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

error
by JeongEunSuk 11 Jan '11

11 Jan '11

Hi all I fitted ZnMgO to know whether Mg is sited on Zn position. the method of fitting as following; 1st : to fit with some Mg located on Zn site. 2nd: to fit with some Mg which position is different from Zn cite The parameters for Mg like bonding length, disorder and others were set. When I was fitting, there are only 8 parameters in both two method. So that independent data point and variables are same. Both 1st and 2nd had same R-factor but reduced chi-square of 1st was lager than that of 2nd. It has been known that R-factor is independent of error( uncertainty in the measurement) but reduced chi-squrare is inverse proportional to error^2. So I think that same R-factor and different reduced chi-square for two method mean the fittings of two method are not different, but error used in reduced chi-square is different. I want to know how the error used in reduced chi-square is decided in FEFFIT code.

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Re: [Ifeffit] Cadmium K-edge
by Alan Du 11 Jan '11

11 Jan '11

Hi Bhoopesh and Scott, I should have given a description of my project. Yes Scott, the work is to investigate the binding mechanisms of aqueous cadmium onto sodium titanate nanotubes. Spectrum of Sample 1 and 2 obtained from merging 9 scans and 4 scans, respectively. A quick check in Athena and, indeed, the white line of Samples are higher than CdO. I'm not sure the reason behind it though. It is likely that cadmium binds to the surface of substrate rather than inside the bulk. The lack of distinct peaks after 1.8 Å means that there are not many scatters around the absorber? Bhoopesh, as requested, I have attached the real part of FT ( http://img585.imageshack.us/i/ftreal.jpg/) I haven't got a chance to interpret them. >From preliminary fitting of Sample 1, the major and minor peaks at 1.8 and 2.3 Å could be described by a Cd-O path (CdO). This interests me because Sample 2 does not have a peak at 2.3 Å, meaning there is another single scattering path for Sample 2?. The peaks at 3 Å were fitted with Cd-Ti path (CdTiO3). No multiple scattering paths used. The best fit goes something like this: **************************************************************************** Independent points = 13.166992187 Number of variables = 8.000000000 Chi-square = 1534.709946959 Reduced Chi-square = 297.021921317 R-factor = 0.000128095 Measurement uncertainty (k) = 0.000060423 Measurement uncertainty (R) = 0.004455442 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.9242390 +/- 0.0509920 (1.0000) enot = 1.3950420 +/- 0.5425380 (0.0000) delr = -0.0872060 +/- 0.0051060 (0.0000) ss = 0.0113250 +/- 0.0008480 (0.0030) amp_2 = 0.2441320 +/- 0.1905250 (1.0000) enot_2 = 22.5261260 +/- 4.5990590 (0.0000) delr_2 = 0.2510860 +/- 0.0719080 (0.0000) ss_2 = 0.0274690 +/- 0.0128040 (0.0030) Correlations between variables: amp_2 and ss_2 --> 0.9342 enot_2 and delr_2 --> 0.9133 amp and ss --> 0.8865 enot and delr --> 0.8632 amp_2 and delr_2 --> 0.3040 delr_2 and ss_2 --> 0.2888 All other correlations are below 0.25 k-range = 2.000 - 9.000 dk = 1.000 k-window = hanning k-weight = 3 R-range = 1.000 - 4.000 dR = 0.000 R-window = hanning fitting space = R background function = none phase correction = none R-factor for this data set = 0.00270 *********************************************************************************** The above enot_2 is on the high side. I am not entirely familiar with the parameters yet. Are there other parameters I should worry about? Cheers, Alan J. DU Nanyang Technological University, Singapore

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sample preparation for liquid samples
by Polzer, Frank 11 Jan '11

11 Jan '11

Dear all, I would like to measure manganese oxide nanoparticles at the Mn K edge. The nanoparticles are affixed to polystyrene latex carrier particles (PS) and the whole composite material (MnO2@PS with ca. 5 m-% MnO2 in the composite) is dispersed in water. Therefore we consider measuring the composite material in the dried state as a powder as well as in the dispersed state in water. The sample preparation for powders to me is quite straight forward, but I would really appreciate if somebody could share his experience with sample preparation and measurements of liquid samples. I think that aqueous samples are best measured in the fluorescence mode. That's why I am concerned of problems like self-absorption and so on. Can anybody tell my what is a good concentration range to overcome effects like self-absorption and how to get good fluorescence data in general? And what kind of sampler holder or materials (cuvettes, etc.) are best suited for aqueous samples? I am looking forward to receiving some helpful replies! Cheers, Frank Dipl. Chem. Frank Polzer F-I2 - Soft Matter and Functional Materials Helmholtzzentrum Berlin für Materialien und Energie Lise-Meitner-Campus Hahn-Meitner-Platz 1 14109 - Berlin Tel.: +49 30 8062-43830 Fax: +49 30 8062-42308 frank.polzer(a)helmholtz-berlin.de<mailto:frank.polzer@helmholtz-berlin.de> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. h.c. mult. Joachim Treusch, Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn- Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Athena crash during LCA
by Scott Calvin 08 Jan '11

