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

particle size and coordination number in Ru nanoparticles on carbon
by Dreher Marian 11 Oct '11

11 Oct '11

Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] lifetime broadening of pre-edge peaks?
by Joshua Kas 10 Oct '11

10 Oct '11

Hi Matthew, This may be a minor (and possibly different) point, but vibrational broadening can be different for different pre-edge peaks. See for example, Keith Gilmore and Eric L Shirley 2010 *J. Phys.: Condens. Matter* *22*315901. Cheers, Josh Kas On Mon, Oct 10, 2011 at 11:42 AM, <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: number of independent points (George Sterbinsky) > 2. Re: lifetime broadening of pre-edge peaks? (Matthew Marcus) > 3. Re: lifetime broadening of pre-edge peaks? (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Oct 2011 14:04:07 -0400 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] number of independent points > Message-ID: > <CALoY8YwBz3jLWTLX+dosjiXs6Fv3RpG_UfG2yEz-X3XVn17abg(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Bruce, Matt, and Jeremy, > > Thank you for explaining this. Your responses are much appreciated. > > George > > On Mon, Oct 10, 2011 at 11:35 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On Monday, October 10, 2011 10:35:12 am George Sterbinsky wrote: > > > Since I haven't received a response to my previous question, I just > > wanted > > > to make sure I asked it clearly. > > > > I suspect the lack of response had more to do with it being a > > non-trivial question asked on a Friday afternoon :) > > > > > To elaborate, I am attaching a log from > > > Athena. The log file lists: > > > > > > "Independent points = 27.057617188" > > > > > > If I attempt to reproduce this result using the equation in the feffit > > > document, I find > > > > > > Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2} = { [2*(14 - 0.5)*(4.2 > - > > > 1.0) / pi] + 2} = 29.50197417, > > > > > > where I have used the k-range and R-range in the log file as kmax, > kmin, > > > Rmax, and Rmin. > > > > > > Can someone explain to me why may calculation does not reproduce the > > number > > > given for "independent points" in the log fie? > > > > George, > > > > A quick examination of the ifeffit source code shows that there are > > two issues: > > > > 1. Regardless of what it may say in the document, Ifeffit uses "+0" > > rather than "+2". See line 345 of > > http://cars9.uchicago.edu/svn/ifeffit/trunk/src/lib/iff_feffit.f > > > > A bit of history: Ed Stern wrote this paper back in 1993: > > http://dx.doi.org/10.1103/PhysRevB.48.9825 > > > > Over the years, many have expressed scepticism of his conclusion. > > The Bayesian work I mentioned earlier suggests quibbling over the > > value of N in the "+N" term misses the bigger issue. Ifeffit's > > use of "+0" provides a conservative yet easily stated estimate of > > Nidp. > > > > 2. The difference to the left of the decimal point has to do with the > > fact that Artemis allows you to pick any value for kmin, kmax, > > rmin, and rmax. When Ifeffit evaluates Nidp (and anything else) > > is actually takes the nearest grid points to those four values. > > The grid in k-space is 0.05 inv. Angstroms. This sets the grid in > > R space to be about 0.03 Angstroms, but not exactly. So the > > values of Rmax and Rmin used by Ifeffit to compute Nidp (and other > > things) are not quite what you specified. > > > > At some point, George, you may want to bite the bullet and look at > > source code. Details are not unknowable, they just might not be > > written down anywhere beside the source code. > > > > Here is the top of Ifeffit: > > http://cars9.uchicago.edu/svn/ifeffit/trunk/ > > > > 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/ifeffit/Demeter > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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lifetime broadening of pre-edge peaks?
by Matthew Marcus 10 Oct '11

10 Oct '11

Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at the main edge? I'm looking into issues of de-noising of XANES epsctra, so need to figure out how narrow real features can be. mam

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number of independent points
by George Sterbinsky 10 Oct '11

