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

lfms1
by Francisco Garcia 21 Jun '11

21 Jun '11

Dear users, I have a question about the value lfms1 is the SCF card. What difference does it make if lfms1=0 (solid) versus lfms1=1 (molecule) for hydrated metal ion clusters? My understanding from the manual is that if the metal is the absorber and I am working with cluster, then lfms1=1. However, if the cluster is sufficiently large (radius=6 Ang--8 Ang), then should it be treated as a solid or molecule? Also, how crucial are the hydrogen atoms in the scattering process? Can the EXAFS spectra be computed with only the metal ion and oxygen positions or the hydrogen positions must be included as well? Thank you.

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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 17 Jun '11

17 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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