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

Postdoctoral position in Yeshiva University and Brookhaven National Laboratory
by Anatoly I Frenkel 20 Jun '14

20 Jun '14

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunity. Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2014. The project title is: "Characterization of structure, diffusion mechanism and optoelectronic properties of doped colloidal semiconductor nanocrystals." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II for X-ray spectroscopy and Center for Functional Nanomaterials for electron microscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods and their applications to nanomaterials, and experience with in situ characterization methods. Working knowledge of Raman spectroscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Use of the 3rd and 4th Parameter
by Michael Kömm 16 Jun '14

16 Jun '14

Hello, I'm trying to make an EXAFS analysis on the Structure of Tb in a borogermanate glass System. The reference is an .cif of Terbium-Gallium-Garnet (TGG). I expect some disorder caused to working in glass. Therefore I would like to use the 3rd and/or the 4th parameter. I tried to set a guess parameter to evaluate those parameters. Could you tell me a reasonable value for these parameters? The 3rd only varies a little bit around its guessed value (+- 0.01) and if I try to do the same with the 4th parameter no fit at all takes place. The errors in the GDS-window are exactly 0.00000 with no fit taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) and the R-factor of the fit is way over the top (>10^20). I've chosen a value of 0.5 for the 3rd and the 4th parameter just to see if they're working and I was only doing a quick first shell fit with the surrounding oxygen-shell. Please can somebody tell me how to deal with this problems. Thanks a lot for your time and efford. Sincerly yours, Michael Kömm

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Ah okay. I think now I get it. Is it correct that in the mu(E) spectrum you plot the total spectrum in blue and in red you chose different fms-radii like 2.5, 3.0, 4.1 to get the XANES spectrum for different shells? Or are the red curves another varied FEFF parameter? Thanks so much for your support! Stefanie

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Dear Bruce, thanks for your answer! My problem is how to get the E/mu information for each single scattering path. If I get it right, the xmu.dat contains the sum of all scattering paths. This is the blue curve in your talk. But there are also the spetra for the first,s econd, third,... path at page 11 in red. I think the information comes from the feff0001.dat. feff0002.dat and so on. But these files do not contain mu! Or do I understand it wrong? I have no data to fit, just the FEFF calculations. Is there any possibility to get the XANES spectrum of all paths and the XANES spectrum of every single path to compare how the single paths influence the complete spectrum? Thanks! Stefanie

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Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount
by madhusmita sahoo 12 Jun '14

12 Jun '14

Dear Members, I would like to know, *Q1)* If there is a screw axis in the system, like the anatase phase of TiO2, whose space group is I41/amd, how should I enter that in the atoms for feff calculation. Kindly tell me which is the correct way. When I entered 141(the space group number) and I41/amd, both generated separate set of atomic positions. The older version of artemis, now the new one(latest version), both generates different set of atomic position with the same crystallographic input, i.e if I enter 141(or I41/amd) in place of space group and run atoms, it generates two different set of co-ordinates in Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same. *Q2)* And when co-ordinates is shifted by certain amount, do we have to enter that in the shift vector as well as while defining the (x y z) of a particular site. Or I should just enter the shift vector and define the co-ordinates at its usual position ( I feel this one is correct). For example in anatase crystal structure the co-ordinates are shifted by (0,0.25,-0.125). So, the inputs can be For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, z= 0 and O (scatterer) x= 0, y=0, z=0.20806 (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally both should give the same result. But it gives different set of atomic positions. Even the same input in different version of artemis is yielding different results(in Artemis 0.8.012 and in Demeter 0.9.18) . I am confused about how atoms work in artemis. I request you to elucidate the correct method. Warm wishes Madhusmita India

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Scattering paths in XANES calculations
by Stefanie Roese 12 Jun '14

