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

About S02
by Zuzaan, Damdinsuren 27 Mar '09

27 Mar '09

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

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Accepting applications for 2009 APS XAFS School, July 6-10, 2009
by Julie Olmsted Cross 23 Mar '09

23 Mar '09

FYI: The application form for the 2009 APS XAFS School is now live at: http://xafs.org/Workshops/APS2009 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Lattice distortion
by Eugenio Otal 23 Mar '09

23 Mar '09

Hi, I am trying to simulate the XANES spectra of erbium in a interstitial site of ZnO, now I am looking for the changes if the erbium atom is not in the center of the site. I done some simulations but I don´t get any change in the spectra with the distortion of the site. Is this possible? I attach the figure of the simulations and the inp files. Thanks, euG --

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Lattice distortion
by Eugenio Otal 20 Mar '09

20 Mar '09

Hi, I am trying to simulate the XANES spectra of erbium in a interstitial site of ZnO, now I am looking for the changes if the erbium atom is not in the center of the site. I done some simulations but I don´t get any change in the spectra with the distortion of the site. Is this possible? I attach the figure of the simulations and the inp files. Thanks, euG

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Athena data
by abhijeet gaur 18 Mar '09

18 Mar '09

Hi Price, Now I got my data imported into Origin. Thanks with regards Abhijeet Gaur Vikram University Ujjain M.P. ( India )

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Re: [Ifeffit] [Ifeffit-devel] import the chi. file from Artemis to Athena
by Bruce Ravel 17 Mar '09

17 Mar '09

Catalin, This is not really a question for the Ifeffit-devel mailing list. I am sending my response to the normal Ifeffit mailing list -- which is the proper place for a question about using the software. On Tuesday 17 March 2009 11:29:10 am Catalin Popescu wrote: > I am trying to align the theory and the data for one of my compounds. I > have difficulties to import in Athena the chi(k)file saved in Artemis. > Whenever i saved my fit data as a chi (k) and I tried to import it in > Athena i am asked to choose the right columns. I tried all the ways to > choose the columns but it doesn't work. How are you saving the chi(k) data from Artemis? Athena expects that its data are chi(k) and NOT k-weighted chi(k). If you are saving the data from Artemis as anything other than un-k-weighted chi(K), the wrong thing will certainly happen in Athena. When importing the chi(k) data back into Athena, you will want to select the first column as k and the second column as chi(k). > Whenever I want to check what I imported I don’t see the right > chi. file so I am assuming that the file saved from Artemis is not > saved as the right file. It’s weird because I know about the > tutorials (MoO3 for example) in which you can import the theory file > into Athena and after to align it to the data. In the case of the > tutorial of Shelly Kelly (background removing procedure for MoO3) > the file containing the theory file is included in .prj file. I am > assuming that it was done directly from Feff. In my case I run the > feff.inp file from Artemis. I already looked in the FAQ Sections and > I only found how to transfer data from Athena to Artemis not the > other way around. Also I saw that Athena import output files like > chi.dat but this format is coming from Feff and is not present in > Artemis. Can you please suggest me a solution? 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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Getting data from athena
by abhijeet gaur 17 Mar '09

17 Mar '09

Hi , I tried the method as told by Bruce & Scott to get the data from Athena and then plot it into Excel or Origin. I got the data of chi(R) in different columns in a notepad file but when I try to copy it in Origin or Excel all the column values got copied into one column , Thus I am not getting the required plot. Please tell me how to get the data plotted in some other plotting software. Abhijeet

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Figure conversion - color to b/w
by Jenny Cai 16 Mar '09

16 Mar '09

Thank you, Bruce and Scott. Actually, I replotted all my figures using EXCEL except this one. It worked well for individual spectrum and linear combination fitting, but in least-squares peak fitting, I couldn't find the data for Gaussian and arctangent step peaks. Could you please let me know where I can find those data? Thanks again. Jenny ________________________________ From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, March 16, 2009 12:34:32 PM Subject: Re: [Ifeffit] Figure conversion - color to b/w On Monday 16 March 2009 12:21:14 pm Jenny Cai wrote: > I submitted a manuscript where XANES least-squares peak fitting was used. A > figure (attached with this email) was copied from Athena. The problem is > that the reviewer asked me to change the color peaks to black and white > with diferent types of lines. I was trying to figure it out by myself, but > failed. Could anyone help me out? Thank you in advance! Jenny, The figures from Ifeffit and friends are not really intended to be of sufficient quality for a publication. See questions 10 and 11 at http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions You may find Richard Mayes' suggestion in the answer to question 10 helpful. Athena gives you quite enough information to replicate your plot in other plotting software. The line shapes are all standard line shapes and the parameters are reported after the fit. 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ________________________________ Now with a new friend-happy design! Try the new Yahoo! Canada Messenger __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.

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Re: [Ifeffit] (no subject)
by Frenkel, Anatoly 16 Mar '09

16 Mar '09

I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case. However, to approach it more rigorously, the first step would be to examine the relative "importance" factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not. Anatoly ________________________________ 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: Wed Mar 11 09:40:31 2009 Subject: [Ifeffit] (no subject) Hi all, I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe distance ~5A). My question is how to fit the model with the data? Can I discard the contribution of multiple scattering effects to the fitting? One most important information that I want to obtain is on the Fe-Fe distance. Is it enough to conclude from the raw data FT that the Fe-Fe distance in my protein sample has been changed in comparison to the Fe-Fe distance in the model (created with Feff using the crystal structure coordinates)? I try fitting using arthemis but got bad and weird results. is there any manual or step-by step guide that I can learn how to fit model of two metal sites to my data? Anther question that I have how can I get to the past discussions in the forum- is there any database for questions and answers that I can learn on the analysis of EXAFS data? Any help will be appreciated, MJacob

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Atoms input file for PdO
by bill.schwartz＠yale.edu 13 Mar '09

13 Mar '09

Greetings I'd like to get an atoms input file for PdO. Can someone point me in the right direction for either obtaining or creating one? Thanks, Bill

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XANES
by Aimee Morey 12 Mar '09

12 Mar '09

I have collected full XANES and EXAFS spectra. I have imported the full spectrum into Athena. I am now trying to analyze using XANES, but I am have trouble figuring out how to set an absolute energy, i.e. 7709 eV = 0 eV or such, and have the energy scaled negatively and positively. It is probably super simple, can anyone please help? Thank you, Aimee -- Aimee M. Morey Graduate Assistant Department of Chemistry, U-3060 University of Connecticut 55 North Eagleville Rd Storrs, CT 06269-3060 Phone # (860) 486 - 6567 Fax # (860) 486 - 2981

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(no subject)
by Michael Jacob 11 Mar '09

11 Mar '09

Hi all, I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe distance ~5A). My question is how to fit the model with the data? Can I discard the contribution of multiple scattering effects to the fitting? One most important information that I want to obtain is on the Fe-Fe distance. Is it enough to conclude from the raw data FT that the Fe-Fe distance in my protein sample has been changed in comparison to the Fe-Fe distance in the model (created with Feff using the crystal structure coordinates)? I try fitting using arthemis but got bad and weird results. is there any manual or step-by step guide that I can learn how to fit model of two metal sites to my data? Anther question that I have how can I get to the past discussions in the forum- is there any database for questions and answers that I can learn on the analysis of EXAFS data? Any help will be appreciated, MJacob

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protonated pentatitanate
by A M 11 Mar '09

11 Mar '09

Dear All I have huge problem with my spectra for protonated pentatitanate ( H2Ti5O11 *3H2O), I’ve tried to build theoretical model for this compound (penta.cif) but unfortunately I have 5 Ti atoms in my formula, so I really don’t know what Ti I should select as a core atom...I tried with 5 different options Ti1....Ti5, so I obtained 5 different models (with distances between Ti-O in first shell sometimes very short 1.59A)... I would be very grateful for any help.... Best regards Marie

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latest version of horae in Debian
by Carlo Segre 08 Mar '09

08 Mar '09

Hi All: After a long delay, I have finally managed to make Debian packages of the new-look horae (after version 069) and upload it to the Debian archive. As usual, I have backported to the current Debian stable (lenny) and to Ubuntu intrepid and jaunty. Because of significant changes, I am not supporting Debian etch or Ubuntu hardy. The old versions of horae are still avilable for those in my archive. The packages can be obtained by putting the appropriate lines on your /etc/apt/sources.list file. Instructions are at http://debian-xray.iit.edu/ Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, 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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Nickel theory
by maho mah 04 Mar '09

04 Mar '09

dear all, I have calculated each one for Ni l2 l3 edges and them together myself .But satellite peak is so broadened in theorical calculation.what will I do for this?? M _________________________________________________________________ Windows Live™ Groups: Create an online spot for your favorite groups to meet. http://windowslive.com/online/groups?ocid=TXT_TAGLM_WL_groups_032009

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Request for Foil Spectra
by Kelly, Shelly 04 Mar '09

04 Mar '09

Hi Everyone, I'm planning on submitting a small EXAFS 14 paper on the comparison of S02 from different beamlines using foils of Cu, Pd, Ag, and Au spectra. I've raided the APS/XOR data for Cu and Ag spectra from all around the APS ring. If you would like to donate foil spectra to the cause, we will include you as an author. Please also send the thickness and source of the foil, the beamline that it was collected on, and a reference for the beamline (if possible). I'm not sure that the paper will include all 4 edges. I'm mostly interested in Cu and Ag since I have a fairly complete set of those already. Thanks for your help, Shelly

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Nickel
by maho mah 03 Mar '09

03 Mar '09

dear all, I am interest in NiTi allow.and I done Total electron yield (TEY) method for NiTi .I would like to see together l3 and l2 edges peak versus theorical Ni L3 and L2 edges.I done it using FEFF8 for theorical calculation but it is not similar measured ones.how can I do for this?especially satellite peak does not seem like measured satellite one. thanks for in advance maho mali _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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Cu data
by abhijeet gaur 03 Mar '09

03 Mar '09

Hello everyone I have some copper foil data that is taken from rotating anode spectrometer. But it has lot of errors.So where can I find Cu data taken from rotating anode on the web so that I can correct my data .If someone can share data with me , then it will also be very helpfull. Abhijeet Gaur

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XANES/EXAFS spectrum of AsF3
by Gleb S. Pokrovski 02 Mar '09

02 Mar '09

Hello, I'm looking for XANES/EXAFS at As K-edge of AsF3 (arsenic(III) fluoride) and/or any other As(III) fluorinated compound. Could someone share such spectra with me if he/she have them? Many thanks in advance Gleb

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(no subject)
by Cammelli Sebastiano 02 Mar '09

02 Mar '09

Dear Feff user I had a problem trying to simulate the EXAFS spectrum of a Cu foil. I found a small shift in the k space and I do not know if it is significant and, if it is, how to correct it. In the doc file I attached you will find the details of the problem, the feff.inp and some explications. Do not worry about its size, pictures are large and the feff.inp takes space... Thank you a lot for your help Sebastiano Sebastiano.cammelli(a)psi.ch

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I got that
by abhijeet gaur 24 Feb '09

24 Feb '09

Thanks Dr. Dominik . I should have tried this on web .Anyways thanks again Sir. Abhijeet

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Attachment
by abhijeet gaur 23 Feb '09

23 Feb '09

Hi Dr. Bruce Actually I got the idea that we had to take into account the multiple scatterring path during fitting. But I am not able open the attachment that you have send , it is some vlc media file. Can you please send it in some other format like pdf.I will be very thankfull to you. Abhijeet

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Neagtive amplitude
by abhijeet gaur 22 Feb '09

22 Feb '09

Hi all, I am fitting a *copper foil* . I am getting a good fit after using the *4 single scattering paths* but in case of *fourth path* I am getting *negative amplitude*. What should be the *probable reason* for that as I am getting a *very good fit*. with thanks Abhijeet Gaur

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Disordered shells
by Eugenio Otal 19 Feb '09

19 Feb '09

Hi all, I need to simulate some structural disorder in the first and second shell of interstitial erbium in ZnO for XANES and EXAFS spectra. Which is the best way to obtain information of the spectra variation with structural changes? If I use DEBYE card, how to correlate temperature with structural parameters? Everything is so quite in the line, no messages since 13/feb... Regards, euG

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Artemis fitting problem
by abhijeet gaur 13 Feb '09

13 Feb '09

Hi every one, Actually I want to know that is it necessary to fit Ei, 3rd, 4th, cumulant in the fitting procedure .If yes then please tell me how to get them involve in the fit .when I give parameter like guess 3rd, guess 4th . Artemis dont take them . One more thing is that I am fitting Cu foil, CuO and Cu2O , so how many number of paths should I take . Abhijeet

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Re: [Ifeffit] SIXPACK
by Matt Newville 13 Feb '09

13 Feb '09

Hi Bounif, I'm actually not responsible for the PCA analysis part of SixPACK, Sam Webb (the author of SixPACK!) is. And I have to admit I don't know all the details beyond what is documented at: http://www-ssrl.slac.stanford.edu/~swebb/spdocs/sixpack_documentation.htm#P… I'll try to answer your questions, and hopefully Sam or someone on this list will correct me: > My question is the following one: > When I calculate the principals components from the data matrix ( sampls ) > I must make a target transformation to obtain the réels compoents which > constitutes mixtures. > 1-a reels components are obtained by the transformationof the principals > components or de target components? I believe it uses the components found from PCA as the pieces with which to build a spectra that matches the target. > 2-How to calculate the concentration of the reels constituents ? I am not sure how to get those numbers directly. If the target transformation works to reproduce your spectra, you could always then try linear combinations to get the sample constituents. I'm not sure that this is guaranteed to work or give a unique answer (say, if all of your samples were truly mixtures of multiple components themselves), but I think that it does normally work in practice with a small number of components and some of them "nearly" endmembers. Cheers, --Matt Newville <newville at cars.uchicago.edu> 2009/2/11 bounif <bounif(a)univ-paris12.fr>: > Dear Newville, > With big enjoyment which I writes you,I am a student in paris 12 > université,I work on the decomposition of the spectre EXAFS of mixtures at > several pure constituents,I test various methods, Among these methods the > principals components analisis(PCA).For this, I use the SIXPACK software > which you are the author. > My question is the following one: > When I calculate the principals components from the data matrix ( sampls ) > I must make a target transformation to obtain the réels compoents which > constitutes mixtures. > 1-a reels components are obtained by the transformationof the principals > components or de target components? > 2-How to calculate the concentration of the reels constituents ? > Very cordially > > > cher Newville, > avec grande joie que je vous écrit,je suis un doctorant à luniversité de > paris 12,je travail sur la décomposition des spectre EXAFS des mélanges en > plusieurs composantes pures,je test différentes méthodes,parmi ces > méthodes l'analyse en composantes principale.pour cela j'utilise le logiciel > SIXPACK dont vous êtes l'auteur. > Ma question est la suivante:quand je calcule les composantes principales > (components) à partir de la matrice des donnés (sampls) je dois effectuer un > transformation pour obtenir les composés réels qui constitue les mélanges. > 1-les composés réel sont obtenus par la transformation des composantes > principales où les composantes cible (target ) ? > 2-comment calculer la concentration des composantes réel? > bien cordialement > > > > > > Bounif Mohamed > > Institut de Chimie et des Matériaux Paris Est (ICMPE) > UMR CNRS-Université Paris 12 n° 7182 > Equipe SAX > 2 à 8 Rue Henri Dunant, 94320 THIAIS France > Tel : +33.1.49.78.13.38 > Fax : +33.1.49.78.12.03 > > > > >

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Re: [Ifeffit] Mo EXAFS
by Matt Newville 13 Feb '09

13 Feb '09

Dear Mehdi, Sorry for taking so long to respond, and hope you'll again forgive me for forwarding this message to the Ifeffit mailing list. I actually have taken very little data on Mo compounds. I don't know what is in the Lytel database for the compounds you list, either. But I'll bet that someone on this list can help you out.... --Matt Mehdi Monir <MXM785(a)bham.ac.uk> wrote: > Dear Matthew > > I am a PhD research student in metallurgy and materials dept. at University of Birmingham . I am working under supervision of Dr. Alison J. Davenport (University of Birmingham) and Prof. Trevor Rayment(Diamond light source). > We are working on a project which is part of an EPSRC -funded program to characterize the chemistry and structure of salt films on Fe, Ni and stainless steel in chloride base solutions with and without other anions, and to explore the use of X-Ray absorption spectroscopy for characterizing chemistry of pits in these materials. > We have done XAS experiments on Mo edge this september at Diamond light source(Synchrotron Facility, Oxfordshire, UK).I am looking for Mo standard spectra like Mo foil, MoAcetate, MoCl3, MoO2, MoCl5 and Na2MoO4 in HCl solutions but unfortunately couldn't find too many ref spectra. > It would be really great help if give me any idea or introduce any resources to find these information. > > Many Thanks > > Mehdi > >

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Co doped znO
by Guvenc Akgul (gakgul) 13 Feb '09

13 Feb '09

dear all I want to figure out and plot theorical Co doped ZnO using FEFF8. how can I do it? thanks guven

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Artemis fitting problem
by abhijeet gaur 07 Feb '09

07 Feb '09

Hi Scott, I know that alpha is not a temperature expansion coefficient .I guess it is a volume expansion coefficient( tell me if I am right). Actually I want to know that is it necessary to fit Ei, 3rd, 4th, cumulant in the fitting procedure .If yes then please tell me how to get them involve in the fit .when I give parameter like guess 3rd, guess 4th . Artemis dont take them . And about Ei I am completely blank.I dont know how to use it and from where i will get it. One more thing is that I am fitting Cu foil, CuO and Cu2O , so how many number of paths should I take . And Thanks a lot for your suggestions With regards Abhijeet

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Lost second shell
by Eugenio Otal 06 Feb '09

06 Feb '09

Hi Carlo, thanks for for help, really interesting your paper about ZnMnO. Cheers, euG

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Co2MnO4 atoms.inp files
by JeongEunSuk 06 Feb '09

06 Feb '09

Hello all I want to get Co2MnO4 atoms.inp. I know that Co2MnO4 is a spinel structure, however I dont know the position of each atom in unit cell. If anyone knows that, please answer me... _________________________________________________________________ 간편하고 정확한 나만의 맞춤 검색, Live Search! http://search.live.com

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An additional beta tester
by Scott Calvin 05 Feb '09

05 Feb '09

Hi Kathy, I just got a late volunteer for beta testing, whom I think will be a good addition: Ryan Hinrichs, professor of Chemistry at Drew University. Knows a little bit about XAFS, partially from collaboration with me, but has never used it himself. E-mail: Hinrich(a)drew.edu (Yes, his name ends in an "s" but his e-mail address does not.) --Scott

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Possible solution to trouble in artemis analysis
by Kleper Oliveira Rocha 05 Feb '09

05 Feb '09

Dear all, Recentilly I post a massage about trouble with analysis in artemis. Well, I think that find the solution. In Portuguese some words are write with symbols like: fam*í*lia (family), prepara*ÇÃ*o (preparation) that are not accept by IFFEFIT programs. In the basis of the instalation of Windows XP in my computer and some folders had this symbols and this caused the trouble in Athena and Artemis. Thanks for all for the help. -- Kleper de Oliveira Rocha Doutorando em Engenharia Química Departamento de Engenharia Química/UFSCar Tels. 55 016 3351-8694

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Lost second shell
by Eugenio Otal 05 Feb '09

05 Feb '09

Dear Carlo, with changes in function of time, you mean that repetitions of the spectra in the same sample are different from the firs to the last? What does this indicates? Thanks for you help, euG

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Artemis parameter
by abhijeet gaur 04 Feb '09

04 Feb '09

Hi Scott, I know that alpha is not a temperature expansion coefficient .I guess it is a volume expansion coefficient( tell me if I am right). Actually I want to know that is it necessary to fit Ei, 3rd, 4th, cumulant in the fitting procedure .If yes then please tell me how to get them involve in the fit .when I give parameter like guess 3rd, guess 4th . Artemis dont take them . And about Ei I am completely blank.I dont know how to use itand from where i will get it. One more thing is that I am fitting Cu foil, CuO and Cu2O , so how many number of paths should I take . And Thanks a lot for your suggestions With regards Abhijeet

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Los
by Eugenio Otal 04 Feb '09

04 Feb '09

Hi everybody, thanks for your time, knowledge and pacience. The first shell is can be fitted by 2 sub shells with this composition: n_first_1 = 2.4702860 r = 1.782161 n_first_2 = 9.2476950 r = 2.342539 This is really far from Zn in ZnO, is closer to Er(OH)3, with 8 between 2.40 and 2.43 and ErOOH presents 7 neighbors between 2.26 and 2.45, with something like 2 sub-shells. Er2O3 has two sites with octahedral simmetry, one is perfectly Oh and the other distorted with 2.21 to 2.36 for Er-O. I chequed the doping element incorporation and found that what I suppose to be 1% is in fact 0.6% (by ICP quantification) the incorporation is less I though. Maybe that is the reason to do not find call parameters change. What kind of difference could I find between nanoparticles and bulk for incorporation? Cheers, euG -- "I posti più caldi nell'inferno sono riservati a coloro che in tempo di grandi crisi morali mantengono la propria neutralità". Dante Alighieri (1265-1321) 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal CINSO - CONICET - CITEFA San Juan Bautista de La Salle 4397. Villa Martelli (B1603 ALO) Buenos Aires TEL: 54 11 4709-8100 Int. 1212. FAX: 54 11 709-8241. E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

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Re: [Ifeffit] Self absorption Correction
by Jens Kruse 03 Feb '09

03 Feb '09

Hi, Thanks Richard and Carlos for the the links. But is the "Fluo"-Algorithm for self absorption correction also valid if I have the concentrated sample (standard) applied as a fine powder to a carbon tape or is it only valid for much much thicker samples? thanks, Jens > ------------------------------ > > Message: 4 > Date: Mon, 2 Feb 2009 09:51:10 -0500 > From: Richard Mayes <rtmayes(a)gmail.com> > Subject: Re: [Ifeffit] Self absorption Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <5a2a54820902020651nfaf1af7q4ec435fc207fc38a(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Jens, > > Since no one has answered yet, I'll chime in. First let me direct you to a > discussion of self-absorption and other sample-related distortions: > http://www.xafs.org/Experiment/OverAbsorption (this is a link from the > tutorials page of www.xafs.org) > > As for your questions: > > I think that you should use the non-normalized XANES data to perform the SA > correction. > > for the angle-in and angle-out meanings, see Grant Bunker's paper on > self-absorption here: > http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf > > Now, how do you determine if you have self-absorption effects? I have to > defer here to those with more experience. What you suggest sounds > appropriate, but I'm not sure how you could determine this without studying > multiple concentrations of your absorber and watch the signals, i.e. does a > 10% increase in absorber concentration translate to a 10% increase in > fluorescence yield (similar to what Matthew Marcus and Alain Manceau > describe in their paper, from the over-absorption link above). > > HTH, > -Rich > > On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse <jens.kruse(a)uni-rostock.de>wrote: > > >> Hi there, >> >> I have measured a pure reference compound with high absorber >> concentration in fluorescence mode (P K-edge XANES). I tried to use the >> Self absorption correction included in Athena but I don't really >> understand the results. >> Fist: Do I have to use the edge step normalized spectrum or the spectrum >> without normalization ? I tried both and the results of course a quite >> different. I would rather use the not normalized spectrum. >> Second: the value "Angel in" is this the angle between the incident >> beam and the sample surface" and "Angle out" the angle between the >> sample surface and the detector position? >> Third: More general- How can I identify a spectrum suffering self >> absorption? Just comparing the relative peak intensities of total >> electron yield signal with the fluorescence yield signal ? >> >> thanks a lot for your comments, >> cheers, >> Jens >> >> -- >> 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 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

3 2

Lost second shell
by Eugenio Otal 03 Feb '09

03 Feb '09

Anatoly, Here I attach some pictures. I also have luminescence measurements an found a great disorder but I could not find changes in the cell parameters by XRD refinements. I perfored XANES simulations for ZnO sustituted by Er and the spectra is really different. I cannot believe that the Er is in Zn site, but maybe the structure changes and the simulation is not so "real". euG

3 2

Re: [Ifeffit] Self absorption Correction
by Carlos Prieto 02 Feb '09

02 Feb '09

Jens, Let me give you an old reference (but still usefull) for the self absorption treatment: R. Castañer and C. Prieto, "Fluorescence detection of EXAFS in thin film samples", J. de Phys. III (France), 7, 337-349 (1997). Best regards Carlos Prieto At 15:51 02/02/2009, you wrote: >Jens, > >Since no one has answered yet, I'll chime >in. First let me direct you to a discussion of >self-absorption and other sample-related >distortions: ><http://www.xafs.org/Experiment/OverAbsorption>http://www.xafs.org/Experiment/OverAbsorption >(this is a link from the tutorials page of <http://www.xafs.org>www.xafs.org) > >As for your questions: > >I think that you should use the non-normalized >XANES data to perform the SA correction. > >for the angle-in and angle-out meanings, see >Grant Bunker's paper on self-absorption >here: ><http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf>http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf > >Now, how do you determine if you have >self-absorption effects? I have to defer here >to those with more experience. What you suggest >sounds appropriate, but I'm not sure how you >could determine this without studying multiple >concentrations of your absorber and watch the >signals, i.e. does a 10% increase in absorber >concentration translate to a 10% increase in >fluorescence yield (similar to what Matthew >Marcus and Alain Manceau describe in their >paper, from the over-absorption link above). > >HTH, >-Rich > >On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse ><<mailto:jens.kruse@uni-rostock.de>jens.kruse(a)uni-rostock.de> wrote: >Hi there, > >I have measured a pure reference compound with high absorber >concentration in fluorescence mode (P K-edge XANES). I tried to use the >Self absorption correction included in Athena but I don't really >understand the results. >Fist: Do I have to use the edge step normalized spectrum or the spectrum >without normalization ? I tried both and the results of course a quite >different. I would rather use the not normalized spectrum. >Second: the value "Angel in" is this the angle between the incident >beam and the sample surface" and "Angle out" the angle between the >sample surface and the detector position? >Third: More general- How can I identify a spectrum suffering self >absorption? Just comparing the relative peak intensities of total >electron yield signal with the fluorescence yield signal ? > >thanks a lot for your comments, >cheers, > Jens > >-- >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 > >_______________________________________________ >Ifeffit mailing list ><mailto:Ifeffit@millenia.cars.aps.anl.gov>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 ================================ Carlos Prieto Instituto de Ciencia de Materiales de Madrid CSIC Cantoblanco, 28049 - MADRID (Spain) Tel.: 91 3349017 e-mail: cprieto(a)icmm.csic.es =================================

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Self absorption Correction
by Jens Kruse 02 Feb '09

02 Feb '09

Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value "Angel in" is this the angle between the incident beam and the sample surface" and "Angle out" the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- 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

2 1

Guessed parameter and Einstien temperature
by abhijeet gaur 02 Feb '09

02 Feb '09

Hi Thanks a lot Scott , I got that how to change ss for difeerent path by using the function debye(temp, thetad).But I am not getting the same result in case of delr . I took the different parameter as follow : guess amp 1 def delr alpha*reff guess enot 0 def ss debye(temp,thetad) set alpha .0002 set thetad 343 set temp 298 But I am not getting a very good fit. The value of debye temperature is 343 for Cu( Kittel book) but I got to know that some persons even guessed the value of thetad as 285+-16 . I am not getting that how we can guess the value of alpha and thetad . Also I am not getting the value of Ei, 3rd and 4th cumulant in the fit results . So How can I get the value of these parameters in the fit results . With thanks Abhijeet Gaur

2 2

Lost second shell
by Eugenio Otal 02 Feb '09

02 Feb '09

Hi all, I am working with Er doped ZnO and the EXAFS measurements (Er L3) shows that I have not a second shell when I perform the FT. I checked that the phase is not destroying the signal, and that is not the guilty guy. I have two possibilities, that the erbium is segregated on the surface of the particles with a strong disordered phase that destroy second shell information (XANES simulation are different from oxide and hydroxides) or that the atoms are isolated in the surface of the particles. Should I use the card for molecules for isolated atoms? And for the disordered phase, what can I do? Is there another possibility to lose the second shell? Thanks in advance, euG

2 1

Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Carlo Segre 01 Feb '09

01 Feb '09

Hi Yordy: I'm sorry. The xdp module is one that was written here by my group to provide I/O for data files produced at our beamline. I have packaged it for Debian but it is not out there for the general public yet. In the program I sent you the xdp module is only used to write out the converted data is a file format that we call SFF (Simple File Format). The xdp module is not necessary if you simply write out the converted data with a more normal set of commands. Your email got me thinking though that I should finish the progrram and make it useful to others. What I did, therefore, is to rewrite the program without the use of xdp and making it a bit more user-friendly. It now also handles both of the filetypes that Matt mentioned on a previous post, and which are documented at http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379… The program now runs fine under Python 2.5 (I don't know about 2.6 but let me know if it has problems!). It is used as a standard *nix filter, that is, rename it to "lytle_convert" (or make a link to it) and make sure it is executable and in the executing PATH so the system can find it. The program is invoked from the command line as $lytle_convert file0 [file1 file2 file3 ... fileN] It does take wildcards so you can process a bunch of files at once. Since all the Lytle database files are of the form "name.ext", the output file name is made to be "name_ext.sff". The program does its best to guess the steps per degree for the olert file type which does not include that information in the header. The d-spacing is assumed to be 1.92017. This may not work for all files (I have not checked and I didn't have time to put in more intelligence right now) so you might need to go in to modify the program to change these defaults. I am thinking that I will add options to let the d-spacing and steps per degree be set on the command line but that will have to wait for later. Enjoy! Carlo On Sat, 31 Jan 2009, Yordy Licea Fonseca wrote: > Hi Carlo, > > I´ve installed Python 2.6 for Windows XP to run your code. Latter I've > installed a numpy 1.2.1 compiled for 2.6. I did neither find the > *Numeric *module > nor the *xdp* module you initialized first in the code. So I've intalled Py > 2.4 version and again numpy, but didn not work. > In 2.6 there is a *math* module that works similar to *Numeric*. As I did > not find what *Numeric.zeros* does in line 32 I could not implement (if it > were possible) with *math.* > Could I use *xdrlib* module instead of *xdp?* > ** > Would you send me or tell me please where to find those modules and which > Python you recommend me to install? > > Best wishes, Yordy > > > > > 2009/1/29 Carlo Segre <segre(a)iit.edu> > >> Ah, just premature sending... >> >> Carlo >> >> On Thu, 29 Jan 2009, Yordy Licea Fonseca wrote: >> >> Hi Carlo and Matt, >>> >>> Thank you very much for your help. >>> >>> Best wishes, >>> >>> Yordy >>> >>> >>> On 29/01/2009, 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. Trouble with fitting with Artemis (Juraci A. Sampaio) >>>> 2. Re: Trouble with fitting with Artemis (Richard Mayes) >>>> 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca) >>>> 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville) >>>> 5. uncertainty in linear combination analysis (Pushan Shah) >>>> 6. Artemis parameters (abhijeet gaur) >>>> 7. Energy shift (Eugenio Otal) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Wed, 28 Jan 2009 15:34:55 -0300 >>>> From: "Juraci A. Sampaio" <jasampaio(a)hotmail.com> >>>> Subject: [Ifeffit] Trouble with fitting with Artemis >>>> To: <ifeffit(a)millenia.cars.aps.anl.gov> >>>> Message-ID: <COL107-W60310E438349CE1C72988AACC80(a)phx.gbl> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> >>>> Hi there!I'm getting the following message when I try to fit my >>>> data:WARNING. The following variables had no effect on the fit: !! >> >>>> amp !! >> >>>> enot !! >> >>>> delr !! >> ss The >>>> data >>>> that I am trying to fit is the Cu metal example that come with the >>>> iffefit >>>> package. I am running Artemis on a Mac, OSX 10.4.11.I could run the >>>> fitting >>>> on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but >>>> it >>>> didn't work.I am wondering what could be wrong with my >>>> machine/software?Thanks a lot.Juraci Sampaio >>>> _________________________________________________________________ >>>> Confira v?deos com not?cias do NY Times, gols direto do Lance, >>>> videocassetadas e muito mais no MSN Video! >>>> http://video.msn.com/?mkt=pt-br >>>>

