[Ifeffit] Athena open data project but not shown the curve

Robert Gordon ragordon at alumni.sfu.ca
Thu Nov 5 11:50:13 CST 2015

Hi Carlos,

Please clarify somethings for me regarding your inquiry.
You have a structural model and you have data.
You calculated a FEFF simulation of your structural model.
You did not use the FEFFNNNN.dat files to try to fit the model to your data,
but instead just did a comparison of the simulated chi(k), presumably
with just some default settings in FEFF.inp in addition to your 
structural model.
Is that correct?

Generally, it is the fit to the data that gives one feedback on the validity
of the structural model (GIGO rules apply).

If you have a model, then you have a model coordination number and can use
a program (e.g. Artemis) to refine amplitude, distance, 
mean-square-relative displacement
and energy shift. Do you need explanations of what these parameters 

So, to address what you were wondering, I believe the answer is 
yes...you need to actually
do a fit, and the goal isn't to get the obtained spectrum to look like 
your simulation.
Data is sacred. The goal is find a model that best reproduces the data 
(within a confidence
level governed by the goodness of fit).


On 11/5/2015 7:06 AM, Carlos Triana Estupinan wrote:
> Dear
> Bruce
> I am doing calculation of EXFAS for a amorphous structure created by 
> molecular dynamics. I am using FEFE to obtain chi(k) and the file xmu, 
> however, when comparing with experimental data with the calculated 
> EXFAS I have the following problems.
> 1) The Fourier transform of the EXAFS calculated by FEFF has the same 
> shape that the experiment spectra, however it is higher in amplitude.
> 2) The calculated EXFAS by FEFF has the same oscillation in K-space, 
> but it does not match the oscillation in K (both of them are shifted 
> to each other).
> I am wondering if I need to do an extra correction to the calculated 
> EXAFS by FEFF in order to match the K-space and the amplitude in 
> R-sapace. Shall I change the energy shift or the Edge step to match 
> the experimental spectra. I so, how can I am sure about the obtained 
> spectra really correspond to my molecular dynamics simulation.
> Thanks for your help.
> Regards.
> 2015-11-03 13:42 GMT+01:00 Bruce Ravel <bravel at bnl.gov 
> <mailto:bravel at bnl.gov>>:
>     On 10/28/2015 08:44 PM, 百度知道用户 wrote:
>         Hi all,
>         I processed a series of data using IFEFFIT Athena, and saved
>         it as a
>         project. Later, when I opened the project in IFEFFIT Athena,
>         the plot
>         window did not show the curve. I tried to open the project in
>         Demeter
>         Athena, but  popuped "Can't call method "datatype" on an undefined
>         value". The data curve was also not shown. I want to know what
>         happened
>         to this? Are the data damaged? I am very thankful if this
>         problem can be
>         solved.
>     It is hard to address a problem like this without an actionable
>     bug report.  See
>     http://bruceravel.github.io/demeter/pods/bugs.pod.html
>     B
>     -- 
>      Bruce Ravel  ------------------------------------ bravel at bnl.gov
>     <mailto:bravel at bnl.gov>
>      National Institute of Standards and Technology
>      Synchrotron Science Group at NSLS-II
>      Building 535A
>      Upton NY, 11973
>      Homepage: http://bruceravel.github.io/home/
>      Software: https://github.com/bruceravel
>      Demeter: http://bruceravel.github.io/demeter/
>     _______________________________________________
>     Ifeffit mailing list
>     Ifeffit at millenia.cars.aps.anl.gov
>     <mailto:Ifeffit at millenia.cars.aps.anl.gov>
>     http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> -- 
> /Carlos Augusto Triana Estupiñan (C.A. Triana-E)
> Physicist
> M.Sc. In Physical Sciences-Research
> PhD Student-Research
> Ångströmlaboratoriet, Lägerhyddsv. 1
> Solid State physics
> Uppsala University, Box 534
> 751 21 Uppsala, Sweden
> Tel: +46 018 471 3144
> e-mail:carlos.triana at angstrom.uu.se 
> <mailto:e-mail%3Acarlos.triana at angstrom.uu.se>
> web:http://www.uu.se//
> // //
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