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

background removal - spline range kmin
by Reagen Lan 23 Apr '13

23 Apr '13

Dear all, For removing the background from a spec with sharp white-line, I understand it is often to put larger value for kmin of Spline range in Athena. However, in my current case, there is a intensive XANES peak at c.a. 16ev after the white-line peak. Thus, should I input kmin in between these two peaks (see attached figure test1.png)? or increase kmin to avoid the second strong peak(attached figure test2.png)? The two conditions do give different chi(R). Please could some body advise? Thanks a lot! Best regards, Zhipeng

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Re: [Ifeffit] ifeffit R-factor
by Matt Newville 18 Apr '13

18 Apr '13

Hi Sandra, On Sat, Apr 6, 2013 at 12:37 PM, Sandra Luber <s.luber(a)pci.uzh.ch> wrote: > Dear Matt Newville, > > I do some fitting with ifeffit using EXAFS data generated by feff. > I wonder how the R-factor is calculated. Unfortunately, > I have not found any definition yet. Would it be possible > that you write me how it is obtained? > This would be great. > > Thanks a lot. > > Best regards > Sandra Luber > The basic definition is R = Sum( |data - fit|^2 ) / Sum( |data|^2 ) The old Feffit document probably has the clearest definition, in its Chapter 5 (pages 16-20 of http://cars.uchicago.edu/~newville/feffit/feffit.pdf ). The definition and briefer explanations are also given in several of the tutorials on http://xafs.org/Tutorials. Thanks for reminding me to put this and related information into the Larch documentation! --Matt

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L-edge soft X-ray data in Artemis and Athena
by Shoaib Muhammad 11 Apr '13

11 Apr '13

Hi, I am a research student and relatively new to XAFS. I have soft X-Ray L-edge data of Mn and Ni. Is it possible to process this data in Athena and then fit in Artemis like usual K-edge data? Thanks -- Shoaib

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ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

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ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

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APS/IIT XAFS Summer School July 8 - 12, 2013
by Robert Gordon 01 Apr '13

01 Apr '13

Notice attached. "This XAFS summer school is a continuation of the week-long summer school offered annually at the Advanced Photon Source, and again the venue will be at IIT in Chicago. Course material will cover fundamental and practical aspects of X-ray Absorption Fine Structure Spectroscopy: sample preparation, experiment, theory, data analysis. One day of hands-on experiments will be carried out by participants at several APS beamlines, followed by a guided data analysis laboratory using Athena/iFEFFIT and other programs. Computers will be available for those participants attending without their own laptops. The target audience is graduate students, postdocs, and other scientists who are new to XAFS and want to use it in their own research. Space is available for up to 40 students. Instructors include: Dr. Steve Heald (ANL), Dr. Matt Newville (UChicago), Prof. Bruce Bunker (U Notre Dame), Prof. Carlo Segre (IIT), Prof. Grant Bunker (IIT), and a number of other experienced XAFS researchers also will participate. The cost of the course is $500 USD, which covers most meals. Students will be responsible for their own housing (available on and off IIT campus) and travel to/from their home institutions. IIT is readily accessible by car, cab, and CTA train from O’Hare and Midway airports. Free time will be available most evenings for participants to visit Chicago attractions such as Grant Park, the Loop, Millennium Park, Lake Michigan; music, architecture, art, theater; Chinatown, White Sox, Field Museum, Shedd Aquarium, Adler Planetarium, and Navy Pier, restaurants, and pubs. Please email bunker(a)iit.edu with subject line “2013 XAFS School” -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

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anisotropic Debye temperatures in reciprocal-space calculations
by Van Der Veen, Renske M. 29 Mar '13

29 Mar '13

Dear FEFF users! I am looking into the use of the DEBYE card in order to calculate the EELS spectrum of graphite at ~800 K. Obviously, graphite is highly anisotropic, such that it would be unphysical to use a single Debye temperature. However, the effective in-plane (a,b axes) and out-of-plane (c axis) Debye temperatures are known for graphite (2500 and 950 K, respectively). I was therefore wondering whether it is possible in FEFF9 to specify two Debye temperatures for the two different crystallographic directions. I am calculating the (oriented) EELS spectrum of graphite in reciprocal space using the RECIPROCAL, LATTICE and ATOMS cards; see feff.inp file below. I am using FEFF version 9.05. In case the use of Debye temperatures is not possible in this way, could anybody recommend another way to take into account the Debye-Waller factors for an anisotropic material such as graphite? Thanks! Best regards, Renske van der Veen -- Dr. Renske M. van der Veen California Institute of Technology Arthur Amos Noyes Laboratory of Chemical Physics 1200 E California Blvd MC 127-72, Pasadena, CA 91125, USA Office: (+1) (626) 395 6530 Mobile: (+1) (626) 808 2635 **** TITLE graphite * C K edge energy = 284.20 eV EDGE K 0.0 CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 1 COREHOLE RPA LDOS -20 10 0.05 * this calculates the density of states EGRID e_grid -3 17 0.3 e_grid last 30 0.4 e_grid last 58 1 ELNES 200 # beam energy in keV 0 0 1 # beam direction in the crystal frame 10 5 # collection semiangle, convergence semiangle (in mrad) 200 1 # q-integration mesh : radial size, angular size 0.0 0.0 # position of the detector (x,y angle in mrad) FMS 7.0 2 EXCHANGE 0 1 0.7 SCF 5 RPATH 0.2 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 6 C 3 2 0.01 1 6 C 3 2 2 2 6 C 3 2 2 RECIPROCAL KMESH 5000 MARKER 1 LATTICE P 2.4612 0.86603 -0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 2.72546 ATOMS * this list contains 251 atoms * * x y z ipot tag distance 0.00000 0.00000 0.68160 1 C1 0.00000 0.00000 2.04479 1 C1 0.57735 0.00000 0.68160 2 C2 0.28868 0.50000 2.04479 2 C2 END

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Demeter 0.9.16
by Bruce Ravel 29 Mar '13

29 Mar '13

Hi, I just tagged a new release of Demeter at https://github.com/bruceravel/demeter and made a link to the new Updater package for Windows at http://bruceravel.github.com/demeter/ This release fixes several issues that have bee raised in the last week or so. For details, see the change log at https://github.com/bruceravel/demeter/blob/master/Changes.org 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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Possible bug in atoms files generation by Artemis
by Devender 29 Mar '13

29 Mar '13

Hi, I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for atoms. Previously, I was using only available option of FEFF6 style. When I tried to run atoms selecting FEFF 8, it generated atoms files but when I tried to run FEFF calculations it produced following errors. Error#1 " Unknown keyword: "EDGE" at line: EDGE L3" Error#2 "Unknown keyword: "exchange" at line: exchange" I worked around first error by replacing "EDGE L3 S02 1.0 "- which was generated by atoms when FEFF8 style is selected. with "HOLE 4 1.0" and deleting Exchange keyword from feff file. After making these edits in feff files, I was able to run FEFF without showing any errors. I have attached all the files with appropriate name. -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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Shifted data in Athena
by George Sterbinsky 27 Mar '13

27 Mar '13

Hello, I have attached an (D)Athena project with containing two groups, imported as a primary data set and a reference. The groups were therefore imported on the same energy grid. However, when plotted, the energy values of the data points for the two groups are clearly shifted with respect to each other. Can someone please explain the origin of this shift? Thank you, George

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