May 2010 - Ifeffit - millenia.cars.aps.anl.gov

update error in Windows 7
by pkraal＠geo.uu.nl 21 May '10

21 May '10

Dear sir or madam, I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution? Regards and many thanks, Peter Kraal.

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fitting
by mohamed sobhy 20 May '10

20 May '10

Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks

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question about E0
by Janeth Lozano 20 May '10

20 May '10

Hi everybody, My question is about the E0, i am making fits where the E0 final is some high, around 8eV, i tried to change the feff calculation with the card EXCHANGE to lower the E0 but it did not work, after the fit i obtained the same E0 around 8 eV, what can i do to improve the E0 around 5 eV, any suggestion? Distance and sigmas are reasonable but my E0 not at all Thanks Janeth Lozano PhD Student mlozano(a)mda.cinvestav.mx

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small screens and my software
by Bruce Ravel 17 May '10

17 May '10

Hi all, Today I received a very common question. An Athena user had just purchased a new laptop and Athena did not display properly on the small screen. When reading in a file, the "OK" button on the column selection dialog was off the bottom of the screen. This question comes up with enough regularity that I wrote a FAQ entry about how to work around this problem. See question 14 at http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions Regards, B -- Bruce Ravel ------------------------------------ bravel(a)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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Sample Charging
by Pralay K. Santra 15 May '10

15 May '10

Hi, I am performing EXAFS experiments on semiconductor nanoparticles. As these samples are highly insulating, they will be charged under the X-ray radiation. Does this charging effect the EXAFS signal (transmission as well as the fluorescence)? If yes, how can one can remove this charging effect? Will it be good enough to mix the sample with graphite and perform the EXAFS? With regards, Pralay. -- Research Student Prof D. D. Sarma's Group (http://sscu.iisc.ernet.in/DDSarma) Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560 012 INDIA Ph No: +91 80 2293 2336 (Extn: 2052) Fax No: +91 80 2360 1310 Mob No: +91 9845123219

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Re: [Ifeffit] Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

---------- Forwarded message ---------- From: Ditty Dixon <ditty.dixon(a)gmail.com> Date: Fri, May 14, 2010 at 4:35 PM Subject: Re: Ifeffit Digest, Vol 87, Issue 18 To: ifeffit(a)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(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)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(a)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(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

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Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 18
by Ditty Dixon 14 May '10

14 May '10

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(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)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(a)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(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

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Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

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(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Differences between fluorescence and > transmission of the same sample > Message-ID: <201005051030.18579.bravel(a)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(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4 > Message-ID: <201005051039.14501.bravel(a)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(a)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(a)tigers.lsu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Differences between fluorescence and transmission > of the same sample > Message-ID: > <z2md94177571005050824k8abda3a0n708eaada202fdc6e(a)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 >

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fitting
by mohamed sobhy 14 May '10

14 May '10

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

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Debye model on Artemis
by Kleber Daum Machado 12 May '10

12 May '10

Hi Matt, Concerning the third cumulant, my problem is to use a particular model for it. Some articles (Frenkel and Rehr, PRB 48 (1993) 585; Araujo et al, PRB 74 (2006) 184102) show how to use the Einstein model on Artemis, since these articles show the expressions that should be defined for sigma^2(T) and C3(T) for this model in Artemis (eqs. 11 and 18 of Frenkel and eqs. 2 and 3 of Araujo). In fact, I have already tested them on my analysis, using the eins function for sigma^2 and defining the C3(T) expression given in those articles in Artemis. I'd like to test Debye model too, and my problem is to use Debye model for sigma^2(T) and C3(T). For sigma^2(T) Artemis has the debye function already predefined. I'd like to use/write an expression for C3(T) considering Debye model, but I didn't find anything about such expression on the literature. Kleber

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