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

Re :Fitting result
by Abhijeet Gaur 21 Jan '10

21 Jan '10

> > Hi Abhijeet, > > I think that there is a problem with you structure for Cu2O. Each Cu > atoms must be coordinated by more than just two O atoms in the first > shell. > > Shelly > > Hi Madam, Is there any problem with the theoretical structure that I generated in Artemis or my experimental data???, I am not getting it. Abhijeet

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Fitting results
by Abhijeet Gaur 21 Jan '10

21 Jan '10

Hello Sir, I had done fitting of a Cu2O data taken at SSRL EXAFS beamline in transmission mode, Stanford, by my research guide Dr. B. D. Shrivastava. I had used here the fiting procedure as discussed before in this mailing list. The fitted curves are coming nice, but the values of some fitting parameters are not reliable as shown * bold* below. *amp = 0.4898160 +/- 0.0469990 (1.0000) * enot = 7.6843630 +/- 0.4828620 (0.0000) alpha = 0.0022670 +/- 0.0030950 (0.0000) * ss011 = 0.0003280 +/- 0.0013130 (0.0030) * sscu11 = 0.0174780 +/- 0.0016220 (0.0030) *sscu11o11 = 0.0470530 +/- 0.0655560 (0.0030) * ss012 = 0.0070100 +/- 0.0044660 (0.0030) sscu12 = 0.0186980 +/- 0.0093570 (0.0030) * ss013cu11 = 0.0088980 +/- 0.0190580 (0.0030) * sscu13 = 0.0196150 +/- 0.0062940 (0.0030) sscu13012 = 0.0084870 +/- 0.0067030 (0.0030) * sscu11cu11 = 0.0071110 +/- 0.0132390 (0.0030) sscu12cu11 = 0.0111440 +/- 0.0139470 (0.0030)* Def parameters (using "FEFF0: Path 1: [O1_1]"): delr = 0.0041920 So, if someone can please tell me that where I had done wrong or what should I do to make things right I will be very thankful. The Artemis project file is attached herewith. With regards Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain (INDIA)

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Problem opening up project files
by Lisa Van Loon 20 Jan '10

20 Jan '10

Hi, I am using Athena in Windows and I have been having trouble with some project files. I would like to determine the cause: after closing the original file I am unable to reopen the project file again properly. I have attached a file to demonstrate the problem (test1.prj) Saving different versions does not help. When I open the file, no spectrum is displayed. (If I click on a file during the importing then that spectrum will remain displayed). At the bottom the "removing background..." never says "done". It seems like everything is working except the graphing window. I haven't been able to determine what is different about this data from other data that opens without any problem. I would appreciate any help with this. Thanks, Lisa Lisa Van Loon, Ph.D. Industrial Research Scientist lisa.vanloon(a)lightsource.ca

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probem with run Athena
by 康明亮 20 Jan '10

20 Jan '10

Dear Matt, Many thanks for your answer yesterday. Since I am a novice, I am now still puzzled to use this software. I just want to process some XANES data for selenium speciation identification. As attached in the annex(three samples and four references, some have analyzed for several times). When open SixPack, I can't import any file from which attached in the enclosure. I don't know whether it is the problem with the format of the data. Thus, I thought probably I need to open the Athena, while it prompted: Cann't execute Grnd.exe.... Sincerely wish to obtain guidance from you. Kind regards Mingliang

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Re: [Ifeffit] consultation
by Jens Kruse 20 Jan '10

20 Jan '10

Hi, I had a similar problem. In my case it was name of the Folder which included the letter "ö". After I changed the name, I had no problem anymore to open the file. In your case I think the "Chinese" letters are the problem. Just change the Folder name, maybe It helps. jens Am 20.01.2010 16:31, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. consultation (???) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Jan 2010 23:31:12 +0800 (CST) > From: ???<kangml(a)163.com> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] consultation > Message-ID: > <16030032.1199091264001472057.JavaMail.coremail(a)app188.163.com> > Content-Type: text/plain; charset="gbk" > > Dear, I want to consult why I can not open the XANES raw data(like the attached file Na2SeO3.dat) by Athena on my laptop(Windows system). It prompt that : coulldn't read...(See the attached picture. file). Wish to obtain help from you.Thanks very muchBest wishesMingliang >

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(no subject)
by JeongEunSuk 20 Jan '10

20 Jan '10

Hi all I have a question for XANES of Zinc compounds. It is known that the pre-edge for Zinc k-edge generally doesnt exist because 3d state of Zinc atom is occupied. However, I got it from ZnMgO with wurtzite structure. 4 oxygen in first shell and 12 zinc in second shell are located around Absorbing atom, Zinc in wurtzite structure. And then I know that some Mg atoms are replaced on zinc site from EXAFS. I wonder the reason for the appearence of pre-edge. Is it structural problem? or substituted Mg? If anybody know reference papers for pre-edge of zinc K-edge, Please answer me. _________________________________________________________________ 새로운 Windows 7: 여러분에게 맞는 최상의 PC를 찾으세요. 자세히 보기. http://windows.microsoft.com/shop

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Re: [Ifeffit] Compiler cannot handle complex function properly
by Ying Zou 15 Jan '10

15 Jan '10

Dear all, One colleague of mine brought up this to my attention. He tried a simple Fourier transformation C code on different machines (PowerPC based MAC G4, Intel based MAC G5, and PCs). The computations yield different results, sometimes on the third significant place. In his Fourier transformation implementation, a standard complex function is called. On MAC boxes, he used GNU C compiler; on PC, MS visual C compiler was used. I have done a little web survey on this issue, it seems that this was reported by others, too; there have been suggestions that it is much more reliable to handle real or imaginary part separately. Since in the Fourier transformation for EXAFS function, complex functions have to be handled too. One thing I would like to know from our Ifeffit Gurus: Are the real and imaginary parts of EXAFS functions been handled separately? Thanks for your attention! Best, Ying ========================== Dr. Ying Zou Research Associate, Physics/UWM 1900 E. Kenwood Blvd. Milwaukee, WI 53217 ==========================

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Job Posting: Post-Doc postion at Missouri State Univ, Material in Extreme Conditions
by Matt Newville 15 Jan '10

15 Jan '10

Hi Folks, Prof. Robert Mayanovic at Missouri Sate University is searching for a post-doctoral associate to work on materials in extreme conditions. More details are at http://xafs.org/Jobs --Matt

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Fwd: regading feff input file of sorbed species
by Bruce Ravel 12 Jan '10

12 Jan '10

Hi everyone, Below is an email I received this morning. I thought I would pass it along to the mailing list. I know that some of you work on projects very close to this fellow's question and thought he would benefit by the wisdom of the masses. Hi Sumit, A few pointers: * There is a wealth of information about Feff and XAFS analysis at http://xafs.org * I strongly encourage you to join and follow this mailing list. I explain the many benefits of the mailing list and offer some advice on using it effectively at this page: http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest As for your question -- there are a number of approaches to the problem of sorbed species that have been adopted by folks working both catalysis, in environmental science, and elsewhere. Obviously, sorbed species are a very important topic in many fields and XAS is very attractive for learning something about them. You would be very well served by examining the very large body of published literature on this topic. Much of that work has been done by people who read this mailing list -- I am hoping some of them will speak up. As I said, there are a number of ways to approach the problem. One fairly simple way is to run atoms on the substrate crystal and then "cut" the resulting cluster to "expose" the surface. What does this mean? The simplest case is to "expose" a (001) surface by simply deleting all atoms from the Feff input file with a positive value for the Z coordinate (assuming, of course, that the crystal is of an orthogonal type -- this "cutting" trick is a bit trickier for other cystal types). Then simply decorate the atoms list with the absorber by placing at coordinates relative to the "exposed" surface that is a plausible place to find that atom. Be sure you set the POTENTIALS list on the Feff input file correctly to account for the newly introduced absorber. This is explained in the Feff documentation and ion several places at xafs.org. Hope that helps, B --------------------------------------------------------------------------------- On Tuesday 12 January 2010, 08:21:04 am, sumitk(a)barc.gov.in wrote: Dear Sir, This is in regrad to the problem in making the FEFF input file for the Eu species sorbed on the the alumina surface. I am Sumit Kumar, Working as Reseach Scholar In Indian Nuclear Establishment. Recenrly I have carried out Eu-L3 EXAFs experiemnt at Elettra Synchrotron EXAFS beamline for delineating Eu species sorbed on alumina and other clay surfaces under different experiemntal/environmental conditions. As I understand for FeFf input file ATOMS SOFTWARE can be used, but as my species are just sorbed/chemical bonded on the surface, I can not take Eu as part of the bulk and then using ATOMS will be not be correct. I need your suggestion in this regard. Pl. suggest how to make the FEFF input file in this case. My problem is similar to one of yours paper sumitted to Geochimica Cosmochimica acta(Zn on Rutile).If you could send FEFF input file file for that work or similar other FEFF input file, it will be of much help to me. With Regards, Sumit Kumar Radiochemistry Division Bhabha Atomic Research Centre, Mumbai, India -------------------------------------------------

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Re: [Ifeffit] How to calculate F-value for XANES PCA results
by Andrew 11 Jan '10

11 Jan '10

Hi everyone, Thank you Dr. Lukens for your help! Let me see if I understand the method that was described for the F-value for the variances using the Fernandez-Garcia definition (that was previously mentioned), and please correct me if I am mistaken. The Principal Component Analysis returns the eigenvectors. Then, to calculate the F-value using the Fernandez-Garcia definition: F-value for component 1 = (variance of eigenvector 1)/ summation[(variance eigenvector 2) + (variance eigenvector 3) + . (variance eigenvector c)] F-value for component 2 = (variance of eigenvector 2)/ summation[(variance eigenvector 3) + (variance eigenvector 4) + . (variance eigenvector c)] F-value for component k = (variance of eigenvector k)/ summation[(variance of eigenvector k+1) + . + (variance of eigenvector c)] Where c is the number of components in the set. Then to calculate the probability of F corresponds to noise, then the that Excel can calculate this using the function Fdist(alpha, degree of freedom 1, degree of freedom 2). Alpha = the confidence interval desired (where 0.05 is generally used) degrees of freedom 1 = # of independent data points - 1 ((this is dependent on the resolution of the beam and Dr. Lukens provided an example calc.)) degree of freedom 2 = number of components on the denominator for the F-value being tested - 1 (i.e. for component k it would equal c-k-1-1 or c-k-2) Then, "if the probability of F less than 5%, these would be the components that you would retain." Are these equations correct? Am I using the correct equation based on the Garcia-Fernandez definition? My main misunderstanding of this was what equation to use for the F-value. Sorry for killing a dead horse, but is this definition of degree of freedom 2 correct? Thanks again for all the help and sorry if this is poorly worded, and if this is on the outer-bounds for an IFEFFIT-relevant question. Andrew

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Fwd: Athena
by Bruce Ravel 11 Jan '10

11 Jan '10

Hi Ronald, I am forwarding my response to your questions to the Ifeffit mailing list. As you will see in my attempt to answer your question, it will be useful to solicit Matt Newville's opinion. This is, of course, the great benefit of a mailing list. Issues with the software are hashed out more quickly and more efficiently when discussed in a public forum. Athena, as we all know, does not actually do much numerical work by itself. Instead it relies upon Matt's Ifeffit for all those chores (which, in turn, uses a variety of freely available numerical packages, including http://www.netlib.org/fftpack/) You ask about the Fourier transform -- Matt explains all of Ifeffit's deep, dark secrets in this part of the reference manual: http://cars9.uchicago.edu/~ifeffit/refman/node141.html I think that all of the discrepancies you are asking about are explained by two things: (1) Ifeffit zero-pads its arrays. (2) Ifeffit treats chi(k) as the real part of the orginal function which is transformed by a complex Fourier transform. Additionally, if you want to do two Foruier transforms in Athena without filtering, you need to explicitly set both FT ranges to the entire data range and you need to set the window sill widths to 0. It is unclear from what you said whether you did that. So, how worried should we be that your software and ours did not do quite the same thing? Not much, I suspect. There are some places where different conventions may have been adopted. In the end, internal consistency is probably the most important thing. Whatever set of conventions Ifeffit uses (and, thus, Athena and Artemis also use), those conventions get used when transforming both theory and data during a fit. Of course, if you still feel I am not understanding part of the problem, please let me know. As I have said many times on this mailing list, the only reason that Athena and Artemis are any good at all is because of the excellent feedback I get from the folks who read this list. Regards, B ---------- Forwarded Message ---------- Subject: Athena Date: Saturday 09 January 2010 From: "Frahm, Ronald, Prof. Dr." <frahm(a)uni-wuppertal.de> To: bravel(a)bnl.gov Dear Bruce, I hope you are doing well! Recently, I just made some calculations using Athena, comparing the results to my own analysis software. With my programs, when I Fourier transform simulated spectar, I get exactly the input amplitude and phase back after a Fourier transform pair. Perhaps I made a mistake using Athena. By importing and transforming a single shell (Feff output, chip001, Cu K-edge) I assumed from your documentation that the 5th column of the backtransform output file is the scattering phase (modulo 2*Pi) for a +...sin() EXAFS formula, and column 4 the modulus. However, Athena's phases seem to be too low by an amount very close to pi/2. Phases: ====== Values at k= 10.0: FEFF input: 37.62 [rad], Athena output: 42.39 [rad] Values at k= 15.0: FEFF input: 60.78 [rad], Athena output: 65.422 [rad] If I calculate chi with the Athena output using Chi(k) = col4 * sin(col5 + 90°) the correct chi in Athena colum 2 is reproduced (see png-files), otherwise there is a significant mismatch. I am also somewhat puzzled about the amplitude in the chi data import, and the amplitude of the resulting backtransform. Is there some scaling/weighting done automatically? Are you calculating the FT by using just the real positive part from 0 to kmax, filling the rest with zeros? The imaginary and real parts of the forward transform look significantly different from my transforms. Perhaps I missed something in your manuals, but there might be an easy explanation for my phase problem! I'd appreciate your comments. Best regards from snowy Germany Ronald ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Prof. Dr. Ronald R. Frahm Fachbereich C / Physik, Bergische Universität Wuppertal Gaußstr. 20, 42097 Wuppertal, Germany E-mail: frahm(a)uni-wuppertal.de phone: +49 202 439-3100, fax: -3101, secretary: -3102 http://hydrogen.physik.uni-wuppertal.de/index.html ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------- -- 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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Installation Problem
by William Diebel 05 Jan '10

05 Jan '10

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Problems with Ifeffit installation
by William Diebel 05 Jan '10

05 Jan '10

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Fitting using Experimental standard
by abhijeet gaur 05 Jan '10

05 Jan '10

A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India)

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Re: [Ifeffit] Fitting using Experimental standard
by Frenkel, Anatoly 05 Jan '10

05 Jan '10

I doctored FEFF path. Not sure if Artemis offers anything better and less intrusive than this trick but I think it is still the only way to use experimental standards for fits (other than the ratio method that is implemented in athena as Bruce desribed, which is used for monoatomic shells only). A. ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Mon Jan 04 22:54:30 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard Ah, I see. I think Artemis has some way of putting in experimental phase and amp, but that may be just to make a "corrected" FT. Is that so? Otherwise, I suppose it should be possible to write a fake FEFF path file and read it in. I guess that's what you did. mam ----- Original Message ----- From: Frenkel, Anatoly <mailto:frenkel@bnl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 7:43 PM Subject: Re: [Ifeffit] Fitting using Experimental standard Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al) Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al) and get a "semi-empirical" Cu->Si "standard". Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam ----- Original Message ----- From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) -------------------------------------------------------------------------------- > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ________________________________ _______________________________________________ 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] Fitting using Experimental standard
by Frenkel, Anatoly 05 Jan '10

05 Jan '10

Thank you, Matthew. As they say in Russia, everything new is well forgotten old. Seriously, that paper was really how to use FEFFIT for both experimental and theoretical standards, not just theoretical. A. ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Mon Jan 04 22:34:56 2010 Subject: Re: [Ifeffit] Fitting using Experimental standard You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of Artemis and the like) as it is now. As shown in the paper, you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple data sets aren't new, either; I used to do that with data taken on dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp) between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the phase+amp for Cu as the central atom and Al as the scatterer. You can't do that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do: Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al) Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al) and get a "semi-empirical" Cu->Si "standard". Why the +- for phase and the */ for amp? You can think of it as extrapolating the log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im(). This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, which they really are. One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam ----- Original Message ----- From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, January 04, 2010 6:21 PM Subject: Re: [Ifeffit] Fitting using Experimental standard I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India) -------------------------------------------------------------------------------- > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Mackale's table
by Neetu parsai 01 Jan '10

01 Jan '10

Happy New year to all I am in need of Mackale's table for backscattering amplitude and phase shift that I want to calculate EXAFS function for some transition metals. with best wishes Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

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installing IFeffit, etc on user accounts
by Elizabeth J. Biddinger 30 Dec '09

30 Dec '09

I recently installed the IFeffit package on a multi-user computer that uses Windows XP Pro. Athena and all of the other programs open and work fine on the administrator account but do not work on the user accounts. If I change one of the users to administrator it also works, but as soon as I change them back to user it again does not work. The Athena version we are using is 0.8.56 if that helps. Network security reasons require that our general users are on "user" not "administrator" logins. Any suggestions on how to get the programs to work in "user" mode? Thanks, Elizabeth Biddinger

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Silver oxide Standard
by Chris Patridge 21 Dec '09

21 Dec '09

hello everyone, I am asking if anyone might have any oxygen K near edge data for silver oxide standards? We forgot to collect the sample at our last beamline time. Thank you in advance, Chris Patridge

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Re: [Ifeffit] spline clamps in ifeffit code
by Bruce Ravel 15 Dec '09

15 Dec '09

On Monday 07 December 2009 05:37:41 am you wrote: > Hi Bruce, > > I have a question concerning the spline clamps in ifeffit. Is there > any possibility to set them directly in the spline() command? I tried > to do it with spline(..., clamp1=0, clamp2=24,...) but it did not work > and by default both spline clamps seem to be zero. Unfortunately I > found nothing about it in the reference guide either. So how can I > configure the clamps in the Ifeffit code? > > Thanks and kind regards, Hi Jan, I am CCing this to the Ifeffit mailing list, which is the better place to ask a question of this sort. I was out of town all of last week -- had you sent this to the mailing list rather than to me directly, you probably would already have received an answer. You seem to have the syntax correct. That is, if you follow along in Athena's Ifeffit buffer, you see that "spline(..., clamp1=0, clamp2=24,...)" is exactly what she does. Anything you see in the Ifeffit buffer should be directly transplantable to an Ifeffit script. Indeed, that is the very purpose of making the Ifeffit buffer available to the user. So, what do you mean that the clamps both seem to be zero? How do you know that? Can you show us an example data file and a short example ifeffit script that demonstrates the problem? It is quite possible that changing the clamp strength will have no significant impact of the background removal. To refresh my memory as I am writing this email, I loaded an iron foil spectrum into Athena. Indeed, changing clamp 2 has little impact on the background removal. But I know from experience that, in general, it does. Just to tell the whole story, I'll point out that the numeric values of the clamp strengths in Athena are configurable. If you go to Edit preferences, then open the clamp group, you will be able to assign new values to the 5 named clamp strengths. HTH, B -- 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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Athena linux version problem
by Nelson Lobo 14 Dec '09

14 Dec '09

Dear Sir I have installed the latest version of Horae 070 in Ubuntu using synaptic package manager. The problem is that I don't see the 'OK' button in Athena 0.8.059 ( ifeffit1.2.11d), after I open a data file. scrolling to bottom of page, dragging the bottom of the page doesn't help either. Please let me know what should be done. My laptop resolution is 1280x800. Attached is a screen shot of the problem. Thanks Nelson

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Re: [Ifeffit] Ifeffit Digest, Vol 82, Issue 3
by Michel Jaouen 07 Dec '09

07 Dec '09

Hi Eugenio, >I want to estimate the influence of every shell in XANES simulations like >Bruce Ravel shown in the publication: "A practical introduction to multiple >scattering theory" >I always done simulations until the system is converged, so now I have a >doubt, should I increse the SCF until convergence and add new shells in FMS >to repeat this kind of results? Just run feff with CONTROL 0 0 1 1 1 1 (you didn't need to recalculate the pot and phase modules) and change the FMS rfms. Best regards, Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI Laboratoire de Physique des Matériaux (PhyMat) UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

1 0

Double crystal monochromator
by sankaran anantharaman 05 Dec '09

05 Dec '09

Hi everyone, Could anyone help me with this. Why is that the Darwin reflectitivity curve plotted versus rotation angle (in text books for example) and rocking curve plotted against rotation angle (observed in the oscilloscope at XAS beamlines for example) look different? I understand that the double crystal rocking curve (photon counts in Ionization chamber1 as a function of Bragg angle) is obtained by rotating the second crystal and recording the photon count. Is it right? Regards, Sankaran Anantharaman

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Shells in XANES
by Eugenio Otal 03 Dec '09

03 Dec '09

Hi, I want to estimate the influence of every shell in XANES simulations like Bruce Ravel shown in the publication: "A practical introduction to multiple scattering theory" I always done simulations until the system is converged, so now I have a doubt, should I increse the SCF until convergence and add new shells in FMS to repeat this kind of results? Thanks in advance, euG

1 0

Mackale's Table for backscattering amplitude
by Neetu parsai 03 Dec '09

03 Dec '09

Hello Can some one send me Mackale's table in which back scattering amplitude and Phase shift values of most of the elements are given. Otherwise can tell me how can I order that table. Thanks with best regards Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

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Open position at HASYLAB
by Welter, Edmund 01 Dec '09

01 Dec '09

Dear XAFS users, if you are interested or know someone who might be interested in a postdoc position in the field of spectroscopy with X-rays, please have a look at our recent job advertisement: http://www.desy.de/v2/docs/1257511440-e.pdf Regards, Edmund Welter

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Re: [Ifeffit] Ifeffit Digest, Vol 81, Issue 25
by Jasquelin Pena 30 Nov '09

30 Nov '09

Scott, .cif files for many minerals can be downloaded from the AMCSD: http://rruff.geo.arizona.edu/AMS/amcsd.php Jasquelin On Mon, 30 Nov 2009, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Request a .cif file for alpha & beta Nickel hydroxide > (Scott Wicker (Student)) > 2. Re: Request a .cif file for alpha & beta Nickel hydroxide > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 29 Nov 2009 12:06:19 -0600 > From: "Scott Wicker (Student)" <scott_wicker_00(a)subr.edu> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Request a .cif file for alpha & beta Nickel > hydroxide > Message-ID: > <301F55994159DB4682AA882A772707E1013EF192(a)primary14.subr.edu> > Content-Type: text/plain; charset="iso-8859-1" > > I would like to request a .cif file for the alpha & beta Nickel hydroxide. If someone also have .cif files for Cobalt hydroxide this will be greatly appreciated. Is there a single crystal data base for .cif files? > > thanks, > > Scott A. Wicker Sr. > Ph.d Graduate Student > Environmental Toxicology > Southern University A & M > Baton Rouge, LA 70813 > School: scott_wicker_00(a)cxs.subr.edu > Home: swicker(a)cox.net > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly > Sent: Fri 11/27/2009 1:12 PM > To: jswashin(a)ncsu.edu; XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Bond length determination EXAFS vs XRD > > XRD measures interplanar spacing, and XAFS - interatomic distances, and they are not the same if disorder is present. Look for articles by Boyce and Mikkelsen, Jr., in Phys Rev B in 1980's who were the first discussing these concepts in GaAs-InAs semiconductors and also KBr-RbBr ionic salts. > They showed that the average structure ascertained by diffraction differs from the local structure measured by EXAFS. > Modern day high energy XRD/PDF measures interatomic distances more accurately than Bragg peak analysis can do but how accurately it agrees with EXAFS is still subject of debates. > Anatoly > > > _____ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Joseph Washington > Sent: Fri 11/27/2009 2:08 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Bond length determination EXAFS vs XRD > > > > Happy Thanksgiving All! > > Can someone, send me some references which explains some of the reasons > why the bond lengths fitted in EXAFS would be different from that fitted > in XRD (assuming that we implemented the crystal model predicted by XRD > correctly in Artemis)? > > I would really appreciate this! > > Sincerely > -- > Joseph Washington > Research Assistant > Department of Physics > North Carolina State University > 431 Riddick Hall > Raleigh, NC 27695-8202 > email: jswashin(a)ncsu.edu > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

1 0

Request a .cif file for alpha & beta Nickel hydroxide
by Eugenio Otal 30 Nov '09

30 Nov '09

Try with this database: http://www.icsd.iqfr.csic.es/ Regards, euG

1 0

Bond length determination EXAFS vs XRD
by Joseph Washington 30 Nov '09

30 Nov '09

Happy Thanksgiving All! Can someone, send me some references which explains some of the reasons why the bond lengths fitted in EXAFS would be different from that fitted in XRD (assuming that we implemented the crystal model predicted by XRD correctly in Artemis)? I would really appreciate this! Sincerely -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswashin(a)ncsu.edu

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Re: [Ifeffit] Path degeneracy modification in feffNNN.dat
by Frenkel, Anatoly 21 Nov '09

