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

Athena and Artemis reference
by IONESCU, Mihail 02 May '07

02 May '07

Dear Bruce, What reference we can give in our papers for using Athena and Artemis packages, which you guys have been provided so generously to the user community? Thanks, Mihail ----------------------------------------------------------------- Dr Mihail Ionescu Senior Research Scientist Ion Beam Accelerator Applications Australian Nuclear Science and Technology Organisation ANSTO Bld. 53, New Illawarra Rd, Lucas Heights, NSW 2234 Australia PMB1, Menai, NSW 2234 Ph: +612 9717 3301 Fax: +612 9717 3257 -----------------------------------------------------------------

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Potential Postdoctoral Position in XAFS
by Bare, Simon R 30 Apr '07

30 Apr '07

POSTDOCTORAL POSITION in XAFS and XRD UOP LLC There is a potential opening for a postdoctoral position in synchrotron radiation research of catalysts and adsorbents with UOP LLC. The successful candidate with work with UOP LLC research scientists and will support UOP LLC exploratory and fundamental industrial research activities primarily at the Advanced Photon Source (APS) at Argonne National Laboratory. UOP LLC, a Honeywell Company, located in northwest suburban Chicago, is an international leader in technology, products, and services for the petroleum processing and separation industries (www.uop.com <http://www.uop.com/> ). The successful candidate will participate in all aspects of experiments related to operating a beamline, collecting, analyzing and interpreting the data. This position requires expertise in techniques of XAFS (preferably with knowledge of Athena/Artemis or Iffeffit software) and XRD, together with hands-on experience with electronic control and measuring equipment and beamline components. A CV with publications list, and the names and addresses of two references, should be sent via e-mail to Dr. Simon Bare at: simon.bare(a)uop.com.

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sum path NAN?
by Mauro Rovezzi 27 Apr '07

27 Apr '07

Dear all, Do you have any idea of what means NAN (Not A Number?) in "sum path" Ifeffit output during the fit? I've already posted this issue in a post dated 2006/10/04 and Bruce asked to me to give him something to reproduce this issue on his computer but this behavior is very unstable and I don't understand how to exactly reproduce it. I would like to know in your opinion what could bring a variable during the minimization process to NAN. In addition, what exactly means the four numbers visible in the "sum path #1 #2 #3 #4" output? It seems to me that, for each path, #2 = delr and #3 = sigma2, isn't it? M. -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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mailing list downtime
by Matt Newville 20 Apr '07

20 Apr '07

Hi Folks, Sorry to bother you with non-XAFS related mail, but I wanted to let you know that the Ifeffit mailing list, web pages (everything on http://cars9.uchicgo.edu, http://millenia.cars.aps.anl.gov, and http://xafs.org) will be unavailable tomorrow (Apr 21), starting around 6am Central Daylight Time (11am UTC) and lasting for around 12 hours. This is due to a scheduled complete power outage to the building housing the server and network equipment. I assume the network equipment and server will come back from the power outage just fine, but will be watching for signs of life. Mail sent to the mailing list during the down time should queue up until the server is back up, but I wouldn't want to guarantee that mail won't get bounced over the weekend. Sorry for the inconvenience, --Matt

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Several Questions
by Edward L. Kunkes 20 Apr '07

20 Apr '07

Hello everyone, I am currently using IFEFFIT to fit LIII edge data collected for Pt, Re and PtRe bi-metallic Nan particles supported on carbon, and I have several questions: 1. I get an So2 value of 0.54 from a first coordination shell fit on Re-foil (this So2 value also seems to work when fitting NH4ReO4-) Has anyone ever worked with Re before and gotten a similar value for So2 ? 2. I model the path for the a single coordination shell as 6 octahedrally arranged nearest neighbor atoms surrounding the absorber atom at a distance equal to that of inter -atomic spacing in the metal. When comparing the IFEFFIT predicted EXAFS for this model to one that is generated by using the first path from a crystallographic model, the two seem slightly different. The nanoparticles are very small (amorphous to XRD), and probably consist of a disordered phase, so I cannot assign a crystal structure. What should I do in this case? 3. I often get high correlations the coordination number and ss, or delEo and dR (the correlations are ~0.8). Using multiple k-weights doesn’t decrease the correlations. What is an acceptable value for these correlations? Thank you very much for taking the time to answer my questions -Ed Kunkes

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Re: [Ifeffit] Structures with multiple crystallographic sites
by Vadim G Palshin 20 Apr '07

20 Apr '07

Matt, Bruce - thank you! I believe I found the problem - Artemis does seem to choke even on 200 paths, especially with the "fit background" option on. At least it does on my office PC - relatively old and weak machine, will start begging for a new one shortly. Sometimes it would generate a long error message starting with "use of uninitialized value in abs at artemis line 12984."; sometimes there is no error message but results would look really strange. Had me so confused that I started to doubt my fitting method. I have since trimmed down the number of paths and variables to a minimum (didn't need that many anyway), and the problem seems to be solved. Thanks again for your responses, gentlemen! Vadim.

