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

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 09 Oct '11

09 Oct '11

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 9
by Soham Mukherjee 09 Oct '11

09 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 06 Oct '11

06 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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