[Ifeffit] Postdoctoral position at Yeshiva University
Dear IFEFFIT subscribers: Please find here the info about the job opening: Postdoctoral position at Yeshiva University Physics Department of Yeshiva University in New York City has immediate opening for a postdoctoral research associate position. The postdoc will investigate thermal, structural and electronic properties of nanocatalysts and contribute to the ongoing research in heterogeneous catalysis. He or she will be stationed at Brookhaven National Laboratory (BNL) and work closely with BNL departments (NSLS, Chemistry, Physics/Materials Science and the CFN) as well as the outside collaborators. Required qualifications: expert knowledge of XAFS and x-ray diffraction and experience with nanomaterials characterization. Hands on experience with vibrational spectroscopies (Raman, IR) and electron microscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel primarily at the Synchrotron Catalysis Consortium (http://www.yu.edu/scc https://webmail.bnl.gov/exchange/frenkel/Drafts/RE:%20[Ifeffit]%20Fe%20K-edge%20second%20shell%20problems.EML/redir.aspx?C=44fc2d9c1c7d43be96daee679b109becURL=http%3a%2f%2fwww.yu.edu%2fscc ) at the National Synchrotron Light Source. Applicants should forward cover letter and CV, and arrange for three letters of recommendation to be sent to Prof. Frenkel at anatoly.fren...@yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel https://webmail.bnl.gov/exchange/frenkel/Drafts/RE:%20[Ifeffit]%20Fe%20K-edge%20second%20shell%20problems.EML/redir.aspx?C=44fc2d9c1c7d43be96daee679b109becURL=http%3a%2f%2fwww.yu.edu%2ffaculty%2fafrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc https://webmail.bnl.gov/exchange/frenkel/Drafts/RE:%20[Ifeffit]%20Fe%20K-edge%20second%20shell%20problems.EML/redir.aspx?C=44fc2d9c1c7d43be96daee679b109becURL=http%3a%2f%2fwww.yu.edu%2fscc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.fren...@yu.edu winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Athena (Question about LC fitting)
I meant fit the standards to the unknown, and I also noticed that Bruce had already replied to the same question below. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Sun 5/15/2011 2:34 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] Athena (Question about LC fitting) It is really important to have the data for the unknown sample and for standards correctly aligned in energy. That means that all of them should be measured in an experiment with the same sample located in the reference position between the transmitted and reference beam detectors. The absorption coefficients of all the reference data should be aligned together in energy. That will ensure that the shifts between the actual data are real and caused by the oxidation state differences. It is sometimes called alignment in absolute energy but it simply means that the shifts are real. When this is taken care of, you can align the standards to the unknown using LCF, and do not float the energy origin corrections (delta E0) of any of the samples used in LCF (either data or standards) since they were already set correctly by experimental conditions. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Yu-Ting Liu Sent: Sun 5/15/2011 1:45 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Athena (Question about LC fitting) Hi, Related to this issue, I have a question about whether alignment is necessary for LCF when the oxidation state among sample and standards is different. I used to align spectra of samples and standards before LCF while handling P. However, I got confused about Se. For Se speciation, I prepared six Se species with oxidation state of -2 (FeSe), 0 (elemental Se), 0 (seleno-cystine), 0 (seleno-methionine), 4 (selenite), and 6 (selenate) to fit samples collected from sediments and biofilms. I am wondering whether the shift of spectra due to the alignment would make standards mis-fit spectral features of samples. Thank you so much for the help! Yu-Ting Liu Yu-Ting (Lusia) Liu Postdoctoral Associate Duke University Civil and Environmental Engineering Durham, NC, 27708-0287 --- Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote: Dear Dr. Ravel, I am doing my PhD in title with identication of Fe-phases in cement hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the fittings. My question is before LC fitting of EXAFS spectra , do I need to calibrate the energy? I have normlized and alligned the spectra very well. The problem is data calibration, when I calibrate the spectra, the energy shifts and it destroys the fitting. Can you please give a clue why this happens or do I make a mistake on the procedure? Thanks so much for your cooperation. Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the data) as a linear combination of two or more other data sets (the standards). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning
Re: [Ifeffit] What does FEFF stand for?
You are both mistaken, but do not check what FEFF is on Urban Dictionary, as it is inappropriate. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Tue 5/10/2011 3:16 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] What does FEFF stand for? On Tuesday, May 10, 2011 03:03:23 pm Scott Calvin wrote: My understanding, although I could be wrong is that the effective part came from an improvement of the theory to account for curved-wave effects. In other words, early theories approximated the photoelectron as a plane wave, but of course it spreads out radially from the absorbing atom. That change necessitated tweaking the definitions of the factors, so it became the effective f. I think you are mistaken. My memory of the etymology has to do with the formalism dating back to Feff5 for computing MS paths. For a purely single scattering theory, you have an F and a phi (without the subscript eff). That is, you can simply compute the scatting function for the one scatterer and be done with it. Feff's path expansion introduced two clever things to the EXAFS business. One is that it provided a formalism for computing a single function that takes into account the angle-dependent scattering functions of all atoms in an arbitrary-geometry multiple scattering path. This allows one to treat a MS path with the familiar SS EXAFS equation only by replacing F and phi with F_eff and phi_eff. That innovation is central to how Ifeffit works. The second clever thing is that it's really fast. That's not such a big deal today, but back in the mid-90s, when a Feff run could take several minutes, a faster algorithm was very welcome indeed. B -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS fromMD simulations
The answer depends, really, on what you want to accomplish. There are several approaches: 1. Full atom-by-atom calculations of EXAFS following an MD trajectory: Riscioni, et al, PRB 83, 115409 (2011). This is required if you have disordered clusters, for example, and your electronic contributions to EXAFS change from atom to atom and you cannot factor them out. 2. Full atom-by-atom calculation of structural (geometric) contributions to EXAFS only, factoring out the electronic contributions: Yevick, Frenkel, PRB 81, 115451 (2010). In the second approach, the advantage is also that if you have small disorder you can calculate it independently from your MD simulations and add it to the structural term that you will obtain from the average coordinates only. Thus, in principle, you will use atom-by-atom calculations only to see if your configurational disorder is something less trivial than a Gaussian, and you would not know without such calculations. Either approach would allow you to match theory to the data without any fitting parameter. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Francisco Garcia Sent: Mon 4/11/2011 4:18 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS fromMD simulations Dear users, I want to compute the average EXAFS spectra usin 500 snapshots of atomic coordinates from my MD simulations. The idea is to compute the EXAFS spectra for each snapshot and then average the spectra over all snapshots (the so-called MD EXAFS approach). I know how to use Artemis to generate the EXAFS spectrum of a single snapshot. However, generating the EXAFS data for each of the 500 snapshots individually will be too time consuming and messy (this is essentially a book-keeping approach). I was wondering if there is a time-saving strategy/script for computing the average EXAFS instead of the snapshot-by-snapshot approach. For example, is it possible to include the coordinates of all the snapshots in a single feff.inp file and feed it to Artemis? Or if I have the feff.inp file for each snapshot, is it possible to write a script for Artemis that will compute each EXAFS spectra individually and dump them in a specified directory? Thank you very much. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fe in glassy ceramics
Diffraction anomalous fine structure seems to the most appropriate method here. Anatoly Frenkel Sent from my mobile phone, please forgive typos. -Original message- From: Andrei Shiryaev a_shiry...@mail.ru To: ifeffit@millenia.cars.aps.anl.gov Sent: Wed, Feb 16, 2011 12:52:38 GMT+00:00 Subject: [Ifeffit] Fe in glassy ceramics ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Distortion of transmission spectra due to particlesize
Jeremy: In your simulation, (c) 1/2 original, 1/2 nothing (a large pinhole) it appears that chi(k) is half intensity of the original spectrum. Does it mean that when the pinhole is present, EXAFS wiggles are half of the original ones in amplitude but the edge step remains the same? Or, equivalently, that the wiggles are the same but the edge step doubled? Either way, I don't think it is the situation you are describing (a large pinhole). If there is a large pinhole made in a perfect foil (say, you removed half of the area of the foil from the footprint of the beam and it just goes through from I0 to I detector, unaffected). Then, if I0 is a well behaving function of energy, i.e., the flux density is constant over the entire sample for all energies, EXAFS in the both cases should be the same. Or I misunderstood your example, or, maybe, the colors? Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Kropf, Arthur Jeremy Sent: Wed 11/24/2010 1:08 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Distortion of transmission spectra due to particlesize It's not that I don't believe in mathematics, but in this case rather than checking the math, I did a simulation. I took a spectrum of a copper foil and then calculated the following: (a) copper foil (original edge step 1.86) (b) 1/3 original, 1/3 with half absorption, and 1/3 with 1/4 absorption (c) 1/2 original, 1/2 nothing (a large pinhole) (d) 1/4 nothing, 1/2 original, 1/4 double (simulating two randomly stacked layers of (c)) Observation 1: Stacking random layers does nothing to improve chi(k) amplitudes as has been discussed. They are identical, but I've offset them by 0.01 units. Observation 2: Pretty awful uniformity gives reasonable EXAFS data. If you don't care too much about absolute N, XANES, or Eo (very small changes), the rest is quite accurate (R, sigma2, relative N). Perhaps I'll simulate a spherical particle next with absorption in the center of 10 absorption lengths or so - probably not an uncommon occurance. Jeremy Chemical Sciences and Engineering Division Argonne National Laboratory Argonne, IL 60439 Ph: 630.252.9398 Fx: 630.252.9917 Email: kr...@anl.gov -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Wednesday, November 24, 2010 10:41 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Distortion of transmission spectra due to particlesize Matt, Your second simulation confirms what I said: The standard deviation in thickness from point to point in a stack of N tapes generally increases as the square root of N (typical statistical behavior). Now follow that through, using, for example, Grant Bunker's formula for the distortion caused by a Gaussian distribution: (mu x)eff = mu x_o - (mu sigma)^2/2 where sigma is the standard deviation of the thickness. So if sigma goes as square root of N, and x_o goes as N, the fractional attenuation of the measured absorption stays constant, and the shape of the measured spectrum stays constant. There is thus no reduction in the distortion of the spectrum by measuring additional layers. Your pinholes simulation, on the other hand, is not the scenario I was describing. I agree it is better to have more thin layers rather than fewer thick layers. My question was whether it is better to have many thin layers compared to fewer thin layers. For the brush sample on tape method of sample preparation, this is more like the question we face when we prepare a sample. Our choice is not to spread a given amount of sample over more tapes, because we're already spreading as thin as we can. Our choice is whether to use more tapes of the same thickness. We don't have to rerun your simulation to see the effect of using tapes of the same thickness. All that happens is that the average thickness and the standard deviation gets multiplied by the number of layers. So now the results are: For 10% pinholes, the results are: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1| 10.0 |0.900 |0.300 | # 5| 10.0 |4.500 |0.675 | #25| 10.0 |22.500 |1.500 | For 5% pinholes: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1| 5.0 |0.950 |0.218 | # 5| 5.0 |4.750 |0.485 | #25| 5.0 |23.750 |1.100 | For 1% pinholes: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1| 1.0 |0.990 |0.099 | # 5| 1.0 |4.950 |0.225 | #25| 1.0 |24.750 |0.500| As before, the standard deviation increases as square root of
