August 2006 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Re: [Ifeffit] OS X: (was: new release (061) of my codes)
by Matt Newville 28 Nov '06

28 Nov '06

Bruce, everyone Mac-interested: I believe many of the problems that have been seen come from the idea that one can install the binary, and then expect upgrading from source to work. I believe this will always be fragile: Mac OS X does not come with an installed compiler for C or Fortran (they are available). For these machines, the standard 'perl Makefile.PL' will fail. Whether this is the cause of the recent problems is a separate question. The way I see it, there are two ways to go here: A) assume that Mac is "just-another-version-of-Unix" so that installations and upgrading from source should work. B) assume that Mac is as special as Windows, and that ALL installations and upgrades need an actual installer or a simple, foolproof upgrade mechanism that involves no users typing at a terminal. An "upgrade" could simply consist of a zip file of new files, but we'd need a program (like exists for Windows) that did this upgrading semi-automatically. If the perl upgrades were "pure perl" and did not include a compilation, it could probably be made to work more reliably. But I don't quite see that as the right solution, because it still expects upgrades to happen with a different model than the original installation. Personally, I'm not thrilled about having to support option A. Option B means that someone will have to do the work of making and testing binary installers and upgrades. It will probably mean having to stick close to Mac OS X upgrade cycle. But I think we need a consensus on this. Any opinions? --Matt

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silly me!
by Bruce Ravel 06 Sep '06

06 Sep '06

Hi folks, It just occured to me that I didn't mention the web page where I document all the changes to my codes in the most recent release. Athena especially has a number of interesting new features. You might want to take a look at this http://cars9.uchicago.edu/iffwiki/HoraeVersion062 B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Alloy EXAFS data fitting
by XQ WANG 31 Aug '06

31 Aug '06

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=weather&FORM=WLMTAG

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Re: problem with normalization
by Bernd Griesebock 31 Aug '06

31 Aug '06

Dear Bruce, thank you very much for the answer. I forgot to say that I load this macro which athena uses for the step function at the very beginning of using ifeffit. Your advise make me looking at my macro file, where I found a little typing error. That was it! Thank you so much! Regards Bernd > Message: 2 > Date: Thu, 31 Aug 2006 09:33:26 -0500 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] problem with normalization > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200608310933.27010.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-6" > > On Thursday 31 August 2006 02:57, Bernd Griesebock wrote: > >> Hi there, >> >> I have a litte question about normalizing data using the commands that >> athena uses. >> >> I used the following commands (in an ifeffit shell), which I copied from >> the ifeffit buffer from athena, but I replaced most of the values with >> the corresponding variables (see at the "set" commands): >> > > I have taken the liberty of numbering and slightly rearranging the lines of > your script. > > > 1 > read_data(file="Rh_sample_11.dat.spektrum.00040", group=rh, no_sort) > 2 > set ___n = npts(rh.1) > 3 > set rh.energy = 1000*rh.1 > 4 > set rh.xmu = (rh.2) / (rh.3) > 5 > pre_edge("rh.energy+0", rh.xmu) > 6 > erase rh.4 > 7 > show e0 > 8 > pre_edge("rh.energy+0", rh.xmu, e0=23228.9989104549, pre1=-150, > 9 > pre2=-30, norm_order=3, norm1=150, norm2=514.053) > 10 > spline("rh.energy+0", rh.xmu, e0=23228.9989104549, rbkg=1.0, kmin=0.5, > 11 > kmax=12.695, kweight=1, dk=0, kwindow=kaiser-bessel, pre1=-150, > 12 > pre2=-30, norm_order=3, norm1=150, norm2=514.053, clamp2=24, > 13 > nclamp=5, interp=quad) > 14 > set rh.preline = pre_offset+pre_slope*(rh.energy + 0) > 15 > set rh.postline = > 16 > norm_c0+norm_c1*(rh.energy+0.000000)+norm_c2*(rh.energy+0.000000)**2 > 17 > step rh.energy e0 rh.theta > 18 > set flat_c0 =norm_c0 - pre_offset > 19 > set flat_c1 =norm_c1 - pre_slope > 20 > set flat_c2 =norm_c2 > 21 > set rh.line = (flat_c0 + flat_c1*(rh.energy+0) + > 22 > flat_c2*(rh.energy+0)**2) > 23 > set rh.flat = (rh.pre + (edge_step - rh.line)*rh.theta) / edge_step > 24 > set rh.fbkg = (rh.bkg-rh.preline+(edge_step-rh.line)*rh.theta)/edge_step > 25 > newplot(rh.energy+0, "1*rh.fbkg+0", xlabel="E (eV)", ylabel="norm > 26 > x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", > 27 > xmin=23028.99891, xmax=24028.99891, style=lines, color="red", > 28 > key=bkg, title="rh_sample_11") > >> At this point athena plots the normalized background function with all >> data points in the post edge region at arround 1. This is exactly what I >> want, but in the ifeffit shell I get an error message: >> ** plot error: no data in y array >> >> Ifeffit> show rh.fbkg >> rh.fbkg = 399 pts [-0.2709E-01: 1.205 ] >> >> So there is data in that array! Using the following plot command: >> >> newplot(rh.energy+0, rh.fbkg, xlabel="E (eV)", ylabel="norm x\gm(E)", >> fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, >> xmax=24028.99891, style=lines, color="red", key=bkg, >> title="rh_sample_11") >> >> plots the background function but not normalized in the sense, that the >> data points in post edge region are at arround 1. >> >> Where is my mistake??? If you need some plot examples please feel free >> to ask for them. >> > > > I suspect that the problem is in line 17 of the ifeffit script. "step" is not > a built-in Ifeffit command. Instead it is a macro that Athena defines when > you start the program. Fire up Athena and look near the beginning of the > ifeffit buffer -- you'll see where the macro is defined. > > The purpose of the macro is to define a step function centered at a given > energy and placed on a particular energy grid. If you don't define this macro > the .theta array is undefined, leading to trouble with the .flat and .fbkg > arrays. > > Hope that helps, > B > > >

