[Ifeffit] Fitting on Athena

Niken Wijaya niken.wijaya at monash.edu
Wed Sep 7 18:52:38 CDT 2011

On 7/09/2011 7:24 AM, Bruce Ravel wrote:
> 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...!
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Hi Bruce,

I think I have to clarify that I used MBACK to do the normalization 
instead of ATHENA. This might as well explain why I got such a high 
value of y-axis offset, why you think I did not choose the right 
parameters for the "pre-edge" and "normalization range" and also why I 
imported the data as normalized mu(E) rather than mu(E). As mentioned in 
the manual, doing normalization in Athena is very subjective, tiny 
difference in the point chosen for both the "pre-edge region" and 
"normalization range" will result in different normalized spectra. Due 
to lack of experience in processing XAFS spectra and noisy spectra 
obtained, I was planning to eliminate this problem by using MBACK. My 
initial plan was to combine the benefit I can get from both ATHENA and 
MBACK. So, I did the normalization using MBACK, then do the 
self-absorption correction and fit the normalized spectra in ATHENA. 
However, looking at your comment, LCF in ATHENA requires edge-step 
normalization, by saying that, does it mean that I cannot normalized my 
spectra using MBACK then fit them in ATHENA?


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