Re: [Ifeffit] Distortion of transmission spectra due to particlesize
You are right about the amplitude factor: it should change. The ln(1+x/2) is not the full story, since x is the exponent: x= exp(-mu*t) and when mu*t is small (thin samples), x is not, and vice versa. More accurate expansion of ln(1+x/2) in the limit of thick and thin samples shows that mu_measured (in thin film with pinholes) and mu in the thin film are differed by a proportinality factor, that is what you are getting. Thanks, Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Wed 11/24/2010 6:35 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Distortion of transmission spectra due to particlesize Hi Jeremy, Anatoly, Thanks, you're absolutely right -- I got the parentheses wrong. Anatoly, However, thickness is present in mu*t only because of the total number of absorbers. There are 1/2 absorbers in the foil with 50% holes, and thus (t*mu)_measured is equal to (1/2) * t*mu_measured. I agree, but I think that you'd have to know your sample was 50% holes to make that work. I was considering 't*mu' to be a single thing quantity (and really meant that to stand for -ln(I_t/I_0) in the sense of the log of intensities sampled by ion chambers, not absolute fluxes). I think it should be (starting with I_t = I_0 * exp(-tmu) ) that a half full / half empty sample will have: I_t = (I_0 + I_0 * exp(-tmu) ) / 2 = I_0 * (1 + exp(-tmu) ) / 2 so that tmu_measured = -ln (I_t / I_0) = -ln( (1 + exp(-tmu))/2) = ln(2) - ln(1+ exp(-tmu)) As for whether there is a reduction in chi(k) of a factor of 2 or not, I think this would depend on the sample thickness (or, the reltive size of tmu to 1) in the portion of the sample that was non-empty. Using this corrected formula on cu foil data (that actually has an edge jump ~= 2.3, so is probably on the thick side, but is still decent data), I do see a reduction in chi(k) that is a little more than a factor of 2, with some k-dependence. Attached is an Athena project of original and half empty data. Am I a pessimist for not calling it half full? --Matt PS: I did this to make the half empty data, then read in the data file into athena. read_data(cu.xmu, group =good) set pinhole.energy = good.energy set pinhole.xmu= -ln( (1 + exp(-good.xmu) )/2) write_data(file=half_empty.xmu, pinhole.energy, pinhole.xmu) winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
That's probably how they discovered graphene, by trying to make exafs sample. Anatoly Sent from my mobile phone, please forgive typos. -Original message- From: Scott Calvin dr.scott.cal...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 Subject: Re: [Ifeffit] Transmission EXAFS sample ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Asymmetric error bars in IFeffit
Scott, It is a strange result. Suppose you fit a bulk metal foil and vary the 1nn coordination number. You will not get 12 +/- 1000. You will get about 12 +/- 0.3 depending on the data quality and the k range, and on the amplitude factor you fix constant. Then, suppose you take your formula for a particle radius from your JAP article and propagate this uncertainty to get the radius uncertainty. That would give you a huge error because you are in the flat region of the N(R) function and R does bit affect N. The meaning of your large error bar is, I think, that you are in such a large limit of sizes that they cannot be inverted to get N and thus the errors cannot be propagated to find Delta R. Why don't you try to obtain N instead of R? You will get much smaller error bars and you can find the lower R limit from your N(R) equation (by plugging in N - deltaN you will find R - delta R). The right limit is infinity as you pointed out. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are characteristic crystallite radii for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with messy chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like the best fit value is 10 nm, and it is probable that the value is at least 4 nm. But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the
Re: [Ifeffit] Asymmetric error bars in IFeffit
On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are characteristic crystallite radii for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with messy chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like the best fit value is 10 nm, and it is probable that the value is at least 4 nm. But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it should possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that
Re: [Ifeffit] Asymmetric error bars in IFeffit
Matthew, if you relied on FEFF as one part of the complex calculation, where the other part was the experimentally extracted one, you could've as well done everything with just FEFF. Why didn't you? A. From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri Oct 22 18:01:17 2010 Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit Another reason, from my point of view, is that FEFF wasn't accurate enough to use on its own without references. Also, it still can be argued that the process of data reduction and filtering produces distortions which aren't captured by using FEFF alone. Further, if one is comparing very similar systems, e.g. bulk and nano of the same stuff, then with the exception of multiple scattering, the one system should be an ideal reference for the other. A trick I used to do: Suppose, for instance, that I wanted to fit a shell of Zn surrounded by Si (not an actual case). There's no Si-rich zinc silicide to use as a reference, but it's not too hard to make theta-CuAl2, a compound in which all Cu atoms are surrounded by Al in the first shell (this was done). From this, amp and phase functions could be extracted which refer to Cu looking at Al (Cu-Al). Next, to transform this into the desired Zn-Si, I would do FEFF calculations on identical structures with the atoms changed around and take: A(Zn-Si, semi-empirical) = A(Cu-Al, expt)*[A(Zn-Si, FEFF)/A(Cu-Al, FEFF)] phi(Zn-Si, semi-empirical) = phi(Cu-Al, expt)+[Phi(Zn-Si, FEFF)-phi(Cu-Al, FEFF)] with A, phi being amplitude and phase for a given shell, and appropriate account being taken of the distance differences involved. This makes sense if you consider A~ = A*exp(i*phi) to be one of the factors in a complex chi~ such that chi = Im(chi~), and you're essentially making a correction to ln(A~). Yes, this was low-rent and subject to errors, but it seemed to make sense provided one didn't try to take it too far, for instance trying to change Al for Au or an oxide for a metal. Brings back memories, not all of them fond :-) mam - Original Message - From: Frenkel, Anatoly mailto:fren...@bnl.gov To: ifeffit@millenia.cars.aps.anl.gov Sent: Friday, October 22, 2010 2:38 PM Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are characteristic crystallite radii for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with messy chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius
Re: [Ifeffit] Multiple scattering paths in fitting
For bond angles, this google search would be helpful: buckling angle multiple scattering xafs Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Abhijeet Gaur Sent: Thu 10/7/2010 3:21 AM To: ifeffit Subject: [Ifeffit] Multiple scattering paths in fitting Hi all, I just read the discussion on sigma^2 values for multiple scattering paths . One thing is clear that inclusion of multiple scattering path may increase the quality of fit. I have also some questions related to MS paths. 1. What else information can be obtained from multiple scattering paths? 2. What values of delr should be relevant for MS paths. 3. How can we determine the bond-angles from multiple-sacttering paths using Artemis fitting method. With thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain. winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Multiple scattering paths in fitting
For relationships between sigma2 for MS and SS paths, some are listed in the Appendix to this article: P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). Anatoly winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28
It is because you made delta E0=0, but the fit gave you delta E0=8. Since the fit agrees with the data in k-space at low wavenumbers (I assume), then the signal with delta E0=0 should not, and vice versa. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Elsa Sileo Sent: Thu 9/30/2010 11:33 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28 Dear Matt, I have to perform EXAFS analysis, and when I tried to fit the first shell, I found deltaE0 values of about 8 eV. Following the paper of Kelly et al (Analysis of soils and minerals using X-ray absorption spectroscopy. In Methods of soil analysis, Part 5: Mineralogical methods; 2008; pp 446) I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. When I compare the experimental and theoretical spectrum I see a mismatch between the position of the nodes at low wavenumbers. Having done this, how I have to proceed to correct the experimental data in order to obtain smalller delta E0 values? Thanks in advance, Elsa --- El mié, 29/9/10, ifeffit-requ...@millenia.cars.aps.anl.gov ifeffit-requ...@millenia.cars.aps.anl.gov escribió: De: ifeffit-requ...@millenia.cars.aps.anl.gov ifeffit-requ...@millenia.cars.aps.anl.gov Asunto: Ifeffit Digest, Vol 91, Issue 28 Para: ifeffit@millenia.cars.aps.anl.gov Fecha: miércoles, 29 de septiembre, 2010 14:00 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov http://es.mc278.mail.yahoo.com/mc/compose?to=ifef...@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-requ...@millenia.cars.aps.anl.gov http://es.mc278.mail.yahoo.com/mc/compose?to=ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov http://es.mc278.mail.yahoo.com/mc/compose?to=ifeffit-ow...@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: Aligning Energy scales (Matt Newville) -- Message: 1 Date: Tue, 28 Sep 2010 12:55:15 -0500 From: Matt Newville newvi...@cars.uchicago.edu http://es.mc278.mail.yahoo.com/mc/compose?to=newvi...@cars.uchicago.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov http://es.mc278.mail.yahoo.com/mc/compose?to=ifef...@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Aligning Energy scales Message-ID: aanlktima_bgt5oo=k-vb-0argwb9ac_w6bcblwgca...@mail.gmail.com http://es.mc278.mail.yahoo.com/mc/compose?to=k-vb-0argwb9ac_w6bcblwgca...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Elsa, It sounds like you want to adjust the data chi(k) so that deltaE0 is 0 in a fit. Is that correct, or are you trying to do something else (say, align the XANES)?If that assumption is correct, you want to change the E0 used to extract chi(k) from the experimental spectra -- the E0 of the background subtraction. That is what sets k for the data. If that's not clear or not the right question, let us know, --Matt On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo si...@qi.fcen.uba.ar http://es.mc278.mail.yahoo.com/mc/compose?to=si...@qi.fcen.uba.ar wrote: I need to align a measured spectra to a theoretically calculated spectra. I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. But I do not know how to use this last theoretical fit to align the spectra. Can somebody help me? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: si...@qi.fcen.uba.ar http://es.mc278.mail.yahoo.com/mc/compose?to=si...@qi.fcen.uba.ar
Re: [Ifeffit] debye function
Just to add: These procedures, described in that article, can be easily implemented in Mathematica. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Tue 8/24/2010 1:23 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] debye function On Tuesday 24 August 2010 12:23:18 pm Kleber Daum Machado wrote: Hi, I'd like to know the explicit mathematical expressions that are represented by the functions debye(temp,thetad) and eins(temp,thetae). Are they given in some documentation file or article? See Extended x-ray absorption fine structure Debye-Waller factors. I. Monatomic crystals E. Sevillano, H. Meuth, J. J. Rehr Phys. Rev. B 20, 4908-4911 (1979) http://link.aps.org/doi/10.1103/PhysRevB.20.4908 B -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Haha