1 0

"Hard tests failed in fovrg"
by tony vitova 30 Jan '09

30 Jan '09

Hi all, I am trying to fit Eu L3 edge EXAFS data of Eu complex whose structure is known (hopefully correct). The default feff6l in Artemis reports an error “Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small“. When I run feff8.2, this error exchanges with the following message “The phase shift correction is accurate to k=19”. I guess that this is not a problem, because my data is until k equal 12 A^-1. However, the fit of the first shell (9O/9N) gives Eo equal to 13, which is unrealistic. This fit with paths calculated with feff6l gives reasonable Eo value. But the phase shifts seem to be calculated incorrectly. I will be very thankful for any hint! Thanks in advance Tonya

3 2

Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Yordy Licea Fonseca 29 Jan '09

29 Jan '09

Hi Carlo and Matt, Thank you very much for your help. Best wishes, Yordy On 29/01/2009, 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. Trouble with fitting with Artemis (Juraci A. Sampaio) > 2. Re: Trouble with fitting with Artemis (Richard Mayes) > 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca) > 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville) > 5. uncertainty in linear combination analysis (Pushan Shah) > 6. Artemis parameters (abhijeet gaur) > 7. Energy shift (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Jan 2009 15:34:55 -0300 > From: "Juraci A. Sampaio" <jasampaio(a)hotmail.com> > Subject: [Ifeffit] Trouble with fitting with Artemis > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <COL107-W60310E438349CE1C72988AACC80(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi there!I'm getting the following message when I try to fit my > data:WARNING. The following variables had no effect on the fit: !! >> > amp !! >> > enot !! >> > delr !! >> ss The data > that I am trying to fit is the Cu metal example that come with the iffefit > package. I am running Artemis on a Mac, OSX 10.4.11.I could run the fitting > on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but it > didn't work.I am wondering what could be wrong with my > machine/software?Thanks a lot.Juraci Sampaio > _________________________________________________________________ > Confira v?deos com not?cias do NY Times, gols direto do Lance, > videocassetadas e muito mais no MSN Video! > http://video.msn.com/?mkt=pt-br >

1 0

Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Yordy Licea Fonseca 29 Jan '09

29 Jan '09

Hi Carlo and Ma On 29/01/2009, 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. Trouble with fitting with Artemis (Juraci A. Sampaio) > 2. Re: Trouble with fitting with Artemis (Richard Mayes) > 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca) > 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville) > 5. uncertainty in linear combination analysis (Pushan Shah) > 6. Artemis parameters (abhijeet gaur) > 7. Energy shift (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Jan 2009 15:34:55 -0300 > From: "Juraci A. Sampaio" <jasampaio(a)hotmail.com> > Subject: [Ifeffit] Trouble with fitting with Artemis > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <COL107-W60310E438349CE1C72988AACC80(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi there!I'm getting the following message when I try to fit my > data:WARNING. The following variables had no effect on the fit: !! >> > amp !! >> > enot !! >> > delr !! >> ss The data > that I am trying to fit is the Cu metal example that come with the iffefit > package. I am running Artemis on a Mac, OSX 10.4.11.I could run the fitting > on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but it > didn't work.I am wondering what could be wrong with my > machine/software?Thanks a lot.Juraci Sampaio > _________________________________________________________________ > Confira v?deos com not?cias do NY Times, gols direto do Lance, > videocassetadas e muito mais no MSN Video! > http://video.msn.com/?mkt=pt-br >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 71, Issue 32
by Juraci A. Sampaio 29 Jan '09

29 Jan '09

Hi Rich,I found out what was wrong. The extend path parameters in the paths tab was on. When I set it as off the fitting worked just fine.Thanks a lot for your help.Juraci> From: ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 71, Issue 32> To: ifeffit(a)millenia.cars.aps.anl.gov> Date: Thu, 29 Jan 2009 07:00:40 -0600> > 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. Trouble with fitting with Artemis (Juraci A. Sampaio)> 2. Re: Trouble with fitting with Artemis (Richard Mayes)> 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca)> 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville)> 5. uncertainty in linear combination analysis (Pushan Shah)> 6. Artemis parameters (abhijeet gaur)> 7. Energy shift (Eugenio Otal)> > > ----------------------------------------------------------------------> > Message: 1> Date: Wed, 28 Jan 2009 15:34:55 -0300> From: "Juraci A. Sampaio" <jasampaio(a)hotmail.com>> Subject: [Ifeffit] Trouble with fitting with Artemis> To: <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID: <COL107-W60310E438349CE1C72988AACC80(a)phx.gbl>> Content-Type: text/plain; charset="iso-8859-1"> > > Hi there!I'm getting the following message when I try to fit my data:WARNING. The following variables had no effect on the fit: !! >> amp !! >> enot !! >> delr !! >> ss The data that I am trying to fit is the Cu metal example that come with the iffefit package. I am running Artemis on a Mac, OSX 10.4.11.I could run the fitting on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but it didn't work.I am wondering what could be wrong with my machine/software?Thanks a lot.Juraci Sampaio> _________________________________________________________________> Confira v?deos com not?cias do NY Times, gols direto do Lance, videocassetadas e muito mais no MSN Video!> http://video.msn.com/?mkt=pt-br> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/eb8… > > ------------------------------> > Message: 2> Date: Wed, 28 Jan 2009 14:29:58 -0500> From: Richard Mayes <rtmayes(a)gmail.com>> Subject: Re: [Ifeffit] Trouble with fitting with Artemis> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID:> <5a2a54820901281129n2b0d8fc4ib02a2ed2faeca8c5(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Juraci,> > Can you please attach a project file so we can look at it and try to find> the problem. My first guess would be the parameters are not defined in the> "guess,def,set" page like they are in the path list but without seeing the> project file, it's hard to be specific.> > -Rich> > On Wed, Jan 28, 2009 at 1:34 PM, Juraci A. Sampaio <jasampaio(a)hotmail.com>wrote:> >> Hi there!>>>> I'm getting the following message when I try to fit my data:>> WARNING. The following variables had no effect on the fit:>> !! >> amp>> !! >> enot>> !! >> delr>> !! >> ss>>>> The data that I am trying to fit is the Cu metal example that come with the>> iffefit package. I am running Artemis on a Mac, OSX 10.4.11.>> I could run the fitting on a mac OSX 10.5 and it worked fine. I reinstall>> the IXAFS package but it didn't work.>>>> I am wondering what could be wrong with my machine/software?>>>> Thanks a lot.>>>>>> Juraci Sampaio>>>>>> ------------------------------>> Not?cias direto do New York Times, gols do Lance, videocassetadas e muitos>> outros v?deos no MSN Videos! Confira j?! <http://video.msn.com/?mkt=pt-br>>>>> _______________________________________________>> Ifeffit mailing list>> Ifeffit(a)millenia.cars.aps.anl.gov>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>>>> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/7f5… > > ------------------------------> > Message: 3> Date: Wed, 28 Jan 2009 18:18:00 -0200> From: Yordy Licea Fonseca <yliceafonseca(a)gmail.com>> Subject: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <6bc7d27d0901281218t6eac4721o1922c155b95a1087(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi,> > Sorry, I could not find enough information.> Would any of you tell me, please, how is the EXAFS data tabulated in Farrel> Lytle data base?> The first column is the energy, what about others?> I would like to obtain the absorption coefficient vs energy from this> file:> > http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095> > Best wishes,> > -- > Yordy E. Licea Fonseca> Departamento de F?sico-Qu?mica> Instituto de Qu?mica-IQ/UFRJ> Laborat?rio de Cat?lise Heterog?nea> Rio de Janeiro, RJ, CEP 21.949-909> Brasil> Email: yliceafonseca(a)gmail.com> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/cea… > > ------------------------------> > Message: 4> Date: Wed, 28 Jan 2009 14:24:22 -0600> From: Matt Newville <newville(a)cars.uchicago.edu>> Subject: Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID:> <b8522e3d0901281224v42f22a8cs6489a5792c4588f0(a)mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1> > Hi Yordy,> > The first column for that file is not energy, it is angular steps. See> http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379…> > and the other posts from earlier today for how to convert this data into mu(E).> > --Matt> > On Wed, Jan 28, 2009 at 2:18 PM, Yordy Licea Fonseca> <yliceafonseca(a)gmail.com> wrote:>> Hi,>>>> Sorry, I could not find enough information.>> Would any of you tell me, please, how is the EXAFS data tabulated in Farrel>> Lytle data base?>> The first column is the energy, what about others?>> I would like to obtain the absorption coefficient vs energy from this>> file:>>>> http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095>>>> Best wishes,>>>> -->> Yordy E. Licea Fonseca>> Departamento de F?sico-Qu?mica>> Instituto de Qu?mica-IQ/UFRJ>> Laborat?rio de Cat?lise Heterog?nea>> Rio de Janeiro, RJ, CEP 21.949-909>> Brasil>> Email: yliceafonseca(a)gmail.com>>>> _______________________________________________>> Ifeffit mailing list>> Ifeffit(a)millenia.cars.aps.anl.gov>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>>>> > > > ------------------------------> > Message: 5> Date: Thu, 29 Jan 2009 13:33:08 +1100> From: "Pushan Shah" <pshah(a)gse.mq.edu.au>> Subject: [Ifeffit] uncertainty in linear combination analysis> To: <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID: <4981B014.0BBD.0060.0(a)gse.mq.edu.au>> Content-Type: text/plain; charset=US-ASCII> > Hello Everyone!> > How can I estimate an uncertainty in linear combination analysis and calculate them in percentage error?> > Many thanks,> Pushan> > > > > > > ------------------------------> > Message: 6> Date: Thu, 29 Jan 2009 15:41:55 +0530> From: abhijeet gaur <abhijeetgaur9(a)gmail.com>> Subject: [Ifeffit] Artemis parameters> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <862a39070901290211s6a928d40yc902a09ff532f2a9(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi> I am fitting a copper foil whose data is taken at room temperature. So> do I need to change the guess value of parameters enot, ss,amp, delr to some> other value or I should take them as the default guess value. Also what> should be the ideal fitting range in R for the copper foil.> > > With thanks> > Abhijeet> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/bd2… > > ------------------------------> > Message: 7> Date: Thu, 29 Jan 2009 11:00:32 -0200> From: Eugenio Otal <eugenioh(a)gmail.com>> Subject: [Ifeffit] Energy shift> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <da22ad30901290500s14de8d2dy4cbaf8ec693e6796(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi Matt,> Thanks for your time, the shift is between calculated and experiment. I> attach two figures with and without correction, it matchs really good if I> change 5.5eV the energy.> Thanks, euG> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > -------------- next part --------------> A non-text attachment was scrubbed...> Name: without energy shift.jpg> Type: image/jpeg> Size: 58982 bytes> Desc: not available> Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > -------------- next part --------------> A non-text attachment was scrubbed...> Name: energy shift.jpg> Type: image/jpeg> Size: 69194 bytes> Desc: not available> Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > > ------------------------------> > _______________________________________________> Ifeffit mailing list> Ifeffit(a)millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > End of Ifeffit Digest, Vol 71, Issue 32> *************************************** _________________________________________________________________ Cansado de espaço para só 50 fotos? Conheça o Spaces, o site de relacionamentos com até 6,000 fotos! http://www.amigosdomessenger.com.br

1 0

Energy shift
by Eugenio Otal 29 Jan '09

29 Jan '09

Hi Matt, Thanks for your time, the shift is between calculated and experiment. I attach two figures with and without correction, it matchs really good if I change 5.5eV the energy. Thanks, euG

2 1

Artemis parameters
by abhijeet gaur 29 Jan '09

29 Jan '09

Hi I am fitting a copper foil whose data is taken at room temperature. So do I need to change the guess value of parameters enot, ss,amp, delr to some other value or I should take them as the default guess value. Also what should be the ideal fitting range in R for the copper foil. With thanks Abhijeet

2 1

uncertainty in linear combination analysis
by Pushan Shah 29 Jan '09

29 Jan '09

Hello Everyone! How can I estimate an uncertainty in linear combination analysis and calculate them in percentage error? Many thanks, Pushan

1 0

about Farrel Lytle data of Na2WO4.2H2O
by Yordy Licea Fonseca 28 Jan '09

28 Jan '09

Hi, Sorry, I could not find enough information. Would any of you tell me, please, how is the EXAFS data tabulated in Farrel Lytle data base? The first column is the energy, what about others? I would like to obtain the absorption coefficient vs energy from this file: http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095 Best wishes, -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

2 1

Trouble with fitting with Artemis
by Juraci A. Sampaio 28 Jan '09

28 Jan '09

Hi there!I'm getting the following message when I try to fit my data:WARNING. The following variables had no effect on the fit: !! >> amp !! >> enot !! >> delr !! >> ss The data that I am trying to fit is the Cu metal example that come with the iffefit package. I am running Artemis on a Mac, OSX 10.4.11.I could run the fitting on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but it didn't work.I am wondering what could be wrong with my machine/software?Thanks a lot.Juraci Sampaio _________________________________________________________________ Confira vídeos com notícias do NY Times, gols direto do Lance, videocassetadas e muito mais no MSN Video! http://video.msn.com/?mkt=pt-br

2 1

EXAFS data
by abhijeet gaur 28 Jan '09

28 Jan '09

Hi We have Farell Lytle type data. When we put that into ATHENA we get the Energy curve. But we are not able to extract that Energy converted data from ATHENA . We tried to import the data in ORIGIN but we could not do so though the graph was imported.So if there is any way to extract the data please let us know. Thanks Abhijeet

4 3

Energy shift
by Eugenio Otal 27 Jan '09

27 Jan '09

Hi all, I finished simulations of Er(OH)3, ErO(OH) and Er2O3, when I compared the spectras with the samples and I found a shift in energy equal to 5.5 eV.Even between the meassured and calculated spectra of Er2O3, which was previously calibrated with a niquel film standard. Is this shift part of the bussines? Thanks, euG

2 1

Re: [Ifeffit] Cumulant expansion fittings
by Patrick Kluth 27 Jan '09

27 Jan '09

Hi Matt, >Of course, XAFS *is* a one-dimensional probe, not a three-dimensional one. >At least ignoring for the moment the angular dependence of multiple >scattering, XAFS is sensitive to g(r) only. Sadly, this is sometimes >forgotten in the literature, and one sees attempts to distinguish >"sigma^2_perpendicular" and "sigma^2_parallel", which is a good sign of a >paper that is complete nonsense. I don`t agree with you in this point. To my understanding, because EXAFS is a one-dimensional probe and it measures the average over instantaneous inter-atomic distances, it is only sensitive to the motion relative to each other along the bond-direction - and thus measures sigma^2_parallel. Combined with XRD which measures the the atomic motion averaged over all directions one can then extract a "sigma^2_perpendicular". If we are talking about the same literature this point is well elaborated in there and I don`t think it is nonsense. Please correct me if I am wrong. Cheers, Patrick --------------------------------------------------------------------- Dr. Patrick Kluth Fellow, ARC Australian Research Fellow Department of Electronic Materials Engineering Research School of Physics and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: patrick.kluth(a)anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------

6 7

small-screen version of Athena document
by Bruce Ravel 26 Jan '09

26 Jan '09

Hi, There is now a version of the Athena User's Guide which is intended for small-screen device (like my the new toy I got this weekend). Here is the URL: http://cars9.uchicago.edu/~ravel/software/doc/Athena/mobile/ This is very similar to the normal html version of the User's Guide, except for a few changes in layout to make it work better on a small screen. The mobile version is not perfect yet, but it is much more legible than the normal version. I have tested it mostly in Explorer on Windows Mobile 6. (I have also tested it under Opera for mobile devices, but I am not happy with how either version gets displayed there.) Hopefully this will be helpful for someone. 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/

4 4

Query regarding measurement uncertainity
by Bindu R. 26 Jan '09

26 Jan '09

Dear all, I have one doubt regarding the measurement uncertainty in R- space (εR). In the manual it is written that εR is evaluated from the rms value of FT in the range 15-20 Å. My doubt is..... In case the FT in R-space does not extend up to the range mentioned above, then how does the fitting program choose the value of εR? Please clarify me this. With best regardsBIndu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

3 2

FEFF calculations for Zeolite
by Feng Wang 23 Jan '09

23 Jan '09

Hi all, My colleague is trying to load Pt into the cages of the zeolite_LTA. It seems the crystallinity was destroyed with small Pt loading (<3%weight)according to the X-ray and e-beam diffraction. I suppose this is not sth new, but it looks intereting to understand the local structural structure with Pt loading, maybe by x-ray absorption or energy loss near-edge structure. Do you know how I should get the FEFF input file for this complex? Also please let me know if you have any relevant reports or your own results for exchange, I will appreciate that, thank you. Sincerely, Feng ==================================== National Institute for Nanotechnology 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

2 1

Cumulant expansion fittings
by umesh palikundwar 22 Jan '09

22 Jan '09

Dear all, Cumulant expansion fittings are generally used, if there are more than one close shells of similar nearest neighbors (if I have understood it correctly). Third and fourth cumulants are used in the fittings to account for non-Gaussian distribution of the neighbors. I would like to known, can one use only fourth cumulant (i.e. without using the third cumulant) in the fittings? I will be highly grateful to get the answer to my query. Umesh _________________________________________________________________ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx

5 10

SCF cards in EXAFS and SO2 of CO, Mn and Cu
by JeongEunSuk 18 Jan '09

18 Jan '09

Hello everyone I am using FEFF8.0 for the analysis of EXAFS. In FEFF, SCF card is for the calculation of self-consistent potential. I usually omitted SCF card for EXAFS. Is it right? Because the potential affects phase shift, I think that SCF card is also used in the analysis of EXAFS. which is correct, using SCF card or not in EXAFS? and I have another requirement. Could I know SO2 of Co, Mn and Cu? If anyone know those, would you show me? _________________________________________________________________ 메신저에서 클럽 이동도 한번에, 클럽을 운영하기 위한 것도 모두 제공! http://groups.live.com/

2 1

book chapter
by Hashem Stietiya 16 Jan '09

16 Jan '09

Dr. Kelly, I would be thrilled if you could send me a copy. Thank you, Hashem Stietiya Louisiana State University -----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: Thursday, January 15, 2009 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 71, Issue 16 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: distinguishing between actual shells and artifacts (Kelly, Shelly) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Jan 2009 13:58:21 -0700 From: "Kelly, Shelly" <Shelly.Kelly(a)uop.com> Subject: Re: [Ifeffit] distinguishing between actual shells and artifacts To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <5A8CCCCD35FC0946BE602D2F43C0218A7DF9FF(a)AZ18EV808.global.ds.honeywell.com> Content-Type: text/plain; charset="iso-8859-1" Hi Hashem, I show one method for doing this in my book chapter Figure 14-23 on page 431. (I feel a bit like a broken record). I will send you a copy if you want. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Voegelin Andreas > Sent: Wednesday, January 14, 2009 9:57 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] distinguishing between actual shells and artifacts > > Hi Hashem > > You can copy-paste the respective EXAFS data in Athena and compare the > backtransforms over the first shell, the first+second shell, the second > shell. > > By comparison of the backtransforms with each other and with the measured > EXAFS, you can see where the second-shell contribution has its origin in > k-space (note that the backtransform is not corrected for the window > function). > > For instance, if the second-shell signal adds to the spectrum in the low-k > range (where noise should not be a problem), it is likely real and might > result, e.g., from multiple scattering among first-shell O atoms. If the > second-shell signal in the backtransform mainly contributes in the high-k > range (where noise or glitches may be a problem), you may be able to see > whether it falls together with obvious artefacts (such as glitches), or > whether the backtransform matches spectral features that you consider to > be real. > > Andreas > > ----------------------------------------------- > Andreas Voegelin, PhD > Soil Chemistry Group > Inst. of Biogeochemistry and Pollutant Dynamics > Dept. of Environmental Sciences > ETH Zurich > Universit?tstrasse 16, CHN F24 > CH-8092 Z?rich, Switzerland > Phone: +41 44 633 61 47 > Fax: +41 44 633 11 18 > E-Mail: voegelin(a)env.ethz.ch > www: http://www.ibp.ethz.ch/people/andreavo > > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > > Of mstiet2(a)lsu.edu > > Sent: Mittwoch, 14. Januar 2009 14:12 > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: [Ifeffit] distinguishing between actual shells and artifacts > > > > Dear all, > > > > I am currently fitting first and second shells with Zn-O and > > Zn-Zn paths,respectively. I get second shell features that > > could be fit quite well, but I am not certain if they are > > actually second shell features or possibly artifacts. For > > some samples I get second shell features that I know should > > not be present. What criteria would you use to distinguish > > between artifacts and actual shells? > > > > Your assistance is appreciated. > > > > Hashem Stietiya > > > > Louisiana State University > > > > > > > > _______________________________________________ > 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 71, Issue 16 ***************************************

7 8

difference between Zn-Zn/Fe and Zn-Fe paths
by Hashem Stietiya 16 Jan '09

16 Jan '09

Dear All, Is there a difference between fitting a second shell with two separate paths (Zn-Zn path and a Zn-Fe path) each with its own parameters and fitting that second shell with a combination of two paths (Zn-Zn/Fe)? When would I choose to do that latter, and how? I hope I made myself clear! Thanks, Hashem Stietiya Louisiana State University

2 1

SCF and FMS radius
by Eugenio Otal 15 Jan '09

15 Jan '09

Hello, I am simulating the XANES spectra of a erbium atom in an interstitial site of ZnO. I needed a SCF radius of 9.75 (316 atoms) and FMS radius of 11.90 (599 atoms) to obtain no change in the simulated spectra (differences of 0.01% or less) Now I am trying to simulate Er(OH)3 and it is using SCF 10.90 (622 atoms) and I still haven found convergence, I will need more even larger radius for FMS. Does the XAS phenomena have this distances? Has this distances physical meaning? Thanks, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 2

distinguishing between actual shells and artifacts
by mstiet2＠lsu.edu 14 Jan '09

14 Jan '09

Dear all, I am currently fitting first and second shells with Zn-O and Zn-Zn paths,respectively. I get second shell features that could be fit quite well, but I am not certain if they are actually second shell features or possibly artifacts. For some samples I get second shell features that I know should not be present. What criteria would you use to distinguish between artifacts and actual shells? Your assistance is appreciated. Hashem Stietiya Louisiana State University

4 3

How to keep enot,delr, and ss within acceptable limits
by Hashem Stietiya 14 Jan '09

14 Jan '09

Dear All, I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr? I appreciate your assistance and guidance. Regards, Hashem Stietiya School of plant, Environmental and Soil Sciences Louisiana State University

5 7

Trouble with fitting with Arthemis
by Kleper Oliveira Rocha 14 Jan '09

14 Jan '09

Hi all, Please, help me. When I try to do any fit in Arthemis, setting all parameters unless one, been this one any of the parameters, the fit gives for the answer -1.0000 +/- 0.000000 like example down. What is happening? ============================================================ Independent points = 8.239257812 Number of variables = 1.000000000 Chi-square = 0.120000000E+37 Reduced Chi-square = 0.165762849E+36 R-factor = NaN Measurement uncertainty (k) = 0.000437667 Measurement uncertainty (R) = 0.000724906 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): * amp = -1.0000000 +/- 0.0000000 (1.0000)* Set parameters: enot = 0 delr = 0 ss = 0.003 c3 = 0.0001 c4 = 0.00001 -- Kleper de Oliveira Rocha Chemical Engenieer Doctorated Tels. 55 016 3351-8694

4 11

Re: [Ifeffit] SCF and FMS radius
by joshua jason kas 14 Jan '09

14 Jan '09

Hi Eugenio, I would call all of the spectra that you sent converged. It is true that they are not the same to all digits of output, but you really don't need things to be that accurate. Theoretical and experimental errors are much larger, especially in the near edge. When converging w.r.t. the SCF and FMS radius, you really only need to be sure that changes in the spectrum due to finite cluster size are small compared to the differences between theory and experiment. You can probably get by with a much smaller cluster even. Cheers, Josh Kas On Mon, 12 Jan 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. SCF and FMS radius (Bruce Ravel, Feng Wang & Josh Kas) > (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Jan 2009 23:40:07 -0200 > From: "Eugenio Otal" <eugenioh(a)gmail.com> > Subject: [Ifeffit] SCF and FMS radius (Bruce Ravel, Feng Wang & Josh > Kas) > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <da22ad30901121740x764c0babjf20f055285a4d9b2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, Feng and Josh, > I am simulating erbium hydroxide from its crystal structure information, > what does really mean well ordered? > Of course I can?t answer you that, I hope someday would know the answer, and > for the dummies question... I see the changes only close to the edge. > I?ll read the paper deeply , and what I see in the abstract, the SCF and FMS > should converge faster. > I attach 3 packages with 3 results and its .inp files, I hope you can help > me. > Thanks in advance, euG >

1 0

looking for Zn(OH)2 EXAFS spectrum
by Samuel Legros 13 Jan '09

13 Jan '09

Hi everybody, I am loking for the Zn(OH)2 EXAFS spectrum. If someone have it, i would be very grateful if he (or she) would like to send it to me. Thank you in advance -- Samuel LEGROS Doctorant CIRAD basé au CEREGE Directeur : Emmanuel DOELSCH Europole de l'arbois BP 80 13545 Aix-en -provence FRANCE Tel : 04 42 97 17 76 Fax : 04 42 97 15 59

1 0

SCF and FMS radius (Bruce Ravel, Feng Wang & Josh Kas)
by Eugenio Otal 13 Jan '09

13 Jan '09

Hi Bruce, Feng and Josh, I am simulating erbium hydroxide from its crystal structure information, what does really mean well ordered? Of course I can´t answer you that, I hope someday would know the answer, and for the dummies question... I see the changes only close to the edge. I´ll read the paper deeply , and what I see in the abstract, the SCF and FMS should converge faster. I attach 3 packages with 3 results and its .inp files, I hope you can help me. Thanks in advance, euG

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 71, Issue 8
by joshua jason kas 12 Jan '09

12 Jan '09

Hi Eugenio, I am not familiar whith the system, but it seems a bit strange to me. What edge are you running? Can you send some of your calculations and a feff input file? I've seen cases where the FMS is still not converged at 1000 atoms, but the SCF radius usually converges much faster. Cheers, Josh Kas > > Hello, > I am simulating the XANES spectra of a erbium atom in an interstitial site > of ZnO. I needed a SCF radius of 9.75 (316 atoms) and FMS radius of 11.90 > (599 atoms) to obtain no change in the simulated spectra (differences of > 0.01% or less) > Now I am trying to simulate Er(OH)3 and it is using SCF 10.90 (622 atoms) > and I still haven found convergence, I will need more even larger radius for > FMS. > Does the XAS phenomena have this distances? Has this distances physical > meaning? > Thanks, euG > > > > > > > > > 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - > > Lic. Eugenio H. Otal > E-mail: eotal(a)citefa.gov.ar > eugenioh(a)gmail.com > > 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - >

1 0

Re: [Ifeffit] SCF and FMS radius
by Feng Wang 12 Jan '09

12 Jan '09

Bruce and Eugenio, It is generally believed that the cluster size (or called spatial resolution) is mainly limited by MFP, to around 1 nm (in the near-edge region), but further spatial limitation may come from elastic scattering (i.e. through phase cancellation). This is what we tried to understand through FEFF calculations in one paper. I put the abstract here in case you want to check: We have investigated the factors that determine the degree of localization of the information obtainable from electron energy loss or x-ray absorption fine structure. Inelastic scattering of the excited core electron limits the volume of specimen contributing to the backscattered intensity to a diameter in the range of 12 nm, dependent on the excited-electron energy and the composition and crystal structure of the sample. Phase cancellation between the backscattered waves further reduces the effective diameter that determines the observed fine structure to below 1 nm. Since the spatial resolution attainable by transmission electron microscopy can approach 0.2 nm or can even be below 0.1 nm (with aberration correction), we predict that delocalization arising from the excited-electron range may limit the resolution of images based on changes in core-loss fine structure. (J. Appl. Phys. 104, 034906 (2008)). Feng > On Sunday 11 January 2009 12:23:26 pm Eugenio Otal wrote: > > I am simulating the XANES spectra of a erbium atom in an interstitial site > > of ZnO. I needed a SCF radius of 9.75 (316 atoms) and FMS radius of 11.90 > > (599 atoms) to obtain no change in the simulated spectra (differences of > > 0.01% or less) > > Now I am trying to simulate Er(OH)3 and it is using SCF 10.90 (622 atoms) > > and I still haven found convergence, I will need more even larger radius > > for FMS. > > Does the XAS phenomena have this distances? Has this distances physical > > meaning? > > Eugenio, > > The mean free path is quite long just above the Fermi energy. It is > conceivable that, in a well ordered material, the cluster size required for > convergence can be quite large. I believe that a very large cluster -- > something like 13 A -- is needed for pure silicon. Of course, I doubt that > erbium hydroxide is that well-ordered! > > So, are you are seeing physics associated with the mean free path or a problem > in Feff's construction of the potentials? I'm afraid I don't know how to > answer that, but hopefully John or one of his gang will weigh in. Do you see > the changes larger than your threshold over the entire data range or only > very close to the edge? > > Good luck, > 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/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ==================================== National Institute for Nanotechnology 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

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How to get the accurate fittting results from the fit in Artemis
by abhijeet gaur 12 Jan '09

12 Jan '09

Hi Actually I trying to learn the fitting procedure in Artemis but I am not getting the actual bond length in the fit results of artemis . So I want to know that that how to get actual parameter from Artemis.And how to exploit the result of Artemis.