21 Nov '09

It takes it from N. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Nov 20 18:57:29 2009 Subject: Re: [Ifeffit] Path degeneracy modification in feffNNN.dat Hi ｔｈｅｒｅ, I have a general question about Artemis. I am going to split a degenerated path with degeneracy N=8 into twoｓ. I noticed that by cloning the path, the "N" in path math expression parameters was halved as "4". However, the degeneracy number in feffNNN.dat remains as "8". For fitting, where will Artemis exactly get this information? Or maybe I　ｓｈｏｕｌｄ　ｍｏｄｉｆｙ　ｆｅｆｆＮＮＮ．ｄａｔ　ｍａｎｕａｌｌｙ？　　Ｔｈａｎｋｓ　ｆｏｒ　ｙｏｕｒ　ｒｅｓｐｏｎｓｅ！＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝Ｄｒ．　Ｙｉｎｇ　ＺｏｕＲｅｓｅａｒｃｈ　Ａｓｓｏｃｉａｔｅ，ＵＷＭ／Ｐｈｙｓｉｃｓ，１９００　Ｅ．　Ｋｅｎｗｏｏｄ　Ｂｌｖｄ，Ｍｉｌｗａｕｋｅｅ，　ＷＩ５３２１７＝＝＝＝＝＝＝＝＝＝＝＝＝＝ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

Re: [Ifeffit] Path degeneracy modification in feffNNN.dat
by Ying Zou 20 Nov '09

20 Nov '09

Hi ｔｈｅｒｅ, I have a general question about Artemis. I am going to split a degenerated path with degeneracy N=8 into twoｓ. I noticed that by cloning the path, the "N" in path math expression parameters was halved as "4". However, the degeneracy number in feffNNN.dat remains as "8". For fitting, where will Artemis exactly get this information? Or maybe I　ｓｈｏｕｌｄ　ｍｏｄｉｆｙ　ｆｅｆｆＮＮＮ．ｄａｔ　ｍａｎｕａｌｌｙ？　　Ｔｈａｎｋｓ　ｆｏｒ　ｙｏｕｒ　ｒｅｓｐｏｎｓｅ！＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝Ｄｒ．　Ｙｉｎｇ　ＺｏｕＲｅｓｅａｒｃｈ　Ａｓｓｏｃｉａｔｅ，ＵＷＭ／Ｐｈｙｓｉｃｓ，１９００　Ｅ．　Ｋｅｎｗｏｏｄ　Ｂｌｖｄ，Ｍｉｌｗａｕｋｅｅ，　ＷＩ５３２１７＝＝＝＝＝＝＝＝＝＝＝＝＝＝

1 0

E0 problems
by Chris Patridge 17 Nov '09

17 Nov '09

Hello, I am having some trouble with a first shell fitting. I have good reason to believe that the compound crystal structure should be quite similar to the starting input structure from other reliable analysis. The closest neighbor paths V-O is 1.61 A away so I set R to 0.8 as a start. I summed what I think are pertinent paths together and tried to fit these paths to a first shell. The bmp file attached contains the fit, summed paths, and the data all in R-space. The fit comes away with a small amplitude, huge E0 of close to -21 eV and negative delr & ss. I have included the artemis project. Is the k-space any indication that the data is too noisy? Any suggestions and or questions would be greatly appreciated. Thank you all, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

1 0

SO2 parameter for Cu2O
by abhijeet gaur 13 Nov '09

13 Nov '09

Hi all, I am fitting Cu2O EXAFS data taken at SSRL using the Artemis. But there is a problem with fitting results that SO2 parameter is coming very low around 0.50. I had also taken Cu2O data from different data bases to check whether theere some problem with my data, but after fitting them, the same problem of low SO2 is coming. In some research papers given SO2 parameter for Cu2O equal to 0.82. But I am unable to get that why all the Cu2O data giving low value of SO2. Is there any other fitting procedure to fit the compounds like Cu2O ?????? With thanks Abhijeet Gaur

2 1

Re: [Ifeffit] Question about ATHENA software
by Bruce Ravel 13 Nov '09

13 Nov '09

Claudia, The implementation of the XANES self-absorption corrections follows the thing that Daniel Haskel wrote up here: http://www.aps.anl.gov/xfd/people/haskel/fluo.html The algorithm used is explained on pages 5-9 of the postscript file on that web page. The angles are defined relative to the surface, not the surface normal. HTH, B PS: You should consider joining the Ifeffit mailing list: (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) It is a very useful resource for siftware and for XAS in general. On Saturday 07 November 2009 02:22:45 pm you wrote: > Dear Bruce Ravel, > > I am a PhD student currently working with the ATHENA software. I came > across a question which I could not answer even after searching the > internet for hours. I hope you might have the time to briefly answer my > question. > > The self-absorption dialog requires the incoming (angle in) and the > outgoing angle (angle out) as an input. My basic question is: Are these > angles referenced to the sample surface or to the normal of the surface? > I would not worry about that if I had measured in 45deg geometry (as in > your tutorial example). However, I did not and therefore it makes a > large difference. > > I strongly apologize bothering you with such a basic question. > Many thanks in advance. > Best regards, > Claudia Fleischmann -- 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/

3 3

SO2 parameter problem
by abhijeet gaur 12 Nov '09

12 Nov '09

Hi all, I am fitting CuO2 EXAFS data taken at SSRL using the Artemis. But there is a problem with fitting results that SO2 parameter is coming very low around 0.50. I had also taken CuO2 data from different data bases to check whether theere some problem with my data, but after fitting them, the same problem of low SO2 is coming. In some research papers given SO2 parameter for CuO2 equal to 0.82. But I am unable to get that why all the CuO2 data giving low value of SO2. Is there any other fitting procedure to fit the compounds like CuO2 ?????? With thanks Abhijeet Gaur

1 0

Why I can't install ifeffit?
by 康明亮 10 Nov '09

10 Nov '09

Dear, I don't konw why I can't intall ifeffit. As I run the Anthena programm, it prompted me the following message: Cannot execute grwnd.exe to open the graphics window. I don;t know how to resolve this problem. wish to obtain guidance. Thank you. Best regards Mingliang

2 1

consultation
by 康明亮 10 Nov '09

10 Nov '09

Dear, I have encountered a problem when using IFEFFIT. As I double click the Athena icon on the desktop, it prompted the following concent: Cannot execute grwnd.exe to open the graphics window. How to resolve this problem? Thank you! Best regards Mingliang

2 1

Athena User Guide—FCFS
by Julie Olmsted Cross 09 Nov '09

09 Nov '09

I have ten copies of the Athena User Guide leftover from the 2009 APS XAFS School. If you want one, send me your mailing address. First come, first served. ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Re: [Ifeffit] Ifeffit Digest, Vol 81, Issue 7
by Khalid, Syed 09 Nov '09

09 Nov '09

The (Passivated Implanted Planar Silicon) PIPS detector that we purchase for our beamlines is model: PD 3000-55-300-AB AB is for BNC connector, if not specified they mail it with an AM (Axial Microdot) connector. PD is partially Depleted, 3000 mm square is the area of the detector. 55 KeV (FWHM) is the energy resolution for alpha particles, and 300 is the thickness of Si in microns. Syed Khalid -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, November 09, 2009 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 81, Issue 7 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: python 2.6 wrapper (Carmelo Prestipino) 2. consultation (???) 3. Re: Question about ATHENA software (Bruce Ravel) 4. PIPs detectors (Bruce Ravel) 5. Re: PIPs detectors (Jeff Terry) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Nov 2009 14:19:42 +0100 From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] python 2.6 wrapper Message-ID: <20091109141942.0tdnvgz3ogcw0ckw(a)160.103.2.152> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear Matt and Carlo I was speaking about windows, sorry for the imprecision. I tested today the file sent by Matt, on my computer all seems to work fine with Python 2.6. Cheers Carmelo Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. python 2.6 wrapper (Carmelo Prestipino) > 2. Re: python 2.6 wrapper (Carlo Segre) > 3. Re: python 2.6 wrapper (Matt Newville) > 4. Re: Ifeffit (Matt Newville) > 5. Re: Ifeffit (Cl?ment Levard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Nov 2009 10:50:25 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] python 2.6 wrapper > Message-ID: <20091106105025.gifreaxeogoc440g(a)160.103.2.152> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear All > I upgraded my my python version on 2.6, I was wondering if is it > available a new Ifeffit wrapper for this version? > Best regards > Carmelo > > -- > > --------------------------------------- > Dr. Carmelo Prestipino > European Synchrotron Radiation Facility > BP220, 38043 Grenoble Cedex, > FRANCE > Tel: +33 (0)4 38 88 19 29 > --------------------------------------- > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Nov 2009 07:46:55 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: <alpine.DEB.1.10.0911060746230.3348(a)arsenide.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > What is your operating system? The gifeffit progrm should work fine with > most versions of python. > > Carlo > > > On Fri, 6 Nov 2009, Carmelo Prestipino wrote: > >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> > > -- > 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 > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Nov 2009 10:46:46 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: > <b8522e3d0911060846t6f7bea35j83dbff53c6c580d2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carmelo, Carlo, > > As Carlo says, on linux there should be no problem with the older > build system.... I'm using python2.6 and Ifeffit on linux. > > So, I'll assume you're asking about Windows. I do not yet have an > executable installer for Python2.6 on Windows. But, if you're brave, > I have something for you to try. In fact, just this past week, as > part of a move to a new Windows build system (see > http://cars9.uchicago.edu/ifeffit/MingwBuild) I've moved from using a > C extension for Python to using Python's ctypes library. This means > that the Ifeffit-Python interface is in pure Python and uses the DLL > directly, which is much better than the previous situation. > > I've tested this with python 2.6 and it works for me on both Windows > and linux, with very minor differences between them. The result > (Ifefffit.py attached) should be viewed as "beta testing" stage -- If > you try it out, I'd love to hear about any issues you have with it. I > don't have a nice installer for this, but you should be able to put > this in any folder that Python will find it. If you don't have > Ifeffit installed to C:\Program Files\Ifeffit, you may need to alter > the top of the script (the set_environ function). > > Cheers, > > --Matt > > > > > On Fri, Nov 6, 2009 at 3:50 AM, Carmelo Prestipino > <carmelo.prestipino(a)esrf.fr> wrote: >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> -- >> >> --------------------------------------- >> Dr. Carmelo Prestipino >> European Synchrotron Radiation Facility >> BP220, 38043 Grenoble Cedex, >> FRANCE >> Tel: +33 (0)4 38 88 19 29 >> --------------------------------------- >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

1 0

PIPs detectors
by Bruce Ravel 09 Nov '09

09 Nov '09

Hi all, A colleague at a company that, for some reason, blocks mail from this mailing list asked me a question the other day that I don't have an immediate answer for. I told him I would pass his question along to the list and forward him any answers. He asks: I've looked over the Canberra website, but I am a little confused about what specifications I should go for. To be absolutely honest, I have never seen a PIPs detector/chip in person as they have always has the Al/Mylar film attached. Would you happen to have a specifications/model list for one of these devices (and the requisite type of BNC connector that I need)? I would greatly appreciate any direction that you could offer. Thanks, B -- 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] python 2.6 wrapper
by Carmelo Prestipino 09 Nov '09

09 Nov '09

Dear Matt and Carlo I was speaking about windows, sorry for the imprecision. I tested today the file sent by Matt, on my computer all seems to work fine with Python 2.6. Cheers Carmelo Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. python 2.6 wrapper (Carmelo Prestipino) > 2. Re: python 2.6 wrapper (Carlo Segre) > 3. Re: python 2.6 wrapper (Matt Newville) > 4. Re: Ifeffit (Matt Newville) > 5. Re: Ifeffit (Cl?ment Levard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Nov 2009 10:50:25 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] python 2.6 wrapper > Message-ID: <20091106105025.gifreaxeogoc440g(a)160.103.2.152> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear All > I upgraded my my python version on 2.6, I was wondering if is it > available a new Ifeffit wrapper for this version? > Best regards > Carmelo > > -- > > --------------------------------------- > Dr. Carmelo Prestipino > European Synchrotron Radiation Facility > BP220, 38043 Grenoble Cedex, > FRANCE > Tel: +33 (0)4 38 88 19 29 > --------------------------------------- > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Nov 2009 07:46:55 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: <alpine.DEB.1.10.0911060746230.3348(a)arsenide.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > What is your operating system? The gifeffit progrm should work fine with > most versions of python. > > Carlo > > > On Fri, 6 Nov 2009, Carmelo Prestipino wrote: > >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> > > -- > 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 > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Nov 2009 10:46:46 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: > <b8522e3d0911060846t6f7bea35j83dbff53c6c580d2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carmelo, Carlo, > > As Carlo says, on linux there should be no problem with the older > build system.... I'm using python2.6 and Ifeffit on linux. > > So, I'll assume you're asking about Windows. I do not yet have an > executable installer for Python2.6 on Windows. But, if you're brave, > I have something for you to try. In fact, just this past week, as > part of a move to a new Windows build system (see > http://cars9.uchicago.edu/ifeffit/MingwBuild) I've moved from using a > C extension for Python to using Python's ctypes library. This means > that the Ifeffit-Python interface is in pure Python and uses the DLL > directly, which is much better than the previous situation. > > I've tested this with python 2.6 and it works for me on both Windows > and linux, with very minor differences between them. The result > (Ifefffit.py attached) should be viewed as "beta testing" stage -- If > you try it out, I'd love to hear about any issues you have with it. I > don't have a nice installer for this, but you should be able to put > this in any folder that Python will find it. If you don't have > Ifeffit installed to C:\Program Files\Ifeffit, you may need to alter > the top of the script (the set_environ function). > > Cheers, > > --Matt > > > > > On Fri, Nov 6, 2009 at 3:50 AM, Carmelo Prestipino > <carmelo.prestipino(a)esrf.fr> wrote: >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> -- >> >> --------------------------------------- >> Dr. Carmelo Prestipino >> European Synchrotron Radiation Facility >> BP220, 38043 Grenoble Cedex, >> FRANCE >> Tel: +33 (0)4 38 88 19 29 >> --------------------------------------- >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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modeling anti-site disorder
by Shashwat 08 Nov '09

08 Nov '09

Dear All, I am studying the local disorder caused in CoGa alloy (B2: CsCl structure) due to ball-milling; it is expected that Ga atoms substitute most of the Co atoms in the Co sublattice after prolonged milling. In order to model this "anti-site" disorder (occupation of Ga atoms on the Co sites) in ATOMS, I am considering to change the occupancies at the corresponding sites as given below: Before ball-milling: site a: occupancy of Ga = 1 site b: occupancy of Co = 1 (standard .cif data) After ball-milling (assuming 80% anti-site concentration): site a: occupancy of Ga = 0.2 (plus compensating vacancies) site b: occupancy of Co = 0.2 site b: occupancy of Ga = 0.8 Could anyone suggest if this approach is reasonable. Many thanks ... Regards, Shashwat

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Re: [Ifeffit] Ifeffit
by Matt Newville 06 Nov '09

06 Nov '09

Hi Clement, I don't have any experience with the windows emulator on Mac OS X, and have only heard reports that it does work. When running atoms.exe on the Windows emulator on Mac OS X, you see: Running "C:\Program Files\Ifeffit\bin\atoms.exe" MetaCinn.inp '\\.host\Shared Folders\Desktop' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. Defaulting to Windows directory. MetaCinn.inp: not a valid input file for Atoms. My guesses are: a) you want to run atoms in a directory without a space in the name b) you want to be sure that the file is has Windows line endings, not Mac OS line endings. Those are guesses, so I'm also CC'ing this to the Ifeffit mailing list, as someone there may have experience with this issue. --Matt 2009/11/5 Clément Levard <clevard(a)stanford.edu> > > Hi Matt, > I am a new postdoc in Gordon Brown's group in Stanford and would like to use you package for XAS analysis. > I am working on Mac, have installed a Windows Emulator. Most of the programs works fine (Sixpack, Athena, Artemis) But I have troubles running Atoms and Feff6l. > Please find in attachment the message I get when I try to run atoms for example. note that the exact same input file works fine on a Windows computer. I have the same kind of error message while running feff6l. > Do you have an idea of what could be the problem ? > thanks a lot for your help! > > -- > Clément Levard > Postdoctoral Scholar > Cell # : 650-521-7096 > Mailing address: > Geological & Environmental Sciences > Green Earth Sciences > 367 Panama Street, room 305 > Stanford University > Stanford, CA 94305-2115

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python 2.6 wrapper
by Carmelo Prestipino 06 Nov '09

06 Nov '09

Dear All I upgraded my my python version on 2.6, I was wondering if is it available a new Ifeffit wrapper for this version? Best regards Carmelo -- --------------------------------------- Dr. Carmelo Prestipino European Synchrotron Radiation Facility BP220, 38043 Grenoble Cedex, FRANCE Tel: +33 (0)4 38 88 19 29 ---------------------------------------

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Two absorbing atom sites
by Yun Luo 05 Nov '09

05 Nov '09

Dear IFEFFIT List, I learned that IFEEFIT can model a single absorber in two different environment. Could anyone direct me to similar studies that have been done or related tutorials? Below are some thoughts and questions: For example, there is 2 wt% A in both M1 and M2 structural sites in crystal X as dopant. I first create 2 FEFF models in Artemis, one has absorbing atom A only in M1 site and the other one has A only in M2 site. In the fitting process, is it correct that I choose paths from both FEFF models and using different Eo and So^2 for M1 and M2 sites? And to model the site occupancy of A in each site, I can create a fraction parameter "a" (which means there are a*2 wt% A in M1 site and (1-a)*2 wt% A in M2 site). Is it correct to apply this fraction parameter only to So^2 to model the site occupancy of A in M1 and M2 site? I am worried this approach will use too many variables. Any suggestions on the constraints/restraints that I can use? Finally, is there anything else that I missed which needs to be considered to do the modeling for this case of two different absorbing atom sites? Any suggestion will be greatly appreciated! Thank you all in advance! Best regards! Yun

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Reference materials for Ca & Cd for XANES
by Varadarajan Sridharan 03 Nov '09

03 Nov '09

Dear Sir, I am planning to carryout the XANES measurements on Cd(1-x)Ca(x)O solid solution to determine the electronic state. Can you suggest me the reference materials for Ca(2+) K-edge and Cd(2+) L-edge for XANES studies. Thanking you in advance V. Sridharan --------- CMPD, IGCAR Kalpakkam, INdia

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Problem with EXAFS simulations: endless loop
by Cammelli Sebastiano 03 Nov '09

03 Nov '09

Dear feff user I try to simulate the EXAFS spectrum of a matrix composed of Fe and Cr (2 atoms on 35) at the Cr K edge. Well, I do not why, but feff (both 8.2 and 8.4) generates an endless loop. Here below I report the feff.inp used. I try even with different value of the SCF card (7.0 1 30 0.05 10) (4.0 1 30 0.05 10) (2.0 1 30 0.2 1) (3.0 1 30 0.2 1) but nothing changes. In order to solve the problem I should not use the SCF card, but this solution brings to a worse evaluation of the E0 and generally, from my little experience, I prefer to use it. The atoms coordinates were calculated by MD. Thank you very much for any help or suggestion. Best Sebastiano TITLE Cr in Fe matrix CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1.003 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4.0 1 30 0.2 1 DEBYE 60 470 0 EXCHANGE 0 0 0 0 CORRECTIONS 0 2.5 EXAFS RPATH 10.0 POTENTIALS 0 24 Cr -1 -1 1 26 Fe -1 -1 2 24 Cr -1 -1 ATOMS -2.83900 -2.83700 -2.83600 1 Fe -1.41600 -1.41600 -1.41500 1 Fe 0.00000 0.00000 0.00000 0 Cr 2.84600 2.84500 2.84300 1 Fe 0.01340 2.84000 2.83900 1 Fe 2.84000 0.01200 2.83900 1 Fe 0.01200 0.01200 2.83200 1 Fe 2.84000 2.83900 0.01050 1 Fe 0.01200 2.83200 0.01000 1 Fe 2.83200 0.01000 0.01000 1 Fe 1.43000 1.42900 1.42800 2 Cr -2.83300 2.84500 2.84300 1 Fe -2.83900 0.01200 2.83900 1 Fe -2.83900 2.83900 0.01050 1 Fe -2.84700 0.01000 0.01000 1 Fe -1.40200 1.41900 1.41800 1 Fe 2.84300 -2.83400 2.84300 1 Fe 0.01050 -2.83900 2.83900 1 Fe 2.83700 -2.84100 0.01050 1 Fe 0.00900 -2.84700 0.01000 1 Fe 1.41800 -1.40300 1.41800 1 Fe -2.83600 -2.83400 2.84300 1 Fe -2.84200 -2.84100 0.01050 1 Fe -1.41000 -1.40900 1.41800 1 Fe 2.84300 2.84200 -2.83600 1 Fe 0.01050 2.83700 -2.84100 1 Fe 2.83700 0.00910 -2.84100 1 Fe 0.00900 0.00870 -2.84700 1 Fe 1.41800 1.41800 -1.40600 1 Fe -2.83600 2.84200 -2.83600 1 Fe -2.84200 0.00910 -2.84100 1 Fe -1.41000 1.41700 -1.41000 1 Fe 2.84100 -2.83700 -2.83600 1 Fe 0.00770 -2.84200 -2.84100 1 Fe 1.41700 -1.41100 -1.41000 1 Fe END

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Re: [Ifeffit] Installing Athena on a Mac
by Bruce Ravel 02 Nov '09

02 Nov '09

Minna, As I point out regularly on the mailing list, I am not a Mac user and do not maintain the mac packages. You really need to inquire on the mailing list for support in that area -- that way you will actually find the people who *can* help you. Here are some recent threads on the mailing list regarding Mac installation issues: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-September/009018.ht… http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-October/009077.html Perhaps your answer is there. If not, please feel free to make a new request for help on the list. Here is more information about the resources available to you: http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest As I explain there, the mailing list should always be your first stop when you have a question about the software. B PS: If any of the Mac users out there would like to update the Macintosh Issues section of http://cars9.uchicago.edu/ifeffit/FAQ/Installing_Ifeffit that would be really splendid. On Monday 02 November 2009 04:09:22 pm you wrote: > Hello Bruce, > > I'm trying to run Athena on a Mac, OS X Version 10.6.1. Following the > instructions at cars9.uchicago.edu/~ravel/software/downloads.html#mac for a > Macintosh OSX download, I went to SourceForge to download Ifeffit. The > latest version does not appear to be available for Mac download, so I > grabbed > Ifeffit-1.2.10.1-Mac10.4_Intel_horae66.dmg<http://sourceforge.net/projects/ >ifeffit/files/ifeffit/1.2.10/Ifeffit-1.2.10.1-Mac10.4_Intel_horae66.dmg/down >load> , because I'm on an Intel Mac, but the installation failed. I then > grabbed > Ifeffit-1.2.10-Mac10.4_PPC_horae066_pkg.dmg<http://sourceforge.net/projects >/ifeffit/files/ifeffit/1.2.10/Ifeffit-1.2.10-Mac10.4_PPC_horae066_pkg.dmg/do >wnload> and the installation appeared to work, but when I went to run > Athena, X11 opened but nothing else happened. I'm not really sure what the > problem is - can you at least give me a suggestion on where to start? > > Thanks for your help! > > Minna R. Krejci > PhD Candidate - Joester Group > Materials Science and Engineering > Northwestern University > > Cook Hall 3021 > Office: 847 491 3584 > Mobile: 330 603 8608 > minna(a)u.northwestern.edu -- 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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Got Athena data plotted
by abhijeet gaur 28 Oct '09

28 Oct '09

Thanks a lot kicaj, I followed the procedure step by step and I got the data plotted in Excel. Thanks again Kicaj. Abhijeet

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Re: [Ifeffit] Normalization in Athena
by Gudrun Lisa Bovenkamp 27 Oct '09

