[Ifeffit] Differences between fluorescence and transmission of the same sample
Shelly Kelly
dr.sdkelly at gmail.com
Fri May 14 11:37:43 CDT 2010
Hi Ditty,
I don't know a lot about fuel cells, but It seems that grazing
incident x-ray absorption spectra might be helpful. This technique
has a small penetration depth into the sample, but needs a larger
surface foot print for the beam to come in at a shallow angle.
Shelly
On Fri, May 14, 2010 at 9:40 AM, Ditty Dixon <ditty.dixon at gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: Ditty Dixon <ditty.dixon at gmail.com>
> Date: Fri, May 14, 2010 at 4:35 PM
> Subject: Re: Ifeffit Digest, Vol 87, Issue 18
> To: ifeffit at millenia.cars.aps.anl.gov
>
>
> Hello Carlo,
>
> Thank you so much.
>
> We already tried with other catalyst like RuSe and CoSe. What was more
> exiting for me was the similarity between the data for anode pellet, cathode
> removed, and fluo data(attachment).
>
> Actually we want to generate exact conditions in a Direct Methanol fuel cell
> (methanol crossover and starvation), so we still like to keep both pt system
> there.
>
> Thank you once again,
>
> Ditty
>
>
>
> On Fri, May 14, 2010 at 3:09 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 (Iztok Ar?on)
>> 2. Re: Differences between fluorescence and transmission of the
>> same sample (Carlo Segre)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 14 May 2010 08:59:20 +0200
>> From: Iztok Ar?on <iztok.arcon at ung.si>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] fitting
>> Message-ID: <4BECF4C8.2090302 at ung.si>
>> Content-Type: text/plain; charset="iso-8859-2"; Format="flowed"
>>
>> Dear Mohamed,
>>
>> There is an example of CeO2 EXAFS analysis, taking into account
>> background problems,
>> in the following paper:
>> *J. Pade?nik Gomil?ek, I. Kozjek-?kofic, N. Bukovec, A. Kodre
>> */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films
>> obtained by sol-gel deposition. /*
>> *Thin solid films, vol. 446, issue 1, (2004) 117-123.
>> regards
>> Iztok Arcon
>>
>> mohamed sobhy wrote:
>>
>> > Dear all
>> > I am trying to use artemis to do fitting to CeO2. But really I cant
>> > get the right way to do that.
>> > During the fitting, I am using amp as set and change in N degeneracy
>> > of the path. attached is the best fit i got but it still not good and
>> > the chi-square is 41.109065479
>> > so can you suggest me what to do
>> >
>> > thanks
>> >
>> > Mohamed
>> >
>> >
>> >------------------------------------------------------------------------
>> >
>> >_______________________________________________
>> >Ifeffit mailing list
>> >Ifeffit at millenia.cars.aps.anl.gov
>> >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> >
>> >
>>
>>
>> --
>> Iztok Arcon
>> University of Nova Gorica
>> Vipavska 13, POB 301
>> 5001 Nova Gorica, Slovenia
>>
>> tel: +386 5 331 5227
>> fax: +386 5 331 5240
>> e-mail: iztok.arcon at ung.si
>> http://www.ung.si/~arcon
>> http://www.ung.si/~arcon/xas
>>
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 14 May 2010 08:09:47 -0500 (CDT)
>> From: Carlo Segre <segre at iit.edu>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Subject: Re: [Ifeffit] Differences between fluorescence and
>> transmission of the same sample
>> Message-ID: <alpine.DEB.2.00.1005140759280.2689 at hydride.iit.edu>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>>
>> Hello Ditty:
>>
>> The problem you have can be solved by not using platinum on both sides.
>> in our group, we just use Pd on the side we are not interested in for a
>> particular experiment, be it anode [0-2] or cathode[3]. As for the
>> qustion about the difference in the two sides in fluorescence mode. It is
>> likely that there is a difference but given that the MEA probably uses a
>> polymer such as nafion means that it is realativley transparent to
>> fluorescence at the Pt L-alpha energy. This means that you have both
>> sides present in the fluorescence, just to different degrees. i am sure
>> that it is possible to get some kind of notion of the difference using
>> such a mixed signal but I don't think you can really do much quantitative
>> analysis. If you add the fact that the "back" side fluorescence is
>> screened differently than the "front" side because of flow channel
>> geometry and other such obstacles, it becomes a very difficult problem.
>> The question you need to ask yourself is whether it is absolutely
>> necessary to have Pt on both electrodes or whether you can draw the
>> conclusions you want by using a less ideal electrode material on the sid
>> you are not studying. This is the approach we have taken.
