Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals

BACKGROUND: Disordered 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. RESULTS: 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. CONCLUSIONS: The 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 MATERIAL: The online version of this article (doi:10.1186/s13321-016-0129-3) contains supplementary material, which is available to authorized users.