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

Core-Shell Spectroscopy session at Denver X-Ray Conference
by Carlo Segre 21 Mar '13

21 Mar '13

Hello All: This year we will once again have a core-shell spectroscopy session at the Denver X-ray Conference. The conference web site is http://www.dxcicdd.com/13/index.htm The conference organizers are accepting abstracts for talks and posters until April 5, 2013 (the web page says that submission is closed but it is really open for this specific session). Bruce Ravel and I are organizing the session and we would like to encourage you to submit your abstracts for talks and posters as soon as possible so that we can keep a yearly meeting where our community can present talks in North America. Denver is a nice centrally located venue where students can easily drive in from many places in North America (certainly from Chicago!) and save some travel costs. There are special student registration rates and there are also funds which students may apply for to defray expenses. I hope that you will participate and encourage your collegues in the field to do so as well. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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(no subject)
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. * 1*. What is the ideal value of R- factor for any fit. 2. * 2. * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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questions related to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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questions regarding to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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controls and data acquisition workshop ot SRI 2013
by Bruce Ravel 13 Mar '13

13 Mar '13

Hi! This year's Pan-American Synchrotron Radiation Instrumentation Conference will be held June 19-21 in Gaithersburg, MD, USA, with satellite workshops on June 17 and 18. Here's the URL: http://pml.nist.gov/Meetings/SRI2013/index.html I am organizing Workshop #8 on June 18th. It will be on the topic of software for beamline controls and data acquisition. If you work in this area, please consider submitting an abstract. Please pass word about this workshop to your favorite beamline scientist or to the controls and acquisition people at your synchrotron. Thanks! Bruce -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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MBACK and Athena
by Bajamundi Cyril 12 Mar '13

12 Mar '13

Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure <Calibrate data> affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal

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Theoretical calculation of Chi(k)
by John Farell 04 Mar '13

04 Mar '13

Dear Sir, I am trying to calculate the value of Chi(k) theoretically. I have taken Fe data. I need the values of scattering amplitude, phase shift at different energies. Where I could get those values ?.. Help me in this regard... Thanking you John

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Calibration for Sb K edge
by Darren Dale 28 Feb '13

28 Feb '13

Hello All, I have the CHESS F3 beamline set up with a dispersive monochromator for XANES at the Sb K edge with ~1 eV resolution. I didn't find a reference spectrum for Sb in Hephaestus, and would like to contribute one. But first I would like to have a little more confidence in the energy calibration. Does anyone know if 30.491 keV corresponds to the inflection point of mu for Sb(0) (or if not, what energy does)? Alternatively, does anyone know the energy of the Sb(0) white line (ideally with a reference)? Thanks, Darren

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Demeter 0.9.15
by Bruce Ravel 28 Feb '13

28 Feb '13

Hi! Today I released an update to Demeter and tagged version 0.9.15 it at GitHub. Windows users can download the updater package from http://bruceravel.github.com/demeter/ Source code installation instructions are near the end of that page. Windows users will notice a new download link for a documentation package. Simply download that package and double-click on it to install the Users' Guides for Athena and Artemis on your computer. If installing from source, the documents will be built and installed as part of the installation. There are a lot of swell new features and important bug fixes in this version. Some of the highlights are: * A fix for last week's report of problems with reference channels * Much improved performance by Athena once data is loaded * Direct links to document pages scattered throughout Athena and Artemis. If you have installed the documentation package, the local version will be displayed in a web browser. If the documentation package is absent, the programs will attempt to fetch the relevant document page from my github site. * Plucking points from the plotting window now works much more reliably For the full list, see https://github.com/bruceravel/demeter/blob/master/Changes.org For those following the development of Matt's Larch project, I have begun work on making Demeter use Larch rather than Ifeffit as its data processing backend. This is going well -- thus far, Athena can import data and do basic data processing using only Larch. Interaction with Larch is normally disabled. If anyone is interested in following along with that development more closely, let me know and I will write a wiki page about how to enable Larch support in Demeter. 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Merging data in Athena
by George Sterbinsky 28 Feb '13

