[Ifeffit] Re: from I.Demchenko (PhD student at the Institute of Physics PAS)

Bruce Ravel ravel at phys.washington.edu
Tue Apr 6 12:40:07 CDT 2004

Hi Iraida,

I hope you don't mind that I CC my reply to the ifeffit mailing list.
I have some suggestions for you, but I thought it might be helpful to
you to see if anyone else has anything to contribute.

(The attachments to Iraida's email included a couple of screenshots
 showing the plotting window with a very good-loooking fit.  She also
 sent the artemis log file showing many of the numbers she quotes

On Tuesday 06 April 2004 12:12 pm, Iraida Demchenko wrote:
> I have a problem with fitting of my data for 0.5 microns  of Ge on
> Si(001) substrate (grown by MBE). The spectrum for K-edge of Ge was
> collected by TY mode. This sample is a standard for my next
> fitting. >From this fitting (for 1 shell) I want to draw
> So^2... But, if I apply a "trick" with k-weight determination as 1
> and So^2 value changing from 0.7 to 1.1 and repetition of this
> operation for k^1, k^2, k^3, I get three parallel lines for
> sigma^2(Ge-Ge) as function of So^2 :(. They aren't crossed in this
> area.

This is kind of surprising to me.  I have used the three-lines trick
many times and have never seen the situation of three parallel lines.
I am a little confused how that is even possible.  One might expect
this trick to do strange things in the case of a first shell that is
not well separated from higher shells, but my memory of Ge is that the
first shell is well separated.

Another situation that might lead to trouble is if strain induced by
the substrate splits the first shell into two well-separated peaks.
However, that does not seem to be the case for you either.  1/2 micron
is (I think) thick enough so that the film should be bulk-like.

Sadly, I am stumped.  Has anyone else ever seen this?

> On the other hand, I tried to fit my data (3 shells, k-w=2; dk=2;
> Hanning; k(3.5-12.3)) and I've obtained: reduced chi-square=10.33;
> R-factor=0.011; So^2=1.22 +/- 0.34; dr_1=0.0107+/-0.006;
> sigma^2_1shell=0.0037+/-0.0019; sigma^2_2=0.0068+/-0.0033;
> sigma^2_5=0.0096+/-0.0041(3 shell) (of course, that errors were
> recalculated(following FEFFIT, p.44). I doubt about the obtained
> value for So^2=1.22 +/-0.34. Within the error, of course, I can say,
> that this value is in the range from 0.6 to1. But, the correlations
> between variables are: amp (So^2) and sigma2_1: 0.916 :(; amp and
> sigma^2_2: 0.498; amp and sigma^2_5: 0.49; sigma^2_1 and sigma^2_2:
> 0.47; sigma^2_1 and sigma^2_5: 0.45.....all other correlations are
> below 0.25. In the attachment there is a log file for this fitting,
> as you can see sigma^2_3 is -0.0055+/-0.016 :(.
> Are there any other ways to determine our So^2? Or these actual results
> (So^2=1.22) we can consider as good? What do You think about this fit?

First, as you say, your value for S02 is not unreasonable in that the
error bar covers a value that one might expect.  Still, you are right
that 1.22 is an oddly large best fit value and suggests that something
else might be happening in the data.

Second, I wouldn't be so concerned about the high correlation between
S02 and sigma^2.  It's normal.  Here is a nice short piece by Matt
about correlations:
The rest of thread might be of interest to you, as well.

At another point in that thread, there is some discussion of how the
normalization is done.  Have you examined that carefully?  If the
post-edge line intersects E0 at an oddly low value, then the
edge-step used in the normalization might be rather too small.  This
is certainly a possibility in fluorescence data where the region after
the edge sometimes sweeps upward.  In that case, the normalization
range is such that the regressed post-edge line can be below the data
near E0.  I explained this in some more detail at
That could be the cause of a best-fit S02 that is larger than 1,
That's my best guess, given that I have not seen the mu(E) data, for
what is happening.

I was bit confused by thing about sigma^2_3.  I saw in the log file
that it was, as you said, negative.  But none of the sigma^2 values
for the paths were negative.  It wasn't clear how that sigma^2 value
was being used.

Hope that helps,

P.S.  I could tell from the log file that you sent me that you are
using a *very* old version of Artemis and presumably of ifeffit as
well.  You may want to download the latest ifeffit installation
package from
and then let the automatic updater bring your computer completely up
to date.  

 Bruce Ravel  ----------------------------------- ravel at phys.washington.edu
 Code 6134, Building 3, Room 405
 Naval Research Laboratory                          phone: (1) 202 767 2268
 Washington DC 20375, USA                             fax: (1) 202 767 4642

 NRL Synchrotron Radiation Consortium (NRL-SRC)
 Beamlines X11a, X11b, X23b
 National Synchrotron Light Source
 Brookhaven National Laboratory, Upton, NY 11973

 My homepage:    http://feff.phys.washington.edu/~ravel 
 EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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