RandSpg: An open-source program for generating atomistic crystal structures with specific spacegroups

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• 作者：Patrick Avery ; Eva Zurek ; ^{ezurek@buffalo.edu}
• 关键词：Crystal structure ; Structure prediction ; Computational crystallography ; Symmetry ; Space group ; Wyckoff position ; Wyckoff site ; Inorganic materials
• 刊名：Computer Physics Communications
• 出版年：2017
• 出版时间：April 2017
• 年：2017
• 卷：213
• 期：Complete
• 页码：208-216
• 全文大小：1320 K
• 卷排序：213

文摘

A new algorithm, RandSpg, that can be used to generate trial crystal structures with specific space groups and compositions is described. The program has been designed for systems where the atoms are independent of one another, and it is therefore primarily suited towards inorganic systems. The structures that are generated adhere to user-defined constraints such as: the lattice shape and size, stoichiometry, set of space groups to be generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally specify if the most general Wyckoff position is to be occupied or constrain select atoms to specific Wyckoff positions. Extensive testing indicates that the algorithm is efficient and reliable. The library is lightweight, portable, dependency-free and is published under a license recognized by the Open Source Initiative. A web interface for the algorithm is publicly accessible at http://xtalopt.openmolecules.net/randSpg/randSpg.html. RandSpg has also been interfaced with the XtalOpt evolutionary algorithm for crystal structure prediction, and it is illustrated that the use of symmetric lattices in the first generation of randomly created individuals decreases the number of structures that need to be optimized to find the global energy minimum.Program summaryProgram Title: RandSpgProgram Files doi:http://dx.doi.org/10.17632/v2nzgmpd37.1Licensing provisions: BSD 3-clause [1]Programming language: C++Nature of problem: Trial structure models are required for: (i) determining the crystal structure of a compound given its powder X-ray diffraction data using the direct space method, (ii) creating the first set of individuals using a priori crystal structure prediction. For both of these problems the initial guess can greatly influence the success rate of the algorithm used for structure determination, especially for crystals with large unit cells. The unit cells of over 99% of inorganic crystals possess some element of symmetry, and it may be possible to obtain partial information about their crystal structures experimentally. Therefore, an algorithm that is able to create trial structures with user-defined constraints including the crystal’s composition, space group and unit cell parameters is desired.Solution method: The RandSpg algorithm is able to determine every possible combination of Wyckoff positions for a given space group and composition. The algorithm randomly picks one of these combinations and adds atoms to particular Wyckoff sites wherein the Cartesian coordinates are chosen randomly such that they satisfy user-defined minimum interatomic distance constraints. In addition, the program can optionally generate crystals where user-defined atoms are placed at specific Wyckoff sites.References:[1]http://opensource.org/licenses/BSD-3-Clause