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


i.godfrey-hclig2XLE9Zaa/9Udqfwiw@public.gmane.org i.godfrey-8xqbrEIV++l3+QwDJ9on6Q@public.gmane.org


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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Matthew Marcus | 26 Nov 21:39 2014

S XANES question

A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a strong peak at 2484eV (calibration:
gypsum white line = 2482.75eV).
There's a shoulder at the nominal position of the sulfate peak.  Now, peaks below sulfate I can understand,
but since there's no such
thing as heptavalent sulfur, what could give a peak *above* the sulfate white line?  Anybody ever seen that? 
Yes, we checked calibration.
Yun Xu | 18 Nov 23:32 2014

experimental standard

Hi all
I have a complex oxide BaTi8-xGaxO16. What standards I should run?
Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as standard, or the simple oxide as BaO, TiO2 Ga2O3?  or is the standard necessary?
Also, I have colleage working on DFT, I assume the theoretical standard is the result from the DFT calculation, and by using the coordinates of the atoms, I can run FEFF and fit the data.
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Bruce Ravel | 11 Nov 16:49 2014

Re: Fwd: Re: Re: problem about negative

On 11/11/2014 10:19 AM, Bruce Ravel wrote:
> Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat
> not smooth.How to distinguish whether a long wavelength oscillation
> appear as a real peak or false one?I am confused about it.
>         I find when I avoid the first scattering peak after white
> line(kmin=4.8 maybe too large),the first peak of R space
> disappeared.Because usually the first scatering peak is related to the
> first coordiantion shell,can I think the first peak in R space less 1A
> is a real peak instead of noise?


As I said yesterday, I don't know anything about your sample, so it is 
hard for me to know what the "right" answer is to your problem.  But I 
can make some observations and some suggestions.

  * Your data range is really short.  As you seem to have noticed 
(judging from the very short k-range in your project file), your data 
has serious systematic problems starting at 9 or 10 inverse Angstroms. 
I cannot quite tell, but your data appear to be transmission data.  Well 
it is possible that you have some instability or nonlinearity at the 
beamline, I would guess that your sample is not very homogeneous.  It is 
possible that more disciplined sample preparation might help extend that 
range of the interpretable data.

  * You are right that slightly increasing the Rbkg value seems to make 
a positive difference in the extracted chi(k) data.  Your data seem to 
be an example of the sort of data I was alluding to yesterday.  The 
background subtraction is difficult because it is difficult to 
distinguish the Fourier components of the background function from the 
Fourier components of the data.  I think that the background subtraction 
with Rbkg=1.1 looks much better than with Rbkg=1.0, but given how 
different they are, you have to be concerned about the correlations 
between the background and the parameters of the data.

It is clear that your data are of the sort for which background 
subtraction is difficult.  So how do you know what is an acceptable 
background subtraction?

Well, using only Fourier methods, I think we have demonstrated that you 
cannot know the right answer without some kind of prior knowledge.

So, how do you get that prior knowledge?

Well, my advice is to first solve some simpler problems.  Measure your 

Measure the common forms of moly oxide and moly sulfide.  Measure moly 
metal.  Analyze all of them.  The advantage of the standards is that you 
know what the answer should be.  Do the data processing and data 
analysis.  Make sure that, when you do the analysis, you get the right 

Having done that exercise, you will then have a lot more knowledge about 
what the various forms of moly oxide look like and what the challenges 
are when doing the data processing and data analysis.

Some questions:

   - Are there any forms of moly oxide for which the bond length is as 
short as 1.6?  If so, do the conditions of formation exist in your 
system?  Is your sample of a valence consistent with the valence of the 
Mo when it has such a short bond?

  - If you convince yourself that it is possible for moly to have an 
oxygen atom at 1.6 or 1.7, what did you have to do with your standard to 
get a sensible analysis of the EXAFS data?  Hopefully, that will guide 
you to doing a sensible analysis of your unknown sample.

  - If none of your moly oxide standards have an O atom at 1.6 or 1.7, 
why do you think it is chemically reasonable for your unknown sample to 
have such a short bond?  If, in fact, that short bond doesn't exist 
elsewhere in nature, why would your sample magically have such a short bond?

  - If you do not believe in such a short bond, then does your 
experience with the standards give you the confidence to increase Rbkg 
such that the low-R signal is removed by the background function?

I completely understand that you have a compelling reason to understand 
your unknown sample and that I am suggesting that you spend a good chunk 
of time measuring and analyzing a bunch of standards that are not your 
actual research project.  That might seem like time that takes you away 
from your real goal, but you have already demonstrated that you are 
stumped by your real goal.  I am saying the only way to get over your 
current hurdle is to take a step back and gain a deeper understanding of 
the data, the physics of EXAFS, the methods of EXAFS analysis, and the 
intricacies of your current problem.



  Bruce Ravel  ------------------------------------ bravel <at> bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
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Katherine M. Davis | 10 Nov 15:34 2014

installing Demeter on Yosemite

Dear all,

I was wondering whether anyone had tried installing the software on the new Mac OS (10.10 Yosemite)? Everything seems to work fine initially. I installed Macports and checked it installed correctly. At least when I test various commands, it seems to work. The sudo port install xorg-server demeter-devel command ran for about 3 hours until it quit. I tried restarting, but whenever I run the command, the following error message appears:

--->  Computing dependencies for xorg-server

--->  Cleaning xorg-server

--->  Computing dependencies for demeter-devel

--->  Configuring demeter-devel

Error: org.macports.configure for port demeter-devel returned: configure failure: command execution failed

Please see the log file for port demeter-devel for details:


To report a bug, follow the instructions in the guide:


Error: Processing of port demeter-devel failed

I will post the log file at the bottom of the email. The last 8 lines are as follows:

:debug:clean No need to upgrade! p5.16-term-twiddle 2.730.0_1 >= p5.16-term-twiddle 2.730.0_1
:debug:clean epoch: in tree: 0 installed: 0
:debug:clean p5.16-text-template 1.460.0_1 exists in the ports tree
:debug:clean p5.16-text-template 1.460.0_1  is the latest installed
:debug:clean p5.16-text-template 1.460.0_1  is active
:debug:clean Merging existing variants '' int 

Would anyone be able to help me with this? Any advice would be useful. Thanks for your time.

Kate Davis

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