>>
>> Cheers,
>>
>> Carlo
>>
>>
>> [0] R. Viswanathan, G. Hou, R. Liu, S.R. Bare, F. Modica, G. Mickelson,
>> C.U. Segre, N.E. Leyarovska, T. Chikyow and E.S. Smotkin, J. Phys. Chem. B
>> 106, 3458 (2002).
>>
>> [1] S. Stoupin, E-H. Chung, S. Chattopadhyay, C.U. Segre and E.S. Smotkin,
>> J. Phys. Chem. B 110, 9932 (2006).
>>
>> [2] S. Stoupin, H. Rivera, Z. Li, C.U. Segre, C. Korzeniewski, D.J.
>> Casadonte, H. Inoue and E.S. Smotkin, Phys. Chem. Chem. Phys. 10,
>> 6430-6437 (2008).
>>
>> [3] Q. Jia, E.A. Lewis, E.S. Smotkin, and C.U. Segre, J. Phys. Conf.
>> Series 190, 012157 (2009)
>>
>> On Fri, 14 May 2010, Ditty Dixon wrote:
>>
>> > Hello ifeffit users,
>> >
>> > I am working in the area of In-situ XAS analysis of Fuel cell catalyst.
>> > The
>> > heart of the fuel cell, MEA(membrane electrode assembly) consist of
>> > nafion
>> > membrane and the catalyst sprayed on both sides which act as Cathode and
>> > Anode(the whole max thickness 1mm). I have a system where Platinum is a
>> > common metal catalyst for both anode and cathode, with anode made of
>> > alloy
>> > of Pt and Ru(nano) ,and Cathode pure Pt(both 2mg/cm2 metal loading).
>> >
>> > An In-situ transmission XAS measurements on such a system gives no
>> > information as the transmission signal will contain both Pt signal from
>> > anode and cathode and two different process taking place oxidation and
>> > reduction. So we deal with the situation by removing the catalyst from
>> > one
>> > side.
>> >
>> > But when we did our measurements in fluorescence(without removing any
>> > catalyst) we got two different signals when we turned the cell 180
>> > degree.
>> > If the anode was facing the fluo detector we got characteristic signal
>> > for
>> > Pt/Ru alloy(dampening in FT) and when cathode was facing, that of pure
>> > Pt.
>> > Is this a solution to separate the signals from anode and cathode
>> > without
>> > removing any catalyst?. I have attached the file for the fluorescence
>> > measurements for my MEA.
>> >
>> > Thanks in Advance,
>> >
>> > Ditty
>> >
>> >
>> >
>> > On Wed, May 5, 2010 at 5:43 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: Differences between fluorescence and transmission of the
>> >> same sample (Bruce Ravel)
>> >> 2. Re: Ifeffit Digest, Vol 87, Issue 4 (Bruce Ravel)
>> >> 3. Differences between fluorescence and transmission of the same
>> >> sample (Andrew Campos)
>> >> 4. Re: Differences between fluorescence and transmission of the
>> >> same sample (Ditty Dixon)
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Wed, 5 May 2010 10:30:18 -0400
>> >> From: Bruce Ravel <bravel at bnl.gov>
>> >> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> >> Subject: Re: [Ifeffit] Differences between fluorescence and
>> >> transmission of the same sample
>> >> Message-ID: <201005051030.18579.bravel at bnl.gov>
>> >> Content-Type: Text/Plain; charset="iso-8859-15"
>> >>
>> >> Andrew,
>> >>
>> >> I suspect that you are seeing what Grant refers to in his tutorials as
>> >> "leakage". That is, your transmission data appears to my eye to be
>> >> what happens when you have a wide spread in sample thickness under the
>> >> beam, ranging from gaps to very thick particles.
>> >>
>> >> If you go to
>> >>
>> >> http://gbxafs.iit.edu/training/tutorials.html
>> >>
>> >> And follow the link to the "Sample preparation" presentation, the
>> >> effect of leakage is shown on slide 16.
>> >>
>> >> On the following slide, Grant points out that this thickness effect
>> >> always reduces amplitudes. That is the case above the edge for your
>> >> data. And if you normalize data distorted in that way, you end up
>> >> with an artificially enhanced pre-edge peak, again as in your data.
>> >>
>> >> My US$0.02,
>> >> B
>> >>
>> >>
>> >> On Wednesday 05 May 2010 09:55:16 am Andrew Campos wrote:
>> >>> 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
>> >>>
>> >>
>> >> --
>> >>
>> >> 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: 2
>> >> Date: Wed, 5 May 2010 10:39:14 -0400
>> >> From: Bruce Ravel <bravel at bnl.gov>
>> >> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> >> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4
>> >> Message-ID: <201005051039.14501.bravel at bnl.gov>
>> >> Content-Type: Text/Plain; charset="iso-8859-1"
>> >>
>> >> On Wednesday 05 May 2010 07:56:47 am baran yildirim wrote:
>> >>> 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.
