On Wed, May 5, 2010 at 3:55 PM,
<ifeffit-request@millenia.cars.aps.anl.gov> wrote:
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Today's Topics:
1. Re: Ifeffit Digest, Vol 87, Issue 4 (baran yildirim)
2. Differences between fluorescence and transmission of the same
sample (Andrew Campos)
----------------------------------------------------------------------
Message: 1
Date: Wed, 5 May 2010 14:56:47 +0300
From: baran yildirim <yildirimbaran@gmail.com>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4
Message-ID: <C5C497A1-0207-4F6E-9167-3840543BC7E9@gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
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:
> Send Ifeffit mailing list submissions to
> ifeffit@millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
> ifeffit-request@millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner@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@cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] fitting simultaneously two different K-edges
> Message-ID:
> <p2tb8522e3d1005031847g176e6685k2c078e39a247135b@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@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@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@lboro.ac.uk>
> To: "ifeffit@millenia.cars.aps.anl.gov"
> <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
>
> ------------------------------
>
> Message: 3
> Date: Tue, 4 May 2010 09:09:31 -0400
> From: Bruce Ravel <bravel@bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> 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/
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 4 May 2010 10:17:35 -0500
> From: Matt Newville <newville@cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] expected network outage to
> millenia.cars.aps.anl.gov
> Message-ID:
> <o2lb8522e3d1005040817nfe57bac2m5f1955ed35fc3356@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@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 87, Issue 4
> **************************************
------------------------------
Message: 2
Date: Wed, 5 May 2010 09:55:16 -0400
From: Andrew Campos <acampo2@tigers.lsu.edu>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Differences between fluorescence and transmission
of the same sample
Message-ID:
<x2gd94177571005050655teffb1ea9xea56a0fdf31ba585@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone,
My lab mates are running in-situ H2 reduction of Cobalt/SiO2 catalysts
using the Co K-edge and are obtaining differences between the
fluorescence and transmission signals. The in-situ cell does have
quite a bit of sample thickness (2-3 mm approx) and I was wondering if
the fluorescence signal only has a penetration depth of a few
micrometers. If this is the case that would explain it where the side
that is further away from the heating element is more oxidized than
the rest of the sample.
Has anyone run into this problem before? We're using the basic
furnace/cryostat unit (in-situ cell manufactured by the exafsco) and a
13 element fluorescence detector (germanium diode).
I appreciate any insight into the issue, I have attached a
fluorescence and transmission spectrum collected at the same time
where the transmission and fluorescence are in the .prj file.
Thanks so much!
Andrew
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