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

Be EXAFS and publication
by Joshua Kas 07 Jul '15

07 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

2 1

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 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

3 2

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

2 3

Demeter OS X plot button colors in Athena
by Schima, Frank 27 Aug '14

27 Aug '14

Hi Bruce, We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4. BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. [cid:F140B9BC-1ABC-4ACE-B222-A833F804F78B] Cheers! Frank

5 10

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

3 3

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

3 2

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

3 2

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

5 4

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/

1 0

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

3 2