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

iXAFS & xQuartz
by Gaspard Jean-Pierre 16 Oct '14

16 Oct '14

Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : "X11 is not installed". I am missing something but I do not know what. Regards JP

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Ke
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Sin Yuen, Thanks for forwarding me that study materials on E0. I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen. Tks! Ke

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Ke
by Ke Yuan 15 Oct '14

15 Oct '14

Hi Bruce, Thanks for your comments! I studied Shelly's paper and found my data does looks different, especially the first peak at 1.9 A, seems it splits into two in my case. I prepared this sample by pressing UO2 powder into a hole (2mm deep), which might have significant self-absorption effect, because it's not dilute and thin. Do you think this will change the peak amplitude? Best, Ke

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Possible bug in Athena during alignment
by Leon Clarke 15 Oct '14

15 Oct '14

I'd like to report a possible bug within Athena. Last week I collected Br K-edge data at the APS and have experienced an issue with Athena during data alignment. The beamline energy required calibration and so I did the following data processing steps, in this order: 1. Completed pre- and post-edge corrections, using windows relative to the actual Br K-edge energy, on the raw data exported from the beamline. (In other words these windows were not energy offsets relative to the actual measured edge position). 2. Used the flatten post-edge feature within Athena. 3. 'Calibrated' (Normalised is a better term really) the first derivative of a NaBr measurement to the Br K-edge energy using the calibrate drop-down option. This resulted in the requirement for a -17.39 eV energy offset. 4. Tried to align all of the sample data to the NaBr 'standard' using the align drop-down option. The issue I have had is with step #4. When I aligned, for several samples the XAFS (XANES) plots went wrong. It seems that Athena was not transforming the pre- and post-edge windows correctly for such a large energy shift, i.e. didn't shift these to lower energies by 17.39 eV, and I think this is a bug within Athena. I hope the above makes sense; I can provide an Athena project file, if required. Many thanks, Leon ----- Dr Leon J. Clarke Senior Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

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Warning "e0 is greater than 10"
by Ke Yuan 15 Oct '14

15 Oct '14

Hello Feff community, I am practicing on using Artemis to fit a UO2 XAFS data I measured. The parameters I used can be found from the pic attached. The Artemis project file is also attached. I have been getting this "e0 greater than 10" warning on many of my fittings. Will picking a slightly different E0 change the result much? Any suggestions on how to improve this fitting? Thanks! Ke -- Ke Yuan PhD Candidate Department of Earth and Environmental Sciences 1100 North University Ave 3021 C.C Little University of Michigan, Ann Arbor MI 48109-1005

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Using artemis to fit EXAFS data with MD- screen message says perl interpreter has stopped working
by Gill, Simerjeet 14 Oct '14

14 Oct '14

I am trying to fit EXAFS data using MD files. I am able to load my MD file and build the histogram but when I try to transfer my ss path for MD, Artemis fails at last step. I see a message on the screen saying Perl interpreter has stopped working (attached). My artemis log file accessed using C:\Users\<username>\AppData\Roaming\Demeter\artemis.log is empty. I am using the latest version of artemis which is 0.9.20. My system is windows 7 with 32-bit operating system. To repeat what I am doing: I load my project file, then Cu.inp file, run atoms and feff, then I load my MD file, build histogram, when I drag the ss path to the path window, the program fails at last binning stage and I see error message-Perl stopped working. I tried looking into iffefit archive using key words "perl interpreter is not working" but could not find it. I will really appreciate help on this. Thanks, Simer

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error message for Athena lauching on mac os 10.9.5
by emmanuelle Montarges-Pelletier 09 Oct '14

09 Oct '14

dear all Until this morning ATHENA installed through mac ports on my computer (OS 10.9.5) was working rather good. However, I have tried to open a .prj file (too large apparently) and the ATHENA-PERL software froze. I quit and tried to relaunch ATHENA, but I had the following message this morning on the terminal window: perl5.16(1177,0x7fff76dad310) 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! Could someone tell me what I am supposed to do? Thanks a lot for your answer Best regards Emmanuelle MONTARGES-PELLETIER Chargée de Recherche CNRS LIEC Laboratoire Interdisciplinaire des Environnements Continentaux UMR 7360 CNRS Université de Lorraine 15 avenue du Charmois F-54500 Vandœuvre-lés-Nancy - France tel 33 (0)3 83 59 62 52 mob 33(0)6 31 33 10 30 Directrice de la Zone Atelier du bassin de la Moselle http://apps.ensic.inpl-nancy.fr/Zam/index_fr.html

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Possible problems with athena
by Paul Fons 08 Oct '14

08 Oct '14

Hello all, I am using the latest version of Demeter (@0.9.20pre10)on the Mac put together by Frank Schima (thank you Frank) and I noticed a problem that I thought I would pass along. This is under OS 10.9 Mavericks with the latest Xquartz (X11) installed. If one outputs a standard (in this case for Fe) file from Hephaestus and attempts to read it in as an "xmu" file in athena, the following happens. The element field is identified as Beryllium and E0 is set to 0. The data while looking fine during the input dialog looks fine. Changing the Element to Fe and specifying the K edge results and selecting a change in E0 (to tabulated value for example) results in the tabulated value popping up in the E0 box, however, plotting results in the same screen values returning Be L2 edge and a value of 0 for E0. Note the strange values for the Pre-edge range as well (12106 to 6053 eV). Fixing this is of no use either as soon as one plots, the strange values return. I have tried reading the data in as both norm(E) and xmu (it is an xmu file) to no avail. Any suggestions as to what I might try next? Cheers, Paul p.s. there are attachments demonstrating the values, but if they get dropped the text description should suffice. Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

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Re: [Ifeffit] Trouble creating feff input file for NaTiO3 cubic perovskite structure
by Badari Rao 08 Oct '14

08 Oct '14

Dear Dr. Bruce, I have attached the datoms.log file and the .inp file used. I am using windows platform. I hope you can get to the root of the problem with this. Regards, Badari On Tue, Sep 30, 2014 at 10:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Date: Tue, 30 Sep 2014 08:21:18 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Trouble creating feff input file for NaTiO3 > cubic perovskite structure > Message-ID: <542AA03E.8070701(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 09/30/2014 05:45 AM, Badari Rao wrote: > > Dear All, > > When I try to feed the following data into the atoms input and run the > > feff calculations, the software just automatically closes. > > space group no: 221 > > a = b = c = 3.88; alpha = beta = gamma = 90; > > atomic coordinates: > > Na: 0.5, 0.5 , 0.5 > > Ti: 0, 0, 0 > > O: 0, 0, 0.5 > > > > Core: Ti > > > > I don't think it is a bug because the calculation works perfectly when I > > replace Na with heavier atoms like K, Mg etc. I would like to know why I > > am not able to create the feff input file using Na. > > I cannot reproduce your problem using the information you've given. > That structural data runs just fine and gives sensible output on both > Windows and linux. > > When making a bug report, you should include the information discussed > in http://bruceravel.github.io/demeter/pods/bugs.pod.html. Without the > information in the error log and without an actionable recipe for > replicating the problem, there is simply nothing that I can do to help. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > -- Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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Update on importing Hephaestus Fe standard
by Paul Fons 07 Oct '14

07 Oct '14

Hi All, I wanted to add a quick update in that the Fe standard from Hephaestus can be imported as a mu(E) file in athena. Perhaps the file type assigned by Hephaestus is the only problem here. Cheers, Paul

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