27 Oct '09

Hi everybody, I am sure that Athena was tested a lot, but as Jeremy pointed out, which I think now is the answer: If the background is substracted before the fitting of the post edge. That is actually how we are normalizing XANES data in our group and that is what I tried in Athena. It is actually working much better with 2. order norm and flattening. Since I do not want to do it by hand for all spectra and import them back into Athena for LCF. This time I attached a the example Athena project file. But with this approach I rarely get the spectrum oscillating around one. I will think about it. Thanks for the hint, Matt, about "no points" in the range. But Athena is acutally complaining, if there are no points to fit the line. Of course, I read the chapter on Normalization in Athena. And what is giving me trouble, why I try the "1-point" approach, is that the small differences in the first post-edge normalization point make a great deal of difference in the normalization of the spectra respective to each other and thus LCF. Finally, I believe it is a very interesting question of taste how to determine the edge step for XANES data or when to substract the background. Or is there any specific reason for a special approach? Thank you all for your help!! Greetings, Lisa > Hi Lisa, > > Be sure that Athena has been rigorously tested and she does know how >to > normalize data. It is much more likely that the default values are >not > the "best" ones for your data. > > My book chapter goes over how Athena normalizes data in detail. If >you > send me your email address I'll send you a copy. In particular see > figure 14-16. > > Cheers, > Shelly > > Shelly, > > I agree that Athena applies its (her) algorithm correctly. Whether >that > algorithm is correct may be a matter of opinion. The apparent > discrepency Lisa sees is due to Athena's algorithm: > > i.e., fit preedge line, fit postedge function to normalization >range, > extrapolate both functions to edge energy to find edge step. > > Another option would be to fit predge line and subtract it. After >that, > fit the post edge normalization range. > > With Athena, if there is a non-zero slope to the preedge line and >you > choose norm order 1, you get Lisa's result. With normalization >order 2 > or 3, the results should either be the same, or at least, much >closer. > > Jeremy > > > > It is a little hard to evaluate your results, Lisa, without an > example. It may help to attach a small project file which > demonstrates your question. > > Without an actual example, I would have to guess that the bottom >line > is an odd choice of parameters. This page from the document might >be > helpful: > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html > > B > > > > Lisa, > > I think the issue you're seeing is most likely due to telling athena > to fit the data between E0+199 and E0+200 with a constant. I'd > recommend expanding that range some to give Athena a chance -- if > there isn't any data between E=E0+199 and E0+200, Athena won't be >able > to figure out what the edge step should be. If you really want >the > edge step to be the value of pre-edge subtracted mu(E) at >E=E0+200eV, > you'll have to do that by hand. > > > --Matt > >

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SrSO4 (Celestite) and SrCO3
by Peter Nico 27 Oct '09

27 Oct '09

Hello All, Would anyone out there have a SrSO4 or SrCO3 standard XANES spectra they would be willing to share? There aren't any in the databases of which I am aware, namely "Lytle, GSECARS, and NSLS X18b." There is a SrCO3 but its really an EXAFS standard (the edge consists of ~3 points.) I am sorry that I can't necessarily promise a publication acknowledgment because I am not sure if the work will ever be published. However, if it is, I'll definitely acknowledge the help. Thanks. --Peter

3 2

Cu oxide fitting
by abhijeet gaur 27 Oct '09

27 Oct '09

Hi all, I had posted a problem related to fitting results of Cu2O. But there are some problems related to the fitting procedure . So now I have used a different fitting procedure, still there are problems with fitting results. like 1. The value of SO2 is coming low. 2. Value of E0 is coming high though I have calibrated the experimental data. 3. The ss (Debye Waller factor) for some of the paths are coming very high. I am not able to understand the value of ss for multiple scattering path. One more problem is that if I try to align the data with theory by adjusting E0 , the data get distorted. The Artemis file is attached herewith. This time I had made fitted the whole data in one fit by taking all parameter as guessed. With thanks Abhijeet Gaur

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atom.inp file for Zr50Cu50
by S. Gautam 27 Oct '09

27 Oct '09

Dear All, Can anyone help me with the atom.inp file for ZrCu bulk metallic glass samples? I am studying the Ag doping effects over the inter-atomic distance and co-ordination number through Artemis. thanking you, sincerely sanjeev --------------- Dr S. Gautam Nano Materials Analysis Center Korea Institue of Science and Technology Republic of Korea -790 784 Phone : +82-54-279-1503 (Off) 1599 (Fax) : +82-10-8061-5767 (Mob) Email : sgautam71(a)kist.re.kr

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suppressing the stdout of FEFF
by Jochen Brendt 26 Oct '09

26 Oct '09

Hello everybody, I want to use FEFF8 in a program loop and redirect the stdout of this programm in a textfile. When I run the loop several times this textfile becomes very large. Does anybody know, if there is a way to suppress the stdout of FEFF8 ? Regards, Jochen

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Rbkg value
by Chris Patridge 26 Oct '09

26 Oct '09

Hello everyone, In removing background, most literature suggests Rbkg value of 1.0 because below this represents mostly noise and low freq components not part of the scattering effect. In using Feff and viewing the individual paths calculated a number of them have paths near 1.5 A, therefore meaning that they have some contributions very close to 1.0 A and below in R space due to phase shift. Has anyone modeled materials which contain these rather short Reff and how did you decide what was scattering and noise? Thank you all, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

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Normalization in Athena
by Gudrun Bovenkamp 26 Oct '09

26 Oct '09

Hey everybody, while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly: Normalization in Athena (post-edge): using 1.order normalization, no flattening (which in this case is irrelevant anyway), points +199 eV and +200 eV above E0. Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value. See the two examples in the attachment. In both examples the normalized spectrum imported from Athena does not have the norm value of 1 at 13235 eV. Why is that? The offset is also not the same for every spectrum. That undoes the normalization routine. Greetings, Lisa

5 4

Xanes with Athena?
by Annette Pietzsch 26 Oct '09

26 Oct '09

Hi, I tried to use the self absorption function of the Athena package (FLUO) with my Xanes data (Fe3O4 at the Fe L3 edge). The program identifies the edge correctly, but gives only a zero line for the correction. I think it might be due to the energy value of the Fe L3 edge emission in the database which is prompted to be zero by Athena. Could this be the reason? If yes, is there a possibility to change the energy database to the correct value? \ Annette

2 1

Cu2O fitting
by abhijeet gaur 26 Oct '09

26 Oct '09

Hi all, I had posted a problem related to fitting results of Cu2O. Bruce sir had suggested me to go through the Metal oxide modelling part of 14 chapter of Soil Analysis book by Shelly D. Kelly madam. I had gone through it and it really helped me in understanding the things in better way. I had done the fitting according to the procedure given in it. But still there are problems with fitting results. like 1. The value of SO2 is coming low. 2. Value of E0 is coming high though I have calibrated the experimental data. 3. The ss (Debye Waller factor) for some of the paths are coming very high. I am not able to understand the value of ss for multiple scattering path. One more problem is that if I I try to align the data with theory by adjusting E0 as given in 14 chapter, the data get distorted. The Artemis file is attached. This time I had made fitted the whole data in one fit by taking all parameter as guessed. With thanks in advance Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain, India

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Installation ifeffit-1.2.4.dmg OS X 10.2.8
by Juergen Roehler 20 Oct '09

20 Oct '09

Hi, I am trying to run Ifeffit on MacOSX 10.2.8 from ifeffit-1.2.4.dmg on a Wallstreet Powerbook (a good old companion ,,,, ) > Ifeffit successfully installed in Applications folder [noname:/Applications/Ifeffit] jroehler% ls artemis icons lib perl5 tkatoms athena include man pgplot >XDarwin started (XFree86 4.2 installed from Fink, runs fine for >other X applications) >Click the perl scripts athena or friends, or run them explicitly >with perl 5.6 - athena & friends won´t start. Asked to choose a >program. Which one? > Try to start from terminal: [noname:/Applications/Ifeffit] jroehler% ./athena Can't locate Tk.pm in @INC (@INC contains: /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl /Network/Library/Perl .) at ./athena line 53. BEGIN failed--compilation aborted at ./athena line 53. Well, the *.pm´s and everything else is in /Applications/Ifeffit/lib/perl5 or /Applications/Ifeffit/, being not in the search tree. Don´t want to modify the system architecture copying /lib/perl5 and the other stuff to somewhere else. How to modify the scripts athena & friends. Other solutions? Would like to start jsut from the icons. Thanks in advance. Juergen ******************************* Juergen Roehler Universitaet zu Koeln Fachgruppe Physik Zuelpicher Str. 77 50937 Koeln mailto:Juergen.Roehler@uni-koeln.de http://www.uni-koeln.de/~abb12 *******************************

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Athena & Artemis crashing
by Chris Patridge 20 Oct '09

20 Oct '09

Hello all, Athena and Artemis have been suddenly crashing lately. There seems to be no single action which causes the crash. I am running on Windows XP Pro with SP3. This has happened only quite recent. Has anyone else experienced this problem? In addition, the autosave does not recover the lost work after crashing? Buena salud, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

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xmu discontinuity
by Lisandro Giovanetti 16 Oct '09

16 Oct '09

Dear fellows, I am working with feff 8.2 trying to simulate Au L3 XANES and in every intent I get an xmu with a strong discontinuity near the infection point. Looking for the origin of this feature I find that is present in xmu0 and in the chi signal. Depending of the value of the Fermi level correction in the EXCHANGE card the discontinuity changes but I never get it disappears. Does anyone have a solution to this problem? I send one of the feff.inp files that I used. Thank you very much. Lisandro TITLE Au Bulk L3 HOLE 4 0 * Au L3 edge (11919.0 eV), second number is S0^2 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 3 EXCHANGE 0 1.0 0.0 NOHOLE *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 5.8 0 *AFOLP 1 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion UNFREEZEF * kmax [ delta_k delta_e ] XANES 5.0 0.05 0.05 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.5 0 RPATH 6.5 NLEG 3 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -20 20 0.5 *** for EXAFS: uncomment the EXAFS card POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.01 1 79 Au_2 3 3 1 2 79 Au_3 3 3 1 3 79 Au_4 3 3 1 ATOMS * this list contains 887 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Au1 0.00000 2.04000 2.04000 0.00000 1 Au1_1 2.88500 -2.04000 2.04000 0.00000 1 Au1_1 2.88500 2.04000 -2.04000 0.00000 1 Au1_1 2.88500 -2.04000 -2.04000 0.00000 1 Au1_1 2.88500 2.04000 0.00000 2.04000 1 Au1_1 2.88500 -2.04000 0.00000 2.04000 1 Au1_1 2.88500 0.00000 2.04000 2.04000 1 Au1_1 2.88500 0.00000 -2.04000 2.04000 1 Au1_1 2.88500 2.04000 0.00000 -2.04000 1 Au1_1 2.88500 -2.04000 0.00000 -2.04000 1 Au1_1 2.88500 0.00000 2.04000 -2.04000 1 Au1_1 2.88500 0.00000 -2.04000 -2.04000 1 Au1_1 2.88500 4.08000 0.00000 0.00000 2 Au1_2 4.08000 -4.08000 0.00000 0.00000 2 Au1_2 4.08000 0.00000 4.08000 0.00000 2 Au1_2 4.08000 0.00000 -4.08000 0.00000 2 Au1_2 4.08000 0.00000 0.00000 4.08000 2 Au1_2 4.08000 0.00000 0.00000 -4.08000 2 Au1_2 4.08000 4.08000 2.04000 2.04000 3 Au1_3 4.99696 -4.08000 2.04000 2.04000 3 Au1_3 4.99696 2.04000 4.08000 2.04000 3 Au1_3 4.99696 -2.04000 4.08000 2.04000 3 Au1_3 4.99696 4.08000 -2.04000 2.04000 3 Au1_3 4.99696 -4.08000 -2.04000 2.04000 3 Au1_3 4.99696 2.04000 -4.08000 2.04000 3 Au1_3 4.99696 -2.04000 -4.08000 2.04000 3 Au1_3 4.99696 2.04000 2.04000 4.08000 3 Au1_3 4.99696 -2.04000 2.04000 4.08000 3 Au1_3 4.99696 2.04000 -2.04000 4.08000 3 Au1_3 4.99696 -2.04000 -2.04000 4.08000 3 Au1_3 4.99696 4.08000 2.04000 -2.04000 3 Au1_3 4.99696 -4.08000 2.04000 -2.04000 3 Au1_3 4.99696 2.04000 4.08000 -2.04000 3 Au1_3 4.99696 -- Lisandro Giovanetti

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Ag NP standards
by Chris Patridge 12 Oct '09

12 Oct '09

Hello all, Our group will be looking at the Ag L-edge soon. I wondered if anyone might have and share some data on Ag nanoparticles. We are running out of time and having trouble synthesizing small size (5-20nm) particles for comparison to our samples of interest. We will be collecting many Ag(salt) Cl, No3, So4 standards if anyone may be in need of those. Buena Salud, Chris Patridge Graduate Student Cell: 315-529-0501

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mailing list outages
by Matt Newville 12 Oct '09

12 Oct '09

Hi Folks, In about 2 hours (noon, Chicago time), I'm going to switch to a new machine as "millenia" which runs this mailing list and the ifeffit web pages. I don't expect serious problems with the web pages. If all goes well, the mailing list will not be out for long enough to notice. But don't be too surprised if mail to the mailing list takes a bit longer than usual this afternoon. Cheers, --Matt Newville

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Fwd: Athena troubleshooting
by Bruce Ravel 12 Oct '09

12 Oct '09

I am forwarding this message to the Ifeffit mailing list, which is the proper forum for Ifeffit software support. Please see http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest I have some comments, which I will post once this gets distributed by the mailing list. B ---------- Forwarded Message ---------- Subject: Athena troubleshooting Date: Wednesday 07 October 2009 From: Tom Malizia <fezzooli(a)gmail.com> To: bravel(a)bnl.gov Hello, this is Tom Malizia. I'm a master's student from the University at Buffalo, and my advisor (Tracy Bank) and I have been granted access to use beamline X11A for the student teacher program. Anyway, I'm emailing because I'm having some trouble with how to manipulate my data and interpret the results. I have run 14 samples (each 4 times) on the beamline, and I'm looking for a shift in the oxidation state of Uranium (4+ to 6+). I'm not sure and can't seem to find any literature on how significant the shift must be to prove anything. Of the 14 samples the uranium peaks for almost all are the samples are at 17160 eV, however a couple samples are at 17158 and another at 17159 eV. The beamline was filtered for both Thorium and Strontium and a zirconium foil standard was implemented. I have aligned all of the zirconium standards peaks, and still have this slight shift in the energy of uranium. Do you have any insight? Also, this is more of a software question. I'm not sure why, but about half of the samples flip their orientation 180 degrees (from positive y to negative y) when "normalizing" them. But when I'm trying to display several samples at once about half are showing positive peaks and half are negative peaks. For instance, samples 10, 3 and 1 don't flip when normalized, however all of the other samples do. If this isn't a good enough explanation I could send files or we could trouble shoot over the phone. I'd like to show as much as I can at the upcoming GSA conference next weekend. I appreciate your time. Thanks so much Tom Malizia University at Buffalo 814-594-4281 cell ------------------------------------------------------- -- 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] Strange problem with FEFF 6L.02
by John McLeod 11 Oct '09

11 Oct '09

I realize this problem might be a bit out of scope for this mailing list, but I was wondering if anyone in the community has any insight into the matter. I was playing around with random clusters of atoms and I noticed that FEFF6 spits out the following error: At line 90 of file istprm.f Fortran runtime error: End of file For a few specific geometries. For most of the structures I have tried FEFF runs fine. I have also tested this on 2 other computers with the same results (all computers are linux machines though, and all with the same FEFF 6L.02 distribution from Artemis 0.8.011). At the end of this email is a sample feff.inp file that produces this error. The second atom, `Se_2' at position (-3.70, -2.63, -3.38) causes the problem. If we move `Se_2' to a new position of (-3.71, -2.63, -3.38) then FEFF runs fine. `Se_2' is over 2.2 angstroms from all other atoms in the cluster. If anyone out there is willing to help me out: 1. Has anyone run into this sort of thing before? 2. Does anyone know why it happens? 3. Do you get the same results as I do with the attached feff.inp? 4. Do the later versions of FEFF have the same problem, or is it native to FEFF6? 5. Is the problem related to my probably outdated version of Artemis? Thanks in advance, John McLeod Department of Physics and Engineering Physics University of Saskatchewan ----------------------------------------------- TITLE Selenium Cluster HOLE 1 1.0 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 3 RMAX 6.0 NLEG 4 POTENTIALS * ipot Z element 0 34 Se 1 34 Se ATOMS * x y z ipot tag distance 0.0 0.0 0.0 0 Se_1 0.0 -3.70 -2.63 -3.38 1 Se_2 5.66 * this atom causes problems * -3.71 -2.63 -3.38 1 Se_2 5.66 * this one does not -2.86 -0.69 -2.42 1 Se_3 3.81 -3.75 0.32 3.27 1 Se_4 4.99 -3.49 -2.06 0.33 1 Se_5 4.07 -1.57 -1.57 4.15 1 Se_6 4.71 0.44 -4.00 -2.28 1 Se_7 4.62 -1.06 0.84 4.08 1 Se_8 4.29 -2.92 1.59 -3.13 1 Se_9 4.56 -3.46 3.66 -1.11 1 Se_10 5.16 -4.87 2.90 1.37 1 Se_11 5.83 -2.64 -3.53 -1.52 1 Se_12 4.66 1.34 -4.46 1.72 1 Se_13 4.97 -0.26 -0.45 -4.18 1 Se_14 4.21 -1.52 -3.36 -3.14 1 Se_15 4.84 -4.85 -0.91 0.69 1 Se_16 4.99 -0.93 -4.90 0.37 1 Se_17 5.00 -0.41 1.95 -3.19 1 Se_18 3.76 0.20 -3.09 2.43 1 Se_19 3.94 -3.19 1.28 -1.23 1 Se_20 3.65 -1.02 1.69 -5.66 1 Se_21 5.99 0.07 3.30 3.46 1 Se_22 4.78 -1.67 4.62 -3.18 1 Se_23 5.85 2.23 -3.69 -3.68 1 Se_24 5.67 1.94 -0.35 -4.32 1 Se_25 4.75 1.23 3.89 -3.49 1 Se_26 5.37 -2.89 3.59 1.53 1 Se_27 4.86 3.71 -1.40 -2.73 1 Se_28 4.82 -1.06 4.39 -0.12 1 Se_29 4.51 3.77 -3.51 -0.02 1 Se_30 5.15 2.74 3.06 2.59 1 Se_31 4.86 2.90 -1.96 4.77 1 Se_32 5.92 2.44 1.72 3.98 1 Se_33 4.97 2.61 4.96 -0.31 1 Se_34 5.61 END -----------------------------------------------

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Cu oxide fitting result
by abhijeet gaur 10 Oct '09

10 Oct '09

Hi all, I am fitting Cu2O data using Artemis. I got a very good fit. But there are problems with the parameters. 1) The value of SO2 is coming very low 2) The value of sigma*2 for different path is coming very different from each other. 3) I have used a number of paths for the fitting as one shell has contribution from many paths. Also the paths are very close to each other (i.e. Reff), So how I should report the fitting results. I am not able to understand these results and also that where I had done mistakes, so please tell me. The Artemis project file is attached herewith

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Re: [Ifeffit] Ifeffit Digest, Vol 80, Issue 7
by abhijeet gaur 10 Oct '09

10 Oct '09

Abhijeet, I took a quick peak at your project and I find it very confusing. In the most recent fit, you are fitting only from 3.5 to 4.4 -- the area under the *third* peak in the data. I don't really know how to comment on this project because you have set a large number of parameters to seemingly arbitrary values. From a numerical perspective, the reason for questions 1 and 2 is because you are attempting to fit only a narrow and of the data and you have set the majority of your parameters. That seems an unlikely strategy to me. I think the best thing you could do would be to fit *all* of your data rather than an arbitrary and small band of it. It would probably be fruitful for you to study carefully Shelly's example of analysis of SnO2 from her recent review chapter. See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2008-July/003641.html and http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-January/004012.html B -- 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 Hello Bruce sir, Thanks for your response. You must be talking about the 14th chapter of the book "Soil and Mineral analysis using XAS". I have that chapter with me. It is very explainatory one. with regards Abhijeet

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Mg K edge measurements
by Amitava D Roy 09 Oct '09

09 Oct '09

Our DCM beamline is capable of measuring magnesium K edge. Amitava Roy J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices Louisiana State University Baton Rouge, LA 70806 reroy(a)lsu.edu

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Fwd: Mg k-edge and Athena Questions
by Bruce Ravel 08 Oct '09

08 Oct '09

I am forwarding this message to the Ifeffit mailing list, which is the proper forum for Ifeffit software support. Please see http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest I have some comments, which I will post once this gets distributed by the mailing list. ---------- Forwarded Message ---------- Subject: Mg k-edge and Athena Questions Date: Wednesday 07 October 2009 From: fang.fang(a)yale.edu To: bravel(a)bnl.gov Dear Bruce, This is Fang from Yale University, Pfefferle and Haller's group. Besides our research on Co/Pt on your X23A2 and X18B, I am mainly involved in the Mg and B edge measurement. I heard from Paul that you also have anongoing project on Mg k-edge, and the updated Athena could import the raw data from X15B. However, after I installed the most recent version of Ifeffit and installed, they still don't recognize the data file. Could you show me how to import the data? Your help will be greatly appreciated. There is another question come with the seasonal shut down of X15B. Do you know any other active beamlines who are willing to put in the effort to scan Mg k-edge? Since NSLS asked us to put in a substitute beamline after we put in this year's proposal, we thought you might have a much better idea of which beamline to turn for this hard range around 1300eV. Many thanks again, Fang ------------------------------------------------------- -- 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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First shell resolution
by Eugenio Otal 08 Oct '09

08 Oct '09

Hi Bruce, thanks for the help, it was really useful. Regards, euG

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First shell resolution
by Eugenio Otal 08 Oct '09

08 Oct '09

Hello, I have a very noisy signal so I have a relative good signal until k =9. I am trying to fit the first shell and want to know if there are a limit for the subshells resolution if the signal is unavailable for k larger than 9. Regards, euG

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Br K-edge exafs spectrum of NaBr(s) or KBr(s)
by Gleb Pokrovski 08 Oct '09

08 Oct '09

Hello, I'm looking for a good exafs spectrum in transmission mode at Br K-edge of NaBr or KBr solids at ambient or low-temperature conditions. Any help will be referenced and acknowledged. Thanks in advance Gleb

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Tenure track position for chemist
by Scott Calvin 06 Oct '09

06 Oct '09

Hi all, Since presumably a lot of people on this list know early-career chemists with an interest in a position where teaching is valued and they can also collaborate closely with a XAFS expert (that's me, I guess), I thought I'd pass along information on our opening: > Sarah Lawrence College, a coeducational liberal arts college > dedicated to individualized education, invites applications from > broadly trained chemists for a tenure-track position beginning > August 1, 2010. The successful candidate will teach general > chemistry, other undergraduate chemistry courses of interest to > liberal arts students, and upper-level courses including physical > chemistry. An interest in environmental science is desirable. A > commitment to working closely with students on an individual basis > is essential. Candidates should have a Ph.D. in Chemistry or expect > to receive one by August 1, 2010. > > Application materials must include: cover letter, CV, statement of > teaching philosophy and research interests, graduate transcript, > descriptions of two courses suitable for liberal arts students, and > three letters of recommendation (at least one of which must address > the candidate's ability to teach general chemistry). Deadline for > applications is November 16, 2009. To apply for the position please > go to: > > https://slc.simplehire.com/applicants/jsp/shared/frameset/Frameset.jsp?time… > For information on Sarah Lawrence College, our curriculum, teaching > methods, and philosophy of education, please see our Web site at: http://www.slc.edu > . > SLC is an Equal Opportunity Employer committed to achieving a > racially and culturally diverse community. --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Ifeffit Digest, Vol 80, Issue 1
by Hashem Stietiya 02 Oct '09

02 Oct '09

Thank you Dr. Segre, So I should not be skeptical if my fitting results return a high Debye Waller value for my first shell as compared with the second shell. I appreciate your help. Hashem Stietiya On Fri, Oct 2, 2009 at 12:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Debye Waller for first shell and second shell (Hashem Stietiya) > 2. Re: Debye Waller for first shell and second shell (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 2 Oct 2009 11:04:45 -0500 > From: Hashem Stietiya <mstiet2(a)tigers.lsu.edu> > Subject: [Ifeffit] Debye Waller for first shell and second shell > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <c7b8f940910020904ged84c20t305a742484dd1f4b(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > Does the Debye Waller value for the first shell have to be smaller than > that > of the second shell? can you have a situation where the Debye Waller value > for the Zn-O first shell is 0.011 and for the Zn-Fe second shell is 0.003? > so if there is thermal or static disorder in the first coordination > shell,that must be the case for the second coordination shell? > > Best Regards, > > Hashem Stietiya > Louisiana State University >

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Debye Waller for first shell and second shell
by Hashem Stietiya 02 Oct '09

02 Oct '09

Dear All, Does the Debye Waller value for the first shell have to be smaller than that of the second shell? can you have a situation where the Debye Waller value for the Zn-O first shell is 0.011 and for the Zn-Fe second shell is 0.003? so if there is thermal or static disorder in the first coordination shell,that must be the case for the second coordination shell? Best Regards, Hashem Stietiya Louisiana State University

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Cementite EXAFS
by Andrew 25 Sep '09

25 Sep '09

Bhoopesh, I would trust the XAFS.org spectrum more than mine, I'm sure that the APS has a better resolution etc. I'm aware that there are other forms of reduced iron carbide, but I did nothing special except for following the Li et al. paper. I then tried to see if the spectrum was similar to both the one on Dr. Newville's database as well as the Iglesia and coworkers' papers, and they were. I know this data is a bit glitchy... and I was pretty much only interested in the XANES. If the person that Dr. Newville is referring to made the Fe3C from the iron melt it would have been a white powder, so they likely did a similar procedure as reducing the Fe2O3 std. to a sufficient temperature (at 1 atm). I have also heard from a former Exxon researcher that when they wanted to make cementite they simply CO reduced Fe2O3 to a sufficient temperature as well. I'm forwarding this directly to your e-mail as well. Hope this helps, if not (try and comparing it with the one on the XAFS.org, I remember when I checked it was similar). Andrew Campos

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Cementite EXAFS - thanks
by Bhoopesh Mishra 24 Sep '09

24 Sep '09

Hi Scott and Mathew, Thanks for pointing me to Matt Newville's archive. It is a great resource to have and I have used it on several occasions. However, what I found on that database is "Fe3C". Since there are couple of different local environments for Fe3C, and not all of them are Cementite - I am not sure if that would be a good standard for me. Nevertheless, it served as a good starting point. It would be great if Andrew can send us his data. Thanks again, Bhoopesh On Thu, Sep 24, 2009 at 11:54 AM, Scott Calvin <SCalvin(a)slc.edu> wrote: > Hi Bhoopesh, > > There are files that are identified as cementite in Matt Newville's > archive: > > http://cars9.uchicago.edu/~newville/ModelLib/search.html<http://cars9.uchicago.edu/%7Enewville/ModelLib/search.html> > > If you manage to get any other data, let me know; I've used the > standard at the link above, but I'd like to confirm it. > > --Scott Calvin > Sarah Lawrence College > > On Sep 24, 2009, at 11:45 AM, bhoopeshm wrote: > > > Dear All, > > I am writing to see if anyone on this mailing list has > > ever measured "Cementite" (Fe3C) EXAFS. It is basically an Iron > > Carbide, nothing exotic at all. > > > > I would be very grateful to anyone who might want to share an EXAFS > > spectrum of Cementite (Fe3C). > > > > > > Regards, > > Bhoopesh > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Cementite EXAFS
by Andrew 24 Sep '09

24 Sep '09

Bhoopesh, There's a paper which says how to make it if you want to run it on your own: "Fe3C, which can form during FTS reactions, was prepared by temperature-programmed reaction (0.167 K/s) of Fe2O3 up to 973 K using CO (Matheson, 99.99%, 107 mol of CO/mol of Fe h) as the reduction and carburization agent. The resulting Fe3C powder was passivated in flowing 1% O2/ He (Matheson, 99.999%, 0.05 mol/h) at room temperature (RT) for 1 h before removing the sample from the synthesis cell." [1] S. Li, G.D. Meitzner and E. Iglesia, J. Phys. Chem. B, 105 (2001) 5743. I made some myself using this method. I would send my spectrum, but if I can recall we had glitches in the EXAFS region. Andrew Campos ** If you want other iron carbides, this will be quite tricky since this is the only one that can be synthesized to a pure extent... obviously one could make cementite to using an iron melt but that requires really high temperature furnaces etc.

