April 2004 - Ifeffit - millenia.cars.aps.anl.gov

new versions of my programs
by Bruce Ravel 22 Apr '04

22 Apr '04

Hi folks, I have just finished the new release of my data analysis programs: Athena 0.8.027 and Artemis 0.7.003. This release contains mostly bug fixes and feature enhancements. As you may recall, last month's release of Artemis generated a very large amount of traffic on this list due to several problems surrounding the new project file format and other file management issues. I have addressed almost all of the problems that were reported and am cautiously optimistic that this release of Artemis will be much more solid than the last. There is one significant new feature in this release -- the program Hephaestus, which will be a permanent part of future releases. Hephaestus replaces the Atoms Periodic Table and expands greatly upon its functionality. I will describe Hephaestus in more detail in a message later this morning. Source code tarballs are already available on my web site and at SourceForge. The Windows updater package will be available soon. Change logs with all the details of the new features of Athena and Artemis are on my web site. Lots of people helped out this time with excellent suggestions and bug reports. Special thanks to Mauro Ravezzi, David Barton, Peter Pfalzer, Gerrit Schmithals, Stanislav Stoupin, and Shelly Kelly. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: Truncate, Post-edge Athena Issues
by Bruce Ravel 21 Apr '04

21 Apr '04

On Tuesday 20 April 2004 11:56 pm, Barton, David (DG) wrote: > One final question. I often see a strong discontinuity near the edge > energy in the background subtraction. The attached Athena project clearly > shows this discontinuity, any thoughts about this? Dave, I am CCing the answer to this one to the mailing list. The background spline is evaluated between the energies (or k values) specified. Outside that range the spline is not evaluated at all. To make the arrays conatining the data and background spectra easier to handle when interacting directly with Ifeffit, Matt wisely chose to make the background array the same length as the data array. At energies within the spline range, the background array contains the background spline. Outside the spline range, that background array contains the original data. Not only does this make the arays the same length, but it makes computation of chi(E) completely trivial -- you can just subtract the background array from the data array point by point. If the first or last few points of the spline are not near in value to the data (which can happen since a spline can be poorly constrained at the ends), then the plot of the data and background arrays will be as you described. The background array will have a discontinuity, but that is not a bug. Regardless of the constraint of the spline near its ends, the criterion for choosing the spline is met. That is, the spline is always chosen to minimize the low-R Fourier components (possibly with respect to a standard spectrum). Sometimes this minimization results in a spline that deviates from the data at the ends. Constraining that deviation is the purpose of the spline clamps. > I typically have ignored this since it is outside the EXAFS fitting > region and the XANES background subtraction routines are not > affected by it. That is completely correct. HTH, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Athena Minor Error
by Norbert Weiher 21 Apr '04

21 Apr '04

Hey Bruce, I found a minor error in athena: When want to select the spline range for my spectrum and accidentially press the "k" button (but have the spectrum plotted in E), athena crashes as soon as I click on the graph to select some value. Its not bothering much (actually I should be aware of pressing the right button - I know :)), just wanted to tell you. Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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noisy spectrum and AUTOBK
by gabriel rosenblum 20 Apr '04

20 Apr '04

Hi all. Sorry for not being specific. I am trying to do background removal with AUTOBK. The parameter emax is present at autobk.inp file under the UWEXAFS package. Emax � means the region after the edge in the xmu file to be taken by AUTOBK to perform the spline. For example, if emax is set to 400 eV, it means the spline and the subtraction will be carried 400 eV over the edge. After the subtraction I FT the data and observe chi(R ). I guess the noise problem is more pronounced 350 to 550 eV over the edge, and not near the edge. However I will sure try the recipe offered by Shelly. Still waiting for an answer. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25� http://photos.yahoo.com/ph/print_splash

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RE: [Ifeffit] Noisy spectrum and AUTOBK
by Kelly, Shelly D. 20 Apr '04