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problem with normalization
by Bernd Griesebock 31 Aug '06

31 Aug '06

Hi there, I have a litte question about normalizing data using the commands that athena uses. I used the following commands (in an ifeffit shell), which I copied from the ifeffit buffer from athena, but I replaced most of the values with the corresponding variables (see at the "set" commands): read_data(file="Rh_sample_11.dat.spektrum.00040", group=rh, no_sort) set ___n = npts(rh.1) set rh.energy = 1000*rh.1 set rh.xmu = (rh.2) / (rh.3) pre_edge("rh.energy+0", rh.xmu) erase rh.4 show e0 pre_edge("rh.energy+0", rh.xmu, e0=23228.9989104549, pre1=-150, pre2=-30, norm_order=3, norm1=150, norm2=514.053) spline("rh.energy+0", rh.xmu, e0=23228.9989104549, rbkg=1.0, kmin=0.5, kmax=12.695, kweight=1, dk=0, kwindow=kaiser-bessel, pre1=-150, pre2=-30, norm_order=3, norm1=150, norm2=514.053, clamp2=24, nclamp=5, interp=quad) set rh.preline = pre_offset+pre_slope*(rh.energy + 0) set rh.postline = norm_c0+norm_c1*(rh.energy+0.000000)+norm_c2*(rh.energy+0.000000)**2 step rh.energy e0 rh.theta set flat_c0 =norm_c0 - pre_offset set flat_c1 =norm_c1 - pre_slope set flat_c2 =norm_c2 set rh.line = (flat_c0 + flat_c1*(rh.energy+0) + flat_c2*(rh.energy+0)**2) set rh.flat = (rh.pre + (edge_step - rh.line)*rh.theta) / edge_step set rh.fbkg = (rh.bkg-rh.preline+(edge_step-rh.line)*rh.theta)/edge_step newplot(rh.energy+0, "1*rh.fbkg+0", xlabel="E (eV)", ylabel="norm x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, xmax=24028.99891, style=lines, color="red", key=bkg, title="rh_sample_11") At this point athena plots the normalized background function with all data points in the post edge region at arround 1. This is exactly what I want, but in the ifeffit shell I get an error message: ** plot error: no data in y array Ifeffit> show rh.fbkg rh.fbkg = 399 pts [-0.2709E-01: 1.205 ] So there is data in that array! Using the following plot command: newplot(rh.energy+0, rh.fbkg, xlabel="E (eV)", ylabel="norm x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82", xmin=23028.99891, xmax=24028.99891, style=lines, color="red", key=bkg, title="rh_sample_11") plots the background function but not normalized in the sense, that the data points in post edge region are at arround 1. Where is my mistake??? If you need some plot examples please feel free to ask for them. Thank you for your help in advance. Best regards Bernd

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Contributions from 2 paths
by McPheeters, Matthew 25 Aug '06

25 Aug '06

Dear All, I am analyzing Neodymium Oxide with G.I.Feffit. I have two paths and I'm having trouble showing the contributions (chi data, Forward and back Fouirer Transform) to the fit from each path. I ran into a problem with the Sigma2 for the second path, sigma2_2. When I guess sigma2_2 I can print out the individual path contributions to the fit with the fitted parameters factored in. If I define, def ( ), sigma2_2 = sigma2_1 then the path contributions that I try to print out do not have the debye-waller parameters factored in. I have tried the analysis with feffit245 and the path contributions it shows seem be consistent with the fit. So, I figure I must be writing something wrong in my command file. I have attached the fit command files, log files, and contribution graphs for when I guess sigma2_2 and define sigma2_2 = sigma2_1. In the graphs black = data, red = fit, green= contribution from path 2, blue= contribution from path 1. Thanks, Matt McPheeters Dr. Mayanovic's Lab Assistant Missouri State University

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Problem loading application on Mac OSX 10.4.7
by chessel＠ualberta.ca 22 Aug '06

22 Aug '06

Hello, I just downloaded ifeffit version - ifeffit-1-1.2.9-Mac10.4_horae62_pkg.dmg - to my Mac - Version 10.4.7 - and am having some trouble running the programs. When I double click on the application file I am prompted to "Please pick an output device;" my choices are either "X11 graphics" or "Aquaterm." When I choose either of them, the application fails and the icon disappears from the dock. Has anyone else encountered this problem? Is there a different version available for Mac OSX 10.4.7? Thanks, Colin

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Mehmet Alper Sahiner/FAC/SHU is out of the office.
by Mehmet Sahiner 22 Aug '06

22 Aug '06

I will be out of the office starting 08/21/2006 and will not return until 09/05/2006. I will be out of the office betwen 8/21/06-9/05/06. Alper

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