Dear All: I would like to attempt fits to the pre-edge features of a set of Fe K-edge XANES spectra for Fe(II) samples that show partial oxidation with the goal of determining whether Fe(III) exists in octahedral or tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001). Broadly, the fitting procedure involves extracting the pre-edge feature from the edge using a spline function and then deconvoluting this feature using a set of pseudo-voigt functions. I believe that I can use the LCF module in Sixpack to fit the feature using the pseudo-voigt functions, but I'm having trouble extracting the pre-edge feature. I've tried using the spline function in Sixpack (and Athena), but I don't have enough options to modify the spline. It seems to me that I need to use a very rigid spline (for instance, one with only 3 or so knots), and that the options in Sixpack and Athena don't allow for this. I heard the program exafspak would allow me more freedom to control the spline function, but I haven't been able to successfully download the program, let alone use it. So, my questions are the following: (1) Is there a program other than exafspak that I could use to fit a spline to my data where I would have more control over the spline options? I would prefer not to use exafspak since my knowledge of unix is nil. (2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd appreciate any tips you might be able to give me on installing the program. I followed the directions for installation provided on the website, but the command to install the program (i.e. "add_exafs") wasn't recognized. Thanks for your help! Sharon
On Friday, June 08, 2012 11:18:25 AM shbone@berkeley.edu wrote:
I've tried using the spline function in Sixpack (and Athena), but I don't have enough options to modify the spline. It seems to me that I need to use a very rigid spline (for instance, one with only 3 or so knots), and that the options in Sixpack and Athena don't allow for this.
Sharon, That is not the problem that the spline in Ifeffit (and therefore in Athena and Sixpack) is designed to solve. The purpose of Ifeffit's spline is to isolate the chi(k) from mu(E) and it only aims to do so reliably above 2 or so inverse Angstroms. There are reasons for that: 1. There are information theoretic limits to how much freedom the chi(k) isolation spline should have. In general, it cannot have enough freedom to reliably go down the edge -- which is the fastest changing part of the data. 2. We typically do our EXAFS analysis starting a few inv. Ang above k=0, so in practice Ifeffit's spline does what we want. 3. The theory for EXAFS analysis is probably unreliable below 2 or 3 inv Ang, but quite reliable above that. So if the spline cannot isolate chi(k) below 2 or 3 and the theory cannot be trusted below 2 or 3, nothing is lost for EXAFS analysis. So, I think your problem is that you are trying to use the wrong tool for the job. You want to treat your XANES data as a generic peak fitting problem. There are many, many options for that. You don't really need to rely upon software written explicitly for XAS data, although many of them do some kind of peak fitting. Athena does, for example, using thinsg like arctangents and gaussians, although it is perhaps not the strongest part of that program. A general peak fitting problem can be dealt with in something like Matlab or Mathematica. It can probably be done reasonably well in Excel. Whatever.... Step-like functions (like an arctangent) are often used to model the edge. I suppose you could use a spline for that, but it may be challenging to give the spline enough freedom to follow the step-like shape but not enough freedom that it wants to follow the peaks in the egde. That's the nice thing about an arctangent or an error function -- purely a broadened step. HTH, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Sharon,
In addition to Bruce's excellent advice on treating pre-edge analysis as a
generic fitting problem, you may also want to have a look at an earlier
systematic survey of Fe pre-edge analysis: Westre, et al., J. Am. Chem.
Soc. 1997, 119, 6297-6314 DOI: 10.1021/ja964352a. Note the constrained
fitting range in that paper, which simplified the fitting problem a bit since they
did not need to worry about accurately fitting the edge step and bumps
along the rising edge using step functions and the like.
The only useful application of EXAFSPAK to your problem would be
to fit the pre-edge data using the EDG_FIT program of that package (this
was used in the Westre paper referred to above). This program has
something of a learning curve to use well. If you have another peak-
fitting program that you like, then it's best to stick with that one.
Good luck,
Erik
--
Erik Farquhar, Ph.D.
Case Center for
Synchrotron Biosciences
Brookhaven National
Lab
NSLS, Building
725A-X3
Upton, NY
11973
efarquhar@bnl.gov
+1-631-344-8174
________________________________
From: "shbone@berkeley.edu"
participants (3)
-
Bruce Ravel -
Erik Farquhar -
shbone＠berkeley.edu