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Query regarding error bars
by Bindu R. 09 Jan '09

09 Jan '09

Hi all, Could any tell me in a simple language about the error bars returned by the EXAFS fitting program? what do they exactly represent?How is it determined?How is the number of iterations decided.In addition to R-factor what are the other parameters which determines a good fit.For a R-factor ~0.001, if the value of chi2~10,000 and reduced chi2 ~ 500, can one consider the fit to be good even if one gets a good match to the experimental spectra. Bindu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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Re: [Ifeffit] posting to the ifeffit mailing list
by JeongEunSuk 07 Jan '09

07 Jan '09

Hello Bruce Ravel I have another questions. I got the charge transfer of TiO2 from FEFF8 as following;Ti: (not absorber) Charge transfer : 0.556 Electron counts for each orbital momentum: 0 0.408 1 6.678 2 2.350 3 0.000O: Charge transfer : -0.280 Electron counts for each orbital momentum: 0 1.843 1 4.354 2 0.087 3 0.000It is known that the electron number of Ti atom ( the atomic number 22) is 1s^2 2s^2 2p^6 3s^2 3p^6 4s^2 3d^2. In the results of FEFF, 0 is s orbital, 1 is p orbital so on.. right? as you know, there is each s-orbital or p-orbital in principal quantum number.which orbital momentum of principle quantum number does 0, 1, 2 and 3 mean? second I cant understand electron counts. I thought that Charge transfer was calculated by electron counts for each orbital momentum, comparing the electron counts of free atom.So I tried to calculate like this: In free oxygen atom case, 2^s has 2 electron, 2^p! has 4 electron. The electron counts calculated by FEFF8 is 1.843 + 4.354 + 0.087 =6.284So charge transfer is 6 - 6.284 = 0.284 The charge thransfer, 0.284, obtained from my calculation is different from the value of FEFF8. How can I get charge transfer form electron counts? > From: bravel(a)bnl.gov> To: eunsuk1986(a)hotmail.com> Subject: posting to the ifeffit mailing list> Date: Mon, 5 Jan 2009 17:10:31 -0500> > > Hi Jeong,> > I think I know what went wrong with your post to the mailing list from last > Friday. I think that you (for some reason) sent the mail to> ifeffit-bounces(a)millenia.cars.aps.anl.gov> rather than to> ifeffit(a)millenia.cars.aps.anl.gov> > The second address is the normal point of entry to the mailing list. The > other address is part of the mailing list administration. I am not sure how > you ended up sending email there. Weird. If you make sure to send your mail > to the second address, it should get posted without any problems.> > If you do have any problems posting to the mailing list, I will probably be > notified automatically. But if you attempt to send mail to the mailing list > and have any problems, please let me know as soon as possible so I can try to > correct the problem.> > 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/ _________________________________________________________________ 블로그에 윈도우 라이브 메신저(베타)를 홍보하면 선물을 드립니다! http://windowslive.msn.co.kr/wlm/customer/view.asp?sectionDiv=2&seq=272

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charge transfer
by Bruce Ravel 05 Jan '09

05 Jan '09

Hi all, The following message from Jeong Eun Suk was not delivered correctly to the mailing list. Fortunately, I noticed the problem and am forwarding it along now. B Original message: what does charge transfer mean in FEFF? I cant understand what the number of charge transfer like 0.058, -0.073 means. The number indicate the number of electron in atom? If anybody knows it, please answer Charge transfer: iph charge(iph) 0 0.058 1 -0.073 2 0.072 -- 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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Problem running Feff through Artemis on Mac OS
by Aaron Slowey 02 Jan '09

02 Jan '09

Hello, I have Artemis running on intel Mac OS 10.4 and am unable to get FEFF to run by using Artemis. I have changed the preferences in the 'atoms' submenu to have feff_version as 7 and template as feff7 and then I have, under the 'feff' submenu, the path to my feff executable, specifically "/Users/aslowey/feff/feff7.exe" I tried removing the .exe -- no go. Then I reverted back to Artemis' default settings (feff version 6) and it still didn't work. I relocated both the feff.inp and feff executable in the same folder, but this also failed. In all cases, the Artemis palettes window opens to the Messages tab with red text that Artemis configured incorrectly...incorrect value of feff->feff_executable. Is there something about Mac OS that FEFF can't work? - Aaron Slowey

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subscription
by 穆鑫 30 Dec '08

30 Dec '08

Hello: I want to subscribe the Ifeffit . Thanks! Happy New year!

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How to identify N and O atoms in the first coordinate
by mzhu＠udel.edu 22 Dec '08

22 Dec '08

Hello all, Merry Christmas! I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. 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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Re: [Ifeffit] How to identify N and O atoms in the first coordinate
by Frenkel, Anatoly 20 Dec '08

20 Dec '08

The fact that PCA tells between known Ni-N and Ni-O complexes by adding one more component when the wrong complex is added (N to O or vice versa) does not mean that there is specific fingerprinting sensitivity to N or O. One needs to demonstrate first that all Ni-N pairs have similar distances and disorder, regardless of their chemical surrounding, and that the same is true for Ni-O. Only in that case your PCA results indeed mean that the Ni sorbed biofilm have both types of bonds. Otherwise you cannot prove that it is Ni-N plus Ni-O vs. a situation where there are two unique types of Ni-O that have not been matched to your Ni-O standard and may thus fool you in thinking that one of them is due to Ni-N instead. Thus, before you conclude that, you should verify whether various Ni-N and Ni-O complexes have same pair properties. From your description it appears not to be the case since you have two components (not one) for your oxygen ligands and nitrogen ligands. Anatoly ----- 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: Fri Dec 19 18:39:24 2008 Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate Hello Anatoly, Thanks for your reply. I could not do it as the literature you mentioned since I do not have detailed structural information as they do. I am wondering if the following method can be justified to indentify nitrogen atoms: 1) EXAFS data of 7 nickel oxygen-coordinated organic and inorganic complexes in which nickel only coordinates to oxygen atoms from carboxyl group, phosphoryl group and water molecules. 2) Fourier back transformation of the peak from 1-2 aus. in R+ delta-R space. This R range must cover the scattering peaks from both nitrogen and oxygen. Then chi functions of these complexes are obtained. 3) A principal component anlaysis (PCA) was performed over the oxygen-coordinated dataset of the chi functions obtained in the step (2). PCA analysis indicated two major components based on the IND values. 4)Then chi functions of two nitrogen-coordinated nickel complexes was obtained using the same method as step 2). It is certain that nitrogen atoms are coordinated to the nickel in the first shell in addition to oxygen atoms. 5) A target transformaiton of the chi function of two nitrogen-coordinated nickel complexes using oxygen-coordianted dataset resulted in the SPOIL values close to 5. Addition of one of the two complexes to the group of nickel complexes in PCA, PCA resulted in 3 components. These indicate that they have different coordination environment to the oxygen-coordinated nickel complexes. It is expected because they have nitrogen in the first shell. 6) A target transformation conducted on a sample of nickel-sorbed biofilm (back fourier transformed chi function in 1-2 aus.) resulted in the value close to 5. It means that the sample can not be represented by the nickel organic group, either. Since the first shell only can have two types of atoms, oxgen and nitrogen. If the nickel sorbed on biofilm can not be represented by the nickel oxygen-coordinated organic group which only has oxygen in the frist shell, it must have nitrogen atoms in the first shell. Also, linear square fitting of the Ni_biofilm with the nitrogen-coordinated complexes resulted in the better goodness than other oxygen-coordinated complexes. Thus, the nitrogen must exist in the first shell of Ni_biofilm sample. Do you think this method is reasonable? 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 ---- Original message ---- >Date: Fri, 19 Dec 2008 16:34:36 -0500 >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" <frenkel(a)bnl.gov>) >Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov>, <ifeffit(a)millenia.cars.aps.anl.gov> > >Dear Mengqiang, > >To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an "inverse" problem ("Which type of neighbors do I have") you cannot do it. However, if you believe you have some knowledge about the type of metal-oxygen bonding: either M=O or a M-O or a M-OH or a M-OH2 (the first one is the shortest and the strongest, the others may have similar interatomic distances but different bond strengths), you can advance somewhat. > >If you have a certain number of distinct models you want to compare the data against, it can be done via a linear combination fitting, or by direct algebraic extraction of any given type of the pair contribution from the data, as described, for example here: > >E. Poverenov, I. Efremenko, A. I. Frenkel, Y. Ben-David, L. J. W. Shimon, G. Leitus, J. M. L. Marin, D. Milstein. A terminal Pt(IV)-oxo complex bearing no stabilizing electron withdrawing ligands and exhibiting diverse reactivity. Nature 255, 1093-1096, 2008. > >See supplementary info to that article for specific details. >Regards, >Anatoly > > >________________________________ > >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of mzhu(a)udel.edu >Sent: Fri 12/19/2008 4:20 PM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] How to identify N and O atoms in the first coordinate > > > >Hello all, > Merry Christmas! > I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. > >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 >_______________________________________________ >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] Problems with feff and crystallographic data (Now with bug report)
by Gregory Merchan 19 Dec '08

19 Dec '08

Hi Hashem, Atoms doesn't handle the occupancy data in the CIF file. See this page for more info: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head-b273ecfd19542ec82… I assume you see a message like this one that I see: This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). If you look on the Atoms tab in Artemis when you open the CIF file, you should see that the co-ordinates for Mg and Al are all 0.00000 ; i.e., all Atoms sees is that they are in the same place. Bruce, here's two bug reports: 1. The warning message above is missing the word "less", as in "separated by _less_ than 0.93 Angstroms" 2. It's an extensive message but doesn't mention this kind of problem. If you want to drive yourself mad with interface stuff, you could catch and highlight these errors on input and disable the controls they affect until the input is corrected. A tricky part of that is making sure the user knows what the highlighting means and has a clue about how to fix the error without - say - throwing up a talking paperclip. A sort of "heavy tooltip" ("lead balloon"?) could be shown - placed so as not to obscure the relevant controls - with a brief message, a way to get to the more help, and dismissal button. An automatic fade out might be nice, not sure. So long as the bad input exists, there should be a way to get the message back, like mousing over the highlighted input or the disabled controls. I don't know of any cross-platform toolkit that makes that kind of thing easy. Cheers, Greg On Thu, Dec 18, 2008 at 10:04 PM, Hashem Stietiya <mstiet2(a)lsu.edu> wrote: > Hello! > > > > I was using Artemis to run feff and generate paths from hydrotalcite. > However, it failed to run and an error message indicated that there is > something wrong with the crystallographic data. I used the crystallographic > data of hydrotalcite from different sources, but encountered the same > problem. Can you please help identify the problem and run feff? > > > > Please find attached the crystallographic data for hydrotalcite. > > > > I appreciate your help. > > > > Regards, > > Hashem Stietiya > > Louisiana State University > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Error bars reported in the curve-fitting analysis in Artemis
by Hiroshi Oji 19 Dec '08

19 Dec '08

Dear all, Could someone tell me how the uncertainities in the fitted variables are estimated in the curve-fitting analysis in Artemis? Thank you very much in advance for your help. Hiroshi Oji -- ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

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Problems with feff and crystallographic data
by Hashem Stietiya 19 Dec '08

19 Dec '08

Hello! I was using Artemis to run feff and generate paths from hydrotalcite. However, it failed to run and an error message indicated that there is something wrong with the crystallographic data. I used the crystallographic data of hydrotalcite from different sources, but encountered the same problem. Can you please help identify the problem and run feff? Please find attached the crystallographic data for hydrotalcite. I appreciate your help. Regards, Hashem Stietiya Louisiana State University

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New windows update
by Matt Newville 17 Dec '08

17 Dec '08

Hi Folks, Bruce and I put together a new Windows updater, and it is now posted and available for download. This should fix several small problems with athena and artemis. It should also fix problems that several people have noticed with the previous update. After the update, the versions should be Athena 0.8.058 Artemis 0.8.013 Ifeffit 1.2.11c If you have any trouble with this update not working to install and run the latest versions, please let us know. --Matt

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fitting ReO2
by Edward L. Kunkes 16 Dec '08

16 Dec '08

Hi everyone, I am trying to do a first shell fit of ReO2 – where there are 2 different Re-O distances in the first coordination shell. Does anyone have an .atoms file or structural information for this material that they would be willing to share ? Thank you very much for your help. -Edward Kunkes Research Assistant Department of Chemical Engineering University of Wisconsin-Madison

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how can i call the function of Athena or Artemis in Python
by goodhei8＠gmail.com 05 Dec '08

05 Dec '08

Such as I want to call calibrate or merge function of Athena in python. Can python glue them together? any document? Jack Song

3 6

How to generate ATOMS file
by milena filadelpho coutinho 04 Dec '08

04 Dec '08

Dear all, I have a simple question.I would like to generate input file (ATOMS) to IFEFFIT. What I have to do? I am still begining my application in EXAFS. thanks Milena. _________________________________________________________________ Confira vídeos com notícias do NY Times, gols direto do Lance, videocassetadas e muito mais no MSN Video! http://video.msn.com/?mkt=pt-br

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remove text
by Guvenc Akgul (gakgul) 02 Dec '08

02 Dec '08

dear all, i have a simple question.I would like to remove texts on graphics window at athena.what can i do this?? thanks guvenc

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Re: [Ifeffit] about wolframite crystallographic file (Ravel, Bruce)
by Yordy Licea Fonseca 26 Nov '08

26 Nov '08

Hi all, In my case, Artemis version 0.8.012 (c), the error in Echo is just: "Artemis trapped one or more errors! Error message dumped to screen." Thank you very much, the problem is solved the way Dominik and Carl have suggested. Best regards, Yordy 2008/11/17 <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: about wolframite crystallographic file (Ravel, Bruce) > 2. Re: about wolframite crystallographic file (Dominik Samuelis) > 3. Re: about wolframite crystallographic file (Ponader, Carl W Dr) > 4. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Mauro Rovezzi) > 5. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 09:16:25 -0500 > From: "Ravel, Bruce" <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] about wolframite crystallographic file > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <8FA2653072F45348BC6E32FEB95CDC62D3D1(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > > Yordy, > > I'll look into this when I get a chance, but that might not be until later > in the week (I am on travel at the moment). > > 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 Yordy Licea > Fonseca > Sent: Sat 11/15/2008 6:36 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] about wolframite crystallographic file > > Hi all, > > As soon as I load this attached CIF crystallographic file from ISCD in > Artemis0.8.012 the software says: > "Artemis trapped one or more errors! Error message dumped to screen." > I can`t go on runnig Atoms as it seems to be a problem with the file. I > have > read the suggestion made in FAQ, but I can not manage to find the error. > Could you help me, please? > It would be nice once the problem been fixed to add this structure to > Matt's > atoms.inp database. > > Thanks you very much, Yordy > > -- > Yordy E. Licea Fonseca > Departamento de F?sico-Qu?mica > Instituto de Qu?mica-IQ/UFRJ > Laborat?rio de Cat?lise Heterog?nea > Rio de Janeiro, RJ, CEP 21.949-909 > Brasil > Email: yliceafonseca(a)gmail.com > >

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Re: [Ifeffit] Hexagonal WO3 (Carlo Segre)
by Yordy Licea Fonseca 26 Nov '08

26 Nov '08

Hi Carlo and Ying, Does it means that if the sample is a random solid solution at experimental temperature, in principle, you would be able to simulate the EXAFS spectra whichever be the Mo/W ratio in the second shell coordination in the Feff.inp, am I right? Thanks, Yordy 2008/11/18 <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: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on > Ubuntu from source (Matt Newville) > 2. Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 3. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Carlo Segre) > 4. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading > to ifeffit-1.2.11b on Ubuntu from source) (Matt Newville) > 5. Hexagonal WO3 (Ying Zhou, Anorganisch-Chemisches Inst.) > 6. Re: Hexagonal WO3 (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Nov 2008 12:30:20 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to > ifeffit-1.2.11b on Ubuntu from source > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171030o2db1e183va43b9dcb4d99705e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > > Carlo Segre wrote: > >> > >> Hi Mauro: > >> > >> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >> unstable and available for Ubuntu intrepid and jaunty in my repository > >> > >> deb http://debian-xray.iit.edu intrepid main contrib non-free > > > > Carlo, > > > > Thank you very much for the package. > > > > Actually, I was able to build/install ifeffit 1.2.11b from source but > > not able to build than the Perl/Python wrappers and so no Horae&Friends > > from Bruce SVN. > > > > Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > > "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > > built from source (Bruce SVN). > > > > Everything seems fine but I still do not understand why ifeffit 1.2.11 > > has all these "IFF str = *" output as stated also by Gareth in his > > "Ifeffit 1.2.11b terminal output" post. Is it normal? > > > > Cheers, > > Mauro > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Nov 2008 17:06:35 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171506h438ba6abke90121bbb1744818(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > and sourceforge.net download sites. > > I have a Windows dll made for this bug fix version. If anyone is > interested, this is currently at > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > This should be a drop-in replacement for the > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > Artemis.exe will not be updated from this dll, as it has this dlls > "compiled in". Bruce will have to make a new Artemis.exe, and then > we'll make a automatic update. > > Sorry for all the trouble, > > --Matt > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi, > > > > This is my fault... and I apologize for the sloppiness and for being > > late in fixing this. I've been mixing 'development/testing' and > > 'production' versions, and haven't been very good at keeping them > > cleanly separated. I think I have this mostly under control now, > > but I will have to work on a decent "test suite". > > > > I think I found another reason to make a 1.2.11c version too, that the > > mixing of "devel" and "production" > > caused an experiment in how fitting was done to be the default, so > > that the reported chi-square doesn't actually match the documentation > > (instead of summing real and imaginary parts, it sums real and > > magnitude components of the misfit, which is part of an experiment to > > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > > another way to report chi-square and misfits is potentially a useful > > approach, but it's not what is documented. Anyway, mixing devel and > > production versions like this (for the past couple years, really) is > > very sloppy on my part, and I apologize again. > > > > I actually have an ubuntu box now, though I built pgplot from source, > > and have never made a .deb file. > > There is a new source kit at > > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > > post this to sourceforge this afternoon, and I'll also make a new DLL > > for Windows and post all of these on the download page. I'll also make > > a new updater for Windows. > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: > >> Carlo Segre wrote: > >>> > >>> Hi Mauro: > >>> > >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>> > >>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >> > >> Carlo, > >> > >> Thank you very much for the package. > >> > >> Actually, I was able to build/install ifeffit 1.2.11b from source but > >> not able to build than the Perl/Python wrappers and so no Horae&Friends > >> from Bruce SVN. > >> > >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >> built from source (Bruce SVN). > >> > >> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >> has all these "IFF str = *" output as stated also by Gareth in his > >> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >> > >> Cheers, > >> Mauro > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > > > > > ------------------------------ > > Message: 3 > Date: Mon, 17 Nov 2008 20:03:06 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: Matt Newville <newville(a)cars.uchicago.edu> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811172002240.3650(a)hydride.iit.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Debian packages have been uploaded to unstable and I am in the process of > building Ubuntu packages for my repository. i expect that they will be up > tonight. > > carlo > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > Hi Folks, > > > > I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > > and sourceforge.net download sites. > > > > I have a Windows dll made for this bug fix version. If anyone is > > interested, this is currently at > > http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > > > > This should be a drop-in replacement for the > > IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > > Artemis.exe will not be updated from this dll, as it has this dlls > > "compiled in". Bruce will have to make a new Artemis.exe, and then > > we'll make a automatic update. > > > > Sorry for all the trouble, > > > > --Matt > > > > > > On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > > <newville(a)cars.uchicago.edu> wrote: > >> Hi, > >> > >> This is my fault... and I apologize for the sloppiness and for being > >> late in fixing this. I've been mixing 'development/testing' and > >> 'production' versions, and haven't been very good at keeping them > >> cleanly separated. I think I have this mostly under control now, > >> but I will have to work on a decent "test suite". > >> > >> I think I found another reason to make a 1.2.11c version too, that the > >> mixing of "devel" and "production" > >> caused an experiment in how fitting was done to be the default, so > >> that the reported chi-square doesn't actually match the documentation > >> (instead of summing real and imaginary parts, it sums real and > >> magnitude components of the misfit, which is part of an experiment to > >> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >> another way to report chi-square and misfits is potentially a useful > >> approach, but it's not what is documented. Anyway, mixing devel and > >> production versions like this (for the past couple years, really) is > >> very sloppy on my part, and I apologize again. > >> > >> I actually have an ubuntu box now, though I built pgplot from source, > >> and have never made a .deb file. > >> There is a new source kit at > >> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >> post this to sourceforge this afternoon, and I'll also make a new DLL > >> for Windows and post all of these on the download page. I'll also make > >> a new updater for Windows. > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>> Carlo Segre wrote: > >>>> > >>>> Hi Mauro: > >>>> > >>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>> unstable and available for Ubuntu intrepid and jaunty in my repository > >>>> > >>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>> > >>> Carlo, > >>> > >>> Thank you very much for the package. > >>> > >>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>> not able to build than the Perl/Python wrappers and so no Horae&Friends > >>> from Bruce SVN. > >>> > >>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>> built from source (Bruce SVN). > >>> > >>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>> has all these "IFF str = *" output as stated also by Gareth in his > >>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>> > >>> Cheers, > >>> Mauro > >>> _______________________________________________ > >>> 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 > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, 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: 4 > Date: Mon, 17 Nov 2008 21:10:51 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] > Upgrading to ifeffit-1.2.11b on Ubuntu from source) > To: segre(a)agni.phys.iit.edu > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0811171910p4509bdacn3dc6ed65606d9580(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks, Carlo! > > --Matt > > > > > On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre <segre(a)iit.edu> wrote: > > > > Debian packages have been uploaded to unstable and I am in the process of > > building Ubuntu packages for my repository. i expect that they will be > up > > tonight. > > > > carlo > > > > On Mon, 17 Nov 2008, Matt Newville wrote: > > > >> Hi Folks, > >> > >> I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu > >> and sourceforge.net download sites. > >> > >> I have a Windows dll made for this bug fix version. If anyone is > >> interested, this is currently at > >> http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll > >> > >> This should be a drop-in replacement for the > >> IFEFFIT_DIR\bin\ifeffit_12.dll on your system. > >> Artemis.exe will not be updated from this dll, as it has this dlls > >> "compiled in". Bruce will have to make a new Artemis.exe, and then > >> we'll make a automatic update. > >> > >> Sorry for all the trouble, > >> > >> --Matt > >> > >> > >> On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville > >> <newville(a)cars.uchicago.edu> wrote: > >>> > >>> Hi, > >>> > >>> This is my fault... and I apologize for the sloppiness and for being > >>> late in fixing this. I've been mixing 'development/testing' and > >>> 'production' versions, and haven't been very good at keeping them > >>> cleanly separated. I think I have this mostly under control now, > >>> but I will have to work on a decent "test suite". > >>> > >>> I think I found another reason to make a 1.2.11c version too, that the > >>> mixing of "devel" and "production" > >>> caused an experiment in how fitting was done to be the default, so > >>> that the reported chi-square doesn't actually match the documentation > >>> (instead of summing real and imaginary parts, it sums real and > >>> magnitude components of the misfit, which is part of an experiment to > >>> see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > >>> another way to report chi-square and misfits is potentially a useful > >>> approach, but it's not what is documented. Anyway, mixing devel and > >>> production versions like this (for the past couple years, really) is > >>> very sloppy on my part, and I apologize again. > >>> > >>> I actually have an ubuntu box now, though I built pgplot from source, > >>> and have never made a .deb file. > >>> There is a new source kit at > >>> http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > >>> post this to sourceforge this afternoon, and I'll also make a new DLL > >>> for Windows and post all of these on the download page. I'll also make > >>> a new updater for Windows. > >>> > >>> --Matt > >>> > >>> > >>> On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> > wrote: > >>>> > >>>> Carlo Segre wrote: > >>>>> > >>>>> Hi Mauro: > >>>>> > >>>>> I have now produced a package of ifeffit 1.2.11b. It is in Debian > >>>>> unstable and available for Ubuntu intrepid and jaunty in my > repository > >>>>> > >>>>> deb http://debian-xray.iit.edu intrepid main contrib non-free > >>>> > >>>> Carlo, > >>>> > >>>> Thank you very much for the package. > >>>> > >>>> Actually, I was able to build/install ifeffit 1.2.11b from source but > >>>> not able to build than the Perl/Python wrappers and so no > Horae&Friends > >>>> from Bruce SVN. > >>>> > >>>> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and > >>>> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" > >>>> built from source (Bruce SVN). > >>>> > >>>> Everything seems fine but I still do not understand why ifeffit 1.2.11 > >>>> has all these "IFF str = *" output as stated also by Gareth in his > >>>> "Ifeffit 1.2.11b terminal output" post. Is it normal? > >>>> > >>>> Cheers, > >>>> Mauro > >>>> _______________________________________________ > >>>> 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 > >> > > > > -- > > Carlo U. Segre -- Professor of Physics > > Associate Dean for Special Projects, 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: 5 > Date: Tue, 18 Nov 2008 17:20:24 +0100 > From: "Ying Zhou, Anorganisch-Chemisches Inst." <ying.zhou(a)aci.uzh.ch> > Subject: [Ifeffit] Hexagonal WO3 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <web-16292974(a)idmailbe2b.unizh.ch> > Content-Type: text/plain;charset=iso-8859-1;format="flowed" > > Dear All > > Recently, I got one compound, W/Mo oxide, which has the similar structure > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this > compound. So, we use the hexagonal WO3 model to refine the structure of our > compounds. My question is that how can I get the FEFF file of this > compound. > Can I directly change some of W to Mo in FEFF file? or Do I need to add the > Mo in the atom file? I do appreciate your help. > > Best wishes > Ying > > > ------------------------------ > > Message: 6 > Date: Tue, 18 Nov 2008 10:33:35 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Hexagonal WO3 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <alpine.DEB.2.00.0811181023390.19806(a)oxide.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Ying: > > On Tue, 18 Nov 2008, Ying Zhou, Anorganisch-Chemisches Inst. wrote: > > > Dear All > > > > Recently, I got one compound, W/Mo oxide, which has the similar structure > > with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of > this > > compound. So, we use the hexagonal WO3 model to refine the structure of > our > > compounds. My question is that how can I get the FEFF file of this > compound. > > Can I directly change some of W to Mo in FEFF file? or Do I need to add > the > > Mo in the atom file? I do appreciate your help. > > > > There are several ways to do this, depending on what you are trying to > find out. If you change W to Mo in the atoms input file than you are > really making MoO3. What it seems like you need to do is to generate the > FEFF input file from the WO3 structure, then replace the central atom with > Mo. This will give you the first path which is likely oxygen. The second > longest set of paths are likely to be W/Mo and you can do two things, one > is to generate a FEFF calculation with W in this position and then make a > second calculation with Mo and use both paths to fit the Mo environment. > You will have to be careful about multiplicities though since by starting > with the WO3 structure, you are assuming some degeneracies in the paths. > The advantage is that you potentially have some multiple scatteing paths > available to use. > > Another approach is to generate the FEFF input file from WO3, look at the > near neighbors and then generate some "quick first shell" paths for the > nearest neighbor (oxygen) and then two fro the next near neighbor (one > with W and one with Mo). The difference here is that you now have > uncorrelated paths with no implied degeneracies. You cannot use this to > fit multiple scattering paths. > > I guess that my approach would be to start with the latter, more simple > approach first to try to understand the problem. If I see that the > environment looks like it is possible to fit with multiple scattering, I > would move to the first approach, being careful to realize that in a solid > sloution compound, the occupancy of the second shell of metal atoms is > probably random and not perfectly ordered like a FEFF input file with > substitutions would be. > > Hope this helps. > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 69, Issue 13 > *************************************** > -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

3 3

Athena problem with integration in Difference of Normalized Spectra (norm(E))
by Zajac, Dariusz 19 Nov '08

19 Nov '08

Hi All, first - I am using Athena 0.8.054 under Windows XP and Adam 0.8.057 under Linux We have checked this problem at 2 computers. I played a little bit with Analysis function - Difference Spectra - norm(E) It works fine when I work with one group - it plots spectrum, difference and program computes the difference and the integral. Now, I want to do the same for marked groups - it computes and makes as new groups the difference spectra. If I want to compute also integrals for marked groups program does not execute operation. Simply it does nothing, or tries to do something with the first marked group, but without result. the error message from shell window is like that: for Athena 0.8.057 Linux: Tk::Error: Can't upgrade that kind of scalar at /usr/bin/athena line 12950. main::diff_marked at /usr/bin/athena line 12950 main::__ANON__ at /usr/bin/athena line 12614 Tk callback for .frame1.frame1.frame2.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) and for Athena 0.8.054 Windows Tk::Error: Can't upgrade that kind of scalar at athena line 12863. main::diff_marked at athena line 12863 main::__ANON__ at athena line 12527 Tk callback for .frame1.frame2.frame2.button Tk::__ANON__ at /PerlApp/Tk.pm line 252 Tk::Button::butUp at /PerlApp/Tk/Button.pm line 111 <ButtonRelease-1> (command bound to event) cheers darek and adam ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------

2 1

Hexagonal WO3
by Ying Zhou, Anorganisch-Chemisches Inst. 18 Nov '08

18 Nov '08

Dear All Recently, I got one compound, W/Mo oxide, which has the similar structure with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this compound. So, we use the hexagonal WO3 model to refine the structure of our compounds. My question is that how can I get the FEFF file of this compound. Can I directly change some of W to Mo in FEFF file? or Do I need to add the Mo in the atom file? I do appreciate your help. Best wishes Ying

2 1

Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
by Matt Newville 18 Nov '08

18 Nov '08

Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls "compiled in". Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi, > > This is my fault... and I apologize for the sloppiness and for being > late in fixing this. I've been mixing 'development/testing' and > 'production' versions, and haven't been very good at keeping them > cleanly separated. I think I have this mostly under control now, > but I will have to work on a decent "test suite". > > I think I found another reason to make a 1.2.11c version too, that the > mixing of "devel" and "production" > caused an experiment in how fitting was done to be the default, so > that the reported chi-square doesn't actually match the documentation > (instead of summing real and imaginary parts, it sums real and > magnitude components of the misfit, which is part of an experiment to > see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for > another way to report chi-square and misfits is potentially a useful > approach, but it's not what is documented. Anyway, mixing devel and > production versions like this (for the past couple years, really) is > very sloppy on my part, and I apologize again. > > I actually have an ubuntu box now, though I built pgplot from source, > and have never made a .deb file. > There is a new source kit at > http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll > post this to sourceforge this afternoon, and I'll also make a new DLL > for Windows and post all of these on the download page. I'll also make > a new updater for Windows. > > --Matt > > > On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi <rovezzi(a)esrf.fr> wrote: >> Carlo Segre wrote: >>> >>> Hi Mauro: >>> >>> I have now produced a package of ifeffit 1.2.11b. It is in Debian >>> unstable and available for Ubuntu intrepid and jaunty in my repository >>> >>> deb http://debian-xray.iit.edu intrepid main contrib non-free >> >> Carlo, >> >> Thank you very much for the package. >> >> Actually, I was able to build/install ifeffit 1.2.11b from source but >> not able to build than the Perl/Python wrappers and so no Horae&Friends >> from Bruce SVN. >> >> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and >> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" >> built from source (Bruce SVN). >> >> Everything seems fine but I still do not understand why ifeffit 1.2.11 >> has all these "IFF str = *" output as stated also by Gareth in his >> "Ifeffit 1.2.11b terminal output" post. Is it normal? >> >> Cheers, >> Mauro >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

2 2

[PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
by Mauro Rovezzi 17 Nov '08

17 Nov '08

Dear all, I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source. First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case. So the only way is to build also PGPLOT from source. Unfortunately the experience has failed both with the "PGPLOT_install" script and following steps in the "install-unix.txt". I have tried many possibilities but the make process interrupts on the drivers compilations. Seen that following "install-unix.txt" gives the same error (but on another driver!) of "PGPLOT_install", let's focus on this last procedure to try debugging the situation: $sudo ./PGPLOT_install ... [all fine until the PGPLOT make] [long list of errors + warnings like:] ... /home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: error: ‘XWdev’ has no member named ‘gc’ ... make: *** [xwdriv_iff.o] Error 1 ... [then the final error due to the bad compilation] collect2: ld returned 1 exit status make: *** [pgdemo1] Error 1 OK, I have described more or less the situation but I would not flood the list with technical mails, so if someone would help me with this issue we can continue in private and then send just the solution to the list. Anyway, the problem is not "urgent" seen that I can work with the 1.2.10 binary installation. Have a nice day! Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

4 7

about wolframite crystallographic file
by Yordy Licea Fonseca 17 Nov '08

17 Nov '08

Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: "Artemis trapped one or more errors! Error message dumped to screen." I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: yliceafonseca(a)gmail.com

4 3

Co doped ZnO
by Guvenc Akgul (gakgul) 16 Nov '08

16 Nov '08

dear all, I have 10%Co doped ZnO EXAFS data and I would like to figure out :Co-Co distance in the 10%Co doped ZnO.what will i do for this?if you can help to me about this i will be very glad. thanks all guvenc

