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

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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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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Open position in XAFS spectroscopy at MAX IV
by Katarina Norén 09 Sep '14

09 Sep '14

Hi, At the MAX IV Laboratory we are looking for a beamline scientist in XAFS spectroscopy with profile in Environmental science for the BALDER beamline at the new 3 GeV ring that will be taken in operation in 2016. Link to the position announcement: http://www.lu.se/lediga-anstallningar-available-jobs?x=0&Dnr=625478&Type=E Best regards, Katarina Norén __________________________________________________ [https://webmail.lu.se/owa/attachment.ashx?id=RgAAAABSBK%2b9jD%2fNQZCL0w%2bj…] Katarina Norén, PhD Manager Hard X-ray Group MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone +46 46 222 68 09 Mobile: +46 709 32 34 23 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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Cursor Issue in Athena Data Import Window
by Godfrey, Ian 05 Sep '14

05 Sep '14

Dear All, This bug report is for a very minor cosmetic issue, but I'm reporting it as it fooled me into thinking Athena had hung and doing a lot of unnecessary troubleshooting - hopefully I can save someone else from the same fate! I experienced this issue with Demeter 0.9.20 on Windows 8 x64 and Windows 7 x64. I don't recall this issue on previous versions of Demeter, but I could be wrong. The bug is as follows. When you open the Athena "Import" window (file > import data) the cursor over the data import window changes to the Windows' busy cursor indefinitely (see screenshot) when it should be the normal cursor (it doesn't impair functionality in anyway - you're still fully able to interact with the window, create plots etc.). Like I said, not a big bug but it led to me wasting a bit of time so I thought I'd report it. Regards, Ian Godfrey (UCL)

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Implementing constraints in EXAFS analysis
by Badari Rao 05 Sep '14

05 Sep '14

Dear Dr. Bruce, I have collected EXAFS data on a ferroelectric perovskite Sodium Bismuth Titanate which has an average rhombohedral R3c structure and am trying to fit the data with R3c as the starting model. But I am having trouble in implementing constraints for the fit. I found a paper authored by you, titled "Local structrue and phase transitions of BaTiO3, Ferroelectrics, 1998, 206-207, pp 407-430". I want to do similar kind of analysis using Artemis on my data. However, I am finding difficulty in understanding how the constraints have been implemented for the refinement of the barium K edge EXAFS, especially those for the bond lengths (Page 416 in the above mentioned article in particular is unclear). Could you please explain how the GDS window and the variables for different paths in this case would look like. Also how do you decide what parameters to refine and what to keep fixed (table IV in the article)? Also can you please suggest some literature for beginners which can guide me in implementing such constraints? Thanking you, -- 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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extract backscattering amplitude and phase shift files after feff calculation
by Matthias Filez 05 Sep '14

05 Sep '14

Dear mailing list user, I would like to obtain the backscattering amplitude and phase shift files, generated during feff calculations, for photo-electron paths used during modelling. These files (containing F(k), *(k)) should be located in some directory but I really cannot find them back. I know this question has been asked before, but no conclusive answer was provided. I use Windows 7, Intel(R) Core(TM) i5-2520M CPU @ 2.5 GHz, 64-bit OS, 4 GB RAM. Currently I employ Demeter 0.9.13. Please provide me your suggestions/solutions, Many thanks in advance, Matthias Filez

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Re: [Ifeffit] EXAFS calculation with large RMAX and NLEG - exceeding path finder limit
by van der Veen, Renske 04 Sep '14

04 Sep '14

Dear Bruce and Josh, Many thanks for your help! I have followed Josh's suggestion and increased the limits of the nx and npx parameters to very large values (nx=10^6, npx = 800.000 in path_tot.f90, npx = 100.000 in ff2x_tot.f90), and recompiled. The npatx parameter was set to 8 already, so I didn't change it. In addition, in order to get enough paths included in the fine structure, I had to increase the np1x parameter from 60.000 to 200.000. I am not quite sure what kind of parameter this is, but by checking the path listing in the xmu.dat file, I find that all important paths up to 8 A are included now. The fine structure looks much more like the experiment now – yay! Unfortunately there are so many paths, that a real EXAFS fitting analysis is impossible. Thanks again & best wishes, Renske -- Dr. Renske M. van der Veen Deutsches Elektronen Synchrotron (DESY) Notkestraße 85, 22607 Hamburg and Max Planck Institute for Biophysical Chemistry Am Faßberg 11, 37077 Göttingen Germany Tel (work): 0551 201 1265 Tel (mobile): 0176 315 05894 http://www.mpibpc.mpg.de/11851537/vanderveen

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