And for the red curve, someone forgot the sample... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Heinz-Eberhard Mahnke Sent: Sun 8/15/2010 12:04 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Haha Hi, nice spectrum. Why is the background so high? someone forgot the filter? Eberhard Mahnke Hi all, For a little comic relief, I just came across this graph: http://www.usablemarkets.com/wp-content/uploads/2010/06/fed-rate-3.jpg I have never seen a graph unrelated to XAFS looks more like (noisy) XAFS data... --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Prof. Dr. Heinz-Eberhard Mahnke Fachbereich Physik Freie Universität Berlin c/o Helmholtz Zentrum Berlin GmbH (vormals Hahn-Meitner-Institut) Bereich Strukturforschung Hahn-Meitner-Platz 1 D-14109 Berlin Tel 0049-(0)30-8062-42715 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting
There is a large number of articles explaining how to fit CeO2 including discussions why multi-electron excitatoins complicate the fit, and some of those authors (e.g., A. Soldatov, but also M. Benfatto) propose first principle methods that account for those. Some papers even show that ignoring those contributions may give a decent fit, but you should be aware of the multitudes of theoretical issues surrounding EXAFS modeling of this system before trying it on your own. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy Sent: Thu 5/13/2010 5:21 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting 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 winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] fitting
Then what I wrote is an overkill... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of María Elena Montero Cabrera Sent: Thu 5/13/2010 5:34 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting I don't know anything about CeO2, but...for me there is something wrong since the Athena fitting, because there are too many peaks below the main one, and specially below 1 A. Am I right or not? Maria Elena 2010/5/13 Frenkel, Anatoly fren...@bnl.gov There is a large number of articles explaining how to fit CeO2 including discussions why multi-electron excitatoins complicate the fit, and some of those authors (e.g., A. Soldatov, but also M. Benfatto) propose first principle methods that account for those. Some papers even show that ignoring those contributions may give a decent fit, but you should be aware of the multitudes of theoretical issues surrounding EXAFS modeling of this system before trying it on your own. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy Sent: Thu 5/13/2010 5:21 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] fitting 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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123 winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Debye model on Artemis
Kleber, Correlated Debye Model (CDM) was proposed by Sevillano, Meuth and Rehr in 1979 in a Phys Rev B artcile. It also shows how to find sigma2(T) from the CDM- and also from Einsten model, by the way. In the former case, you take phonon density of states in Debye approximation (where it is proportional to the square of the mode frequency) and projoect it on the direction of the bond between the atoms, so the modified projected density of states is used to calculate vibrational amplitudes. Similarly, it can be used to calculate not vibrational amplitudes but third cumulant but it has not been done with CDM to my knowledge. It was done only for the Einstein moedl in the subsequent papers though, as you and Bruce wrote. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Kleber Daum Machado Sent: Wed 5/12/2010 1:59 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Debye model on Artemis 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Differences between fluorescence and transmission of thesame sample
What can be done in this case, is not to use either flourescence or transmission data, - because both are bad by the reasons Bruce explained - but use corrections, if you cannot change your experimental geometry (different concentration of the sample or different thickness or different reactor cell). What we do in these cases, if we must keep original thick sample for fluorescence measurements, we make the same sample prepared for transmission on a tape or as a pellet, that gives proper thickness to be free of any leakage or thickness effects that reduce oscillation intensity or introduce noise due to poor statistics. Then we compare EXAFS oscillations plotted together for the two samples: one measured in fluorescence in the cell you want to use in your in situ experiment, and the other meausred in tranmission in ideal conditions. The former will have reduced intensity. You can manually find scaling factor that is needed to match two intensities. Based on many early papers (e.g., Kim, Stern and Heald, Physical Review B, Thickness effect in EXAFS data or something like that), this scaling factor is approximately constant. Once you found it, then you can take all your in situ data in flourescence and later on, during data processing and analysis, correct all the EXAFS data by scaling them up with the same factor. Don't change the sample geometry midway, and do not apply similar correction to recover XANES. Other strategies should be used for XANES corrections. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Andrew Campos Sent: Wed 5/5/2010 11:24 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Differences between fluorescence and transmission of thesame sample 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 winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] energy resolution
This is a quote from Joseph Dvorak' report on energy resolution measurements at the NSLS beamlines: The energy resolution was measured as follows. A Si 220 crystal was used as an analyzer crystal. This was placed in the hutch in near back reflection condition (87 deg inc). The reflected x-rays were detected with a Si photodiode. Oriented as such, the analyzer crystal reflects at its fundamental (3233 eV) and all higher order reflections (440, 660, ...). The beamline monochromator was then scanned successively through the various reflections of the analyzer crystal. Since the energy bandpass of the analyzer crystal in back reflection is very narrow compared to the fundamental of the beamline monochromator (true for all the higher order analyzer crystal reflections, and possibly true for the fundamental depending on the monochromator crystal), a measurement of the width of the reflected beam gives a direct measurement of the energy resolution. The second monochromator crystal was set to full tune. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Matthew Sent: Wed 5/5/2010 2:42 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] energy resolution That method only works at one energy, and assumes something about the width of the V2O5 feature. Another possible method might be to measure, in back-reflection, a high-order Bragg reflection from a Si crystal. For instance, the 555 reflection would be at 9.9keV. If you put up a 111 Si crystal and did a transmission scan, maybe you could detect the reflection as a transmission dip. You would then play with the orientation of the crystal so that the energy at which this dip occurred was as low as possible, meaning that you were at back-reflection. This condition is useful because it gives the least sensitivity to beam divergence. You could then calculate the Darwin broadening of the 555 reflection to correct the observed value. By choosing different reflections, you could measure the resolution at different energies. Of course, I haven't tried this myself. mam - Original Message - From: Bruce Ravel bra...@bnl.gov To: mrceo...@yahoo.com.ar; XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Wednesday, May 05, 2010 11:19 AM Subject: Re: [Ifeffit] energy resolution On Wednesday 05 May 2010 02:12:38 pm M Ceolin wrote: Hi all. I would like to know if anyone knows an experimental method to determine the energy resolution in the XANES region of a XAS spectrum. I do not explored the previous entries in the list so I beg you pardon if it was already discussed. Thank you for the information. Hi Marcelo, A few years back the folks at the APS used the method described about half-way down the page at: http://xafs.org/APSXAFS/APS_XOR_Eval One example evaluation is shown at http://xafs.org/APSXAFS/APS_XOR_Eval/20BM/EResolution HTH, B -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Logicused in Artemis to do the error minimization
Bruce, Some time ago I was trying to find a reference (and failed) explaining the relationship between the error bar reported by the fitting algorithm of ifeffit and one standard deviation in the fitting parameter. From your reply below it appears that they are the same (error bars reported by ifeffit are 1 sigma). I have read in a few old xafs papers stating, without proof, that the error bars (also obtained by the same Levenberg-Marquardt algorithm) in the fits correspond to the 95% confidence intervals which means that they are much larger than 1 sigmal, more like 3 sigma. Can you comment more on your statement about 1 sigma, or give a reference? Thank you, Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Mon 3/8/2010 9:11 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Logicused in Artemis to do the error minimization On Monday 08 March 2010 01:24:17 am Pralay K Santra wrote: Dear All, After the final fitting in Artemis, we get the (i) total error; (ii) the final value of the parameters; (iii) the error in the parameters as well as (iv) the dependencies among the parameters. What is kind of logic used in Artemis to calculate these values? Is it Genetic optimization procedure used in this process? Can anyone help me by giving some references. I was going through the old posts and found two posts. One is this one: http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling and the other one mentioned in the same. I am sorry to ask for some help which is not directly related to the XAFS. I am not really clear how a question about error analysis could be considered as not directly related to XAFS. To my mind, error analysis is at the foundation of any scientific activity. Ifeffit uses a Levenberg-Marquardt steepest descent algorithm to find the parameters values which minimize chi-squared, which is computed in the standard fashion (Bevington's Data Reduction and Error Analysis for the Physical Sciences is my favorite text on the subject). The uncertainties are the diagonal elements of the covarience matrix, albeit scaled by the square root of reduced chi-square. The reason for this is that it is somewhere between extraordinarily difficult and impossible to fully evaluate the measurement uncertainty in an XAFS experiment. As a result, chi-square is scaled incorectly. By rescaling the diagonal elements of the covarience matrix, we are assuming that every fit is a good fit and that the only problem is the evaluation of uncertainties. Thus, if a fit is -- by some criterion -- good and is the one that you want to publish, the error bars reported by Ifeffit are 1-sigma error bars. The correlations are taken from the off-diagonal elements of the covarience matrix. Those need not be scaled and aren't. The formulas for chi-square, reduced chi-square, and the R-factor are given on pages 16 and following of this postscript file http://cars.uchicago.edu/~newville/feffit/feffit.ps My own take, for what it's worth, on all of this is explained on pages 6 to 15 of this presentation: http://xafs.org/Workshops/APS2009?action=AttachFiledo=viewtarget=Ravel_advanced_topics.pdf B PS: Phys. Rev. B 70, 104102 (2004) and J. Synchrotron Rad. (2005). 12, 70-74 are interesting papers about Bayesian approaches to EXAFS analysis. Ifeffit does not do Bayesian analysis. But you seem interested, so I thought I would point them out. -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Logicused in Artemis to do the error minimization
