Hi
Timm,
You
can use an expression that will return only positive values for you
variables.
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.
HTH
Shelly
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