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

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 04 Jan '10

04 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 04 Jan '10

04 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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