I meant that error bars are related to standard deviations of the mean, not standard deviations... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Mon 3/8/2010 9:25 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Logicused in Artemis to do the error minimization Bruce, Some time ago I was trying to find a reference (and failed) explaining the relationship between the error bar reported by the fitting algorithm of ifeffit and one standard deviation in the fitting parameter. From your reply below it appears that they are the same (error bars reported by ifeffit are 1 sigma). I have read in a few old xafs papers stating, without proof, that the error bars (also obtained by the same Levenberg-Marquardt algorithm) in the fits correspond to the 95% confidence intervals which means that they are much larger than 1 sigmal, more like 3 sigma. Can you comment more on your statement about 1 sigma, or give a reference? Thank you, Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Mon 3/8/2010 9:11 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Logicused in Artemis to do the error minimization On Monday 08 March 2010 01:24:17 am Pralay K Santra wrote: Dear All, After the final fitting in Artemis, we get the (i) total error; (ii) the final value of the parameters; (iii) the error in the parameters as well as (iv) the dependencies among the parameters. What is kind of logic used in Artemis to calculate these values? Is it Genetic optimization procedure used in this process? Can anyone help me by giving some references. I was going through the old posts and found two posts. One is this one: http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling and the other one mentioned in the same. I am sorry to ask for some help which is not directly related to the XAFS. I am not really clear how a question about error analysis could be considered as not directly related to XAFS. To my mind, error analysis is at the foundation of any scientific activity. Ifeffit uses a Levenberg-Marquardt steepest descent algorithm to find the parameters values which minimize chi-squared, which is computed in the standard fashion (Bevington's Data Reduction and Error Analysis for the Physical Sciences is my favorite text on the subject). The uncertainties are the diagonal elements of the covarience matrix, albeit scaled by the square root of reduced chi-square. The reason for this is that it is somewhere between extraordinarily difficult and impossible to fully evaluate the measurement uncertainty in an XAFS experiment. As a result, chi-square is scaled incorectly. By rescaling the diagonal elements of the covarience matrix, we are assuming that every fit is a good fit and that the only problem is the evaluation of uncertainties. Thus, if a fit is -- by some criterion -- good and is the one that you want to publish, the error bars reported by Ifeffit are 1-sigma error bars. The correlations are taken from the off-diagonal elements of the covarience matrix. Those need not be scaled and aren't. The formulas for chi-square, reduced chi-square, and the R-factor are given on pages 16 and following of this postscript file http://cars.uchicago.edu/~newville/feffit/feffit.ps My own take, for what it's worth, on all of this is explained on pages 6 to 15 of this presentation: http://xafs.org/Workshops/APS2009?action=AttachFiledo=viewtarget=Ravel_advanced_topics.pdf B PS: Phys. Rev. B 70, 104102 (2004) and J. Synchrotron Rad. (2005). 12, 70-74 are interesting papers about Bayesian approaches to EXAFS analysis. Ifeffit does not do Bayesian analysis. But you seem interested, so I thought I would point them out. -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting using Experimental standard
I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting using Experimental standard
Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. - Original Message - From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu-Si) = Amp_exp(Cu-Al)*Amp_Feff(Cu-Si)/Amp_Feff(Cu-Al) Phi(Cu-Si) = Phi_exp(Cu-Al)+Phi_Feff(Cu-Si)-Phi_Feff(Cu-Al) and get a semi-empirical Cu-Si standard. Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam - Original Message - From: Frenkel, Anatoly fren...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting using Experimental standard
I doctored FEFF path. Not sure if Artemis offers anything better and less intrusive than this trick but I think it is still the only way to use experimental standards for fits (other than the ratio method that is implemented in athena as Bruce desribed, which is used for monoatomic shells only). A. From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Mon Jan 04 22:54:30 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard Ah, I see. I think Artemis has some way of putting in experimental phase and amp, but that may be just to make a corrected FT. Is that so? Otherwise, I suppose it should be possible to write a fake FEFF path file and read it in. I guess that's what you did. mam - Original Message - From: Frenkel, Anatoly mailto:fren...@bnl.gov To: ifeffit@millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 7:43 PM Subject: Re: [Ifeffit] Fitting using Experimental standard Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. - Original Message - From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu-Si) = Amp_exp(Cu-Al)*Amp_Feff(Cu-Si)/Amp_Feff(Cu-Al) Phi(Cu-Si) = Phi_exp(Cu-Al)+Phi_Feff(Cu-Si)-Phi_Feff(Cu-Al) and get a semi-empirical Cu-Si standard. Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam - Original Message - From: Frenkel, Anatoly fren...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input
Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD
A correction to Matt's email: In random alloys, smaller size atoms and larger size atoms are at different average distances (measured by EXAFS and other local-structure-sensitive techniques, e.g., XRD/PDF) that are, respectively, smaller and larger than the distance between the average lattice points (measured by XRD). Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Wed 12/30/2009 11:47 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD Hi Scott, I believe we had a conversation about this last January. XAFS is not sensitive to the crystallographic lattice constants. It measures the spacing between atoms. Because of thermal vibrations and other disorder terms, the average distance between atoms is larger than the distance between the lattice points. --Matt On Fri, Dec 25, 2009 at 12:04 PM, Scott Calvin scal...@slc.edu wrote: Merry Christmas, everyone! Yes, I'm pondering EXAFS on Christmas... Here's an issue that I bet has been worked out, and I bet someone on this list knows the result and where it's been published. It's well known that the MSRD (sigma squared) for EXAFS differs substantially from the Debye-Waller factor in XRD, because the first is the variance in the interatomic distance, and the second is the variance in the atomic position relative to a lattice point. But what about the lattice parameter implied by the nearest-neighbor distance in EXAFS as compared to the lattice parameter found by XRD? It is certainly true that in most materials, particularly highly symmetric materials, the nearest-neighbor pair distribution function is not Gaussian, and generally has a long tail on the high-r side. (This is largely because the hard-core repulsion keeps the atoms from getting much closer than their equilibrium positions.) So imagine a set of atoms undergoing thermal vibrations around a set of lattice points. For concreteness, let's consider an fcc material like copper metal. The lattice points themselves are further apart than they would be without vibration, sure, but that's not the question. The question is whether the square root of two multiplied by the average nearest-neighbor distance is still equal to the spacing between lattice points. My hunch is that the answer is no, and that the EXAFS implied value will be slightly larger. While the average structure is still closed-packed, the local structure will not be. And in a local structure that is not closed-packed, the atoms will occasionally find positions quite far from each other, but will never be very close. In a limiting case where melting is approached, it's possible to imagine an atom migrating away from its lattice point altogether, leaving a distorted region around the defect. While XRD would suppress the defect, EXAFS would dutifully average in the slightly longer nearest-neighbor distances associated with it. Just to be clear, I am not talking about limitations in some particular EXAFS model used in curve-fitting. For example, constraining the third cumulant to be zero is known to yield fits with nearest-neighbor parameters that are systematically reduced. In fact, limitations like that mean the question can't be answered just by looking at a set of experimental results: I can make my fitted lattice parameter for copper metal go up or down a little bit by changing details of a fitting model or tinkering with parameters that themselves have some uncertainty associated with them, like the photoelectron's mean free path. (Fortunately, this kind of tinkering will affect standards and samples in similar ways, and thus don't affect my confidence in EXAFS analysis as a tool for investigating quantitatively differences between samples, or between samples and a standard.) My question is about the ACTUAL pair distribution function in a real fcc metal. To the degree it's a question about analysis, it's about XRD: In an fcc metal should the expectation value of the nearest-neighbor separation, multiplied by the square root of two, equal the lattice spacing as determined by XRD? --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD
Big deal... We have final exams on Christmas... Anatoly Frenkel Yeshiva University From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Fri 12/25/2009 1:04 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Lattice parameters: EXAFS vs. XRD Merry Christmas, everyone! Yes, I'm pondering EXAFS on Christmas... Here's an issue that I bet has been worked out, and I bet someone on this list knows the result and where it's been published. It's well known that the MSRD (sigma squared) for EXAFS differs substantially from the Debye-Waller factor in XRD, because the first is the variance in the interatomic distance, and the second is the variance in the atomic position relative to a lattice point. But what about the lattice parameter implied by the nearest-neighbor distance in EXAFS as compared to the lattice parameter found by XRD? It is certainly true that in most materials, particularly highly symmetric materials, the nearest-neighbor pair distribution function is not Gaussian, and generally has a long tail on the high-r side. (This is largely because the hard-core repulsion keeps the atoms from getting much closer than their equilibrium positions.) So imagine a set of atoms undergoing thermal vibrations around a set of lattice points. For concreteness, let's consider an fcc material like copper metal. The lattice points themselves are further apart than they would be without vibration, sure, but that's not the question. The question is whether the square root of two multiplied by the average nearest- neighbor distance is still equal to the spacing between lattice points. My hunch is that the answer is no, and that the EXAFS implied value will be slightly larger. While the average structure is still closed- packed, the local structure will not be. And in a local structure that is not closed-packed, the atoms will occasionally find positions quite far from each other, but will never be very close. In a limiting case where melting is approached, it's possible to imagine an atom migrating away from its lattice point altogether, leaving a distorted region around the defect. While XRD would suppress the defect, EXAFS would dutifully average in the slightly longer nearest-neighbor distances associated with it. Just to be clear, I am not talking about limitations in some particular EXAFS model used in curve-fitting. For example, constraining the third cumulant to be zero is known to yield fits with nearest-neighbor parameters that are systematically reduced. In fact, limitations like that mean the question can't be answered just by looking at a set of experimental results: I can make my fitted lattice parameter for copper metal go up or down a little bit by changing details of a fitting model or tinkering with parameters that themselves have some uncertainty associated with them, like the photoelectron's mean free path. (Fortunately, this kind of tinkering will affect standards and samples in similar ways, and thus don't affect my confidence in EXAFS analysis as a tool for investigating quantitatively differences between samples, or between samples and a standard.) My question is about the ACTUAL pair distribution function in a real fcc metal. To the degree it's a question about analysis, it's about XRD: In an fcc metal should the expectation value of the nearest-neighbor separation, multiplied by the square root of two, equal the lattice spacing as determined by XRD? --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Path degeneracy modification in feffNNN.dat
It takes it from N. Anatoly - Original Message - From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Fri Nov 20 18:57:29 2009 Subject: Re: [Ifeffit] Path degeneracy modification in feffNNN.dat Hi ｔｈｅｒｅ, I have a general question about Artemis. I am going to split a degenerated path with degeneracy N=8 into twoｓ. I noticed that by cloning the path, the N in path math expression parameters was halved as 4. However, the degeneracy number in feffNNN.dat remains as 8. For fitting, where will Artemis exactly get this information? Or maybe I ｓｈｏｕｌｄ ｍｏｄｉｆｙ ｆｅｆｆＮＮＮ．ｄａｔ ｍａｎｕａｌｌｙ？ Ｔｈａｎｋｓ ｆｏｒ ｙｏｕｒ ｒｅｓｐｏｎｓｅ！ ＝＝＝ Ｄｒ． Ｙｉｎｇ Ｚｏｕ Ｒｅｓｅａｒｃｈ Ａｓｓｏｃｉａｔｅ， ＵＷＭ／Ｐｈｙｓｉｃｓ， １９００ Ｅ． Ｋｅｎｗｏｏｄ Ｂｌｖｄ， Ｍｉｌｗａｕｋｅｅ， ＷＩ５３２１７ ＝＝ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Bug in Athena?