2 1

Sealed Sample Cell
by Bhoopesh Mishra 12 Nov '08

12 Nov '08

Dear All, I am planning to conduct an EXAFS experiment which involves dealing with methyl mercury. Obviously, I want to be as cautious as I can in sealing the sample. In that connection, I am wondering if anyone on this forum can advise me regarding the best way to have a completely sealed (air tight) sample holder. My requirements are given below. Third requirement is not as important as the first two. 1. Sample cell (or the front and rear exit) should be made of low scattering material that would not attenuate photons too much at ~ 10-12 keV. 2. The sample cell should be a perfectly sealed, as gaseous phase methyl mercury or even di-methyl mercury could be produced in the cell. 3. I would like to inject solution using syringe in the sealed sample holder (if possible, this requirement is not necessary). Among several possibilities, I am thinking of designing a cuvette shaped rectangular box with a thin bottom section, and probably using some sort of polypropylene such that scattering is as low as possible. It should be easy to put two silicon rubber septa on the top. Other possibility could be using a thick Beryllium window (and please forgive my naivete' here - isn't there some restriction in using Be) on both the front and back of a rectangular or cylindrical box with rubber stopper at the top. The easiest and probably the best would be to have a commercially available sample cell that can serve my purpose. I don't know any commercially available product like that. But I suspect, people who work with volatile material and/or radioactive material might know a lot about it. If you know anything, please write me back. Any comments, suggestions, or criticism would be highly appreciated. PS: Sealing with kapton tape (or any other thin film) might not be enough in this case as gaseous phase methyl mercury might diffuse through kapton, and also air might diffuse through kapton making the inside of the cell environment aerobic while I need to do this experiment anaerobically. Thanks for your help! Bhoopesh

3 2

problem on opening data file
by Ruoshuang Huang 11 Nov '08

11 Nov '08

Hello All, Recently I found that I could not open my EXAFS data files using Athena any more. Previously I had no problem using Athena to do data analysis (the last time was in last year). Now when I try to open a data file, a small window appears saying this file 'could not be read by ifeffit as a data file'. This happened to both the old data files that could be opened previously and new ones that were obtained recently. All the raw data were taken on beamline X10C at NSLS in the format of .xfs. I appreciate it if someone could help and give me some suggestions. I've attached one of my data files as an example. Thank you so much, Ruoshuang

5 4

Athena's application
by abhijeet gaur 06 Nov '08

06 Nov '08

> I am doing my research work on EXAFS . For > that I am using the software ATHENA for analyzing my data > which my guide had brought from SSRL ( USA ) . But there is > some problem in that , Athena is taking the data and > plotting it but is not giving the required parameters. I am > sending you the copy of that data . So if you can go through > it and suggest me what is the problem , I wil be very > thankfull . > > > > > > > Did you know? You can CHAT without downloading > messenger. Go to http://in.webmessenger.yahoo.com/ Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

2 1

Synchrotron Environmental Science meeting, Dec 11-13th, 2008 San Francisco CA
by Peter Nico 06 Nov '08

06 Nov '08

Hello All, I thought some readers of this list might be interested in the Synchrotron Environmental Science meeting described below and at the following link. http://esd.lbl.gov/sesIV08/index.html Even if I do say so myself, I think its going to be a very interesting conference form both a synchrotron science and environmental science point of view. Plus, its always nice to go to California in the winter. :) Thanks. --Peter *Synchrotron Environmental Science IV (SES-IV) Meeting, December 11 -- 13, 2008* <http://esd.lbl.gov/sesIV08/> * PREREGISTRATION DEADLINE IS NOV 14!* After Nov. 14, registration fees will increase. Please register at: http://www.regonline.com/Checkin.asp?EventId=649848 *PROGRAM HIGHLIGHTS INCLUDE:* * Key note perspective talks on CO2 sequestration, atmospheric chemistry, environmental remediation science, and marine sciences from world-leading scientists, with emphasis on the potential roles of synchrotron techniques. * Talks on new and emerging synchrotron techniques * Talks on developments in data acquisition hardware and software * Hands-on sessions at SSRL and ALS beam lines for prospective and new users * Introductory-level talks for prospective and new users * Facility reports from North American synchrotron sources * Poster session * * *CONFERENCE HOTEL INFORMATION -- Lodging Deadline is NOVEMBER 14* The lodging deadline for the Conference Hotel is also November 14th, however space is limited and is not guaranteed. The $152.00/per night rate at the Westin is actually less than the Government allowable in San Francisco of $164.00. Also, our rate is even lower than that offered through AGU of $164/night. You may extend your stay through the entire AGU session. You can make your lodging reservations for the Conference hotel by visiting: http://esd.lbl.gov/sesIV08/accomodations.html * ** KEY DATES:* *Early Discount Registration Closes November 14, 2008 Discount Lodging Registration Closes November 14, 2008* SES IV Conference Dates December 11 -- 13, 2008 Hands on Sessions December 11, 2008 Poster Session Evening, December 12, 2008 *COMPLETE MEETING PROGRAM* The complete Synchrotron Environmental Science IV (SES-IV) 2008 Meeting agenda is available at: http://esd.lbl.gov/sesIV08/program.html As you will see, the conference has a very exciting program! *HANDS ON SESSION:* On Thursday, December 11, there will be a tour and hands on training at beam lines at ALS or SSRL See web for more details and to enroll: http://esd.lbl.gov/sesIV08/session.html *QUESTIONS?* Please direct all questions or comments to CAValladao(a)lbl.gov. Best Regards, SES-IV 2008 Organizing Committee

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Re: [Ifeffit] Ifeffit Digest, Vol 69, Issue 3
by Gudrun Bovenkamp 04 Nov '08

04 Nov '08

Dear Bruce, thanks for your detailed answer. I tried Athena, Arthemis and the Six Pack programs. For all these programs it was not possible to open a certain file or save a project to a certain location. I also tried as you wanted me to get some error messages through the DOS command console, but the program just ended and did not send any comment to the cmd! It seems as if it ended in a correct way. And: the problem occurred just recently. I was wondering if anyone else had this problem. But it did not seem so. I talked to my administrator....and he suggested to delete my profile and renew it. Now the problem is solved. It was something on my computer. I am so sorry that I bothered you with this. Thanks, anyway. You are just great! Lisa

2 1

Fwd: ifeffit installation
by Makarand R. Gogate 04 Nov '08

04 Nov '08

--- the forwarded message follows ---

2 1

Problem with new ifeffit version
by Gudrun Bovenkamp 03 Nov '08

03 Nov '08

Dear Matt, Bruce and Sam, I just installed the new ifeffit 1.2.11 version (including) update von my windows pc (OS windows xp). The program works fine so far, but when I want to open or save a file, project or xmu the program just ends (without any error message). The only way to use data is by loading recent files. Am I the only one with this problem? Thanks for your help, Lisa

2 1

a big big thank-you
by Bosman, Eckhard 03 Nov '08

03 Nov '08

Hi, a few days ago I finished my diploma thesis (Modeling of XANES-Spectra). Now, the thesis is submitted and I want to thank you all very much for your great and quick help over the past months. I bring the odysseus explanation well to mind :-) Thanks a lot, Eckhard --- Eckhard Bosman eckhard.bosman(a)stud.uni-goettingen.de ecbo2000(a)gmx.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

2 1

XANES calculation at Al-L23 edge for gamma alumina by FEFF8
by Daesung Park 02 Nov '08

02 Nov '08

hi everyone, I want to calculate XANES at Al-L23 edge for gamma alumina. It was knon that gamma alumina has a defected spinel structure. There are 4- and 6-coordinated aluminium atoms by oxygen in the structure. And 16.77% vacancies exist at 6-coordinated aluminium stie. For calculating XANES, I produced randomly vacancies in the input file. And then I calculated XANES for two different crystallographic sites, since they have different surroundings. Finally, spectra calculated were weighted to reproduce total spectrum. However, I could not get similiar total spectrum comparing to experimental one. Maybe can someone help me to calculate Al-L23 edge for gamma alumina? Best regards Daesung Park

1 0

Re: [Ifeffit] Your internet exchange with "Chachi" about FeCo, last year
by Dominik Samuelis 31 Oct '08

31 Oct '08

Dear Dr. English, unfortunately, I am not a metals and intermetallics expert. I mostly work on oxides and related phases. Nevertheless, I've now ordered your original TMS paper from our library. As soon as I've found the time to read your analysis, I'll get in touch with you. There might be a good chance that EXAFS could give additional insight into these fine domain structures, since - as you wrote - many atoms will have a large number of wrong next neighbors. Maybe, there are also some intermetallics experts on this list, who could comment on this more knowledgeably. Best regards, Dominik Samuelis > Dear Sir: I just ran across your exchange of ideas on FeCo order etc. > about this time last year. I did some experiments in the mid 60s > (Trans. Met. Soc AIME 236 (1966) 14ff.) on FeCo2V and showed that the > superlattice xray line [100} can be seen in brine-quenched thin strips > if the XRD is done with CoKa radiation. The lines are very broad in > as-quenched state and the peak narrows gradually with time of > reheating to a few hundred degrees C. > The interpretation was that we were seeing APB domains which were > unexpected but seemed obvious in hindsight--two interpenetrating, > multiply-connected domains sort of like "swiss cheese" (J. W. Cahn > called it "sponge" at the time--he wrote an elegant mathematical > analysis that appeared in Acta Met.). The "scale" of interconnection > changes with time at temperature as the structure coarsens to reduce > the energy associated with APB. I thought the picture was confusing > since "perfect order with very fine domain size" could as well be > descri bed as partial, or incomplete order due to large number of > wrong near neighbors. I don't know if there are other alloys or > chemical combinations in which B2 order is present with very fine > domain structure such as I described. I am not aware of any other work > that confirmed or reinterpreted my results. Any comments? -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 68, Issue 29
by daesung 30 Oct '08

30 Oct '08

Dear J. Rehr, it is an interesting issue for me. I thought that FEFF calculates for L2 and L3 absorption edges if I use EDGE L3 card, since they overlap in a small energy region. Now I understand why I had bad results for L23 edge calculations. However, where can I find scripts for adding FEFF results for two edges? Are they somewhere in FEFF 8 documents? Please give me more informations Daesung Park On Thursday 30 October 2008 18:00:01 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. Fe_L2L3 (Guvenc Akgul (gakgul)) > 2. Re: Fe_L2L3 (John J. Rehr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Oct 2008 16:17:10 -0500 > From: "Guvenc Akgul (gakgul)" <gakgul(a)aps.anl.gov> > Subject: [Ifeffit] Fe_L2L3 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <fb33bc484270.49088c86(a)aps.anl.gov> > Content-Type: text/plain; charset=us-ascii > > dear all, > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical > .how can I do this using FEFF? > > thanks > > guven > > > ------------------------------ > > Message: 2 > Date: Wed, 29 Oct 2008 20:03:51 -0700 (PDT) > From: "John J. Rehr" <jjr(a)phys.washington.edu> > Subject: Re: [Ifeffit] Fe_L2L3 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.64.0810292003250.16641(a)donatello.phys.washington.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Subject: Re: [Ifeffit] Fe_L2L3 > > Dear Guvenc, > > It's pretty easy, but you have to do the calculation edge by edge and > then add, i.e., two calculations, one with > > EDGE L3 > > and one with > > EDGE L2 > > The FEFF project has scripts for adding FEFF results for two edges - send > email to jjr(a)phys.washington.edu for details. > > J. Rehr > > On Wed, 29 Oct 2008, Guvenc Akgul (gakgul) wrote: > > dear all, > > > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical > > .how can I do this using FEFF? > > > > thanks > > > > guven > > _______________________________________________ > > 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 68, Issue 29 > ***************************************

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Re: [Ifeffit] Fe_L2L3
by John J. Rehr 30 Oct '08

30 Oct '08

Subject: Re: [Ifeffit] Fe_L2L3 Dear Guvenc, It's pretty easy, but you have to do the calculation edge by edge and then add, i.e., two calculations, one with EDGE L3 and one with EDGE L2 The FEFF project has scripts for adding FEFF results for two edges - send email to jjr(a)phys.washington.edu for details. J. Rehr On Wed, 29 Oct 2008, Guvenc Akgul (gakgul) wrote: > dear all, > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical .how > can I do this using FEFF? > > thanks > > guven > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

Fe_L2L3
by Guvenc Akgul (gakgul) 29 Oct '08

29 Oct '08

dear all, I have to calculate L3 and L2 absorption edges for pure Fe as theorical .how can I do this using FEFF? thanks guven

1 0

Re: [Ifeffit] Normalization of XANES spectra
by Jens Kruse 29 Oct '08

29 Oct '08

Thanks for your replay and sorry for the confusing question. but I think it not getting better. Scott, you are right LCF would be helpful but even with lot of standards it is hard to get a meaningful result from low concentrated samples at the N k-edge. I think my problem is than I don`t understand the physical meaning of a edge step normalized spectra. Is it the spectrum 1 x-ray photon would produce? Is it right that I loose the information of the absolute concentration after normalization so that I still can identify relative proportions of different compounds with in a sample but I can`t compare different spectra in an absolute way anymore? The extreme case would be a comparison of pure and a diluted spectra. 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. Normalization of XANES spectra (Jens Kruse) > 2. Re: Normalization of XANES spectra (Frenkel, Anatoly) > 3. Re: Normalization of XANES spectra (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Oct 2008 15:02:54 +0100 > From: Jens Kruse <jens.kruse(a)uni-rostock.de> > Subject: [Ifeffit] Normalization of XANES spectra > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <49086D0E.2000603(a)uni-rostock.de> > Content-Type: text/plain; charset="ISO-8859-15"; format=flowed > > Hi everyone, > > I have a general question: > I know Normalizing is something we do so that we can compare samples > measured > under different experimental conditions (removes the effect of different > gains ...) but I have problems in understanding and applying > normalization when also quantitative conclusions are needed when > comparing different spectra. > > If I have two XANES spectra (a) and (b) measure under the same > conditions but with different concentration of the absorbing atom with > in different molecules.If both normalized spectra show a peak 1 , but > this peak is higher in intensity in spectrum (a) than in spectrum (b), > does this mean that compound which produced peak 1 is also absolute > higher in concentration in sample/spectrum (a) or do I loose this > information after normalization? > Or can I just say: in the normalized spectrum (a) peak 1 is higher than > peak 2 suggesting that the compound leading to peak 1 is more abundant > (just relative proportions).But I can't say: The intensity of peak 1 in > the also normalized spectrum 2 is lower than in spectrum one, Therefore, > the compound leading to peak 1 is less abundant in spectrum/sample 2. ???? > > > I hope somebody can help me to understand this issue. > > Thanks a lot, > > jens > > -- 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

3 2

Your internet exchange with "Chachi" about FeCo last year
by Alan English 29 Oct '08

29 Oct '08

Dear Sir: I just ran across your exchange of ideas on FeCo order etc. about this time last year. I did some experiments in the mid 60s (Trans. Met. Soc AIME 236 (1966) 14ff.) on FeCo2V and showed that the superlattice xray line [100} can be seen in brine-quenched thin strips if the XRD is done with CoKa radiation. The lines are very broad in as-quenched state and the peak narrows gradually with time of reheating to a few hundred degrees C. The interpretation was that we were seeing APB domains which were unexpected but seemed obvious in hindsight--two interpenetrating, multiply-connected domains sort of like "swiss cheese" (J. W. Cahn called it "sponge" at the time--he wrote an elegant mathematical analysis that appeared in Acta Met.). The "scale" of interconnection changes with time at temperature as the structure coarsens to reduce the energy associated with APB. I thought the picture was confusing since "perfect order with very fine domain size" could as well be described as partial, or incomplete order due to large number of wrong near neighbors. I don't know if there are other alloys or chemical combinations in which B2 order is present with very fine domain structure such as I described. I am not aware of any other work that confirmed or reinterpreted my results. Any comments? Alan English Summit NJ

1 0

Fe L2 L3
by Guvenc Akgul (gakgul) 29 Oct '08

29 Oct '08

dear all, I have to calculate L3 and L2 absorption edges for pure Fe.how can I do this? thanks guven

1 0

Normalization of XANES spectra
by Jens Kruse 29 Oct '08

29 Oct '08

Hi everyone, I have a general question: I know Normalizing is something we do so that we can compare samples measured under different experimental conditions (removes the effect of different gains ...) but I have problems in understanding and applying normalization when also quantitative conclusions are needed when comparing different spectra. If I have two XANES spectra (a) and (b) measure under the same conditions but with different concentration of the absorbing atom with in different molecules.If both normalized spectra show a peak 1 , but this peak is higher in intensity in spectrum (a) than in spectrum (b), does this mean that compound which produced peak 1 is also absolute higher in concentration in sample/spectrum (a) or do I loose this information after normalization? Or can I just say: in the normalized spectrum (a) peak 1 is higher than peak 2 suggesting that the compound leading to peak 1 is more abundant (just relative proportions).But I can't say: The intensity of peak 1 in the also normalized spectrum 2 is lower than in spectrum one, Therefore, the compound leading to peak 1 is less abundant in spectrum/sample 2. ???? I hope somebody can help me to understand this issue. Thanks a lot, jens -- 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

2 1

Re: [Ifeffit] Normalization of XANES spectra
by Frenkel, Anatoly 29 Oct '08

29 Oct '08

Jens: This example may help you understand your problem: if compound a) has a small fraction of metal Cu mixed with a large fraction of oxidized Cu, while a compound b) has it the other way around, then the main (1s - 4p) absorption peak in compound a) will be smaller than in b) after edge step normalization. Edge step normalization allows to view all features in XANES and EXAFS regions as if caused by an x-absorption process in a singe atom located in a concentration-average environment of all species in the sample that contain that element. Thus, the edge step normalization does have sensitivity to the composition of the sampe. Or, I misunderstood your question? 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: Wed Oct 29 10:02:54 2008 Subject: [Ifeffit] Normalization of XANES spectra Hi everyone, I have a general question: I know Normalizing is something we do so that we can compare samples measured under different experimental conditions (removes the effect of different gains ...) but I have problems in understanding and applying normalization when also quantitative conclusions are needed when comparing different spectra. If I have two XANES spectra (a) and (b) measure under the same conditions but with different concentration of the absorbing atom with in different molecules.If both normalized spectra show a peak 1 , but this peak is higher in intensity in spectrum (a) than in spectrum (b), does this mean that compound which produced peak 1 is also absolute higher in concentration in sample/spectrum (a) or do I loose this information after normalization? Or can I just say: in the normalized spectrum (a) peak 1 is higher than peak 2 suggesting that the compound leading to peak 1 is more abundant (just relative proportions).But I can't say: The intensity of peak 1 in the also normalized spectrum 2 is lower than in spectrum one, Therefore, the compound leading to peak 1 is less abundant in spectrum/sample 2. ???? I hope somebody can help me to understand this issue. Thanks a lot, jens -- 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 _______________________________________________ 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] Fit XANES spectra using Athena
by Frenkel, Anatoly 28 Oct '08

28 Oct '08

PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum. 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: Sun Oct 26 13:05:32 2008 Subject: Re: [Ifeffit] Fit XANES spectra using Athena Jenny, I'm relatively new to the community XAFS, and have not done any sulfur work thus far... but have you considered doing a principal component analysis on the XANES of your samples? This method should help you identify how many phases are present (assuming that all of your samples aren't exactly identical; however the maximum number of independent phases it will return is the number of samples you tested), and with your standards you might be able to eliminate some of the phases (from the standards) as well as identify some of the phases that are in your sample. (There is software that will do this in the IFFEFIT package under Sixpack --> 'pc analysis') Andrew Campos _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

3 2

Re: [Ifeffit] EXAFS simulations
by Frommer Jakob 26 Oct '08

26 Oct '08

Ciao Sebastiano, did you use the mu-column of the xmu.dat? If so, the main difference between the chi.dat and the xmu.dat is that the mue_0 (as calculated by FEFF) is already subtracted in the former while it needs to be subtracted by Athena in the latter. Some of the difficulties you mentioned are thus due to problems of Athena to do a decent background (i.e. mue_0 and normalization) processing if there is no pre-edge region. Thus the effect of changing the absorption energy in Cu Bulk 4 from 8988.430eV to 8988.431eV is not caused by a *wrong* Enot but by a change in the edge-jump of almost 50% (due to a different *pre-edge*). Thus using the chi.dat seems to be the better (i.e. more reproducible) choice in this case (a precautionary note though: the mue_0 as calculated by FEFF will most likely differ between the central and the peripheral atoms; this may be part of the cluster-effect or an artifact (I assume that this is only a problem in the XANES region but I don't know, so you should check this by plotting the single mue_0). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Fri 10/24/2008 09:57 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 21 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: Fit XANES spectra using Athena (Adam Webb) 2. EXAFS simulations (Cammelli Sebastiano) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Oct 2008 07:39:55 +0200 From: Adam Webb <adam.webb(a)desy.de> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <49015FAB.5060802(a)desy.de> Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I don't know what exactly you are trying to do so I can't say which method is better but I can make a comment. It all comes down to the number of independent variables. The Gaussian and step functions are independent of each other. The heights, widths and positions can all be adjusted. In the linear combination you change everything together so for example, the ratio of the peak height and the step height doesn't change. The result is that you need more spectra to get the same number of degrees of freedom as in the least-squares peak fit. Cheers, Adam Jenny Cai wrote: > Hello everyone, > > Sorry for bothering you again. > > I am using least-squares peak fit and linear combination fit to analyze > my samples. I have spent tons of time on it, and it really makes me > crazy. Why can't I get consistent results from these two methods? > > Please see the attached file. Both of these methods work well > individually, but linear combination fit always need more peaks than > peak fit to get an 'ok' fitting. Should I stick on one method for all my > samples, no matter what results the other one gives? It is confusing me > so much. Could anyone help me out? > > Thank you in advance for your help! > > > Jenny > > ------------------------------ Message: 2 Date: Fri, 24 Oct 2008 09:57:35 +0200 From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> Subject: [Ifeffit] EXAFS simulations To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <AD99CE4B84C4D3468F69B0E4FB345D5804A5E78C(a)MAILBOX0A.psi.ch> Content-Type: text/plain; charset="us-ascii" Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli

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Re: [Ifeffit] Fit XANES spectra using Athena
by Andrew Campos 26 Oct '08

26 Oct '08

Jenny, I'm relatively new to the community XAFS, and have not done any sulfur work thus far... but have you considered doing a principal component analysis on the XANES of your samples? This method should help you identify how many phases are present (assuming that all of your samples aren't exactly identical; however the maximum number of independent phases it will return is the number of samples you tested), and with your standards you might be able to eliminate some of the phases (from the standards) as well as identify some of the phases that are in your sample. (There is software that will do this in the IFFEFIT package under Sixpack --> 'pc analysis') Andrew Campos

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Fw: Re: Fit XANES spectra using Athena
by Jenny Cai 26 Oct '08

26 Oct '08

Sorry, Bruce. I have to send it again to the group. -Jenny --- On Sun, 10/26/08, Jenny Cai <jennyh_cai(a)yahoo.ca> wrote: From: Jenny Cai <jennyh_cai(a)yahoo.ca> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "Bruce Ravel" <bravel(a)bnl.gov> Received: Sunday, October 26, 2008, 2:08 AM Hi everyone, Thank you for your reply. I understand the difference between peak fitting and linear combination fitting. It is like, If I don't know anything about my sample, peak fitting should be used. If I know the components of my sample, I can use linear combination. That is why I use peak fitting first, because I know very little about my sample. However, what I am thinking is that from the results of peak fitting, I know there may be some types of sulphur in my sample, and based on the peak positions, I can chose the standards for linear combination fitting. I can't use linear combination fitting in the first place, because I don't exactly know what sulphur forms in my sample, and I may miss an important species if I chose the wrong standards. However, I still want to try linear combination after peak fitting, because I think the linear combination fitting may be more accurate than peak fitting. It uses the whole spectrum of the standard, while the peak fitting neglectes the effect of small features on the fitting. Does it make sense? My samples are fluid coke and their activation products. They have reduced and oxidized sulphur species, more likely in organic forms. I have 26 standards covering the sulphur oxidation states from elemental sulphur to sulphate. Most of them are organic sulphur. Any more suggestions? Thank you! Best regards, Jenny --- On Fri, 10/24/08, Bruce Ravel <bravel(a)bnl.gov> wrote: From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Received: Friday, October 24, 2008, 9:06 AM On Friday 24 October 2008 00:59:21 Jenny Cai wrote: > Hello everyone, > > Sorry for bothering you again. > > I am using least-squares peak fit and linear combination fit to analyze my > samples. I have spent tons of time on it, and it really makes me crazy. Why > can't I get consistent results from these two methods? > > Please see the attached file. Both of these methods work well individually, > but linear combination fit always need more peaks than peak fit to get an > 'ok' fitting. Should I stick on one method for all my samples, no matter > what results the other one gives? It is confusing me so much. Could anyone > help me out? Jenny, I think you are comparing apples and oranges. I certainly think you are looking for some correspondance between peak fitting and linear combination fitting that probably does not exist. When doing linear combination fitting, you are making the implicit assumption that your data can be described in that way. Suppose that you go to the chemical cabinet and grab jars of 5 stable, non-reactive chemicals. Scoop out a spatula-full of each and mix them together very well in ajar. Then scoop out a bit of the mixture, spread it on a piece of tape, and measure some XAS. In that case, we certainly expect LCF to work well. The measured spectrum should be a linear combination of the spectra from each of the 5 original materials in proportion that has something to do with how many absorber atoms were in each scoop. Now suppose that you take a scoop of soil from a swamp. You might expect that your metal atom is distributed among oxide and sulfide species. You measure some xas on the swamp soil and on a library of standards. You may find that you can do LCF using some mixture of oxides and sulfide, or you might not. That may mean that you neglected to consider an important standard, a carbide, for example. *Or* it might mean that the oxides and sulfides in the real sample include some kind of exotic organic species that isn't quite like the standards you have available. In the latter case, your LCF fit results will be approximate in the best scenario. So, you don't say anything about what sulfur species you are using as standards, nor do you say anything about what the sample is. Should you expect a perfect fit from some number of standards? Do you know for a fact that your standard is simply a linear combination of standards. That is, should you expect the LCF to tell you what the components *are* or should you expect the LCF to tell what the sample resembles? As for the peak fitting, what do each of the line shapes mean physically? Chemically? No XAS data is described by a single Gaussian. Neither is any XAS data described by a single arc-tangent. So why should the number of lineshapes required to generate a mathematical function that resembles your data be related to the number of species you require in a linear combination fit? You seem to making yourself crazy based on the assumption that there is some magical relationship between the six lineshapes you used in the peak fitting and the number of standards you use in the linear combination fitting. It seems to me that you would make yourself a lot less crazy if you didn't cling to this unsubstantiated assumption. 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Now with a new friend-happy design! Try the new Yahoo! Canada Messenger __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.

3 2

feff8
by Guvenc Akgul (gakgul) 24 Oct '08

24 Oct '08

Hi all, I want to calculate L2and L3 absorption edges for Fe as theoretical. Where can I find feff8 software programme?? thanks guven

2 1

Reference spectra for KCl
by shiryaev＠crys.ras.ru 24 Oct '08

24 Oct '08

Hi everybody, I would greatly appreciate if someone could provide me with K K-edge spectra for KCl and K2CO3. Cl K-edge in KCl would be useful too. Thanks in advance, Andrei Shiryaev Institute of crystallography, Moscow, Russia

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EXAFS simulations
by Cammelli Sebastiano 24 Oct '08

24 Oct '08

Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli

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Re: [Ifeffit] Crytallites AND polycrystalline - Artemis handling?
by Scott Calvin 20 Oct '08

20 Oct '08

Sure, Joseph. These were nanoparticles made with a reverse micellar method. Past experience has shown that this synthesis produces a passivating oxide layer on an iron core; the passivating layer is usually amorphous, which is a good thing; hematite has a lattice mismatch and thus doesn't passivate. Linear combination analysis suggested this samples was 75% metal and 25 +/- 5% oxide. A typical amp entry is: S02_Fe*Frac_bcc*(1-3/4*reff/R_Fe+1/16*(reff/R_Fe)^3) S02_Fe is just the usual S02 factor, and "should" be from 0.70 to 1.0. It's lower than that in the fit I've sent you; that's one of the indications the fit may not yet be done. (I've actually gone much further with this fit, but that would have made for a more confusing file.) Frac_bcc is the fraction of iron atoms in an ordinary bcc metal environment. In the fit I sent you, it optimizes to 34 +/ 9%. Notice that's consistent with the linear combination analysis. That makes me happy. R_Fe is the radius of the core, modeled as a sphere. The formula in which it appears accounts for the reduction in average coordination number due to surface termination, and is discussed in several of my papers, including my articles: S. Calvin et al., Appl. Phys. Lett. 87, 233102 (2005) and S Calvin et al, Phys. Scr. T115 744-748 (2005). The oxide amp entry is much simpler: S02_Fe*Frac_Ox*2 Frac_Ox is 1-Frac_Bcc; i.e. what's not metal is oxide. The factor of 2 is just because I was working with a path from hematite that had coordination number of 3 (there's some splitting in hematite); I multipled by 2 to get an assumed coordination number of 6. Much of my subsequent fitting has been using bond valence theory to try to distinguish between coordination of 4 or 6 for the amorphous oxide. --Scott Calvin Sarah Lawrence College On Oct 20, 2008, at 8:46 AM, Joseph Washington wrote: > Scott, > Thank you very much. I am looking at this file and I understand > everything as far as the isotropic expansion terms in the delr and > the debye term. Can you clarify the amp math expression? Also, just > so we're on the same page, tell me a little about this system? > > Thank you again for your help! > > Joseph > > Scott Calvin wrote: >> Hi Joe, >> Here's an in-progress Artemis file for a system with some broad >> similarities to the one your describe. Perhaps it will help. >> Disclaimer: This is /not/ a final fit! >> --Scott >> ------------------------------------------------------------------------ >> On Oct 17, 2008, at 2:15 PM, Joseph Washington wrote: >>> Hello all, >>> I am working on analyzing Ge edge EXAFS data of an annealed sample >>> which >>> is likely to be Ge-Te crystallites with some amorphous material at >>> the >>> grain boundary (or perhaps, just Ge-N crystal material at the >>> interface). I do not have any information about the grain size, only >>> possible constituents for the grain and the boundary. Can anyone >>> give me >>> some examples of how Artemis might handle this? >>>

1 0

question
by Guvenc Akgul (gakgul) 17 Oct '08

17 Oct '08

Hi, This question very important for me.I have 5% Ti doped ZnO data.It includes not only Zn-K-edge but also Ti-K -edge data.I would like to figure out in following distances and Coordination numbers of them 1)Zn-O 2)Zn-Ti 3)Zn-Zn 4)O-O 5)Ti-Ti 6)Ti-O How can I do them?If you can help to me I will be very glad.Thanks for your help best regards guvenc

5 4

Ifeffit 1.2.11b terminal output
by Gareth Jones 14 Oct '08

14 Oct '08

Hi all, The newest Ifeffit release dumps a whole lot of text to stdout. I've attached an example (hope that's okay), showing how it prevents the proper configuration of the Perl wrapper for Horae (see my previous post about the missing Ifeffit.pm file). Similar output is produced when using the Horae programs with the out-of-date wrapper, and even when running "ifeffit --help". This is in Ubuntu 8.04.1 (two machines), with gcc/gfortran 4.2.3-2ubuntu7 and pgplot 5.2.2-11ubuntu1, and Ifeffit 1.2.10a works fine. Is this normal, or did I manage to break Ifeffit somehow? Thanks, Gareth

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Horae 067 missing Ifeffit.pm (with solution)
by Gareth Jones 14 Oct '08

