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

athena working issues on windows 8 and Ubuntu 14.04
by huyanyun＠physics.utoronto.ca 31 Jul '14

31 Jul '14

Hi All, I am writing to inquire if Demeter(athena, artemis) works on a 64-bit windows 8 system. I was trying to install Demeter 0.9.20 (downloaded from http://bruceravel.github.io/demeter/)on my 64-bit windows 8 laptop. It seems install well, at least there were no problems coming out during the installation. However, when I opened Athena, and imported data (an EXAFS data file end with .dat), there was no graphic window and no data was imported into Arthena, which stopped me proceeding. I had similar problems when I tried to install the Updater package (version 0.9.18.2) after the 0.9.13 Installer package was installed. Has anyone known if this problem was caused by the incompatibility between Demeter and Windows 8, or because I didn't install any supported package? Or how can I resolve this issue? I also tried to install the source code of demeter (version 0.9.20) following the instructions on http://bruceravel.github.io/demeter/pods/installation.pod.html. All procedures (step 1 to 4 in the section 'BUILD DEMETER AND ITS DEPENDENCIES') went smoothly on my Ubuntu 14.04. When it was done, I typed 'athena' or 'artemis' in the terminal under the demeter directory and athena or artemis were launched. But the graphic interface is still PGPLOT, rather than GNUPLOT, although I have installed GNUPLOT before I built demeter. Besides that, the data column window opened through 'open files' cannot be imported, as there is no 'OK' button in the bottom left. Also, the athena version shown is 0.8.061, rather than 0.9.20 which is the version number of demeter I built. I was really confused about these working issues, stopping me at the very beginning of data processing. I'd appreciate a lot if anyone could let me know how to solve the above problems. Does anyone else have similar issues? I look forward to hearing from you soon. All the best, Yanyun Hu PhD student in Physics, University of Toronto

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Import XAFS Data from Farrel Lytle Database (http://ixs.iit.edu/database/)
by Peng Liu 30 Jul '14

30 Jul '14

Hi all, I searched the Farel Lytle Database and looked like I found chalcopyrite spectra for Cu from http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Cu/index.html. I downloaded the data, but I can not import into Athena. I looked into the data, it looked wired for me. The first column doesn't look like energy for Cu. I am wondering if anyone have any idea how to import or transfer the data. I attached the data file. Regards, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu(a)uwaterloo.ca

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Quick first shell fit - Artemis
by Karin Julius 30 Jul '14

30 Jul '14

Hello, I'm trying to do a quick first shell fit with Artemis for my EXAFS measurement of 0.1 M auqeous solution of RbCl. I'm especially interested in the first hydration shell of the Rb ion. So I made an atoms input file with Rb and O in Rock salt structure. But how do I consider the Cl ion in the quick first shell fit? I don't think I can overlook the scattering on the Cl ions. Best regards, Karin

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Can the degeneracy (N) in Artemis be a variable?
by Peng Liu 28 Jul '14

28 Jul '14

Hi all, When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it? Thanks for your reply, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu(a)uwaterloo.ca

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Fwd: problems by using Artemis and Demeter
by Bruce Ravel 28 Jul '14

28 Jul '14

Marika, I am responding via the Ifeffit mailing list, which is the appropriate venue for questions about the software. Please use it. It is to your significant benefit to use the mailing list as it exposes you to other people who may be able to answer your questions. This is particularly useful at a time when I am on vacation, as I was for the last several days. You did not identify the version of Artemis that you are using, although your email suggests that you are not using the most current version. I simply do not have the resources to provide support for any but the most recent version of my software. Your postscript comment is similarly ambiguous in that you did not tell me what file you were attempting to import nor what actions you took. See this page of the document: http://bruceravel.github.io/demeter/artug/startup/main.html#thefilemenu and, in particular, note the explanation of the "Import" submenu, which provides a tool for importing project files (.apj) from the very old version of Artemis. As I have discussed many times on the mailing list, .apj file import is spotty, but has imporved over time as people have reported problems in a way that is clear and actionable. Cheers, B -------- Forwarded Message -------- Subject: problems by using Artemis and Demeter Date: Thu, 24 Jul 2014 17:26:57 +0200 From: Vespa, Marika (INE) <marika.vespa(a)kit.edu> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Dear Bruce, I encountered a problem that Artemis is only showing the fit results in the top of the results window: Later where a summary is usually shown it is left blank: R-factor for this data set = 0.46013 pathdegen amp sigma^2 e0 reff delta_R R ------------------------------------------------------------------------ I started a new project sequentially reading the FEFF paths and the problem appear after I have read in the fist C-path (U_oxo_carboante.prj). Would you have any idea? Best regards, Marika P.S. I have tried to use Demeter, but there I was not able to open a saved project -- 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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Fwd: from Rui Si at SSRF: help needed
by Bruce Ravel 18 Jul '14

