[Ifeffit] Artemis fit results question

Kelly, Shelly D. SKelly at anl.gov
Tue Aug 31 09:06:54 CDT 2004

Hi Timm,
You can use an expression that will return only positive values for you
sigma2 = abs(ss)
guess    ss
This will force the model to use a positive values for sigma2.  You can
also use a penalty factor to keep the value inbetween a given range of
values.  I believe that there is an example of that in the Artemis or
Ifeffit manual. 
-Most often negative values is a strong indication that something in the
model is not quite right.  Be sure to look at your data and fits showing
the individual contribution from each path in the real or imaginary part
of the FT.    A negative sigma2 value or a really small sigma2 value
usually indicates one of two different things.  1)  You have included
too much noise in the FT which is randomly adding signal all over in
R-space hence your sigma2 values are unrealistically small to
compensate.  To check for this case,  reduce the k-max value in the FT
of the data by 1 1/angstrom and see what happens in the fit.  2)  The
path type is not right.  sigma2 is small because you actually need more
electron density for that scattering path.  Hence try a path with larger
Negative values for the degeneracy would indicate that the path length
and/or atom type is not correct.  Set the degeneracy, sigma2, and delr
to some reasonable values then look at the real/imaginary part of the FT
for the data, fit and the contribution from the path of interest.  Look
to see if the signal from the path of interest has a positive
contribution to the data before you try to optimize the parameters.
Here is my rule of thumb for reasonable sigma2 (units= angstroms2)
sigma2 = 0.001 to 0.003 for double bonds that do not participate in
binding to another atom.  i.e. for the axial oxygen atoms of a uranyl
moiety, UO2.
sigma2 = 0.003 to 0.008 for "normal"  well ordered shells.  Like for Cu
metal.  This is the usual range.
sigma2= 0.009 to 0.015  for disordered shells that are rather weekly
bound.  i.e. for the equatorial oxygen atom of the uranyl.  There is
usually 4 to 6 of them and they are not well ordered.  Some times these
shells can be split into two shells given enough data range in k-space.
sigma2=0.015 to 0.025  for really soft bonds like solutions or squishy
metals (AgCl)
Sigma2 values also depend on the distance.  The rules given above are
for 1st and 2nd shells of atoms.

-----Original Message-----
From: Strathmann, Timothy J. 
Sent: Monday, August 30, 2004 3:42 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Artemis fit results question

This may be a question related to Artemis or to EXAFS fitting in general
for a relative newcomer. Over the past months, when I've fit EXAFS data
using Artemis and feff-derived single-scattering paths, I sometimes end
up with best fit values for 2nd-shell coordination numbers or sigma
squared values that are negative. Do these values have any meaning, or
do they most likely signify that the chosen paths are not appropriate
for fitting the spectral region in question? Also, is there a way to
constrain the parameters to only consider positive values. Thanks.


Timm Strathmann

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