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

Two plotting related glitches in Athena
by Godfrey, Ian 04 Mar '15

04 Mar '15

?Dear All, I encountered two (apparent) bugs related to plotting data in Athena. In both cases I think they're best expressed via video screencaps so please see the links with each bug report (both of these links are valid for 10 days only). Both of these are occurring in Athena 0.9.21 x64 on Windows 8.1 Enterprise x64. An Athena log file is attached. 1) Sometimes lines on a plot disappear when zooming/scrolling. This typically happens with steeper lines. In the video you can see it occurring when I scroll up and down - sometimes it also occurs immediately when I try and zoom in. (I guess this could be an issue with GNUPlot, rather than Athena?) Video: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=1… Password: 2725d459 2) When using the pluck function to set indicators (possibly in other situations too, although I haven't noticed it there) if you don't double click to pluck the point fast enough after clicking the pluck button the software plucks a nonsense value instead. (The halo around the cursor is supposed to show when I click, but it seems to show up when I leave the cursor stationary and at some other times too, so don't rely too much on that... when I don't double click the point I've left the cursor entirely off the Athena windows). (Sometimes when this happens it seems that you need to replot the graph to be able to pluck again, but I can't reliably reproduce that behaviour.) Video: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=3… Password: 2725d459 Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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International EXAFS Conference XAFS16
by Lichtenberg, Henning (IKFT) 04 Mar '15

04 Mar '15

Abstract Deadline for the International XAFS Conference in Karlsruhe (www.xafs16.org<http://www.xafs16.org>) extended until March 15,2015 Dear colleagues of earlier XAFS conferences Good news about the XAFS16 conference, which will take place in Karlsruhe/Germany 23 – 28 August 2015: More than 300 abstracts have arrived in our system during the last 3 days just before the deadline. Most popular at the moment are topics like EXAFS in materials science, instrumentation, new spectroscopic methods, energy-related materials and catalysis (please refer to the site: http://www.xafs16.org) The strength of the conference is that theory and instrumentation on the one hand and applications on the other hand talk to each other! Many have asked us about the extension of the deadline so that we have prolonged the abstract submission deadline until March 15, 2015. Please submit your abstract in time! The reviewing process will start immediately afterwards. Later abstracts may be considered as poster but this also depends on whether we still have enough space. During the next days we will also update the plenary and keynote speaker list. So please have a glance on the homepage www.xafs16.org<http://www.xafs16.org> from time to time. Special sessions like an industrial session as well as 3 satellite meetings are planned. We already now look forward to a successful conference and look forward to contributions in all 16 topics. Best regards, in the name of the IXAS society and the local organizing committee. Jan-Dierk Grunwaldt Chairman XAFS16 [cid:image001.jpg@01D0553A.FD9D8F50]<http://www.xafs16.org/> --------------------------------------------------------------------- Prof. Dr. Jan-Dierk Grunwaldt Chair in Chemical Technology and Catalysis grunwaldt(a)kit.edu<mailto:grunwaldt@kit.edu>; www.itcp.kit.edu/grunwaldt/<http://www.itcp.kit.edu/grunwaldt/> Tel.: +49 721 608-42120, Fax: -44805, Sekr. Tel.: -42121, -43064 Karlsruhe Institute of Technology (KIT) Director at the Institute for Chemical Technology and Polymer Chemistry (ITCP) Engesserstr. 20, 76131 Karlsruhe, Germany Director at the Institute for Catalysis Research and Technology (IKFT) Herman-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany KIT - Universität des Landes Baden-Württemberg und nationales Großforschungszentrum in der Helmholtz-Gemeinschaft

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problem plotting in Athena after installation of Demeter 0.9.21 on Windows 64bit
by kirshstein＠gmail.com 03 Mar '15

03 Mar '15

Hello, I have just installed Demeter and the first thing Athena does, when asked to plot (mu(E)) of an averaged standard spectrum (S-K-edge of CaSO4, averaged in sixpack), is to give the following error message: "Use of uninitialized value in multiplication(*) at C:/strawberry/perl/site/lib/Math/Spline.pm line 36." Also E0 is 0 and in front of a red background. So it seems to have trouble finding E0. But why? What does this mean? What do I have to do to get athena to work? attached is the CaSO4 spectrum in question. Thanks! Yael Kirsch

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Feature request - Hephaestus: Plot multiple standards at once
by Godfrey, Ian 02 Mar '15

02 Mar '15

Dear All, I'm using Hephaestus' standards library to help with some XANES fingerprinting and it's very useful. I would find it quite helpful to be able to select two (or more) standards from the list and plot them on the same graph for comparison. Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Pb compound determination fitting issue
by Pieter Tack 25 Feb '15

