June 2011 - Ifeffit - millenia.cars.aps.anl.gov

Fwd: problem with horae installation on ubuntu 11.04
by Bruce Ravel 21 Jun '11

21 Jun '11

Samuel, As you can see, I am forwarding this to the mailing list. It seems to me that you do not have pgplot installed. On ubuntu this package is called "pgplot5". Have you installed it? I would have thought that the pgplot package would have been a dependency of the ifeffit package. Carlo: can you shed any light on Samuel's problem? Rgeards, B ---------- Forwarded Message ---------- Subject: problem with horae installation on ubuntu 11.04 Date: Tuesday, June 21, 2011, 08:19:46 am From: Bickel Sämi <bickels(a)student.ethz.ch> To: "bravel(a)anl.gov" <bravel(a)anl.gov> hi this is probably a stupid question but i'm quite stuck here. i need the athena software but it doesen't load. it termines with the error: > bickels@bickels-laptop:/$ athena > /usr/bin/perl: symbol lookup error: /usr/local/lib/perl/5.10.1/auto/Ifeffit/Ifeffit.so: undefined symbol: pgqndt_ > i tried compiling the ifeffit-perl but it did not work. also i don't know if i got another version of perl.. but i installed ifeffit trough synaptic. im a newbie and this is probably no big issue.. thanks and have a nice day samuel bickel ----------------------------------------- -- 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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Re: [Ifeffit] SS and MS contributions to EXAFS
by Scott Calvin 18 Jun '11

18 Jun '11

Hi Francisco, Following up on Matt's comment, a FEFF calculation with default option assigns sigma2 to be 0, and that probably won't result in relative contributions between SS and MS that look much like what happens in the real material. A better strategy would be to read the calculation into Artemis, as Matt suggests, and use a Debye model for the sigma2 for the paths, trying a few different Debye temperatures to get a sense of how it affects the relative contributions. While the Debye model is not an appropriate model for quantitatively fitting most materials, at least it takes a stab at how sigma2 might depend on R, which will help with understanding how important the MS paths are to chi(k). --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 7:21 PM, Matt Newville wrote: > Hi Francisco, > > On Fri, Jun 17, 2011 at 7:34 PM, Francisco Garcia > <garcia.ff.000(a)gmail.com> wrote: >> Dear users, >> >> I would like to quantify the single scattering (SS) and multiple >> scattering (MS) contributions to the EXAFS spectra over a range of k >> values. I adopted the following approach and I would like ask >> experienced users if my approach is sound: >> >> (1) Run a regular EXAFS (default NLEG=8); I assume this includes all >> possible scattering paths. Call the chi(k) data chi.dat >> (2) Run another EXAFS but this time I set NLEG=2. I assume this is >> for >> all SS contributions. Call the chi(k) data chi_ss.dat >> (3) To obtain the MS contribution, I subtracted chi_ss.dat from >> chi.dat >> >> If my approach is faulty, can you tell me how to remedy it? >> >> Thank you. > > That approach would work under the assumption that the atomic > coordinates in the feff.inp file fully described the distribution of > atoms in the system. If, on the other hand, the feff.inp had an > idealized structure, then the approach would model the MS > contributions for that structure. For example, a feff.inp file often > assumes no static or thermal disorder in the system. In that case, > the MS contributions would have no disorder terms (eg, sigma^2) > applied to them. > > An equivalent approach that may be somewhat simpler would be to use > Artemis to run the Feff calculation with NLEG=8 (4 is probably good > enough below 6Ang in most structures), read in all the paths, and sum > the paths with NLEG>2. > > --Matt

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SS and MS contributions to EXAFS
by Francisco Garcia 18 Jun '11

18 Jun '11

Dear users, I would like to quantify the single scattering (SS) and multiple scattering (MS) contributions to the EXAFS spectra over a range of k values. I adopted the following approach and I would like ask experienced users if my approach is sound: (1) Run a regular EXAFS (default NLEG=8); I assume this includes all possible scattering paths. Call the chi(k) data chi.dat (2) Run another EXAFS but this time I set NLEG=2. I assume this is for all SS contributions. Call the chi(k) data chi_ss.dat (3) To obtain the MS contribution, I subtracted chi_ss.dat from chi.dat If my approach is faulty, can you tell me how to remedy it? Thank you.