Yay! Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Thu 11/19/2009 2:59 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Bug in Athena? Hi Scott On Thu, Nov 19, 2009 at 9:50 AM, Scott Calvin scal...@slc.edu wrote: Hi Matt, I'm the one who requested the merged reference channel. If the data is ideal, of course only one reference scan is needed. But there are two common ways it can be nonideal that are relevant: 1) The monochromator does not hold calibration; i.e. there is an energy shift between scans 2) The reference channel is very noisy, perhaps because of an inherently thick sample If 1) is a significant problem and 2) is not, then it makes sense to align the scans using the reference, at which point any reference scan will do for determination of the chemical shift of the merged data from the sample. If 2) is a significant problem and 1) is not, then it makes sense to merge the references along with the sample data, because that will make it easier to determine the chemical shift. For this case, wouldn't it be better to measure the reference separately to determine the chemical shift, and not rely on the reference channel for this purpose? How often is the reference channel both noisy AND improved by merging? That would imply a transmission measurement that was poor due to low flux. But if this is because the sample is thick as you suggest, the x-rays hitting the reference could be dominated by harmonics, and the reference data may just be bad, not noisy due to counting statistics. --Matt PS: I think that means I agree with Anatoly! ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] modeling anti-site disorder
I would make a feff.inp file corresponding to the Co as a central atom in CoGa in its original CsCl structure. Then, I would substitute all Ga atoms by Co (the two sites are crystallographically equivalent in the bcc lattice, and there is no need to do it separately for Cs and Cl sites). That would give me Co-Co contributions for all single scattering, and Co-Co-Co...-Co contributions for all multiple-scattering paths. Then, I would do the same by making a feff.inp file for Ga as an absorber in its CsCl structure. Then, again, substitute all Co for Ga and create Ga-Ga and Ga-Ga-Ga...--Ga contributions. If you REALLY want to include multiple-scattering contributions of collenear paths (going from the corner through the body center through the opposite corner along the cube diagonal) you would have to also generate mixed multiple-scattering paths by leaving one and/or two shells around Co(Ga) un-substituted in such models. That would give you Co-Ga-Ga, Co-Ga-Co, etc. linkages and their corresponding double and triple scattering collinear paths. In short, it is just to make a number of models and save the resulting feff.dat paths on your disk for each of them, and make a table for yourself, which one corresponds to what linkage. Then, you can add them all together in your fitting model and vary their mixing fractions. For example, if you want to fit the first shell only, you should fit it as: x*chi(Co-Co) + (1-x) chi(Co-Ga) for Co edge. It is of course best to do it by fitting Co and Ga edge concurrently, within the same run of your fitting program, by imposing multiple constratints on your Co-Ga distances, mixing fractions and debye-waller factors. There are large number of papers describing multiple data set (multiple edge) fitting schemes in alloys which use this very simple method. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Shashwat Sent: Fri 11/6/2009 9:37 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] modeling anti-site disorder Dear All, I am studying the local disorder caused in CoGa alloy (B2: CsCl structure) due to ball-milling; it is expected that Ga atoms substitute most of the Co atoms in the Co sublattice after prolonged milling. In order to model this anti-site disorder (occupation of Ga atoms on the Co sites) in ATOMS, I am considering to change the occupancies at the corresponding sites as given below: Before ball-milling: site a: occupancy of Ga = 1 site b: occupancy of Co = 1 (standard .cif data) After ball-milling (assuming 80% anti-site concentration): site a: occupancy of Ga = 0.2 (plus compensating vacancies) site b: occupancy of Co = 0.2 site b: occupancy of Ga = 0.8 Could anyone suggest if this approach is reasonable. Many thanks ... Regards, Shashwat winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] modeling anti-site disorder
Since in your case it is not a random alloy (I just realized that Co does not substitute for Ga, only Ga for Co, and thus this material should have compensating vacancies on Ga sites), you should include the possibility of vacancy in your fitting scheme. For the first neighbors it will be: chi(Co-1NN) = chi(Co-Ga)*y1 where y is the Ga site occupancy (provided that chi(Co-Ga) was obtained for a model CsCl structure with 8 nearest neighbors per atom). chi(Ga-1NN) = chi(Ga-Co)*x + chi(Ga-Ga)*y2 where x + y are less than 1 (again, provided that each contribution was calculated for the ideal CsCl structure where Ga substituted for Co as described below). It also help that your alloy has a 50/50 composition of Ga and Co - it is only in that case y1 is always equal to y2 and you should constrain it as such in the fit. Then, when you do the fit to the 1NN shell, do it simultaneously for both Ga and Co edges, and vary x and y. It is not easy to say in advance what kind of uncertainties you will be getting since you will vary two parameters, not one as it is usually done in the case of random alloys, and if the correlations will be large you may decide to introduce another contraint, e.g., a known value of site occupancy of Ga (i.e., y = 0.2). Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Sun 11/8/2009 12:15 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] modeling anti-site disorder I would make a feff.inp file corresponding to the Co as a central atom in CoGa in its original CsCl structure. Then, I would substitute all Ga atoms by Co (the two sites are crystallographically equivalent in the bcc lattice, and there is no need to do it separately for Cs and Cl sites). That would give me Co-Co contributions for all single scattering, and Co-Co-Co...-Co contributions for all multiple-scattering paths. Then, I would do the same by making a feff.inp file for Ga as an absorber in its CsCl structure. Then, again, substitute all Co for Ga and create Ga-Ga and Ga-Ga-Ga...--Ga contributions. If you REALLY want to include multiple-scattering contributions of collenear paths (going from the corner through the body center through the opposite corner along the cube diagonal) you would have to also generate mixed multiple-scattering paths by leaving one and/or two shells around Co(Ga) un-substituted in such models. That would give you Co-Ga-Ga, Co-Ga-Co, etc. linkages and their corresponding double and triple scattering collinear paths. In short, it is just to make a number of models and save the resulting feff.dat paths on your disk for each of them, and make a table for yourself, which one corresponds to what linkage. Then, you can add them all together in your fitting model and vary their mixing fractions. For example, if you want to fit the first shell only, you should fit it as: x*chi(Co-Co) + (1-x) chi(Co-Ga) for Co edge. It is of course best to do it by fitting Co and Ga edge concurrently, within the same run of your fitting program, by imposing multiple constratints on your Co-Ga distances, mixing fractions and debye-waller factors. There are large number of papers describing multiple data set (multiple edge) fitting schemes in alloys which use this very simple method. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Shashwat Sent: Fri 11/6/2009 9:37 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] modeling anti-site disorder Dear All, I am studying the local disorder caused in CoGa alloy (B2: CsCl structure) due to ball-milling; it is expected that Ga atoms substitute most of the Co atoms in the Co sublattice after prolonged milling. In order to model this anti-site disorder (occupation of Ga atoms on the Co sites) in ATOMS, I am considering to change the occupancies at the corresponding sites as given below: Before ball-milling: site a: occupancy of Ga = 1 site b: occupancy of Co = 1 (standard .cif data) After ball-milling (assuming 80% anti-site concentration): site a: occupancy of Ga = 0.2 (plus compensating vacancies) site b: occupancy of Co = 0.2 site b: occupancy of Ga = 0.8 Could anyone suggest if this approach is reasonable. Many thanks ... Regards, Shashwat winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] new release of my software
It is when you take a bug from a pot and then put it back in the pot. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Julie Olmsted Cross Sent: Wed 7/1/2009 4:47 PM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] new release of my software What is a repoted bug? On Jul 1, 2009, at 2:30 PM, Bruce Ravel wrote: repoted ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
Just a comment, to add some sanity in this discussion: FEFF6 is overestimating delta E0 for Pt and a few other metals. I forgot the reason but it could be the cause of a problem. I think FEFF8 is doing a better job. Fortunately - and it was checked - no other problems occur, just E0 values change, when one usees FEFF8 instead of FEFF6 in most cases. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Kropf, Arthur Jeremy Sent: Fri 6/19/2009 3:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, etc., there is no reason to assume that Eo is on the lower energy side of the peak. Jeremy Kropf -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Zajac, Dariusz A. Sent: Friday, June 19, 2009 9:45 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Scott, I am afraid that E0 jumps over the edge - see bmp's in the attachment (files with enot_12 means E0=12...). Hovewer 12 eV is still less than k=3 (the starting k value). Can it influence? I did also once more fit with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can see in the attachment too... I hope you and anyone from the mailing list don't mind that I am attaching so many files... cheers darek -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 2:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Darek, OK, so if the K, H, and O don't affect the fit much for the C and N, and the K, H, and O are returning nonsensical values, then a logical possibility is that the E0's for C and N are correct. If you add 12 eV to the E0 you chose in Athena, where in the spectrum does it fall? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W-C and W-C-N bondings. This sample is an reference sample for other cyano-brigded networks. So you suggest to focuse on K ions? how can it help with first 2 peaks? K is at ~5A. I have analysed in larger R space only to see how the spectrum behave. contribution from K, O etc. at k highers than 5A is for me too low to analyse it resonable for such compound. I have attached in the previus post the last version of results. Anyway, enots for C and N do not change if I am enlarging R region (when I am including next paths, also for K). about material I am quite sure ;) and crystal structure is from literature in the attachment you will find bmp file of the fit: data, fit, bkg and K path. fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - first C cheers darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Multiple data set fit
I don't think there is much published on that, so it is worth trying and see what you get. Anatoly -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Debora Meira Sent: Friday, April 17, 2009 10:23 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Multiple data set fit Dear all, I'd like to know a reference that has multiple set data fit as a function of temperature in nanoparticles. Is the relation of Debye Waller factor (s2 = ss2 + sd2) valid for the higher shells? In particular, can I use the Einstein model for sd2? Thanks in advance, Débora Débora M Meira Universidade Federal de São Carlos Pós-Graduação em Engenharia Química Laboratório de Catálise Tel: (16) 92461134 / (16) 34125935 _ Descubra quais produtos Windows Live tem mais a ver com você! Faça o teste! http://www.windowslive.com.br ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] huge S02 value ??
