[Ifeffit] Autobk parameters

[Kelly, Shelly D.]

Hi Stefano,

> 1) I understand that energy calibration should be performed, and I 
> did so by using the atomic edge energy. I also understand that this 
> parameter could be fluctuating in the subsequent fitting. Any comment 
> on this procedure?

I agree that all the energy shift stuff can be confusing.  The important
end result for Extended X-ray Absorption Fine Structure Analysis is to
get the energy-grid of the data to match the energy-grid of the theory
with the zero energy of the photo-electron somewhere on the absorption
edge.  In the process of doing this you may have more than one data set
from the same sample with different energy-grids... Furthermore you may
have more than one sample which may have different energy-grid from the
other samples and the theory.  Then to make things all the more
complicated X-rays can change the oxidation state of metals in organic
materials.  So that the energy grid is supposed to be different and the
data is useless.  

After all that, here are some answers.

1) Always measure a foil reference at the same time that you measure any
EXAFS data.  It is easy to do.  Here is a reference for how to do it
when your sample is too thick and you can not simply put the foil behind
the It ion chamber. J L Cross and A I Frenkel. "Use of scattered
radiation for absolute energy calibration." Rev. Sci. Instrum. 70: pp
38-40, 1998 

2)  Align each data scan:
2a) Without an energy reference.  Align the data to one of the data sets
(remember which one you used) so that the edges are all right on top of
each other. Each sample has it's own energy-grid.

2b) By using the energy reference of the foil measured simultaneously
with each scan.     Align all the reference spectra to one of the
reference spectra.  Then shift each of the data sets that belong to the
reference spectra by the same amount. Now each scan is independently
aligned and you have an absolute energy reference for each scan.   This
is useful for XANES comparisons or if you suspect changes in the data
while the measurement was taking place.  The difference in energy from
the reference to the data or from one data set to another is a real
change and can be used to "say" stuff about the sample.

3) Check the alignment:  Plot all the normalized xmu(E) data from the
same sample in Athena, zoom in on the edge region -20 to 20 eV and take
a good look.  Hopefully they all line up.  If there is a systematic
change in the edge features?  If so how much...less than 10 % (which is
about the accuracy of the measurement).  This means that you can most
likely still use the data but that you have changes happening to your
sample while the measurement was taking place and you should fix that
next time.

4) Now the problem of alignment is somewhat smaller.  All the data sets
have the same energy grid if you used 2b...or all the data sets have
there own energy grid if you used 2a.  Now we need to align the data and
the theory.  To do this there are two steps.  Choosing a zero energy of
the photo-electron to define the k-grid in converting the data to
chi(k), and then aligning the chi(k) data with the theory chi(k).

5) Choosing a Ezero in Athena:  Pick any point that you like on the edge
for Ezero in Athena.  Plot the xmu data with the background and pre-edge
and post-edge range.  A circle on the plot shows the position of Ezero.
Then right click The Ezero to set this energy to be the same value for
all the data sets from this sample.  Then plot the chi(k) data and see
that the curves all look the same at low k-values. If not adjust Ezero a
bit for the data sets that are different to get the chi(k) data to look
the same.  Then average the chi(k) data and write it out so that you can
align it with the theory in Artemis.

6)  Aligning data to theory:  Read the data into Artemis.  Read in what
you think should work for a first shell feffxxxxx.dat file.  Fit the
data to the first shell.  Plot the data and the theory in chi(k), take a
look at the deltaE value from the fit.  This value for deltaE is telling
you how much the theory had to move to match-up with your choice of
Ezero that you picked in step 5.  If you think that the theory is
correct and deltaE is larger than a few eV then you need to adjust your
chi(k) data.  But first write out what the theory should look like if
you choose Ezero just right.

6b)  Making a standard:  In Artemis, set all the parameters to their
best-fit values, except for deltaE.  Set deltaE to zero and run the fit
again.  This is not really a fit.  There are no parameters to optimize.
Now the theory is showing you what the data should look like if you
choose the perfect value for Ezero and the perfect background function
in step 5.

7) Redo the background and energy choice:  In Athena open up the
chi(k).fit that was produced by step 6b.  This is the "standard" that
you can use to help get Ezero and the background correct.  Then select
individual scans taken from the sample and then open the standard menu
and choose the theory chi(k) data.  Right click on the standard to use
the same standard for all data sets.  Redo the background removal.  Plot
the chi(k) data and the standard.  If they are different at low k you
need to adjust Ezero so that they start at the same place.  When you are
done adjusting your choice for Ezero, plot the xmu(E) data and make sure
that the circle that is your value for Ezero is on the edge.  If it
isn't, then the theory that you used to align the data doesn't work..and
you need to start over in step 6.  If the value is on the edge some
where, right click on the Ezero choice and set its value for Ezero of
all the scans.  Then merge all the data in chi(k) and write it out for
use in Artemis...as you did the first time making sure that all the
scans have a similar bkg.  

8) Redo the fit:  Now the data and the theory are aligned and you can
redo the fit varying all the parameters...deltaE in Artemis should be
small..and the background should give a nice match at low-r values.
Often this entire procedure is used at the end of your analysis to make
a nice figure for publication.

9) Bonus of using an energy reference:  If you used an energy reference
measured simultaneously with the data sets then in the end you can
simultaneously fit the different samples with only one deltaE in the fit
for all of the samples.  If you aligned each one independently then each
data set should have it's own deltaE value..unless you have more
information and can prove that they should be the same.

HTH
Shelly