14 Oct '08

Hi everyone, This is a follow-up for a problem I encountered at the XAS08 PSI workshop, solved by Bruce, but it should probably be archived here in case anyone else discovers it. The Problem: Installation of Ifeffit and Horae following the build-from-source instructions [http://cars9.uchicago.edu/~ravel/software/downloads.html] appears to work, but Horae programs fail to start due to a missing "Ifeffit.pm" in "$prefix/lib/perl/...". You may at this point have copied Ifeffit.pm from the Ifeffit build tree, which at first seems to fix the problem. However, certain operations that require data to be copied between Perl/Horae and Ifeffit fail - in my case copying a group in Athena yields an apparently empty (or corrupt) group. This is reproducible for affected groups, but not all groups are affected. De-glitching is another test. The Solution: The Ifeffit Perl wrapper is apparently out-of-date. Bruce's Subversion repository contains an updated wrapper (libperlxray/Ifeffit) that fixes the problem, but hasn't been released as a source tarball yet - there are Subversion installation instructions at http://cars9.uchicago.edu/iffwiki/BruceRavel/EvolvingSoftware. Installation of the libperlxray/Ifeffit wrapper should be enough - you can use the release versions of the rest of Horae, but you may need Ifeffit 1.2.10a rather than 1.2.11b (more on this in another post). Anyway thanks to Bruce for figuring it out (and I hope my description isn't too inaccurate!) Gareth

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feff.inp trouble geometry
by penelope arancegui 13 Oct '08

13 Oct '08

Hi everyone, I'm having some trouble with a feff.inp file. I changed the geometry of a 13-atom Pd molecule but I don't know why FEFF8 doesn't read the archive. Using the cristollagraphy database for this molecule, ATOMS generated the following file: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** 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 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 3 3 0.001 1 46 Pd 3 3 4 ATOMS * this list contains 13 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 1 Pd 0.00000 0 1.99550 1.99550 0.00000 0 Pd 2.82206 1 -1.99550 1.99550 0.00000 1 Pd 2.82206 2 1.99550 -1.99550 0.00000 1 Pd 2.82206 3 -1.99550 -1.99550 0.00000 1 Pd 2.82206 4 1.99550 0.00000 1.99550 1 Pd 2.82206 5 -1.99550 0.00000 1.99550 1 Pd 2.82206 6 0.00000 1.99550 1.99550 1 Pd 2.82206 7 0.00000 -1.99550 1.99550 1 Pd 2.82206 8 1.99550 0.00000 -1.99550 1 Pd 2.82206 9 -1.99550 0.00000 -1.99550 1 Pd 2.82206 10 0.00000 1.99550 -1.99550 1 Pd 2.82206 11 0.00000 -1.99550 -1.99550 1 Pd 2.82206 12 END With the coordinates I want to use, the file would be: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350 eV EDGE K S02 1 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** 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 4 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 1 46 Pd ATOMS * this list contains 13 atoms * x y z ipot tag distance 0 0 0 0 Pd 0 0 0 0 2.822 1 Pd 2.82206 1 2.52407 0 1.26204 1 Pd 2.82206 2 0.779982 2.40054 1.26204 1 Pd 2.82206 3 -2.04202 1.48361 1.26204 1 Pd 2.82206 4 -2.04202 -1.48361 1.26204 1 Pd 2.82206 5 0.779982 -2.40054 1.26204 1 Pd 2.82206 6 2.04202 -1.48361 -1.26204 1 Pd 2.82206 7 2.04202 1.48361 -1.26204 1 Pd 2.82206 8 -0.779982 2.40054 -1.26204 1 Pd 2.82206 9 -2.52407 0 -1.26204 1 Pd 2.82206 10 -0.779982 -2.40054 -1.26204 1 Pd 2.82206 11 0 0 -2.822 1 Pd 2.82206 12 END Do I need to modify something else besides the coordinates? Thank you for your help. Penelope _________________________________________________________________ Realiza búsquedas en Internet y llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx

2 1

Estimation of S02
by Hiroshi Oji 13 Oct '08

13 Oct '08

Dear all, Could you give me some advice on estimating the intrinsic loss factor (S02)? I am trying to estimate the S02 value in the curve-fitting analysis for Zr K-edge EXAFS. To do this, I did the curve-fitting analysis on the first shell of Fourier transform of Zr-K EXAFS of Zr-foil by Artemis. However, there was a marked difference between the amps obtained by the fitting, depending on the "Fit k-weights" as follows. kw amp 1 0.8145660 +/- 0.0486470 2 0.9230700 +/- 0.0673820 3 1.0439100 +/- 0.0854950 1,2,3 0.9081570 +/- 0.0722180 Is this a usual thing? I can't find the reasonable explanation why S02 depends on "Fit k-weights". I attached the Artemis project file. Thank you in advance for your cooperation. Hiroshi Oji ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

4 6

more on update problem
by Matthew 07 Oct '08

07 Oct '08

The update that causes the problem is Update 10 (iff_010.zip). When I re-downloaded from Sourceforge and let it do that update, it worked. mam

1 0

problem with Runner
by Matthew 07 Oct '08

07 Oct '08

I just let Runner do the update to Ifeffit10 on a PC under XP, and now when I try to run any of the programs, the splash screen shows for a fraction of a second and the program dies. What's going on? mam

1 0

Broadening
by Eugenio Otal 06 Oct '08

06 Oct '08

Hi Matt, I have measured the XAFS spectra by absorption. I really want to avoid obtain over detailed simulated spectras with a LDOS broadening smaller than core-hole broadening. So, I want to know the logical criteria to use the eimag in LDOS card. Thanks, euG Hi Eugenio, On Wed, Oct 1, 2008 at 7:42 AM, Eugenio Otal <eugenioh at gmail.com <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>> wrote: >* Hello everybody, *>* I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole *>* broadening is 4.163, which value should I use in LDOS broadening to *>* reproduce the experimental spectra. *>* Thanks, euG * What experimental LDOS data do you have? If you've measured it by x-ray absorption (which is not exactly the LDOS), you'll need to include both the experimental energy broadening, and include the core-hole broadening. --Matt

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Re: [Ifeffit] What confidence limit is implied in the error bars
by Andrew Campos 03 Oct '08

03 Oct '08

Everyone, Thank you so much for all the help. I very much appreciate the help and the advice on how to approach this problem. I have a MUCH better idea now of what downfalls, considerations, and benefits that are associated with the least-squares fitting and the errors associated with this technique. Sincerely, Andrew Campos

1 0

Re: [Ifeffit] What confidence limit is implied in the error bars forleast-squares fitting in Athena
by Don R Baker 03 Oct '08

03 Oct '08

Hi Shelly, I am very interested in Andrew's question too, but I am to ignorant to fully understand your response. Could you please provide some more detail? For example, when you state "a large source of uncertainty can come from the representation of the standards in matching the species in the sample." do you mean that heterogeneities (as Bruce mentioned in his email) in the standards are propagated into the fits of the unknowns? Or instead do you mean that an inappropriate choice of standards can create unreliability in the fit? I would appreciate any details you can add to your repsonse. Thanks, Don On Thu, 2008-02-10 at 14:22 -0700, Kelly, Shelly wrote: > Hi Andrew, > > > > If you are fitting XANES spectra with standards, a large source of > uncertainty can come from the representation of the standards in > matching the species in the sample. > > > > Shelly > > > > > ______________________________________________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Andrew > Sent: Thursday, October 02, 2008 3:49 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] What confidence limit is implied in the error bars > forleast-squares fitting in Athena > > > > Hi everyone, > > > > I’m fitting data with the least-squares method in Athena and am not > sure what the error bars correspond to. What I mean, are these 95% > confidence limits, or is it some other statistical way for error > analysis? If Athena says the weight of one phase is 0.049 (0.003), > what confidence are in the 0.003 error bar reported by Athena? > > > > (I have done a PCA of the XANES, and XRDs of the samples and am pretty > confident in the phases that I’m fitting). > > > > I greatly appreciate the help! > > > > Andrew Campos > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University, Montreal, QC CANADA phone: 1-514-398-7485

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What confidence limit is implied in the error bars for least-squares fitting in Athena
by Andrew 02 Oct '08

02 Oct '08

Hi everyone, I'm fitting data with the least-squares method in Athena and am not sure what the error bars correspond to. What I mean, are these 95% confidence limits, or is it some other statistical way for error analysis? If Athena says the weight of one phase is 0.049 (0.003), what confidence are in the 0.003 error bar reported by Athena? (I have done a PCA of the XANES, and XRDs of the samples and am pretty confident in the phases that I'm fitting). I greatly appreciate the help! Andrew Campos

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Re: [Ifeffit] Ifeffit Digest, Vol 68, Issue 3
by Frommer Jakob 02 Oct '08

02 Oct '08

Hi Renske, I still think your problem is related to the potentials. If you unzip your artemis project and look in one of the feffXXXX.dat files in the folder data0.feff3 (this calculations was done with the solvent_O) you will find the calculated R_MTs in the first lines - for ipot3 (O) this is 1.6. Do the same with the data0.feff7 folder (apparently this calculation was done without the solvent O - even though the feff.inp says something different) and you will find 0.728. FEFF (always?) uses the closest atom (relative to the ipot=0-atom) to determine the unique potentials to be used for all atoms with the same ipot (in the manual it is stated that FEFF takes the first atom in the atoms-list but in your case just changing the position in the list did change nothing whereas increasing the distance to 3.3 (the O_t_1 atoms are at 3.266) did yield a different R_MT - but maybe I am wrong). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thu 10/2/2008 06:37 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, 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: Athena Peak Fitting (Matt Newville) 2. Re: Independence of scattering paths? (van der Veen Renske) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Oct 2008 16:23:34 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Athena Peak Fitting To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0810011423g68bb1b81g143ed34a0569a471(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I would say that method 2 looks better, as the fit over the whole of the specified fitting range is clearly better. I wouldn't necessarily say that "peak 1" in this fit -- I'm assuming you mean the highest energy peak at ~2488.3eV -- is too broad. At that high energy (definitely into the EXAFS region), the idea of peaks coming from specific electronic transitions breaks down, and EXAFS oscillations can be that broad in energy. It seems that you need this "broad peak" because you're fitting out past 2500 eV. I think that's OK (that third broad peak may not be a single electronic transition but is still useful for identifying species). But, if you'd rather not have to use the broader peak, you might also try fitting just the two sharper peaks at lower energy, say out to 2485 eV. Hope that helps, --Matt On Wed, Oct 1, 2008 at 1:31 PM, Jenny Cai <jennyh_cai(a)yahoo.ca> wrote: > Hi Everyone, > > I am using Athena peak fitting function to fit the sulfur spectrum of my > coke sample. I checked everywhere, but couldn't get detailed instruction for > using this function. So, I attached a file with this email to get help. > Could you please take a look at it, and tell me if I did the fitting right > (in terms of fitting procedure only)? > > I did the fitting in two ways, and I know both of them have problems. For > instance, in the first case, I can't get a good step line and have to cut > off the tail of the spectrum. In the second one, peak 1 is way too broad, > but if I cut it off, the fitting will be very poor. So, please tell me which > way is better, or you have some ideas to improve the fitting. > > Thank you in advance! > > > Best, > > Jenny > > ________________________________ > > Yahoo! Canada Toolbar : Search from anywhere on the web and bookmark your > favourite sites. Download it now! > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ Message: 2 Date: Thu, 2 Oct 2008 06:36:48 +0200 From: "van der Veen Renske" <Renske.vanderveen(a)psi.ch> Subject: Re: [Ifeffit] Independence of scattering paths? To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <67F374811ED3544C8543E6C0EE5EAA4B02AFEC8E(a)MAILBOX0B.psi.ch> Content-Type: text/plain; charset="us-ascii" Dear Bruce and Jakob Thanks for your replies. I realize that I should have been a bit more precise in where I actually put this extra atom: it is placed outside the molecule at an axial position of the absorbing Pt atom, representing an ethanol solvent molecule that coordinates. It is not placed between any other atoms that are included in the fit/sum, so the MT potentials should not be disturbed. Thanks to the nice presentation of scattering paths in Artemis, I am sure that I chose the same scattering paths involving the same atoms for both sums. I attached an Artemis project to make things more clear. Thanks a lot & best wishes, Renske > > On Friday 26 September 2008 22:38:58 van der Veen Renske wrote: > > I have a question concerning the independence of scattering > pathways. > > I fitted the EXAFS signal of a molecule consisting of 30 atoms (the > > related FEFF calculation is called calc 1). To see the > effect of the > > surrounding solvent molecules in the chi(k) data, I added > an O-atom in > > the coordinate list of the FEFF input file at an arbitrary distance > > from the absorbing atom (in this case Pt) and I re-ran FEFF > (calc 2). > > As a check within calc 2, I generated the sum of the same > scattering > > paths that were used in the fitting model of calc 1 using > the therein > > obtained structural fit parameters. The new O-atom was not > included in this sum. > > I expected the sum within calc 2 to be identical to the fit > of calc 1 > > based on the fact that the original atoms can not sense the > presence > > of the new O-atom (independence of scattering paths). BUT: the > > resulting sum was significantly different from the fit! > > It is a little hard to answer this question since you > described it to us rather than showing it to us with project > file(s). I have a couple of suggestions, but without being > able to examine what you did, I cannot be sure that either is > relevant. (You can insert here my standard diatribe on the > topic of how to ask questions.) > > One suggestion is to be very careful that you are including > the same set of paths in the calculation. When you add an > atom to a feff.inp file, the indexing of the paths change in > a way that may be hard to predict. Just blindly summing up > the first N paths may not do what you want. > > The other suggestion is to check that you did not place the > oxygen atom in a position that dramatically altered the > muffin tin radii. > The potantials calculation can change quite if you insert an > atom at an arbitrary loctation such that the muffin tin radii > have to be very different for some atoms. > > 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] Independence of scattering paths?
by van der Veen Renske 02 Oct '08

02 Oct '08

Dear Bruce and Jakob Thanks for your replies. I realize that I should have been a bit more precise in where I actually put this extra atom: it is placed outside the molecule at an axial position of the absorbing Pt atom, representing an ethanol solvent molecule that coordinates. It is not placed between any other atoms that are included in the fit/sum, so the MT potentials should not be disturbed. Thanks to the nice presentation of scattering paths in Artemis, I am sure that I chose the same scattering paths involving the same atoms for both sums. I attached an Artemis project to make things more clear. Thanks a lot & best wishes, Renske > > On Friday 26 September 2008 22:38:58 van der Veen Renske wrote: > > I have a question concerning the independence of scattering > pathways. > > I fitted the EXAFS signal of a molecule consisting of 30 atoms (the > > related FEFF calculation is called calc 1). To see the > effect of the > > surrounding solvent molecules in the chi(k) data, I added > an O-atom in > > the coordinate list of the FEFF input file at an arbitrary distance > > from the absorbing atom (in this case Pt) and I re-ran FEFF > (calc 2). > > As a check within calc 2, I generated the sum of the same > scattering > > paths that were used in the fitting model of calc 1 using > the therein > > obtained structural fit parameters. The new O-atom was not > included in this sum. > > I expected the sum within calc 2 to be identical to the fit > of calc 1 > > based on the fact that the original atoms can not sense the > presence > > of the new O-atom (independence of scattering paths). BUT: the > > resulting sum was significantly different from the fit! > > It is a little hard to answer this question since you > described it to us rather than showing it to us with project > file(s). I have a couple of suggestions, but without being > able to examine what you did, I cannot be sure that either is > relevant. (You can insert here my standard diatribe on the > topic of how to ask questions.) > > One suggestion is to be very careful that you are including > the same set of paths in the calculation. When you add an > atom to a feff.inp file, the indexing of the paths change in > a way that may be hard to predict. Just blindly summing up > the first N paths may not do what you want. > > The other suggestion is to check that you did not place the > oxygen atom in a position that dramatically altered the > muffin tin radii. > The potantials calculation can change quite if you insert an > atom at an arbitrary loctation such that the muffin tin radii > have to be very different for some atoms. > > 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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update for Windows, fixing problems with Athena/Artemis
by Matt Newville 01 Oct '08

01 Oct '08

Hi Folks, I just put up a Windows updater with new versions of Athena and Artemis which (should / seems to) fix the "Athena is stuck" problems seen be various people. Details on what else changed are below. All windows users with Ifeffit 1.2.10 and 1.2.11 should install this update. If you're still using an older version, beware that this update will be binary incompatible with that version, and you should upgrade to 1.2.11 before installing this update. If you've been having troubles with Athena/Artemis "getting stuck" and these persist after installing this update, please let us know!! --Matt =========== This update to Ifeffit 1.2.11 for Windows corrects several problems with the prior release related to building the Athena et al executables against the wrong version of the Ifeffit library. This update includes newly rebuilt executables for Athena, Artemis, Hephaestus, and Atoms. Additionally, the following features have been added to Athena: 1. Filename are sorted when importing multiple files. 2. Corrected a problem related to importing chi(k) data that do not start at 0. 3. Filetype plugins have been added for: - SSRL binary files - SSRL ASCII files - SSRL MicroEXAFS files - files from the CLS HXMA beamline - files from Photon Factory beamline 12C Enjoy! Bruce Ravel 25 Sep. 2008 ===========

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Broadening
by Eugenio Otal 01 Oct '08

01 Oct '08

Hello everybody, I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole broadening is 4.163, which value should I use in LDOS broadening to reproduce the experimental spectra. Thanks, euG

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Independence of scattering paths?
by van der Veen Renske 01 Oct '08

01 Oct '08

Hello! I have a question concerning the independence of scattering pathways. I fitted the EXAFS signal of a molecule consisting of 30 atoms (the related FEFF calculation is called calc 1). To see the effect of the surrounding solvent molecules in the chi(k) data, I added an O-atom in the coordinate list of the FEFF input file at an arbitrary distance from the absorbing atom (in this case Pt) and I re-ran FEFF (calc 2). As a check within calc 2, I generated the sum of the same scattering paths that were used in the fitting model of calc 1 using the therein obtained structural fit parameters. The new O-atom was not included in this sum. I expected the sum within calc 2 to be identical to the fit of calc 1 based on the fact that the original atoms can not sense the presence of the new O-atom (independence of scattering paths). BUT: the resulting sum was significantly different from the fit! Am I overlooking something here? Aren't the calculated backscatter amplitudes and phases independent from each other? I am using Artemis version 0.8.007, Windows XP, Ifeffit 1.2.9. Thank you! Best regards, Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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Re: [Ifeffit] Independence of scattering paths? (van der Veen Renske)
by Frommer Jakob 30 Sep '08

30 Sep '08

Hi Renske, I am not sure whether I fully understand your question but here is my *two-cent-explanation*: FEFF's first step is to calculate the potentials - since it is a real space code based on the muffin-tin approximation the surrounding of an atom determines the actual scattering potential (even if you are not doing a self-consistent calculation). Since the potentials in turn determine the backscattering amplitudes and phase shifts, placing an additional atom randomly in a structure is certainly not a good idea. A possible work-around may be to find a *similar* (but known) structure with oxygen ligands and combine these two calculations in artemis (for multiple scattering however the geometry can matter a lot). If your solvent contains oxygen already you may (at least as a first approximation and for single scattering) just duplicate that path in artemis. Regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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plot linetypes option in athena windows version
by Malte Schulz 22 Sep '08

22 Sep '08

Hi there, I would like to export graphics from Athena to use them in my b&w printed thesis. Therefore it would be really useful to have Athena cycle through linetypes instead of colors. I found the "linetypes" option in the "plot" section of the preferences menu. However it doesn't seem to have any effect. I am using Athena v. 0.8.056 for windows. Malte

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export from large Athena projects
by shiryaev＠crys.ras.ru 19 Sep '08

19 Sep '08

Hi, It seems that there is a problem in exporting normalised data files from large (i.e. >10 curves) Athena projects: Exported data are cut in energy. When one exports the files one by one, this problem does not occurs. All the best, Andrei

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[ATOMS] supercell input file
by Mauro Rovezzi 19 Sep '08

19 Sep '08

Dear all, I would like to submit to your attention a problem with Atoms that I still do not understand. What I would like to do is to generate a FEFF input file starting from a supercell, that is repeating the unit cell NXxNYxNZ times and create the crystal with the resulting box. An example is given in the attached _test-atoms.inp_ created following this procedure: from wurtzite GaN (a,c cell parameters) that we describe with 2 atoms I reduce the symmetry and I use 4 atoms, then I create a 72 atoms supercell - 4*(3x3x2) - that has 3ax3ax2c dimensions and finally I tell atoms to use "P1" space group in order to replicate the supercell in x,y,z space and shift at the center the absorbing atom. Here the *problem*: the resulting _test-feff8.inp_ present good values of distances but strangely it has generated an additional Fe potential (there is just 1 Fe absorbing atom in the box/list). This is annoying because I have to remove manually the wrong "ipot" to run FEFF. Is it a stupid mistake generating the Atoms input file or is it an odd behaviour? Cheers, Mauro PS: Atoms 3.0.1 (linux) 05/08/15 PPS: Do not pay attention to coordinates and distances, these are just test-files! -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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XANES peak fitting
by Dominik Samuelis 18 Sep '08

18 Sep '08

Dear Jenny, although it doesn't exactly look like the software in your attached word file (this probably is some special XPS instrument software), peak fitting can very nicely be done with the Athena program (Analysis -> Peak fit). It's got all the features that you'd expect from a peak fitting software (difference plot, component plot, the possibility to fix certain values, and an almost arbitrary number of gaussians :-) ). If you are not restricted to the ifeffit package, the Peak Fitting Module in OriginLab's Origin Pro also produces nice results. It's not free software, though. Cheers, dominik Am 18.09.2008 um 21:45 schrieb ifeffit- request(a)millenia.cars.aps.anl.gov: > From: Jenny Cai <jennyh_cai(a)yahoo.ca> > Subject: [Ifeffit] XANES peak fitting > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <407251.2113.qm(a)web88208.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > > Could anyone tell me which software in Ifeffit package can do peak > fitting like the one shown in the attached file? > > Thank you in advance! > > Jenny Cai > -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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Re: [Ifeffit] CFAVERAGE CARD
by joshua jason kas 18 Sep '08

18 Sep '08

Hi Cammelli, feff8 is hard coded to accept only 1000 atoms or less. The error message is not very informative and I don't think it applies to your case. What you want to do is recompile change the parameter natx in the source code to something larger, maybe 3000, and recompile. If you do not have the source code, you can find it at the feff webpage with the same username and password that was used to obtain your executable. Cheers, Josh Kas On Thu, 18 Sep 2008, 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. CFAVERAGE CARD (Cammelli Sebastiano) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 Sep 2008 15:59:43 +0200 > From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> > Subject: [Ifeffit] CFAVERAGE CARD > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <AD99CE4B84C4D3468F69B0E4FB345D58048FE174(a)MAILBOX0A.psi.ch> > Content-Type: text/plain; charset="us-ascii" > > Dear Iffefit user > > I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS > simulations. > > I need to simulate a cluster with 1481 atoms, let's say in a first > moment, composed of only Cu atoms. > > Without this card the simulations crashed and it was suggested to "Use > or reduce rclabs in CFAVERAGE card Or increase parameter natx and > recompile". > > I tried with different indexes: > > CFAVERAGE 1 -1 7 > > CFAVERAGE 0 -1 6... > > I could run EXAFS simulations but I could not get xmu.dat. > > FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is > NOT used). But how could I simulate larger clusters (with more then > 1000atoms)? > > Here I send you a copy of the feff.inp, I do not write here below all > the atoms between the 1st and the 37th shell because I do not want to > make this mail too large, but I attach the original file. > > > > TITLE A > > *cluster 1481 atoms > > CONTROL 1 1 1 1 1 1 > > PRINT 0 0 0 0 0 0 > > RMULTIPLIER 1 > > LDOS -30 20 0.2 > > EDGE K > > S02 1.0 > > SCF 4 0 30 0.2 1 > > NLEG 5 > > DEBYE 15 343 0 > > EXAFS > > RPATH 10.0 > > POTENTIALS > > 0 29 Cu 3 3 0.0010 > > 1 29 Cu 3 3 1.0 > > > > ATOMS * this list contains 1481 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Cu_1 0.00000 > > 1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 > > 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 > > .... > > 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > END > > > > > > Best > > Sebastiano Cammelli > > > >

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CFAVERAGE CARD
by Cammelli Sebastiano 18 Sep '08

18 Sep '08

Dear Iffefit user I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS simulations. I need to simulate a cluster with 1481 atoms, let's say in a first moment, composed of only Cu atoms. Without this card the simulations crashed and it was suggested to "Use or reduce rclabs in CFAVERAGE card Or increase parameter natx and recompile". I tried with different indexes: CFAVERAGE 1 -1 7 CFAVERAGE 0 -1 6... I could run EXAFS simulations but I could not get xmu.dat. FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is NOT used). But how could I simulate larger clusters (with more then 1000atoms)? Here I send you a copy of the feff.inp, I do not write here below all the atoms between the 1st and the 37th shell because I do not want to make this mail too large, but I attach the original file. TITLE A *cluster 1481 atoms CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 NLEG 5 DEBYE 15 343 0 EXAFS RPATH 10.0 POTENTIALS 0 29 Cu 3 3 0.0010 1 29 Cu 3 3 1.0 ATOMS * this list contains 1481 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Cu_1 0.00000 1.80753 1.80753 0.00000 1 Cu_1 2.55623 -1.80753 1.80753 0.00000 1 Cu_1 2.55623 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 1.80753 0.00000 1.80753 1 Cu_1 2.55623 -1.80753 0.00000 1.80753 1 Cu_1 2.55623 0.00000 1.80753 1.80753 1 Cu_1 2.55623 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 .... 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 END Best Sebastiano Cammelli

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 15 Sep '08

15 Sep '08

Thanks for checking this so quick. To give more details: after I have merged the datafiles I can not plot the data in any space anymore. Athena seems to process the data for plotting, but the plot program GrWnd does not respond, so this kind of problem is probably related to GrWnd only. However, when trying to merge something else inside this file, for example only 2 scans, the resulting merged datagroup is identical to the initial one, so Athena is not working properly too. Regards Timna-Josua Kuehn

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 12 Sep '08

12 Sep '08

Hi again, I attached a standard athena project file to this mail, in order to demonstrate the bug that follows a merging process. The project file contains 4 standard EXAFS measurements of a PtCo3/C nanoparticle (+ref) which shall be merged. As I told before the merging works, but afterwards I can not do anything else, the program hangs up. This bug does appear under Windows XP.c With best regards Timna-Josua Kuehn

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Re: [Ifeffit] broken feffit
by Matt Newville 09 Sep '08

09 Sep '08

Hi Shelly, On Tue, Sep 9, 2008 at 4:04 PM, Shelly Kelly <dr.sdkelly(a)gmail.com> wrote: > Hi Matt, > > I'm likely the last person on earth using this software....but feffit seems > to be broken in the latest version ifeffit-1.2.11a. > > I'm proud to have triggered the message: > >>>feffit error > routine fitfft failed internal test. > program error: contact matt > Fatel Error: feffit error Oh thanks! When playing around with Ifeffit this summer, I completely forgot about Feffit (what was I thinking about?). It is completely broken (but fortunately, it's a simple fix!). This is now fixed in svn, and I'll post a 1.2.11b tar ball to the cars ifeffit download site right away. > I went back to the version distributed with 1.2.9 and that one works for me. This doesn't affect Windows users, as the version of Feffit there is old enough to not have this bug. --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 15
by Khalid, Syed 09 Sep '08

09 Sep '08

Matt, We do use a cam when doing QEXAFS. Along with time and detector values we record the Bragg angle of the Si(111) monochromator as a function of optical encoder readout. The encoder values are random numbers but linear with the Bragg angle. Under normal routine QEXAFS we have developed programs to convert the QEAXFS data and make it compatible with Athena analysis. That works fine. In this particular case I wanted to compare Ni EXAFS scan done in conventional way to the one I got in 100 ms. For this particular scan I could not use the programs that we developed (for data conversion to Athena compatible, for many reasons). I wanted to see how a time axis converted to energy, compares with conventional EXAFS at FFT stage. It was also to find out, as you mentioned, if two energy points will match, then will it compare to conventional EXAFS in this particular case?? 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: Tuesday, September 09, 2008 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 15 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: Ifeffit Digest, Vol 67, Issue 12 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Sep 2008 11:14:12 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12 To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809090914o2e3d6773n370158b56f370077(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Syed, Adam, I think the suggestion from Adam and one of the suggestions from Anatoly assume the energy linear in time. Is that the really case? For quick-scanning modes, many beamlines run the mono at a constant angular velocity, so that time maps linearly to angle, which then needs to be converted (non-linearly) to energy. Then again, some quick-scanning beamlines use a special cam drive, in which neither angle nor energy would be linear in time. Again, you need know these details in order to correctly assign energies to the data. None of it is particularly difficult, so there's no point in guessing, and stretching or massaging the energy scale until two energy points correct does not mean the rest are correct. You need to find out from the beamline how the data mapped onto energy and fix that. While you can probably use Ifeffit macros within Athena to do this correction, this is really a job for the beamline, not for Athena. Having an option in Athena that allowed the user to say "I don't know why my energy scale is bad, but can you please stretch the energies so that these two energies are what I'd like them to be" is a horrible idea. --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 67, Issue 15 ***************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12
by Khalid, Syed 09 Sep '08

09 Sep '08

That is correct: It is a QEXAFS scan of Ni foil as a function of time. Please see the data attached as a .txt file. The first column is time, second I0, and third It. I can plot this in Athena, time appears at energy axis. I can set the first derivative to 8333.0 eV ( changing X-axis from time to energy ). If I have another known energy point of Ni scan ( which is not a problem ) then I can convert the time axis to correct energy axis and proceed with normal analysis. Is that possible? -----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: Tuesday, September 09, 2008 9:23 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 12 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: ODP: enrgy-axis-expansion (Bruce Ravel) 2. Re: ODP: enrgy-axis-expansion (Matt Newville) 3. Re: Bugs in Athena under Windows (Matt Newville) 4. Noise level in XANES spectrum (Pushan Shah) 5. Re: ODP: enrgy-axis-expansion (Zajac, Dariusz) 6. Re: Noise level in XANES spectrum (Zajac, Dariusz) 7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 16:59:08 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081659.08948.bravel(a)bnl.gov> Content-Type: text/plain; charset="utf-8" On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: > I do not clearly understood what you mean. could you explain it more > precisely? do you want to replace the x scale from energy to time? if you > want only set the edge energy use E0 Apparently (and Khalid or Anatoly should correct me if I am wrong), they are collecting data as a function of time in quick scan mode. They then have the problem of converting time to energy. If the mono speed is recorded somehow incorrectly, then there is an accordian effect throughout the data. I think that Khalid wants to be able to adjust this accordian effect to correct the energy scale of teh 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/ ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 16:18:55 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081418h564560d4n2fed4de0223e227(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Khalid, I agree with Dariusz: I do not understand the question. I have a hard time believing it is "the beamline cannot provide data as a function of energy, can Athena do this for me automatically?" (if it is, the answer is definitely 'No!'). Could you explain what you're trying to do? --Matt ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 16:24:45 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Bugs in Athena under Windows To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081424x5a6135dfk3aefb0e4a13c3bce(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Timna, Posting a project would definitely help here, as would clarify "since the last two versions ..." to say explicitly which versions do and do not work. My suspicion is that this related to the bug noted last week (and possibly another recent vague report of "not working") that is due to the latest version of athena -for-windows being hard-linked to pre-final-release of the ifeffit dll which is making athena's ifeffit session get stuck in an unresponsive state. I believe the only cure is a new version of athena. Again, if you could post a project that demonstrates the problem, that would be most helpful. --Matt ------------------------------ Message: 4 Date: Tue, 09 Sep 2008 15:48:51 +1000 From: "Pushan Shah" <pshah(a)gse.mq.edu.au> Subject: [Ifeffit] Noise level in XANES spectrum To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <48C69AE2.0BBD.0060.0(a)gse.mq.edu.au> Content-Type: text/plain; charset=US-ASCII Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan ------------------------------ Message: 5 Date: Tue, 9 Sep 2008 10:03:46 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "Bruce Ravel" <bravel(a)bnl.gov>, "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" hi so, I think, in case of converting time scale to energy - this should be supported by beamline (beamline scientist) somehow... if there is any nonlinearity of the converion factor (Anatoly - what whould happened if D parameter is time/energy dependent?) I think only reference spectra can help - do you have it Syed? if you have all needed parameters the calibration can be relatively quickly done in some other programs, also in macro (for many files) but that's my speculations kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Monday, September 08, 2008 10:59 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion > > >On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: >> I do not clearly understood what you mean. could you explain it more >> precisely? do you want to replace the x scale from energy to >time? if >> you want only set the edge energy use E0 > > >Apparently (and Khalid or Anatoly should correct me if I am >wrong), they are collecting data as a function of time in >quick scan mode. They then have the problem of converting >time to energy. If the mono speed is recorded somehow >incorrectly, then there is an accordian effect throughout the >data. I think that Khalid wants to be able to adjust this >accordian effect to correct the energy scale of teh 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/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 6 Date: Tue, 9 Sep 2008 10:12:42 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] Noise level in XANES spectrum To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" Hi Pushan, can you tell more about the experiment and the way of data collecting? how did you measure your samples? which method did you use? what kind of samples do you have? the answer of your question is not stricted, but generaly I would say that the noise level should be independent of the samples, did you change something on the beamline or program between samples/measurements? e.g. sample time, no. of repeats, you moved in /out detector, amplification gain, etc.... kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Pushan Shah >Sent: Tuesday, September 09, 2008 7:49 AM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] Noise level in XANES spectrum > > >Hello Everyone, > >I have a general question regarding noise level of XANES >spectrum. I have collected XANES data for an element which is >present in ppm level in my samples. > >Some samples are exhibiting varying degree of noise in XANES >spectrum. > >Is the noise level of XANES spectrum would be proportional or >consistent with the concentration of the sample? As XANES >spectra for some of my samples with relatively higher >concentration of this element are exhibiting greater level of >noise than those with relatively lower concentrations. Will >sample matrix play any role in the noise level? > >Thanks and I appreciate your help. > >regards, >Pushan > > > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 7 Date: Tue, 9 Sep 2008 09:22:14 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD18B(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? 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: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ 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] Ifeffit Digest, Vol 67, Issue 11
by Khalid, Syed 09 Sep '08