Hi Mengqiang, I have done fits of aqueous solution of NiSO4 before and obtained S02 of 0.8 for the octahedrally coordinated Ni-O shell. You did not send the mu(E) data, just chi(k), so I was not able to compare my and your raw data fully, just in k-space. Here is what I found: my data is in perfect agreement in k-space with yours, only if I move E0 down to the pre-edge region, and I suspect, therefore, it is where you chose your E0. As a result, the entire, very intense, main absorption peak became a part of your EXAFS, increasing the intensity of the k-space signal (since it became the first half-cycle of the EXAFS oscillation), and thus you got such a large S02. If you move your E0 to half-the edge jump, your result will be the same as mine, 0.8 Let me know if it helped, Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of m...@udel.edu Sent: Sat 4/4/2009 10:04 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] huge S02 value ?? Hello everyone, I have been fitting EXAFS of NiSO4 aqueous solution. The feff files were created from Ni(OH)2 using Feff7.00. During the fitting, coordination number was fixed as 6. The S02 derived from fitting is 1.22. I tried other materials for creating feff files, such as NiCO3 and NiPO4, and I got the similar S02 values. I also tried Feff6, it did not result in a reasonable S02 value, either. Anyone can tell me why it led to such high S02 value? The data file and feff input file (Feff 7) are attached. Thanks in advance. Best wishes, Mengqiang Zhu --- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Mixed Multiple scattering shell
Could be helpful: RbBr, KBr, RbCl, AgBr(x)Cl(1-x) etc.l: A. Frenkel, E. A. Stern, M. Qian, and M. Newville, Multiple - scattering x-ray-absorption fine-structure analysis and thermal expansion of alkali halides, Phys. Rev. B 48 , 12449 (1993). A. Frenkel, E. A. Stern, A. Voronel, M. Qian, and M. Newville, Buckled crystalline structure in mixed ionic salts, Phys. Rev. Lett., 71 , 3485 (1993). A. Frenkel, E. A. Stern, A. Voronel, M. Qian, and M. Newville, Solving the structure of disordered mixed salts, Phys. Rev. B 49 , 11662 (1994). A. Frenkel, A. Voronel, A. Katzir, M. Newville, and E. A. Stern, Buckled crystalline structure of disordered mixed salts, Physica B 208 209 , 334 (1995). Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Joseph Washington Sent: Wed 4/1/2009 1:55 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Mixed Multiple scattering shell Hello all, I was wondering if anyone can send any useful hints or tips for parameterizing a mixed multiple scattering shell comprised of two NaCl type strucutres, like the AgBr(1-x)Cl(x) example. Has anyone worked on fitting the third shell in that example? I am looking for examples of nacl rocksalt-like FEFF calculations that have successfully parametrized multiple scattering path contributions. Right now, after running feff, I'm using a different delr / ss term for each multiple scattering path I include. Does anyone have any clever ways of representing these in terms of the delr/ss in the first shell? Also, FEFF is telling me that the amp and mixing terms are almost completely correlated and this cause the amp term to blow up. Thanks all, I really appreciate the assistance! Joseph winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] (no subject)
I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case. However, to approach it more rigorously, the first step would be to examine the relative importance factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Wed Mar 11 09:40:31 2009 Subject: [Ifeffit] (no subject) Hi all, I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe distance ~5A). My question is how to fit the model with the data? Can I discard the contribution of multiple scattering effects to the fitting? One most important information that I want to obtain is on the Fe-Fe distance. Is it enough to conclude from the raw data FT that the Fe-Fe distance in my protein sample has been changed in comparison to the Fe-Fe distance in the model (created with Feff using the crystal structure coordinates)? I try fitting using arthemis but got bad and weird results. is there any manual or step-by step guide that I can learn how to fit model of two metal sites to my data? Anther question that I have how can I get to the past discussions in the forum- is there any database for questions and answers that I can learn on the analysis of EXAFS data? Any help will be appreciated, MJacob ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Lost second shell
Eugenio, The possibilities depend on the actual data at hand. Not seeing second shell is a relative term. Do you mean that you do not see it above noise? Then, technically, you cannot say that you do not have a second shell. Er may substitute for Zn and you will still have Er-Zn contributions expected for ZnO structure, but they will be disordered due to the large DWF and thus hide under the noise level which can be estimated as the FT magnitude at high r. However, If the data is of high quality, and you see well defined first peak (Er-O) in r-space and have negligible noise level, then you may say, with confidence, that Er does not enter ZnO lattice substitutionally. Then, indeed, it may be a surface sorption of some sort which is usually accompanied by high disorder in the second shell, as was shown to be the case in similar examples, e.g., Pb sorption of iron oxides. If you sent an image of your data in k-space and r-space it would be easier to judge. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Eugenio Otal Sent: Sun 2/1/2009 9:52 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Lost second shell Hi all, I am working with Er doped ZnO and the EXAFS measurements (Er L3) shows that I have not a second shell when I perform the FT. I checked that the phase is not destroying the signal, and that is not the guilty guy. I have two possibilities, that the erbium is segregated on the surface of the particles with a strong disordered phase that destroy second shell information (XANES simulation are different from oxide and hydroxides) or that the atoms are isolated in the surface of the particles. Should I use the card for molecules for isolated atoms? And for the disordered phase, what can I do? Is there another possibility to lose the second shell? Thanks in advance, euG winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] small-screen version of Athena document
Bruce and Matt: When Athena and Artemis are completely moved to BlackBerry and iPhone, there will be a number of really nice options out there. For example, ringtones for a really bad fit should be made very unpleasant, and even more so, when Delta E0 is out of bounds, or r-factor is greater than 0.02.. Anatoly -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Ravel, Bruce Sent: Monday, January 26, 2009 10:02 AM To: XAFS Analysis Using Ifeffit Subject: [Ifeffit] small-screen version of Athena document Hi, There is now a version of the Athena User's Guide which is intended for small-screen device (like my the new toy I got this weekend). Here is the URL: http://cars9.uchicago.edu/~ravel/software/doc/Athena/mobile/ This is very similar to the normal html version of the User's Guide, except for a few changes in layout to make it work better on a small screen. The mobile version is not perfect yet, but it is much more legible than the normal version. I have tested it mostly in Explorer on Windows Mobile 6. (I have also tested it under Opera for mobile devices, but I am not happy with how either version gets displayed there.) Hopefully this will be helpful for someone. Regards, B -- Bruce Ravel bra...@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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Cumulant expansion fittings
Hi Scott, Third cumulant in your example will not be zero because this arrangement is symmetric only on the average. Locally, the interatomic pair potential (and the cumulants are the measures of the effective pair potential) which is the sum of the two potentials - between the interestitial and its neighbors on the opposite sides)- is still asymmetric, since the repulsive bruch of the potential is steeper than the attractive brunch. You can model your situation using two anharmonic pair potentials, e.g., Morse potential (see, for example, Rehr-Hung's paper in Phys Rev B in the 1990's, and I've done such calculations too, just in the case you described) and you will obtain that the effective pair potential is still analytically anharmonic and it has a non-zero third cumulant. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Wed 1/21/2009 10:00 AM To: XAFS Analysis using Ifeffit Cc: Scott Calvin Subject: Re: [Ifeffit] Cumulant expansion fittings Hi Umesh, At first, that seems to me like a very odd thing to do. What motivates it in your case? I say that because the cumulant expansion is a series expansion like, for example, a Taylor expansion: each successive term is typically supposed to be a smaller correction than the previous one. Of course, the third cumulant implies a radially skewed distribution, which the fourth cumulant does not (i.e. the third cumulant implies that the distribution is not symmetric about some distance). If I think about it, I can perhaps construct a situation where I expect that distribution to be symmetric, but not harmonic. For example, suppose there is a rigid lattice of atoms, with other atoms arranged interstitially half-way between lattice points. If the lattice atoms are treated as nearly fixed and are all of one type, then the interstitial atoms are equally likely to be less than half-way as more than half-way from one to the next. Thus, the third cumulant is zero by symmetry. The distribution may be very far from harmonic, though; in fact, it may have two minima that are not re! solved (one slightly closer to one lattice atom, one slightly closer to the other). In that case, I'd think fitting a fourth cumulant but not a third would be justified. The bottom line is that you should have a good physical reason, having to do with symmetries, for using the fourth without the third. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 9:35 AM, umesh palikundwar wrote: Dear all, Cumulant expansion fittings are generally used, if there are more than one close shells of similar nearest neighbors (if I have understood it correctly). Third and fourth cumulants are used in the fittings to account for non-Gaussian distribution of the neighbors. I would like to known, can one use only fourth cumulant (i.e. without using the third cumulant) in the fittings? I will be highly grateful to get the answer to my query. Umesh ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Cumulant expansion fittings
quickly explore issues with computer precision of floating point numbers). The second option (often called a histogram approach in the Ifeffit world, and modeled somewhat after The GNXAS Approach) has been used successfully a number of times. --Matt On Jan 21, 2009, at 10:12 AM, Frenkel, Anatoly wrote: Hi Scott, Third cumulant in your example will not be zero because this arrangement is symmetric only on the average. Locally, the interatomic pair potential (and the cumulants are the measures of the effective pair potential) which is the sum of the two potentials - between the interestitial and its neighbors on the opposite sides)- is still asymmetric, since the repulsive bruch of the potential is steeper than the attractive brunch. You can model your situation using two anharmonic pair potentials, e.g., Morse potential (see, for example, Rehr-Hung's paper in Phys Rev B in the 1990's, and I've done such calculations too, just in the case you described) and you will obtain that the effective pair potential is still analytically anharmonic and it has a non-zero third cumulant. Anatoly ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Cumulant expansion fittings
