Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4

Dear IFEFFIT researchers, My problem is similar; I am trying to simulate a doped crystal (different than chp 10 in Atemis doc, this time impurity atom is subjected to XAS) and the host is similar to inverse-spinel type: include both tetrahedral and octahedral sites in its structure. The dopant may settle in tetrahedral or octahedral sites. 1- I managed to simulate the doped structure as changing the FEFF inp file manually (first I run Atoms as if impurity ions settle in all sites and then keep it in 0 potential and change the 1st potential with the original atom) and did it for both sites, thus i have 2 batch of paths and then fit it. It seems it works (Question: Do you think what i am doing is logical? or any other suggestion? ) 2- But problems do not end :) Another problem is impurity ion may take different valences: it can be trivalent or divalent. In FEFF 9.0 i found kinda solution using ION command, it doesnt do what i exactly want but i can get some idea on what happens if the charge distribution changes. But unfortunately, i cant try it in ARTEMIS since i can not install FEFF 9.0 in ARTEMIS. As far as i understood the program structure is changed completely. But I didnt give up :)I generated the chi file in FEFF 9.0 and load it in ARTEMIS and continue to analyze but the results are not promising. (Question: Is there any way to run it together? and any suggestion in changing the valance? ) 3-Final problem "The concentration of the dopant in the structure". I tried to change the occupancy, there is no option in "feff inp" but just SO2 parameter, i changed the SO2 parameters as suggested in previous mail, although I can not guess the SO2 parameter changing with the occupancy. The results are not satisfactory, initial trial with just one octa & one tetra configuration seems more logical. Again i didnt give up; I generated another crude solution: there are 30 sites in unit cell and %10 concentration means doping in 3 sites, so i generated 2 octa 1 tetra batch of paths(and vice versa) and tried to merge&fit it. But still no success and then i gave up !! (Question: Any help?? ) 4- Extra problem regarding FEFF 9.0. I change the paths dat file manually and unclick the paths box and give arbitrary feff inp file. I thought it has a modular structure and all modules read the previous file as an input, so whatever i give as a feff inp the final graph is the result of paths.dat is my assumption right? Thanks in advance for your help Regards, baran On May 4, 2010, at 8:00 PM, ifeffit-request@millenia.cars.aps.anl.gov wrote:

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Today's Topics:

1. Re: fitting simultaneously two different K-edges (Matt Newville) 2. S02 parameter (Enzo Liotti) 3. Re: S02 parameter (Bruce Ravel) 4. expected network outage to millenia.cars.aps.anl.gov (Matt Newville)

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Message: 1 Date: Mon, 3 May 2010 20:47:02 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting simultaneously two different K-edges Message-ID: Content-Type: text/plain; charset=UTF-8

Dear Maria,

If you haven't already done so, I would suggest that you begin by separately fitting the data for each edge on each sample. This will give you a good understanding of the local structure around each metal ion. Once you have this intimacy with the structural models, you will be able to tell what might be constrained between the two different metal atoms. Once you get to that point, getting the software to combine the fits will not seem very hard ;).

--Matt

2010/5/1 Mar?a Elena Montero Cabrera :

...

Dear friends, Sam Webb, Bruce Ravel or any other,

I have XAFS measurements, performed at SSRL at room temperature, of three compounds. All compounds have multielemental character and I have K- edge XAFS of two elements in each compound. It is desirable to make IFEFFIT fitting of both edges simultaneously. In all cases random solution of competing elements is assumed, but there are ferroelectricity, superconductivity or magnetic behaviors that are desirable to be explained. In each case, XAFS would confirm or reject the random character of the solution. I am not such an expert for resolving by myself how to fit together two edges using Artemis software. I'll present each case in the following:

1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+? compounds series was studied in both Ru and Nb K-edges. Changes in interatomic distances that could be obtained by EXAFS would tell something about oxygen octahedra around Ru and Nb.

2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated by XAFS in both Fe and Cr K-edges. Possible distortion of oxygen octahedra around both Fe(III) and Cr(III) cations would tell something about not confirmed ferroelectricity.

3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was studied by its Fe and Ti K-edges. Interatomic distances that could be obtained by EXAFS are interesting for checking possible preferential occupation of sites by Fe or Ti atoms.

Would any of you, please, suggest how to use Artemis or Sixpack for solving these problems?

Sincerely yours

-- Mar?a Elena

Dra. Mar?a Elena Montero Cabrera Departamento de Medio Ambiente y Energ?a Centro de Investigaci?n en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. M?xico Tel (614) 4391123

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Message: 2 Date: Tue, 4 May 2010 12:09:33 +0100 From: Enzo Liotti To: "ifeffit@millenia.cars.aps.anl.gov" Subject: [Ifeffit] S02 parameter Message-ID: <225D20E4A8281F4E9DCFE465D9B75D0B102BCF75D3@STAFFMBX-1.lunet.lboro.ac.uk

...

Content-Type: text/plain; charset="us-ascii"

Hello,

I'm trying to use EXAFS to study the intermetallics present in a complex Al alloy. The three main phases present in the alloy are Al3Ti, Al13Cr2 and Al13Fe4. The first is tetragonal and the other two are monoclinic.