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Structures with multiple crystallographic sites
by Vadim G Palshin 20 Apr '07

20 Apr '07

>Do a Feff calculation with each unique Co site as the absorbing atom, >then use paths from each calculation, weighted by the fractional site >occupancy. >Cheers, >--Matt Thanks, Matt! Yes, that's exactly what I tried doing. It's a simple cubic lattice with 20 atoms per unit cell, 8 of one type (Co1) and 12 of the other (Co2). So I did two FEFF runs in the same Artemis project, with Co1 and Co2 as the core atom, and multiplied their respective amplitudes by 0.4 and 0.6. Then I noticed that if I calculate a sum of all included paths I get a different FT spectrum than if the sums are calculated separately for the two FEFF runs and averaged (with correct weighting) outside of Artemis. Of course, it is a bit late here and I could be missing some obvious mistake. On the other hand, I am trying for 1.6-5.5 angstrom fitting range, which involves 70+ paths for Co1 core and ~120 for Co2. Is it possible that Artemis does not like to deal with too many paths and/or variables? I better go check the manual... :o) Regards. Vadim.

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Structures with multiple crystallographic sites
by Vadim G Palshin 19 Apr '07

19 Apr '07

Hello, everyone! I am trying to fit various metallic Co spectra (nanoparticles) and one of the structural models, the epsilon-Co phase, has two unique crystallographic sites for Co. How does one tackle fitting a dataset with multiple crystallographic sites? Thanks! Vadim.

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question concerning Hephaestus
by I.Reitz 17 Apr '07

17 Apr '07

Dear list members, can you please tell me, what the ion chamber utility calculates. I did not understand the perl code. Does it give me first the percentage absorbed via Beers law und then give me the Nbofphotonsabsorbed, that means the flux absorbed in the chamber or is the result that gives the program out the "number of transmitted photons" after the chamber? Thank you Irmi -- ********************************************* I. Reitz German Cancer Research Center DKFZ, E0401 Dept. of Medical Physics in Radiation Therapy Im Neuenheimer Feld 280 D – 69120 Heidelberg Phone: +49 - 6221 42-2455 Fax: +49 - 6221 42-2572 Email: I.Reitz(a)dkfz.de *********************************************

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Doubts
by Shiju N. R. 16 Apr '07

16 Apr '07

Hi, I am Shiju and I work as a research associate at the Chemical Engineering department of University of Cincinnati. We are working on the conversion of light alkanes using mixed oxide catalysts. We are trying to understand the structure of a Mo based mixed oxide catalyst that is highly active for this reaction using XAFS and have some data of this catalyst, collected at NSLS. Since I am new to XAFS, I am trying to learn it myself. I am using Athena and Artemis. I am trying to use MoO3 as a model compound for understanding the Mo local structure in my catalyst. By following Scott Calvin's ZnO example (which is highly helpful for beginners like me), I was able to get a reasonable fit for MoO3 structure. For the next step (fitting my Mo catalyst), I would like to seek help regarding the procedure I should follow. I would like to describe my understanding to approach the fitting of my Mo catalyst and please let me know if I am right or wrong. I am going to take same MoO3 structure to form the theory and import the same paths which were used to fit model MoO3 structure. Then I will set the values of S02 and sigma2 to that obtained for MoO3 and allow E0 and delr to vary during the fitting. Please let me know if this is right approach. I tried once this way, also introducing the concept suggested by Bruce Ravel to find the coordination in one of the earlier posts. I used the expression S02 = ni*amp, where i represents each path, keeping the degeneracy of each path as 1. I was able to get a fit, however, ni are fractions and their sum is much less than 6, while I am expecting an octahedral coordination of Mo in my catalyst. Is it due to any mistake in my approach? what should I do to correct it? Please excuse if these questions seem silly... I am just a beginner in XAFS! Shiju Dr. Shiju. N. R. Research associate Chemical and Material Engineering University of Cincinnati Ohio USA --------------------------------- Yahoo! Mail is the world's favourite email. Don't settle for less, sign up for your freeaccount today.

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