28 Feb '13

I am writing to make you aware of what I believe to be a bug in (D)Athena. To demonstrate the problem, I have attached a project file containing two groups. Both groups have the same energy range but were measured with slightly different point spacings. Attempting to merge the two groups results in Athena excluding one of the groups from the merge "for being too short." Thank you, George

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Peakfit tool - determination of width
by Gudrun Lisa Bovenkamp 22 Feb '13

22 Feb '13

Hey Bruce, I was wondering how the width in the peak fitting tool of Athena is connected to the real data. What I mean is: A gaussian peak with a width of 1 (eV ?) seems to have a FWHM of 2 eV. Is it possible that you mean with "the Gaussians (...) are unit normlized (...)" the width is actually "sigma" and the amplitude is actually "mu" in the pure formula? Thanks, Lisa

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Error in second shell fit
by Devender 22 Feb '13

22 Feb '13

Hi, I am trying to fit Bi2Te3 exafs data using artemis. I am able to fit first shell (screenshot of fit is attached, I have also attached 'atoms' and 'feff' files for reference) but when I am trying to include second shell, I am getting the error (attached file- Fit_error.log). Error reads that- "The R effective for this path is well beyond the rmax value of its Data object." but I am already using Rmax of 6 A and Reff of these path are less than 5 A in my fit. I will appreciate if anyone can guide me or point me where I am making mistake. Regards, -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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Re: [Ifeffit] Importing Multiple Data Sets into Athena
by John Hayes 21 Feb '13

21 Feb '13

Hello, I am having some issues when importing multiple data sets into Athena. When I try to import more than one file at a time only the reference sample data from the first file are imported and the subsequent files do not import the reference data (only a straight line is imported). There is an error that is reported, and I have saved the error log [log.txt] and attached it in the zip file (as well as the dathena.log file and some sample spectra files). The spectra files are of the Mo K-edge and the reference is an Mo foil. These spectra were collected using the HXMA beamline, and as such, I am using the HXMA plug-in to import the data. The relevant columns for the reference are: col 2: energy col 6: I1 col 7: I2 I searched the archive and found what I think is a similar issue (link: www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03454.html) and hope I'm not over-reporting the error (sorry in advance if I am), but the previous report seemed somewhat different, in that there was an issue with the wrong edge being chosen for the test and ref data (best I can tell). I do have the work around of importing each file individually, so this is no more than an inconvenience, but I thought I'd report it and see if maybe someone had some up with a more elegant solution. I am currently using version 9.14 on a 64-bit windows platform. Thanks in advance for any advice or help the community can provide! -- John Hayes The Grosvenor Group Dept. of Chemistry University of Saskatchewan Two fish are in a tank. One turns to the other and says, "You man the guns, I'll drive."

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Fwd: Re: Use of feff8 with D-artemis?
by Bruce Ravel 20 Feb '13

20 Feb '13

On Thursday, July 12, 2012 05:31:19 PM you wrote: > > I wonder why the new Artemis (from Demeter) is limited to feff6 or feff7 as > the old ifeffit can deals with feff8 and feff9. > > Is it a wish? When you published data using feff7, the reviewers first note > that you should have used more actual version. I would challenge a reviewer to come up with a reliable study demonstrating that Feff8 or Feff9 provides a statistically significant improvement to EXAFS analysis. Obviously, I am not saying that full multiple scattering, self-consistency, and the various potential improvements in Feff9 are not relevant to XANES calculations or to Feff's treatment of other spectroscopies. What I am saying is that it has not been rigorously demonstrated that those things have an impact on the calculation of the extended EXAFS such that the analysis is improved in a statistically meaningful way. In short, I find that such arguments from reviewers boil down to "Feff8 is 33% better than Feff6 because 8 is 33% bigger than 6!" > Is it planned that D-Artemis will work with feff8 too? > > I am using the other programs of Demeter but still have to stick to the old > Artemis as none of my files can be read by D-Artemis (always error due to > feff8 or feff9 files by importing old project) That said, there is no good reason that artemis should not be able to use Feff8 or 9 if you want to do so. I suppose that laziness is the best explanation for why it doesn't yet. The Atoms portion of Demeter writes Feff8 files. The Atoms portion of Artemis simply has the line of code for using that part of Demeter commented out. That's trivial to fix. Getting Demeter to use Feff8 instead of Feff6 is not a lot of work, but it is also not a trivial amount of work. I will put this at the top of my to do list. Given that I will soon be leaving for conferences in distant places on the globe, I probably won't be able to release a version of Demeter that uses Feff8 effectively until Spetember. 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ----------------------------------------- -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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phase correction
by wangshaofeng＠iae.ac.cn 20 Feb '13

