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 mailto:bravel@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@bnl.gov mailto:bravel@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@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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/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@angstrom.uu.se mailto:e-mail%3Acarlos.triana@angstrom.uu.se web:http://www.uu.se//

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Hi Carlos, My previous exposure to MD for EXAFS was as part of a collaboration here: J. Synchrotron Rad. (2013). 20, 555–566 There, to get estimates of energy shift and amplitude (So^2), a simplified model was used to fit the experimental data. In your case, that could be done by performing a FEFF calculation for an atom best representing the average. The FEFF calculation won't include deviations in Eo or So^2 or even temperature effects by default. DEBYE, s02 (or HOLE or EDGE), and CORRECTIONS cards could be used in generating the FEFF chi.dat. If your MD simulation gives you N, R and sig^2 for each shell (and each atom) you wish to include in your comparison, then you can implement the Eo-shift and amplitude values from the simplified fit in each shell of a simulation (using the FEFFNNNN.dat files) up to whatever shell you have the energy to try to include in the simulation...I would suggest starting with the first shell and include the second once you get a good agreement with the first. There may still be deviations in peak position between experiment and calculation. That can be considered by examination of a known standard. You should consider the same k-space ranges for experiment and theory when comparing your own results...comparison itself would be done in R-space, particularly if only using a few shells. For comparison with the results of others, it would depend on available data ranges and quality as to how to proceed. e.g. If I analyse 3 to 18 A-1 and want to compare to someone else who analysed 3 to 10 A-1 due to their data limits, then I should also look at my results over their range to give a fair comparison. If the reverse situation is present, then the comparison is only within the limits of available data. regards, Robert On 11/5/2015 10:31 AM, Carlos Triana Estupinan wrote:

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 mailto:ragordon@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.