20 Apr '04

Hi Gabi, I need some more information to address your concerns. See below: > I have a question regarding noisy EXAFS, since I > analyze biological zinc samples. I have seen Bruce's > data and it is quiet as a sleeping snail all the way > till chi(k)=16, however I have a completely different > situation since I encounter noise at high chi(k) and I > need an advice from whoever can supply it. > As I use AUTOBK with emax set to maximum I observe > chi(k) which is quiet at 0-9, and at 9-12 I obsrerve > clearly the oscillations but with the addition of > small spikes resulting from noise. At chi (R ) I see > the first shell peak at 1.5A with amplitude of 1. > Adjacent to this peak I observe a small peak at 1A > with 0.5 amplitude. What is emax? Do you mean that you set Ezero to the maximum of the first derivative of the xmu data? What does the background function look like? Does it have a large spike right at the beginning? If so adjusting Ezero can help reduce that. Usually kmin should be small like zero. The exception being if you have a large white line (peak at the top of the absorption step). Then you want to increase kmin to help the bkg go over the white line >As I change Rbkg and Knin I cannot > get rid of the small peak; the left region of the > small peak is situated between 0.5 to 1A at chi(R ), If you increase Rbkg to 2.5 you must be able to get rid of the low r peak. Although I don't recommend that you do that, for real. Try it, just for fun and see. Often the low r peaks really don't matter. To get rid of them, the most robust method is to fit the first shell peak with a theory then pull the fit back into Athena and remove the background with the fit as a "standard". --see below for a recipe. > and my attempts to keep this region "clean" failed. > However, if I lower emax to 400, corresponding to > approx. 10 at chi(K), and Fourier-transform the region > between 2 to 9 (the quiet region), the small peak > disappears and the region at Chi (R ) between 0 to 1A > is "clean", but since I utilize less information the > peaks at chi (R ) have lower resolution. > My questions are: > 1. What is the source of the small peak ? > 2. Is it a real contribution from scattering ligands ? > 3. How should I treat the small peak. > 4. Should I get rid of it by all means ? if so, how ? I don't understand the emax variable. But, Since the low r peak disappears as you move the k-range up a bit then I believe the low r peak is an incorrect bkg removal that can be fixed by including a standard in Athena. Here is a recipe to get a nice background function. I'm sure Bruce and Matt have this written down somewhere too. 1) Fit the first shell in Artemis. Using a limited k-range where you are really confident that the oscillations are not distorted by the bkg. k=[2:9] determine a value for deltaE, deltaR and N or SO2. DetlaR, N or SO2, should be reasonable. The value for DeltaE depends on your choice in Athena. 2) You have to decide if you original choice of Ezero (in Athena) was close enough. If deltaE (from the Artemis fit) is more than +/- 10eV you need to go back into Athena move Ezero and redo step 1. The rule is: deltaE + Ezero should be somewhere on the edge of the xmu data. 2b) If you can not get a reasonable deltaE then rethink your theory. Maybe R in the theory is way wrong? Maybe two shells are needed instead of one? Or maybe Ezero in Athena is way off? Maybe your k-range needs to be even smaller. 2c) Still having trouble with step 1? --you can also change the k-weight for the background removal. For this first step it is often useful to crank it up, so that the higher k-region has a nice bkg and then just don't use the low k-region in the fit to get the theory to "line up" with the data. For example: use k=[4:12] in Artemis, with k-weight=3 in Athena for the background. 3) Now you have a theory for the first shell peak with an Ezero somewhere on the edge, we want to match-up the data and theory before the first shell peak. Go back into Athena, read in the fit in k-space. Then highlight your data, pull down the standard menu and select the theory data file. Redo the bkg by plotting both the theory and the data in k-space. They should look similar at low k. Then plot the FT (using the same parameters as you did in Artemis) and they should look similar below the edge. 3b) If not: --If they do not cross zero in k-space (at low k-values) at the same places you need to adjust Ezero. --If they do not have the same amplitude you may need to adjust Rbkg slightly. Remember Rbkg can not be greater than Kmin in for the data region used in Artemis, but they can be equal and often are equal. 4) Redo the fit and add some more shells as needed, increase the data range in k-space. See how much data you can use and still get reasonable fit and uncertainties. 5) At the very end you might want to repeat this procedure to make a pretty picture for your pub. HTH Shelly

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Noisy spectrum and AUTOBK
by gabriel rosenblum 20 Apr '04

20 Apr '04

Hi all I have a question regarding noisy EXAFS, since I analyze biological zinc samples. I have seen Bruce�s data and it is quiet as a sleeping snail all the way till chi(k)=16, however I have a completely different situation since I encounter noise at high chi(k) and I need an advice from whoever can supply it. As I use AUTOBK with emax set to maximum I observe chi(k) which is quiet at 0-9, and at 9-12 I obsrerve clearly the oscillations but with the addition of small spikes resulting from noise. At chi (R ) I see the first shell peak at 1.5A with amplitude of 1. Adjacent to this peak I observe a small peak at 1A with 0.5 amplitude. As I change Rbkg and Knin I cannot get rid of the small peak; the left region of the small peak is situated between 0.5 to 1A at chi(R ), and my attempts to keep this region �clean� failed. However, if I lower emax to 400, corresponding to approx. 10 at chi(K), and fourier-transform the region between 2 to 9 (the quiet region), the small peak disappears and the region at Chi (R ) between 0 to 1A is �clean�, but since I utilize less information the peaks at chi (R ) have lower resolution. My questions are: 1. What is the source of the small peak ? 2. Is it a real contribution from scattering ligands ? 3. How should I treat the small peak. 4. Should I get rid of it by all means ? if so, how ? My confusion arises from the fact that AUTOBK should get rid of atomic exafs at chi(k), consequently, the contributions at chi (R ) between 0 to 1A should get lower. In my case it seems that this contribution is lower, but it still exist with half the amplitude of the first shell peak. Any help would be appreciated. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25� http://photos.yahoo.com/ph/print_splash