09 Sep '08

Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? 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: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
by Frenkel, Anatoly 09 Sep '08

09 Sep '08

No, if you enter any number in the energy shift window, the entire scale is shifted. This linear scaling can be done only for small shifts, in XANES region. For larger shifts you need parabolic correction, or even use a splice method where different corrections are applied to different sub-ranges of the data, and then the entire (supposedly, correct) energy range is spliced from Such corrected ranges. Suppose, you took data at the beamline where you discovered there is energy tracking problem, which is reproducible. Then you can fix it, assuming you collected also data in a reference foil and can compare such data against a "standard" data of the foil. It is very time consuming but doable. 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: Tue Sep 09 09:22:14 2008 Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? 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: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Noise level in XANES spectrum
by Pushan Shah 09 Sep '08

09 Sep '08

Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan

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enrgy-axis-expansion
by Khalid, Syed 09 Sep '08

09 Sep '08

Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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Bugs in Athena under Windows
by Timna-Josua Kuehn 08 Sep '08

08 Sep '08

Hello, since the last two versions of Athena under Windows some serious bugs have appeared. Whenever I merge some datasets, Athena somehow breaks down afterwards. The window is still open, but I can not plot anything, nor do any other operation. The same happens when I try to align or convolute some spectrum. Thanks for checking this. Timna

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FW: enrgy-axis-expansion
by Khalid, Syed 08 Sep '08

08 Sep '08

-----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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A problem with Athena
by NIRAWAT THAMMAJAK 08 Sep '08

08 Sep '08

Hello, May I ask a short question here. I don't know why now Athena cannot open any data files. It is said "you have not used any memory yet" in the bottom.* *I have tried to go back and used the older version (1.2.10), which once it used to work very well, and it started to have the same problem. I've heard about bug stuff in a former mailing list, but i don't know how to solve it. It would be very grateful if you could let me know a short solution for this. Please accept my appreciation for your kindly help. Best Regards, Nirawat. -- Nirawat Thammajak Research and Academic Division, National Synchrotron Research Center, PO Box 93, Nakhon Ratchasima 30000 Thailand. Tel. (+66) 044-217040 ext. 504 Fax (+66) 044-217047

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Re: [Ifeffit] lanthanides convergence
by Eugenio Otal 06 Sep '08

06 Sep '08

Dear Micah, I attach six xmu.dat files and its feff.inp files. The atoms range is from 230 to 488 atoms. The convergence for SCF is achieved but not for FMS, I have some more files with problem to converge the FMS, but the server is in back up process in this moment, I will post them ASAP if necessary. I found the core-hole broadening in xmu.dat, but which is a correct criteria to choose the broadening for the LDOS? Thanks in advance, euG Eugenio, Can you post some of your xmu.dat files generated with various cluster sizes? That might give a clue as to what is going on. > If I increase the broadening for the LDOS, the default is 0.1eV for > the one exported by Arthemis and 0.2eV is shown in the manual, the > last one is still small compared with 4.16 eV. Which is a good > criteria to choose it and where I can find the core hole broadening > value? > The core-hole broadening in eV is reported in the header of xmu.dat as Gam_ch. Here is the relevant line from one of my files: # Gam_ch=8.302E+00 H-L exch Vi= 2.000E+00 Vr= 0.000E+00 > I will quit the LDOS card to obtain results faster, but pot.bin > will be generated anyway (I will leave the CONTROL card option on), > if not, is it needed for another calculation? The calculations > (without the LDOS) and the spectra will be obtained like before? > You can compute pot.bin once and do subsequent calculations with CONTROL 0 1 1 1 1 1. This will cause FEFF to skip the potentials calculation and use the result (saved in pot.bin) of the previous run. There is no need to recalculate the potentials for each run in a convergence test unless you are converging parameters relevant to the potentials calculation. Best Wishes, Micah Prange 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Re: [Ifeffit] lanthanides convergence
by Eugenio Otal 05 Sep '08

05 Sep '08

Hi Joshua, I can not find convergence on the absorption spectra. It is very hard to believe that 500 atoms is not enough to find a converged spectra. If I increase the broadening for the LDOS, the default is 0.1eV for the one exported by Arthemis and 0.2eV is shown in the manual, the last one is still small compared with 4.16 eV. Which is a good criteria to choose it and where I can find the core hole broadening value? I will quit the LDOS card to obtain results faster, but pot.bin will be generated anyway (I will leave the CONTROL card option on), if not, is it needed for another calculation? The calculations (without the LDOS) and the spectra will be obtained like before? I will implement the lanczos algorithm too and parameter nex to obtain faster results with a bigger number of atoms. Cheers, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Hi Eugenio, I have a question for you, When you say that convergence is not reached, do you mean convergence of the absoption spectrum or convergence of the LDOS? These are very different since the absorption has core-hole and self-energy broadening included. I noticed that you use 0.1 eV broadening for the LDOS, which is much smaller than the core hole broadening which is 4.16eV. Also, the calculation will be much quicker if you do not run LDOS since FEFF does the matrix inversion for each unique potential and energy when the LDOS card is present. Otherwise, the inversion is only done for the central atom potential at each energy. Cheers, Josh Kas > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** 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 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

2 1

chi(k) Athena bug?
by Olivier 04 Sep '08

04 Sep '08

Dear all, I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k. When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just froze. Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success. In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data. To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval. Do you also experience this tiny Athena 0.8.056 (XP OS) bug? Or is there a workaround? Best regards, Oli ++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat(a)env.ethz.ch

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Re: [Ifeffit] lanthanides convergence
by joshua jason kas 03 Sep '08

03 Sep '08

Hi Eugenio, I have a question for you, When you say that convergence is not reached, do you mean convergence of the absoption spectrum or convergence of the LDOS? These are very different since the absorption has core-hole and self-energy broadening included. I noticed that you use 0.1 eV broadening for the LDOS, which is much smaller than the core hole broadening which is 4.16eV. Also, the calculation will be much quicker if you do not run LDOS since FEFF does the matrix inversion for each unique potential and energy when the LDOS card is present. Otherwise, the inversion is only done for the central atom potential at each energy. Cheers, Josh Kas > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** 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 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

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Re: [Ifeffit] Problem reproducing spectrum for Ti complex (Josh Kas)
by joshua jason kas 03 Sep '08

03 Sep '08

Hi Janine, I think that distortions could play a role here. When I shift the central Ti atom by 0.1 angstroms in plane (perpendicular to the Cl bonds) to break the planar symmetry, I get a clear double pre-edge peak. 0.1 angstroms may be a bit large but 0.05 is certainly not, since 0.003 angstroms**2 is a very reasonable value for sigma**2. You could also estimate the distortion if you have more information about the debye waller factors, or even better, you could perform a molecular dynamics simulation and do a configurational average of the XANES spectra from snapshots. Below is the feff.inp file that I used. You might want to play with shifting the Ti atom in different directions too. Cheers, Josh Kas TITLE TiPcCl2 molecule Geom1acc CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 9.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 0 0 0 *Dirac Hara, -1eV Fermi level shift, -3 broadening SCF 8.0 1 *includes second coordination shell XANES 6.0 0.03 0.001 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 SIG2 0.005 * emin emax eimag * LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS 0 0.1 0 0 0 -0.00040276 -2.1184 -0.28392 2 2.13734 -2.11835 0.00044201 -0.284329 2 2.13734 0.00049691 2.11839 -0.284036 2 2.13734 2.11844 -0.00045764 -0.283627 2 2.13734 -0.00040584 6.782e-05 2.45003 4 2.45003 0.00040523 -6.766e-05 -2.45005 4 2.45005 -1.14859 2.9207 -0.359915 1 3.159 -1.14983 -2.92023 -0.359755 1 3.159 -2.92016 1.14988 -0.36016 1 3.159 -2.92065 -1.14866 -0.360097 1 3.159 1.14871 -2.92072 -0.359374 1 3.159 1.14995 2.92021 -0.359534 1 3.159 2.92028 -1.1499 -0.359129 1 3.159 2.92077 1.14864 -0.359192 1 3.159 -2.49915 2.50027 -0.371632 2 3.5546 -2.50021 -2.49922 -0.371494 2 3.5546 2.49928 -2.50029 -0.370665 2 3.5546 2.50034 2.4992 -0.370803 2 3.5546 -0.692606 4.24003 -0.468777 1 4.32173 -0.694406 -4.23976 -0.468544 1 4.32173 -4.23967 0.694471 -0.469267 1 4.32173 -4.23997 -0.692696 -0.469229 1 4.32173 0.692761 -4.24006 -0.468314 1 4.32173 0.694562 4.23974 -0.468547 1 4.32173 4.23983 -0.694497 -0.467823 1 4.32173 4.24012 0.69267 -0.467862 1 4.32173 -1.42292 5.42169 -0.582346 1 5.63547 -1.42522 -5.42112 -0.582048 1 5.63547 -5.42101 1.4253 -0.582898 1 5.63547 -5.42161 -1.42303 -0.58282 1 5.63547 1.42311 -5.42172 -0.581576 1 5.63547 1.42541 5.42109 -0.581873 1 5.63547 5.4212 -1.42533 -0.581023 1 5.63547 5.42181 1.423 -0.581101 1 5.63547 -2.50314 5.41265 -0.586151 3 5.99217 -2.50544 -5.41162 -0.585854 3 5.99217 -5.41151 2.50552 -0.586554 3 5.99217 -5.41257 -2.50326 -0.586416 3 5.99217 2.50334 -5.41269 -0.585024 3 5.99217 2.50564 5.41159 -0.585321 3 5.99217 5.4117 -2.50555 -0.584622 3 5.99217 5.41277 2.50322 -0.584759 3 5.99217 -0.705001 6.62658 -0.692551 1 6.69987 -0.707815 -6.62632 -0.692187 1 6.69987 -6.62618 0.707911 -0.693369 1 6.69987 -6.62648 -0.705135 -0.69333 1 6.69987 0.70523 -6.62662 -0.691953 1 6.69987 0.708044 6.62628 -0.692316 1 6.69987 6.62641 -0.707949 -0.691134 1 6.69987 6.62671 0.705096 -0.691173 1 6.69987 -1.23945 7.56123 -0.780998 3 7.70184 -1.24266 -7.56074 -0.780583 3 7.70184 -7.56059 1.24277 -0.781872 3 7.70184 -7.56112 -1.2396 -0.781804 3 7.70184 1.23971 -7.56127 -0.780172 3 7.70184 1.24292 7.5607 -0.780587 3 7.70184 7.56085 -1.24281 -0.779298 3 7.70184 7.56138 1.23956 -0.779366 3 7.70184 END On Thu, 28 Aug 2008, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 1. Problem reproducing spectrum for Ti complex (Janine GRATTAGE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 28 Aug 2008 10:42:31 +0200 > From: Janine GRATTAGE <janine.grattage(a)esrf.fr> > Subject: [Ifeffit] Problem reproducing spectrum for Ti complex > To: Ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <48B664F7.6010704(a)esrf.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Dear IFEFFIT mailing list, > > I have been trying to reproduce the XANES spectrum of a titanium > compound (titanium phthalocyanine dichloride) using FEFF 8.4. The > overall shape is reproduced reasonably well, but I wanted to ask the > mailing list users if they have any ideas as to how to improve the > details such as the pre-edge (to give two distinct peaks) and peak > positions over the absorption edge. > > I have attached a file showing the experimental spectrum, two FEFF input > files and the corresponding XMU output files. These two files have the > same atomic co-ordinates for the molecule, but one has 'standard' > broadening and the Fermi level has been shifted by -1eV (geom1) where > the other has reduced experimental broadening (-3) a shifted Fermi > level, and smaller step size (geom1acc). > > I have tried changing the geometry of the molecule by moving one or both > of the Cl atoms, and by trying a flat molecular geometry rather than the > 'umbrella' shape in the attached files, but the spectra attached are the > best match to experiment. Any help or suggestions on improvements would > be greatly appreciated. > > Best regards and thanks in advance, > > Janine Grattage > > -- > 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 > >

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Re: [Ifeffit] lanthanides convergence
by hebhop＠u.washington.edu 02 Sep '08

02 Sep '08

Hi Eugenio, You can use the lanczos algorithm for the matrix inverse. This is specified by setting the fourth option to the FMS card to 2. FMS 5.0 0 2 Also, make sure that the number of energy points is not set too large, that is check the parameter nex in the code. Set it to 150 or so. I have a feeling that it is set to 400. These two things should reduce the time by a factor of 4 at least. Cheers, Josh Kas > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: lanthanides convergence (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Sep 2008 23:58:55 -0300 > From: "Eugenio Otal" <eugenioh(a)gmail.com> > Subject: Re: [Ifeffit] lanthanides convergence > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <da22ad30809011958g484a5cfr750341645402fb74(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** 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 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

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lanthanides convergence
by Eugenio Otal 02 Sep '08

02 Sep '08

Bruce, I am running feff to model XANES of Erbium doped ZnO. I have a big problem to find the convergence of FMS in this kind of systems. I increased the atoms number in feff code to nclusx=500 and still have not found convergence. Should I increase the nclusx to a bigger number?, is there a limit for this number independent from the computer RAM or I do have another chance?. Thanks for your time and patience. 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Eugenio H. Otal CINSO - CONICET - CITEFA eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 2

Problem reproducing spectrum for Ti complex
by Janine GRATTAGE 29 Aug '08

29 Aug '08

Dear IFEFFIT mailing list, I have been trying to reproduce the XANES spectrum of a titanium compound (titanium phthalocyanine dichloride) using FEFF 8.4. The overall shape is reproduced reasonably well, but I wanted to ask the mailing list users if they have any ideas as to how to improve the details such as the pre-edge (to give two distinct peaks) and peak positions over the absorption edge. I have attached a file showing the experimental spectrum, two FEFF input files and the corresponding XMU output files. These two files have the same atomic co-ordinates for the molecule, but one has 'standard' broadening and the Fermi level has been shifted by -1eV (geom1) where the other has reduced experimental broadening (-3) a shifted Fermi level, and smaller step size (geom1acc). I have tried changing the geometry of the molecule by moving one or both of the Cl atoms, and by trying a flat molecular geometry rather than the 'umbrella' shape in the attached files, but the spectra attached are the best match to experiment. Any help or suggestions on improvements would be greatly appreciated. Best regards and thanks in advance, Janine Grattage -- 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 TITLE TiPcCl2 molecule Geom1acc CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1. -3. *Dirac Hara, -1eV Fermi level shift, -3 broadening SCF 4 *includes second coordination shell XANES 6.0 0.03 0.001 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule Geom1acc Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi=-3.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax= 0.100, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.8609E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4966.250 -12.512 -0.540 9.13165E-04 3.37112E-03 -2.45795E-03 4966.484 -12.279 -0.480 1.06274E-03 4.18380E-03 -3.12106E-03 4966.689 -12.074 -0.420 1.27282E-03 5.35021E-03 -4.07739E-03 4966.868 -11.895 -0.360 1.58625E-03 7.11910E-03 -5.53285E-03 4967.019 -11.744 -0.300 2.09217E-03 1.00069E-02 -7.91471E-03 4967.142 -11.621 -0.240 3.00252E-03 1.52351E-02 -1.22326E-02 4967.238 -11.525 -0.180 4.92381E-03 2.62777E-02 -2.13539E-02 4967.307 -11.456 -0.120 1.00982E-02 5.59015E-02 -4.58033E-02 4967.348 -11.415 -0.060 2.70590E-02 1.52513E-01 -1.25454E-01 4967.351 -11.412 -0.051 3.08226E-02 1.73905E-01 -1.43082E-01 4967.361 -11.402 0.000 4.35361E-02 2.46060E-01 -2.02524E-01 4967.365 -11.398 0.030 4.81925E-02 2.72502E-01 -2.24310E-01 4967.375 -11.388 0.060 5.99908E-02 3.39822E-01 -2.79831E-01 4967.392 -11.371 0.090 7.06798E-02 4.01939E-01 -3.31259E-01 4967.416 -11.347 0.120 7.66663E-02 4.38394E-01 -3.61727E-01 4967.447 -11.316 0.150 7.97483E-02 4.59111E-01 -3.79362E-01 4967.485 -11.278 0.180 8.14520E-02 4.72336E-01 -3.90884E-01 4967.529 -11.233 0.210 8.25377E-02 4.81982E-01 -3.99444E-01 4967.581 -11.182 0.240 8.33826E-02 4.89861E-01 -4.06478E-01 4967.639 -11.124 0.270 8.41397E-02 4.96841E-01 -4.12701E-01 4967.704 -11.059 0.300 8.48985E-02 5.03368E-01 -4.18469E-01 4967.776 -10.987 0.330 8.56237E-02 5.09640E-01 -4.24016E-01 4967.855 -10.908 0.360 8.62149E-02 5.15699E-01 -4.29484E-01 4967.941 -10.822 0.390 8.67731E-02 5.21557E-01 -4.34784E-01 4968.034 -10.729 0.420 8.78023E-02 5.27174E-01 -4.39371E-01 4968.133 -10.630 0.450 9.10340E-02 5.32553E-01 -4.41519E-01 4968.239 -10.524 0.480 1.04529E-01 5.37749E-01 -4.33220E-01 4968.352 -10.411 0.510 1.23575E-01 5.42866E-01 -4.19290E-01 4968.472 -10.291 0.540 1.10145E-01 5.48027E-01 -4.37883E-01 4968.599 -10.164 0.570 1.15424E-01 5.53380E-01 -4.37956E-01 4968.733 -10.030 0.600 1.29776E-01 5.59004E-01 -4.29228E-01 4968.874 -9.889 0.630 1.40253E-01 5.64967E-01 -4.24714E-01 4969.021 -9.742 0.660 1.30116E-01 5.71309E-01 -4.41194E-01 4969.175 -9.588 0.690 1.02880E-01 5.78006E-01 -4.75126E-01 4969.337 -9.426 0.720 7.82317E-02 5.85054E-01 -5.06823E-01 4969.505 -9.258 0.750 6.27424E-02 5.92438E-01 -5.29696E-01 4969.679 -9.084 0.780 5.40260E-02 6.00135E-01 -5.46109E-01 4969.861 -8.902 0.810 4.93417E-02 6.08094E-01 -5.58753E-01 4970.050 -8.713 0.840 4.72836E-02 6.16308E-01 -5.69025E-01 4970.245 -8.518 0.870 4.73852E-02 6.24726E-01 -5.77341E-01 4970.448 -8.315 0.900 5.02215E-02 6.33358E-01 -5.83136E-01 4970.657 -8.106 0.930 5.67812E-02 6.42152E-01 -5.85370E-01 4970.873 -7.890 0.960 6.13993E-02 6.51085E-01 -5.89686E-01 4971.096 -7.667 0.990 5.66943E-02 6.60139E-01 -6.03445E-01 4971.325 -7.438 1.020 6.16275E-02 6.69310E-01 -6.07683E-01 4971.562 -7.201 1.050 7.15826E-02 6.78561E-01 -6.06979E-01 4971.805 -6.958 1.080 6.00972E-02 6.87872E-01 -6.27775E-01 4972.056 -6.707 1.110 6.50374E-02 6.97223E-01 -6.32185E-01 4972.313 -6.450 1.140 7.38111E-02 7.06611E-01 -6.32800E-01 4972.577 -6.186 1.170 8.62661E-02 7.16016E-01 -6.29750E-01 4972.848 -5.915 1.200 1.03456E-01 7.25401E-01 -6.21944E-01 4973.126 -5.637 1.230 1.26524E-01 7.34746E-01 -6.08222E-01 4973.410 -5.353 1.260 1.54971E-01 7.44066E-01 -5.89095E-01 4973.702 -5.061 1.290 1.82740E-01 7.53341E-01 -5.70601E-01 4974.000 -4.763 1.320 2.00380E-01 7.62518E-01 -5.62138E-01 4974.305 -4.458 1.350 2.11141E-01 7.71629E-01 -5.60487E-01 4974.617 -4.146 1.380 2.30273E-01 7.80636E-01 -5.50363E-01 4974.936 -3.827 1.410 2.66899E-01 7.89521E-01 -5.22623E-01 4975.262 -3.501 1.440 3.21552E-01 7.98299E-01 -4.76747E-01 4975.594 -3.169 1.470 3.88177E-01 8.06915E-01 -4.18738E-01 4975.934 -2.829 1.500 4.53793E-01 8.15386E-01 -3.61592E-01 4976.280 -2.483 1.530 5.03101E-01 8.23710E-01 -3.20609E-01 4976.633 -2.130 1.560 5.32723E-01 8.31850E-01 -2.99127E-01 4976.993 -1.769 1.590 5.66560E-01 8.39805E-01 -2.73245E-01 4977.360 -1.403 1.620 6.34775E-01 8.47573E-01 -2.12798E-01 4977.734 -1.029 1.650 6.84473E-01 8.55136E-01 -1.70663E-01 4978.115 -0.648 1.680 6.71745E-01 8.62493E-01 -1.90748E-01 4978.502 -0.261 1.710 7.03172E-01 8.69644E-01 -1.66472E-01 4978.897 0.134 1.740 7.94749E-01 8.76587E-01 -8.18378E-02 4979.298 0.535 1.770 8.38553E-01 8.83285E-01 -4.47320E-02 4979.706 0.943 1.800 8.11564E-01 8.89757E-01 -7.81934E-02 4980.121 1.358 1.830 8.36275E-01 8.96019E-01 -5.97439E-02 4980.542 1.780 1.860 9.16563E-01 9.02018E-01 1.45451E-02 4980.971 2.208 1.890 1.00872E+00 9.07788E-01 1.00932E-01 4981.407 2.644 1.920 1.08114E+00 9.13312E-01 1.67828E-01 4981.849 3.086 1.950 1.11955E+00 9.18608E-01 2.00945E-01 4982.298 3.535 1.980 1.13308E+00 9.23657E-01 2.09423E-01 4982.754 3.991 2.010 1.14273E+00 9.28461E-01 2.14271E-01 4983.217 4.454 2.040 1.15283E+00 9.33035E-01 2.19790E-01 4983.687 4.924 2.070 1.15849E+00 9.37346E-01 2.21143E-01 4984.163 5.401 2.100 1.16452E+00 9.41447E-01 2.23068E-01 4984.647 5.884 2.130 1.18412E+00 9.45303E-01 2.38817E-01 4985.137 6.374 2.160 1.21498E+00 9.48932E-01 2.66044E-01 4985.634 6.872 2.190 1.24240E+00 9.52334E-01 2.90069E-01 4986.139 7.376 2.220 1.25155E+00 9.55511E-01 2.96036E-01 4986.649 7.887 2.250 1.23876E+00 9.58461E-01 2.80303E-01 4987.167 8.404 2.280 1.21617E+00 9.61204E-01 2.54969E-01 4987.692 8.929 2.310 1.20218E+00 9.63742E-01 2.38437E-01 4988.223 9.460 2.340 1.21246E+00 9.66074E-01 2.46388E-01 4988.762 9.999 2.370 1.25770E+00 9.68220E-01 2.89477E-01 4989.307 10.544 2.400 1.32791E+00 9.70161E-01 3.57749E-01 4989.859 11.096 2.430 1.38130E+00 9.71917E-01 4.09379E-01 4990.418 11.655 2.460 1.38220E+00 9.73507E-01 4.08696E-01 4990.984 12.221 2.490 1.34139E+00 9.74933E-01 3.66459E-01 4991.556 12.793 2.520 1.29626E+00 9.76174E-01 3.20089E-01 4992.136 13.373 2.550 1.27334E+00 9.77270E-01 2.96074E-01 4992.722 13.959 2.580 1.27044E+00 9.78222E-01 2.92220E-01 4993.315 14.552 2.610 1.26795E+00 9.79029E-01 2.88916E-01 4993.915 15.153 2.640 1.25051E+00 9.79692E-01 2.70818E-01 4994.522 15.759 2.670 1.21688E+00 9.80191E-01 2.36689E-01 TITLE TiPcCl2 molecule Geom1 CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1 *Dirac Hara, -1eV Fermi level shift SCF 4 *includes second coordination shell XANES 6.0 0.05 0.01 AFOLP 1.2 CRITERION 0 0 *use all paths *RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule (positions calculated from ADF) Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi= 0.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax=-1.000, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.6992E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4964.275 -14.488 -0.900 1.44077E-02 3.21565E-02 -1.77488E-02 4964.923 -13.840 -0.800 1.61993E-02 3.95010E-02 -2.33017E-02 4965.495 -13.268 -0.700 1.84771E-02 4.97434E-02 -3.12663E-02 4965.990 -12.773 -0.600 2.15278E-02 6.45932E-02 -4.30654E-02 4966.409 -12.354 -0.500 2.58451E-02 8.69527E-02 -6.11076E-02 4966.752 -12.011 -0.400 3.21686E-02 1.21157E-01 -8.89880E-02 4967.019 -11.744 -0.300 4.10037E-02 1.70217E-01 -1.29214E-01 4967.209 -11.554 -0.200 5.09103E-02 2.25913E-01 -1.75002E-01 4967.323 -11.440 -0.100 5.83015E-02 2.67539E-01 -2.09238E-01 4967.351 -11.412 -0.051 6.02274E-02 2.78296E-01 -2.18069E-01 4967.361 -11.402 0.000 6.09319E-02 2.82145E-01 -2.21213E-01 4967.371 -11.392 0.050 6.15821E-02 2.85805E-01 -2.24223E-01 4967.400 -11.363 0.100 6.35112E-02 2.96793E-01 -2.33281E-01 4967.447 -11.316 0.150 6.67307E-02 3.14931E-01 -2.48200E-01 4967.514 -11.249 0.200 7.10829E-02 3.39349E-01 -2.68267E-01 4967.600 -11.163 0.250 7.62645E-02 3.68148E-01 -2.91884E-01 4967.704 -11.059 0.300 8.19260E-02 3.98629E-01 -3.16703E-01 4967.828 -10.935 0.350 8.77714E-02 4.28185E-01 -3.40413E-01 4967.971 -10.792 0.400 9.37945E-02 4.55258E-01 -3.61463E-01 4968.133 -10.630 0.450 1.00145E-01 4.79354E-01 -3.79209E-01 4968.314 -10.449 0.500 1.06691E-01 5.00709E-01 -3.94018E-01 4968.514 -10.249 0.550 1.12394E-01 5.19879E-01 -4.07485E-01 4968.733 -10.030 0.600 1.15591E-01 5.37511E-01 -4.21920E-01 4968.971 -9.792 0.650 1.13910E-01 5.54177E-01 -4.40267E-01 4969.228 -9.535 0.700 1.06198E-01 5.70351E-01 -4.64152E-01 4969.505 -9.258 0.750 9.61631E-02 5.86343E-01 -4.90179E-01 4969.800 -8.963 0.800 8.86382E-02 6.02345E-01 -5.13707E-01 4970.114 -8.649 0.850 8.55330E-02 6.18458E-01 -5.32925E-01 4970.448 -8.315 0.900 8.67318E-02 6.34730E-01 -5.47998E-01 4970.800 -7.963 0.950 9.08250E-02 6.51152E-01 -5.60327E-01 4971.171 -7.592 1.000 9.64994E-02 6.67694E-01 -5.71195E-01 4971.562 -7.201 1.050 1.03277E-01 6.84334E-01 -5.81056E-01 4971.972 -6.791 1.100 1.11508E-01 7.01012E-01 -5.89504E-01 4972.400 -6.363 1.150 1.27017E-01 7.17678E-01 -5.90661E-01 4972.848 -5.915 1.200 1.51783E-01 7.34259E-01 -5.82476E-01 4973.315 -5.448 1.250 1.85121E-01 7.50729E-01 -5.65608E-01 4973.800 -4.963 1.300 2.22060E-01 7.66999E-01 -5.44939E-01 4974.305 -4.458 1.350 2.60104E-01 7.83015E-01 -5.22911E-01 4974.829 -3.934 1.400 3.10517E-01 7.98732E-01 -4.88216E-01 4975.372 -3.391 1.450 3.82202E-01 8.14085E-01 -4.31883E-01 4975.934 -2.829 1.500 4.63881E-01 8.29030E-01 -3.65149E-01 4976.515 -2.248 1.550 5.37065E-01 8.43501E-01 -3.06436E-01 4977.115 -1.648 1.600 6.07253E-01 8.57469E-01 -2.50216E-01 4977.734 -1.029 1.650 6.73937E-01 8.70893E-01 -1.96956E-01 4978.372 -0.391 1.700 7.30804E-01 8.83727E-01 -1.52923E-01 4979.030 0.267 1.750 8.02516E-01 8.95956E-01 -9.34395E-02 4979.706 0.943 1.800 8.54202E-01 9.07537E-01 -5.33342E-02 4980.401 1.638 1.850 9.26242E-01 9.18471E-01 7.77126E-03 4981.115 2.353 1.900 1.02684E+00 9.28720E-01 9.81182E-02 4981.849 3.086 1.950 1.10155E+00 9.38305E-01 1.63246E-01 4982.601 3.838 2.000 1.13866E+00 9.47198E-01 1.91459E-01 4983.373 4.610 2.050 1.16173E+00 9.55400E-01 2.06331E-01 4984.163 5.401 2.100 1.18362E+00 9.62930E-01 2.20694E-01 4984.973 6.210 2.150 1.21605E+00 9.69805E-01 2.46241E-01 4985.802 7.039 2.200 1.24599E+00 9.76015E-01 2.69973E-01 4986.649 7.887 2.250 1.25003E+00 9.81596E-01 2.68433E-01 4987.516 8.753 2.300 1.24364E+00 9.86570E-01 2.57068E-01 4988.402 9.639 2.350 1.26862E+00 9.90955E-01 2.77669E-01 4989.307 10.544 2.400 1.33164E+00 9.94768E-01 3.36871E-01 4990.231 11.468 2.450 1.36605E+00 9.98067E-01 3.67984E-01 4991.174 12.411 2.500 1.33716E+00 1.00084E+00 3.36318E-01 4992.136 13.373 2.550 1.30098E+00 1.00317E+00 2.97807E-01 4993.117 14.354 2.600 1.28188E+00 1.00505E+00 2.76824E-01 4994.117 15.354 2.650 1.24913E+00 1.00652E+00 2.42606E-01 4995.136 16.373 2.700 1.19116E+00 1.00762E+00 1.83538E-01 4996.174 17.412 2.750 1.12334E+00 1.00839E+00 1.14945E-01 4997.232 18.469 2.800 1.05879E+00 1.00886E+00 4.99339E-02 4998.308 19.545 2.850 1.00361E+00 1.00905E+00 -5.44234E-03 4999.403 20.640 2.900 9.66190E-01 1.00899E+00 -4.28024E-02 5000.518 21.755 2.950 9.53894E-01 1.00874E+00 -5.48451E-02 5001.651 22.888 3.000 9.61104E-01 1.00831E+00 -4.72049E-02 5002.804 24.041 3.050 9.70657E-01 1.00771E+00 -3.70537E-02 5003.975 25.212 3.100 9.65699E-01 1.00699E+00 -4.12896E-02 5005.166 26.403 3.150 9.43779E-01 1.00616E+00 -6.23849E-02 5006.376 27.613 3.200 9.12270E-01 1.00527E+00 -9.29971E-02 5007.604 28.841 3.250 8.79909E-01 1.00430E+00 -1.24395E-01 5008.852 30.089 3.300 8.53592E-01 1.00330E+00 -1.49707E-01 5010.119 31.356 3.350 8.37319E-01 1.00228E+00 -1.64962E-01 5011.405 32.642 3.400 8.32342E-01 1.00126E+00 -1.68915E-01 5012.710 33.947 3.450 8.37897E-01 1.00024E+00 -1.62341E-01 5014.034 35.271 3.500 8.52224E-01 9.99254E-01 -1.47030E-01 5015.377 36.614 3.550 8.73066E-01 9.98292E-01 -1.25226E-01 5016.739 37.976 3.600 8.98424E-01 9.97383E-01 -9.89589E-02 5018.120 39.357 3.650 9.25999E-01 9.96535E-01 -7.05367E-02 5019.520 40.757 3.700 9.53423E-01 9.95731E-01 -4.23079E-02 5020.939 42.176 3.750 9.78294E-01 9.94988E-01 -1.66939E-02 5022.378 43.615 3.800 9.98847E-01 9.94307E-01 4.53986E-03 5023.835 45.072 3.850 1.01451E+00 9.93705E-01 2.08018E-02 5025.311 46.548 3.900 1.02568E+00 9.93184E-01 3.25003E-02 5026.807 48.044 3.950 1.03332E+00 9.92711E-01 4.06132E-02 5028.321 49.558 4.000 1.03851E+00 9.92313E-01 4.61965E-02 5029.855 51.092 4.050 1.04223E+00 9.91980E-01 5.02542E-02 5031.407 52.644 4.100 1.04512E+00 9.91711E-01 5.34115E-02 5032.979 54.216 4.150 1.04746E+00 9.91501E-01 5.59600E-02 5034.570 55.807 4.200 1.04937E+00 9.91335E-01 5.80315E-02 5036.179 57.416 4.250 1.05095E+00 9.91211E-01 5.97411E-02 5037.808 59.045 4.300 1.05246E+00 9.91143E-01 6.13166E-02 5039.456 60.693 4.350 1.05412E+00 9.91101E-01 6.30208E-02 5041.123 62.360 4.400 1.05575E+00 9.91083E-01 6.46637E-02 5042.809 64.046 4.450 1.05588E+00 9.91095E-01 6.47840E-02

