September 2014 - Ifeffit - millenia.cars.aps.anl.gov

Be EXAFS and publication
by Joshua Kas 08 Jul '15

08 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

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Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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save Artemis project and cannot find Path List information when reopen
by huyanyun＠physics.utoronto.ca 27 Oct '14

27 Oct '14

Hi all, I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something. I attached one of my artemis project file and the most recent log file I saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'. Best, Yanyun ----- Attachments (links will expire on 28/02/15): 1. CoedgeforGa0.15 fitting.fpj (7.7 MB) [application/zip] Download link: https://webmail.physics.utoronto.ca/imp/attachment.php?id=53ffbffa-2424-413…

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simulating As K edge XANES using full multi scatering method
by Shaofeng Wang 24 Oct '14

24 Oct '14

Dear all, Does anyone have experience for simulating As K edge XANES using multi-scatering method or some other methods. Please introduce some papers or articles to me. Any help is appreciated. Regards, Shaofeng

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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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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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Trouble creating feff input file for NaTiO3 cubic perovskite structure
by Badari Rao 30 Sep '14

30 Sep '14

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. -- Yours Sincerely 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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FEff
by Carlos Triana Estupinan 29 Sep '14

29 Sep '14

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 -- *Carlos Augusto Triana Estupiñan (C.A. Triana-E) Physicist M.Sc. In Physical Sciences-Research PhD Student-Research Ångströmlaboratoriet, Lägerhyddsv. 1 Solid State physics Uppsala University, Box 534 751 21 Uppsala, Sweden Tel: +46 018 471 3144 e-mail:carlos.triana@angstrom.uu.se <e-mail%3Acarlos.triana(a)angstrom.uu.se> web:http://www.uu.se/ <http://www.uu.se/>*

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Inconsistency of the amplitude reduction factor
by HOON Kim 18 Sep '14

18 Sep '14

Hello, I am a bit confused about the amplitude reduction factor (S0^2), in a sense that whether this factor must be determined by fitting or constrained by a reference value for a specific element. I'm dealing with a cathode composite (for lithium-ion battery) comprised of two crystal phases. During charge-discharge, the amplitude reduction factor changes and at a certain state of charge (SOC) it changes a lot such as from 0.77 to 0.67. My understanding is that it may reflect the phase transition of the material into the amplitude reduction factor. But, I'm not sure ... I need advice on this. Thank you ! Kind Regards,HOON

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