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

Reminder: NASCCSC Abstracts Deadline
by Carlo Segre 07 Feb '11

07 Feb '11

Hello All: In case you had not seen this notice, the Second Annual North american Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs this on August 1-5. This years conference will have special sessions on catalysis and 5f electron systems. Abstract sumissions will be open probably until March 1, 2011. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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R dependence of S02
by Scott Calvin 04 Feb '11

04 Feb '11

Hi all, I've been pondering how much R dependence we should expect to see in S02; that is, how much R dependence is shown by intrinsic losses. I've looked at quite a bit of the literature, not to mention old threads from this mailing list. One recent (2002) reference is this one by Campbell et al.: http://prb.aps.org/pdf/PRB/v65/i6/e064107 My understanding is that S02 is intended to account for intrinsic losses; that is, those that are determined when the core hole forms. Extrinsic losses, such as inelastic scattering of the photoelectron and the effect of the core-hole lifetime, are accounted for by a mean free path term. The mathematics of how ifeffit implements this are here: http://cars9.uchicago.edu/~newville/feffit/feffit.ps Intrinsic losses are dependent on k for at least two reasons. One is that the cross-section of the intrinsic effects themselves depends on the energy of the incident x-ray. This is evident if one thinks in terms of shake-up and shake-off events. But another reason is that shake-up and shake-off events rob some energy from the primary photoelectron. At low k, ten or twenty electron volts can alter the phase of the primary photoelectron significantly, and thus shake-up and shake-off events will tend to cancel each other out. But at high k, the energy robbed from the photoelectron is less significant, because the EXAFS oscillations are more spread out in energy. Thus, shake-up and shake-off events, while still occurring, will not suppress the EXAFS amplitude as much at high k. S02 therefore gradually rises through most of the EXAFS region to reach a limiting value of 1 well above the top of the EXAFS region. The latter effect--the fact that removing a specified amount of energy from the primary photoelectron has less of an effect at high k than at low--also implies an R dependence. Low R oscillations are further apart in energy than high R oscillations, and thus over a specified k range low R oscillations should be less affected. In other words, S02 should show a modest decrease with increasing R over typical EXAFS ranges. Some papers, in particular those with John Rehr as an author, confirm that S02 should have an R dependence, but don't discuss the implications much. While ifeffit allows for floating ei, a parameter related to the mean free path, as I understand it that will still give a damping of the amplitude that is exponential in R. It seems to me that the S02 dependence on R, in contrast, is likely to be more gentle. Why is this important? Several authors, including myself, have analyzed crystallite size and/ or morphology by comparing the coordination number of successive scattering shells. This is potentially much more accurate than just finding the first-shell coordination number, because it is independent of any amplitude effects that are independent of R, such as normalization errors and many experimental effects. Errors in the mean free path are a bit more significant, but the exponential dependence of the mean free path gives it a very different shape than effects from size and morphology. But an R-dependence of S02 would be troubling, as the functional form might look a bit more like a size effect. So one question is this: does anyone have an order-of-magnitude estimate of how much R dependence to expect in S02 over the EXAFS range? If over a range of 2 to 6 angstroms S02 changed by even a few percent, that could have a significant effect on the kind of size analyses I mentioned in the preceding paragraph. Of course, another question is if I've completely blown it anywhere in my discussion above; I've just been puzzling this out over the last few days! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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EXAFS fitting method
by Abhijeet Gaur 30 Jan '11

30 Jan '11

Hi all, As I understand, the EXAFS fitting procedure using Artemis, for generating a theoretical model requires the crystal structure parameter like space group, cell parameters and *specially* *atom coordinates* etc. For this we have to perform XRD measurements of single crystals of the samples. I have some questions (1) In case we dont have the XRD data of a sample then how can the EXAFS analysis be done of that sample? (2) If we have already performed the XRD on the sample then by doing EXAFS what additional information are we getting ? (3) If the answer to the first question is that - *use the crystal structure of a * * similar sample,* then what are the conditions under which we can use the known crystal structure of one sample for other samples ? Thanks in advance Abhijeet Gaur

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Fwd: Horae-70 installation problem
by Bruce Ravel 18 Jan '11

18 Jan '11

Hi all, Has anyone here ever used security enhanced linux? I got the following bug report from an SELinux user which includes an error message from one of SELinux security systems. Never having used SELinux myself, I don't quite understand the problem Dr. Pan is observing once he uses chcon to change the security state of the ifeffit library. And I don't have a machine on which to explore this problem. I am hoping someone here might be more knowledgable than I. If anyone can offer any assistance to Dr. Pan, that would be great. Thanks, B ---------- Forwarded Message ---------- Subject: Horae-70 installation problem Date: Saturday, January 15, 2011, 01:34:29 am From: Guoqiang PAN <gqpan(a)ustc.edu.cn> To: Bruce Ravel <bravel(a)bnl.gov> Dear Dr. Ravel Hi, thank you very much for the horae-70 for artemis, athema and hephaestus XAFS software. Due to the detail for the installation, I have installed in my PC linux of Fedora Core 10. When artemis has been installed, it was failed to run correctly. There is a detailed explanation of it in the attachment. I fixed it using chcon -t textrel_shlib_t '/usr/local/lib/perl5/site_perl/5.10.1/i686-linux/auto/Ifeffit/Ifeffit.so' Afterwards, it seems work, but the data in the interface panel could not be changed,please refer to the attached snapshot pictures. My system information as follows: [gqpan@localhost horae-070]$ uname -a Linux localhost.localdomain 2.6.27.5-117.fc10.i686 #1 SMP Tue Nov 18 12:19:59 EST 2008 i686 i686 i386 GNU/Linux Thank you for your help! Best regards! Guoqiang PAN National synchrotron Radiation Laboratory University of Science & Technology of China ----------------------------------------- -- 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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Liquid gold-Latex suspension measurements
by Julian Kaiser 14 Jan '11

14 Jan '11

Dear Colleagues, I would like to measure some Gold-Nanoparticles that are embedded in a kind of polymer-matrix consisting of a polystyrene-core and some polyelectrolyte-chains. The total amount of gold in the suspension will be 0.025-0.05 percent by weight. The idea is to place the sample in a polystyrene cuvette with approximately 1 mm diameter (sample) and (2x) 1 mm (polystyrene). We've tried once to measure in transmission mode, where we had some problems maybe due to the absorption of water and polystyrene. Measurements in fluorescence mode might also cause problems by self-absorption and the absorption of the polystyrene again. Does anybody have good experience with liquid measurements of diluted samples? Best regards, Julian ========================================= Julian Kaiser Helmholtz-Zentrum Berlin für Materialien und Energie Hahn-Meitner-Platz 1, D-14109 Berlin Tel. +49 30 8062 - 43029 Mail: Julian.Kaiser(a)helmholtz-berlin.de ========================================= Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583 =========================================

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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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