Conventions and acknowledgements

The best way to learn how to use ATHENA is to use ATHENA. Poke at the buttons, poke at the menus, try things just to see what happens. And above all, remember the physical and mathematical meanings of your data and of the data analysis techniques and think about how actions in ATHENA relate to those meanings.

ATHENA is a powerful and versatile program capable of supporting almost all of your common (and not-so-common) XAS data processing chores. It is not, however, a particularly intuitive program. I doubt that any XAS program could be intuitive. On top of that, ATHENA has accumulated lots of features over the years. Many of these features are necessary for high-quality data processing, others are bells and whistles intended to make data processing more convenient or more fun.

This document attempts to be a comprehensive overview of all of ATHENA's features. There are lots of words, but also lots of pictures. Feel free to jump around and to focus on the parts most directly relevant to your immediate needs. I hope you find this document and the program helpful.


Layout and typesetting conventions

Here is a summary of fonts, colors, and symbols used to denote different kinds of text. Note that some of these may appear the same in certain presentation media.

Caution! Points that require special attention are written inside of attention-grabbing boxes.

To do! Notes about features missing from the document are indicated like this.

To do! Features that have been recently added to ATHENA are indicated like this if they have not yet been properly documented.

Essential topic
This symbol indicates a section describing one of ATHENA's features that I consider especially powerful and central to the effective use of the program.

Advanced topic
This symbol indicates a section with difficult information that newcomers to ATHENA might pass over on their first reading of this document.

The html version of this document makes use of HTML 4.1 character entities (mostly Greek symbols) and will not display correctly in very old browsers.



I have to thank Matt Newville, of course. Without IFEFFIT there wouldn't be an ATHENA. One afternoon over coffee, Julie Cross and Shelly Kelly lit the spark that eventually lead to the first version of this document. Some content of this document was inspired by the XAS review article by Shelly Kelly and Dean Hesterberg (S.D. Kelly, D. Hesterberg, B. Ravel, Methods of soil analysis, (2008) p. 387-483), the first draft of which I had the pleasure of editing and the final draft of which I ended up on the author list. I have a huge debt of gratitude to all the folks on the IFEFFIT mailing list. Without the incredible support and wonderful feedback that I've received over the years, ATHENA would be a shadow of what it is today.

The following great software tools were used to create this document:

Almost all screenshots were made of either ATHENA or the Gnuplot window on my KDE desktop. The screenshots of spreadsheets made from a report file and an LCF fit report are displayed in LibreOffice.

The images of the Tholos temple on the front page and the Klimt painting Pallas Athena in the navigation box of the html document are from

The image used as the ATHENA program icon is from a “Terracotta lekythos depicting Athena holding a spear and aphlaston.”. The image is licensed as Creative Commons Attribution-Share Alike 3.0 and can be found at Wikimedia Commons.


Data citations


Installing Athena on your computer

Linux, BSD, and other unixes
It is not especially hard to build ATHENA from source code. The procedure is explained in detail on this web page: An excellent addendum to those instructions is at

Debian and debian-based Linux
Coming soon....

Follow the links on the Demeter homepage to download the installer and updater packages. Just download, double-click, and answer the questions.

Coming soon....


Building this document from source


Obtaining the document source

The source files and all images files for this document can be downloaded using Git. To grab the source, you will need an Git client on your computer. This command checks a copy of the source out and downloads it onto your computer:

    git clone

This document is written using The Template Toolkit. It requires the perl interpreter and a fairly complete installation of version 2 of The Template Toolkit to build. If TT2 is not available as a package for your system (it is available as a pre-compiled package for many versions of Linux; a ppm file for ActivePerl on Windows exists; a Fink package for OSX exists) it can be downloaded from its website and installed by hand or downloaded using perl's CPAN utility. You will also need to install the Image::Size, PPI::HTML, and Syntax::Highlight::Perl modules. Compiling the LATEX version of the document will require a fairly complete LATEX installation as I make use of many styles, including amsmath, amsfonts, amssymb, floatflt, wrapfig, fancybox, fancyhdr, keystroke, varioref, hyperref, and more. (I have no experience building the PDF document on any system other than linux.)

Once TT2 and the other modules are installed, building the document should be quite simple. TT2's ttree program is used to recurse the through the directory structure containing the templates. The bin/build, and bin/tex scripts are wrappers around ttree. They invokes a number of important command line options and pass any further command line options to ttree.

TT2 was chosen for this project because it is an excellent templating tool. A templating tool was chosen because the strong separation of format and content was attractive to me. The template source is used to generate html and PDF versions of the document as well as the pod format used by ATHENA's internal document viewer.

Contributions to the document are extremely welcome. The very best sort of contribution would be to directly edit the source templates and commit your changes to the SVN repository. The second best sort would be a patch file against the templates in the repository. If TT2 is more than you want to deal with, but you have corrections to suggest, I'd cheerfully accept almost any other format for the contribution. (Although I have to discourage using an html editing tool like FrontPage to edit the html directly. Tools like that tend to insert lots of additional html tags into the text, making it more difficult for me to incorporate your changes into the source.)


Building the html document

After downloading and unpacking the source for DEMETER, you must configure it to build correctly on your computer. This is simple:

cd doc/aug

To build the entire document as html

./bin/build -a

Individual pages can be built by specifying them on the command line:

./bin/build bkg/


Building the LaTeX document

The LATEX document is built by

./bin/tex -a
cd tex/
pdflatex athena.ltx
pdflatex athena.ltx

You need to run pdflatex two or three times to get all of the section numbering and cross referencing correct. The varioref package, used to handle cross-referencing, is sometimes a little fragile. If you see the following error message: simply hit return. The message should disappear when you recompile the document.

! Package varioref Error: vref at page boundary 142-143 (may loop).


Using the document with Athena

The html document files can be used by ATHENA. They are installed at the time that DEMETER is installed (and they can be installed on a Windows machine by downloading and installing the documentation package). If the html pages cannot be found, ATHENA will try to use your internet connection to fetch them from the Demeter homepage.