Marcelo Alves | 16 Jan 16:21 2015

Exploring XANES data for getting EXAFS results

Hi all,

I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells.

I think that could be very interesting for low Z elements such as P, S, Ca, K, Al, etc in diluted samples.

Thanks in advance.

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Miller, BradleyW | 14 Jan 16:53 2015

Demeter installation



I’m trying to install Demeter software package on my govt. computer which is under a degree of lock down. I have full admin rights but its still not running.


Here is the explanation from IT support.


it wants to install on C:\strawberry and the C: drive is locked down here and all our programs need to be installed to C:\program files (x86) and when I tried to install there it told me that it didn't like spaces in the directory and I went ahead and install where it wanted and now program will not run due to security “



Any suggestions?


Thanks for your time.




Bradley W Miller, PhD

Environmental Scientist

US Environmental Protection Agency

National Enforcement Investigations Center

Denver Federal Center, Bldg 25 Door E3

PO Box 25227

Denver, CO  80225

Office: 303-462-9150

Mobile: 863-258-7989

Fax: 303-462-9028


The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley



Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency. 



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Angel Yanguas-Gil | 31 Dec 05:46 2014

is there any ongoing effort to integrate feff and larch?

So far it seems from the sphinx doc that feff cannot be called from
larch. Is there any ongoing effort to implement that? The simplest way
would be to create a python module to generate the corresponding
feff.inp file, but I'd hate to duplicate someone else's work.


Edmund Welter | 22 Dec 15:23 2014

Job offer at DESY

Dear colleagues,

DESY offers a postdoc position at the new PETRA III extension EXAFS
beamline P64. If you are interested in details please visit:

If you should know of a colleague who might be interested in the
advertised position please feel free to forward this mail. In case you
have any question please do not hesitate to contact me (preferentially
not via this mail list...)

Best regards,

Edmund Welter
Godfrey, Ian | 18 Dec 10:19 2014

Handling large data sets in Athena (and energy dispersive calibration)

Dear All,


Here’s an issue I recently encountered while trying to handle some very large in situ datasets in Athena; it may be by design/an inherent limitation, rather than a bug, though:


(I am running Demeter 0.9.21 pre and Demeter 0.9.20 , both x64 on Windows 8.1 x64 on separate machines).


Each of my datafiles contains over 300 columns of u(E) data as space delimited plain text, however when I try and import them to Athena the import window will only display checkboxes up to column 87.


I’ve attached an example datafile and a logfile to this email. (The data is very poor, but that shouldn’t be an issue for debugging…) I’ve also attached a copy of the datafile as it came from the beamline – this also displays the issue, so it’s nothing I’ve done to the file.


On a related note, is it possible for the energy dispersive data calibration to be added back to Athena? To get the calibration parameters for this data I had to use the (very) old version!







Ian Godfrey


PhD Student,

UCL/JAIST Programme


Industrial Doctorate Centre in Molecular Modelling and Materials Science,

Department of Chemistry,

University College London




School of Materials Science,

Japan Advanced Institute of Science and Technology




Attachment (dathena.log): application/octet-stream, 1678 bytes
Attachment (citrate_003_log_0_calibrated): application/octet-stream, 2921 KiB
Attachment (citrate_003_log_0): application/octet-stream, 3879 KiB
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Jean-Baptiste ABBE | 9 Dec 10:46 2014

Bug report - autosave on mac

Hi everybody,

I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days.
Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue.
Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens :
1) athena launch, a little bit longer than usual
2) a box appear to give me choice to recover data by importing it from autosave or not
3) I can’t select anaything and the rainbow wheel of death appears.
After a few hours, nothing changes… and I have to terminate the programm manually.

So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions :

I tried to find the autosave file : nothing
I tried to uninstall and reinstall macports : nothing
I tried to uninstall macports and install the demeter-devel : nothing
In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment.

I will try again other solutions, but I will gladly accept any kind of help to solve my issues.

Thank you

ABBE J-Baptiste
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Sanson Andrea | 5 Dec 15:07 2014

non-standard space group P 21/n

Dear all

does anyone know if is it possible to create with ATOMS
the non-standard space group P 21/n ?

Space group keywords are listed at the atoms website
but no keyword for P 21/n group is available.