10 Oct '11

Hello, I am wondering what values Artemis/feffit use for kmax and kmin when calculating the number of independent points (Nidp) for a fit done in R-space, where according the feffit document, Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I have tried using the Fourier transform range for kmax and kmin, but this does not give agreement with the value of Nidp reported by Artermis. Thank you, George

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Re: [Ifeffit] number of independent points
by Matt Newville 10 Oct '11

10 Oct '11

Of course. I do agree with both Jeremy and Bruce. -Matt On Oct 10, 2011 10:07 AM, "Bruce Ravel" <bravel(a)bnl.gov> wrote: > On Monday, October 10, 2011 10:48:25 am Kropf, Arthur Jeremy wrote: > > Perhaps there is a more subtle analysis of the data range, but I doubt > > it, since Matt is on record as suggesting that people not place too much > > emphasis on the exact value of N-idp, if I recall correctly. You can > > scale your chi-square, reduced chi-square, and errors using whatever > > value of N-idp you prefer. > > The papers by Rossner and Krappe (for instance, > http://dx.doi.org/10.1103/PhysRevB.66.184303) use a Bayesian approach > to evaluate the actual information content in an EXAFS signal. > Unsurprisingly, the Bayesian analysis finds something we should > already know -- the EXAFS signal is not an ideally packed sum of sine > waves. Consequently, the actual information content is rather less > than the Nyquist criterion. > > That is the context of the suggestion not to place to much emphasis on > the Nyquist number. (Since Jeremy invoked Matt, I should say that I > suspect that Matt would more or less agree with what I am saying > here.) It gives us a number to work with in evaluating the statistics > in Ifeffit. The interpretation of Ifeffit's statistical analysis > (which is a simple Gaussian analysis for a problem that is ill-posed > in the Guassian sense) has been a frequent topic of conversation on > this mailinglist over the years. It is also a topic in this talk that > I sometimes give: https://github.com/bruceravel/XAS- > Education/downloads/atea.pdf > > All that said, the question of the formula used and the value reported > in Artemis is a valid one. I don't recall off the top of my head, > but I will look at the codes. > > 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/ifeffit/Demeter > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Soham Mukherjee has invited you to open a Google mail account
by Soham Mukherjee 10 Oct '11

10 Oct '11

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 9
by Soham Mukherjee 10 Oct '11

10 Oct '11

For the first shell, I used cubic phase as my starting model and that gave a pretty good fit. However, when I take wurtzite phase as my starting model and vary two bond lengths (both Zn-S, with the axial bond longer by only 0.004 Ang) independently, my delr and ss go crazy. I think that as the first two S subshells are so close to each other, my data can't identify them (delr and ss) independently. So I defined their delr and ss to be same and the results match pretty well with the cubic phase. The r-factor and reduced-chi square with the two models are very similar.Thanks a lot ! On Sun, Oct 9, 2011 at 10:30 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. lifetime broadening of pre-edge peaks? (Matthew Marcus) > 2. Re: Zinc Sulfide fitting (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 08 Oct 2011 14:36:56 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] lifetime broadening of pre-edge peaks? > Message-ID: <4E90C278.3060602(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at > the main edge? I'm looking into issues of de-noising of XANES epsctra, so > need to figure out how narrow real features can be. > mam > > > ------------------------------ > > Message: 2 > Date: Sun, 9 Oct 2011 07:06:52 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Zinc Sulfide fitting > Message-ID: <BLU151-W2672826EC60532B7643F18DAFF0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > hello > > Two phase can be mixed in ZnS. You need to check r-factor and reduced-chi > squrare with two model. > If you want to fit only first shell, > I suggest. > first use cubic zinc-blende model in FEFF, and check goodness of fit. > second, fix the bond length of 3 bonding length and change the bond length > of a rest. > when you use my suggestion, the variables in Artemis is delrS1(changable), > sigmaS1(changable), others(fix) > > > > > Date: Thu, 6 Oct 2011 13:32:24 +0530 > From: soham.chem(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Zinc Sulfide fitting > > Dear Ifeffit Community, > > Zinc Sulfide exists largely in two phases, either the cubic zinc-blende > (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. > > The details of the NN distances are as follows :- > 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are > 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; > 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur > bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 > axially > elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 > Angstroms ! > > I am performing a first shell fit to Zinc Sulfide which exists in the > wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking > the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is > that since bond distances are higher in a hexagonal phase than the cubic > phase, I end up with a considerable delr as I underestimated my starting > bond length value. Taking a wurtzite model involves defining two different > bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in > the > FEFF, whose sigma^2 values are quite similar. This gives unusually large > delr values and high sigma^2 for the longer axial bond, which looks > suspicious ! > > Do I really need to define the two bond distances separately of so close > values? Or taking a cubic phase will be sufficient? Please find the > attached > project file (artemis.apj) where I have tried out some simulations with > both > cubic and hexagonal models. > > Here are a few details you asked for :- > > The sample is a thin layer, it's pretty homogeneous and had no pinholes > during measurements. The fit details are :- > k_min = 2, k_max = 14 > R_min = 1, R_max = 3 > The potential is self consistent in these calculations > Fitting was performed in the R-space > > Best regards, > Soham. > > _______________________________________________ Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Zinc Sulfide fitting
by grant bunker 09 Oct '11