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mu(E) of theoretically calculated spectra
by abhijeet gaur 24 Sep '09

24 Sep '09

Hi all, I am doing the theoretical fitting using Artemis. But I am unable to get the mu(E) of theoretically calculated spectra in Artemis. If I got it correctly, Artemis plot the theoretical spectra using FEFF code. But it gives chi(k) and chi(R). Is there any way to get mu(E) from this chi(k) spectra. Or in order get the theoretically calculated mu(E) spectrum of the given structure , we have to use FEFF code alone. How it can be done? with thanks Abhijeet Gaur Vikram University Ujjain (INDIA)

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job postings
by Matt Newville 22 Sep '09

22 Sep '09

Hi Folks, There have been two post-doc positions posted at http://xafs.org/Jobs recently. If you know of anyone who might be interested, please pass these along. Cheers, --Matt Newville

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Re: [Ifeffit] Ifeffit Digest, Vol 79, Issue 9
by abhijeet gaur 20 Sep '09

20 Sep '09

The FEFF6L distributed with Ifeffit is only set up to calculate EXAFS. If you want the near edge structure, you will have to use FEFF8 separately. Hello Carlo Sir, Sorry to give you trouble again about the same reply of yours. Is it possible to get mu(E) of EXAFS, say beyond 20-50 eV through FEFF6L distributed with Ifeffit . with regards Abhijeet

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Re: [Ifeffit] Ifeffit Digest, Vol 79, Issue 8
by abhijeet gaur 19 Sep '09

19 Sep '09

Hi Abhijeet: The FEFF6L distributed with Ifeffit is only set up to calculate EXAFS. If you want the near edge structure, you will have to use FEFF8 separately. Cheers, Carlo Hello Carlo Sir, Thanks for your quick response. But if you can tell me, from where I can get FEFF8 to calculate the near edge structure, it will be very helpful to me. with regards Abhijeet

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XANES spectrum of cobalt carbide
by Xiaoming Wang 19 Sep '09

19 Sep '09

Dear All, I am doing the analysis of some unknown cobalt-containing samples, and I suspect that there might be cobalt carbide there. Thus I am wondering if anybody has a cobalt K edge XANES spectrum of cobalt carbide to share. Your help will be greatly appreciated! Many thanks! Xiaoming Wang Yale University

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GAANN Fellowships for Synchrotron Radiation
by Carlo Segre 18 Sep '09

18 Sep '09

Hello All: I apologize in advance for filling your INBOX with this if it is not relevant. We have recently been awarded a number of fellowships from the Department of Education GAANN program. Our fellowships are specifically for synchrotron radiation research in the Physics program. The announcement link is below. If anyone knows of students interested in this opportunity, please let them know. http://www.iit.edu/research/undergraduate_research/news/gaan_award.shtml 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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Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
by Joel Kelly 16 Sep '09

16 Sep '09

Hello, I recently upgraded to OS 10.6 (snow leopard) on my intel Mac. It comes with version 2.3.4 of X11. Now, I can't seem to run any of the Horae GUI applications! I've tried launching Athena from iXAFS or from the stand alone IFEFFIT suite. When I run iXAFS, the normal launch window with Athena, Artemis, Hephaestus and the iXAFS shell appears. Clicking on the Athena, Artemis, and icons Hephaestus causes X11 to launch with an xterm window, but Aquaterm does not load. However, the iXAFS shell seems to load, though I'm not experienced enough with the shell to know if it's fine or not. Upon launching the Athena standalone program from IFEFFIT (downloaded here: http://cars9.uchicago.edu/~ifeffit/src/Ifeffit-1.2.10-Mac10.4_Intel_horae06…) clicking on "X11 graphics" launches xterm but not Aquaterm, and clicking on "Aquaterm" closes the program. Not sure if this is a Snow Leopard related problem or not- there has been a new version of X11 released (2.4) that is unsupported in OS 10.6, and unfortunately it doesn't seem to allow me to install a previous 2.3.2 version. Looks like I'll have to downgrade back to Leopard, these cat names are getting confusing. Has anyone experienced anything similar, or have any insight on how to fix the problem? Best regards, Joel Kelly University of Alberta

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8 coordination crystal
by mohamed sobhy 15 Sep '09

15 Sep '09

Dear I am trying to simulate CeO2 crystal lattice but I found that in Artemis documentations the following Currently the following coordination geomatries are available: * 4-coordinate crystal * 6-coordinate crystal * octahedral molecule * tetrahedral molecule * square-planar molecule CeO2 has coordination no of 8, so what is the meaning of that Also is there any manual or working examples for Artemis Thnaks Mohamed

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simplr question
by yavuz al 08 Sep '09

08 Sep '09

Dear all, I have just started the using athena and artemis but I wanna learn that what does it means: degen ? So2 ? eo ? dr ? ss2 ? plase help to me about this. yavuzal _________________________________________________________________ With Windows Live, you can organize, edit, and share your photos. http://www.windowslive.com/Desktop/PhotoGallery

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Re: [Ifeffit] Linear combination fitting reports
by Jens Kruse 02 Sep '09

02 Sep '09

Thanks for the fast answers. Attached is a screenshot. Maybe I just read the pages incorrectly. cheers, Jens ifeffit-request(a)millenia.cars.aps.anl.gov schrieb: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Linear combination fitting reports (Jens Kruse) > 2. Re: Linear combination fitting reports (Bruce Ravel) > 3. Re: Linear combination fitting reports (Kelly, Shelly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Sep 2009 10:13:55 +0200 > From: Jens Kruse <jens.kruse(a)uni-rostock.de> > Subject: [Ifeffit] Linear combination fitting reports > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <4A9E2943.5020408(a)uni-rostock.de> > Content-Type: text/plain; charset="ISO-8859-15"; format=flowed > > Hi, > > I have only two short questions. Is it possible that values for > chi-square and reduced chi-square given in the "Fit results" and the > "Combinatorics" page are inverted within Athena? > In the CSV report for all fits, which of these both columns ("chisqr", > "chinu" ) is chi-square and which is reduced chi-square? > > thanks, > Jens > > > > > ------------------------------ > > Message: 2 > Date: Wed, 2 Sep 2009 09:40:48 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Linear combination fitting reports > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200909020940.48150.bravel(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Wednesday 02 September 2009 04:13:55 am Jens Kruse wrote: > >> Hi, >> >> I have only two short questions. Is it possible that values for >> chi-square and reduced chi-square given in the "Fit results" and the >> "Combinatorics" page are inverted within Athena? >> > > I tried running a combinatorial LCF series just before writing this > email and I think these numbers are reported correctly. If you think > otherwise, you will need to show me an example. > > Of course, the values for both R-factor and reduced chi-square are > rather peculiar in Athena's LC fitting, as explained in the manual: > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/analysis/lcf.html > > > >> In the CSV report for all fits, which of these both columns ("chisqr", >> "chinu" ) is chi-square and which is reduced chi-square? >> > > I don't think these are reported wrongly. As I discuss in the manual, > it is hard to know how to evaluate chi-nu in a XANES fit. I use > epsilon=1 (for want of a better number) and I use the number of points > in the data as the number of independent measurements. There are > typically of the order of 100 points in a XANES scan, so chi-nu tends > to be about 2 orders of magnitude smaller than chi-square, which > itself is very small due to the value of epsilon. > > All of this just underscores the squishiness of the statistical > parameters in this context. Interpreting LCF results requies the use > of prior knowledge and a very conservative interpretation of what > Athena reports. > > B > > > > -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190

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Linear combination fitting reports
by Jens Kruse 02 Sep '09

02 Sep '09

Hi, I have only two short questions. Is it possible that values for chi-square and reduced chi-square given in the "Fit results" and the "Combinatorics" page are inverted within Athena? In the CSV report for all fits, which of these both columns ("chisqr", "chinu" ) is chi-square and which is reduced chi-square? thanks, Jens

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 78, Issue 27
by Kevin McPeak 31 Aug '09

31 Aug '09

Andreas, Thanks for your input. We did you use a Zn foil reference and I had aligned the scans in Athena using the auto align feature (to the smoothed derivative). But do to your and Carlo Segre's suggestions I re-checked the alignment, this time zooming very closely. I noticed that a few of the reference scans were +/-0.1 eV misaligned from the reference standard. After the re-alignment the IND value now reaches a minimum at 2 components. Thanks so much for the suggestion! You really can't be too careful with the alignment. Kevin On Fri, Aug 28, 2009 at 1:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Determining the correct number of components from PCA > (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Aug 2009 23:12:12 +0200 > From: "Voegelin, Andreas" <Andreas.Voegelin(a)eawag.ch> > Subject: Re: [Ifeffit] Determining the correct number of components > from PCA > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <9B57B672CD2140498D728E4524354F4264D5BF(a)EA-MAIL.eawag.wroot.emp-eaw.ch> > > Content-Type: text/plain; charset="us-ascii" > > Hi Kevin > > Maybe the 3rd component is not due to noise but accounts for very small > shifts in energy calibration between scans (considering that the > reconstructed white-line is shifted to higher energies in the > 2-component reconstruction). Do you have a reference foil measured with > each scan to exactly align the spectra or some other way to check for > small shifts in energy calibration? > > Best regards, > > Andreas > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kevin > McPeak > Sent: Donnerstag, 27. August 2009 07:23 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Determining the correct number of components from PCA > > Hi all, > > I have a question about the "best" method to use to decide the correct > number of components in a system based on a PCA. Myself and a > collaborator took in-situ XANES scans of the formation of ZnO in > aqueous solution. We have a series of scans from this experiment and I > have done a PCA on them using SIXPack. After doing the PCA I unchecked > the components until I could no longer visually reconstruct the series > of scans accurately (by visual determination). Using this visual > method I only need 2 components. But if I go by the minimum of the IND > function (what the SIXPack user guide recommends) I should use three > components. > > I have posted the sample/reconstruction plots for 2 and 3 component > reconstructions here (the scan I chose to reconstruct is > representative of the data series): > > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_2comp. > html > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_3comp. > html > > The main difference between the two plots is that the 3 component > reconstruction fits the edge region better. Zoom in (hold down the > right mouse button) and you'll see what I'm talking about. That said I > really have my doubts about 3 components being necessary, the visual > differences are so slight that I can't help but think that these > differences are just part of the noise. As for 2 or 3 components being > physically possible, both are feasible give the chemistry involved. > > SIXPack does not provide IE or F test, so I plotted the IND results > vs. number of components for all the reactions. Except for the lowest > concentration the IND value reached a minimum at 3 components for all > the reactions. You can see the plot of IND value vs. number of > components here: > > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_ind_results.html > > The IND minimum is rather broad. Are there other techniques that I > should be using to determine the number of components from the PCA? I > look forward to your feedback. > > Kevin McPeak > kmm333(a)drexel.edu > -- > PhD Candidate > Chemical Engineering > Drexel University > > P.S If you use Firefox or Safari you can zoom in on these plots by > holding down the right mouse button and making a box. Release the > right mouse button to zoom in on that box. Press the left arrow button > to the left of the plot to un-zoom. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 78, Issue 27 > *************************************** >

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Determining the correct number of components from PCA
by Kevin McPeak 27 Aug '09

27 Aug '09

Hi all, I have a question about the "best" method to use to decide the correct number of components in a system based on a PCA. Myself and a collaborator took in-situ XANES scans of the formation of ZnO in aqueous solution. We have a series of scans from this experiment and I have done a PCA on them using SIXPack. After doing the PCA I unchecked the components until I could no longer visually reconstruct the series of scans accurately (by visual determination). Using this visual method I only need 2 components. But if I go by the minimum of the IND function (what the SIXPack user guide recommends) I should use three components. I have posted the sample/reconstruction plots for 2 and 3 component reconstructions here (the scan I chose to reconstruct is representative of the data series): http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_2comp.html http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_3comp.html The main difference between the two plots is that the 3 component reconstruction fits the edge region better. Zoom in (hold down the right mouse button) and you'll see what I'm talking about. That said I really have my doubts about 3 components being necessary, the visual differences are so slight that I can't help but think that these differences are just part of the noise. As for 2 or 3 components being physically possible, both are feasible give the chemistry involved. SIXPack does not provide IE or F test, so I plotted the IND results vs. number of components for all the reactions. Except for the lowest concentration the IND value reached a minimum at 3 components for all the reactions. You can see the plot of IND value vs. number of components here: http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_ind_results.html The IND minimum is rather broad. Are there other techniques that I should be using to determine the number of components from the PCA? I look forward to your feedback. Kevin McPeak kmm333(a)drexel.edu -- PhD Candidate Chemical Engineering Drexel University P.S If you use Firefox or Safari you can zoom in on these plots by holding down the right mouse button and making a box. Release the right mouse button to zoom in on that box. Press the left arrow button to the left of the plot to un-zoom.

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Energy Units in phminNN.dat
by Krayzman, Victor 26 Aug '09

26 Aug '09

Who knows what are energy units and energy origin in files phminMM.dat and phaseNN.dat created by FEFF8.2? Are they Rydbergs or atomic units? Thanks. Victor Krayzman

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Athena error reading file
by Christopher Allen 26 Aug '09

26 Aug '09

Hi everyone, I have two scans taken at x19a of the NSLS (attached) recently that won't open in Athena. Scans before and after these two had no problem, but these give the error reading file message. This was true using whatever version of Athena is on their beamline computer and also version 0.8.056. Thank you in advance, Chris ---------------------------- Chris Allen Northeastern University for Renewable Energy Technology 317 Egan Research Center 360 Huntington Avenue Boston, Ma 02115 617-373-5630

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Re: [Ifeffit] Ifeffit Digest, Vol 78, Issue 23
by Liu Lei 26 Aug '09

26 Aug '09

Hello,I will cancel the booking. Best Regards! ifeffit-request(a)millenia.cars.aps.anl.gov 写: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Vanadium pre edge peak contributes to K-space? (Bruce Ravel) > 2. Re: Vanadium pre edge peak contributes to K-space? > (Chris Patridge) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Aug 2009 11:32:41 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Vanadium pre edge peak contributes to K-space? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200908251132.41271.bravel(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Tuesday 25 August 2009 11:02:26 am Chris Patridge wrote: >> Hello all, >> >> After calibration, alignment and merging V K edge data, there seems to >> be a large peak in R space below 1 A. From most examples and readings, >> this would seem to be noise since atoms do not reside that close to each >> other. Adding a background addresses this noise but then the number of >> variables becomes too large and meaningless to the first shell R space >> range. I believe the problem lies with the large pre edge feature seen >> with high valence state Vanadium compounds. Any suggestions on how to >> work through this and make realistic EXAFS analysis on these compounds. >> >> Thanks everyone, > > > Didn't Richard Mayes answer this same question from you last month? > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-July/004365.html > > In my experience, Richard's answer was spot on for V K edge data. > > If Richard's good advice didn't help, then you need to be more > explicit about what the problem is, perhaps by posting a small athena > project file that demonstrates the problem. > > B > > > -- > > 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/ > > > > > ------------------------------ > > Message: 2 > Date: Tue, 25 Aug 2009 11:44:38 -0400 > From: Chris Patridge <patridge(a)buffalo.edu> > Subject: Re: [Ifeffit] Vanadium pre edge peak contributes to K-space? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <4A9406E6.9070808(a)buffalo.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Bruce Ravel wrote: >> On Tuesday 25 August 2009 11:02:26 am Chris Patridge wrote: >> >>> Hello all, >>> >>> After calibration, alignment and merging V K edge data, there seems to >>> be a large peak in R space below 1 A. From most examples and readings, >>> this would seem to be noise since atoms do not reside that close to each >>> other. Adding a background addresses this noise but then the number of >>> variables becomes too large and meaningless to the first shell R space >>> range. I believe the problem lies with the large pre edge feature seen >>> with high valence state Vanadium compounds. Any suggestions on how to >>> work through this and make realistic EXAFS analysis on these compounds. >>> >>> Thanks everyone, >>> >> >> >> Didn't Richard Mayes answer this same question from you last month? >> >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-July/004365.html >> >> In my experience, Richard's answer was spot on for V K edge data. >> >> If Richard's good advice didn't help, then you need to be more >> explicit about what the problem is, perhaps by posting a small athena >> project file that demonstrates the problem. >> >> B >> >> >> > Yes it is a very similar question. I did make this type of correction > by setting E0 myself. When moving to R space the data shows significant > intensity below 1 A which I thought was noise but it may not be. Are > these low A signals data or noise is my main concern because EXAFS > fitting does not fit all that well which then would point me to my model > as the problem which I think i understand. > > Thank you all for your patience, > > -- > Christopher J. Patridge > Graduate Student > SUNY Buffalo - Dept of Chemistry > 716-645-6800 x 2110 > 315-529-0501 > >

1 0

Vanadium pre edge peak contributes to K-space?
by Chris Patridge 25 Aug '09

25 Aug '09

Hello all, After calibration, alignment and merging V K edge data, there seems to be a large peak in R space below 1 A. From most examples and readings, this would seem to be noise since atoms do not reside that close to each other. Adding a background addresses this noise but then the number of variables becomes too large and meaningless to the first shell R space range. I believe the problem lies with the large pre edge feature seen with high valence state Vanadium compounds. Any suggestions on how to work through this and make realistic EXAFS analysis on these compounds. Thanks everyone, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

4 6

a question
by Dr Somaditya Sen 25 Aug '09

25 Aug '09

Hi All I am having problems in comparing the real bond length as obtained from EXAFS data and Reitveld analysis of XRD data of te same sample. The bond lengths as observed from the XAFS data seems to be much smaller that that from XRD. Is there some multiplication factor known in literature to address this issue? S Sen

3 2

R space merged data bitmap
by Chris Patridge 25 Aug '09

25 Aug '09

Sorry I forget to add bitmap for my questions. I will not double post anymore. Thanks again, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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Re: [Ifeffit] Using Ifeffit in Perl
by bravel＠bnl.gov 25 Aug '09

25 Aug '09

Jan, Are you using Strawberry or ActiveState? B ------Original Message------ From: Jan Stoetzel Sender: ifeffit-bounces(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov ReplyTo: XAFS Analysis using Ifeffit Subject: [Ifeffit] Using Ifeffit in Perl Sent: Aug 24, 2009 9:25 AM Hi, I have a little problem, probably/hopefully not so complicated: I want to include the Ifeffit functions in my Perl scripts which I want to use in Windows XP via the cmd.exe. So I installed Ifeffit with the Windows Installer, found some ifeffit.pm module and included it somewhere in the @inc folders. Now, if I call "use Ifeffit" in my scripts it doesn´t work with the message: "Can´t locate loadable object for module Ifeffit in @INC... Compilation failed". Any idea of what is going wrong here? Some precompilation necessary? Thanks, Jan -- Dipl.-Phys. Jan Stötzel Fachbereich C / Physik, Bergische Universität Wuppertal Gaußstr. 20, D-42097 Wuppertal, Germany E-mail: j.stoetzel(a)uni-wuppertal.de phone: +49 202 439-3105, fax: -3101, secretary: -3102 http://hydrogen.physik.uni-wuppertal.de/index.html _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Sent on the Now Network� from my Sprint® BlackBerry

2 1

Using Ifeffit in Perl
by Jan Stoetzel 24 Aug '09

24 Aug '09

Hi, I have a little problem, probably/hopefully not so complicated: I want to include the Ifeffit functions in my Perl scripts which I want to use in Windows XP via the cmd.exe. So I installed Ifeffit with the Windows Installer, found some ifeffit.pm module and included it somewhere in the @inc folders. Now, if I call "use Ifeffit" in my scripts it doesn´t work with the message: "Can´t locate loadable object for module Ifeffit in @INC... Compilation failed". Any idea of what is going wrong here? Some precompilation necessary? Thanks, Jan -- Dipl.-Phys. Jan Stötzel Fachbereich C / Physik, Bergische Universität Wuppertal Gaußstr. 20, D-42097 Wuppertal, Germany E-mail: j.stoetzel(a)uni-wuppertal.de phone: +49 202 439-3105, fax: -3101, secretary: -3102 http://hydrogen.physik.uni-wuppertal.de/index.html

2 1

limits for second shell
by Eugenio Otal 24 Aug '09

24 Aug '09

Hello everybody thanks for the help. best regards for everyone

1 0

Principle Component Analysis
by abhijeet gaur 22 Aug '09

22 Aug '09

Hi all, I am trying to understand the method of Principal Component Analysis. What is PCA, On what principle it works, How it can be applied to system and to what type of system it can be applied. I am trying to find the answers of these questions. If someone can please tell me where I can find the literature related to these questions, I will be very thankful. with thanks Abhijeet Gaur

3 2

limits for second shell
by Eugenio Otal 21 Aug '09

21 Aug '09

Hi, I have a sample of a pure Er2O3 (blue line in the attached graph) and a sample of doped ZnO with erbium that has segregated the same oxide (red line) by thermal treatmen. The signal for de segregated oxide gets noisy around k=9 because the sample is so diluted, but the radial distribution shows second shell signal, smaller than the pre oxide, but still a signal. My doubt is about how to know if the second shell is real and if that second shell can be useful to obtain information. Is there a criteria to know that? Some limit in k-space? Thanks, euG

5 4

limits for second shell
by Eugenio Otal 21 Aug '09

21 Aug '09

Hi Scott, thanks, I deeply appreciate your help, like Theseus leaving the labyrinth. Best regards, euG

1 0

limits for second shell
by Eugenio Otal 21 Aug '09

21 Aug '09

Hi, thanks for the help. Let me be more clear. I am trying to know the limits to use information from the second shell, from XRD I found that the phase is present, but I want to know if I can use the signal to obtain more information about second neighbors. I have this sample and some more where I find a second shell signal, the doubt is about how far can I trust in this information, is there a limit in k-space to believe in the information of the second shell and try to fit it? I attach the R-space graph with the same limits for the FT, there are still differences, what should I check to be sure the information I can get from the second shell is trustable and not a problem of the noisy signal? Thanks, euG

2 1

Pellet sample preparation
by Dominik Samuelis 21 Aug '09

21 Aug '09

Dear list, for many years, I have used "Merck Uvasol Polyethylene for spectroscopy" PE powder as a diluent and binder for pressing self-supporting pellets especially of air-sensitive substances. When I today wanted to order a new bottle, I had to learn that it's not available anymore (actually, since 2002... :-)). Does anyone of you know about any other supplier of spectroscopy-grade polyethylene powder? And more general, which binder/diluent do you use for preparing pellets of sensitive substances ? Best regards, Dominik -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