To create the theoretical model in Artemis I inserted in Atoms the crystallographic informations available in literature and I run it and FEFF. Since in the monoclinic structure the absorbing atom occupies more than one position I created as many FEFF calculations as the number of positions of the Absorbing atom changing every time the core atom in the Atoms page.

My question now regards the S02 parameter (path amplitude), how do I model it when I've got more than one FEFF calculation for a single compound? and how do I do when I have more than one compound with more than one FEFF calculation each ones (for example if I have a mixture of two similar intermetallics like Al3Ti and Al11Ti5 )?

Best regards

Enzo

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Message: 3 Date: Tue, 4 May 2010 09:09:31 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] S02 parameter Message-ID: <201005040909.31674.bravel@bnl.gov> Content-Type: Text/Plain; charset="iso-8859-1"

On Tuesday 04 May 2010 07:09:33 am Enzo Liotti wrote:

...

Hello,

I'm trying to use EXAFS to study the intermetallics present in a complex Al alloy. The three main phases present in the alloy are Al3Ti, Al13Cr2 and Al13Fe4. The first is tetragonal and the other two are monoclinic.

To create the theoretical model in Artemis I inserted in Atoms the crystallographic informations available in literature and I run it and FEFF. Since in the monoclinic structure the absorbing atom occupies more than one position I created as many FEFF calculations as the number of positions of the Absorbing atom changing every time the core atom in the Atoms page.

My question now regards the S02 parameter (path amplitude), how do I model it when I've got more than one FEFF calculation for a single compound? and how do I do when I have more than one compound with more than one FEFF calculation each ones (for example if I have a mixture of two similar intermetallics like Al3Ti and Al11Ti5 )?

As a purely practical matter (without any consideration of physics or of how the theory works), there are two options. You either make them all the same or you don't make them all the same.

That's not a very profound answer, I admit, but if you start to scratch the surface, you'll eventually find a way to think about this sort of question.

In purely statistical terms, you are asking whether or not to add more parameters. In this case, as in every case, that is a simple enough thing to test. Try making a fit with all S02 parameters the same, then try making a fit with two or more being different. If the fit is improved in the sense of the reduced chi-square being significantly smaller, then you may have improved the quality of the fit. Another way to state this question is: "Do the data support the evaluation of more than one such parameter?" A question of the "do the data support support" variety is always easy to answer -- you just try it and see.

Of course, these are not arbitrary parameters -- they have specific meaning. In the case of S02, this parameter is a measure of the non-unity overlap of the electronic states of the absorbing atom before and after the creation of the core-hole. That is, it is somehow a measure of the relaxation of the electrons in the presence of the core hole. As such, we expect S02 to be a number around, but smaller than, 1.

However, there are a lot of things that effect the amplitude in an EXAFS analysis. Problems with the sample, with the linearity of the detectors, with the processing of the data, or even with the theory can all contribute to the evaluation of the EXAFS amplitude. All those effects are difficult or impossible to distinguish from the physical S02 in a statistical sense. Thus, your measure of S02 in EXAFS analysis includes the effect of relaxation in the presence of a core-hole, but it also includes all those others issues that may or may not exist in your data.

For many years, the concept of "chemical transferability" has been currency in the EXAFS community. That is, we presume that for properly created and measured samples of the same absorber and edge, the S02 value for one such sample can be used in teh analysis of another. Stated another way, S02 is a property of the species of the absorber. Some years ago, Frank Bridges and his group published such a survey. Recent work from John Rehr's group has elaborated on this, demonstrating that S02 is, in the strictest sense, neither transferable nor constant in energy. However, these effects are small such that chemical transferability remains a useful and defensible practice in many EXAFS analyses.

So, back to your question -- how do you deal with S02 in a mixed compound or in a compound with multiple crystallographic sites? Or, more generally, how do you deal with S02 when you have to run Feff more than once to perform a single fit?

Well ... you either make them all the same or you don't make them all the same.

Regardless of how you proceed, you need to verify that your choice is statistically defensible. More importantly, if you introduce more than one such parameter, you need to be able justify that decision in terms of the physics or chemistry. In the case of a mixed compound, you need to be able to explain why the amplitudes for the species in the mixture should be different. If you have no such physical or chemical explanation, then you have to ask yourself if the parameter you added was not just a "fudge factor" that made the fit better numerically without adding meaning to your results.

Fortunately, Artemis makes it relatively easy to tie parameter values together and to allow them to float separately. (Pro tip: Use def parameters.)

As a general practice, I would start with a single S02 and see how the fit goes. If it goes well, I might declare victory and move on. If it goes poorly, I might consider introducing other S02 parameters, taking care that I can defend the choice statistically and physically.

HTH, B

--

Bruce Ravel ------------------------------------ bravel@bnl.gov

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

My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Message: 4 Date: Tue, 4 May 2010 10:17:35 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: [Ifeffit] expected network outage to millenia.cars.aps.anl.gov Message-ID: Content-Type: text/plain; charset=ISO-8859-1

Hi Folks,

The APS networking people will be doing some hardware work next week which means that millenia.cars.aps.anl.gov will be inaccessible to the outside world May 10,11,12, and 17. Because of this, xafs.org, the Ifeffit wiki, and this mailing list will all appear to be down on these days.

--Matt

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End of Ifeffit Digest, Vol 87, Issue 4 **************************************