2 1

Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, Nice to get so prompt response from Bruce and Scott, thanks for their effort to make this list vital! Looks like "amp" is a factor which can be reduced. Then there is a question: how would all paths be sorted? by Reff or by "amp"? More techically related another question is then: can FEFFIT and FEFF work seamless together on this? Is there any presumption in FEFFIT (or more explicityly, ARTEMIS/ATHENA) which assumes all the paths have been sorted by descending "amp" down from 100% with ascending REFF? The background story behind this: using the same structural model (thanks Bruce!), I tried to fit either use paths from FEFF840 or from FEFF6. The fitting with FEFF6 paths does a quite good job, giving a R_factor~1%, reduced chi square~ 90. Yet the one with FEFF840 paths terminates abnormally because two parameters cannot be determined. Attached please find two ARTEMIS project files. And appreciate for comments! Ying Ying Zou Research Assoc., Dr. Phys. Physics Department, UWM

2 1

Re: [Ifeffit] Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, While I am calculating FEFF path through Feff8.40 using the "feff8.inp" as attached, I notice that the value of "amp" shown on "FEFF interpretation page" for some paths goes over 100%. For example, path 14 has a Reff=3.9317 far away from first shell, yet it has an "amp"=169.913. On the contrary, if I do the same in Artemis through embedded Feff6.0(using "feff6.inp"), none of paths has an "amp" over 100%. I am guessing this could be all right because Feff8 is using curved waves Feff6 instead plane waves. Any comments on this would be greatly appreciated! Ying Ying Zou Research Assoc., Dr.Phys. Physics Department, UWM =======================feff8.inp======================================= * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END ============================================================================ ========================feff6.inp========================================== * This feff6 input file was generated by Artemis 0.8.011 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 2.06 microns, unit edge step: 13.38 microns * specific gravity = 7.942 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00048 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title Pb Ti O3 * title Glazer A M * title # Powder profile refinement of lead zirconate titanate at several temperatures. * title # II. Pure PbTiO3 * title # Locality: synthetic * title # Sample: T = 25 C * space = P 4 m m * a = 3.9050 b = 3.9050 c = 4.1560 * alpha = 90.0 beta = 90.0 gamma = 90.0 * core = Ti edge = K * atoms * ! elem x y z tag occ * Pb 0.00000 0.00000 0.00000 Pb 1.00000 * Ti 0.50000 0.50000 0.53900 Ti 1.00000 * O 0.50000 0.50000 0.11400 Oapical 1.00000 * O 0.50000 0.00000 0.61700 Oplanar 1.00000 * ----------------------------------------------------------------- TITLE Pb Ti O3 TITLE Glazer A M TITLE # Powder profile refinement of lead zirconate titanate at several temperatures. TITLE # II. Pure PbTiO3 TITLE # Locality: synthetic TITLE # Sample: T = 25 C HOLE 1 1.0 * Ti K edge (4966.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 4.29550 *CRITERIA curved plane *DEBYE temp debye-temp NLEG 4 POTENTIALS * ipot Z element 0 22 Ti 1 82 Pb 2 22 Ti 3 8 O ATOMS * this list contains 25 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 3 Oapical_1 1.76630 1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 -1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 0.00000 1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 -1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 0.00000 2.38970 3 Oapical_2 2.38970 1.95250 1.95250 1.91592 1 Pb_1 3.36084 -1.95250 1.95250 1.91592 1 Pb_1 3.36084 1.95250 -1.95250 1.91592 1 Pb_1 3.36084 -1.95250 -1.95250 1.91592 1 Pb_1 3.36084 1.95250 1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 1.95250 -2.24008 1 Pb_2 3.55563 1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 3.90500 0.00000 0.00000 2 Ti_1 3.90500 -3.90500 0.00000 0.00000 2 Ti_1 3.90500 0.00000 3.90500 0.00000 2 Ti_1 3.90500 0.00000 -3.90500 0.00000 2 Ti_1 3.90500 0.00000 0.00000 4.15600 2 Ti_2 4.15600 0.00000 0.00000 -4.15600 2 Ti_2 4.15600 3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 -3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 0.00000 3.90500 -1.76630 3 Oapical_3 4.28589 0.00000 -3.90500 -1.76630 3 Oapical_3 4.28589 END ========================================================================

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Re: [Ifeffit] charge transfer by SCF in FEFF8 and simulation for charge disproportionation
by Ying Zou 28 Aug '08

28 Aug '08

Dear all, I am doing a SCF calculation by Feff8.40 for a model compound PbTiO3. However, the obtained charge transfer deviates far away from its well-known formal oxidation state. According to common electron negativity data, the oxidation state would be: Pb 2+ Ti 4+ O 2- The SCF run gave out charge transfer for those atoms as following: Pb 0.717 Ti 0.181 O -0.300 After I read through the existing threads on charge transfer in this list, I know that transfered charge FEFF gives out is just a portion of general formal oxidation state. Can we undderstand that this is just ionic portion for entire bonding? Such as for oxygen, "-0.300" is ionic bonding, while the rest of valency (-1.700) exists as covalent bonding, which doesn't have apparent charge transfer by definition. Another related question is then: is there any way in FEFF to take into account this "covalence" part? (maybe deriving from overlapping area of mufftin-potential?) I think this may be crucial for a self-consistent analysis of charge disproportionation. Any comments on this would be greatly appreciated. Attached please see"atom.inp" and "feff.inp". Thanks so much! Ying Ying Zou Research associate,Dr. Phys. Physics Department, UWM ***************atoms.inp*********************************** ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = Perovskite: PbTiO3 space = p 4 m m a = 3.9050 b = 3.9050 c = 4.1560 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ti edge = K rmax = 4.2950 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.00000 Pb 1.00000 Ti 0.50000 0.50000 0.53900 Ti 1.00000 O 0.50000 0.50000 0.11400 Oapical 1.00000 O 0.50000 0.00000 0.61700 Oplanar 1.00000 ****************************************************************** ************feff.inp*************************************** * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END *******************************************************************

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Re: [Ifeffit] Quick question about atoms.exe and .cif files
by Bruce Ravel 26 Aug '08

26 Aug '08

On Tuesday 26 August 2008 01:44:03 you wrote: > Hi Bruce, > > I have atoms running well, but whenever I input a simple diamond > structure .cif file (like the attached silicon.cif file), I get the wrong > structure. I've tried everything that I could think of, but it doesn't > work. I'm not sure if it is something I'm doing wrong, or something > intrinsic in the .cif file. I'm currently running the command line program > with the command "atoms.exe -u -o "silicon.inf" "Silicon.cif"", with the > files being appropriately loaded. If you get the chance could you tell me > if it is an easy problem that I can quickly fix (and the solution), or if > it is something more in depth: I'd appreciate it. > > Zak I am forwarding this question to the Ifeffit mailing list. This is the sort of question for which that forum was created. Please make use of it. http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest As the warning message says, "F d -3 m" is one of those space groups in the International Tables that offers two choices for the position of the origin. There is no way to correct that from the command line, so your two options are: 1. Use Artemis to generate your unit cell file and apply the shift vector given in the warning message or 2. Edit the cif file to put the Si atom at (1/8,1/8,1/8) 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/

1 0

(no subject)
by Hashem Stietiya 25 Aug '08

25 Aug '08

Dr. Calvin, I appreciate your prompt reply. I will work on your suggestions and get back to you soon. Meanwhile, can you please tell what is meant by 'A Bessel window with a smoothing parameter of 4?' I read that in a couple of publications where they indicate that is used to suppress artifacts. Is the smoothing parameter the dk? Thanks again. Regards, Hashem Stietiya Louisiana State University

2 1

asking questions effectively
by Bruce Ravel 25 Aug '08

25 Aug '08

Hi folks, When I returned from the dentist's office this afternoon, there were 2 questions on the mailing list. Both were interesting questions but neither really included enough information to definatively solve the problem. Please remember that the folks who answer questions on the maililng list can only do so effectively if you provide enough information that the problem can be reproduced on their own computers. Often, this involves attaching a small project file which demonstrates the problem to your email. 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/

1 0

Background Subtraction
by Hashem Stietiya 25 Aug '08

25 Aug '08

Dear Dr. Ravel, I am trying to optimize background removal of my spectra by setting the Rbkg to half the distance of the first shell peak. However, when I import my spectra in ATHENA, I notice that the edge step is a very large number and when converting to R space there are no well defined peaks. If I click on 'fix step', the R space becomes comprehendible and peaks appear. Do I continue using the 'fix step' and then setting Rbkg to half the distance of the first shell peak? I appreciate your help. Regards, Hashem Stietiya

3 2

Re: [Ifeffit] Energy shift (???)
by Frommer Jakob 19 Aug '08

19 Aug '08

Hi eunsuk1986 (unfortunately you did not share your full name with us...) I had some trouble with reading your feff.inp. Nevertheless the problem of the absolute alignment of FEFF xmu and experimental data has been the subject of earlier questions. I' am citing form a list contribution of J. Rehr (Aug 3rd 2003): "The FEFF calculation of the absolute energy is not meant to be highly accurate, and errors of several eV for K-shells of large Z atoms are not unusal. Thus you did nothing wrong in the input file. To match FEFF and experiment you *always* have to shift the FEFF absolute threshold to match experiment.". There is no way (I am aware of) to tell FEFF do this absolute shift (you can and you often need to shift the position of the Fermi level though) but you can do this with every plot program. Thus you should not worry too much about the absolute energies in your xmu but a lot about relative energies (i.e. the positions of the single resonances). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mon 8/18/2008 09:46 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 66, Issue 9 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. Energy shift (???) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Aug 2008 16:46:26 +0900 From: ??? <eunsuk1986(a)hotmail.com> Subject: [Ifeffit] Energy shift To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <COL101-W46347AB6CA04C793B53D5FDA6E0(a)phx.gbl> Content-Type: text/plain; charset="ks_c_5601-1987" Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ ???? ???, ???? ?? ???? ???? ??? Windows Live Hotmail! ?? ???? ???! http://www.hotmail.com <http://www.hotmail.com/>

1 0

Energy shift
by 정은석 18 Aug '08

18 Aug '08

Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ 강력해진 보안성, 아웃룩을 닮아 편리해진 기능들로 무장한 Windows Live Hotmail! 지금 로그인해 보세요! http://www.hotmail.com

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Artemis bug in new version
by van der Veen Renske 15 Aug '08

15 Aug '08

Hello! I just downloaded the new version of Ifeffit (1.2.11) and I am happy with it except for a small bug that wasn't present in the previous version. I am used to work with many different FEFF calculations for the same data set, all with the same fit model. I usually copy the path parameters from one calculation to all the others by using <right click> "Paths -> Export these path parameters... -> to SELECTED paths". Although a bit cumbersome for many paths and calculations, it worked fine in the previous version of Artemis. In the new version, it does exactly the opposite from what I want: it exports the path parameters to all the paths EXCEPT the ones I selected. Is there a chance to fix this, or does anybody know a more cunning way to copy the path parameters from one calculation to the others on a path-by-path basis? Thanks in advance! Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

2 2

The first step involve in Bio-physics simulation
by 沛昌蔡 15 Aug '08

15 Aug '08

Dear Prof. and authors: We have involved Bio-physics experiment recently, but we have no idea about the simulation softwave (free is better), and our protein sample is rod figure, so do you have any idea about the simulation, such as vibration mode, absorption, molecular structure. We are so appreciate with your information. Thanks for your time and feedback! Tsai pei-chang _________________________________________________________________________________________________________ 知識+ 的電玩高手全都在這裡！ http://tw.knowledge.yahoo.com/dir/group_buzz?time=total&type=article&sid=39…

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Bug: Can't type into Athena on Linux
by Gregory Merchan 14 Aug '08

14 Aug '08

Hi everyone, We uncovered a bug that affects Athena and friends. When SCIM is running, Perl/Tk programs do not respond to keyboard events. These reports have more information: https://bugzilla.novell.com/show_bug.cgi?id=77424 https://bugzilla.novell.com/show_bug.cgi?id=309794 (Googled for those links. We were running an up-to-date Ubuntu.) This affected Horae 066 and I've not yet tested the latest release. Hope this helps, Greg P.S. - Now googling the symptoms should be useful. I don´t expect a fix, since the problem is upstream.

2 1

Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 14 Aug '08

14 Aug '08

Hello, I made as you said and now everything is working! Thanks!! Gilberto

4 3

update to ifeffit source kit
by Matt Newville 13 Aug '08

13 Aug '08

Hi Folks, I found a serious bug in the ifeffit-1.2.11 source code kit that was on the cars.uchicago.edu and sourceforge.net sites. This bug would become readily apparent, as many operations beyond the simplest tests will not work correctly, so like any actual use of Athena would be clearly wrong. Sorry for any trouble! I uploaded a fixed source code kit (ifeffit-1.2.11a.tar.gz) to both the cars.uchicago.edu and sourceforge.net sites. This bug does not affect the Windows binaries. --Matt

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Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 12 Aug '08

12 Aug '08

Hello again, I tried to install the new package of both ifeffit(1.2.11) and horae (0.67) but it also didn't work. I first removed any file related to ifeffit and horae that I could find. Pgplot, ifeffit, Xray-Absorption, Xray-Scattering and Chemistry-Formula installation runned without error and I could open ifeffit on command line. But the error mensage below appeared when I runned the "perl Build.PL" on horae. ... Checking whether your kit is complete... Looks good Checking prerequisites... Package 'Config::IniFiles' already declared with version '2.39', ignoring subsequent declaration. Looks good Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'horae' version '067' ... Even though this error I runned ./Build and ./Build install and no error appeared. But when I tried to run athena (it also happens on artemis) the error appeared: ...... Can't locate Ifeffit.pm in @INC (@INC contains: /usr/lib/perl5/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at /usr/bin/athena line 67. BEGIN failed--compilation aborted at /usr/bin/athena line 67. ..... I looked for the Ifeffit.pm file on /usr/lib/perl5 and it doesnt exist. Thanks, Gilberto ps: I will write on the FAQ as soon as possible... :)

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new software releases
by Bruce Ravel 11 Aug '08

11 Aug '08

Hi folks, I just uploaded source code and a Windows installer for Ifeffit 1.2.11 to SourceForge. Both are also available for download from the Ifeffit web site. Source code packages for my programs (Athena, Artemis, Hephaestus) can be found at SourceForge or on my website. Macintosh installer packages will be available soon. For the windows users, the new installer package has a number of advantages, including: * New compilation of ifeffit, resulting in noticeably faster execution compared to the 1.2.10 release * Latest versions of SixPack, Athena, Artemis, and Hephaestus * Perl 5.8 and PerlApp 7.2 were used to build my programs, solving a number of performance issues reported in recent months * The Athena User's Guide is included in the package and the html version is now used as the internal documentation in Athena We recommend that all windows users upgrade to the new version. As always, let us know about any issues, comments, or suggestions that you might have. This version was used successfully at the APS XAFS Summer School last week. While not an exhaustive testing, it seems to be a good release so far. 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/

1 0

several FEFF-questions
by Bosman, Eckhard 11 Aug '08

11 Aug '08

Hello, i read in the FEFF 8.4 manual, that the 6 modules are executed in ascending order. But now i'm confused concerning the modules 3 till 5. In module 3 the full multiple scattering is calculated. But only after this module the path enumeration (module 4) and the scattering amplitudes (module 5) are computed. I thought the path enumeration and the scattering amplitudes are required for calculation of the full multiple scattering? Why are these quantities calculated after the fms module? In my opinion this doesn't make sense. Another question affects the paper (page 9 and 10) of Zabinsky et al (attached). In the section "path enumeration" (respectively one side bevor) he introduced the quantity r_tot = total path length and R = r_tot/2 = effective path length. My question is, what is the meaning of the effective path length? In my opinion r_tot is the way and the way back? And R < r_tot is the path length without negligible contributions (scattering amplitude,...), is this right? The next question concerns the XANES-Card. What is the meaning of k respectively xkmax? In my opinion k is the wavenumber (of the photo electron wave?) which occurs in the xmu.dat in the third column, isn't it? Many thanks for your help! best regards, Eckhard

2 1

Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 11 Aug '08

11 Aug '08

hello, I have a amd 64 bits computer running opensuse 11. I tried to install ifeffit on it and it was very complicated. After some modifications on the makefile of PGPlot (as showed here: http://proteus.pha.jhu.edu/~dks/Unixtips/index.html) and during the horae install (http://cars9.uchicago.edu/pipermail/ifeffit/2006-September/002621.html and http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2008-January/003481.html) After those changes the artemis is working well, but athena is not... the program opens but I can not open any file. When I opened athena on terminal and tried to open a file the error below appeares. Tk::Error: Failed to AUTOLOAD 'Tk::FBox::_get_select_Path' at /usr/bin/athena line 5212 Carp::croak at /usr/lib/perl5/5.10.0/Carp.pm line 44 Tk::Widget::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Widget.pm line 347 Tk::FBox::Done at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 909 Tk::FBox::VerifyFileName at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 678 Tk::FBox::ActivateEnt at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 647 Tk::FBox::OkCmd at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 815 Tk callback for .fbox.frame1.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) Thanks, Gilberto

2 1

[OT] Ball&sticks open source Perl/Python libraries
by Mauro Rovezzi 31 Jul '08

31 Jul '08

Dear all, I'm sorry if I introduce an off-topic (OT) subject but I would like to ask if you have knowledge of a simple ball&stick open source library that could be called from Perl or Python in order to generate "on the fly" theoretical paths visualization (or any atomic structure). At the moment the simplest (and useful!) utility I have found is XBS (http://ihp02.ihp-ffo.de/~msm/) but it is not the best solution because it needs input files and the output quality is low. Thanks for your help, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

2 1

reference spectra for Cu(OH)2
by Zajac, Dariusz 30 Jul '08

30 Jul '08

Hi all, as now we have a time for XAS spectra requests, I would like to ask you also for one. I need spectra of Cu(OH)_{2}. If someone could help I would preciate. Thanks in advance 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 ------------------------------------------------------------------------

4 7

Re: [Ifeffit] Ifeffit Digest, Vol 65, Issue 21
by sankaran anantharaman 30 Jul '08

