[Ifeffit] Differences between fluorescence and transmission of the same sample
Ditty Dixon
ditty.dixon at gmail.com
Wed May 5 10:42:59 CDT 2010
Hello Andrew,
We have similar situation in our fuel cell in-situ measurements, our
membrane electrode assembly having a thickness approx 1mm is usually coated
with Pt/C on one side(Cathode), and PtRu/C(alloy) on the other side(anode).
We usually get a pronounced signal of the sample facing the fluorescence
detector. For eg in our case if the Anode is facing the fluorescence
detector we get a lower white line and a splitting in the FT which is
characteristic of the Pt/Ru alloy nanoparticles and the transmission signal
is completely different.
Best Wishes,
Ditty
On Wed, May 5, 2010 at 3:55 PM,
<ifeffit-request at millenia.cars.aps.anl.gov>wrote:
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> Today's Topics:
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> 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 at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4
> Message-ID: <C5C497A1-0207-4F6E-9167-3840543BC7E9 at 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 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/<http://cars9.uchicago.edu/%7Eravel/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
> > **************************************
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 May 2010 09:55:16 -0400
> From: Andrew Campos <acampo2 at tigers.lsu.edu>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Differences between fluorescence and transmission
> of the same sample
> Message-ID:
> <x2gd94177571005050655teffb1ea9xea56a0fdf31ba585 at 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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> ------------------------------
>
> _______________________________________________
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>
> End of Ifeffit Digest, Vol 87, Issue 5
> **************************************
>
--
Ditty Dixon
Institut für Materialwissenschaft
Technische Universität Darmstadt
Petersenstr. 23
64287 Darmstadt
Ph 00496151165498
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