Hi Scott, It could be an interesting direction, to use these type of lattice calculations to predict, as you suggested, what type of structures (or host compounds, for dopands), will, if not make it zero, which is probably impossible, but minimize third cumulant. Thus, it may be a rational way to design materials, at least hypothetically, with controlled thermal expansion, or even the lack of thereof. I do not care that someone may jump in and patent it, but I will appreciate a Porsche, if possible, when it is licensed. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Wed 1/21/2009 10:30 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Cumulant expansion fittings Anatoly, You're right--3 dimensions ruins my symmetry argument. My mistake. On the other hand, I still suspect that there exists a realistic case where forcing the third cumulant to zero cause a much smaller increase in chi-square than forcing the fourth cumulant to zero; e.g., a broad, flat radial distribution function. For those of you out there who are relative novices, this is an entertaining and informative discussion, but I don't want to lose track of the practical point: It is very rare to find a system where the fourth cumulant is both necessary and sufficient. Either the potentials are close enough to harmonic that the fourth cumulant makes little difference, or they are so far from harmonic that the fourth cumulant alone is not enough. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 10:11 PM, Frenkel, Anatoly wrote: Thus, I am pretty much convinced, unless there is some mistake in my reasoning, that no case exists in 3D with a zero third cumulant. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] difference between Zn-Zn/Fe and Zn-Fe paths
Hashem, it is not very clear, give mode details for each fitting scheme. Anatoly -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Hashem Stietiya Sent: Friday, January 16, 2009 12:13 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] difference between Zn-Zn/Fe and Zn-Fe paths Dear All, Is there a difference between fitting a second shell with two separate paths (Zn-Zn path and a Zn-Fe path) each with its own parameters and fitting that second shell with a combination of two paths (Zn-Zn/Fe)? When would I choose to do that latter, and how? I hope I made myself clear! Thanks, Hashem Stietiya Louisiana State University ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] How to identify N and O atoms in the first coordinate
Dear Mengqiang, To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an inverse problem (Which type of neighbors do I have) you cannot do it. However, if you believe you have some knowledge about the type of metal-oxygen bonding: either M=O or a M-O or a M-OH or a M-OH2 (the first one is the shortest and the strongest, the others may have similar interatomic distances but different bond strengths), you can advance somewhat. If you have a certain number of distinct models you want to compare the data against, it can be done via a linear combination fitting, or by direct algebraic extraction of any given type of the pair contribution from the data, as described, for example here: E. Poverenov, I. Efremenko, A. I. Frenkel, Y. Ben-David, L. J. W. Shimon, G. Leitus, J. M. L. Marin, D. Milstein. A terminal Pt(IV)-oxo complex bearing no stabilizing electron withdrawing ligands and exhibiting diverse reactivity. Nature 255, 1093-1096, 2008. See supplementary info to that article for specific details. Regards, Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of m...@udel.edu Sent: Fri 12/19/2008 4:20 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] How to identify N and O atoms in the first coordinate Hello all, Merry Christmas! I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. Best wishes, Mengqiang Zhu --- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Normalization of XANES spectra
Jens: This example may help you understand your problem: if compound a) has a small fraction of metal Cu mixed with a large fraction of oxidized Cu, while a compound b) has it the other way around, then the main (1s - 4p) absorption peak in compound a) will be smaller than in b) after edge step normalization. Edge step normalization allows to view all features in XANES and EXAFS regions as if caused by an x-absorption process in a singe atom located in a concentration-average environment of all species in the sample that contain that element. Thus, the edge step normalization does have sensitivity to the composition of the sampe. Or, I misunderstood your question? Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Wed Oct 29 10:02:54 2008 Subject: [Ifeffit] Normalization of XANES spectra Hi everyone, I have a general question: I know Normalizing is something we do so that we can compare samples measured under different experimental conditions (removes the effect of different gains ...) but I have problems in understanding and applying normalization when also quantitative conclusions are needed when comparing different spectra. If I have two XANES spectra (a) and (b) measure under the same conditions but with different concentration of the absorbing atom with in different molecules.If both normalized spectra show a peak 1 , but this peak is higher in intensity in spectrum (a) than in spectrum (b), does this mean that compound which produced peak 1 is also absolute higher in concentration in sample/spectrum (a) or do I loose this information after normalization? Or can I just say: in the normalized spectrum (a) peak 1 is higher than peak 2 suggesting that the compound leading to peak 1 is more abundant (just relative proportions).But I can't say: The intensity of peak 1 in the also normalized spectrum 2 is lower than in spectrum one, Therefore, the compound leading to peak 1 is less abundant in spectrum/sample 2. I hope somebody can help me to understand this issue. Thanks a lot, jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fit XANES spectra using Athena
PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Sun Oct 26 13:05:32 2008 Subject: Re: [Ifeffit] Fit XANES spectra using Athena Jenny, I'm relatively new to the community XAFS, and have not done any sulfur work thus far... but have you considered doing a principal component analysis on the XANES of your samples? This method should help you identify how many phases are present (assuming that all of your samples aren't exactly identical; however the maximum number of independent phases it will return is the number of samples you tested), and with your standards you might be able to eliminate some of the phases (from the standards) as well as identify some of the phases that are in your sample. (There is software that will do this in the IFFEFIT package under Sixpack -- 'pc analysis') Andrew Campos ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Comparison of amp between Feff8.40 and feff6 - Curved waves or Plane waves?
By looking at the FEFF.inp file it appears that the path in question is a Ti-O-Ti where the angle of this linkage is very close to 180 degree (had it been 180 degree, the total length would be not 3.9317 but either 3.90500 or 4.15600. In a perovskite with Ti on center such angle would be 180 degree but in your input file you have TiO6 octahedron displaced relative to the Pb corners in 100 direction (also known as tetragonal distortion). Still, the angle is close to 180 degree which makes a contribution of forward scattering, triple-scattering paths that go through O in forward direction twice, the strongest - and that should explain why your path amplitude increased over 100 percent. Why the two programs give different amplitude, must be a bug, as Bruce and Scott explained. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Ying Zou Sent: Thursday, August 28, 2008 6:42 PM To: ifeffit Subject: Re: [Ifeffit] Comparison of amp between Feff8.40 and feff6 - Curved waves or Plane waves? Dear all, While I am calculating FEFF path through Feff8.40 using the feff8.inp as attached, I notice that the value of amp shown on FEFF interpretation page for some paths goes over 100%. For example, path 14 has a Reff=3.9317 far away from first shell, yet it has an amp=169.913. On the contrary, if I do the same in Artemis through embedded Feff6.0(using feff6.inp), none of paths has an amp over 100%. I am guessing this could be all right because Feff8 is using curved waves Feff6 instead plane waves. Any comments on this would be greatly appreciated! Ying Ying Zou Research Assoc., Dr.Phys. Physics Department, UWM ===feff8.inp=== * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * potxsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 * *RPATH 0.1 * emin emax resolution *LDOS -2020 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22Ti -1 -1 0 18O -1 -1 3 2 82Pb -1 -1 1 3 22Ti -1 -1 1 ATOMS 0.0 0.0 0.00 Ti 0.0 0.0 0.0-1.766301 Oapical 1.76630 1.95250 0.0 0.324171 Oplanar 1.97923 0.0-1.95250 0.324171 Oplanar 1.97923 -1.95250 0.0 0.324171 Oplanar 1.97923 0.0 1.95250 0.324171 Oplanar 1.97923 0.0 0.0 2.389701 Oapical 2.38970 -1.95250-1.95250 1.915922 Pb 3.36084 1.95250-1.95250 1.915922 Pb 3.36084 -1.95250 1.95250 1.915922 Pb 3.36084 1.95250 1.95250 1.915922 Pb 3.36084 1.95250-1.95250-2.240082 Pb 3.55563 -1.95250 1.95250-2.240082 Pb 3.55563 -1.95250-1.95250-2.240082 Pb 3.55563 1.95250 1.95250-2.240082 Pb 3.55563 -3.90500 0.0 0.03 Ti 3.90500 0.0 3.90500 0.03 Ti 3.90500 3.90500 0.0 0.03 Ti 3.90500 0.0-3.90500 0.03 Ti 3.90500 0.0 0.0 4.156003 Ti 4.15600 0.0 0.0-4.156003 Ti 4.15600 3.90500 0.0-1.766301 Oapical 4.28589 0.0-3.90500-1.766301 Oapical 4.28589 -3.90500 0.0-1.766301 Oapical 4.28589 0.0 3.90500-1.766301 Oapical 4.28589 END feff6.inp== * This
Re: [Ifeffit] questions concerning paper
We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and mythological sense. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: Ravel, Bruce; XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Thu May 22 14:30:38 2008 Subject: Re: [Ifeffit] questions concerning paper I loved it also, thanks Matt :-) May i cite your Odysseus explanation in my diploma thesis? ;) Original-Nachricht Datum: Thu, 22 May 2008 12:40:01 -0400 Von: Bruce Ravel [EMAIL PROTECTED] An: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Betreff: Re: [Ifeffit] questions concerning paper Matt, That was awesome! I **loved** the Odysseus explanation of the exafs equation. Quite possibly the best Ifeffit mailing list post ever. B -- Bruce Ravel [EMAIL PROTECTED] 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/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/[EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter
There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species. Please clarify. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe SCK·CEN Disclaimer http://www.sckcen.be/emaildisclaimer.html ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter
