bravel at anl.gov
Wed Nov 9 10:07:48 CST 2005
> 1) After a normalization of the data, i put the data in "Athena" turn
> on the options: "pre-edge line", "post-edge line" and then "normalized"
> (in fact i usually turn the option "flatten" on, in dispite of the fact
> that i don´t know what that means, what that means?), i save using the
> option "Save chi(k)" in "file".
Flattening in the "Background removal" section of the in-program
The quadratic polynomial which is regressed after the edge is
normally used only to determine the edge step. It is quite possible
for a set of properly normalized spectra to overplot very nicely as
chi(k) but not as norm(E). This is because the standard
normalization does not alter the shape of the background function
beyond the edge. If there is variation in the over-all slope beyond
the edge, a set of overplotted norm(E) spectra will form a sort of
fan beyond the edge. Flattening is a visualization trick which
subtracts the linear and quadratic portions of the post-edge
polynomial from the data in such a way that the flattened,
normalized spectrum oscillates around 1. Thus, much of the variation
in the background functions in an ensemble of data can be suppressed
when plotting. This is particularly useful when making plots of
The flattening is purely visual. The subtraction of the post-edge
linear and quadratic portions of the background is made only for
plotting. chi(k) is not in any way affected by the flattening
In the Background removal section of the main window, there is a
check button which turns flattening on and off for the data
group. When flattening is turned off, the standard norm(E) spectrum
will be plotted. Flattening is controlled group-by-group, so it is
possible to make a multiple data set plot in which some spectra are
flattened and others are not.
> 2)Then i open the program "Artemis" and insert the data saved in
> the step "1)" in the column of the middle i click with the right button
> of the mouse and select the option "theory",
A much easier and more flexible way of doing this is to save your
Athena work as a project file and to import that project file in
Artemis. Artemis will display a page that allows you to select the
record from the Athena project that you want to import and analyze.
> "atoms" and insert the
> spatial group, unit cell parameter, and atomic location (here its
> important to say that the compound that i'm studying is LaCaMnRuO6 the
> measure of x-ray absorption was performed in the K-edge of the Mn, we
> are interested in
> Mn-O ligands so in "Artemis" i only put the data of the Mn and O,
I am not certain what you mean by this. On the atoms page, you want
to include the complete crystal structure, then choose the Mn atom as
the central atom. When you run Atoms, the crystal data will be used
to make a radially sorted list of atomic coordinates centered around a
Mn atom. Feff then uses this list of atomic coordinates to compute
the theory. You absolutely should not remove atoms from the list used
in the Feff calculation unless you really know what you are doing.
> 3)I click in the option "run atoms" for each atoms that i inserted the
> information, choosing 10 paths in each step, i click the in the option
> "run feff" for each atom that i inserted the information (again), after
> that, i click in "Fit" then appears in the screem the advise: "there
> is something wrong with your math expressions" (or something like that) i
> ignore that advise and go on, but the big problem is that the fit
> appears very poor!
Well, that's what happens when you ignore her sensible advice! ;-)
Seriously, you seem to understand the outline of the steps required to
do a fit, but I suspect that you are not appreciating the details of
making a proper fitting model.
It is very rare that you get to just push the big green button without
neediong to think about the details of the model that you are using to
fit the spectrum.
I could write on and on about this topic, but I think it would be
fruitful for you to follow the example that Scott Calvin wrote up.
And download the ZnO example. This consists of a series of Artemis
project files. Scott wrote comments in the journals of each project
to walk you through the process of using Artemis to fit real data. I
think that it would be helpful to you to work through this example
carefully. I suspect that doing so will help to clear up some of your
If, after working through Scott's example, you still have questions --
we on the mailing list will be glad to help you out.
Bruce Ravel ---------------------------------------------- bravel at anl.gov
Molecular Environmental Science Group, Building 203, Room E-165
MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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