ATOMS 3.0

Bruce Ravel
Version 3.0beta1

Abstract:

ATOMS is a program for generating lists of atomic coordinates from crystallographic data. The primary use of ATOMS is to create input files suitable for running the ab initio XAFS program FEFF. For that purpose, the list is sorted by radial distance from an atom chosen as the central atom. ATOMS can also generate other sorts of lists as well as calculate estimations of the bulk absorption and density of the crystal and various corrections to EXAFS data due to experimental effects.

ATOMS is also a package containing the program ATOMS and various related materials. There are versions of the program ATOMS which run from a command line, use a graphical interface, or are served over the Web and accessed by a browser. All versions of ATOMS use the same set of object-oriented tools for crystallography, access to x-ray absorption databases, and access to structural data.

ATOMS is written entirely in Perl, an object-oriented, interpreted language which can be run on a wide variety of platforms and operating systems. ATOMS is an Free Software (or Open Source or Software Libre, as you wish) product. This means that you can reuse or redistribute any or all of ATOMS in a manner consistent with the Perl Artistic License (see App. ). In particular, this means that you may freely contribute to the development of ATOMS or use its programs and object-oriented tools for projects of your own.

This document is copyright © 1999,2000 Bruce Ravel.

Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies.

Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one.

Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the author.

Acknowledgements:

A lot of people have contributed in some manner to the development of ATOMS. Without their gracious contributions of time, energy, advice, and criticism ATOMS would not be what it is now. A few people are in the Hall of Fame:

Matt Newville

Matt wrote the module 'CLdata.pm' and adapted all of the Fortran code that it uses from the original Brennan/Cowen source. He also created the file 'mcmaster.dat' and influenced much of the design of 'Absorption.pm'. He was my earliest alpha tester and has always been my best, harshest, and most useful critic. He also hosts the very first site using WebATOMS.

Tim Elam

During a sabbatical, Tim put together the most complete collection of edge and line energies and absorption cross sections that I know of. He graciously donated his work to the ATOMS project. It is the default in TkATOMS and the only choice in APT.

Shelly Kelly

Shelly was one of my earliest alpha testers, wrote code that inspired the Molecule panel in TkATOMS, and is working on code to transform geometrical information from ATOMS into useful instructions for FEFFIT.

Daniel Haskel

Dani kindly spent hours translating all of the language data used by ATOMS into Spanish, thus helping me introduce internationalization to the code.

Stéphane Grenier

Stéphane contributed the French translation of the language data.

Thorsten Buhrmester

Thorsten contributed the German translation of the language data.

I also would like to thank the people whose contributions, suggestions, and helpful bug reports have helped shape ATOMS: Chuck Bouldin, Hannes Fischer, Glenn ``Full'' Forney, Chris Glover, John Rehr, Hubert Renevier, Julia Wienold, Andrzej Wilamowski, my mom Fran Ravel, and my nephew Gabriel. Gabe, at age 5, is actually quite concerned with the symmetry properties of Legos and not at all with the symmetry properties of crystals, but it pleases me to mention him here nonetheless.

The original version of ATOMS benefited from the advice and support of Boyan Boyanovich, Julie Cross, Ed Stern, Hans Stragier, Kalle Voss, Steve Zabinsky, and Yanjun Zhang. One of the early inspirations for the original version of ATOMS was the program SEXIE by Bernhard Rupp.