>> >>
>> >> Indeed. Similar enough that you also should read the paper by Scott
>> >> Calvin that I suggested to Maria Elena.
>> >>
>> >>> 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? )
>> >>
>> >> I think that's a good approach.
>> >>
>> >> Question 15 at
>> >>
>> >> http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling
>> >>
>> >> gives a bit more information. The link to the page authored by Scott
>> >> is quite useful.
>> >>
>> >>
>> >>> 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? )
>> >>
>> >> Artemis does not support Feff9 at this time.
>> >>
>> >> I actually have not played around with Feff9 yet, myself, so I won't
>> >> be able to help with the rest. Perhaps one of the Seattlites can help
>> >> ....
>> >>
>> >> 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: 3
>> >> Date: Wed, 5 May 2010 11:24:16 -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:
>> >> <z2md94177571005050824k8abda3a0n708eaada202fdc6e at mail.gmail.com>
>> >> Content-Type: text/plain; charset="iso-8859-1"
>> >>
>> >> Dr. Ravel,
>> >>
>> >> Thanks so much for the link and the advice! I appreciate it greatly. I
>> >> will advise my lab mates as such and may have to only use the
>> >> fluorescence data if that is indeed the case.
>> >>
>> >> I also included the file where the lower temperature is included and
>> >> you might come to the same conclusion. The samples that I ran were
>> >> pre-sieved, and the ones included in the .prj file aren't so that
>> >> should be pursued prior to running the experiment. If they crush the
>> >> particle and sieve the sample, I think that we can be more certain
>> >> that this is not the case. This was very helpful!
>> >>
>> >> Andrew
>> >> -------------- next part --------------
>> >> A non-text attachment was scrubbed...
>> >> Name: Fluorescence and transmission.prj
>> >> Type: application/octet-stream
>> >> Size: 13112 bytes
>> >> Desc: not available
>> >> URL: <
>> >>
>> >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20100505/d4d81d96/attachment-0001.obj
>> >>>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 4
>> >> Date: Wed, 5 May 2010 17:42:59 +0200
>> >> From: Ditty Dixon <ditty.dixon at gmail.com>
>> >> To: ifeffit at millenia.cars.aps.anl.gov
>> >> Subject: Re: [Ifeffit] Differences between fluorescence and
>> >> transmission of the same sample
>> >> Message-ID:
>> >> <j2j6d89d2891005050842y193522e0i5deed33ab905627f at mail.gmail.com>
>> >> Content-Type: text/plain; charset="iso-8859-1"
>> >>
>> >> 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:
>> >>
>> >>> 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: 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/>
>> >> <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
>> >>> -------------- next part --------------
>> >>> A non-text attachment was scrubbed...
>> >>> Name: Fluorescence and transmission.prj
>> >>> Type: application/octet-stream
>> >>> Size: 7244 bytes
>> >>> Desc: not available
>> >>> URL: <
>> >>>
>> >>
>> >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20100505/bb37469e/attachment.obj
>> >>>>
>> >>>
>> >>> ------------------------------
>> >>>
>> >>> _______________________________________________
>> >>> 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 5
>> >>> **************************************
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> Ditty Dixon
>> >> Institut f?r Materialwissenschaft
>> >> Technische Universit?t Darmstadt
>> >> Petersenstr. 23
>> >> 64287 Darmstadt
>> >> Ph 00496151165498
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >> URL: <
>> >>
>> >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20100505/bee2d9dd/attachment.htm
>> >>>
>> >>
>> >> ------------------------------
>> >>
>> >> _______________________________________________
>> >> 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 6
>> >> **************************************
>> >>
>> >
>> >
>> >
>> >
>>
>> --
>> Carlo U. Segre -- Professor of Physics
>> Associate Dean for Graduate Admissions, Graduate College
>> Illinois Institute of Technology
>> Voice: 312.567.3498 Fax: 312.567.3494
>> segre at iit.edu http://www.iit.edu/~segre segre at debian.org
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 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 18
>> ***************************************
>
>
>
> --
> Ditty Dixon
> Institut für Materialwissenschaft
> Technische Universität Darmstadt
> Petersenstr. 23
> 64287 Darmstadt
> Ph 00496151165498
>
>
>
> --
> Ditty Dixon
> Institut für Materialwissenschaft
> Technische Universität Darmstadt
> Petersenstr. 23
> 64287 Darmstadt
> Ph 00496151165498
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
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