20 Feb '13

Hi Bruce, How can I open the phase correction function in fitting using demeter athena and artemis? cheers, Shaofeng

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Building perl wrapper for ifeffit on OS X Lion for Demeter
by Lyle Gordon 18 Feb '13

18 Feb '13

Dear Ifeffit experts, I am working on building Demeter on OS X. In the process I am trying to build ifeffit, including the perl bindings on OS X. However, upon following the instructions I get a range of errors when I try to build the perl bindings. The main ifeffit libraries appear to build just fine. This might be something trivial as I don't have much OS X experience. Following the (slightly out of date) instructions... cd ./wrappers/perl perl Makefile.PL see output: http://pastebin.com/TGzVjrpi sudo make install see output: http://pastebin.com/qkMYhYsP Any help would be greatly appreciated. Thanks very much, Lyle -- Lyle Gordon Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Cook Hall 2036 Evanston, IL 60208 Tel: (847) 491-3584 Mobile: (847) 400-4071 http://lylegordon.ca

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Hephaestus crash
by Darren Dale 17 Feb '13

17 Feb '13

Hello all, I'm working on getting my ifeffit/demeter environment together, following the instructions at http://bruceravel.github.com/demeter/pods/installation.pod.html . When I run hephaestus, select F'/F'', and then select any element in the table, the program bails and I get some feedback in the terminal: Can't use string ("Demeter") as a HASH ref while "strict refs" in use at accessor Demeter::devflag (defined at /home/darren/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter.pm line 100) line 8. Sometimes, "<F> line 29." is appended to that error message. I'm running the forthcoming kubuntu 13.04. Any ideas how I can improve my install? Thanks, Darren

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demeter windows download
by Darren Dale 17 Feb '13

17 Feb '13

Hello Bruce, All, I wanted to install Demeter on my windows computer this morning. I followed links to instructions at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in turns links to https://github.com/bruceravel/demeter/downloads . Unfortunately, github recently discontinued the downloads service, so that is not a functioning link anymore. Is there a new location available to find the installer? Thanks, Darren

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problem of paths calculation
by wangshaofeng＠iae.ac.cn 17 Feb '13

17 Feb '13

Hello Bruce, I am using demeter-atoms to calculate paths using a cif file (see attachment). When I run feff to calculate paths, there is a dialog box saying "You have defined ipot #1 but not used it in the atoms list". If I change the core atom from Ni to S, the calculation can be done. So how to solve this problem. Shaofeng

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Athena doesn't start - Larch server not running
by Ivan Stijepovic 16 Feb '13

16 Feb '13

Dear Bruce and other people in the list, I have just installed Demeter from the git on Ubuntu 12.04 using instructions given by Dave Hughes ( https://gist.github.com/waveform80/3959252) Everything went fine during installation but then I tried to start Athena using *dathena* command from the terminal and I got this message: Demeter says: Uh oh! You have requested using Larch, but there is no Larch server running! Then I installed Larch (with some problems during installation, but that is different story) and again tried starting Athena with the same result. When I tried starting Larch in a server mode with *larch -r* command it didn't offer a possibility to start Athena in the same terminal window. Then I opened a new tab in the terminal and just typed *dathena* and the GUI appeared. Now, I have two questions: 1. Do I have to start Larch server every time like this before using Athena or is there some other solution for this? 2. I tried Artemis without Larch server running and didn't get the error message. Is Artemis independent from Larch or are there some problems that might occur later? -- Best wishes, Dr Ivan Stijepović Department of Materials Engineering Faculty of Technology University of Novi Sad Bul. cara Lazara 1 21000 Novi Sad Serbia tel: +381 21 485 3750 fax: +381 21 450 413 e-mail: ivan.stijepovic(a)gmail.com

