [5], infra-red or X-ray adsorption near-edge structure (XANES) are relevant to reveal and characterize point defects to understand how they affect the materials properties [6, 7]
In b and c are two configurations satisfying the restrictions on H atoms positions that result in correlated disorder in this system, with space groups Cmc21(36) and c Cc (9), respectively for example, the total number of unique configurations will be 11 million, which is too large to process in the same way as the initial cell
Summary
This paper describes a software named supercell, which has been designed to facilitate the construction of structural models for the description of vacancy or substitution defects in otherwise periodically-ordered (crystalline) materials. The presented software allows to apply the supercell approximation systematically with an all-in-one implementation of algorithms for structure manipulation, supercell generation, permutations of atoms and vacancies, charge balancing, detecting symmetry-equivalent structures, Coulomb energy calculations and sampling output configurations. The mathematical and physical backgrounds of the program are presented, along with an explanation of the main algorithms and relevant technical details of their implementation. Practical applications of the program to different types of solid-state materials are given to illustrate some of its potential fields of application. Comparisons of the various algorithms implemented within supercell with similar solutions are presented where possible
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