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On 7/09/2011 7:24 AM, Bruce Ravel wrote:
<blockquote cite="mid:email@example.com" type="cite">
<pre wrap="">On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote:
<pre wrap="">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
<a class="moz-txt-link-freetext" href="http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html">http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html</a>
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
<a class="moz-txt-link-freetext" href="http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.html">http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.html</a>
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
<a class="moz-txt-link-freetext" href="http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html#datatypesandenergyunits">http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html#datatypesandenergyunits</a>
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
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
<pre wrap="">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
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.
<pre wrap="">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.
<a class="moz-txt-link-freetext" href="http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.html">http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.html</a>
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:
<a class="moz-txt-link-freetext" href="http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf">http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf</a>
<pre wrap="">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.
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
Ifeffit mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Ifeffit@millenia.cars.aps.anl.gov">Ifeffit@millenia.cars.aps.anl.gov</a>
<a class="moz-txt-link-freetext" href="http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit">http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit</a>
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