09 Oct '11

Soham - I don't think you will be able to resolve the small (.0044) distance difference between one S and 3 others. That corresponds to a sigma squared of only 3.6*10^(-6). If you wanted to resolve them by going to higher k you would have to go out to k=pi/(.0088 A) ~ 357 inverse angstroms, which might be a bit of a challenge. More fundamentally the delr parameter that you float would be nearly 100% correlated with the sigma squared, if you are also floating that. The numerical instability associated with parameter correlation can be expected to give you crazy values for both delr and ss (and correspondingly large error bars), which I think you are getting. So the 4 S atoms are effectively at the same distance. It's to just treat them as a single shell of 4 S atoms and describe the mean and SS of that distribution. It's really all the data can tell you without bringing some other information into the fitting process. hope that helps Grant Bunker

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Zinc Sulfide fitting
by Soham Mukherjee 08 Oct '11

08 Oct '11

Dear Ifeffit Community, Zinc Sulfide exists largely in two phases, either the cubic zinc-blende (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. The details of the NN distances are as follows :- 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 axially elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 Angstroms ! I am performing a first shell fit to Zinc Sulfide which exists in the wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is that since bond distances are higher in a hexagonal phase than the cubic phase, I end up with a considerable delr as I underestimated my starting bond length value. Taking a wurtzite model involves defining two different bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in the FEFF, whose sigma^2 values are quite similar. This gives unusually large delr values and high sigma^2 for the longer axial bond, which looks suspicious ! Do I really need to define the two bond distances separately of so close values? Or taking a cubic phase will be sufficient? Please find the attached project file (artemis.apj) where I have tried out some simulations with both cubic and hexagonal models. Here are a few details you asked for :- The sample is a thin layer, it's pretty homogeneous and had no pinholes during measurements. The fit details are :- k_min = 2, k_max = 14 R_min = 1, R_max = 3 The potential is self consistent in these calculations Fitting was performed in the R-space Best regards, Soham.

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controlling valence state in FEFF9 XANES sims
by Matthew Marcus 07 Oct '11

07 Oct '11

I'm involved in a project involving mixed Fe-Cr oxides. There's some evidence that the presence of Fe2+ in these oxides causes distinctive features to appear in the XANES at the Cr K-edge. I would like to simulate this situation to see if a valence effect could really explain it. However, FEFF9 doesn't seem to have an obvious mechanism for controlling the valence of the atoms or even assuring charge neutrality of the cluster. For instance, as a test, I simulated goethite (FeO(OH)) with and without the H atoms and got almost the same result, even though charge balance works for FeO(OH) and not for FeO(O<nothing>). I know that there is the ION card, but it's not clear how to choose the value so as to get a given formal oxidation state or how to determine what charges are present on any atoms in the cluster. Any ideas out there? Also, I find that the XANES is best simulated if I make S02=0.7 or so. If S02=1, the features are too intense. mam