4 3

limits for second shell
by Eugenio Otal 21 Aug '09

21 Aug '09

Carlo, deeply sorry, the problems to work pass midnight. Regards, euG

1 0

Chi in arthemis
by Eugenio Otal 19 Aug '09

19 Aug '09

Hi Scott, here I copy a part of the report: Independent points = 6.222656250 Number of variables = 4.000000000 Chi-square = 247.145092496 Reduced Chi-square = 111.193574128 R-factor = 0.017422216 Guess parameters +/- uncertainties (initial guess): amp = 6.7815290 +/- 1.4687660 (1.0000) enot = 2.2173620 +/- 2.1499920 (0.0000) delr = 0.0514640 +/- 0.0163900 (0.0000) ss = 0.0074020 +/- 0.0025220 (0.0030) I see that the R-factor is pretty good, 1.74%, amp is high cause is correlated with the coordination number and always have big errors., delr has the error of the total distance, so it is ok, but ss and enot have a a really big error, is this normal? Thanks, euG

4 5

Chi in arthemis
by Eugenio Otal 18 Aug '09

18 Aug '09

Hi Scott, Thanks for you help. Best Regards, euG

1 0

Chi in arthemis
by Eugenio Otal 18 Aug '09

18 Aug '09

Hi Scott, I forget the amp, I left the N =1, that is the mistake, sorry I have de S02 from other oxide to transfer it. I found that error bars in Ifeffit are scaled by Chi2 reduced, so should I transform the error or inform them directly as reported? Regards, euG

2 1

Chi in arthemis
by Eugenio Otal 18 Aug '09

18 Aug '09

Hi all, I see that the reports of the fits a perform in arthemis have Chi really big. The fit is really good and the Chi should be closer to 1 than to 100. The problem, is what should I report as the Chi. Uncertain in delr or ss have the same problem, are big like the results. I found the topic in the list but not a good answer to what should I report. Thanks, euG

2 1

Athena User Guide–All copies spoken for
by Julie Olmsted Cross 12 Aug '09

12 Aug '09

All 10 copies of the Athena User Guide have been spoken for. Many thanks, Julie ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Re: [Ifeffit] Ifeffit Digest, Vol 78, Issue 8
by abhijeet gaur 12 Aug '09

12 Aug '09

Re ( Athena User Guide) Hello, Is it the same user guide that comes with the ATHENA software ? If not I also need a copy. Abhijeet On 8/12/09, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Athena User Guide?FCFS (Julie Olmsted Cross) > 2. Re: Athena User Guide?FCFS (Stefano Ciurli) > 3. Re: Athena User Guide?FCFS (Julie Olmsted Cross) > 4. Athena User Guide?All gone (Julie Olmsted Cross) > 5. Re: Athena User Guide?FCFS (goodhei8(a)gmail.com) > 6. Re: Athena User Guide?FCFS (valmor) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Aug 2009 14:21:16 -0500 > From: Julie Olmsted Cross <jox(a)aps.anl.gov> > Subject: Re: [Ifeffit] Athena User Guide?FCFS > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <ABF43A66-D8BB-4A49-83B4-031CE3290B06(a)aps.anl.gov> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > I just found two more, bringing the total to 12. I'll give you two. > > On Aug 11, 2009, at 1:49 PM, Matt Newville wrote: > > > I never got one.... > > > > --Matt > > > > On Tue, Aug 11, 2009 at 1:47 PM, Julie Olmsted > > Cross<jox(a)aps.anl.gov> wrote: > >> I have ten copies of the Athena User Guide leftover from the 2009 > >> APS XAFS > >> School. If you want one, send me your mailing address. First come, > >> first > >> served. > >> > >> ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > >> Dr. Julie O. Cross > >> User Technical Interface > >> APS Engineering Support Division > >> Argonne National Laboratory > >> 9700 South Cass Ave., Bldg. 401/B4204 > >> Argonne IL 60439-4801 > >> tel: 630 252 0592 > >> fax: 630 252 7187 > >> ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > >> > >> > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > Dr. Julie O. Cross > User Technical Interface > APS Engineering Support Division > Argonne National Laboratory > 9700 South Cass Ave., Bldg. 401/B4204 > Argonne IL 60439-4801 > > tel: 630 252 0592 > fax: 630 252 7187 > ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Aug 2009 21:27:14 +0200 > From: Stefano Ciurli <stefano.ciurli(a)unibo.it> > Subject: Re: [Ifeffit] Athena User Guide?FCFS > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <B486A028-9A31-4E68-9994-9337A62C7DCC(a)unibo.it> > Content-Type: text/plain; charset="us-ascii" > > I would like one > Stefano > > On 11 ago 2009, at 20:47, Julie Olmsted Cross wrote: > > > I have ten copies of the Athena User Guide leftover from the 2009 > > APS XAFS School. If you want one, send me your mailing address. > > First come, first served > > ______________________________ > > Stefano Ciurli > Laboratory of Bioinorganic Chemistry > http://bioinorg.agrsci.unibo.it/ > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > http://www.cerm.unifi.it/home/ > http://www.isa.unibo.it/ISA/ > http://www.biocomp.unibo.it/unibonet/ > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high" > >

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Athena User Guide—All gone
by Julie Olmsted Cross 11 Aug '09

11 Aug '09

~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Re: [Ifeffit] Athena User Guide—FCFS
by Frantisek Majs 11 Aug '09

11 Aug '09

Franta Majs Apt 1725 124 Grande Brook Circle Wakefield RI 02879 ---- Original message ---- >Date: Tue, 11 Aug 2009 13:47:29 -0500 >From: Julie Olmsted Cross <jox(a)aps.anl.gov> >Subject: [Ifeffit] Athena User Guide—FCFS >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > I have ten copies of the Athena User Guide leftover > from the 2009 APS XAFS School. If you want one, send > me your mailing address. First come, first served. > > ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ > Dr. Julie O. Cross > User Technical Interface > APS Engineering Support Division > Argonne National Laboratory > 9700 South Cass Ave., Bldg. 401/B4204 > Argonne IL 60439-4801 > tel: 630 252 0592 > fax: 630 252 7187 > ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ >________________ >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Is it legitimate to merge transmission data with fluorescence data?
by jrkizews＠ncsu.edu 11 Aug '09

11 Aug '09

Dear XAFS community members, I have a question concerning data merge. We normally collect XAFS data in both transmission mode and fluorescence mode. We normally have to merge a few scans to enhance signal-to-noise ratio. For one particular sample, I want to know if it is legitimate to merge its transmission scans with its fluorescence scans to improve data quality? I appreciate any input. Regards. Fiona Kizewski North Carolina State University Department of Chemistry

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Re: [Ifeffit] Installation of FEFF8 on IFEFFIT
by Bruce Ravel 11 Aug '09

11 Aug '09

> I have a question of the FEFF8 installation in IFEFFIT on a window XP. > I know that the IFEFFIT includes FEFF6, and I have the licence of FEFF8. > I have used IFEFFIT with FEFF6 on the window and FEFF8 in a LINUX system. > Now I want to use the FEFF6 on the windos XP. > After I unzipped the ifeffit package, I find binary files, including > feff6l.exe, in the bin directory. May I copy the FEFF8.exp file into the > directory and rename FEFF8.exe to feff6l.exe? Or is there any other way to > select different versions of FEFF from Atermis? Han, I am CCing my answer to the Ifeffit mailing list, as this is an appropriate question for the list. Artemis is quite happy using Feff8 for EXAFS analysis, although the advantage of Feff8 for EXAFS analysis over Feff6 is rather marginal. You will need to configure Artemis to use Feff8 correctly. In the Edit menu, select Edit preferences. Change the Atoms->feff_version parameter to 8. Then change the Feff->feff_executable parameter to the fully qualified location of the Feff8 executable. That is, you must type in something like "C:\Software\Feff8\feff8.exe". To the best of my knowledge, that will work correctly. B -- 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] Kapton in glove box (Todd Monson)
by Monson, Todd 06 Aug '09

06 Aug '09

Thanks for all your comments regarding kapton tape and measuring air and moisture sensitive compounds. Many of my samples are indeed air sensitive and not just moisture sensitive (iron nanoparticles). If my particles are dispersed in solvent will the kapton be resistant to that solvent (at least during the time that the solvent is evaporating from the tape in the glove box)? Darek mentioned kapton dots - could you tell me where I can purchase these? Thanks again for everyone's help, I thought this mailing list was primarily for software related questions but I am finding it is useful to get help on any XAFS related questions. Todd -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: August 06, 2009 1:50 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 78, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Kapton in glove box (Scott Calvin) 2. Re: Kapton in glove box (Zajac, Dariusz A.) 3. Re: Kapton in glove box (Maurits van den Berg) ---------------------------------------------------------------------- Message: 1 Date: Wed, 05 Aug 2009 20:47:48 -0400 From: Scott Calvin <SCalvin(a)slc.edu> Subject: Re: [Ifeffit] Kapton in glove box To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: Scott Calvin <scalvin(a)slc.edu> Message-ID: <025FE360-0E9F-4421-A22D-2074D838AFB7(a)slc.edu> Content-Type: text/plain; charset="us-ascii" Good point on the cardboard, Richard. I always pre-cut strips of Kapton tape, so that I wasn't bringing in cardboard at all. --Scott Calvin Sarah Lawrence College On Aug 5, 2009, at 8:13 PM, Richard Mayes wrote: > Todd, > > Are you working with oxygen sensitive or moisture sensitive samples > (or both)? If it's just moisture sensitive, then you can use regular > 2-sided tape from your local office supply and polypropylene film to > seal samples in polycarbonate or aluminum holders (or even pellets if > you're lucky enough to be able to press pellets that hold their > shape). Chemplex Industries is where I have gotten the polypropylene > films I have used (and Kapton as well - www.findtape.com also has a > good selection of Kapton tape). > > I used this method with many samples that involved heavily chlorided > titanium on silica and had few problems if they're used within 5-7 > days after packing in a glove box (the samples with problems resulted > from improperly sealed samples). You can get jars (baby food jars > work very well to ship individual samples) to store the samples for > shipping and if you pack the jars in the glove box, you will have the > box atmosphere in the jars, for a little while anyway. > > A note on oxygen sensitivity (and to an extent moisture > sensitivity): you probably already know this, but I'll say it > anyway...if cardboard is present in the role of Kapton tape, you may > have oxygen/water diffusion from the cardboard for a few days after > you take it into the box. Our rule of thumb was to pull vacuum on > anything involving cardboard for at least 48 hrs before taking it into > the box. All that to say, take your supplies into the box a few days > ahead of time to allow your box catalyst to take care of any residual > oxygen/water that make their way in. > > HTH, > -Richard

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Kapton in glove box
by Scott Calvin 06 Aug '09

06 Aug '09

Hi Todd, I've taken the liberty of posting your question to the Ifeffit mailing list. You're likely to get more accurate and quicker answers to these kinds of questions there. (For the rest of you: Todd is asking about the technique of preparing air-sensitive samples in a glove box, putting them on Kapton tape, sealing them in plastic bags, and transporting them to the beamline, shooting right through the bags.) I'll take my shots, though: It's hard for me to imagine adsorbed oxygen on the Kapton being more significant than the other sources of stray oxygen that can be present in a glove box. After all, the Kapton's in there too. And I don't think it's going to be more significant than the oxygen that diffuses through the plastic bags during transport. The thinner the Kapton tape, the better, as that will minimize the absorption due to the tape. It used to be hard to find 1 mil Kapton tape with adhesive, but now it's easy. Hephaestus will give you the absorption of Kapton, so you can judge how big an effect it will be at the energies at which you'll work. --Scott Calvin Sarah Lawrence College On Aug 4, 2009, at 2:39 PM, Monson, Todd wrote: > Scott, > > Thanks. Is it pretty reasonable to assume that the kapton tape that > you put your samples on doesn’t have any adsorbed oxygen that could > affect your samples? Do you do anything to clean the kapton? Where > are some good places to buy the kapton (and do you need to purchase > rather thin kapton tape for doing XAFS)? > > Thanks again, > > Todd > > From: Scott Calvin > Sent: August 04, 2009 11:34 AM > To: Monson, Todd > Cc: Scott Calvin > Subject: Re: mossbauer > > Hi Todd, > > Regular zip-loc bags work just fine. For heat sealers I've used > everything from a heat sealer manufactured for the purpose to a > little propane torch--even a cigarette lighter should work. Putting > one sealed bag inside another, if the energy you're working at > allows it, seems to work quite well. > > --Scott > > > On Aug 4, 2009, at 1:15 PM, Monson, Todd wrote: > > > Scott, > > I had another question – what kind of plastic bags and heat sealers > do you use for sealing up your air-sensitive XAFS samples? And > where could I buy them? > > Thanks, > > Todd >

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Re: [Ifeffit] Ifeffit Digest, Vol 77, Issue 30
by Eugenio Otal 04 Aug '09

04 Aug '09

Hi Rafael, I usually use the same compiler with the option -o only I will try the -O0 option. Thanks, euG 2009/7/31 <ifeffit-request(a)millenia.cars.aps.anl.gov> > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: NLEG (Rafael Rodr?guez Pappalardo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jul 2009 12:22:47 +0200 > From: Rafael Rodr?guez Pappalardo <rafapa(a)us.es> > Subject: Re: [Ifeffit] NLEG > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <200907301222.47267.rafapa(a)us.es> > Content-Type: Text/Plain; charset="us-ascii" > > Dear Eugenio, > which compiler was used to compile FEFF? > I have "solved" the problem compiling with Intel Fortran with -O0. > > Best regards, > > Rafael > -- > Dr. Rafael R. Pappalardo > Dept. of Physical Chemistry, Univ. de Sevilla (Spain) > e-mail: rafapa(a)us.es > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 77, Issue 30 > *************************************** >

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conventional unit cell to primitive cell
by Mudit Dixit 30 Jul '09

30 Jul '09

Dear sir , If you have found any way convert conventional unit cell to primitive cell please tell me I am also looking for it. I have material studio if you know how to do it material studio please tell me. -- With Best Regards, Mudit Dixit JRF c/o Dr. Saurav Pal Physical Chemistry Division, Center For Excellence in Advance Computing PUNE ,INDIA

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Re: [Ifeffit] NLEG
by Rafael Rodríguez Pappalardo 30 Jul '09

30 Jul '09

Dear Eugenio, which compiler was used to compile FEFF? I have "solved" the problem compiling with Intel Fortran with -O0. Best regards, Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: rafapa(a)us.es

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Comparing similar peak positions in Fourier transform with fitting results
by Hashem Stietiya 29 Jul '09

29 Jul '09

Greetings to all, I am working on Zn binding to Fe and Al oxides and I am trying to fit the second and third shells. I have three spectra from three samples that differ in a particular treatment. Visually speaking, the Fourier transforms for all these spectra show second and third shells at 2.6 and 3.2A (uncorrected for phase shift), respectively. I fit the second shell with Fe and the third shell with Al. From the fitting results I obtained the Zn-Fe and Zn-Al radial distances for the second and third shells. However, these Zn-Fe and Zn-Al radial distances were different among the samples. For example, the Zn-Fe radial distance was 3.18A for sample 1, 3.44A for sample 2 and 3.51A for sample 3. My question is: if the peaks in the Fourier transforms are at the same position for all samples, why is it that the fitting shows that the radial distances are actually different? NOTE: I fit the 1st,2nd and 3rd shells(R range:1.0-3.2A) together. Thank you, Hashem Stietiya School of Plant, Soil and Environmental Sciences Louisiana State University

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Re: [Ifeffit] background subtraction
by umesh palikundwar 28 Jul '09

28 Jul '09

Go through the Athena Manual and the project files therein. Umesh > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 77, Issue 26 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sun, 26 Jul 2009 12:00:02 -0500 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. background subtraction (yavuz al) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Jul 2009 16:04:41 -0700 > From: yavuz al <yavuzal1(a)hotmail.com> > Subject: [Ifeffit] background subtraction > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <BLU116-W2649DF9BAA31B6973E611892190(a)phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > > Hi all, > > I have some Zn L2-L3-edge XANES spectra. I am not sure how to remove the > background and normalize these data using athena?If you can help me about this I will be very glad > > thanks > yavuzz > _________________________________________________________________ > Windows Live? SkyDrive?: Store, access, and share your photos. See how. > http://windowslive.com/Online/SkyDrive?ocid=TXT_TAGLM_WL_CS_SD_photos_072009 >

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edge height proportional to the molar density?
by Haiyan Zhao 25 Jul '09

25 Jul '09

I am wondering whether the edge height could be used to estimate molar density or not. If so, is there any reference about such kind of calculation? Thanks! Haiyan

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background subtraction
by yavuz al 24 Jul '09

24 Jul '09

Hi all, I have some Zn L2-L3-edge XANES spectra. I am not sure how to remove the background and normalize these data using athena?If you can help me about this I will be very glad thanks yavuzz _________________________________________________________________ Windows Live™ SkyDrive™: Store, access, and share your photos. See how. http://windowslive.com/Online/SkyDrive?ocid=TXT_TAGLM_WL_CS_SD_photos_072009

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Sorry
by Chris Patridge 23 Jul '09

23 Jul '09

I forgot to post a bitmap of the spectra of the previous message. Thank you all. -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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Proper data processing in Athena with large pre-edge features
by Chris Patridge 22 Jul '09

22 Jul '09

Hi everyone, I am working on Vanadium K-edge EXAFS with various VxOx oxides. My question concerns deciding E0 and background spline in Athena. The K edge at 5465eV has a large peak before the edge jump and when subtracting the background and moving to K-space using the default settings, the Bkgd looks incorrect. Any suggestions on how to set the background for further processing? Thank you everyone as this is my firstpost and first EXAFS analysis, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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Re: [Ifeffit] Ifeffit Digest, Vol 77, Issue 19
by abhijeet gaur 21 Jul '09

21 Jul '09

Re :inquire (Makoto Matsuura) Dear Makoto, I also encountered the same problem you are facing now. The basic problem is that when you save k chik or k2 chik in Athena and then get it imported in Artemis then the data is already k weighted and when you again try to weight it in Artemis, the data gets disturb. So, you have to save simply chik of your data in Athena and then import it into Artemis.Then in Artemis you can weight your data as you have done in Athena and it will look same as Athena plot. Also from Artemis you can select the groups of which you which you need chi k or chir and then you can go for option save selected groups in Artemis. You will get all the data in one file . then you cam import it in Origin or any other software by import single ascii option. In your case you save chir data the real part, imaginary part also got saved with magnitude, so if you need your fourier transform as seen in Athena, you just plot the magnitude column with data. I think this will work Abhijeet Gaur School of Studies in Physics Vikram University Ujjain ( India) On 7/21/09, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. inquire (Makoto Matsuura) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 21 Jul 2009 15:28:34 +0900 > From: "Makoto Matsuura" <m_matsuura(a)imr.tohoku.ac.jp> > Subject: [Ifeffit] inquire > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <000601ca09cc$790f3aa0$6b2dafe0$(a)tohoku.ac.jp> > Content-Type: text/plain; charset="us-ascii" > > Hi! > > I'm annoyed with the mismach of Fourier transform between Athena and > Arthemis. The k-weighting (k^1), k-window( Kaiser Bessel) and k-range are > kept same for both. The input chi-data and resultant Fourier transforms are > attached. > > One more question of Arthemis is that when I try to output data of chi(k) > or chi(r) from menu of File, null data file comes out while right data can > be obtained for the fitted data. How can I get data of chi(k) or chi(r) in > ascii format for Arthemis? Thank you. > ======================================================================== > Makoto Matsuura > > IMR Tohoku Univ. Sendai, Japan > > ========================================================================= > >

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inquire
by Makoto Matsuura 21 Jul '09

21 Jul '09

Hi! I'm annoyed with the mismach of Fourier transform between Athena and Arthemis. The k-weighting (k^1), k-window( Kaiser Bessel) and k-range are kept same for both. The input chi-data and resultant Fourier transforms are attached. One more question of Arthemis is that when I try to output data of chi(k) or chi(r) from menu of File, null data file comes out while right data can be obtained for the fitted data. How can I get data of chi(k) or chi(r) in ascii format for Arthemis? Thank you. ======================================================================== Makoto Matsuura IMR Tohoku Univ. Sendai, Japan =========================================================================

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Re: [Ifeffit] atoms location in feff.inp
by Eugenio Otal 17 Jul '09

17 Jul '09

Yes, that is the point, I need to move the central atom from 0,0,0 to change the symmetry. Now everything gonna be more easy. Thanks, euG I am not sure I quite understand the question, but ... The central atom does not need to be at (0,0,0) in the feff.inp file. Atoms puts it there for the convenience of the human reading the feff.inp file, but that is not a requirement. It also does not need to be the first item in the atoms list. HTH, B

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atoms location in feff.inp
by Eugenio Otal 17 Jul '09

17 Jul '09

Hi, I am performing some XANES simulations of site distortion in ZnO, and found some problems to change atoms position and run atoms. I want to know if is the same to change the atoms position of the ipot0 in the feff.inp file. Thanks, euG

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Re: [Ifeffit] Error in paths with ifeffit
by Bruce Ravel 16 Jul '09

16 Jul '09

On Thursday 16 July 2009 04:42:41 pm you wrote: > When I try to obtain the path with the attached > cif file, I find distance As_O(8) = 2.142 A, this > is uncorrect, because there is no oxygen atom at that distance. > What is going on? Hi Elsa, For some reason, Artemis does the wrong thing with the setting of the space group. According to your CIF file, the proper setting of the space group is P 21/n. For some reason, when Artemis reads that CIF file, it uses P 21/c as the space group symbol. That is strange behavior -- I will have to investigate what is going on. The work-around on the Atoms page in Artemis is to change the space group to "P 21/n" before running feff. If you are using Atoms at the command line, you will have to tell Atoms to write out an atoms.inp file, edit that, then run feff. That's all a bit irritating, but it is at least workable. When I ran your cif file after specifying "P 21/n" on the Atoms page, I got this for the first several neighbors: 0.00000 0.00000 0.00000 0 As1 0.00000 -0.46784 -0.12630 1.58774 4 O3_1 1.66004 -0.88804 -0.96644 -1.02986 4 O1_1 1.66830 1.65544 -0.19677 -0.19615 4 O2_1 1.67859 -0.36279 1.66519 -0.35929 4 O4_1 1.74171 -0.22909 1.88872 -1.29544 1 H1_1 2.30172 2.26346 1.49452 0.40642 1 H13_1 2.74263 2.03956 -2.01248 0.21917 1 H10_1 2.87366 1.14080 -0.11749 2.64281 1 H8_1 2.88092 2.08625 -0.17254 -2.02856 1 H5_1 2.91501 -2.72907 -0.44011 -1.05767 1 H9_1 2.95976 That looks more like what you were expecting.... B PS: The proper address for the mailing list is ifeffit(a)millenia.cars.aps.anl.gov rather than ifeffit-owner@... Mail to ifeffit-owner goes just to Matt and I rather than to the whole list. -- 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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post-doc position
by Matt Newville 16 Jul '09

16 Jul '09

Hi Folks, A Post-Doctoral position using XAFS in Earth Sciences is open at St. Francis Xavier University, working with Alan Anderson. More details are at http://xafs.org/Jobs --Matt

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Re: [Ifeffit] Athena XFit report, possible (minor) bug.
by Bruce Ravel 16 Jul '09

16 Jul '09

On Wednesday 15 July 2009 09:33:25 pm you wrote: > Hi Bruce, > > I was looking at some Co data this morning, and having a problem whereby > the XFit program Spline was crashing when trying to read in an XFit report > output from Athena 0.8.059. After some head scratching and fidling, I > figured out it was because the XFit report had used Cobolt as the absorber > instead of Cobalt. I'm not even 100% sure this is directly related to > Athena, although I couldn't find any reference to Cobolt or Cobalt in the > raw ESRF data. Stacey, Wow. The word "Cobalt" is misspelled in the tool that Athena uses to translate between Z number and element name. This is my favorite kind of bug -- one that is not my fault ;-) I'll update that tool on the machine that I use to build windows executables. The next time I build and release a windows executable, this will be fixed. In the meantime, you will need to manually fix that misspelling for all you Co data. B -- 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] Ifeffit Digest, Vol 77, Issue 11
by Zuzaan, Damdinsuren 10 Jul '09

10 Jul '09

Dear all, It is possible to use in Artemis several paths from 2 different FEFF input files in one fit for the unknow sample? Also could I manipulate directly in the feff input file, I mean change elements and so on. Thanks, Damdin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Monday, July 06, 2009 9:39 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 77, Issue 11 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. xanes_normalization range (Arezki, Bahia) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jul 2009 21:36:42 +0200 From: "Arezki, Bahia" <Bahia.Arezki(a)uni-siegen.de> Subject: [Ifeffit] xanes_normalization range To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7093842D66DA64CB51A0EEC99D6BBA31504137B82(a)MAIL30.uni-siegen.de> Content-Type: text/plain; charset="iso-8859-1" Dear IFEFFIT users, I have some problems/doubts with quite basic questions concerning xanes processing. In particular the normalization range. Can anyone please look at my project and tell me if my data processing is correct ? The xanes are at the Fe K-edge, of a F(II)-complex, taken at different temperatures. In fact my question concerns the choice of the starting value for the normalization range. I obtain reasonable lines with a starting point from more that 100 eV after E0. Is it correct to start so far from the edge?? should one start just after the broad feature (onset of exafs ? ) ? if I start the post-edge normalization before ..I obtain different results when I compare the different xanes.. thanks for your help, best regards, bahia