30 Jul '08

Hi Darek, If you have not found the spectrum in the database, here you go... -Sankaran Uni Stuttgart ! ! Comments %c EXAFS-Scan started at 28-Nov-2006 00:54:18, ended 02:23:54 Name: cuoh2_00002 from 8689 to 10175.77 Cu 0.8mu, MOT8 at 62.2 Counter readings are offset corrected and normalized to 1s, the offsets are: C1 0 C2 0 C3 0 C5 0 C1 0.1 C2 0.1 C3 0.1 C5 0 ! ! Parameter %p ! ! The EXAFS Scan Regions ! ! Energy Delta Sample_Time Edge Power ! 8689 1 1 0 0 ! 8949 0.5 1 0 0 ! 9019 0.818 1 8979 1 ! 10179 0 0 0 0 ! ENERGY = 8979 THETA2 = 12.72019 THETA1 = 12.72019 MC2_Z = 33.63474 EXIT_SLIT_TOP = 0.5000014 EXIT_SLIT_BOTTOM = -0.5 EXIT_SLIT_LEFT = 4 EXIT_SLIT_RIGHT = -4 SAMPLE_HEIGHT = 62.2 REFERENCE_HEIGHT = 40.01077 MONO_ENTR_SLIT = -60 PLANE_MIRR_SLIT = 0.5000793 PLANE_MIRR_THETA = -0.1680022 PLANE_MIRR_TRANSL = -32 PLANE_MIRR_HEIGHT = 0 REFL_SLIT_TOP = 2 REFL_SLIT_BOTTOM = -2 REFL_SLIT_LEFT = 8.5 REFL_SLIT_RIGHT = -7.5 TORO_MIRR_THETA = 0.01400023 TORO_MIRR_TRANSL = 5.7 TORO_MIRR_RHO_OLD = -0.5101779 TORO_MIRR_HEIGHT = 2.6 WHITE_SLIT_TOP = 0.9 WHITE_SLIT_BOTTOM = -0.9 TORO_MIRR_RHO = -0.4290012 MOT26 = -73 SAMPLE_HEIGHT_OLD = 24.50071 SAMPLE_RHO = 93 DET_VER = 10.5 MOT30 = 0 HE_KRYO_HEIGHT = 78.89 SAMPLE_HORIZONTAL = 84 ! ! Data %d Col 1 CUOH2_00002 FLOAT Col 2 CUOH2_00002 FLOAT Col 3 CUOH2_00002_REF FLOAT Col 4 cuoh2_00002_C1_SCAN_C1 FLOAT Col 5 cuoh2_00002_C2_SCAN_C2 FLOAT Col 6 cuoh2_00002_C3_SCAN_C3 FLOAT Col 7 cuoh2_00002_C5_SCAN_C4 FLOAT Col 8 CUOH2_00002_IDORIS FLOAT Col 9 CUOH2_00002_DELTA FLOAT Col 10 CUOH2_00002_SAMPLE_TIME FLOAT 8688.999 -0.9160514 -1.616946 79421 198505 1000005 582 140.702 1 1 8690.005 -0.916195 -1.616891 79414 198516 1000005 582 140.6929 1 1 8690.995 -0.9167968 -1.616227 79419 198648 1000006 581 140.6842 1 1 8692.002 -0.9169251 -1.616085 79420 198676 1000005 581 140.674 1 1 8692.992 -0.9172173 -1.616071 79398 198679 1000006 581 140.6638 1 1 8694 -0.9173985 -1.61589 79398 198715 1000006 581 140.6554 1 1 8695.007 -0.9175774 -1.616 79375 198693 1000006 581 140.6465 1 1 8695.998 -0.9180022 -1.61531 79396 198830 1000005 582 140.637 1 1 8697.006 -0.9181758 -1.6152 79391 198852 1000006 581 140.6282 1 1 8697.998 -0.9184055 -1.615411 79356 198810 1000005 581 140.6196 1 1 8699.006 -0.9188882 -1.614879 79360 198916 1000006 581 140.6109 1 1 8699.998 -0.919215 -1.614577 79358 198976 1000006 582 140.6004 1 1 8701.006 -0.9190844 -1.614758 79354 198940 1000006 581 140.5925 1 1 8702 -0.9195341 -1.614271 79357 199037 1000006 581 140.5798 1 1 8703.009 -0.9196827 -1.614235 79348 199044 1000006 582 140.5725 1 1 8704.002 -0.9202557 -1.613763 79340 199138 1000006 581 140.5607 1 1 8704.995 -0.9202415 -1.614004 79322 199090 1000006 581 140.5531 1 1 8706.005 -0.9206479 -1.613522 79328 199186 1000006 581 140.5436 1 1 8706.998 -0.9208564 -1.613352 79325 199220 1000006 581 140.5332 1 1 8707.992 -0.9210504 -1.61332 79312 199226 1000005 580 140.524 1 1 8709.004 -0.9215401 -1.612919 79305 199306 1000005 581 140.5152 1 1 8709.998 -0.9218105 -1.612548 79313 199380 1000005 581 140.5069 1 1 8710.993 -0.9218587 -1.612589 79306 199372 1000006 581 140.4979 1 1 8712.004 -0.9224178 -1.612042 79305 199481 1000006 580 140.4869 1 1 8712.999 -0.9223476 -1.612111 79305 199467 1000005 581 140.4789 1 1 8713.994 -0.9228746 -1.611686 79297 199552 1000006 581 140.4701 1 1 8715.007 -0.9229347 -1.611626 79297 199564 1000006 581 140.4633 1 1 8716.003 -0.9232742 -1.611475 79282 199594 1000005 581 140.4522 1 1 8716.999 -0.9237504 -1.61105 79278 199679 1000006 581 140.4415 1 1 8717.995 -0.9235653 -1.611261 79276 199637 1000006 581 140.4301 1 1 8718.992 -0.9242787 -1.610533 79277 199782 1000005 580 140.4213 1 1 8720.005 -0.9240496 -1.610915 79265 199706 1000006 581 140.4116 1 1 8721.002 -0.9245644 -1.610298 79273 199829 1000005 581 140.4038 1 1 8722 -0.9251846 -1.609943 79252 199900 1000005 581 140.3925 1 1 8722.997 -0.9253718 -1.609719 79255 199945 1000006 581 140.3823 1 1 8723.995 -0.9256028 -1.609589 79247 199971 1000006 581 140.3733 1 1 8724.993 -0.9256823 -1.609458 79251 199997 1000005 581 140.364 1 1 8726.008 -0.925855 -1.609564 79229 199976 1000006 581 140.3555 1 1 8727.006 -0.9264488 -1.608869 79237 200115 1000006 581 140.344 1 1 8728.005 -0.9264717 -1.608884 79234 200112 1000006 580 140.338 1 1 8729.004 -0.927026 -1.608544 79217 200180 1000006 581 140.3279 1 1 8730.003 -0.9269611 -1.608609 79217 200167 1000006 581 140.3182 1 1 8731.003 -0.9277296 -1.60779 79221 200331 1000006 581 140.3119 1 1 8732.002 -0.9276711 -1.607974 79211 200294 1000005 581 140.3007 1 1 8733.002 -0.9277956 -1.607825 79213 200324 1000006 582 140.2908 1 1 8734.003 -0.9280737 -1.60785 79189 200319 1000006 582 140.2835 1 1 8735.003 -0.9282715 -1.607501 79201 200389 1000006 581 140.273 1 1 8736.004 -0.9286039 -1.607421 79181 200405 1000006 581 140.2634 1 1 8737.005 -0.9287407 -1.607246 79184 200440 1000006 581 140.2543 1 1 8738.006 -0.9291416 -1.606998 79172 200490 1000007 580 140.2447 1 1 8739.007 -0.9293418 -1.606847 79168 200520 1000006 581 140.236 1 1 8739.992 -0.929958 -1.606269 79165 200636 1000006 581 140.2262 1 1 8740.994 -0.9298488 -1.606593 79148 200571 1000006 581 140.2196 1 1 8741.996 -0.9302292 -1.606149 79153 200660 1000006 581 140.2088 1 1 8742.998 -0.9306677 -1.605712 79153 200748 1000007 581 140.1994 1 1 8744.001 -0.9305344 -1.605756 79160 200739 1000006 581 140.1887 1 1 8745.004 -0.9311802 -1.605502 79129 200790 1000006 581 140.1833 1 1 8746.006 -0.9314628 -1.605143 79135 200862 1000006 581 140.1717 1 1 8746.993 -0.9318132 -1.604919 79125 200907 1000006 581 140.1613 1 1 8747.997 -0.9318757 -1.605034 79111 200884 1000006 581 140.1561 1 1 8749 -0.9325858 -1.604387 79106 201014 1000006 581 140.1431 1 1 8750.005 -0.9325852 -1.604501 79097 200991 1000006 581 140.1333 1 1 8750.991 -0.932791 -1.604257 79100 201040 1000006 581 140.1257 1 1 8751.996 -0.9329993 -1.604162 79091 201059 1000005 580 140.1168 1 1 8753.001 -0.9332858 -1.604053 79077 201081 1000006 581 140.1051 1 1 8754.006 -0.9335842 -1.603615 79088 201169 1000005 581 140.0964 1 1 8754.994 -0.9340215 -1.603318 79077 201229 1000006 580 140.089 1 1 8756 -0.9343268 -1.603138 79067 201265 1000005 580 140.0784 1 1 8757.006 -0.933955 -1.603561 79063 201180 1000006 581 140.0686 1 1 8757.994 -0.9349874 -1.602478 79067 201398 1000006 581 140.0589 1 1 8759 -0.9348328 -1.602861 79049 201321 1000006 581 140.0515 1 1 8760.007 -0.9350347 -1.602836 79035 201326 1000006 581 140.0409 1 1 8760.997 -0.9354887 -1.60223 79047 201448 1000006 580 140.0314 1 1 8762.004 -0.9356693 -1.602151 79039 201464 1000006 581 140.0201 1 1 8762.994 -0.9357593 -1.602224 79026 201449 1000005 581 140.0117 1 1 8764.002 -0.9361541 -1.601843 79025 201526 1000006 581 140.0029 1 1 8764.993 -0.9364461 -1.601639 79018 201567 1000006 580 139.9928 1 1 8766 -0.9369649 -1.60102 79026 201692 1000006 580 139.9855 1 1 8766.992 -0.9367937 -1.60143 79007 201609 1000005 580 139.9747 1 1 8768 -0.9372631 -1.601 79004 201696 1000006 581 139.9644 1 1 8768.992 -0.9377688 -1.60038 79013 201821 1000006 580 139.9571 1 1 8770.001 -0.9377069 -1.600682 78994 201760 1000006 581 139.9463 1 1 8770.993 -0.9379404 -1.600473 78992 201802 1000005 581 139.9344 1 1 8772.002 -0.938574 -1.599815 78994 201935 1000006 581 139.9287 1 1 8772.995 -0.9387199 -1.599885 78977 201921 1000006 581 139.9177 1 1 8774.005 -0.9390368 -1.599568 78977 201985 1000006 581 139.908 1 1 8774.998 -0.9392062 -1.599449 78973 202009 1000006 581 139.8988 1 1 8776.009 -0.9393038 -1.599502 78961 201998 1000005 581 139.8904 1 1 8777.002 -0.9398196 -1.599038 78957 202092 1000006 580 139.8799 1 1 8777.996 -0.939939 -1.599261 78930 202047 1000006 581 139.873 1 1 8779.007 -0.9400718 -1.598988 78941 202102 1000005 581 139.8622 1 1 8780.002 -0.9404982 -1.598499 78946 202201 1000006 581 139.8542 1 1 8780.996 -0.9407615 -1.598285 78942 202244 1000005 581 139.846 1 1 8782.008 -0.9411249 -1.598024 78934 202297 1000006 580 139.8362 1 1 8783.003 -0.9412766 -1.598113 78915 202279 1000006 581 139.8263 1 1 8783.998 -0.9413125 -1.598127 78911 202276 1000005 581 139.8191 1 1 8784.993 -0.941655 -1.597748 78914 202353 1000006 581 139.8055 1 1 8786.006 -0.9417889 -1.597435 78928 202416 1000005 581 139.7979 1 1 8787.002 -0.942345 -1.597184 78904 202467 1000006 581 139.7871 1 1 8787.998 -0.9426057 -1.597075 78892 202489 1000005 582 139.7815 1 1 8788.995 -0.9430081 -1.596483 78907 202609 1000006 581 139.7697 1 1 8790.008 -0.9426519 -1.597283 78872 202447 1000006 581 139.7613 1 1 8791.005 -0.9436069 -1.596227 78880 202661 1000006 581 139.7515 1 1 8792.002 -0.9436469 -1.59639 78864 202628 1000006 581 139.7449 1 1 8793 -0.9438987 -1.595871 78885 202733 1000006 580 139.7354 1 1 8793.997 -0.9439424 -1.59598 78873 202711 1000006 581 139.7269 1 1 8794.995 -0.9440198 -1.596118 78856 202683 1000006 581 139.718 1 1 8795.994 -0.9443827 -1.595768 78855 202754 1000006 581 139.7064 1 1 8796.992 -0.9447399 -1.595486 78849 202811 1000005 581 139.699 1 1 8798.007 -0.9448519 -1.595413 78846 202826 1000006 581 139.6903 1 1 8799.006 -0.9452216 -1.595043 78846 202901 1000006 581 139.6779 1 1 8800.005 -0.9456637 -1.594639 78843 202983 1000006 581 139.6713 1 1 8801.005 -0.9456754 -1.594944 78818 202921 1000005 581 139.6606 1 1 8802.005 -0.9462643 -1.594278 78824 203056 1000005 582 139.6509 1 1 8803.004 -0.9464955 -1.594289 78805 203054 1000006 581 139.6404 1 1 8804.004 -0.9465467 -1.594137 78813 203085 1000006 581 139.6337 1 1 8805.004 -0.9468311 -1.593979 78803 203117 1000006 581 139.6222 1 1 8806.005 -0.9468906 -1.594096 78789 203093 1000005 581 139.6141 1 1 8807.006 -0.9473912 -1.593546 78793 203205 1000006 581 139.6044 1 1 8808.007 -0.947979 -1.593033 78787 203309 1000005 581 139.5968 1 1 8809.008 -0.9478374 -1.59329 78778 203257 1000006 581 139.5856 1 1 8809.992 -0.9481491 -1.592876 78786 203341 1000005 581 139.5781 1 1 8810.994 -0.9487299 -1.592474 78772 203423 1000006 581 139.5689 1 1 8811.996 -0.9484674 -1.592596 78783 203398 1000005 581 139.5594 1 1 8812.999 -0.9487922 -1.592361 78776 203446 1000006 580 139.549 1 1 8814.001 -0.9490617 -1.592218 78766 203475 1000006 582 139.5415 1 1 8815.003 -0.9495506 -1.591804 78760 203559 1000005 581 139.5314 1 1 8816.006 -0.9497918 -1.591653 78753 203590 1000006 581 139.5231 1 1 8816.992 -0.9498103 -1.591824 78738 203555 1000005 580 139.5118 1 1 8817.996 -0.9505261 -1.590779 78764 203768 1000006 581 139.5008 1 1 8818.999 -0.9502358 -1.591564 78725 203608 1000005 581 139.4947 1 1 8820.003 -0.9506068 -1.591054 78736 203712 1000006 580 139.4828 1 1 8821.008 -0.9508154 -1.591136 78713 203695 1000005 581 139.4776 1 1 8821.994 -0.9510984 -1.590588 78734 203807 1000006 581 139.4662 1 1 8822.999 -0.9511608 -1.590843 78709 203755 1000006 581 139.4567 1 1 8824.003 -0.9518704 -1.590082 78713 203910 1000005 581 139.451 1 1 8824.992 -0.9517537 -1.590442 78694 203837 1000007 581 139.4392 1 1 8825.997 -0.9518046 -1.59016 78712 203894 1000005 582 139.4327 1 1 8827.002 -0.9523791 -1.589955 78683 203936 1000006 581 139.4202 1 1 8827.991 -0.9525576 -1.589764 78684 203975 1000006 581 139.4131 1 1 8828.997 -0.9531137 -1.589475 78663 204034 1000006 581 139.4049 1 1 8830.003 -0.9530785 -1.589078 78697 204115 1000006 581 139.3936 1 1 8830.992 -0.9533434 -1.589092 78675 204112 1000006 581 139.3837 1 1 8831.999 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188090.8 581.4554 131.8056 3.496 4.26 9713.459 -0.1824195 -0.7516828 74319.62 89192.29 189138.1 581.7757 131.783 3.505 4.28 9716.945 -0.183632 -0.7557339 74303.27 89280.84 190094.4 581.3084 131.757 3.513 4.28 9720.477 -0.1852446 -0.7564353 74277.91 89394.41 190469.8 581.6279 131.7345 3.521 4.3 9723.989 -0.18661 -0.7602264 74269.77 89506.74 191433.5 581.3953 131.71 3.53 4.3 9727.525 -0.1882126 -0.7622097 74262.03 89640.97 192101.2 581.4814 131.6872 3.538 4.32 9731.064 -0.1897114 -0.7663843 74245.6 89755.55 193151.4 581.4814 131.6647 3.546 4.32 9734.605 -0.1913879 -0.7673346 74223.96 89879.95 193603 581.106 131.6408 3.555 4.34 9738.149 -0.1924753 -0.7704337 74219.12 89971.88 194402.5 581.3364 131.6174 3.563 4.34 9741.717 -0.1941731 -0.7727069 74201.38 90103.21 195129.4 581.1926 131.5921 3.571 4.36 9745.286 -0.1954897 -0.7756405 74198.62 90218.58 195953.2 581.1926 131.5687 3.58 4.36 9748.879 -0.1972325 -0.7773853 74178.08 90350.91 196583.3 581.2785 131.5416 3.588 4.38 9752.454 -0.1983988 -0.7814649 74165.75 90441.32 197584.5 581.5068 131.5199 3.597 4.38 9756.053 -0.2000841 -0.7825196 74158.86 90585.45 198108.2 581.5909 131.4965 3.605 4.4 9759.674 -0.2010596 -0.787679 74146.59 90658.86 199294.3 581.8182 131.4742 3.613 4.4 9763.278 -0.2027545 -0.7890071 74126.47 90788.01 199843.4 581.4479 131.4521 3.622 4.42 9766.905 -0.2042531 -0.7915499 74112.67 90907.23 200615.4 581.6742 131.4262 3.63 4.42 9770.535 -0.2055488 -0.7944462 74093.7 91001.8 201406.5 581.5315 131.4013 3.638 4.44 9774.168 -0.2070249 -0.7970237 74077.25 91115.99 202179.7 581.7568 131.3792 3.647 4.44 9777.824 -0.2082031 -0.8031633 74061.88 91204.48 203622.4 581.6143 131.3541 3.655 4.46 9781.482 -0.2097286 -0.8047759 74045.52 91323.54 204217.3 581.8386 131.3307 3.663 4.46 9785.145 -0.2112285 -0.8070495 74033.48 91445.76 204956 581.4732 131.3036 3.672 4.48 9788.809 -0.2126778 -0.8099405 74019.2 91560.71 205807.8 581.4732 131.2805 3.68 4.48 9792.497 -0.2138429 -0.8145974 74001.34 91645.34 206959.6 581.1111 131.2562 3.688 4.5 9796.188 -0.2153694 -0.8171718 73995.78 91778.45 207794.4 581.5555 131.2299 3.697 4.5 9799.882 -0.2169705 -0.8197341 73985.4 91912.61 208632.1 581.8584 131.2065 3.705 4.52 9803.579 -0.2188276 -0.8212922 73976.21 92072.02 209319.8 581.0573 131.1819 3.713 4.54 9807.299 -0.2202323 -0.8233477 73951.54 92170.7 209975.3 581.0573 131.1584 3.722 4.54 9811.022 -0.2214481 -0.8277655 73920.84 92244.52 211073.9 581.579 131.132 3.73 4.56 9814.748 -0.2229134 -0.8313667 73930.7 92392.11 212174.3 581.579 131.1076 3.739 4.56 9818.498 -0.2242077 -0.8357968 73902.62 92476.64 213311.4 581.441 131.0814 3.747 4.58 9822.229 -0.2259346 -0.8372965 73884.5 92613.76 213948.2 581.6594 131.0585 3.755 4.58 9825.985 -0.2275993 -0.8394876 73886.74 92770.88 214781.3 581.3044 131.0333 3.764 4.6 9829.764 -0.2289489 -0.8420216 73863.7 92867.18 215549.8 581.3044 131.0102 3.772 4.6 9833.525 -0.2301332 -0.8469578 73846.54 92955.63 216822.7 581.6017 130.9845 3.78 4.62 9837.311 -0.2316851 -0.8518745 73840.7 93092.64 218212.6 581.1688 130.9587 3.789 4.62 9841.1 -0.2331145 -0.8530397 73824.36 93205.17 218731 580.819 130.9328 3.797 4.64 9844.89 -0.2347148 -0.8559673 73814.88 93342.46 219695.5 580.6035 130.9058 3.805 4.64 9848.705 -0.2361134 -0.8592763 73788.84 93440.13 220654.3 581.1159 130.8839 3.814 4.66 9852.524 -0.2375821 -0.8624155 73785.62 93573.39 221663.7 581.1159 130.8582 3.822 4.66 9856.346 -0.2389406 -0.866123 73765.81 93675.43 222729.7 580.9829 130.8306 3.83 4.68 9860.17 -0.240465 -0.8694502 73750.22 93798.51 223765.6 580.9829 130.8087 3.839 4.68 9864.019 -0.2416302 -0.8724822 73746.38 93902.98 224695.1 581.4894 130.7789 3.847 4.7 9867.849 -0.2433288 -0.8744358 73720.64 94029.79 225438.5 581.2766 130.7556 3.856 4.7 9871.702 -0.2449749 -0.8757373 73718.86 94182.42 226098.5 581.1441 130.7328 3.864 4.72 9875.581 -0.2466001 -0.8782026 73696.83 94307.42 226957.4 581.1441 130.7064 3.872 4.72 9879.443 -0.2476443 -0.882942 73674.9 94377.85 228205.9 581.2236 130.6818 3.881 4.74 9883.327 -0.2493295 -0.8849612 73670.05 94530.8 229037.8 581.0127 130.6553 3.889 4.74 9887.216 -0.2505484 -0.8890806 73644.95 94613.86 230185.3 581.3025 130.6294 3.897 4.76 9891.127 -0.2520224 -0.8923002 73628.57 94732.35 231216.8 581.3025 130.6058 3.906 4.76 9895.021 -0.2531911 -0.8955087 73615.06 94825.73 232188.5 581.5899 130.5789 3.914 4.78 9898.939 -0.2547251 -0.897184 73602.92 94955.64 232896.4 581.3807 130.5542 3.922 4.78 9902.861 -0.2562643 -0.8992658 73585 95078.75 233684.4 581.25 130.5272 3.931 4.8 9906.787 -0.2575805 -0.9034094 73567.91 95181.88 234909.2 581.25 130.5025 3.939 4.8 9910.735 -0.2590616 -0.9044798 73555.8 95307.26 235470.5 581.3278 130.4763 3.947 4.82 9914.688 -0.2602722 -0.9104101 73539.41 95401.45 237105.2 581.5353 130.4504 3.956 4.82 9918.644 -0.2615568 -0.9142758 73534.71 95517.97 238314.2 581.6116 130.4231 3.964 4.84 9922.603 -0.2632515 -0.9167878 73518.18 95658.47 239265.1 581.405 130.3946 3.972 4.84 9926.564 -0.2646601 -0.9183254 73502.47 95772.84 239919.8 581.0699 130.3719 3.981 4.86 9930.552 -0.2662603 -0.9214873 73466.46 95879.22 240946.9 580.8642 130.3465 3.989 4.86 9934.541 -0.2677618 -0.9252858 73465.57 96022.12 242224.4 581.1475 130.3204 3.998 4.88 9938.534 -0.2690301 -0.9300012 73451.84 96126.02 243632.6 581.5574 130.2921 4.006 4.88 9942.553 -0.2706184 -0.933166 73441.84 96265.71 244760 582.0408 130.2672 4.014 4.9 9946.574 -0.2723669 -0.9340918 73425.91 96413.27 245362.2 581.4286 130.2403 4.023 4.9 9950.578 -0.2735913 -0.9381644 73398.17 96494.91 246572.2 581.3008 130.2155 4.031 4.92 9954.627 -0.2755136 -0.9409024 73400.41 96683.53 247731.5 581.504 130.1908 4.039 4.92 9958.658 -0.2770178 -0.9434696 73389.88 96815.18 248706.5 581.3765 130.164 4.048 4.94 9962.714 -0.2779255 -0.9507638 73368.83 96875.3 250682.8 581.5789 130.1392 4.056 4.94 9966.753 -0.279907 -0.9512416 73344.96 97035.88 251218.3 581.25 130.1112 4.064 4.96 9970.837 -0.2812562 -0.9547032 73332.66 97150.6 252387.5 581.4516 130.0859 4.073 4.96 9974.902 -0.2827646 -0.958266 73315.66 97274.7 253611.8 581.5261 130.0606 4.081 4.98 9978.974 -0.2844347 -0.9605305 73301.2 97418.07 254561.4 581.3253 130.0328 4.089 4.98 9983.066 -0.2862177 -0.9627611 73293 97581 255556.6 581.4 130.005 4.098 5 9987.165 -0.2873286 -0.9677265 73266.53 97654.19 257021.3 581.2749 129.9807 4.106 5.02 9991.288 -0.2889409 -0.9701182 73261.75 97805.38 258035.7 581.2749 129.9503 4.115 5.02 9995.393 -0.2902907 -0.9737609 73244.84 97914.88 259267.3 581.3492 129.928 4.123 5.04 9999.523 -0.2918433 -0.9756314 73240.28 98060.91 260140.1 581.3492 129.9023 4.131 5.04 10003.66 -0.2937176 -0.9782977 73223.32 98222.13 261263.4 581.4229 129.8761 4.14 5.06 10007.79 -0.2948881 -0.9833791 73201.98 98308.5 262825.3 581.2253 129.8505 4.148 5.06 10011.93 -0.2965294 -0.985831 73194.29 98459.65 263875.6 581.1024 129.8213 4.156 5.08 10016.1 -0.2980552 -0.9879006 73178.55 98588.78 264769.1 581.2992 129.7939 4.165 5.08 10020.27 -0.2989719 -0.9939678 73154.71 98647.06 266537.8 580.9804 129.7717 4.173 5.1 10024.44 -0.3009697 -0.9957541 73139.02 98823.14 267491 581.1765 129.7409 4.181 5.1 10028.62 -0.3022175 -1.000394 73134.38 98940.23 269053.3 581.4453 129.7136 4.19 5.12 10032.8 -0.3035528 -1.00374 73104.69 99032.23 270206.1 581.4453 129.6855 4.198 5.12 10037 -0.3049954 -1.004922 73079.96 99141.64 270824.7 580.7393 129.659 4.206 5.14 10041.21 -0.3067298 -1.005635 73069.84 99300 271450.8 580.9338 129.6328 4.215 5.14 10045.42 -0.3081777 -1.009801 73054.27 99422.68 272920.6 581.3954 129.605 4.223 5.16 10049.64 -0.309582 -1.012877 73037.21 99539.15 274082.2 581.3954 129.5743 4.232 5.16 10053.88 -0.3105683 -1.016986 73020.85 99615.06 275420.7 581.4672 129.5518 4.24 5.18 10058.12 -0.3121064 -1.019782 72999.62 99739.38 276536.5 581.2742 129.523 4.248 5.18 10062.38 -0.3135855 -1.021047 72995.2 99880.97 277279.4 580.9615 129.4976 4.257 5.2 10066.63 -0.3147411 -1.025627 72978.27 99973.27 278809.8 580.9615 129.4716 4.265 5.2 10070.88 -0.3162828 -1.028625 72959.2 100101.3 280005.2 581.4177 129.4412 4.273 5.22 10075.16 -0.3174573 -1.032887 72938.12 100190 281450.4 581.4177 129.4168 4.282 5.22 10079.45 -0.3187815 -1.037973 72934.73 100318.1 283247.2 581.6794 129.3876 4.29 5.24 10083.74 -0.3202578 -1.040198 72920.23 100446.4 284240.8 581.8702 129.3656 4.298 5.24 10088.03 -0.3216768 -1.043282 72895.81 100555.3 285427.9 581.749 129.3376 4.307 5.26 10092.35 -0.323152 -1.045373 72871.48 100670.1 286352.1 581.5589 129.3069 4.315 5.26 10096.65 -0.3248683 -1.046986 72874.43 100847.2 287318.8 581.6288 129.2836 4.323 5.28 10100.98 -0.3260214 -1.051646 72851.13 100931.2 288901.5 581.8182 129.2527 4.332 5.28 10105.31 -0.3278494 -1.052939 72827.16 101082.6 289709.2 580.9434 129.2268 4.34 5.3 10109.66 -0.3293603 -1.056046 72798.11 101195.1 290933.9 581.3207 129.1986 4.348 5.3 10114 -0.3306668 -1.060307 72789.09 101314.8 292522 581.3909 129.173 4.357 5.32 10118.36 -0.3323018 -1.063432 72773.87 101459.4 293856.2 581.5789 129.1455 4.365 5.32 10122.73 -0.333741 -1.065545 72758.23 101583.7 294838.8 581.4606 129.117 4.374 5.34 10127.1 -0.3353355 -1.070271 72740.07 101720.4 296634.1 581.6479 129.0906 4.382 5.34 10131.48 -0.3369642 -1.074219 72736.2 101880.8 298276.8 581.3433 129.0607 4.39 5.36 10135.88 -0.3385116 -1.077082 72719.21 102014.7 299525.4 581.3433 129.034 4.399 5.36 10140.28 -0.3399971 -1.081194 72695.91 102133.6 301110.2 581.2267 129.0084 4.407 5.38 10144.69 -0.3415332 -1.083918 72693.3 102287 302384.9 581.4126 128.9791 4.415 5.38 10149.1 -0.3433089 -1.086838 72674.07 102441.7 303727.8 581.2963 128.9538 4.424 5.4 10153.52 -0.3447922 -1.090293 72658.7 102572 305166.8 581.4814 128.9231 4.432 5.4 10157.97 -0.3461569 -1.094603 72633.95 102677.1 306798.7 581.9188 128.8965 4.44 5.42 10162.39 -0.3477357 -1.096089 72625.83 102827.9 307706.3 581.9188 128.8687 4.449 5.42 10166.84 -0.3492052 -1.100713 72596.51 102937.5 309461.9 581.6176 128.8397 4.457 5.44 10171.3 -0.3507942 -1.104715 72591.91 103094.7 311177.2 581.6176 128.8124 4.465 5.44 10175.78 -0.3524879 -1.107431 72563.19 103228.6 312428.8 581.685 128.7832 4.465 5.46

2 1

reference spetra fo CoSi
by Cserháti Csaba 30 Jul '08

30 Jul '08

Dear all, I would like to ask if anyone has a reference spectra of CoSi. I would appreciate if someone could help. Thanks in advance! Csaba Cserhati P.S. I have already checked the databases you offered to Darek.

1 0

Proper link for Lytle Database
by Carlo Segre 29 Jul '08

29 Jul '08

Hello All: I have reworked the database web site a bit and I would appreciate it if the following URL is used to access it in the future. It would make my life a lot easier if I knew where users entered the database. http://ixs.iit.edu/database/ I took the liberty of continuing the association with the IXAS. If there is an objection, please let me know. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, 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

1 0

Zn xanes
by Michel Jaouen 25 Jul '08

25 Jul '08

Hi everybody, I wish to know if somedody can send me a reference xanes spectrum for pure Zn (ascii file)? That would be great.... Thank you everybody 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 __________________________________________

4 3

Bond lengths
by Bindu R. 25 Jul '08

25 Jul '08

Hi, Could you please clarify me, up to what decimal place in the bond lengths obtained from EXAFS fitting is reliable? If there are changes in the bond lengths in the fourth decimal place around the region of phase transition, can one consider this as a genuine one even though the error bars obtained from the EXAFS fitting are more than the variation in the bond lengths? Regards Bindu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/

2 1

Fwd: Re: Athena/Artemis
by Bruce Ravel 24 Jul '08

24 Jul '08

Hi gang, I received an interesting question this afternoon about EXAFS parameters and I thought that Olivier would benefit by hearing what more people than just me would have to say about this topic. He asks: Can you point me to documentation about the third and fourth cumulants? Since I study glasses, which are highly disordered, I would like to measure the anharmonicity parameters. What are typical values for C3 and C4? Grant Bunker has a very useful paper on the cumulants in Nucl. Instrum, and Meth. (1983) v. 207, p 437-444. Anatoly's paper on cumulants Phys. Rev. B 48, 585 - 588 (1993) is also handy and should give you some sense of what size the C3 and C4 parameters should be. In my experience, C3 and C4 should be smaller than sigma^2 -- perhaps by about 1 and 2 orders of magnitude, respectively. When they get much bigger than that, one can reasonably ask whether a short cumulant expansion (that is, an expansion out to only the 4th cumulant) is really adequate for describing the distribution of atoms in such a disordered material. There are people who have been applying reverse monte carlo or molecular dynamics to come up with better descriptions of highly disordered materials. Hopefully others will contribute to answering your questions. B Olivier: Sorry for switching languages on you -- hopefully it will prove useful to hear from others on the list. Je m'excuse de changer de langue pour cette conversacion -- on espere que il y aura des autres response utils ici sur la liste. ---------- Forwarded Message ---------- Subject: Re: Athena/Artemis Date: Thursday 24 July 2008 From: Olivier Villain <olivier.villain(a)impmc.jussieu.fr> To: Bruce Ravel <bravel(a)bnl.gov> Pourrais-tu m'indiquer où est l'aide concernant les paramètres 3rd et 4th ? Comme j'étudie des verres, donc du désordre, j'aimerais essayer des paramètres d'anharmonicité. Quelles sont les valeurs typiques ? Quelle est l'unité ? Je n'ai pas réussi à trouver ça dans l'aide. J'espère que je ne suis pas trop lourd... A bientôt, Olivier ------------------------------------------------------- -- 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

Installation of the last versions on XP
by shiryaev＠crys.ras.ru 23 Jul '08

23 Jul '08

Hi Matt, I have a message pretty similar to what Kleper sees (both problems he has located: "could not read bitmap...." and "can´t open \share\per1\Xray\space_groups.db:"). This is indeed sounds like non-ASCII names on my computer. Would be nice to find a way to overcome the problem without logging as another user. Thanks in advance, A.Shiryaev

2 2

Installation of the last versions on XP
by shiryaev＠crys.ras.ru 22 Jul '08

22 Jul '08

Hi everybody, Perhaps you may hep to resolve the following problem: I have no problems in installing and working with Ifeffit-1.2.6 on my Windows XP laptops. The problem concerns working with later versions: 1.2.9 and 1.2.10. There are no error messages on installation, but neither Athena not Artemis work. What can I change in setup? Thanks in advance, A.Shiryaev

5 6

Linear Combination Fitting - More Questions
by Gudrun Lisa Bovenkamp 17 Jul '08

17 Jul '08

Hi everyone, I just learned that before Athena there was no such program to check on all combinations, so it was not that confusing - or just more work? I think this feature of Athena is very good tool, but when I really do not know what is in my sample how can it help? I try to answer it myself and someone can correct me: Certainly not all of my, say 10 reference spektra, are that similar that I can get several LCFs with the same say R-factor. So, I will get some clue to narrow the components. But still there can be, for example: Standard-combi 1, 2, 3 equal to 1, 4, 6. So, my analysis gives two solutions and one must be wrong, but both can be wrong. How can I tell? Can a PCA help me in this case? The results change significantly when I change the normalization. How do I know what is the 'correct' adjustment? - Yes, I read the Athena turorials, but I got no answers from there. I searched quite a while to find a complete documentation of the LCF formula used in Athena, but I could not find it. Many thanks, Lisa

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 65, Issue 10
by sankaran anantharaman 17 Jul '08

17 Jul '08

Hi Richard, If I could intervene in your discussion, a suitable phrase is already in use to differentiate the EXAFS Debye-Waller factor from that obtained in X-Ray diffraction..."Debye-Waller-like factor". Reference : M. Bauer, H. Bertagnolli:X-ray absorption spectroscopy - The Method and its application, Bunsen-Magazin, 9. Jahrgang, 6/2007, p.216 Regards, Sankaran Anantharaman Universität Stuttgart Institute of Physical Chemistry Research group of Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart > Bruce, > > While you're on your soapbox, if we drop "Debye-Waller factor" to describe > the EXAFS disorder term, would you suggest using only "disorder" or do you > have a better phrase to use? > > Rich > > -- > Richard Mayes > > Barnes Group > 450/452 Buehler Hall > Department of Chemistry > University of Tennessee > Knoxville, TN 37996 > > > >

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quotation of figures
by s440697＠stud.uni-goettingen.de 17 Jul '08

17 Jul '08

Hi, i have a print out of a talk (about XANES, XAFS and multiple scattering...) and i want to cite some figures (attached). Can anybody tell me the author etc...? I searched everywhere on the web (on several sites of XAFS-Summer Schools...). Unfortunately i do not have the talk as pdf-file only the print out. Maybe the talk is from Matt Newville? Maybe anybody recalls on this talk/slides or recognizes them? Thanks for your help. Have a nice day, Eckhard --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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third cumulant
by grant bunker 16 Jul '08

16 Jul '08

Matthew - as you know, it's trivial to just let b=1/a and the write the distribution as (x-x)^s Exp[- (x-x0)/b] so that the gaussian limit is obtained as b->0. So infinite parameters are not a problem. Your suggestion and other observations are quite right. In fact, if convoluting distributions is ok, you can use whatever your favorites are, since cumulants just add under convolution. grant On Jul 16, 2008, at 11:08 AM, ifeffit- request(a)millenia.cars.aps.anl.gov wrote: > OK, here's my $0.02. I've used the convolution of an exponential > tail function > exp(-(r-r0)/w) (r-r0)*w >= 0 > 0 (r-r0)*r < 0 > > with a Gaussian. This avoids having to have parameters go to > infinity to approach a gaussian. This function > is a little unwieldy in real space but is simple in k-space. > mam

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FEFF-SCF and Enot in Artemis
by Frommer Jakob 16 Jul '08

16 Jul '08

Dear all! Recently I read the two inspiring XAFS13-contributions of Shelly and Bruce dealing with the energy-shift (p.132) and the use of SCF-calculations (p. 137). In this respect I have a question regarding the Enot parameter in Artemis: Plotting the mue (4th column in xmu.dat) of a FEFF8.4 SCF calculation (of a transition metal oxide; here: Fe or Cr) against the second column ("e") of xmu.dat, I end up with a fairly decent reconstruction of my experimental XANES: the onset of the pre-edge resonances is located at negative energies (if I am right this is referred to as E_0 (bottom of the conduction band)) and the energy zero (i.e. Fermi energy) is located somewhere in the rising part of the absorption edge. If I then use the same (SCF) potentials and let FEFF do a path-expansion run, the header of the feffnnnn.dat contains a (negative) quantity called "edge", which gives exactly the difference between E_0 and E_fermi (as also explained in Matt's article: J. Sync. Rad., 2001, pp. 96-100). In the xmu.dat, k seems to be calculated relative to E_0 (i.e. to a negative energy in the 2nd ("e") column). Plotting a path in Artemis (or the xmu calculated for a single path) I had the impression that again k is referenced to E_0 (onset of the pre-edge feature) rather than to E_fermi (somewhere in the rising part of the edge). Is this true? Assuming that I set the E0-parameter in Athena to the first inflection point of the main edge (so in the upper nomenclature to something like E_Fermi) and assuming further that I do a shell-fit in Artemis, wouldn't I expect to end up (in an ideal case) with an Enot similar to the quantity "edge" given in the feffnnnn.dat rather than a Enot of (close to) 0? I also found a mailing-list contribution (dating back to 2004) of Wojciech and Matt addressing a similar topic - still it is not clear to me what the effect on Artemis' Enot will be. I hope I did not confuse too many things. I will greatly appreciate any hint clarifying this situation. With many thanks and best regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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cumulant/rdf question
by grant bunker 15 Jul '08

15 Jul '08

re the cumulant <--> rdf connection This isn't a general solution, but it may work well for your system. A poisson distribution (x-x)^s Exp[-a (x-x0)] is a pretty flexible for moderately skewed distributions, permitting variable C2 and C3 by adjusting parameters s and a. For large s and small a the distribution approaches a gaussian. Expressions for cumulants etc are in Yang et al, JNCS Volume 210, Number 2, March 1997 have fun - gb > matt, > > I have a problem with an exafs analysis: > from the exafs analysis (with feffit2.98) of the first shell of a > disordered > system > I get the first three cumulants. > now, I wander how can reconstruct from them the radial distribution > function > which is the best solution? I have tried with the skew-normal > distribution, > but for the high skewness (ratio of third cumulant to sigma3) > values I get - that is around 2.5 - it is not well defined. > Do you have a suggestion? > Thanks,

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polarization
by Asma Tougerti 15 Jul '08

15 Jul '08

Hi, I study the sorption of Ni on single crystals of alumina by exafs . the angle made between the electric field and the sample is 90 and 0 . I read in “Exafs analysis using feff and feffit , matthew Newville, j.synchrotron rad (2201), 8,96-100” that we can use feff and feffit to calculate exafs spectra . I have three questions: In this reference authors uses a feff7 Can I use feff6 or I need a feef recent version ? There is a manual that explain how to write a feffit.inp file? How I can include the polarization dependence on my calculation? Asma

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