08 Jan '11

Hi Matt and Jeff, I just upgraded to 0.8.061, and it works in that version, so apparently whatever the bug was has been fixed. Thanks for checking it out for me! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 8, 2011, at 7:08 AM, Matt Newville wrote: > Hi Scott, > > Like for Jeff, the chi(k) LCA fit works for me with Athea 0.8.061 on > OSX 10.6. If I had to make a guess or recommendation for something > to try it would be this: > > Standard2 extends to pretty far out in K (>20Ang^-1) and Standard2 is > pretty glitchy beyond 12Ang^-1 or so. You might try truncating the > data and/or removing the obvious glitches before doing the background > subtraction and LCA fit. > Again, that's a guess. > > Does the latest iXAFS3 not work for you on 10.5.8? I haven't tried > it, but the intention was that it would work on 10.5. > > --Matt >

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Athena crash during LCA
by Scott Calvin 08 Jan '11

08 Jan '11

Hi all, Athena has been crashing for me during one particular linear combination analysis, and I'm wondering if any of you have an explanation. A project file which demonstrates the problem is attached. I am using Athena 0.8.054 with ifeffit 1.2.10 on a MacBook Pro using OS 10.5.8. The behavior can be seen by trying to fit the Data group by using a linear combination of Standard 1 and Standard 2 in chi(k). It gets as far as "plotting in k-space from group 'Data'...done!' and then hangs, with the watch icon remaining indefinitely. This doesn't happen in norm(E) or deriv(E) fits, and doesn't happen when Standard 1 is not used. But Standard 1 appears to have uncorrupted chi(k) data when plotted directly. Standard 1 is from one of the XDAC lines at NSLS, as are the standards that work. I've tried saving Standard 1 and reading it in as a new group, but no luck. I've also looked at the data in Standard 1, and I don't see anything out of place, such as a place where the energy backs up. I've tried starting the chi(k) file with zero values, truncating the end values, and changing the background spline to end at the same point the data does. And it always hangs at the same point. Any ideas? I'd like to use this data for a workshop next week! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Re: [Ifeffit] Athena crash during LCA
by Scott Calvin 07 Jan '11

07 Jan '11

Jeff--sorry, I guess my grammar got a little convoluted. It DOES work with norm(E) and deriv(E) fitting for me as well. It does NOT work with chi(k) fitting for me. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 7, 2011, at 7:58 PM, Jeff Terry wrote: > Did not try really hard to work with it. > > Fitting Data as norm(E) from -20.000 to 30.000 > > Fit included 98 data points and 3 variables > R-factor = 0.000263 > chi-square = 0.04347 > reduced chi-square = 0.0004482 > > group weight > ======================================= > 2: Standard 1 1.000(0.000) > 3: Standard 2 0.455(0.000) > > > group e0 shift > ======================================= > 2: Standard 1 -0.905( 0.000) > 3: Standard 2 -0.905( 0.000) > > > > <PastedGraphic-1.pdf> > > On Jan 7, 2011, at 8:07 PM, Scott Calvin wrote: > >> Hi all, >> >> Athena has been crashing for me during one particular linear >> combination analysis, and I'm wondering if any of you have an >> explanation. A project file which demonstrates the problem is >> attached. I am using Athena 0.8.054 with ifeffit 1.2.10 on a >> MacBook Pro using OS 10.5.8. >> >> The behavior can be seen by trying to fit the Data group by using a >> linear combination of Standard 1 and Standard 2 in chi(k). It gets >> as far as "plotting in k-space from group 'Data'...done!' and then >> hangs, with the watch icon remaining indefinitely. This doesn't >> happen in norm(E) or deriv(E) fits, and doesn't happen when >> Standard 1 is not used. But Standard 1 appears to have uncorrupted >> chi(k) data when plotted directly. Standard 1 is from one of the >> XDAC lines at NSLS, as are the standards that work. >> >> I've tried saving Standard 1 and reading it in as a new group, but >> no luck. I've also looked at the data in Standard 1, and I don't >> see anything out of place, such as a place where the energy backs >> up. I've tried starting the chi(k) file with zero values, >> truncating the end values, and changing the background spline to >> end at the same point the data does. And it always hangs at the >> same point. >> >> Any ideas? I'd like to use this data for a workshop next week! >> >> --Scott Calvin >> Faculty at Sarah Lawrence College >> Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >> >> <LCACrash.prj> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: [Ifeffit] Problem with Athena
by Bruce Ravel 07 Jan '11

