[Ifeffit] doubts

Bruce Ravel bravel at anl.gov
Wed Nov 9 10:07:48 CST 2005

Hi Marcos,

> 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
  XANES data.

  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,
> right?)

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.
Look at:


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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