[Ifeffit] Possible bug in Athena during alignment

Christopher Patridge patridge at buffalo.edu
Wed Oct 15 09:47:30 CDT 2014


I am not sure I understand but from what you wrote, did you try to align the data sets to the NaBr standard or did you align the standard associated with each data set to the NaBr standard?  Using the align tool in Athena, one should align the same type of data, i.e. the same sample such as NaBr.  If the samples you try to align are different, then the align function will have some trouble, particularly if there are unique XANES features.  On the other point, a 17 eV shift is not out of the ordinary and Athena does a fine job even as large as 25 eV in my experience with Ag K edge.  calibrate and normalize can not be interchanged unless again I don't understand the problem completely.  Calibrate has to do with the energy scale of the data and normalize has to do with the intensity of the signal at each energy point.

please clarify,

Dr. Christopher Patridge
Assistant Professor of Chemistry
Dept of Math and Natural Science
D'youville College
320 Porter Ave., Buffalo, NY 14201
Phone: 716-829-8096
Email: patridgc at dyc.edu

On Oct 15, 2014, at 10:21 AM, Leon Clarke <L.Clarke at mmu.ac.uk> wrote:

> I’d like to report a possible bug within Athena.
> Last week I collected Br K-edge data at the APS and have experienced an issue with Athena during data alignment. The beamline energy required calibration and so I did the following data processing steps, in this order:
> 1.       Completed pre- and post-edge corrections, using windows relative to the actual Br K-edge energy, on the raw data exported from the beamline. (In other words these windows were not energy offsets relative to the actual measured edge position).
> 2.       Used the flatten post-edge feature within Athena.
> 3.       ‘Calibrated’ (Normalised is a better term really) the first derivative of a NaBr measurement to the Br K-edge energy using the calibrate drop-down option. This resulted in the requirement for a -17.39 eV energy offset.
> 4.       Tried to align all of the sample data to the NaBr ‘standard’ using the align drop-down option.
> The issue I have had is with step #4. When I aligned, for several samples the XAFS (XANES) plots went wrong. It seems that Athena was not transforming the pre- and post-edge windows correctly for such a large energy shift, i.e. didn’t shift these to lower energies by 17.39 eV, and I think this is a bug within Athena.
> I hope the above makes sense; I can provide an Athena project file, if required.
> Many thanks, Leon
> -----
> Dr Leon J. Clarke
> Senior Lecturer in Environmental Analytical Chemistry
> Division of Chemistry and Environmental Sciences
> School of Science and the Environment
> Faculty of Science and Engineering
> Manchester Metropolitan University
> John Dalton East
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> Manchester
> M1 5GD
> E-mail: l.clarke at mmu.ac.uk
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