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What you see is "not" what you get: help
by Ismael Graff 10 Jul '09

10 Jul '09

Hi folks, I´ve been working on Xanes peaks fitting with Athena (last version) and I found a strange behaviour. I get a "good" fit looking to the Graphics Window of Athena and to the minimized parameters (R-factor, etc). However, when I use the data of the fit generated by Athena "write a log file" feature and plot them in Origin, the fit looks bad! In order to get a "good looking" fit in Origin I have to change the parameters ad-hoc in Athena fitting dialog box. When I do this, the fit looks bad in Athena Graphics window and better in Origin. The values that are inserted ad-hoc in Athena are not the optimized ones from the fitting procedure output. I have attached the log file from Athena fit and two figures: a PS figure from Athena and a JPG figure from Origin. It resembles that the generated data from Athena are not exactly these ones that I see in the Graphics window! I´m looking for help from someone out there. Kind regards, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418

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running diffkk and deltaf
by marie-helene.tuilier＠uha.fr 09 Jul '09

09 Jul '09

Hello everyone, First, I would like to pay homage to the authors of that fairly user-friendly software, which is very useful for a diffusion of XAFS technique. Thanks to the detailed explanation found in the various tutorials, I became able to use it almost without any help. Despite every thing, I encounter now some difficulties running DIFFKK and DELTAF in IFEFFIT. I am trying to reduce DAFS data of a metallic nitride film at the Ti K-edge and I need anomalous scattering factors. First I built diffkk.inp and deltaf.inp files following the instructions given by Matt Newville and Julie O. Cross in the Diffkk tutorial. Then, I begin to run diffkk in ifeffit 1.2.11c as follows: ifeffit> run diffkk ifeffit> read diffkk.inp or ifeffit> run deltaf ifeffit> read deltaf.inp I become only a file named userenv.log with such comments: " cannot process autoexec.bat". Perhaps I loaded a wrong version of IFEFFIT. Thank you in advance. Marie-Hélène Diffkk.inp %Anomalous scattering at Ti K-edge% Title=Ti0.5Al0.5N (2microns) XAFS data out = C:\Program Files\Ifeffit\Ti05diffkk.fpp %output file name xmu= C:\Program Files\Ifeffit\L27ACIEReldeg.xmu %xmu data file name isfeff=false %is this a feff xmu.dat ? encol=1 % energy column mucol=2 % mu(E) column iz=22 % z of central atom (Ti) e0=4968.0000 % edge energy egrid= 1.0000 % energy grid ewidth=1.2000 % for broadening Cromer-Liberman f"(E) elow=70.0000 % how far below the data range to go ehigh=500.0000 % how far above the data range to go %------------------------% Deltaf.inp %Bare atom resonant scattering factors at Ti K-edge% Title=Ti0.5Al0.5N (2microns) delta f" out = C:\Program Files\Ifeffit\Ti05deltaf.fpp %output file name iz=22 % z of central atom (Ti) e0=4968.0000 % edge energy ehigh=500 % how far above the data range to go elow=70 % how far below the data range to go egrid= 1 % energy grid ewidth=1.2 % for broadening Cromer-Liberman f"(E) end %------------------------%

2 1

xanes_normalization range
by Arezki, Bahia 06 Jul '09

06 Jul '09

Dear IFEFFIT users, I have some problems/doubts with quite basic questions concerning xanes processing. In particular the normalization range. Can anyone please look at my project and tell me if my data processing is correct ? The xanes are at the Fe K-edge, of a F(II)-complex, taken at different temperatures. In fact my question concerns the choice of the starting value for the normalization range. I obtain reasonable lines with a starting point from more that 100 eV after E0. Is it correct to start so far from the edge?? should one start just after the broad feature (onset of exafs ? ) ? if I start the post-edge normalization before ..I obtain different results when I compare the different xanes.. thanks for your help, best regards, bahia

1 0

new release of my software
by Bruce Ravel 05 Jul '09

05 Jul '09

Hi everyone, Windows users should soon see that an update is available. This is a relatively small thing -- it contains a new build of Athena with fixes for several recently repoted bugs. As always, it should get installed sometime soon when you fire up one of the Ifeffit programs. For those who build from source, I have also uploaded a new tarball to my web site (already there) and to SourceForge (available soon). Along with the bug fixes to Athena, this new tarball (horae-070) is my attempt to address the serious problems many of you have had in recent months trying to get my codes installed from source. The current tarball contains all of horae as well as all of my libperlxray modules. It also includes all the files required to install the Athena User's Guide (which is why the new tarball is so much larger than previous ones). I have writen a general build script and attempted to explain the installation procedures clearly is files fouond at the top of tarball. Let me know how it goes. For those of you who use the SVN server for the source code, that remains a useful alternative to using the tarball. There is no code in the tarball that is not in the SVN repository. Regards, B -- 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] Ifeffit Digest, Vol 77, Issue 8
by abhijeet gaur 05 Jul '09

05 Jul '09

Hello Sir, I am fitting Cu2O at room temperature. I got the point. So, the negative value of SS parameter is due to the low value of SO2 guessed by artemis. I have done the fitting again by fixing the value of SO2 to 0.7. Now I am gettig positive value of SS parameter which is around 0.007. Please tell me from where I can get the standard value of SO2 calculated theoretically in the literature. with regards Abhijeet Gaur Dear Abhijit, > > > > The parameters So2 and SS are highly correlated. The negative value of SS > does not make any physical significance. It may be due that Artemis is > conveging for lower value of So2. In your case (So2=0.552 or 0.61) it is > very low. Generelly, it should be in the range of 0.7 to 1. It will be > better if you fix So2 for the standard value calulated theoretically in the > literature or you can try to get approximated value of SS for So2 around 0.8 > to 0.9. > > > > regards > > > > Umesh Palikundwar > > Department of Physics > > RTM Nagpur University, > > Nagpur-440033 > > _________________________________________________________________ > Missed any of the IPL matches ? Catch a recap of all the action on MSN > Videos > http://msnvideos.in/iplt20/msnvideoplayer.aspx >

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Re : Cu2O fitting
by abhijeet gaur 04 Jul '09

04 Jul '09

Hi all, Thanks for the response. I am sorry as I should attach the figure in a viewable format. Anyways now I am attaching a the artemis project file in which I had used a set positive value for the SS parameter of first path. I am not able to understand the reason for negative SS value. Thanks again Abhijeet Gaur

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Re: [Ifeffit] Fitting Cu2O
by umesh palikundwar 04 Jul '09

04 Jul '09

> Hi all, > I am fitting Cu2O data. But when I fit the first shell using the > first path, I got the guess value for SS parameter negative which is around > -0.0028 and also the guessed value for SO2 parameter comes out to be around > 0.52. Are these values logically correct as I am getting a nice fit. > Also when I use the same SS parameter but with positive sign for the > first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to > be 0.61. > When I fit the higher shells by using the same SO2 and Enot value for > other paths, the value of SS parameter for these paths is coming very high , > i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher > values of SS parameter correct. The resulting figure is attached. > > with thanks > > Abhijeet Gaur > > School of Studies in Physics > > Vikram University, Ujjain, INDIA. Dear Abhijit, The parameters So2 and SS are highly correlated. The negative value of SS does not make any physical significance. It may be due that Artemis is conveging for lower value of So2. In your case (So2=0.552 or 0.61) it is very low. Generelly, it should be in the range of 0.7 to 1. It will be better if you fix So2 for the standard value calulated theoretically in the literature or you can try to get approximated value of SS for So2 around 0.8 to 0.9. regards Umesh Palikundwar Department of Physics RTM Nagpur University, Nagpur-440033 _________________________________________________________________ Missed any of the IPL matches ? Catch a recap of all the action on MSN Videos http://msnvideos.in/iplt20/msnvideoplayer.aspx

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Re: [Ifeffit] orbital configuration (FEFF8)
by joshua jason kas 04 Jul '09

04 Jul '09

Hi Iraida, I believe there are a few issues here that could be addressed/explained. First, the electronic configuration given at the end of the potentials is only the configuration of the valence electrons. For example the absorbing oxygen should be interpreted as 0 0 1.953 ~2s2 0 1 5.159 ~2p5 (The ~1 extra valence electron for the absorbing atom is due to the attractive core hole) 0 2 0.040 0 3 0.000 while for Cd 1 0 0.723 ~5s1 1 1 0.711 ~5p1 1 2 10.149 ~4d10 1 3 0.000 Here, the differences from the atomic configuration of 4d10 5s2 are due to the fact that this is a self-consistent solid state configuration, i.e. the valence electrons were allowed to relax and were effected by the solid state potential. That being said, there are ways to change the initial configuration for the elements, but you would have to change the source code and recompile. I don't think this is what you want to do though. As for improving your results, there may be a variety of things that you can do. Off hand your input file looks pretty good. One thing you might try is using the card UNFREEZEF which allows the d electrons from the Cd to tranfer to f states which can sometimes be important when the d band is full. I hope that my answer helps some, at least in interpreting FEFFs output. Josh Kas > Hi everyone,I > would like to calculate K-edge of oxygen XANES spectrum for CdO film. I > attached my feff.inp file to this e-mail. When I check log1.dat file I > observe next information: > "... > Electronic configuration > iph il N_el > 0 0 1.953 //comment: 0-centr.atom (O) > 0 1 5.159 > 0 2 0.040 > 0 3 0.000 > 1 0 0.723 //comment: 1-Cd > 1 1 0.711 > 1 2 10.149 > 1 3 0.000 > 2 0 1.921 //comment: 2-O > 2 1 4.443 > 2 2 0.052 > 2 3 0.000 > mu_new= -5.168 > Charge transfer: iph charge(iph) > 0 -0.152 > 1 0.417 > 2 -0.417 > Done with module 1: potentials." > > As > is well known, orbital configuration for Cd and O is: 4d10 5s2 and 1s2 > 2s2 2p4, respectively. I think that obtained results for Cd differ much > according to presented orbital configuration (s,p). So, my question is: > do there exist some possibilities to change something in my feff.inp > file to improve the results? > > Best regards, > Iraida. > > > >

2 1

Fitting Cu2O
by abhijeet gaur 03 Jul '09

03 Jul '09

Hi all, I am fitting Cu2O data. But when I fit the first shell using the first path, I got the guess value for SS parameter negative which is around -0.0028 and also the guessed value for SO2 parameter comes out to be around 0.52. Are these values logically correct as I am getting a nice fit. Also when I use the same SS parameter but with positive sign for the first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to be 0.61. When I fit the higher shells by using the same SO2 and Enot value for other paths, the value of SS parameter for these paths is coming very high , i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher values of SS parameter correct. The resulting figure is attached. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain, INDIA.

2 1

Fitting Cu2O
by abhijeet gaur 03 Jul '09

03 Jul '09

Hi all, I am fitting Cu2O data. But when I fit the first shell using the first path, I got the guess value for SS parameter negative which is around -0.0028 and also the guessed value for SO2 parameter comes out to be around 0.52. Are these values logically correct as I am getting a nice fit. Also when I use the same SS parameter but with positive sign for the first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to be 0.61. When I fit the higher shells by using the same SO2 and Enot value for other paths, the value of SS parameter for these paths is coming very high , i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher values of SS parameter correct. The resulting figure is attached. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain, INDIA.

1 0

orbital configuration (FEFF8)
by Dream Dream 02 Jul '09

02 Jul '09

Hi everyone,I would like to calculate K-edge of oxygen XANES spectrum for CdO film. I attached my feff.inp file to this e-mail. When I check log1.dat file I observe next information: "... Electronic configuration iph il N_el 0 0 1.953 //comment: 0-centr.atom (O) 0 1 5.159 0 2 0.040 0 3 0.000 1 0 0.723 //comment: 1-Cd 1 1 0.711 1 2 10.149 1 3 0.000 2 0 1.921 //comment: 2-O 2 1 4.443 2 2 0.052 2 3 0.000 mu_new= -5.168 Charge transfer: iph charge(iph) 0 -0.152 1 0.417 2 -0.417 Done with module 1: potentials." As is well known, orbital configuration for Cd and O is: 4d10 5s2 and 1s2 2s2 2p4, respectively. I think that obtained results for Cd differ much according to presented orbital configuration (s,p). So, my question is: do there exist some possibilities to change something in my feff.inp file to improve the results? Best regards, Iraida.

1 0

problem with Athena's E0 !
by Arezki, Bahia 01 Jul '09

01 Jul '09

Hi all, I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct? I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step? I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case. Thanks so much for your time, Bahia

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Re: [Ifeffit] plotting anotation
by Bruce Ravel 30 Jun '09

30 Jun '09

Hi Dr. Matsuura, I am answering CCing this email to the Ifeffit Mailing List http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the most appropriate forum for asking questions about the software. If you have not yet joined the mailing list, we encourage you to do so. I have also taken the liberty of converting the image file you attached into a format that everyone will be able to view. On Tuesday 30 June 2009 02:49:51 am you wrote: > Dear Bruce Ravel > > I'm a beginner of IFEFFIT. I'm pleased if you could ask following > questions about plotting in Artemis. > > 1) In a plotted figure as attached, annotation shows "2/path #". What > does it mean letter" 2". Presumably, you have more than one Feff calculation in your Artemis project, one of which still has its default name of "Feff2". To save horizontal space in the legend of the plot, I have Artemis drop the ltters "Feff". So, that legend entry means "Path N from Feff calculation 2". > 2) In the plotted figure attached, the sum of each path constituent is > not equal to fitting data. The reason of why. In Ifeffit, we use a complex Fourier transform to convert chi(k) to chi(R), thus chi(R) is a complex function. When the fit is evaluated, the real part of the theoretical chi(R) is compared to the real part of the data chi(R) and the imaginary part is compared to the imaginary part. You have plotted the magnitude of this complex function. You should not expect the sum of the moduli of the paths to equal the modulus of the sum of the paths. For a complex function, summation and mudulus are not commutative operations. B > > > > *************************************************************************** >* ****************** > > Metallic Glass Inorganic Materials Joinning Technology Development > > Institute for Materials Research, Tohoku University,Sendai, 980-8577,Japan > > Dr. Makoto Matsuura > > e-mail:m_matsuura@imr.tohoku.ac.jp > > *************************************************************************** >* ******************* -- 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/

1 0

Fwd: Follow-up on your Athena issue
by Bruce Ravel 24 Jun '09

24 Jun '09

Gautier, First off: USE THE MAILING LIST! That's what it's there for. Why ask two people for help when you can ask hundreds? As you say, you are not the first to see this behavior, but I am not among those who have witnessed this. It is, of course, hard for me to troubleshoot a problem that I have never seen and don't know how to reproduce. The only helpful thing that comes to mind is to ask if there are any non-lower-ascii characters in the path either to the folder where Ifeffit is installed or to the folder where your data lives. At some point in the last couple years, I thought I had fixed the issues with nono-lower-ascii characters -- but who knows? Perhaps you keep your data in folder called "données" or "データ". If so, try installing Ifeffit in a place with only lower-ascii characters and do the same with your data. No guarantees, but it is something to try. B ---------- Forwarded Message ---------- Subject: Follow-up on your Athena issue Date: Wednesday 24 June 2009 From: Gautier Landrot <landrot(a)udel.edu> To: n.thammajak(a)gmail.com Dear Dr. Thammajak: I noticed on the Ifeffit email list that you posted last year a message about a problem you had on Athena. I currently do have the same problem with my athena, the symptoms I have are the same than those described in your post: 1) Any single XAFS spectrum, which could be opened with Athena before the problem occurred, cannot be opened anymore. Only a message saying "you have not used any memory yet" appears at the bottom of the Athena Window. Oddly, old saved project files can still be opened. Then, when the data is opened from these old projects, new project cannot be saved (nothing happens when I try to save a project). Data files are not corrupted or have strange format, since the files could be opened before the problem occurred. Also I can open the data with Athena installed on other PCs without any problem. 2) The main Athena window won't close. The only way to close that window is to force quit the program. 3) I checked the command rpompt window, and ran Athena, as Bruce Ravel suggested in his reply. A message says "Ifeffit checked for updates recently. Your version of Ifeffit is up to date". That's it. No error message obviously... 4) I reinstalled both Athena and Windows XP, but the problem still occurs. I don't think anybody from the Ifeffit email list found the source of your issue. Is your Athena working now? If yes, have you figured what was the problem? Thanks a lot, Gautier ----------- Gautier Landrot graduate student University of Delaware Plant and Soil Sc. Dept. Environmental Soil Chemistry Group 152 Townsend Hall Newark, DE 19711 (302)831-1230 http://ag.udel.edu/SoilChem/landrot.html ------------------------------------------------------- -- 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/

1 0

Artemis multiple edge refinement problem
by alessandro di domenico 24 Jun '09

24 Jun '09

Hello to everyone; I'm a master thesist student in physics and I'mdoing a XAS analysis on bimetallic nanoparticles. my problem is that when I try to do a refinement on two different edges (K-Pd and L3-Au) Artemis changes one of the experimental data-set. Say that I have the data set for the K-edge of Pd and L3-edge of Au (which are plotted correctly); after the fit one of the two data set are plotted different. it seems that experimental data have been modified.... I don't know what to do about it; maybe I'm doing something wrong but unfortunately there isn't a complete guide to artemis . On the internet i have found some pdf which deals with the argument but don't focus on the procedure that one has to do in the program. Has someone ever had this problem, and if not can someone suggest me a "tutorial" on multiple edge refinement with artemis that I can follow step by step? Thank you alessandro

2 2

Re: [Ifeffit] Edge step
by Eugenio Otal 24 Jun '09

24 Jun '09

Bruce, I supposed the answer would be a little inconvenient truth. I will follow your wise words. Thanks, euG Eugenio, I am afraid that the question, as posed, is somewhat unanswerable. Careful alignment (preferably to a reference) is essential and you should take care to use the same parameters for every data set. I don't know how to advise you about "rightness", but consistency is certainly a must-do. If you are looking at subtle changes in the XANES features, you might consider turning off the "flattening" display trick that Athena uses for displaying XANES data. HTH, B

1 0

Re: [Ifeffit] Interpolating in feff - the Lead Titanate example
by Matt Newville 23 Jun '09

23 Jun '09

Hi Joseph, On Mon, Jun 22, 2009 at 8:15 PM, joseph washington<jswashin(a)ncsu.edu> wrote: > Hi Matt, > Thanks for your reply. I actually did not diliberately modify the > intermediate FEFF files. I think you should probably post the input file. > Up to this point, I beleive that I've been > following Bruce's example consistently. Its only when I noticed that the > path lengths were showing up differently that I started opening feff files. Which example is that? > Furthermore, it may be that this is just a bug because if I import the > "misbehaving" path into the list of paths for fitting in Artemis, it then > shows the correct path length there. So wierd - it says it is 5.9211 in > feff2019.dat but it says its 5.9179 when you import it for fitting. Yeah, I agree...that looks like a problem. --Matt

1 0

Re: [Ifeffit] Primitive unit cell from .cif file
by joshua jason kas 22 Jun '09

22 Jun '09

Thanks everyone for your suggestions! I have tried the following things. I used atoms (webATOMS) to generate a p1.inp file using diamond as an example, but this gives me the conventional cell with 8 atoms in it instead of the 2 atom primitive cell. Am I doing something wrong? The input file came from the atoms database and the output is as follows: * * "F d -3 m" appears in the International Tables with * multiple choices of origin. If the atoms list seems wrong, you * should use a shift vector of: * -0.125, -0.125, -0.125 * * ! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = name: diamond title = formula: C title = sites: C1 title = refer1: Kittel, ISSP title = refer2: title = schoen: title = notes1: diamond structure space p 1 ! original space group: F d -3 m a = 3.5670 b = 3.5670 c = 3.5670 alpha = 90.0 beta = 90.0 gamma = 90.0 core = C1_1 edge = K rmax = 6.0 atoms ! elem x y z tag occ C 0.12500 0.12500 0.12500 C1_1 1 C 0.12500 0.62500 0.62500 C1_2 1 C 0.62500 0.12500 0.62500 C1_3 1 C 0.62500 0.62500 0.12500 C1_4 1 C 0.87500 0.37500 0.37500 C1_5 1 C 0.87500 0.87500 0.87500 C1_6 1 C 0.37500 0.37500 0.87500 C1_7 1 C 0.37500 0.87500 0.37500 C1_8 1 I also tried the Mercury demo, but all editing features are disabled. I will try Diamond now. Just to give some motivation here, I am working with abinit (along with feff) to produce optical spectra. If I use a conventional cell, the calculations become much more time consuming, so ideally I want to use a primitive cell. Thanks again for all your help! Josh > Hi Josh, > You may try Diamond Demo version which is free. > > http://www.crystalimpact.com/diamond/download.htm I will give this a try. > > Hi Josh, > > If I understand your question, I think that Atoms does what you want. Running the command line tool as "atoms -p" turns the attached cif file into the attached "p1.inp" file. You can do the same thing inside of Artemis using "write special output" in the Theory menu. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas > Sent: Wed 6/17/2009 2:16 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Primitive unit cell from .cif file > > Hi everyone, > I was wondering if there is a simple (free) utility for producing a > primitive cell (not conventional) from an asymmetric cell and space group. > Basically, I want to be able to easily go from a crystallographic > information file to a primitive unit cell. I know that there are ways to > do this within applications like material studio, but these are expensive. > Any help would be appreciated. > Thanks, > Josh Kas > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

4 3

Edge step
by Eugenio Otal 22 Jun '09

22 Jun '09

Hi, I am looking for some small differences in XANES spectra and want to know how to set the edge step to a "right" value. The differences are around 2 eV shift and a change in the edge step is critical. Thanks euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 1

problem with E0 (enot) parameters
by Zajac, Dariusz A. 22 Jun '09

22 Jun '09

Hi all, can anybody help me and send some link about problems with enot in Artemis? in google, tutorials I couldn't find any help. Of course are few posts about delr or ss parameters, but enot is somehow omited (or I can not find it...) the problem is with fiting K4W(CN)8*2H2O at W:L3 edge. fit and others parameters looks ok, except enot for C and N, where both are around 12 and don't want to fit to other values... thanks darek ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

