Crystal Structure Visualizations in Three Dimensions with Database Support
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Crystal structure visualizations in three dimensions with database support P. Moeck1, O. Čertík1,2, G. Upreti1, W. Garrick3, P. Fraundorf4 1
Department of Physics, Portland State University, P.O. Box 751, Portland, OR 97207-0751, [email protected] 2 Faculty of Mathematics and Physics, Charles University of Prague, Ke Karlovu 3, 121 16 Praha, The Czech Republic 3 Academic & Research Computing for Instruction and Research Services and the Office of Information Technology, Portland State University, Portland, OR 97201 4 Department of Physics and Astronomy and Center for Molecular Electronics, University of Missouri at St. Louis, MO 53121 ABSTRACT Crystallographic databases for inorganic materials that are freely accessible over the internet are reviewed. The Nano-Crystallography Database project is described. Instructions are given on how to visualize in three dimensions the atomic arrangements of the several thousand entries of the Crystallography Open Database. 1. INTRODUCTION Courses in materials science and engineering, crystal physics, crystal chemistry, and mineralogy typically employ two-dimensional sketches of the atomic arrangement in crystal structures and unit cells. The chapter on ideal crystal structures of the widely used introductory materials science and engineering text by Schaffer et al. [1] contains for example 14 such sketches. Textbooks on mineralogy contain a much larger number of such sketches (e.g. Hibbard’s text [2] features a picture with more than ten ball-and-stick models on the dedication page and approximately one hundred sketches of atomic arrangements in crystal structures and unit cells in the body of the text). Physical three-dimensional models of crystal structures and unit cells are also popular. While academic departments in the developed part of the world may possess some tens of such three-dimensional models and allow their students to explore those hands on, their counterparts in the developing part of the world may consider such models too expensive and fragile for class room usages. To help remedying this situation we made a survey on crystallographic databases that are freely accessible on the internet and also started our own nano-crystallography database project with on line three-dimensional (3D) visualizations of ideal and real structures. This paper reports on both the results of the survey and our ongoing project. 2. FREE INTERNET ACCESSIBLE CRYSTALLOGRAPHIC DATABASES Fifteen years after the development of the World Wide Web, there is already a variety of internet based free access crystallographic databases. In this part of the paper we discuss only the subset of free databases that deals primarily with inorganic crystals. The free database MINCRYST [3] is maintained and hosted by the Russian Academy of Sciences and contains more than 6,000 entries for minerals from which X-ray powder
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diffractograms can be calculated on the fly. 3D visualization of the entries are provided by means of the java-based freeware program “Jmol” [4]. The Naval
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