{"title":"<i>Polynator</i>: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures","authors":"Lukas Link, Rainer Niewa","doi":"10.1107/s1600576723008476","DOIUrl":null,"url":null,"abstract":"Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"97 1","pages":"0"},"PeriodicalIF":6.1000,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Applied Crystallography","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1107/s1600576723008476","RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0
Abstract
Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.
期刊介绍:
Many research topics in condensed matter research, materials science and the life sciences make use of crystallographic methods to study crystalline and non-crystalline matter with neutrons, X-rays and electrons. Articles published in the Journal of Applied Crystallography focus on these methods and their use in identifying structural and diffusion-controlled phase transformations, structure-property relationships, structural changes of defects, interfaces and surfaces, etc. Developments of instrumentation and crystallographic apparatus, theory and interpretation, numerical analysis and other related subjects are also covered. The journal is the primary place where crystallographic computer program information is published.