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[proposal] Artemis plotting option
by mauro＠rulp.org 20 Apr '04

20 Apr '04

Hi, I would like to know if it is possible to include in Artemis the "stack" plotting option, like the Athena's one. In fact, setting a y-offset value for the selected chi/paths/residual could be very useful. Thanks, M -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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S02-Interpretation
by Norbert Weiher 20 Apr '04

20 Apr '04

Dear Friends, I would like to ask a question on the interpretation of S02 in a fit. Although there has been some discussion on this parameter, I did not find exactly what I was looking for. Here it goes: To my knowledge, S02 accounts for intrinsic as well as extrinsic losses in the sample. Now, if I have two samples and determined the S02 value according to the way which Bruce has in his supplement to the FEFFIT course, I find two differing values for electrochemically prepared oxide (0.74) and crystalline gold oxide (0.92). This difference is independent of beamlines I measured and I can exclude quite safely that it is just a measurement error - it comes up with any spectrum I recorded on these systems. When discussing this with my colleagues, we interpreted the S02 difference as an indication of more disorder in case of the electrochemical system (which would well fit to my picture of the whole thing). BUT: Is there any physical reason to assign a difference in S02 (for "chemically equivalent" systems, where just the preparation is different) to a structural disorder? Regards, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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Windows Update
by Matt Newville 19 Apr '04

19 Apr '04

Hi Folks, I've posted a windows update that includes Bruce's latest Athena, and Hephaestus, that he described a week ago. It also has a couple other fixes: - a problem with runprog.exe got fixed so that running autobk,feffit, and feff6 now works correctly for directories that contain a space in their name. - the updater now includes two additional parameters that may help those people who were having problems with the updater timing out before downloading files. These are both in updates\updater.ini: timeout_connect is the time in seconds to connect to to http://cars9.uchicago.edu to read what the update level is and verify that a connection can be made. timout_download is the time in seconds to download a zip file. If you have problems with the updater, try increasing these numbers from their default values of 60seconds and 2400seconds. Sorry for taking so long on this. --Matt

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introducing Hephaestus ...
by Bruce Ravel 19 Apr '04

19 Apr '04

Hi folks, In his workshop he has handmaidens he has forged out of gold who can move and who help him in his work. ... With Athena, he [is] important in the life of the city. The two [are] the patrons of handicrafts, the arts which along with agriculture are the support of civilization. "Mythology", Edith Hamilton The big new feature in the latest release is a new program called Hephaestus -- in keeping with the Greek mythology theme. Hephaestus combines the functions of the old Atoms Periodic Table with a bunch of other small utilities based on the priodic table and on tabels of x-ray absorption coefficients. Hephaestus supercedes both the Atoms Periodic Table and the TkFormula programs, both of which are being retired. You should find that Hephaestus is a very handy tool both at home and at the beamline. Along with displaying edge and line energies, and computing absorption lengths of elements and compounds, Hephaestus offers tools for computing the absorption of ion chambers, displaying the anomalous scattering factors of the elements, and displaying chemical data about the elements. Here is a web page with descriptions and a few screenshots: http://leonardo.phys.washington.edu/~ravel/software/exafs/abouthephaestus.h… The Windows updater does not install shortcuts to the desktop or to the Start menu, so Windows users might want to do so by hand. The updater will put the hephaestus.exe and .bat files in the normal Ifeffit place and you will find the hephaestus.ico icon file there as well. It should be a simple matter to modify the desktop and Start menu shortcuts for the Atoms Periodic Table to launch hephaestus instead. If you do not know how this is done, post a question to the mailing list and hopefully someone will explain. For the unix users, there is an icon file for use on the desktop in the Ifeffit/lib/hephaestus directory when you unpack the source code tarball. The file vulcan.gif is the intended icon file. I hope that you will find Hephaestus useful and I look forward to hearing people's suggestions for improving it. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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