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Temp effect
by Hana 17 Jun '11

17 Jun '11

Dear EXAFS experts, I am quite a beginner, and that's might be an ignorant question but really important to my work, so I would be happy to get a direction: what would be the right way to weigh in the effect of temperature in soils samples, since solutions like Debye models will not fit to my understanding? specifically, I am trying to compare my measurements(collected at 10K) to literature data of these metals adsorbed on iron oxides (collected at room temperature). I would appreciate any advise, Hana

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Re: [Ifeffit] McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

I apologize if I have abused the list while working on my text. I will find a different channel for raising these questions and requests once the current discussion is complete. --Scott On Jun 16, 2011, at 8:11 PM, Matt Newville wrote: > Hope that helps. I have to admit I'm a little uneasy with the > frequency of "I've been pondering..." discussion topics alternating > with requests to review book chapters, and find myself being more > cautious in my response than I would if someone was actually asking a > question. On the other hand, I don't think anyone would object if > you added a button to Athena that normalized the data in a way that > included a correction for the expected decay of mu(E).

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Re: [Ifeffit] McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

Thanks, all! Here's what I got out of the discussion: FEFF is calculating the "correct" chi(k), and applying an approximate correction introduces additional sources of error. But the only way to measure chi(k) is to extract it from unnormalized data, and the original definition of chi was an arbitrary, if sensible, one: chi(E) = mu(E)/mu_o(E) - 1. And mu_o(E), while not known with great accuracy, depends only on the element and the edge (perhaps excepting minor contributions from AXAFS). Not applying a correction, whether McMaster or something more accurate (such as the ones Anatoly and John suggested), is equivalent to using the approximation mu_o(E) = mu_o(E_o), which is less accurate than the alternatives. On the other hand, the effect is almost entirely a shift in the absolute (as opposed to relative) value of sigma^2. Considering that, it seems to me that this would be a good option for Athena when calculating chi(k). (I think it would be more problematic to apply when calculating normalized energy-space data, as in that case the correction would depend on instrumental effects and the absorption of other edges in the sample.) So, Bruce, I guess this was first a discussion and then a feature request. :) --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 4:14 AM, John J. Rehr wrote: > Hi Scott et al., > > Thanks for bringing up this issue. Whether or not McMaster > corrections > are useful does seem to depend on details of the measurement. But > my question is: for the cases where they are useful, can one do > better? As the data & theory get better and better, perhaps we > should try > to extract more accurate cross sections mu(E). For example, is it at > all > of interest to have embedded atom cross-sections to replace the atomic > based Cromer-Liberman cross sections or empirical tables? > > John > > > On Thu, 16 Jun 2011, Scott Calvin wrote: > >> Hi all, >> I've been pondering the McMaster correction recently. >> >> My understanding is that it is a correction because while chi(k) is >> defined >> relative to the embedded-atom background mu_o(E), we almost always >> extract >> it from our data by normalizing by the edge step. Since mu_o(E) drops >> gradually above the edge, the normalization procedure results in >> oscillations that are too small well above edge, which the McMaster >> correction then compensates for. It's also my understanding that this >> correction is the same whether the data is measured in absorption or >> fluorescence, because in this context mu_o(E) refers only to >> absorption due >> to the edge of interest, which is a characteristic of the atom in >> its local >> environment and is thus independent of measurement mode. >> >> So here's my question: why is existing software structured so that >> we have >> to put this factor in by hand? Feff, for instance, could simply >> define >> chi(k) consistently with the usual procedure, so that it was >> normalized by >> the edge step rather than mu_o(E). A card could be set to turn that >> off if a >> user desired. Alternatively, a correction could be done to the >> experimental >> data by Athena, or automatically within the fitting procedure by >> Ifeffit. >> >> Of course, having more than one of those options could cause >> trouble, just >> as the ability to put sigma2 into a feff calculation and in to >> Ifeffit >> sometimes does now. But wouldn't it make sense to have it available >> (perhaps >> even the default) at one of those stages? >> >> --Scott Calvin >> Sarah Lawrence College

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McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

Hi all, I've been pondering the McMaster correction recently. My understanding is that it is a correction because while chi(k) is defined relative to the embedded-atom background mu_o(E), we almost always extract it from our data by normalizing by the edge step. Since mu_o(E) drops gradually above the edge, the normalization procedure results in oscillations that are too small well above edge, which the McMaster correction then compensates for. It's also my understanding that this correction is the same whether the data is measured in absorption or fluorescence, because in this context mu_o(E) refers only to absorption due to the edge of interest, which is a characteristic of the atom in its local environment and is thus independent of measurement mode. So here's my question: why is existing software structured so that we have to put this factor in by hand? Feff, for instance, could simply define chi(k) consistently with the usual procedure, so that it was normalized by the edge step rather than mu_o(E). A card could be set to turn that off if a user desired. Alternatively, a correction could be done to the experimental data by Athena, or automatically within the fitting procedure by Ifeffit. Of course, having more than one of those options could cause trouble, just as the ability to put sigma2 into a feff calculation and in to Ifeffit sometimes does now. But wouldn't it make sense to have it available (perhaps even the default) at one of those stages? --Scott Calvin Sarah Lawrence College

