[Ifeffit] Ifeffit Digest, Vol 87, Issue 4

Wed May 5 06:56:47 CDT 2010

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 at millenia.cars.aps.anl.gov  
wrote:

> Send Ifeffit mailing list submissions to
> 	ifeffit at millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
> 	ifeffit-request at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> 	ifeffit-owner at millenia.cars.aps.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 3 May 2010 20:47:02 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] fitting simultaneously two different K-edges
> Message-ID:
> 	<p2tb8522e3d1005031847g176e6685k2c078e39a247135b at mail.gmail.com>
> 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 <elena.montero at cimav.edu.mx>:
>> 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
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 4 May 2010 12:09:33 +0100
> From: Enzo Liotti <E.Liotti at lboro.ac.uk>
> To: "ifeffit at millenia.cars.aps.anl.gov"
> 	<ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] S02 parameter
> Message-ID:
> 	<225D20E4A8281F4E9DCFE465D9B75D0B102BCF75D3 at 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
>
> ------------------------------
>
> Message: 3
> Date: Tue, 4 May 2010 09:09:31 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] S02 parameter
> Message-ID: <201005040909.31674.bravel at 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 at 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/
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 4 May 2010 10:17:35 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] expected network outage to
> 	millenia.cars.aps.anl.gov
> Message-ID:
> 	<o2lb8522e3d1005040817nfe57bac2m5f1955ed35fc3356 at mail.gmail.com>
> 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
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 87, Issue 4
> **************************************