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d-band vacancies vs d-band center
by Qingying Jia 06 Oct '11

06 Oct '11

Hi All: I am wondering whether there is a specific correlation between d-band vacancies vs d-band center of Pt. We can acquire experimental d-band vacancies of Pt by XAFS from Pt LIII & LII XANES. I assume the downshift of d-band relative to Fermi level (lower d-band center) caused by for example alloying with the second metal will reduce the d-band vacancies since the part above Fermi level gets reduced. But it seems like it is not always true. I appreciate if someone can explain the correlation between these two or give relevant references. Regards, Jias

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 4
by Soham Mukherjee 06 Oct '11

06 Oct '11

Dear Ifeffit Community, The attachment didn't open ?! I am resending the same. In any case, I will give all the details :- The sample is a thin layer, it's pretty homogeneous and had no pinholes during measurements. The fit details are :- k_min = 2, k_max = 14 R_min = 1, R_max = 3 The potential is self consistent in these calculations Fitting was performed in the R-space Best regards, Soham. On Thu, Oct 6, 2011 at 12:50 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: Energy shift (Dr. Dariusz A. Zaj?c) > 2. Zinc Sulfide fitting (Soham Mukherjee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Oct 2011 08:45:05 +0200 > From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy shift > Message-ID: <4E8D4E71.2000309(a)ifj.edu.pl> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Your attachment do not help in this case... > Do you know something more about sample? I suppose it is a thin layer. > Have you checked if you have no defects, vacancies, etc? > I suppose that you can follow instructions given in this post > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-January/008522.html > but you can be also interested in this topic: > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-June/004293.html > and especially in last posts. > you can also try this suggestion > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-June/009471.html > > In general - could you precise, what is k_{min} for your fit, and did > you use self consistent potential in calculations? > > > > > > W dniu 11-10-06 02:28, JeongEunSuk pisze: > > Thank Dariuz and Bruce. > > TiO is deposited on Si substrate and PtO is fabricated on TiO2. > > I measered EXAFS with Pt L3 edge(11563eV) and The model is decided > > from FEFF8.0. > > PtO has only fist shell like attached files So I chose the simple > > model with octahedral structure (probe atom Pt, others O) > > When the EXAFS was fitted by feffit, the variables were three eo(Enot > > in Artemis, energy shift), do1(distance factor), sigo1(debye-waller > > factor). > > the results of fit is as following > > variable best fit value uncertainty initial guess > > eo = 19.283398 1.726426 0.000000 > > do1 = -0.023227 0.009557 0.096000 > > sigo1 = 0.003790 0.000583 0.003047 > > r-factor: 11 > > reduced-chi square: 95 > > > > Energy shift by fit shows an amount of difference from Pt L3 edge. It > > is my problem. > > To reduce the energy shift, I tried to remove background carefully > > again and to change distance Pt-O. > > However the result was failed. > > > > > > > > ------------------------------------------------------------------------ > > Date: Wed, 5 Oct 2011 08:24:16 +0200 > > From: kicaj(a)ifj.edu.pl > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Energy shift > > > > Hi, > > could say more precise what kind of energy shift you are talking > > about? the position of the white line or the Enot in Artemis. How big > > it is? Which version of Feff do you use? What do you mean writing > > "removing background carefully"? Background in the EXAFS fit? Any > > pictures to illustrate problem are welcome > > > > W dniu 11-10-05 03:25, JeongEunSuk pisze: > > > > Hell all > > I have the study for PtO nanoparticles with EXAFS. > > When I fitted the data to model, I had a problem for energy shift. > > I thought that the energy shift obtained from fitting must be > > below White line. However it was over white line. > > Although I removed background carefully and changed bond length in > > model, the energy shift was still big. > > I want to know other factors which affect energy shift. > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto: > Ifeffit(a)millenia.cars.aps.anl.gov> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > _______________________________________________ Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Zinc Sulfide fitting
by Soham Mukherjee 06 Oct '11