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EXAFS modules
by Joshua Kas 14 Jun '11

14 Jun '11

Hi Francisco, This depends on which version of FEFF you are using. The following shows the executables needed for EXAFS in feff9 and feff8. The names are different, so I have put the corresponding module in parentheses. FEFF9 FEFF8 rdinp rdinp atomic ffmod1 (atomic and pot) pot ffmod2 (xsph) xsph ffmod4 (path) path ffmod5 (genfmt) genfmt ffmod6 (ff2x) ff2x Cheers, Josh Kas > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2011 12:22:16 -0700 > From: Francisco Garcia <garcia.ff.000(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] EXAFS modules > Message-ID: <BANLkTimTXXPzOh-sFoYaq_kE3v0pq4BAYA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear users, > > Which of the following modules are needed to compute only the EXAFS > spectra (that is, chi.dat)?: > > ipot > ixsph > ifms > ipaths > igenfmt > iff2x > > Thank you. > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 100, Issue 9 > *************************************** >

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EXAFS modules
by Francisco Garcia 13 Jun '11

13 Jun '11

Dear users, Which of the following modules are needed to compute only the EXAFS spectra (that is, chi.dat)?: ipot ixsph ifms ipaths igenfmt iff2x Thank you.

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Fe foil at 900 C
by KONG Quingyu 12 Jun '11

12 Jun '11

Hello, We are measuring the kinetic of carbon nanotubes using Fe as catalytic element. To analyze the data, we need the Gamma iron (Fe fcc, iron foil measured with a temperature between 910 and 1400 C) EXAFS spectrum. We appreciate if anyone could send us this spectrum. Thanks a lot in advance, Sincerely Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Wednesday, June 08, 2011 9:03 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 100, Issue 6 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: Question about shift in E0 (Christopher Patridge) 2. Re: Question about shift in E0 (Brandon Reese) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2011 21:55:25 -0400 From: Christopher Patridge <patridge(a)buffalo.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Question about shift in E0 Message-ID: <D53A5E8D-B912-4E7B-A567-2E0BB79B4B06(a)buffalo.edu> Content-Type: text/plain; charset="us-ascii" Brandon, I have a question about your method. You mention that you pick E0 based on the 1st peak of the derivative for each sample then extract chi(k). Have you tried constraining E0 across the set? I have thought that in order to make a good comparison between samples in a set, a common E0 should be chosen in order to replicate closely the background function across the whole set. Constraining may also provide a trend in the fitting. Buena salud, Chris On Jun 6, 2011, at 6:46 PM, Brandon Reese <bjreese(a)gmail.com> wrote: > Kicaj and Matt, > > Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis. > > I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides. > > I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way? > > Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous? > > I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same. > > Would there be some reasonable way in a multi-data set fit to constrain the Enot's? > > Brandon > > On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > HI Brandon, > > If I understand right (and to echo Darius's questions), it seems like > you measure samples with a metal reference, and aligned the spectra in > Athena so that the references matched. That's a fine way to go. I > would ask: how big were the needed energy shifts? > Are the experimental mu(E) spectra aligned well at this point? If > you're studying metal oxides with different oxygen content, you might > very well see oxidation in the XANES. If I understand correctly, > you're saying you don't see this. > > Then, you extracted the chi(k) from the aligned spectra. How much did > E0 vary for the shifted spectra in this background-subtraction step? > > Then, you pulled these chi(k) into Artemis, and see different E0 > shifts in the fits. This E0 is a little different, in that it is the > E0 shift applied to the Feff calculation to match the experimental > spectra. If you use different paths or different calculations, such > E0 shifts might happen, and wouldn't be highly meaningful. > > I know that's not a complete answer, but hopefully that and Darius's > questions will help, > > --Matt > > PS on Q2: 1/ (kR)^2 vs 1 / kR^2 > > This is probably either a typo, or a different convention based on the > definition of f(k) as the electron scattering amplitude. In the Feff > world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to > k*f(k). > _______________________________________________ > 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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