This directory contains the crystallographic data for Iron Sulfide
(pyrite, FeS2) along with a transmission scan of FeS2 taken at room
temperature at beamline 13BM at the APS.  The data was taken from
Matt's data archive at
     [[http://cars9.uchicago.edu/~newville/ModelLib/search.html]]
     
This is sufficient information to begin a fitting project for FeS2.
In this readme file, I'll write steps to take to work through this
example.  You should not consider this to be a recipe -- at each step
you should play around with the settings in either Athena or Artemis
to understand fully these data and the programs.

 1.  Fire up Athena.  Import the data file.

 2.  Find a set of parameters that gives a good background removal and
     Fourier transform.  Note that the first couple data points in the
     pre-edge are odd -- be sure to select pre-edge parameters that
     avoid that bit of data.

 3.  Save the data to a project file.  You can ow close Athena.

 4.  Fire up Artemis.

 5.  Import the data from the Athena file that you just saved.

 6.  Import the crystallographic data contained in the file FeS2.inp.
     Run Atoms.  Note that you can set the cluster size independently of
     Rmax, the length of the longest path to be calculated.

 7.  Verify that the Feff input data is reasonable, then run Feff.

 8.  Select the first 10 paths in the path interpretation by clicking
     on path #1 then clicking on path #10 while holding the shift key.
     Drag and drop these paths onto the Data window.

 9.  Use the plot transfer buttons (the little red and blue buttons in
     the upper left corner of the Data and Path windows to move data
     and paths into the plotting list.  The buttons at the top of the
     Plot window are used to plot the contents of the plotting window.

     * Put the data and the first path in the plotting list.  See how
       it contributes spectral weight in the region of the first peak.

     * Clear the plotting list and put the data and the next three
       singel scattering paths in the plotting list.  Where do those
       paths contribute spectral weight?

     * Plot the various multiple scattering pathss along with the
       data.  Do anyof these MS paths seem like they might be
       important contributions to the fit?

 10. Click the GDS button to open the parameters window.  Create 4
     guess parameters called "amp", "enot", "delr", and "ss".  The
     initial guess for amp should be 1.  ss should be 0.003.  The
     other two can be 0.

 11. Deploy these four parameters as the path parameter values for the
     first shell.

 12. Exclude all paths after the first one from the fit.  One way of
     doing this is to select the first path, choose "mark after
     current" from the Mark menu, the "exclude marked" from the
     Actions menu.

 13. Set the fit range appropriate for a first shell fit.  Include
     only those path or paths which contribute strongly under the
     first peak.  Hit the big green button and examine your first
     shell fit results.  Do the parameters make physical sense?

 14. Extend the fit range to cover the split peak between 2.3 and 3.9
     Angstroms.  Include each of the first four SS paths in the fit.

 15. Now you need to set parameters for the paths you just included.
     It is reasonable to use the same S02 and E0 parameters for each
     path.  Should Delta R be the same for each path?  Should sigma^2?
     Come up with some reasonable parameterization, either by making
     interesting constraints between the paths or by creating new
     guess parameters as needed.

 16. Make a fit using your parameterization.  Are the best fit values
     reasonable?  How might you change the parameterization?  Is it
     possible to make constraints between the paths?

 17. FeS2 is a cubic material (it's space group is Pa3 -- a cubic
     group).  This means we can use the trick of modeling the delta R
     parameters by an isotropic expansion coefficient.  Discard
     whatever Delta R parameters you might have.  Define Delta R for
     each path to be "alpha*reff".  Remember that "reff" always
     evaluates to the nominal path length as used in Feff when a path
     parameter math expression is interpreted.  Make alpha a guess
     parameter.

 18. What other paths contribute significant spectral weight in the
     region between 2.3 and 3.7 Angstroms?  Consider including
     important MS paths and the fourth shell S atom to the fit.  How
     about paths 13 and 14, which are collinear paths involving the
     absorber and 1st shell S atoms?

 19. Can you think of a way to approximate the sigma^2 for the MS paths
     using math expressions, def parameters, and the sigma^2 parameters
     that are used to fit the SS paths?
     
 20. The 2nd and 3rd shells are both S and are relatively close
     together in length.  Test to see if the data support measuring
     sigma^2 independently for those two paths by comparing a fit in
     which they are constrained to be to same to a fit in which the
     float freely.

 21. If you look at the atoms information, you will see that this
     structure is actually defined by two parameters -- the lattice
     constant and the position of the S atom.  The variation in the
     lattice constant is accommodated in our fit using the isotropic
     expansion constant alpha.  How might you include the possibility
     of refining the S coordinate in the fit?