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Re: [Ifeffit] Demeter administator mode.
by Bruce Ravel 13 Feb '13

13 Feb '13

On Tuesday, February 12, 2013 04:19:55 PM you wrote: > Dear Bruce, > I am researcher from ICIQ, Spain and we produced some data at ALBA > synchrotron light facility in Barcelona ,Spain. My question is about > Demeter software in administrator mode. It works in only admin mode so it > can’t be used to normal users in our institute workgroup. Is there any > solution to this problem ? Atul, First off, I am CCing my answer to the Ifeffit mailing list, which is the appropriate venue for questions about the software. You can join the mailing list at http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Secondly, I provide instructions for submitting a useful and actionable bug report at http://bruceravel.github.com/demeter/pods/bugs.pod.html The advantage of following those instructions is that, including sending the log file with the initial report, it expedites my ability to understand the problem you are having. Finally, I think I recognize the problem you are having. Demeter attempts to write to "%APPDAtA%\demeter" where %APPDATA% is typically C:\Users\<username>\AppData\Roaming\ on Win 7 and C:\Documents and Settings\<username>\Application Data\ on Win XP. In the last release, I attempted to fix a problem whereby "%APPDAtA%\demeter" was not created at the time of installation. Athena or Artemis would then try to write to that location and fail because that folder did not exist. My "solution" in the last release was not correct and I hope to fix that in the upcoming release. The likliest solution to your problem is to create that folder by hand for each user, then try running the programs again. If that does not work, then please report back *to* *the* *mailing* *list* and I will again try to figure out what the problem is. 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Molybdenum nitride spectrum for Mo k and/or Mo L3 edge
by Soma Chattopadhyay 12 Feb '13

12 Feb '13

Hello Was wondering if anybody has a Mo k edge and/or L3 edge exafs spectra/spectrum (preferable with Mo foil in reference) for the compound molybdenum Nitride and can send me data. Will appreciate very much. Thanks Soma

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Basic question in normalization and background removal
by Bajamundi Cyril 08 Feb '13

08 Feb '13

Hello, I have here a very basic XANES data processing. I am but a novice in this XANES analysis. In Bruce's lecture "Athena: Data processing I<mms://diamstream02.diamond.ac.uk/xafs-2011-2>" posted in the Diamond Light Source website, he used the Fe_lepidocrocite.000 example to show how background removal and normalization is done. For the normalization range he used the range 150 - 742.610 because his original photon energy scan range is quite long [ Emin: -200 and Emax: 800]. However, say that your original scan range is only short e.g. within the range Emin : -30 to Emax: 80, such that you don't see the non-wiggly range and you only see the a short portion of the post edge range, how does one set the normalization range for this data? Since I'm very new to XANES analysis, I keep second-guessing my choice of normalization range. Your patience for answering this simple question will definitely help me in moving to the actual fingerprinting analysis that I need to do with my sample. Many thanks. Warm regards, Cyril [cid:image004.jpg@01CE05DE.B8F89320] [cid:image007.jpg@01CE05DE.B8F89320]

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XAS position in Industry
by Shelly Kelly 06 Feb '13

06 Feb '13

Dear XAS Community, We have a position open at UOP LLC, A Honeywell Company to support our XAS/tomography group. The position description can be found under Req number 00213183 at http://www.careersathoneywell.com/en/home. Please apply through the web site. Thank-you, Shelly Kelly

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Open post-doc position in Korea
by Deok-Yong Cho 03 Feb '13

03 Feb '13

Dear Ifeffit users: To whom interested in post-doc position in Korea: A two-year contract post-doc position is open in the Center for Functional Interfaces of Correlated Electron Systems (CFI-CES), Institute for Basic Science (IBS), located in Seoul National University, Seoul, Korea. We expect he/she will perform spectroscopic analysis including IR spectroscopy (Spectroscopic ellipsometry and FT-IR) at the institute and synchrotron experiments such as soft/hard x-ray absorption spectroscopy and XAFS analysis for new functional oxide materials (mainly strongly-correlated electron system). Please find enclosed document for more details. Best Regards, Deok-Yong Cho Spectroscopy team in CFI-CES, Institute for Basic Science (IBS), Seoul National University

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