[Ifeffit] Artemis fit results question

Timm Strathmann strthmnn at uiuc.edu
Tue Aug 31 09:33:47 CDT 2004

Shelly, Bruce

  Thanks for the advice. I'll try your suggestions. The negative parameters
usually only appear when I try fitting the FT using an alternative path to
the one that I believe is correct, or when I try improving the fit of broad
second-shell peaks by considering 2 paths instead of 1. I've been assuming
that the negative values were indicative of the second possibility you
indicated, but wanted to verify this. I'll certainly tryout the suggestions
you both made. Thanks.





Timothy J. Strathmann
Environmental Engineering and Science Program
Department of Civil and Environmental Engineering
3209 Newmark Civil Engineering Laboratory
205 North Mathews Avenue
Urbana, IL 61801-2352


phone: 217-244-4679
fax: 217-333-6968
strthmnn at uiuc.edu



-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Kelly,
Shelly D.
Sent: Tuesday, August 31, 2004 9:07 AM
To: XAFS Analysis using Ifeffit
Subject: RE: [Ifeffit] Artemis fit results question


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 Z.  


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)  values

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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