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

trial release #9 for Windows for Demeter 0.9.20
by Bruce Ravel 09 Jul '14

09 Jul '14

As I promised Badari yesterday, I have a new trial release for Demeter on Windows: 64 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… 32 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… This fixes both of the issues Badari reported. It also fixes Margaret Anne's problem with the Spec file with a really long line without needing a plugin. There are also a number of improvements to Atoms even compared to the previous trial release. An update to demeter-devel on MacPorts is not yet available, but will be soon. Those who build Demeter from source can clonw from the head of the github repository. Cheers, 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://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Demeter-devel Athena on OS 10.9.4
by Emmanuelle Montarges-Pelletier 08 Jul '14

08 Jul '14

Dear all I have just installed Demeter-devel on a computer Mac OS X 10.9.4, following the suggestions of Frank Schima and the different steps for installing xcode and command tools, macports, Xquartz. The mailing list was really helpful, thanks! After having written Athena on a terminal window I have apparently the same "freezing" phenomena reported earlier by Margaret Hinkle, July 4th 2014 " With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'.". I don't know how to solve this Athena blocking and completely lost when I read the solution provided by Bruce " Look for the '[athena]' section of demeter.ini, which should be in '$HOME/.horae'. Set the "tips" parameter to "false". That will suppress the tips dialog." I really tried to do on my own,...but I have to be honest, I don't know how to change the tips parameter. I would need a specific lesson, something entitled "demeter for dummies". So, could someone help me? Thanks for your answer Best Regards Emmanuelle -- ................................................. Emmanuelle Montarges-pelletier CR CNRS LIEC UMR 7360 CNRS-Université Lorraine 15 avenue du Charmois BP40 54500 Vandoeuvre les Nancy France tel 33 (0)3 83 59 62 52 fax 33 (0)3 83 59 62 55 mob 33 (0)6 31 33 10 30 emmanuelle.montarges(a)univ-lorraine.fr Zone Atelier Moselle http://www.ensic.inpl-nancy.fr/Zam/

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Possibly will join, I am from MPI- Stuttgart. EOM
by Devender 08 Jul '14

08 Jul '14

On Tue, Jul 8, 2014 at 12:54 PM, Edmund Welter <edmund.welter(a)desy.de> wrote: > Dear mail list users, > > > as you probably know the next XAFS conference (XAFS 16) will be held > from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main > conference a small number of Satellite meetings will be organised. One of > these meetings will be organised at the DESY site in Hamburg, Germany. The > title of this Satellite meetings is: “Data acquisition, treatment, storage > – quality assurance in XAFS spectroscopy“. Almost 5 years after the Q2XAFS > workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate > the developments during the last 5 years and to discuss strategies for > further improvement of XAFS data taking and XAFS data evaluation and > storage. > > First information about the meeting is summarised in the attached flyer > and on the meeting's webpage (see: > https://indico.desy.de/conferenceDisplay.py?confId=10169) The > information on the webpage will be updated and further information > especially about registration, travel and accommodation added as soon as it > becomes available. > > Please send me a mail if you have any comment, suggestions for further > session topics and/or questions! I am also interested in getting a first > impression about the possible number of participants and would therefore > appreciate if you send me (edmund.welter(a)desy.de) a short notice if you > could imagine to participate in the meeting. > > > Best regards > > Edmund Welter > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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XAFS 16 Sat. Meeting announcement
by Edmund Welter 08 Jul '14

08 Jul '14

Dear mail list users, as you probably know the next XAFS conference (XAFS 16) will be held from August 23rd to 28th 2015 in Karlsruhe, Germany. Around the main conference a small number of Satellite meetings will be organised. One of these meetings will be organised at the DESY site in Hamburg, Germany. The title of this Satellite meetings is: "Data acquisition, treatment, storage -- quality assurance in XAFS spectroscopy". Almost 5 years after the Q2XAFS workshop in Tsukuba, Japan the idea behind this meeting is, to recapitulate the developments during the last 5 years and to discuss strategies for further improvement of XAFS data taking and XAFS data evaluation and storage. First information about the meeting is summarised in the attached flyer and on the meeting's webpage (see: https://indico.desy.de/conferenceDisplay.py?confId=10169) The information on the webpage will be updated and further information especially about registration, travel and accommodation added as soon as it becomes available. Please send me a mail if you have any comment, suggestions for further session topics and/or questions! I am also interested in getting a first impression about the possible number of participants and would therefore appreciate if you send me (edmund.welter(a)desy.de) a short notice if you could imagine to participate in the meeting. Best regards Edmund Welter

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Re: [Ifeffit] How to distinguish whether the coordination
by Michael Weir 07 Jul '14

