The XAFS Toolbox

A Worked Example for the UWXAFS Package

In Appendix A of the Autobk document and Appendix A of the Feffit document, an entire worked example of the UWXAFS package is described. Read those carefully then download the appropriate archive file listed below. All of the input and data files needed to run the example are contained in the archive files at the end of this page.

• A list of the files in the example

Example Input Files for Atoms

Follow this link for various example input files for the program atoms.

A Searchable Archive of Input Files for Atoms

More examples for ATOMS, with a search engine to help you find the atoms.inp file you're looking for. Follow this link here to visit the archive.

feffit.el

This is an Emacs major mode with special features for editing input files to the UWXAFS programs. This package consists of a file of emacs-lisp code and documentation. See the comments at the top of the lisp codes for complete installation instructions. Follow this link for feff.el and other lisp scripts.

fd2fi

This is a utility for converting the files.dat file generated by FEFF into a template of a feffit.inp file used for running FEFFIT. The template contains most of the keywords you will need for a FEFFIT run followed by blanks for you to fill in with the appropriate values This is a perl script, so requires that you have perl available on your machine. Fortunately perl is commonly available on most UNIX machines and can be compiled for just about any other machine or operating system, including VMS, MACs, OS/2, and the Microsoft operating systems. Follow this link for fd2fi and other lisp scripts.

McBook: McMaster Tables

McBook is a 181-page book of the McMaster data for absorption cross-sections of most of the atoms in the Periodic Table. It is available in a choice of two PostScript files. One makes an 8.5x11in book, and the other makes a 7.25x9.25in book (which looks way better).
Last Update: July 5, 1996. M Newville

• McBook Home Page with Postscript files ready to download.

FLUO: Correcting XANES for self absorption in fluorescence data

FLUO is a computer program that corrects XANES data measured with the fluorescence technique for self-absorption effects. These effects are most significant when the element whose XANES is measured is concentrated and/or when it is a heavy atom surrounded by lighter atoms. The program can be used to correct data taken on liquid solutions as well as on crystalline and amorphous solids. The code can also be used for energy alignment of several data scans and to calculate their energy derivatives.
Last Update: May 27, 1999. D. Haskel

• FLUO: source code and postscript documentation
• Linux ELF 32-bit executable
• Windows 95, 98, NT executable

UWXFGUI: Graphical User Interface to UWXAFS software for Windows (95/98/NT) system

If you have Microsoft Visual Basic on your system, you do not need the vb_lib.zip file. After unziping the uwxfgui.zip file, look at the enclosed help file for installation procedure. Windows ZIP utility has been used to generate these files, and it is an exception to the statement below.

• uwxfgui.zip program files
• vb_lib.zip library files

RUNFIT: Systematically determining atomic positions to get a match to XAFS data

XAFS and diffraction spectroscopies give complementary information about a crystal structure. Often at high pressures or temperatures diffraction spectroscopy has been used to determine the space group of the crystal structure and the unit cell dimensions for the space group but there is insufficient data to determine the atomic positions within the unit cell. Since the atomic positions along with the already known unit cell dimensions and space group give the local atomic structure, the atomic positions can be determined from XAFS data. It is the goal of these programs (runfit and mkfit) to automate the process of systematically determining the atomic positions to get a match to the XAFS data. This process uses the unit cell dimensions and the space group, the results of diffraction, so that the final structure is consistent with both XAFS and Diffraction spectroscopies. The programs (runfit and mkfit) have not been fully tested out yet. We appreciate for your comments and suggestions.

• runfit.tar

Intrp

This is a perl script for helping you organize and interpret the output of Feff. It reads feff.inp, paths.dat, and files.dat and writes a file called intrp.dat. The output file contains information about the paths calculated by Feff in an easy-to-read table. It is intended to read a feff.inp file as written by Atoms v. 242 or higher and the paths.dat and files.dat of Feff v. 5.04 or higher. For now, the only documentation is in the script itself. Use the -h command line switch to read the documentation. A proper document will be written one of these days... Follow this link for intrp and other lisp scripts.

The Toolbox Archive

This is a compressed and archived file containing many of the things referenced on this page. The Unix version is tarred and gzipped. The DOS version is ZIPed.

• Unix, 381 kb
• DOS and other computers, 402 kb

Other Useful Links

Help Compiling The UWXAFS 3.0 Software

We are maintaining a help page containing compiler flags that give the best results for compiling the UWXAFS software on different platforms and under different compilers. You can add to the list if you have experience on a compiler that is not on the list. Follow this link to see the compiler help page.

IDP

IDP allows the user to view data interactively, and do some simple manipulations of the data. This program requires special binary files, called UWEXAFS binary files. Although the UWXAFS 3.0 programs can use this special file type, IDP is not maintained by the programmers of the UWXAFS Project. IDP is archived at Illinois Institute of technology.

Gnuplot

Gnuplot is a freely available data plotting program available for a wide variety of platforms. While the programmers of the UWXAFS project have nothing to do with the development and maintenance of Gnuplot, it comes highly recommended by them. Click here to reach the official Gnuplot archive.

Fudgit

Fudgit is a freely available, interactive driver for Gnuplot. It allows for such useful XAFS analysis tasks as e0 shifts, k-weighting, and Fourier transforms. Click here to reach the Fudgit archive.

ZIP

A unix version of the zip utility was used to create archive files for the UWXAFS Web site. The advantage of this format is that utilities exist on virtually all types of computers for extracting files from this sort of archive. Look at The Info-Zip page for information about using the zip format on your computer. I have stored text files in these archives with the MS-DOS end-of-line convention. If you use the zip files to download the UWXAFS package onto a computer that is not an MS-DOS sort of computer, be sure to read the instructions that come with the zip utility for your computer to extract text files with the correct end-of-line character.

GNU-VMS project

A fellow named Richard Levitte maintains VMS ports of the GNU software. You can find gzip at his site. There may be a version of tar. With these, you should be able to access the Unix archive files contained on the UWXAFS site. Click here to see the GNU-VMS home page.