12 Jun '14

Dear all, I am performing XANES calculations for silver clusters with FEFF. Aditional to my XANES results, I would like to get information about the participating scattering paths and how they influence my spectra. In detail I want to get the same pictures that Bruce ravel used in his talk "a practical introduction to multiple scattering theory" from page 11. I have performed calculations for XANES using the rpath algorithm to obtain the feffnnnn.dat files. I already checked, that the course of the rpath spectra agrees to the fms calculations in ordner to make sure that the algorithm converged. But now I fail at getting the plots with the Energy at the x-axis and the normailzed mu at the y-axis likle Bruce did it in his talk. Which program was used there? Athena? And how can I get the energy/mu-information out of my feffnnn.dat files to compare to the total spectrum? I think I am quite close to the solution, but it does not work. Thanks in advance for every help! Steffi

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Demeter on Mac OS X
by Juliana Fonseca de Lima 06 Jun '14

06 Jun '14

Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Cheers, Juliana

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Demeter-devel port added in Macports for OS X
by Schima, Frank 06 Jun '14

06 Jun '14

OS X Users, I have created a new port in Macports for demeter-devel based on the 0.9.20 version which is still in development. This has important fixes for the black window problem in Artemis. To install it, simply run the following commands in Terminal: sudo port selfupdate sudo port uninstall demeter sudo port install demeter-devel Feedback appreciated. I have only tested it on OS X 10.9.3 so far. Just keep in mind that the “devel” part means that this is not a release version and problems may exist. Cheers! Frank

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Help
by Dien.Li＠srs.gov 06 Jun '14

06 Jun '14

HI, all I am a beginner user of Athena and Artemis and ATOMS. It is very nice to find Athena and Artemis manuals, they are helpful: 1. Do you have FeS2 and other Fe mineral EXAFS data as described in your manual, and associated data files, so that I can practice following your manual. 2. When I ran ATOMS standing alone, to input the crystal structure data that have more than 7 atom sites. I could not add a site by clicking "Add a Site" button, is there a problem for ATOMS, or it may be related to our SRNL security system. 3. Currently, my project is to study U adsorption to natural organic matter and minerals (e.g., goethite) surfaces, do you have any template files available for calculating FEFF or if you can instruct me where I can start for such systems: for example, uranyl-C or uranyl-goethite surfaces. 4. How to define the fitting models and GDS parameters for such U systems. Thanks you so much for your help. Dien Li, Ph.D. Fellow Scientist Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Aligning EXAFS E0 to Theory
by Carter Abney 05 Jun '14

05 Jun '14

Hello, Everyone - This is my first time trying to work through EXAFS analysis of experimental data, and I've got what (I think) should be a fairly straightforward question. I'm trying to minimize my delta E0 by aligning the EXAFS data with my best fit (i.e. - align the k-grid of the data with the k-grid of the theory to obtain a small delta E0). However, I have been unsuccessful in "reading the theoretical chi(k) spectrum into Athena<http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02494.ht…>" to accomplish this. I assume the crux of the problem is the format in which I am exporting my theoretical chi(k) spectrum from Artemis. The only way I have been able to export the data with Artemis so Athena can import it is to click the "Save next plot to a file" button, which then allows me to save the data as a text file. I know I need chi(k) data that is not k-weighted<http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg01623.ht…>, so I plot the best fit with k-weight of 0 in k space with deltaE0 equal to 0. Considering the problems I've had, I'm assuming somewhere in this process is where I'm going wrong. When I import this data, I have four columns: k, experimental data, fit, window. Since k is the wavenumber of the photoelectron, I choose that as "Energy." Then I select column 3, the best fit, as "Numerator," and change the data type to chi(k). I then import the data. I've attached two pngs to this e-mail which, assuming they come through, should display the Athena data import window and the corresponding plot of chi(k). When I plot this data in k-space or R-space using Artemis, the resulting plots look appropriate. When I try to align the experimental EXAFS data in Athena, I know it aligns the first derivative of E for the selected data to the first derivative of E for the standard. I want my best fit to be the standard to which the data is aligned. However, I cannot plot chi(k) data in E, which causes me to believe I shouldn't be able to align data to the first derivative of E. True enough, when I try to auto align, I get impossible values for E0 adjustment. Clearly I'm doing something wrong - possibly even several somethings wrong. Any guidance would be greatly appreciated. Thanks, - Carter

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