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

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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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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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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Re: [Ifeffit] Athena data exporting
by Bruce Ravel 03 Sep '14

03 Sep '14

On 09/03/2014 03:21 PM, Dissanayake, Amila C wrote: > Dear Bruce, > > I am Amila Dissanayake, a Ph.D intern at Pacific Northwest National Lab. > I am analyzing XAS data using Athena. But when I am trying to save a > list of data group (about 6 data group) using “ Save marked group > as..” command, all the data groups are not saving into different > columns. When I try to load this file into Origin I could find only just > two columns of data. Could you help me to sort out this problem. I am CCing my answer to the Ifeffit Mailing List, which is the appropriate place to ask questions about the software. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ You should address any follow up questions to the list. You've not offered enough information that I can even venture a guess as to what is happening. You have not told me what version of the software you are using. You've not provided an example of a project file that triggers the problem. You have not provided a recipe that would allow me to reproduce the problem on my computer. Alas, there's nothing for me to comment on. The "Save marked groups" feature works for me -- I just tried it on both the linux and Windows machines here in my office. Works fine. No one else has ever raised this problem. The one thing that occurs to me is that you may not understand what is meant by the phrase "marked groups". Have you read this page from the document? http://bruceravel.github.io/demeter/aug/ui/mark.html 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/

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