6 15

Re: [Ifeffit] problem with E0 (enot) parameters
by joshua jason kas 20 Jun '09

20 Jun '09

As Anatoly mentioned, feff6 overestimates e0 (the Fermi energy). This is at least partially due to the use of overlapped atomic potential. The problem is fixed when the self-consistent potentials are used in feff8. If no self-consistency is used, I believe feff6 and feff8 give very similar results. Josh > From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> > Subject: Re: [Ifeffit] problem with E0 (enot) parameters > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov>, > "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <CCBF39F82283424BBB90EA208CD9DE80EBB710(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Just a comment, to add some sanity in this discussion: > > FEFF6 is overestimating delta E0 for Pt and a few other metals. I > forgot the reason but it could be the cause of a problem. > I think FEFF8 is doing a better job. Fortunately - and it was checked - > no other problems occur, just E0 values change, when one usees FEFF8 > instead of FEFF6 in most cases. > > Anatoly > > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Kropf, Arthur Jeremy > Sent: Fri 6/19/2009 3:41 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] problem with E0 (enot) parameters > > > > With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, > etc., there is no reason to assume that Eo is on the lower energy side > of the peak. > > Jeremy Kropf > >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >> Of Zajac, Dariusz A. >> Sent: Friday, June 19, 2009 9:45 AM >> To: XAFS Analysis using Ifeffit >> Subject: Re: [Ifeffit] problem with E0 (enot) parameters >> >> Hi Scott, >> I am afraid that E0 jumps over the edge - see bmp's in the >> attachment (files with enot_12 means E0=12...). Hovewer 12 eV >> is still less than >> k=3 (the starting k value). Can it influence? I did also once >> more fit with R from 1.7 to 4A. Fits of first 2 peaks are >> identical - you can see in the attachment too... >> I hope you and anyone from the mailing list don't mind that I >> am attaching so many files... >> >> cheers >> darek >> >>> -----Original Message----- >>> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >>> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >> Of Scott >>> Calvin >>> Sent: Friday, June 19, 2009 2:49 PM >>> To: XAFS Analysis using Ifeffit >>> Subject: Re: [Ifeffit] problem with E0 (enot) parameters >>> >>> >>> Hi Darek, >>> >>> OK, so if the K, H, and O don't affect the fit much for the C and N, >>> and the K, H, and O are returning nonsensical values, then a logical >>> possibility is that the E0's for C and N are correct. If you >> add 12 eV >>> to the E0 you chose in Athena, where in the spectrum does it >> fall? Is >>> it still before the white line? If so, it seems to me you >> don't have a >>> problem. If not, then we have to ponder further. >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> >>> On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: >>> >>>> Hi Scott, >>>> look also at H and O, >>>> but for me and for this fit important are only W-C and W-C-N >>> bondings. >>>> This sample is an reference sample for other cyano-brigded >> networks. >>>> So >>>> you suggest to focuse on K ions? how can it help with first >>> 2 peaks? K >>>> is at ~5A. >>>> I have analysed in larger R space only to see how the >>> spectrum behave. >>>> contribution from K, O etc. at k highers than 5A is for me >> too low to >>>> analyse it resonable for such compound. >>>> I have attached in the previus post the last version of results. >>>> Anyway, >>>> enots for C and N do not change if I am enlarging R region >> (when I am >>>> including next paths, also for K). >>>> about material I am quite sure ;) and crystal structure is from >>>> literature >>>> >>>> in the attachment you will find bmp file of the fit: data, >> fit, bkg >>>> and K path. >>>> fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase >> correction - first >>>> C >>>> >>>> cheers >>>> darek >>>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > Message: 3 > Date: Sat, 20 Jun 2009 10:37:09 +0200 > From: "Zajac, Dariusz A." <dariusz.zajac(a)desy.de> > Subject: [Ifeffit] ODP: problem with E0 (enot) parameters > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <35E004AD6290A7438FCA34BBF325F4160C57F8(a)ADXV2.win.desy.de> > Content-Type: text/plain; charset="iso-8859-2" > > Dear Jeremy, > thanks for your reply. This fits to my results and to my "feeling", but is any physical meaning behind it? > cheers > darek > > > > -----Wiadomo?? oryginalna----- > Od: ifeffit-bounces(a)millenia.cars.aps.anl.gov w imieniu Kropf, Arthur Jeremy > Wys?ano: Pt 2009-06-19 21:41 > Do: XAFS Analysis using Ifeffit > Temat: Re: [Ifeffit] problem with E0 (enot) parameters > > With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, > etc., there is no reason to assume that Eo is on the lower energy side > of the peak. > > Jeremy Kropf > >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >> Of Zajac, Dariusz A. >> Sent: Friday, June 19, 2009 9:45 AM >> To: XAFS Analysis using Ifeffit >> Subject: Re: [Ifeffit] problem with E0 (enot) parameters >> >> Hi Scott, >> I am afraid that E0 jumps over the edge - see bmp's in the >> attachment (files with enot_12 means E0=12...). Hovewer 12 eV >> is still less than >> k=3 (the starting k value). Can it influence? I did also once >> more fit with R from 1.7 to 4A. Fits of first 2 peaks are >> identical - you can see in the attachment too... >> I hope you and anyone from the mailing list don't mind that I >> am attaching so many files... >> >> cheers >> darek >> >>> -----Original Message----- >>> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >>> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >> Of Scott >>> Calvin >>> Sent: Friday, June 19, 2009 2:49 PM >>> To: XAFS Analysis using Ifeffit >>> Subject: Re: [Ifeffit] problem with E0 (enot) parameters >>> >>> >>> Hi Darek, >>> >>> OK, so if the K, H, and O don't affect the fit much for the C and N, >>> and the K, H, and O are returning nonsensical values, then a logical >>> possibility is that the E0's for C and N are correct. If you >> add 12 eV >>> to the E0 you chose in Athena, where in the spectrum does it >> fall? Is >>> it still before the white line? If so, it seems to me you >> don't have a >>> problem. If not, then we have to ponder further. >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> >>> On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: >>> >>>> Hi Scott, >>>> look also at H and O, >>>> but for me and for this fit important are only W-C and W-C-N >>> bondings. >>>> This sample is an reference sample for other cyano-brigded >> networks. >>>> So >>>> you suggest to focuse on K ions? how can it help with first >>> 2 peaks? K >>>> is at ~5A. >>>> I have analysed in larger R space only to see how the >>> spectrum behave. >>>> contribution from K, O etc. at k highers than 5A is for me >> too low to >>>> analyse it resonable for such compound. >>>> I have attached in the previus post the last version of results. >>>> Anyway, >>>> enots for C and N do not change if I am enlarging R region >> (when I am >>>> including next paths, also for K). >>>> about material I am quite sure ;) and crystal structure is from >>>> literature >>>> >>>> in the attachment you will find bmp file of the fit: data, >> fit, bkg >>>> and K path. >>>> fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase >> correction - first >>>> C >>>> >>>> cheers >>>> darek >>>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Sat, 20 Jun 2009 12:44:34 +0200 > From: Stefan Mangold <stefan.mangold(a)iss.fzk.de> > Subject: Re: [Ifeffit] problem with E0 (enot) parameters > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <6F3358E1-7C2C-4FA2-B3B3-AD9FF7B0C5F3(a)iss.fzk.de> > Content-Type: text/plain; charset="iso-8859-1" > > Please do not attach 10 Mb of data on your Mails. Just send an Link to > an Web-space with your e-mail. People can then download the stuff if > needed. > > Best regards > > Stefan > > Am 19.06.2009 um 16:44 schrieb Zajac, Dariusz A.: > >> Hi Scott, >> I am afraid that E0 jumps over the edge - see bmp's in the attachment >> (files with enot_12 means E0=12...). Hovewer 12 eV is still less than >> k=3 (the starting k value). Can it influence? I did also once more fit >> with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can >> see >> in the attachment too... >> I hope you and anyone from the mailing list don't mind that I am >> attaching so many files... >> >> cheers >> darek >> >>> -----Original Message----- >>> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >>> [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >>> Of Scott Calvin >>> Sent: Friday, June 19, 2009 2:49 PM >>> To: XAFS Analysis using Ifeffit >>> Subject: Re: [Ifeffit] problem with E0 (enot) parameters >>> >>> >>> Hi Darek, >>> >>> OK, so if the K, H, and O don't affect the fit much for the C and N, >>> and the K, H, and O are returning nonsensical values, then a logical >>> possibility is that the E0's for C and N are correct. If you >>> add 12 eV >>> to the E0 you chose in Athena, where in the spectrum does it fall? Is >>> it still before the white line? If so, it seems to me you >>> don't have a >>> problem. If not, then we have to ponder further. >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> >>> On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: >>> >>>> Hi Scott, >>>> look also at H and O, >>>> but for me and for this fit important are only W-C and W-C-N >>> bondings. >>>> This sample is an reference sample for other cyano-brigded networks. >>>> So >>>> you suggest to focuse on K ions? how can it help with first >>> 2 peaks? K >>>> is at ~5A. >>>> I have analysed in larger R space only to see how the >>> spectrum behave. >>>> contribution from K, O etc. at k highers than 5A is for me too low >>>> to >>>> analyse it resonable for such compound. >>>> I have attached in the previus post the last version of results. >>>> Anyway, >>>> enots for C and N do not change if I am enlarging R region (when I >>>> am >>>> including next paths, also for K). >>>> about material I am quite sure ;) and crystal structure is from >>>> literature >>>> >>>> in the attachment you will find bmp file of the fit: data, fit, bkg >>>> and >>>> K path. >>>> fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - >>>> first C >>>> >>>> cheers >>>> darek >>>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> < >> K4W >> (CN >> )8_enot_12 >> .bmp >>> >> < >> K4W >> (CN >> )8_enot_0.bmp><K4WCN8_b.apj><K4W(CN)8_2.bmp><K4W(CN)8_2q.bmp><mime- >> attachment.txt> > > -- > Dr. Stefan Mangold > Institut f?r Synchrotronstrahlung > Forschungszentrum Karlsruhe > Tel.: +49-7247-826073 > >

1 0

Re: [Ifeffit] Primitive unit cell from .cif file
by joshua jason kas 19 Jun '09

19 Jun '09

Hi Bruce, > I don't really understand what you are driving at, but it seems as > though you want to express Diamond as a simple cubic cell with a two > atom basis? Yes, that would be the case for diamond, but for an arbitrary crystal structure specified as in a .cif I would like to find the primitive cell, i.e. the unit cell of smallest volume. > I don't really understand how that > will save you time in > abinit, but, of course, I am not a crystallographer.... Smaller volume means less bands to obtain the same energy range. > PS. Doesn't abinit understand crystal symmetry? Maybe. I couldn't get it to reproduce the diamond structure using only one atom in the cell, but I haven't been using it for very long, and will probably go to the abinit list for this. > Why can't you just tell it that it's diamond and has the symmetry of > diamond? For our application, we can't really use the symmetry at this point. Would be good if we can in the future, but for now we really need input that includes all atoms in the primitive unit cell. Again, thanks to everyone for your time. I hope this was not too far out in left field for this mailing list. Apologies if it was. Josh Kas > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas > Sent: Thu 6/18/2009 2:41 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Primitive unit cell from .cif file > > Thanks everyone for your suggestions! I have tried the following things. > I used atoms (webATOMS) to generate a p1.inp file using diamond as an > example, but this gives me the conventional cell with 8 atoms in > it instead of the 2 atom primitive cell. Am I doing something wrong? > The input file came from the atoms database and the output is as follows: > > * > * "F d -3 m" appears in the International Tables with > * multiple choices of origin. If the atoms list seems wrong, you > * should use a shift vector of: > * -0.125, -0.125, -0.125 > * > * > ! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10) > ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > title = name: diamond > title = formula: C > title = sites: C1 > title = refer1: Kittel, ISSP > title = refer2: > title = schoen: > title = notes1: diamond structure > space p 1 ! original space group: F d -3 m > a = 3.5670 b = 3.5670 c = 3.5670 > alpha = 90.0 beta = 90.0 gamma = 90.0 > core = C1_1 edge = K rmax = 6.0 > atoms > ! elem x y z tag occ > C 0.12500 0.12500 0.12500 C1_1 1 > C 0.12500 0.62500 0.62500 C1_2 1 > C 0.62500 0.12500 0.62500 C1_3 1 > C 0.62500 0.62500 0.12500 C1_4 1 > C 0.87500 0.37500 0.37500 C1_5 1 > C 0.87500 0.87500 0.87500 C1_6 1 > C 0.37500 0.37500 0.87500 C1_7 1 > C 0.37500 0.87500 0.37500 C1_8 1 > > I also tried the Mercury demo, but all editing features are disabled. > > I will try Diamond now. > > Just to give some motivation here, I am working with abinit (along with > feff) to produce optical spectra. If I use a conventional cell, the > calculations become much more time consuming, so ideally I want to use a > primitive cell. > Thanks again for all your help! > Josh > >> Hi Josh, >> You may try Diamond Demo version which is free. >> >> http://www.crystalimpact.com/diamond/download.htm > I will give this a try. > > >> >> Hi Josh, >> >> If I understand your question, I think that Atoms does what you want. Running the command line tool as "atoms -p" turns the attached cif file into the attached "p1.inp" file. You can do the same thing inside of Artemis using "write special output" in the Theory menu. > >> >> B >> >> -- >> Bruce Ravel ----------------------------------- bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Methods Group at Brookhaven National Laboratory >> Building 535A >> Upton NY, 11973 >> >> My homepage: http://cars9.uchicago.edu/~ravel >> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >> >> >> >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas >> Sent: Wed 6/17/2009 2:16 PM >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] Primitive unit cell from .cif file >> >> Hi everyone, >> I was wondering if there is a simple (free) utility for producing a >> primitive cell (not conventional) from an asymmetric cell and space group. >> Basically, I want to be able to easily go from a crystallographic >> information file to a primitive unit cell. I know that there are ways to >> do this within applications like material studio, but these are expensive. >> Any help would be appreciated. >> Thanks, >> Josh Kas >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >>

2 1

Radial distribution
by Eugenio Otal 18 Jun '09

18 Jun '09

Hi Shelly, thanks, I will try this. Cheers, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

1 0

Radial distribution
by Eugenio Otal 18 Jun '09

18 Jun '09

Hi, I performed EXAFS simulation and want to obtain the radial distribution of the signal. I tried with athena but I cannot process it like experimental signal. Is there any trick to transform the signal into radial distribution? Thanks, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 1

Primitive unit cell from .cif file
by Eugenio Otal 18 Jun '09

18 Jun '09

Josh, you can also try with Mercury, has a free version at: http://www.ccdc.cam.ac.uk/products/mercury/ Hope it helps, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Hi Josh, You may try Diamond Demo version which is free. http://www.crystalimpact.com/diamond/download.htm Good luck, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ---- Original message ---- >*Date: Wed, 17 Jun 2009 11:16:49 -0700 (PDT) *>*From: ifeffit-bounces at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> (on behalf of joshua jason kas <hebhop at u.washington.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>) *>*Subject: [Ifeffit] Primitive unit cell from .cif file *>*To: ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> *>* *>*Hi everyone, *>*I was wondering if there is a simple (free) utility for producing a *>*primitive cell (not conventional) from an asymmetric cell and space group. *>*Basically, I want to be able to easily go from a crystallographic *>*information file to a primitive unit cell. I know that there are ways to *>*do this within applications like material studio, but these are expensive. *>*Any help would be appreciated. *>*Thanks, *>*Josh Kas *>*_______________________________________________ *>*Ifeffit mailing list *>*Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> *>*http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit *

1 0

Primitive unit cell from .cif file
by joshua jason kas 17 Jun '09

17 Jun '09

Hi everyone, I was wondering if there is a simple (free) utility for producing a primitive cell (not conventional) from an asymmetric cell and space group. Basically, I want to be able to easily go from a crystallographic information file to a primitive unit cell. I know that there are ways to do this within applications like material studio, but these are expensive. Any help would be appreciated. Thanks, Josh Kas

3 2

Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2
by joshua jason kas 12 Jun '09

12 Jun '09

> And yet, the documentation for the CORRECTIONS keyword says: > > "The real energy shift vrcorr moves E0 in the final \chi(k) and > the imaginary energy shift vicorr adds broadening to the > result. The real energy shift is useful to correct the error in > FEFF's Fermi level estimate and the imaginary part can be used to > correct for experimental resolution or errors in the core-hole > lifetime." > > And a couple of sentences later: > > "The imaginary energy is typically used to correct for instrument > broadening or as a correction to the mean free path calculated by > feff." > > Perhaps the document should be updated to explain more clearly what > CORRECTIONS actually does. Thank you Bruce. I will try to clear up the documentation. Let me state more clearly how these two cards can be used to change the broadening of the spectrum. In the EXCHANGE card, the user can use negative values to offset the core hole broadening. The CORRECTIONS card can only be used to add to the total (previous) broadening, which is given by the half width at half max, Gamma_CH/2 + vi, where vi is the broadening from the EXCHANGE card and Gamma_CH is the core hole broadening. The benefit of using the CORRECTIONS card is that it is very fast since you can skip the matrix inversion for the FMS calculation. Thus a good way to use the two cards together is to reduce the broadening via EXCHANGE by a bit too much (use an overestimate as a first try), then use the CORRECTIONS card to fine tune the broadening. Cheers, Josh correctly. > 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/ > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 76, Issue 8 > ************************************** >

1 0

how to reduce the core-hole lifetime broadening in feff8.2
by joshua jason kas 11 Jun '09

11 Jun '09

Hi Tony, As mentioned already, you can use the EXCHANGE card with negative values to reduce the core-hole broadening. Note however that this will not work with the CORRECTIONS card. Josh Kas > Message: 1 > Date: Thu, 11 Jun 2009 05:58:53 -0700 (PDT) > From: tony vitova <tony_vitova(a)yahoo.com> > Subject: [Ifeffit] how to reduce the core-hole lifetime broadening in > feff8.2 > To: Ifeffit List <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <204685.79014.qm(a)web54505.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear?all, > ? > Could somebody give me a hint how to reduce the core-hole lifetime broadening in feff8.2? Do I?need to change the source code? I have partial fluorescence yield XANES spectrum whose White Line is narrow than the one in the calculation. > ? > Thanks for any help > ? > Tonya > > > >

2 1

how to reduce the core-hole lifetime broadening in feff8.2
by tony vitova 11 Jun '09

11 Jun '09

Dear all, Could somebody give me a hint how to reduce the core-hole lifetime broadening in feff8.2? Do I need to change the source code? I have partial fluorescence yield XANES spectrum whose White Line is narrow than the one in the calculation. Thanks for any help Tonya

4 3

Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2
by tony vitova 11 Jun '09

11 Jun '09

Hi Janine and Bruce, Thanks a lot! I didn't think that the EXCHANGE card might take and negative values... Tonya --- On Thu, 6/11/09, Janine GRATTAGE <janine.grattage(a)esrf.fr> wrote: From: Janine GRATTAGE <janine.grattage(a)esrf.fr> Subject: Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2 To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Date: Thursday, June 11, 2009, 5:29 PM Hi Tonya, I use the EXCHANGE card to reduce the applied broadening in my spectra. If you set the third parameter in the card to a number less than zero (up to about -5 in my experience) then the broadening is reduced and you can calculate high resolution type XANES spectra. This applies only to some inherent limit in the calculations where further reducing the parameter has no effect. You can look up the EXCHANGE card on the feff wiki as it also can be used to change the exchange model and the position of the Fermi level. Hope that helps you! Janine tony vitova wrote: > Dear all, > > Could somebody give me a hint how to reduce the core-hole lifetime > broadening in feff8.2? Do I need to change the source code? I have > partial fluorescence yield XANES spectrum whose White Line is narrow > than the one in the calculation. > > Thanks for any help > > Tonya > > > ------------------------------------------------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Dr Janine GRATTAGE Postdoctoral Fellow, ID26 European Synchrotron Radiation Facility (ESRF) Sector 26, BP 220 6, rue Jules Horowitz, 38043 Grenoble, Cedex 9, FRANCE Tel: +33(0)4 38 88 19 30 Email: janine.grattage(a)esrf.fr _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

Xanes peaks fitting with Athena: no data on output
by Ismael Graff 10 Jun '09

10 Jun '09

Hi dears, I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following: # Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail! All the best, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418

3 5

pgplot on mac os x 10.5.7
by Matthew Ginder-Vogel 09 Jun '09

09 Jun '09

Hi Renske, Thanks for the info. It worked for me as well. However, now I'm running the older version of ifeffit. Has anyone had success with version 1.2.10? Thanks, Matt On Thu, Jun 4, 2009 at 1:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) > (Renske van der Veen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 04 Jun 2009 10:01:56 +0200 > From: Renske van der Veen <renske.vanderveen(a)psi.ch> > Subject: Re: [Ifeffit] pgplot on mac os x 10.5.6 (Matthew > Ginder-Vogel) > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <C64D4C14.B00%renske.vanderveen(a)psi.ch<C64D4C14.B00%25renske.vanderveen(a)psi.ch> > > > Content-Type: text/plain; charset="US-ASCII" > > Hello, > > I encountered the same problem with the 1.2.10 version of ifeffit > (ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg downloaded via > http://cars9.uchicago.edu/ifeffit/Downloads) on my Mac (also Mac OS X > version 10.5.6). > > Instead I downloaded iXAFS (iXAFSinstall.tar.gz) from the same website for > which pgplot works fine. > > Best regards, > Renske > > > On 02.06.09 19:00, "ifeffit-request(a)millenia.cars.aps.anl.gov" > <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > > pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) > > Message: 1 > Date: Mon, 1 Jun 2009 15:53:33 -0400 > From: Matthew Ginder-Vogel <mattgv(a)udel.edu> > Subject: [Ifeffit] pgplot on mac os x 10.5.6 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <f637a5340906011253m3b98d3deld2452f2511c3f355(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Everyone, > > Does anyone else have problems with pgplot on macs? > > There is no text on any plot that I make using Athena/Artemis. This > includes the axis labels, the legend, and the tick labels. > > I've tried on several macs and the problem is the same on all of them. > > Any advice? > > Thanks, > > Matt > > -- > ******************************************* > Matthew Ginder-Vogel > Post Doctoral Researcher > Center for Critical Zone Research > Environmental Soil Chemistry > University of Delaware > http://ag.udel.edu/SoilChem/gindervogel.html > (302) 831-0608 > mattgv(a)udel.edu > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 76, Issue 3 > ************************************** > -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Re: [Ifeffit] pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel)
by Renske van der Veen 04 Jun '09

04 Jun '09

Hello, I encountered the same problem with the 1.2.10 version of ifeffit (ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg downloaded via http://cars9.uchicago.edu/ifeffit/Downloads) on my Mac (also Mac OS X version 10.5.6). Instead I downloaded iXAFS (iXAFSinstall.tar.gz) from the same website for which pgplot works fine. Best regards, Renske On 02.06.09 19:00, "ifeffit-request(a)millenia.cars.aps.anl.gov" <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) Message: 1 Date: Mon, 1 Jun 2009 15:53:33 -0400 From: Matthew Ginder-Vogel <mattgv(a)udel.edu> Subject: [Ifeffit] pgplot on mac os x 10.5.6 To: ifeffit(a)millenia.cars.aps.anl.gov Message-ID: <f637a5340906011253m3b98d3deld2452f2511c3f355(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello Everyone, Does anyone else have problems with pgplot on macs? There is no text on any plot that I make using Athena/Artemis. This includes the axis labels, the legend, and the tick labels. I've tried on several macs and the problem is the same on all of them. Any advice? Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu

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post-doc job postings
by Matt Newville 03 Jun '09

03 Jun '09

Hi, There are a couple of new listings for Post-Doc positions at http//xafs.org/Jobs. If you or someone you know may be interested, please pass these along. --Matt

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Re: [Ifeffit] Problems with potential overlap for small molecule
by joshua jason kas 02 Jun '09

02 Jun '09

Hi Renske, In order to solve the overlap problem, I tried some of the standard methods of fixing these problems, i.e. using the FOLP cards and such with no luck. This will take some time to debug, but we are looking into it. As for the negative density problem, this is something that we have worked on, and know how to fix, but will also take some time. Cheers, Josh Kas > Dear FEFF users, > > I have a FEFF8.4-related question concerning the abortion of the potential > module in a XANES calculation for a small molecule in solution. It might not > be totally appropriate for the ifeffit mailing list, but the FEFFusers > mailing list doesn?t seem to be used very often. I have looked through the > archive, but I haven?t found an entry with this specific problem. > > I am trying to simulate the L3-edge XANES spectrum for the linear I3- > molecule (I-I-I) embedded in a solvent with O-H groups. In order to simulate > the scattering from the solvent, I have put two O-H groups at either end of > the molecule with the H-atoms pointing towards the I-atoms (expected charge > transfer from I3- towards solvent). The I-H and I-O distances are taken from > ab initio calculations in the literature, the O-H distance is well-known and > amounts to 0.96 A. It is also known from the literature on similar ions in > solution that the H-atoms contribute to the XANES and should therefore be > included. > > I pasted my feff.inp file below. > > Running this file results in abortion at the beginning of the potential > module: > > ... > Number of processors = 12 > Calculating potentials ... > free atom potential and density for atom type 0 > MOVRLP-1 > Abnormal termination on processor 8 > [n7:09539] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with > errorcode 512 > ... > > It seems to occur when it is trying to overlap the potentials (MOVRLP-1). I > tried including the FOLP 2 0.8 card as suggested for H-atoms in the manual, > but this does not help. > > It seems like the O-H bond <1 A is too small: moving the O atoms further > away such that the O-H bond is 1.05 A ?solves? the problem, although this is > not what I want. But: moving the H atom closer to the I atom while keeping > the O positions fixed, which increases the O-H bond as well, does not help! > Also, to make things even more complicated, excluding the H-atoms fully, > i.e. putting only two O-atoms at 3.5 A from the iodines, results in the > WARNING during the SCF loop that the interstitial potential level lies > higher than the Fermi energy (moving the O atom closer to ca. 2 A removes > this message). In addition, certain combinations of H- and O- positions give > the output ?negative dens? during the SCF loop, for which I checked that > FOLP 2 0.8 did not help... > > It is obvious that FEFF has problems with generating the MT potentials for a > small and ?open? system such as the one here. Did somebody encounter similar > problems (abortion, Ei>Ef, negative dens) for systems like this? Is there > something wrong with my input cards? > > I?d appreciate any help. > > Best regards, > Renske van der Veen > > P.s. I am running the parallel version of FEFF8.4 on Linux > > *** > > TITLE I3- XANES spectrum > > * I L3 edge energy = 4557.0 eV > EDGE L3 > S02 1.0 > > CONTROL 1 1 1 1 1 1 > SIG2 0.01 > > PRINT 1 0 0 0 0 0 > EXCHANGE 0 0.0 0.0 0 > > SCF 10 1 30 0.2 1 > > LDOS -30 60 -1 > > XANES 6 > > FMS 10 1 > UNFR > > POTENTIALS > 0 53 I 3 4 > 1 53 I 3 4 > 2 1 H > 3 8 O 2 3 > > *FOLP 2 0.8 > > ATOMS > 0.0000 0.0000 0.0000 0 > -2.91 0.0000 0.0000 1 > 2.91 0.0000 0.0000 1 > -5.45 0.0000 0.0000 2 > 5.45 0.0000 0.0000 2 > -6.41 0.0000 0.0000 3 > 6.41 0.0000 0.0000 3 > END > >

1 0

pgplot on mac os x 10.5.6
by Matthew Ginder-Vogel 01 Jun '09

01 Jun '09

Hello Everyone, Does anyone else have problems with pgplot on macs? There is no text on any plot that I make using Athena/Artemis. This includes the axis labels, the legend, and the tick labels. I've tried on several macs and the problem is the same on all of them. Any advice? Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

