[Ifeffit] Fitting on Athena

Tue Sep 6 16:24:10 CDT 2011

On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote:
> 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 
> fitting), the intensity of the fitting spectra is higher than the actual 
> sample. This is I believe due to the higher intensity of the individual 
> standard compounds when compared to the spectra of my samples (i.e. 
> filename: ifeffitlist-intensity). This is the case for every fitting I 
> did for my sample so I am just not sure with the fitting results.

Well, there are a lot of problems contributing to your confusion.

One thing that probably doesn't help, but which certainly isn't the
central problem, is that you have extremely large values for the
y-axis offset parameter of several of the standards.  This makes it
difficult to plot normalized spectra in an unconfusing way.

Your central problem is that, for most of the data groups, the values
of parameters for the pre-edge and normalization lines are not well
chosen.  It would seem that you trusted the default values without
checking them.  See

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html

In your case, the default values resulted in unusably short ranges for
thepre-edge line or the post-edge line or both.  The moral of this
story is to plot the data with its pre- and post-edge lines to verify
that the values result in sensible normalization.  See

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.html

You also had a problem that some of your data were somehow imported as
normalized mu(E) rather than as mu(E) or xanes(E).  See

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html#datatypesandenergyunits

This is usually not a good idea as it tells Athena that your data are
already reliably normalized and should not be further processed.
Those data, however, were not unit edge-step normalized, which is what
the LCF utility requires.  The way to fix that in an existing Athena
project file is explained just a little further down on that same
page.

Once I fixed the datatype for all of your groups and performed a
sensible normalization for your data, I got the LCF fit shown in the
attached image.  Not great, but not the ridiculous result you were
getting with so many things done wrongly in your project file.

I think that the underlying problem is that you expected Athena to
magically do the right thing with your data without verifying its
results.  Or, perhaps, you plowed forward without fully understanding
how to use the program.  The documentation isn't exactly exciting
reading, but it doesn't completely suck.  You might want to bookmark
its URL.

> 2. If we see figure "ifeffitlist-sample39", we can see that the spectra 
> has different slopes on the pre and post-edge region. When I used MBACK 
> for background removal, the normalized spectra is weird, illustrated in 
> "sample39-fig-norm.pdf". What is the best way to fix this issue? I have 
> 5 samples with this feature that I cannot process due to the weird 
> normalized spectra.

Well, MBACk isn't my thing, so I can only comment on it in general
terms.  I suspect that you would get better results if you severely
truncated your data, say from about 2455 to 2515.  Something wonky
happens in that spectrum at the beginning and the end.  I suspect that
MBACK is having trouble figuring out what part of the data is actually
the edge step.

> 3. Regarding the self-absorption correction, I was not aware that Athena 
> has this function. I will have a look at the manual again. Thank you for 
> letting me know.

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.html

Again, not exciting ... doesn't suck ... bookmark.

Here's a talk I gave at the University of Ghent last January on the
topic of self-absortion corrections.  It may be of some help to you:

  http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf

> 4. With the 3rd derivative spectrum, I did indeed derive it from the 
> normalized values. As you can see from the file I attached earlier, from 
> the experts points of view, do you think I should go on with the Nth 
> derivative spectra or due to the very low signal-to-noise ratio of the 
> spectra, I should just focus on the absorption spectra?

I don't really have an opinion one way or the other about the 3rd
derivative.  The folks from Stanford and CLS who do a lot of sulfur
work have made extensive use of the 3rd derivative and they are really
smart people.  I haven't done a lot of S work in my own career and
none of Athena's users have ever asked for a 3rd derivative option, so
Athena doesn't currently do that.

B

PS: Doesn't it just blow your mind how there is a strong correlation
between quality and clarity of the question and specificity of the
answer?  Amazing...!

-- 

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software:  http://cars9.uchicago.edu/ifeffit/Demeter
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