07 Jan '11

Hi Samer, I am CCing my response to the Ifeffit mailing list. I ask that questions about the software be directed to the mailing list rather than to me personally. The file that you attached is from the SSRL Data Collector. This is one of the formats supported by a filetype plugin. See http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/plugin.html As explained on that page, from the "Settings" menu, select "Plugin registry", then click on the button labeled "SSRLA". Athena will then be able to import your file. If you do not have that plugin on your computer for some reason (for example, if you are running a somewhat old version of Athena), a copy can be found at http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… Place that file in C:\Program File\Ifeffit\horae\Ifeffit\Plugins\Filetype\Athena\ if you are a windows user or in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ on linux. There is a similar location on a Mac, but I don't know its path off the top of my head. B On Friday, January 07, 2011 05:46:13 am you wrote: > Dear Mr. Bruce, > > > > At first I wish you a happy new year and a very successful 2011! > > I have problem with opening the Roble files with Athena (see pleas attached > file). > > I get the following error: the file could not be read by ifeffit as data > file. > > Our Athena version is 0.8.061. > > > > Could you please help me? > > 　 > > Thanks in advance. > > > > With best wishes, > > > > Samer Amayri > __________________________________________________________________ > Dr. Samer Amayri > Institut für Kernchemie > der Universität Mainz > Fritz-Strassmann Weg 2 > D-55128 Mainz > Telefon: +496131 39-25317/25307 (Lab.) > Handy: 017621805879 > Fax-Nr. +496131 39-24510 > E-mail: amayri(a)uni-mainz.de<mailto:amayri@uni-mainz.de> -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Cadmium K-edge
by Scott Calvin 06 Jan '11

06 Jan '11

Hi Alan, (To the list: I discussed Alan's system a bit with him when he came to SSRL, but don't recall the details. That's why in this reply I have a little more knowledge about it than what he posted yesterday.) I suspect the peak at 2.3 A does indeed represent structure of some kind. Your k-space data for sample 1 has very little noise, so I don't think it's spurious in that sense. What strikes me about your data is that the FT's have so little structure beyond the 1.8 A peak. I don't recall exactly the nature of your system: it was cadmium loaded on to the surface of a substrate, but I don't recall what the substrate was. If it's low-Z (for example, silica), then the scattering off of whatever the oxygen is bonded to (in my example, silicon) would show up pretty weakly, and that could be the peak at 2.3 A. It's absence in sample 2 could represent the cadmium ion being less selective about what surface site it bonds to, so that the Cd-Si distance (in my example) varies and the peak washes out. That's all just an example of the kind of thing that could be responsible for what you're seeing. I agree that a good plan is to use a Cd-O structure to at least let you model the first peak. For the second peak, though, you may have to take more inspiration from the structure of the substrate than the structure of Cd-O. It's also intriguing that the white line in your sample is larger than in the CdO standard from the database. Someone with more XANES experience than I might be able to suggest why that is--something about these being bound to the surface? Is my recollection of your system correct? If so, what was the substrate? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 5, 2011, at 11:23 PM, Alan Du wrote: > > Hi all, > > I processed my XAS data and compare them with standards from Farrel > Lytle Database. (http://img717.imageshack.us/i/xasw.jpg/) > > In the RSF, both sample 1 and 2 has a major peak at R = ca. 1.8 A. > sample 1 has an additional peak at R = ca. 2.3 A. I wonder if this > tiny peak is significant. > > It seems both samples has peak positions similar to those of CdO > standard, which sound logical because the cadmium will bind to the > surface oxygen of the material. > > I looking at fitting sample 1 and 2 using whatever crystallographic > info of CdO I can get my hands on. > > Wonder if the plan make sense. > > Happy new year, > Alan

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Cadmium K-edge
by Alan Du 06 Jan '11

06 Jan '11

Hi all, I processed my XAS data and compare them with standards from Farrel Lytle Database. (http://img717.imageshack.us/i/xasw.jpg/) In the RSF, both sample 1 and 2 has a major peak at R = ca. 1.8 A. sample 1 has an additional peak at R = ca. 2.3 A. I wonder if this tiny peak is significant. It seems both samples has peak positions similar to those of CdO standard, which sound logical because the cadmium will bind to the surface oxygen of the material. I looking at fitting sample 1 and 2 using whatever crystallographic info of CdO I can get my hands on. Wonder if the plan make sense. Happy new year, Alan

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Ifeffit "print" command question
by Kelly, Tony D Ctr USAF AETC AFIT/ENP 31 Dec '10

31 Dec '10

To whom it may concern, I have recently downloaded Ifeffit for Mac OS X from your website. I am hoping to be able to use it with EXAFS data as the FEFF6 website led me to your application. I am currently working through the tutorial. However, every time I try to use the print command to make a literal string statement, all I get is 0.0000 back. Example: print " the square root of ", number, " is ", sqrt(number) 0.0 99.0000000 0.0000000 9.94987437 print "Hi mom" 0.000000000 Any thoughts? Thanks, Tony Tony Kelly, M.S. DTRA PhD Student Department of Engineering Physics Air Force Institute of Technology Office: (937)255-3636 ext 7300

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