An option could be, if you collected just one spectrum, to construct 1st shell EXAFS data for each compound using FEFF and use a linear combination option of Athena to see if there is any value of the mixing fraction of these two theoretical compounds that resemble good fit. You will still need to know the best fit value of S02 obtained previously from standard uranium compounds and use same sigma2 for all U-O bonds. You can define your fitting range using large value of kmin to emphasize the first shell signal better, and do fititing in k space with k-weighting of 1 for the same reason. It can all be done witinin Athena. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Tue Apr 29 10:23:10 2008 Subject: Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species. Please clarify. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples. Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach. Can someone comment on this? Many thanks in advance, Christophe SCK·CEN Disclaimer http://www.sckcen.be/emaildisclaimer.html ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] cofe2o4 chi data
I have it. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Tai-Yen Chen Sent: Monday, January 14, 2008 12:27 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] cofe2o4 chi data Dear all Does anyone have cofe2o4 chi data by anychance or know where I can find the data? thanks a lot!! Best Regard. TaiYen Chen 979-739-7772 Department of Chemistry Texas AM University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Log-Ratio
It adds (or subtracts) 2pi to the phase difference between the unkown and the standard as some times it does not eztrapolate to zero as 2k*delta r term should. Anatoly -Original Message- From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Wed Dec 05 06:22:28 2007 Subject: [Ifeffit] Log-Ratio Dear all, i have a question to the Log-Ratio/Phase-Differnce Analysis in Athena. What means the parameter 2pi jump? I did not find any help file for the ratio method. Best regards Jörg Haug ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Exafs distance resolution
Yes and a very important one - see Ed Stern's talk at the 2001 EXAFS workshop advanced methods and tricks etc. His talk is online. Anatoly -Original Message- From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Tue Nov 27 04:44:48 2007 Subject: [Ifeffit] Exafs distance resolution Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to the fourier transform traditionally used for exafs analysis. If exafs fitting is done in k-space, on the raw exafs data without applying fourier or any other filtering transformation is there a physical limitation determining exafs bond distance resolution? This question comes down to the following practical problem. If one has a theoretical model developed using computational chemistry that predicts two different bond lengths within one shell, e.g. an octahedral metal center surrounded by 6 oxygen atoms and this shell is predicted to be split in three subshells for wich the bond length differs only 0.05 angstroms; and this model can be fit very well in k-space with the splitted shell, off course keeping the number of fit parameters below the nyquist criterion. Is there in such a case any physical reason not to fit the experimental data with the splitted shell , but with an averaged 6-atom shell with a larger Debye Waller factor? Best regards, Eric Breynaert ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] [howto] configurational average in EXAFS with FEFF
Mauro, If I do understand your question correctly, you may be asking how to handle a multiple of inequivalent sites in atomic clusters with N atoms, where each atom generates a unique sequence of single- and multiple-scattering paths. A possible solution is given in this article: D. Glasner and A. I. Frenkel Geometrical characteristics of regular polyhedra: Application to EXAFS studies of nanoclusters AIP Conf. Proc. 882 , 746-748 (2007). https://exchange2000.bnl.gov/exchange/frenkel/Drafts/RE:%20%5BIfeffit%5D%20%5Bhowto%5D%20configurational%20average%20in%20EXAFS%20with%20FEFF.EML/XAFS13-Proc/clusters-geometry.pdf The PDF is here: http://pubweb.bnl.gov/users/frenkel/www/XAFS13-Proc/clusters-geometry.pdf It is the same type of averaging and radial distribution analysis approach that you are proposing unless I misunderstood your question. Anatoly From: [EMAIL PROTECTED] on behalf of Mauro Rovezzi Sent: Tue 3/27/2007 9:38 AM To: Ifeffit-ML Subject: [Ifeffit] [howto] configurational average in EXAFS with FEFF Dear all, I would like your point of view on how to approach configurational average in EXAFS analysis with FEFF (let's not consider GNXAS for the moment). In particular, I'm trying to combine ab-initio DFT numerical simulations with EXAFS for doped semiconductors where in the minimized cluster there are N absorbing atoms. Usually I don't use the CFAVERAGE card because fractional degeneracies are not taken into account and, to have a qualitative analysis, I calculate an extended-XANES (up to 8.0 A^-1) for each cluster - where each absorbing atom is shifted to (0,0,0) - and then I average over all single-cluster signals. Well, at this point my question is: how to proceed in the quantitative analysis with Ifeffit? In fact, considering only single-scattering expansion for all the clusters the result could be seen as a radial distribution for each scattering pair where the integral gives the coordination number and the FWHM a structural Debye-Waller factor. How to combine these informations? Thanks for the answers, Mauro -- Mauro Rovezzi [EMAIL PROTECTED] PhD student - GILDA BM08 c/o ESRF (Grenoble, FR) ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] E0 for bulk crystals and nanoparticles
That's true - if there are no shift-like changes in XANES, E0 may be constrained. Anatoly From: [EMAIL PROTECTED] on behalf of Scott Calvin Sent: Sun 2/25/2007 10:20 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] E0 for bulk crystals and nanoparticles Hi again, Hmm...Anatoly makes good points here. But I'd say that most of those kinds of things should give changes in XANES. If you don't see changes in XANES as you change the temperature, I'd still feel pretty comfortable constraining the E0 to be the same for all temperatures between 10 and 300 K. And that lets you decouple E0 from lattice expansion and the third cumulant, which was your goal. --Scott Calvin Sarah Lawrence College At 10:06 PM 2/25/2007, Anatoly wrote: Leandro - depending on the details of your system and treatment, electronic structure of the nanoparticle may or may not change at elevated temperatures. It may change as a result of hydrogen chemisorption, charge exchange with support, ligand desorption, oxidation, etc. As a result, you may observe changes in XANES that may be due to the change in core hole screening or Fermi energy change or both (depending on the degree of metallicity of the nanoparticle). There are many references in literature demonsrating each effect that I mentioned. Thus, keeping E0 the same at all temperatures may or may not be wise, depending on the magnitude of the edge shift that can, in principle, be observed at different temperatures. If that happens, you may want to compare the resuls obtained by keeping E0 the same vs those when E0 was allowed to vary independently for each scan. In short, there is no one fits all answer. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Alloy EXAFS data fitting
Hey Xianqin, If it is a (bulk) alloy system, and if A-A and A-B are 1NN pairs, then, unless there is a phase transition or other perturbations that can involve chemical changes either within the sample of heterogeneous (say, nanophase formation of different composition) or homogeneous (say, ordering changes from random solid solution to an intermetallic compound, as in Au3Cu etc.) the coord. numbers should stay the same. Thus, it is not physical to vary them differently. Thus, if the coord. number of the A-1NN is 12 (as in fcc) then set NB=12-NA worry only that NA comes out to be between 0 and 12. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of XQ WANG Sent: Thursday, August 31, 2006 2:54 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Alloy EXAFS data fitting Dear all, I am trying to understand some EXAFS data collected on an alloy system (sorry I can't say it since these are not my data). It is a two-element alloy system, name AB. Their fitting results showed that A-B coordination number and A-A coordination number did not follow the similar trend with the temperature increase. I am just wondering if this case is possible? I had thought if A-A and A-B are from the same compound, they should follow the same trend. Maybe I am wrong. Another question is whether it is OK to combine coordination of A-A in A compound with CN of A-A in AB alloy if these two A-A bond distances are very close? If this case is OK, then combination of A-A CN and CN of A-B could follow differnt trend (I guess). But I thought we could not combine CN from different materials. Maybe I am wrong again?? Please let me know any suggestions concerning this situation. Thanks! Xianqin _ Check the weather nationwide with MSN Search: Try it now! http://search.msn.com/results.aspx?q=weatherFORM=WLMTAG ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
RE: [Ifeffit] Right way of choosing E0 in Athena
Vadim, The ss2 of multiple-scattering (ms) paths and single-scattering (ss) paths are not simply related unless the legs in the ms paths are collinear. In that case, as published in Frenkel, Stern, Qian, Newville, Phys. Rev. B, 48, 12449 (1993), if the intervening atom is a first nearest neighbor of the absorber, this atom, to a good approximation, does not affect the ss2 of the double scattering and triple-scattering path connecting the absorber, the 1NN and the 1NN to the intervening atom in the forward scattering direction. It also describes other relationships between the ss2 of the 1NN path and the ms paths when the intervening atom is the absorber. The complete set of these relationships can be found in the Appendix of an article by D. Pease, A. Frenkel et al., - I will send it to you as an attachement in a separate email. Anatoly Frenkel Yeshiva University -Original Message- From: [EMAIL PROTECTED] on behalf of Vadim G Palshin Sent: Sun 7/2/2006 5:25 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Right way of choosing E0 in Athena Since you know the spectra are well calibrated relative to one another, I would use a single E0 for all background subtractions. In such a situation, I tend to play with the background parameters for one of the spectra and then apply these background parameters to all other spectra. Thanks, Matt! Yes, that's pretty much what I have been doing, just had some trouble getting reasonable fit values for E0's in my last set of samples. Aligning chi(k) of the standard to theory - great guide, Shelly! - and then applying the same parameters to the other spectra helped solve this. Now, more questions: 1. Many experts advise to do multiple k-weight fitting to deal with correlated variables. Should one always use multiple k-weights, or is it better to switch to one kw value once the correlations are taken care of - to refine the remaining variables? Does it make any difference? 2. When modeling the Debye-Waller factors for multiple-scattering paths, is it possible to express them in terms of the sigma^2's of single-scattering paths that correspond to the atoms involved in the multiple scattering events; i.e. for a core-atomA-atomB-core path, can sigma^2 be obtained by some combination of core-atomA and core-atomB sigmas? It seems intuitively that they should be related, and also that the amplitudes of multiple scattering paths should be more sensitive to disorder. Does this make any sense? Thanks again for your replies! Vadim. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