1 0

Problems with potential overlap for small molecule
by Renske van der Veen 20 May '09

20 May '09

Dear FEFF users, I have a FEFF8.4-related question concerning the abortion of the potential module in a XANES calculation for a small molecule in solution. It might not be totally appropriate for the ifeffit mailing list, but the FEFFusers mailing list doesn¹t seem to be used very often. I have looked through the archive, but I haven¹t found an entry with this specific problem. I am trying to simulate the L3-edge XANES spectrum for the linear I3- molecule (I-I-I) embedded in a solvent with O-H groups. In order to simulate the scattering from the solvent, I have put two O-H groups at either end of the molecule with the H-atoms pointing towards the I-atoms (expected charge transfer from I3- towards solvent). The I-H and I-O distances are taken from ab initio calculations in the literature, the O-H distance is well-known and amounts to 0.96 A. It is also known from the literature on similar ions in solution that the H-atoms contribute to the XANES and should therefore be included. I pasted my feff.inp file below. Running this file results in abortion at the beginning of the potential module: ... Number of processors = 12 Calculating potentials ... free atom potential and density for atom type 0 MOVRLP-1 Abnormal termination on processor 8 [n7:09539] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with errorcode 512 ... It seems to occur when it is trying to overlap the potentials (MOVRLP-1). I tried including the FOLP 2 0.8 card as suggested for H-atoms in the manual, but this does not help. It seems like the O-H bond <1 A is too small: moving the O atoms further away such that the O-H bond is 1.05 A ³solves² the problem, although this is not what I want. But: moving the H atom closer to the I atom while keeping the O positions fixed, which increases the O-H bond as well, does not help! Also, to make things even more complicated, excluding the H-atoms fully, i.e. putting only two O-atoms at 3.5 A from the iodines, results in the WARNING during the SCF loop that the interstitial potential level lies higher than the Fermi energy (moving the O atom closer to ca. 2 A removes this message). In addition, certain combinations of H- and O- positions give the output ³negative dens² during the SCF loop, for which I checked that FOLP 2 0.8 did not help... It is obvious that FEFF has problems with generating the MT potentials for a small and ³open² system such as the one here. Did somebody encounter similar problems (abortion, Ei>Ef, negative dens) for systems like this? Is there something wrong with my input cards? I¹d appreciate any help. Best regards, Renske van der Veen P.s. I am running the parallel version of FEFF8.4 on Linux *** TITLE I3- XANES spectrum * I L3 edge energy = 4557.0 eV EDGE L3 S02 1.0 CONTROL 1 1 1 1 1 1 SIG2 0.01 PRINT 1 0 0 0 0 0 EXCHANGE 0 0.0 0.0 0 SCF 10 1 30 0.2 1 LDOS -30 60 -1 XANES 6 FMS 10 1 UNFR POTENTIALS 0 53 I 3 4 1 53 I 3 4 2 1 H 3 8 O 2 3 *FOLP 2 0.8 ATOMS 0.0000 0.0000 0.0000 0 -2.91 0.0000 0.0000 1 2.91 0.0000 0.0000 1 -5.45 0.0000 0.0000 2 5.45 0.0000 0.0000 2 -6.41 0.0000 0.0000 3 6.41 0.0000 0.0000 3 END

1 0

Polarization vector in FEFF calculation
by Yun Luo 15 May '09

15 May '09

Dear All, I have a quick question regarding the polarization vector in FEFF calculation. There is a card of "POLARIZATION x y z" that we can use to count in polarization effect in FEFF calculation. I just want to make sure that the x, y, z coordinates of the polarization vector is in the crystal Cartesian base. For example, if the direction of the electric field of the incident beam is along the a axis of the crystal, then I can use the card "POLARIZATION 1 0 0" in the FEFF input file to do the calculation. Is this correct? Thank you very much! Best Yun

2 1

Artemis and Athena
by Chris Patridge 08 May '09

08 May '09

Hello everyone, I am starting the tutorials that are provided with the ifeffit package. Do the examples in the package have additional text files to explain some of the steps involved with the various fits for the more complicated samples? Thank you all, Chris

1 0

Fitting procedure
by abhijeet gaur 01 May '09

01 May '09

Hello Matt Sir, Thanks a lot. I will include the error bars in fitted value for sure. with regards Abhijeet Gaur

4 3

Inviting you to Multiply
by kaswat nano (via Multiply) 27 Apr '09

27 Apr '09

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1 0

Fitting procedure
by abhijeet gaur 24 Apr '09

24 Apr '09

Hello Matt Sir, Thanks a lot for your valuable sugestions. I had fitted the Cu foil spectra as you suggested. I had taken same SO2 value for all the paths and after fitting the first shell , making its parameter fix when fitting second shell I changed the fit R range 2.9- 3.7 in order to make the contribution of first shell negligible. I got a nice fit. The values of different parameters I got are as follows : E 0=2.90 eV , SO2= 0.72 1st shell R = 2.54, delR= -0.011, SS2=0.0083 2nd shell R= 3.69, delR= 0.080, SS2=0.0088 The experimental data is taken at room temperature. Are these parameters within the experimental error limit. Please tell me with regards Abhijeet Gaur

2 1

Can't locate Ifeffit.pm
by Silvio Levy 21 Apr '09

21 Apr '09

Hi, I've installed horae on a new laptop after a hiatus. When I try to run athena or artemis I get the message Can't locate Ifeffit.pm in @INC (@INC contains: ... Setup: ifeffit-1.2.11c horae-069 Ubuntu 8.04.1 There is an Ifeffit.pm (in fact two) in the ifeffit-1.2.11c source directory, so I added it to the PERL5LIB path. But this didn't solve the problem; it just pushed it a few yards further. Now I get Can't locate loadable object for module Ifeffit in @INC (@INC contains: ... Anybody know the solution? Note to Bruce: the instructions in 0INSTALL still say 'perl Makefile.PL; make; make install' but the correct thing seems to be 'perl Build.PL; Build; Build install' as I found on one of your web pages. Thanks in advance Silvio

3 2

Fitting procedure
by abhijeet gaur 20 Apr '09

20 Apr '09

I want to add some more things I have done 1) E0 is kept same for all the shells 2) All other parameters like SO2 , del r , SS2 are calculated separately for different shells. So. is there problem with taking different SO2 for different shells. Surely del r and SO2 will be different for different shells , If I got it right. Abhijeet

2 1

NLEG
by Eugenio Otal 20 Apr '09

20 Apr '09

Hi, I am performing some XANES simulation with feff. I want to know somethings about an extra shoulder so I am using NLEG card. I have no problem with NLEG = 1 - 3, but NLEG > 3, I found a error: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% WARNING!! Two non-degenerate paths, hashed to the same hash key!! 0.12036490409027290344E+09 0.12042092980933572352E+09 3 3 npat0, npat iat, ipot0, ipot, ipat0, ipat 1 1 1 2 2 2 0 0 0 0 3 1 1 2 1 ileg, rx0,ry0,rz0, rx1,ry1,rz1 1 0.0000000000E+00 -1.3877787808E-16 1 0.0000000000E+00 0.0000000000E+00 1 1.9402260780E+00 1.9402260780E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 2 0.0000000000E+00 0.0000000000E+00 3 0.0000000000E+00 1.7760854959E+00 3 0.0000000000E+00 0.0000000000E+00 3 1.9402260780E+00 -7.8094518185E-01 hash error that is what I found in output file and the simulation crashed. Is there somehow to solve this and continue the job? Thanks in advanced, euG

1 0

Fitting procedure
by abhijeet gaur 19 Apr '09

19 Apr '09

Hi all, I think there is a lot of confusion over the method that i used for fitting, So I should make it clear here. In this method I fit the first shell by taking into account only first shell R range i.e. 1.5 - 2.7. Then after getting a nice fit for the first shell, I extract its parameters and make them set in Artemis. Then I include the second shell by increasing R range to 1.5 - 3.6. In the same manner I fit the first three shells of copper foil and the parameters I got for them are reasonably good. The problem of high SO2 only lies with one of my foil data which is not as good as other data. For other good data I got SO2 value for second shell within the exceptable limit. One more thing I want to say is that we can check the corelation between different parameters of shells by making them guess during any step of the fitting e.g. during the fitting of second shell we can make any parameter of the first shell to vary and check its corelation with them. But if I am counting the first shell data twice, I will include only second shell R range after first shell fit.I think it will not make any difference to results. If yes please tell me the reasons. with thanks Abhijeet gaur

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Re: [Ifeffit] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

Oops, please ignore my message - sent it to the wrong address!!! --------- Message sent via my BlackBerry Wireless Device ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Sat Apr 18 14:56:35 2009 Subject: Re: [Ifeffit] Fitting procedure They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ 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] Fitting procedure
by Chappell, Mark A ERDC-EL-MS 18 Apr '09

18 Apr '09

They're on theur way back to Vicksburg. I yried to guide them from home but couldn't figure out where she was. By 230, she hung it up and turned back --------- Message sent via my BlackBerry Wireless Device ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Sat Apr 18 12:57:18 2009 Subject: Re: [Ifeffit] Fitting procedure Hi Adam, I am confused by this thread too! As you say, the original issue involved using S02 for individual shells of data on Cu foil. Of course, having separate S02 for each shell is not usually necessary to model Cu foil -- in fact I can't think of a case where it is needed. But since S02 is 100% with N, and ~95% correlated with sigma2, it is easy to have S02 vary per shell if one allows it to happen. Whether that's a good idea or not depends on how you interpret the results. Most people choose to fix a single S02 and vary N. Lots of people fit spectra with one S02 and an N for each shell, so I don't think the number of free parameters is necessarily a big issue. In a follow-up message, Scott seemed (to me) to be more concerned about whether it was reasonable to "fix parameters for the first shell" when fitting a second or higher shells, not so much with the issue of what parameters were being refined. There weren't explicit details on what was fixed or what fitting ranges or parameters were used for the higher shells. Scott suggested (I believe) that "fixing the first shell" and fitting the second shell was not a good idea, and asked to hear differing views. I find the approach of "fit the first shell, then fix those parameters and fit the second shell" to be a reasonable way to start, so I responded. I would not call this approach "acceptable, but generally not preferred" -- I would say it has actual merit. Yes, it is often a good idea to check a fit to the whole spectrum toward the end of an analysis. But in a fit to the whole spectrum, the quality of the fit to the more subtle features (the finer structure) can often get lost in the fit to the more dominant features of the spectra. That is why we subtract mu0(E), after all. I don't see Fourier filtering as a bad idea for analyzing higher shells. But perhaps I am just not understanding what Scott and Shelly recommend??? --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting procedure
by abhijeet gaur 18 Apr '09

18 Apr '09

Hi all, Thanks to all the concerned persons for having such a wonderful discussion over fitting procedure. I am able to understand the things better by going through these discussions. But what I am trying to say is that I had first applied the fitting procedure in which I make the parameters of all paths( included in the fit) to vary simultaneously, but the problem is that I am not able to get a good fit and the parameters for different paths are also coming absurd like very low amplitude etc. For days I have been trying this method of fitting but not able to get good results.I tried different models also like Debye & Einstien model, I used the relation del r= alpha* Reff but it doesn't work. Then I switch to this the method in which we fit the first shell, get the parameters fix them and then go for the next shell and in this way e fix the whole spectra. The results I got are extremely good. Thus I am using this method. Abhijeet Gaur

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Multiple data set fit
by Debora Meira 18 Apr '09

18 Apr '09

Dear all, I'd like to know a reference that has multiple set data fit as a function of temperature in nanoparticles. Is the relation of Debye Waller factor (s2 = ss2 + sd2) valid for the higher shells? In particular, can I use the Einstein model for sd2? Thanks in advance, Débora Débora M Meira Universidade Federal de São Carlos Pós-Graduação em Engenharia Química Laboratório de Catálise Tel: (16) 92461134 / (16) 34125935 _________________________________________________________________ Faça já uma busa e ganhe um wink do Messenger. Está esperando o que? É grátis! http://www.ibud.com.br/

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R quality factor in k space
by Cammelli Sebastiano 17 Apr '09

17 Apr '09

Dear iffefit user, I found on a paper (E.A. Stern et al. /Physica B 208&209 (1995) 117 120) the definition of R quality factor as: R_factor ≡ < ∆chi(R space))> = √[ ∑ |chi_C(Ri) – chi_E(Ri)|2 / ∑( chi_E(Ri))2] ----> formula 3 Where Chi(Ri) is a complex function (imaginary and real part of the XAFS spectra in the R space), C concerns the calculated XAFS spectrum, while E refers to the experimental XAFS spectrum. In the case of a linear combination fitting on the k space performed by ATHENA, the <∆chi> needs a correction. Is it correct to write: R_factor ≡ < ∆chi(k space))> = √[ ∑ (chi_C(ki) – chi_E(ki))2 / ∑( chi_E(ki))2] ? Where Chi_C(ki) = x1*chi1(k)+x2*chi2(k) : chi1 and chi2 are the EXAFS functions of the two reference samples used for the linear combination procedure and x1, x2 (with 0<x1,x2<1 and x1+x2=1) are their weight; Chi_E(k) is the EXAFS experimental function of the investigated sample. Best regards Sebastiano Cammelli

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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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Fwd: Questions about Athena & FEFF
by Bruce Ravel 15 Apr '09

15 Apr '09

Pascal, I am answering your question on the Ifeffit mailing list, which is the most appropriate venue for questions of this sort. Please read this page: http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest If I understand your question, you are asking about whether it is appropriate to run Feff with a small cluster. The canonical answer to that question is that you want to use a large cluster whenever possible so that the muffin tin potential is well constrained. Sometimes, with a very small cluster, the algorithm Feff uses to compute the muffin tin radii can result in radii that are unphysically large, resulting in an unphysical calculation. Of course, that is a somewhat hand-waving answer. It is hard to know without actually running a calculation whether the problem with muffin tin radii will actually happen. I have comfortably published results which use very small clusters indeed. In your case, as in so many cases, the best advice I can give is to try it both ways and see what happens. That is, you can try doing a XANES calculation (Are you using Feff8? You didn't say...) with the small cluster and comparing it to the Feff8 calculation which uses a large cluster to compute the potentials and small cluster to compute the full multiple scattering XANES. See the Feff document at http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Document… for details about how to set parameters in the feff.inp file to make that happen. Regards, B ---------- Forwarded Message ---------- Subject: Questions about Athena & FEFF Date: Wednesday 15 April 2009 From: "Pascal G. YOT" <pascal.yot(a)univ-montp2.fr> To: bravel(a)bnl.gov Dear Prof. Ravel, I'm working on data coming from XAFS measurements carried out at Pb-L3 edge on lead containing glassy samples. Three reducing agent are used to reduce lead(+II) inside the original glass at high temperature. Our samples contain then a fraction is in fcc lead(0) form and one other fraction of lead(+II) still remaining inside the glassy framework. EXAFS analysis show a decrease of the Pb-O coordination number from 3 (for original glass) to lower CN (1 in extreme case). My major concern is the analysis of XANES, some modifications are observed on the finger prints. I've try to fit the spectra using linear combination fitting module from Athena using lead and original glass spectrum with poor result as you have understand. I need then to generated model XANES spectra for the CN. As I'm not an expert of FEFF, I need some advices. Can I use a cluster PbOx ((d=2.23 A) with coordinate for Pb and O coming from lead oxide) containing few atoms? Is the obtained spectra reliable to give a "good" fit? I hope my questions are clear for you. Thanks in advance for your remarks. Best regards Dr. Pascal Yot ------------------------------------------------------- -- 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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Basic questions
by haiyan 15 Apr '09

15 Apr '09

Dr. Kelly, May I get a copy about setting k-range? Thanks1 Haiyan Zhao Chemical Engineering Department Virginia Tech Blacksburg, VA 24060 Hi Andy, I have a book chapter that details how to set the k-range for a data set. It also talks about Rbkg in detail. If you want a copy just send me an email. Cheers, Shelly

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residual saving
by Guvenc Akgul 15 Apr '09

15 Apr '09

dear all, I need save residual as k^3*Chi(k) but I could not save it because it is saving only as Chi(k).how can do for this? thanks in advance guvenc

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High SO2
by abhijeet gaur 12 Apr '09

12 Apr '09

Hello Scott Sir, I got that ifeffit basically works on the principle of making the theoretical data look similar to experimental data. But what I know about fitting is that we have to first fit the first shell and then keeping the first shell parameter constant , we go for the next shell. Is it not right. Please tell me Abhijeet Gaur

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High SO2 value
by abhijeet gaur 09 Apr '09

09 Apr '09

Hi all, I am fitting a copper foil. I fit the first shell by using first ss path and got it fitted nicely. Then keeping the parameters for the first shell to be fixed , I tried to fit the second shell by taking first and second ss but it is always coming a littel displaced and not fitting well also. But when I added the the third ms path to it , the fit becomes very nice. But the problem is that parameters for third path are coming very bad. And one more problem is that the value of SO2 for second shell is coming very high around 1.5. I am not able to understand the results. Thanks in advance Abhijeet Gaur

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Linear combination fitting
by Guvenc Akgul 09 Apr '09

09 Apr '09

Dear all, I have done Ti doped ZnO EXAFS data analysis but I guess it is getting mixture structure at high concentration for example 55% Ti doped ZnO.Also I done linear combination fit , but at fitting space norm(E),ZnO weight is 0.779 and ZnTiO3 is 0.221 then I changed fitting space is chi(k) ZnO weight is getting 25.2 and ZnTiO3 is getting 74.8 and it is not same like at fitting space norm(E) why? regards guven

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huge S02 value ??
by mzhu＠udel.edu 07 Apr '09

07 Apr '09

Hello everyone, I have been fitting EXAFS of NiSO4 aqueous solution. The feff files were created from Ni(OH)2 using Feff7.00. During the fitting, coordination number was fixed as 6. The S02 derived from fitting is 1.22. I tried other materials for creating feff files, such as NiCO3 and NiPO4, and I got the similar S02 values. I also tried Feff6, it did not result in a reasonable S02 value, either. Anyone can tell me why it led to such high S02 value? The data file and feff input file (Feff 7) are attached. Thanks in advance. Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

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Basic questions
by Andy Connelly 06 Apr '09

06 Apr '09

Some really quick basic questions. I am working with EXAFS spectra of silicate glasses at various edges (including S and Fe K edges) and I am having a really difficult time pinning down the structures. Clearly with glasses I can't always be sure of the oxygen co-ordination and so I have to refine this value which is one among many problems. Just to check I have things right: 1. Are there any problems if I set the R-range min to the same value as Rbkg? 2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems? 3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances? 4. If I have a calculated Fe3+-O path from a 4 and 6 co-ordinate reference are these equivalent? Obviously, they will give a different bond length and the MS paths will change but if I am only fitting a first shell is there anything different. I think the answer involves the muffin tin potentials but I'm a little out of my depth there. Any advice about solving glass structures more than welcome. Whatever I try I can't get realistic results out. Thank you for your time, Andy Connelly

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Ab initio calculations
by Luanga Nchari 06 Apr '09

06 Apr '09

I would like to do ab initio calculations to get a theoretical XANES spectra. I have XYZ coordinates..... Could somebody remind me how I can run this on my PC. Cheers, Luanga

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Mixed Multiple scattering shell
by Joseph Washington 01 Apr '09

01 Apr '09

Hello all, I was wondering if anyone can send any useful hints or tips for parameterizing a mixed multiple scattering shell comprised of two NaCl type strucutres, like the AgBr(1-x)Cl(x) example. Has anyone worked on fitting the third shell in that example? I am looking for examples of nacl rocksalt-like FEFF calculations that have successfully parametrized multiple scattering path contributions. Right now, after running feff, I'm using a different delr / ss term for each multiple scattering path I include. Does anyone have any clever ways of representing these in terms of the delr/ss in the first shell? Also, FEFF is telling me that the amp and mixing terms are almost completely correlated and this cause the amp term to blow up. Thanks all, I really appreciate the assistance! Joseph

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Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 25
by Zuzaan, Damdinsuren 31 Mar '09

31 Mar '09

Hi Matt, >From the raw data I can recognize columns with dead time information. Also I am waiting reply from beamline scientists. Anyway, could you give me some detailed information how to do this dead time correction with Ifeffit commands or within Athena. Thank you in advance. Cheers, Damdin ------------------------------ Message: 2 Date: Mon, 30 Mar 2009 10:18:43 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903300818w355650dfub735bf29165fc0a1(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Damdin, > I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). > So I think the small S02 and N are due to deadtime effect. Yes, a slightly saturated detector can cause an S02 that is a little smaller than normal. > It is possible to do it in Athena? In general, athena doesn't have buttons or a page to do dead time corrections. This is because there isn't a single, consistent way to store the dead time information. You might want to consult with the beamline scientist for how to make these corrections. If you know what columns in your data file hold the dead time information (and what the columns are holding), it's possible to do this with Ifeffit commands (within athena, even). Cheers, --Matt Newville <newville at cars.uchicago.edu>

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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] Ifeffit Digest, Vol 73, Issue 24
by Zuzaan, Damdinsuren 30 Mar '09

30 Mar '09

Hello everyone, Shelly, Matt, Scott many thanks for your reply. I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). So I think the small S02 and N are due to deadtime effect. It is possible to do it in Athena? Damdin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, March 28, 2009 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 73, Issue 24 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: About S02 (Matt Newville) 2. Re: About S02 (Scott Calvin) ---------------------------------------------------------------------- Message: 1 Date: Fri, 27 Mar 2009 16:28:46 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0903271428i7c6ea611l325443292de87b45(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Damdin, An XAFS book or theory that says "S02 must be between 0.8 and 1" overstates the case. In simplest terms, S02 is a fudge factor. There is a theoretical basis for it (passive electron overlap), but much of this can also be folded into other "loss terms" that are due to inelastic scattering events for the photo-electron. These should be part of the EXAFS calculation from, say, Feff, but are hard to do well to high precision. When using Feff, Ifeffit, Artemis, it does turn out that, in most cases, the calculated amplitudes tend to overestimate the experimental amplitudes, and that applying a constant S02 between 0.8 and 1.0 works reasonably well. That is hardly a "must be" between 0.8 and 1. In addition to the theoretical issues of Feff not-quite-correctly calculating S02, there are experimental factors that affect the XAFS amplitude: the estimate of the edge step being the most important, but also the energy resolution of the incident x-rays and sample-dependent issues such as pinholes, and for fluorescence measurements detector deadtime and self-absorption. There is an understandable desire to turn these observation into a rule-of-thumb and then into some sort of rule that can be pointed to as if to say "this analysis is wrong" or "this analysis is correct". As is normal for such rules-of-thumb, it is sometimes broken. Of course the main trouble with the uncertainty of which S02 to use is that for a single-shell analysis, one cannot distinguish S02 from the coordination number. That is, the EXAFS amplitude for S02=1, N=4 is the same as for S02=0.8, N=5, and for S02=0.67, N=6. Distinguishing these cases is hard (don't let anyone tell you they aren't or that there is a button in Artemis that fixes this problem). If you need to distinguish N=5 from N=6, you better be pretty confident that your data and analysis have a good value for S02. The classic approach to this is to measure a data on a "standard" is free from amplitude-reducing artifacts and for which the coordination number is well-defined as easy to extract from the data, measure this at the same beamline conditions (energy resolution, harmonic content) as your unknown sample, and then work to be highly consistent in setting the edge step. The S02 applied to the standard to get the correct coordination number is then applied to the unknown data to get its coordination number. There are many ways for such an analysis to fall short of perfect, but it is generally the best we can do. --Matt On Fri, Mar 27, 2009 at 8:19 AM, Zuzaan, Damdinsuren <zuzaan(a)uni-mainz.de> wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ Message: 2 Date: Fri, 27 Mar 2009 19:23:29 -0400 From: Scott Calvin <SCalvin(a)slc.edu> Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <E7658A83-0512-4A17-ACC0-1CC7A2A7F831(a)slc.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Damdin, Matt and Shelly have answered this very well, but I have one more thought to add. You have a mineralogical sample and apparently have a pretty good idea what the mineral is, since you're not varying r or n. Under those circumstances, you probably have a hypothesis as to the structure beyond the nearest-neighbor. If you include more than one path in your fit, the inability to distinguish coordination number from S02 is reduced, and more importantly for your purposes, the correlation between S02 and sigma2 is also reduced. If it stays the same when you add more paths, it can help increase your confidence that the low S02 in your fit is appropriate. --Scott Calvin Sarah Lawrence College On Mar 27, 2009, at 9:19 AM, Zuzaan, Damdinsuren wrote: > Hello everyone, > > I am graduate student and doing EXAFS in my research. > > My question is about S02. From the XAFS books or theory it says that > this value must be between 0.8 to 1, but in the literature some people > used different values like 0.25 or 1.4. In my case I fitted > experimental RDF of my standard sample by holding the known r and n > values for each path, while varying E0, S02 and sigma2. Obtained E0 > and S02 values were holded for unknown sample and rest were floated > freely. S02 were 0.64. So my question is that this relatively small > S02 value could affect the mineralogical interpretations made in my > study. Should I refit it using high value? Thanks in advance > > Regards, > > Damdin ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 73, Issue 24 ***************************************

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