07 Jul '14

Hi Matt and Zhan, I think this is the point where adding another approach would be very useful. In my limited experience, XAFS was much more powerful when combined with other techniques to eliminate potential models. We also needed to use our "chemical sense". Is there a reason you would suspect Se, Ge, Ga, or any of the other elements in your material? Could you use your beamline to look for these elements by a quick scan of one of their stronger transitions? If there is a full coordination shell, detecting the other element this way is feasible. However, as someone else mentioned recently, dopants would be much more difficult to detect. Is there another analytical technique you could use to narrow down the possible elements in your system? I hope that answering those questions helps you answer your question about the system. Also, thank you Bruce, Matt, Scott and others for the very useful discussions on this list. Michael Weir Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei <zhanfei(a)ihep.ac.cn> wrote: > Hi Matti? > Thanks for your attention and patience. > The back fourier transform of the specific peak (use window)of Chi(R) > gives the amplitude,donated by amp_bft?As in previous mails,I ask whether > the compare the amp_bft and the amplitude of specific Z number element can > determine the Z. > Sorry, I'm not sure I understand this. I didn't understand the figure you attached in your earlier mail. Generally speaking, I find back-transformed data to be not very useful -- making any sense of these requires very well isolated shells of atoms. The amplitude of the back-transformed chi(k) (is that what you mean by amp_bft??) has many contributions, and is not simply f(k). It will have Z dependence, but it will have other dependencies too. > And thanks for telling me the useful trick using the total phase shift of > the specific element. > > > The discrepancy between R and Rphcor is below,the Zn and Br is close to > Se(the best fit)'s 0.013, > Yes, Ge actually gives the closest match, and Se the second closest match, and I left Ga out of the test. I would probably say that anything closer that 0.015 Ang (and, really, maybe 0.02 Ang) is pretty darn close. So the phase-correction approach appears to be (in this case) not as sensitive to Z as the reduced chi-square, but does provides a check on self-consistency. The fits with Zn and Rb are noticeably worse than the fit with Se... hence Z +/- 3 or perhaps 5 seems like a reasonable rule of thumb, and sometimes one might be able to do better. > should the enot also be important criterion in this trick?and dose the > plus or minus of enot indicate the lighter or higher element relative to > the specific coordination shell? > Well, an E0 shift > 10 eV probably indicating that something is off .... but that could be just the selection of E0 for the experimental data. I wouldn't put much meaning of the absolute value of E0 though for any single fit. "a bond valence sum can be an independent check on the consistency of N, > R, and valence",can your give the ref. paper of this method? Thanks > > http://en.wikipedia.org/wiki/Bond_valence_method The idea is that N, R, and valence are not independent. --Matt --

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Multiple phases in samples
by Dien.Li＠srs.gov 07 Jul '14

07 Jul '14

Hi, All "Assuming" there are multiple phases in one sample, saying, U on goethite, U on organic matter, and uraninite, how to fit the EXAFS data using Artemis? 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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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Chris, I am facing the same problem in both windows xp (32 bit) as well as windows 7 (64 bit) operating systems. Dear Matt, These two problems are not file specific since I have confirmed it with many files and also with different systems. (windows xp as well as windows 7). Dear Bruce, Thank you for taking note of the problem. - Badari

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Demeter-devel MacPorts Athena issues & work-around
by Margaret Hinkle 07 Jul '14

07 Jul '14

Dear OS X Users, First let me thank Frank Schima for fixing the issues with Artemis and ATOMS with his new demeter-devel Macports download -- I (and all Mac users) greatly appreciate it! I thought I would bring two issues with Macports Athena to your attention... FYI, I am using Mac OS X Mavericks v. 10.9.4, with an Intel processor. I followed the directions found here today to delete the old version of demeter and download the new one: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04404.ht… Issue 1. With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'. I had a feeling it was an issue with the Tip of the Day popping up, so I edited the Athena.pm file (in the UI folder), and edited line 197 from ‘$app->show_tip if Demeter->co->default('athena', 'tips');’ TO ‘$app->show_tip if Demeter->co->default('athena', 'tip');’ (honestly, I don't know enough about this code to be able to give it a real option that would turn off the Tip of the Day as the default, so I just hoped this would make the program give me general error in the GUI but that Athena could still load). Luckily, my not-fix fix worked. I get an error every time I open it, but after clicking 'OK', Athena behaves just like normal. I hope you can use this information to provide a real fix to the problem! Issue 2. I can only load data files into Athena if there are no headers of any sort -- commenting out each header line with a # or % does not work. When I try to load in a .dat file with a commented-out header, I get the following error message in Terminal: 'At line 436 of file iff_show.f Fortran runtime error: End of record' followed by Athena quitting itself. This is an issue with both the regular Macports demeter download and the demeter-devel download. These data files loaded in just fine to the old iXAFS version of Athena, and on a PC. Is there a plugin I should be using in the Demeter versions? If I delete the header, or load it in from a .prj file, everything works just fine. So it is not huge issue, as I do have a work around. Thank you, Frank, for the new version of Demeter, and thank you all for any thoughts you have on Issue 2. Best regards, Margaret Anne ------------------------------------ Margaret Anne G. Hinkle Ph.D. Candidate Earth and Planetary Sciences Washington University in St. Louis Rudolph Hall Campus Box 1169 1 Brookings Drive St. Louis, MO 63130 email: mhinkle(a)eps.wustl.edu website: aqgeochem.wustl.edu

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Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Sir, I am facing two problems while handling files in Athena. First of all, when I freshly open Athena and import a file, it gives some kind of warning, which says can't locate Encoding/FixLatin/XS.pm in @NIC.. etc. I have attached a screenshot of the warning message. However, I could continue with my work without any problem, and importing more files did not give this warning. The second problem, which is a major one is that I am not able to use the "align data" option. Whenever I select my data and click on "align data", the software crashes and closes. kindly look into this issue. I would also like to mention that both these bugs were not present in the earlier version: Demeter 0.9.20_pre5. 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. [image: Inline image 2]

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How to distinguish whether the coordination element is heavy or light
by ZHAN Fei 07 Jul '14

07 Jul '14

Dear all, when I try to solve my question{[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that},I find a method from Prof.Calvin to distinguish whether coordination shell is composed by light or heavy element: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-December/007983.html A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen. But I still don't know ,why it works. Thanks for your patience, Sincerely, zhanfei

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