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

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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fitting mixture
by kaziz sameh 06 Oct '14

06 Oct '14

hi, i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum and think there is a mixture of Pd in staple and in centre. could you help me how to do the fitting mixture.

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ifeffit on Mac 10.8.5
by Gaspard Jean-Pierre 05 Oct '14

05 Oct '14

Hello, I am working on a MacBook under OS X.8.5 I downloaded iXAFS. When I try to start iXAFS, the system answers (in French): "Impossible to open because it comes from an unidentified developer." In the new OS, it is difficult to start an application that is not validated by Apple. Is there a way to start iXAFS ? Thank you for your help. Regards JP Gasaprd

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problems re-opening Athena project
by Foster, Andrea 03 Oct '14

03 Oct '14

Hello all, I am an experienced EXAFS person, but not having a lot of luck using Athena. I am trying to set up an Athena project for linear combo fitting. I can get the data + model compounds imported, and I can save a project file. However, after saving and closing the file, the next time I try to open, I am asked to re-import the data from the project file (I think this is a normal part of Athena)... [image: Inline image 4] ...but when I try to select importing as chi(k) instead of u(E), I get the following message [image: Inline image 2] after "ok-ing" this message away, I can't get any farther. Importing the data as u(E) doesn't give the appropriate results. I am also attaching the aforementioned project file. thanks for any help with this, andrea ________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

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Help
by johnny huertas 03 Oct '14

03 Oct '14

Good afternoon:My name is Jhonny, I work at PUC-Rio in Brazil and I'm having hard difficult to fit the ZrO2 tetragonal. I create the INP file using the follow structural data Space group: p21/ca=5.1490b=5.2070c=5.3160alpha=90beta=99.2250gamma=90Zr (0.2750; 0.03900; 0.2090)O (0.0650; 0.3260; 0.3100)O (0.4610; 0.7570; 0.4790) Several paths were created, but when I start to fit each path a message of ABORT appear saying "you have 3 variables but only 2 independent measurements in 1 data set"One more thing, each path has 1 coordination number (deg)I don't know what to do, I need some help.Thank. Jhonny Huertas Flores Rio de Janeiro-Brasil

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Problems with Athena
by Austin Krehel 02 Oct '14

02 Oct '14

Dear IFEFFIT Representative, I am a graduate student and am just now learning about EXAFS data plotting. I am having a problem with opening the data that I collected last month at Bulk-XANES line X11A (NSLS). I have tried the new and old versions of Athena, and they are both not reading the .001 files, which according to my professor, should be read since this has worked for him in the past on the old version. When I try opening the files, it says they "could not be read by ifeffit as a data file". I have attached one of the .001 files, in case that may help. And help or suggestions will be greatly appreciated. Thanks. -- Austin W. Krehel Kansas State University M.Sc. Geology, Class of 2016 Ph: (810)-358-3505

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