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

The missing feff paths
by 史乾涛 14 Aug '14

14 Aug '14

Hi, I have a problem when I used Demeter 9.18 or 9.20. The Artemis window only show parts of the calculated feff paths such as the followed figure (only 0, 4, 5, 6, 7, 10 paths of the first 10 paths were shown, and where is the other paths?). Did anyone meet this problem and how did you treat it? Many thanks! best regards, Qiantao Shi Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

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help with XAFS spectrum of NbS2
by Yuanyuan Li 10 Aug '14

10 Aug '14

Hi, We have measured some Nb doped MoS2 samples and want to compare Nb edges of these samples with standard NbS2. If someone has it and would like to share it, it would be great help to us. Thank you very much! Best, Yuanyuan Li Physics Department Yeshiva University

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Re: [Ifeffit] space group P 4/mmc ?
by Bruce Ravel 08 Aug '14

08 Aug '14

On 08/08/2014 03:33 PM, Marinkovic, Nebojsa wrote: > Bruce, > I found the PtO strucutre (WJ Moore, JACS 63 (1941) 1392) reported as P > 4/m m c , but Atoms says "invalid space group". Any clues? > Thanks, > Ned > Hi Ned, I am CCing my answer to the Ifeffit Mailing List since I think this question of general interest. The author is using archaic notation, which is a common problem with crystallography references from the early decades of the 20th century. "P 4/m m c" does not exist in the modern International Tables of Crystallography. See http://en.wikipedia.org/wiki/List_of_space_groups Happily the author also gives the Schoenflies notation. "D^9_4h" is "P 42/m m c" in modern notation. The majority of the symbols Artemis recognizes are given in the Artemis Users' Guide: http://bruceravel.github.io/demeter/artug/atoms/space.html although perhaps not in the most useful manner. The wikipedia page is also useful for resolving a Schoenflies symbol to the corresponding Hermann-Maguin symbol. You can also simply use the Schoenflies symbol in Artemis. The string "D^9_4h" should be recognized by Atoms as the same as "P 42/m m c". 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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Undo in Athena
by Peng Liu 01 Aug '14

01 Aug '14

Hello everyone, I have one more question about undo in Athena, e.g. I accidentally deleted one of the good spectra, how I can get it back. In word, I can go to Edit and click undo, but I haven't found it in Athena. Thanks for your time, 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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larch warning about epics plugin
by Johan Nilsson 01 Aug '14

01 Aug '14

Hello, Today I reinstalled larch after upgrading my computer to Ubuntu 14.04. I downloaded the latest source and installed all the recommended dependencies except PyEpics and then continued with the install. Everything went smoothly and larch appears to be working as it should. However when I start the program I get warning messages about the epics plugin $ larch Larch 0.9.23 (8-Apr-2014) M. Newville, T. Trainor using python 2.7.6, numpy 1.8.1, wx-enabled, wx version 2.8.12.1 Warning: /usr/share/larch/plugins/epics/xrfcontrol.py is not a valid plugin error: ImportError('cannot import name ROI',) Warning: /usr/share/larch/plugins/epics/xrf_detectors.py is not a valid plugin error: ImportError('cannot import name ROI',) Warning: /usr/share/larch/plugins/epics/xspress3.py is not a valid plugin error: ImportError('cannot import name ROI',) I have no plans to use this plugin but I tried to install PyEpics to see if anything would change but it did not. Is this a bug or is there some configuration I can change to get rid of the warnings? --Johan

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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 31 Jul '14

31 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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