American mineralogist crystal structure database

Abstract

A database has been constructed that contains all the crystal structures previously published in the American Mineralogist. The database is called “The American Mineralogist Crystal Structure Database” and is freely accessible from the websites of the Mineralogical Society of America at http://www.minsocam.org/MSA/Crystal_Database.html and the University of Arizona. In addition to the database, a suite of interactive software is provided that can be used to view and manipulate the crystal structures and compute different properties of a crystal such as geometry, diffraction patterns, and procrystal electron densities. The database is set up so that the data can be easily incorporated into other software packages. Included at the website is an evolving set of guides to instruct the user and help with classroom education. parameters; (5) incorporating comments from either the original authors or ourselves when changes are made to the originally published data. Each record in the database consists of a bibliographic reference, cell parameters, symmetry, atomic positions, displacement parameters, and site occupancies. An example of a data set is provided in Figure 1. The first part of each data set contains identifying information, bibliography and notes, while the second part contains the crystallographic parameters. The first line of a data file contains an identifier, such as the name of the mineral or formula of the chemical species. The next line(s) contain the names of the authors, each separated by a comma. This is followed by the journal reference, title of the paper, and additional notes. The crystallographic data begins with a listing of the cell parameters and space group. If the data is given with respect to a non-standard space group origin then an asterisk precedes the space group symbol and the next line contains the translation vector from the standard origin. The 1952 edition of the International Tables for X-ray Crystallography are used to define the standard origin. The rest of the data set is a fixed-formatted listing of the atoms, their positional and displacement parameters, and occupancies. A header is provided that defines rightjustified columns. The name of each atom identifies the occupying elements, with additional identifiers added when appropriate. For instance, “Oco” identifies a particular oxygen atom in the albite structure. Some data sets report a crystallographic site occupied by molecular species rather than elemental, such as OH, water or methane. In most of these cases the atom name is denoted by molecular formula. For example, “CH4” denotes methane, and “Wat” denotes water. The displacement factors are tabulated in one of two formats, U’s or b’s