[Ifeffit] Right way of choosing E0 in Athena

Kelly, Shelly D. SKelly at anl.gov
Thu Jun 29 09:08:42 CDT 2006

Hi Gerrit,

My web page has a couple of examples that I think you will find helpful.
Take a look at http://www.mesg.anl.gov/Skelly.html .  The "Basics of
EXAFS data analysis 2004" presentation and the tutorial on background
removal for MoO3 will answer most of your questions.  The alignment of
measured spectra for EXAFS analysis can be different than the alignment
of spectra for XANES analysis.  My presentations address the issue of
alignment for EXAFS analysis.  

Briefly, The important consideration in EXAFS analysis is aligning the
chi(k) data to each other to get a consistent background and aligning
the data to the theory.  If the different spectra have a similar edge
shape then a consistent background removal can be achieved by aligning
the spectra relative to each other and choosing exactly the same bkg
parameters for all. Go into the align spectra menu, choose the first
spectra as the reference and then align all the other spectra to the
first spectra.  Once that is done go back to the background removal
page.  Make the background the way you want for the first spectra and
then right click on the "background parameters" heading and set those
parameters to all the spectra.  Then compare the chi(k) spectra with a
low k-weight so you can see if they are aligned (spectra should cross
zero at the same k-value).  Sometimes I need to tweak the value for E0
by ~ 1eV or so to get them exactly the same.

BTW, I have a poster at the EXAFS conference later this month about
these issues.  I will put the poster on my web page when it is done...

Good luck

Shelly Kelly
Argonne National Laboratory
Bldg 203, RM E113
9700 S. Cass Ave
Argonne, IL 60439

Molecular Environmental Science Group
skelly at anl.gov
phone: 630-252-7376

-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Gerrit
Sent: Thursday, June 29, 2006 8:48 AM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Right way of choosing E0 in Athena

Vadim G Palshin schrieb:
> Hi everyone,
> I have the following question: I have a set of spectra collected in
> transmission with 3 ionization chambers and a standard between 2nd and
> ion chambers for calibration, so I know my spectra are nicely
> relative to each other. Should I then force Athena(/autobk) to use the
> E0 for all of them (e.g. use the atomic value) or let it find E0
> independently for each sample? Thanks!
> Vadim.


I wrote the message below a few days ago and when I wanted to post it to
the mailing list I noticed that Vadim already posed a related question.
Sorry for not supplying an answer but to extend the list of
questions :( ...

Recently I stumled across a behaviour in Athena I did not understand
while discussing with a collegue how to choose the right E0 for
background subtraction in Athena. I would be glad if I could benefit
from the expertise of the members of this mailing-list.

The initial question was how to choose a value for E0 when comparing
samples with mixtures and the measurements of the pure compounds (e.g.
iron, iron-oxide and a sample containing a mixture of both). Usually in
this case I set E0 to the atomic value for all samples (Assuming I can
be sure that the monochromator was calibrated to return a correct
absolute energy. Otherwise I do an appropriate energy-calibration with
reference to a standard measured at the same time before entering
Athena). I do that to ensure a uniform background subtraction for all
samples. However, for a system of e.g. Se, RuSe2 and a mixture of both,
the atomic value E0 can be quite far away from the inflection point of
the RuSe2- and mixture-samples. So the first question would be: is it
better to use the same E0 for all samples or to somehow adjust the E0 to
the inflection point of the specific sample?

In this context my idea of the algorithm of background subtraction was
that a shift of E0 could be completely compensated for by appropriatly
shifting all other parameters in the backward direction. E.g. when
shifting E0 by 4 eV I should end with the same FT when shifting the
values for pre-edge range, normalization range, spline range and k-range
by the same amount. However, a test revealed that only the pre-edge
lines and post-edge lines are identical. The background splines are
different and the FTs differ quite significantly from each other. Is my
general assumption wrong?

Another question (more cosmetic) concerns the use of 'E0' and 'E shift'
as it is irrelevant which parameter to adjust to achieve an energy
shift. Is it a good idea to set E0 always to the atomic value and use 'E
shift' for entering the offset? Actually this is the way I prefer to do
it although Athena initially does not set 'E shift'. I also have a kind
of feature request in this context and would be interested if others
would also benefit from it: for some samples the initial value Athena
picks for E0 is obviously inadequat, e.g. when it chooses a prepeak as
inflection point. As a consequence the parameters for background
subtraction are also inadequate. After choosing a right value for E0 a
new feature could be: "automatically adjust background parameters with
regard to the current E0", so one could still benefit from Athenas
auto-function. Usually I adjust these parameters anyway but it would
simplify doing a quick first look at the data.

Thanks for any help,

Gerrit Schmithals
Hahn-Meitner-Institute Berlin

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