06 Oct '11

Zinc Sulfide exists largely in two phases, either the cubic zinc-blende (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. The details of the NN distances are as follows :- 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 axially elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 Angstroms ! I am performing a first shell fit to Zinc Sulfide which exists in the wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is that since bond distances are higher in a hexagonal phase than the cubic phase, I end up with a considerable delr as I underestimated my starting bond length value. Taking a wurtzite model involves defining two different bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in the FEFF, whose sigma^2 values are quite similar. This gives unusually large delr values and high sigma^2 for the longer axial bond, which looks suspicious ! Do I really need to define the two bond distances separately of so close values? Or taking a cubic phase will be sufficient? Please find the attached project file (artemis.apj) where I have tried out some simulations with both cubic and hexagonal models. With best regards, Soham.

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Energy shift
by JeongEunSuk 06 Oct '11

06 Oct '11

Hell all I have the study for PtO nanoparticles with EXAFS. When I fitted the data to model, I had a problem for energy shift. I thought that the energy shift obtained from fitting must be below White line. However it was over white line. Although I removed background carefully and changed bond length in model, the energy shift was still big. I want to know other factors which affect energy shift.

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Fit in TiO2
by Kleper Rocha 05 Oct '11

05 Oct '11

2 1

Au-foil (fcc) splitted peak
by Kaiser, Julian 04 Oct '11

04 Oct '11

Dear Ifeffit Community, I'm trying to understand a basic question about an ordinary gold-foil in the fcc-crystal structure. If the spectra is plotted in the R-space, one will find two main-peaks at approx. 2.497 and 2.964 Angström that both should be attributed to the first shell. (see attached plot "Au_foil.pdf") Would this mean, one can find a peak-splitting in the 1st NN shell? And if yes, why? Maby I am compleately wrong and the second peak demonstrates already the second shell.(?) But I think the second shell should not start below 4.07825 Armströng. I think most of fcc metal crystals show this behavior. Of cause it also varys depending on the k-weight(kw=2 in the attachment). Thanks a lot in advanced, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Absorption versus energy plot
by Francisco Garcia 04 Oct '11

04 Oct '11

Dear users, Can someone kindly explain how I can obtain the X-ray absorption versus energy plot (specifically which file contains the data) in FEFF9. I want to depict a single plot where I can clearly show the XANES and EXAFS regions. Thank you very much.

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Fit with Artemis in Demeter
by Kleper Rocha 30 Sep '11

30 Sep '11

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Preparation help with fly ash sample with diluted Tl
by Mengling Yi Stuckman 30 Sep '11

30 Sep '11

Dear Ifeffit Community, I am currently working on project "Evaluating Speciation of Thallium in Coal Fly Ash". The project was accepted by APS and we will conduct our measurement on beamline 5-BM-D. My fly ash sample has Tl concentration ranging from 0.5ppm to 13ppm. How can I know whether the sample can generate enough photon counts if using fluorescence mode? what would be the appropriate sample preparation procedure I should follow? Is there any interference I should pay attention to? I understand that I should use Hephaestus, but I don't know how to do that if my sample contains lots of different oxides. I attached the elemental composition in this email. Most metals should be in form of oxides, or sulfates. Any input would be highly appreciated, Mengling

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Re: [Ifeffit] Preparation help with fly ash sample with
by fred.mosselmans＠diamond.ac.uk 30 Sep '11

30 Sep '11

Dear Mengling, As Caroline Peacock from Leeds has successfully done Tl L3 microXAFS on some samples on I18 at diamond, I Have a little experience. She has a paper on the work currently in review. As Matt says if you have Pb in the sample your data is limited to just under 350 eV (10 k). Micro EXAFS past 10 k is quite hard but feasible and the big advantage is your localised concs. are possibly (probably?) a lot higher than for the bulk. If the Tl was equally distributed at 13 ppm max then micro Xanes might work, XAFS wont - but i think that's not likely. Thus with a local high concentration you might with time get 12 k XAFS from the Tl. As for using a total yield detector the big advantage is that they are count rate unlimited so you don't have to worry about count rate saturating your detector and can have it dead close to the sample to get the maximum Tl counts. Even with Al attenuation which will remove the Fe signal quicker than the Tl you are throwing away some Tl counts. Hence for XANES in particular it may be advantageous. Cheers Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Fly ash sample with diluted Tl
by Mengling Yi Stuckman 29 Sep '11

