January 2011 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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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 12 Jan '11

12 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 12 Jan '11

12 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 08 Jan '11

08 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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