Thanks for any suggestion.
Best regards,
Badari Rao | 3 Dec 13:54 2014

A small query on constricting mean square displacement in multi-edge EXAFS refinement

Dear All,

Suppose I have a compound, say AB. I have the EXAFS data from both A-edge as well as B-edge and I am simultaneously refining these data.
Would it be correct to force the mean square displacement of the A-B path in both the edges to be the same?

-- Regards,
Badari Narayana. A. R.
Ph.D Student, Nanoscience and Nanotechnology,
c/o Prof Rajeev Ranjan,
Electroceramics Lab,
Department of Materials Engineering,
Indian Institute of Science.

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pushkar shejwalkar | 3 Dec 02:22 2014

Regarding a fit for Fe(OTf)2

Dear All,
            I am experiencing problem during my fit for Fe(OTf)2 anhydrous. The problem is as follows.
I collected the data and used a model to fit. The fitting values and other technical information is as below. The basic problem is Fe(OTf)2 in anhydrous condition is probably not cyrstalline because of which there are no crystal data available. Although .cif file is available for hexahydrate and tetra acetonitrile. But obviously it is not directly useful as I am looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit information is given. Is this fit acceptable?

Now two questions
1) Why do I not see any scattering or peak for Fe-S. I expected S to be a strong scatterer and would  show a peak. Under given circumstances it looks like Fe is all surrounded by water and no triflate is present near Fe at all. Is this assumption even make sense (when the bottle said anhydrous) The bottle was not kept under inert condition (and its my fault), but does it mean Fe(OTf)2 is so hygroscopic and that it can actually form such hexahydrate to the full extent?
OR there is some inherent problem with my fitting and collection itself. I used RBKG=1.0

2) Is anybody working on Fe(OTf)2 and had such or any other problem indicating that Fe(OTf)2 by itself is a bad choice of precursor because of its reactivity. Also any comments on purification method etc. does anybody know if crystal structure is available for Fe(OTf)2 anhydrous? I could not find it on the quick search or on CCDC. Any other site where I can get crystal data and .cif information?

Thank you very much for all the help, I hope the question is asked appropriately and all the other information is provided, however, if anybody needs any other information please let me know.
Thank you in an anticipation

Independent points          : 16.1250000
Number of variables         : 4
Chi-square                  : 7324.9401796
Reduced chi-square          : 604.1187777                                       
R-factor                    : 0.0195782                                         
Measurement uncertainty (k) : 0.0001264
Measurement uncertainty (R) : 0.0004142
Number of data sets         : 1

guess parameters:                                                               
  SO                 =   1.06525455    # +/-   0.05504541     [1.00000]
  delE               =  -2.32587026    # +/-   0.59606221     [-2.77870]
  delR               =   0.00911122    # +/-   0.00503027     [-0.02322]
  ss                 =   0.00706809    # +/-   0.00071967     [0.00300]

Correlations between variables:                                                 
                delr & dele               -->  0.9154
                  ss & so                 -->  0.9023
All other correlations below 0.4

 name        N       S02     sigma^2   e0     delr     Reff     R
 O1.1      6.000   1.065   0.00707  -2.326  0.00911  2.09150  2.10061

Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,

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Lichtenberg, Henning (IKFT | 2 Dec 17:16 2014

open position at KIT

Dear XAS community,
we have an open position in the field of EXAFS and operando spectroscopy in our group. For further information see the attached job description. Please feel to contact us also if you are interested in a beamline scientist position or x-ray microscopy. 
with best regards,
Henning Lichtenberg
Attachment (PostDoc-ITCP-EXAFS.pdf): application/pdf, 86 KiB
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kaziz sameh | 27 Nov 10:13 2014

Fit a mixture

Dear All,
I look for advice or document that can help me to fit the FT EXAFS data of Pd2Au36(SR)24.
The situation is as follows:
In the sample there is 3 sites of the Pd ( in staples, in surface or in the core). the spectrum that I have presents  a first bond of Pd_S and second bond of Pd_Au, so the palladium should be in the staples or in the surface because in core we cannot see Pd-S, but other results of the same sample confirm that the palladium is in core.
I concluded that there is a mixture of some nano (x ) with Pd in staple and another nano(y) with Pd in core  such y>x.
Note that I fit the data with Pd2Au36(SR)24 structure in which I put the 2 palladium in the staple and I have got a good fit (attached) but I think that is not logical.
If you can help me with an idea how to fit this mixture, I would be very grateful.
Attachment (fit.docx): application/vnd.openxmlformats-officedocument.wordprocessingml.document, 58 KiB
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