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

Thu Nov 5 12:31:40 CST 2015

Hello
ROBERT

Thanks for your kind answer
I have an amorphous structure with 216 atoms, 72 of them are absorbing
atoms. So, I did FEFF calculation for each of those absorber to get
individual EXAFS, and then I dis an average of them to get an averaged
EXAFS (total EXAFS).
I don't want to refine a structural model, but I want to compare the
experimental EXAFS data with the averaged EXAFS I got for my model.

My question is, if I get the EXAFS just from FEFF calculation (chi(k) or
xmu.dat), then I can import it to artemis, and compare with the
experimental (but without do any fiting), just to compare EXAFSs. From FEFF
I can obtain chi(k), u, u0, and X as a function of energy. Which of those
(chi(k), u, u0, and X) should I compare with the experimental data.

Also, if I compare mi experimental EXAFS with other EXAFS spectra already
published in papers, should be the EXAFS the same or it depends on the
range for the fourier transform.

regards.

2015-11-05 18:50 GMT+01:00 Robert Gordon <ragordon at alumni.sfu.ca>:

> 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
> represent?
>
> 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).
>
> regards,
> Robert
>
>
> 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>:
>
>> 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>
>> 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
>> 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
> <e-mail%3Acarlos.triana at angstrom.uu.se> web:http://www.uu.se/
> <http://www.uu.se/>*
>
>
> _______________________________________________
> Ifeffit mailing listIfeffit at millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
> _______________________________________________
> Ifeffit mailing list
> 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
<e-mail%3Acarlos.triana at angstrom.uu.se> web:http://www.uu.se/
<http://www.uu.se/>*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151105/740d8929/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 27872 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151105/740d8929/attachment.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 80677 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151105/740d8929/attachment-0001.jpe>