18 Jul '14

Hi Rui, I am CCing my answer to you and to the Ifeffit Mailing List. It's always a good idea to use the mailing list as it greatly increases the number of eyes that get to look at your question. If you reply to this, please do so via the mailing list. In the PDF file you attached, you asked these two questions: (1) Why the second peak (ca. 3 Å) in experimental data is missing in the Co3O4 model? I do not know anything about your sample, so this is a tough question. Are you certain of its phase purity? Could there be another form of cobalt oxide present in the sample? (2) Why need to add the “shift vector” suggested by Artemis? Actually, no action is required and the software change the Co core from 0.125, 0.125, 0.125 to 0.5 0.5 0.5, and keep the shift vector as 0 0 0. The purpose of the shift vector is explained here: http://bruceravel.github.io/demeter/artug/atoms/space.html#multipleoriginsa… In the case of the CIF file you attached, the shift vecotr does not seem required. The list of atomic coordinates without the shift vecotr looks right to me. B -------- Original Message -------- Subject: from Rui Si at SSRF: help needed Date: Tue, 15 Jul 2014 07:33:31 +0000 From: 司锐 <sirui(a)sinap.ac.cn> To: bravel(a)bnl.gov <bravel(a)bnl.gov> Hi Bruce, Here, I have a question needs your help on the EXAFS fittings. When I tried to fit the Co3O4 standard (cif and apj file attached), there was a "shift vector" problem, which has been resulted in the mismatch between experimental data and theoretic model. Please see the details in the attachment. I am not familiar with crystal models, and thus I cannot find the key. Could you please help me? Many thanks! Best, Rui ---------------------------------------------------------- Dr. Rui Si Shanghai Institute of Applied Physics, Chinese Academy Sciences Shanghai Synchrotron Radiation Facility Address: 239 Zhangheng Rd, Pudong District Shanghai 201204, China E-mail: sirui(a)sinap.ac.cn Tel: (86)21-33932079 Cell:(86)13301753969

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demeter-devel: Athena autosave hang issue
by Jennifer Carter 16 Jul '14

16 Jul '14

Installed the newest version of the software for the Mac OS X earlier this week. v129-22-124-229:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) Now when I try to run athena the software hangs on an autosave file. I am unable to click either button the the pop-up menu to advance the software and I get the "application not responding" error. I searched for an athena.autosave file, as discussed in a previous thread about this issue, but don't find one. v129-22-124-229:~ jwc137$ find athena.autosave find: athena.autosave: No such file or directory Cheers Jennifer ᐧ

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Re: [Ifeffit] crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 16 Jul '14

16 Jul '14

Dear Prof. Frenkel, Many thanks for your detailed explanation about my queries. I would appreciate if you could send me the electronic copy of your article (at Jatinkumar.rana(a)helmholtz-berlin.de ): D. Glasner and A. I. Frenkel Geometrical characteristics of regular polyhedra: Application to EXAFS studies of nanoclusters AIP Conf. Proc. 882, 746-748 (2007). We may have further discussion on this topic, once I go through the suggested literature. With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 16 July, 2014 03:19 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 137, Issue 42 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: ATOM and GDS (Sin Yuen Chang) 2. Re: ATOM and GDS (Bruce Ravel) 3. Re: crystallite size determination by EXAFS (Anatoly I Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 15 Jul 2014 17:27:50 +0000 From: Sin Yuen Chang <sinyuen.chang(a)postgrad.manchester.ac.uk> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <62C8FAC78934514E930100B52B3D4A17010AC2C612(a)MBXP05.ds.man.ac.uk> Content-Type: text/plain; charset="us-ascii" Hi Dien Li, I had the same problem with ATOM in Demeter version 0.9.18 used in Windows 7, the "Add a site" icon doesn't work for me for some reasons. To add another row of atomic coordinate, what works for me is: 1. right click on any space on the table of atomic coordinate. 2. choose "Copy site" 3. right click again 4. choose "Paste site" [cid:image001.png@01CFA05A.7CE0C5C0] Hope this helps, Sin Yuen -- Sin Yuen, Chang PhD Student, School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL Manchester. From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Dien.Li(a)srs.gov Sent: 14 July 2014 21:26 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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crystallite size determination by EXAFS
by Rana, Jatinkumar Kantilal 15 Jul '14

15 Jul '14

Dear all, I have some questions regarding crystallite size determination by EXAFS. I am investigating a system where there is a formation of metallic Cu in the system. I could see the presence of metallic Cu in the sample by XRD and EXAFS. However, high resolution TEM does not show any evidence of metallic Cu, perhaps the crystallite size is much smaller than the resolving power of the microscope and/or these crystallites are highly disordered. Nevertheless, I thought of estimating the size of Cu crystallites by EXAFS. I know at least two approaches described by two prominent members of the mailing list, Scott Calvin and Anatoly Frenkel. The approach by Scott Calvin (http://link.aip.org/link/JAPIAU/v94/i1/p778/s1&Agg=doi) estimates crystallite size based on an assumption that they are spherical in shape. On the other hand, Anatoly Frenkel’s approach estimates both size and shape of crystallites based on the number of neighbors in each coordination shell obtained from EXAFS fit http://pubs.acs.org/doi/abs/10.1021/jp012769j I have questions about the second approach. I would like to know how to calculate the number of neighbors in various coordination shells as a function of cluster size for different shapes ? Conversely, if one knows the number of neighbors in various shells from EXAFS fits, then how to correlate those numbers to clusters of different sizes and shapes as discussed by Anatoly Frenkel. I know my questions are very specific, but I am sure many in the list would have already tried both these approaches and may provide some valuable insights. Many thanks in advance ! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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ATOM and GDS
by Dien.Li＠srs.gov 15 Jul '14

15 Jul '14

HI, Bruce and Matt For the Demeter version I am using, I found that I could just enter 8 atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in ATOMS, and define more variables in GDS? and How? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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