29 Sep '11

Dear Ifeffit Community, I am currently working on project "Evaluating Speciation of Thallium in Coal Fly Ash". The project was accepted by APS and we will conduct our measurement on beamline 5-BM-D. My fly ash sample has Tl concentration ranging from 0.5ppm to 13ppm. How can I know whether the sample can generate enough photon counts if using fluorescence mode? what would be the appropriate sample preparation procedure I should follow? Is there any interference I should pay attention to? I understand that I should use Hephaestus, but I don't know how to do that if my sample contains lots of different oxides. I attached the elemental composition in this email. Most metals should be in form of oxides, or sulfates. Any input would be highly appreciated, Mengling -- Mengling Yi Stuckman Graduate Research Assistant Civil and Environmental Engineering and Geodetic Science Ohio State University 2070 Neil Ave., Columbus, OH, 43210

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Artemis fitting k-weight
by George Sterbinsky 20 Sep '11

20 Sep '11

Hello, When fitting data in Artemis with the "other k weight" box checked and the kw = 1, 2, or 3 boxes unchecked, I find that the log file lists "k-weight = 1, kw", where kw is the value I entered into the "other k weight" text box. If I choose 0 as the other k weight, then the log file lists "k-weight = 1". Is it possible to run a fit in Artemis using only a k-weight of something other than 1, 2, or 3? Thank you, George

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Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon
by Anatoly I Frenkel 20 Sep '11

20 Sep '11

Ru oxidizes easily. Since you fixed CN in bulk Ru as total 12 in the fit to hcp Ru it probably gave you a small amplitude factor for the foil. Thus when you transferred that small amplitude factor to fit NP Ru it resulted in large CN. We use freshly made Ru powders as standards. What amplitude factor have you got from the foil? Anatoly Sent from my mobile phone, please forgive typos. -----Original message----- From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: Dreher Marian <Marian.Dreher(a)psi.ch>, "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:27:57 GMT+00:00 Subject: Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon You have to be careful using Ru foil. Sent from my mobile phone, please forgive typos. -----Original message----- From: Dreher Marian <Marian.Dreher(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:00:15 GMT+00:00 Subject: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon
by Anatoly I Frenkel 20 Sep '11

20 Sep '11

You have to be careful using Ru foil. Sent from my mobile phone, please forgive typos. -----Original message----- From: Dreher Marian <Marian.Dreher(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue, Sep 20, 2011 18:00:15 GMT+00:00 Subject: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] Spline range?
by Matt Newville 19 Sep '11

19 Sep '11

Wei, On Sun, Sep 18, 2011 at 9:10 AM, Wei Li <weili(a)udel.edu> wrote: > Dear all, > > I am wondering about what range should be chosen in Athena? Some literature > says from 1 to the end; some says from 0.5 to the end. What literature says this? Do you mean to imply that someone is saying it should be 0.5 or 1.0, and *not* some other value? In principle, the background should start at k=0, and one should use k-weight=1, as Integral_E=E0^E=infinity chi(E) dE = 0 Integral_k=0^k=infinity chi(k) * k * dk = 0 In practice, that is nearly useless beyond the suggestion that the integral (which is to say, the DC component), *should* be zero. Using kmin between 0 and 1 and k-weight between 0 and 2 usually "work best", especially in the sense of "stable". In my experience, the value of E0 is much more important than kmin, and it is hard to predict whether k-weight = 1 or 2 works better. My advice is to not over-think or spend too much time worrying about background subtraction. --Matt

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