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

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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Re: [Ifeffit] Problems with Athena
by fred.mosselmans＠diamond.ac.uk 02 Oct '14

02 Oct '14

Hi Austin, Bruce Ravel could surely point out what it is , but there is probably something Athena doesn't like in your header (blank lines??) removing it and then reading the file in works fine (obviously you may want to note of the column headings ) Thanks Fred Mosselmans -----Original Message----- From: ifeffit-request(a)millenia.cars.aps.anl.gov [mailto:ifeffit-request@millenia.cars.aps.anl.gov] Sent: 02 October 2014 13:21 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 140, Issue 2 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Problems with Athena (Austin Krehel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Oct 2014 21:58:34 -0500 From: Austin Krehel <awkrehel(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Problems with Athena Message-ID: <CAOgu4qpAAuzH_hTUn1n_E-MErnhYv96DqjxnzFf1jaHBLSxB2g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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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Re: [Ifeffit] FEff (Joshua Kas)
by Joshua Kas 30 Sep '14

30 Sep '14

Hi Carlos and Matt, Matt is correct that the CFAVERAGE card averages over a variety of absorbing atoms specified within the input file, with amplitude fixed to 1. In addition, CFAVERAGE only works in FEFF8.4 and earlier, and only if you have the monolithic version (i.e., feff is a single executable, not a script that runs several executables). We intend to improve the capabilities of feff9/jfeff to include more possibilities in terms of averaging over the absorption of different sites within a feff.inp file, or averaging over multiple input files, but for now, you will have to perform the averaging yourself. Cheers, Josh Kas On Tue, Sep 30, 2014 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: FEff (Matt Newville) > 2. Trouble creating feff input file for NaTiO3 cubic perovskite > structure (Badari Rao) > 3. Re: Trouble creating feff input file for NaTiO3 cubic > perovskite structure (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 Sep 2014 12:47:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] FEff > Message-ID: > < > CA+7ESbqpUvDtwnjXumeqWo2DMwvw15nyUOfjPq5jnV8t5EJviw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Mon, Sep 29, 2014 at 11:48 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 09/29/2014 11:44 AM, Carlos Triana Estupinan wrote: > > > >> Dear > >> Feff group > >> > >> I am Carlos Triana, and I want ask you the following. > >> I am trying to calculate the feff.inp file for a theoretical amorphous > >> structure composed by a supercell with 24 Ti atoms surrounding by 48 > >> oxygen atoms with different coordination. In amorphous materials or > >> materials with distortions from regular crystals, the absorbing atoms > >> may have different surroundings. > >> My question is how can I build the feff.inp file in this case, shall I > >> define the 24 Ti atoms like absorbing atoms, because in this case the > >> feff does not works. > >> What can I do in this case, how can I build the feff.inp file with > >> different environments > >> > >> I will be very grateful for your help > >> > > > > I'd like to follow up on Matt's comment. > > > > I presume you have some way of knowing a list of Cartesian coordinates > for > > the atoms in your cluster. If so, the discussion on pages 7-10 of this > > talk should be helpful, with the caveat that your input file needs to be > > appropriate to the version of Feff you intend to use. > > > > https://speakerdeck.com/bruceravel/modeling-non- > > crystalline-samples?slide=9 > > > > Make one input file for each Ti atom serving as the absorber. As Matt > > said, take care not to overwrite your results. > > > > Were this my problem, I would prefer to organize and perform N > > calculation, then add them up myself. That said, Feff does provide a > > simple sort of configuration average. Look up "CFAVERAGE" in the Feff > > document. > > > > B > > > > > I believe CFAVERAGE does not work as advertised. I haven't checked this > recently, but my recollection is that using CFAVERAGE always ends up giving > a coordination number that is a whole number, which cannot always be the > case. That might depend on versions of Feff, and I'd be happy to shown to > be wrong about this. > > Can anyone else verify or shed light on this? > > --Matt >

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