25 Feb '15

Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

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Re: [Ifeffit] Pb compound determination fitting issue
by fred.mosselmans＠diamond.ac.uk 25 Feb '15

25 Feb '15

-----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: 25 February 2015 10:48 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 144, Issue 11 Hi Pieter Apologies for confusing you, By 1 and 3 I meant fit 3 O, fit 5 S in the history. I had to fix S02 as the data range gives only 3 -4 paras and it flew off initially. Sorry Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 10:45:15 +0000 From: <fred.mosselmans(a)diamond.ac.uk> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Pb compound determination fitting issue Message-ID: <CF65047C5B0562499EAFF9FBBC542D6485DF0819(a)EXCHMBX01.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear Pieter, You wouldn't start with Pb exafs if you had the choice. Pb has a lot of structural disorder in its compounds and is very thermally wobbly leading to poor signal to noise data. I think your dataset is only good to 7 -8 inverse A. That said I think you can learn something about the sample. Was the sample cold? eg in a cryostat when measured this is about the only way to get OK Pb data from anything but a solid state system with ordered atoms. In fit 1 (see the history) in the attached project file I use the first shell of massicot and this doesn't give a good fit but nothing ridiculous , in fit 3 I sued the cerrusite 1st shell and e0 goes along way and the first shell distance contracts a lot. This suggests you are likely have O in the first shell and by playing around more, e.g. Shortening the data range in Athena to improve the data reduction you should be able to get a better fit than with just one button press, however the useable data range is small so it will be not great In accuracy terms. Also you might try comparing the XANES to literature data though the core hole size in Pb L3 washes out xanes a bit so its not the best. Regards Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 11:20:17 +0100 From: Pieter Tack <Pieter.Tack(a)ugent.be> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Pb compound determination fitting issue Message-ID: <20150225112017.Horde.GS9lWdD6UQ5U7aHhPZgmRhA(a)webmail.ugent.be> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"; DelSp="Yes" Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

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Re: [Ifeffit] Pb compound determination fitting issue
by fred.mosselmans＠diamond.ac.uk 25 Feb '15

25 Feb '15

Dear Pieter, You wouldn't start with Pb exafs if you had the choice. Pb has a lot of structural disorder in its compounds and is very thermally wobbly leading to poor signal to noise data. I think your dataset is only good to 7 -8 inverse A. That said I think you can learn something about the sample. Was the sample cold? eg in a cryostat when measured this is about the only way to get OK Pb data from anything but a solid state system with ordered atoms. In fit 1 (see the history) in the attached project file I use the first shell of massicot and this doesn't give a good fit but nothing ridiculous , in fit 3 I sued the cerrusite 1st shell and e0 goes along way and the first shell distance contracts a lot. This suggests you are likely have O in the first shell and by playing around more, e.g. Shortening the data range in Athena to improve the data reduction you should be able to get a better fit than with just one button press, however the useable data range is small so it will be not great In accuracy terms. Also you might try comparing the XANES to literature data though the core hole size in Pb L3 washes out xanes a bit so its not the best. Regards Fred ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Feb 2015 11:20:17 +0100 From: Pieter Tack <Pieter.Tack(a)ugent.be> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Pb compound determination fitting issue Message-ID: <20150225112017.Horde.GS9lWdD6UQ5U7aHhPZgmRhA(a)webmail.ugent.be> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"; DelSp="Yes" Hi everyone, I recently acquired an EXAFS data set (albeit somewhat noisy) on the Pb-L3 edge. I have normalized it using Athena, and tried to fit the first shell using Artemis. I attached the Athena project file as well as the Artemis project file of what I obtained thus far. We have reason to believe the unknown compound is PbO or PbS (or a mixture). However, when I look at the R space curve, the first coordination shell is at rather low path distance (1.7 A), whereas one would expect larger bond distances for PbO and PbS. I found that a similar bond distance as to what the experimental spectrum shows can be found in PbCO3, but a fit using the mineral data of PbCO3 also doesn't do the trick. In any case, no matter what I try to fit in Artemis, nothing seems decent. Is the EXAFS fitting simply impossible due to the noisy data, did I extract my Chi(k) wrong or am I encountering some other issue? I realize it's probably not much to go on, but I'm rather new to EXAFS analysis so any help/advice is appreciated. Thanks a lot in advance! Best regards, Pieter Tack -- X-Ray Micro-Spectroscopy and Imaging Group Department of Analytical Chemistry Ghent University Krijgslaan 281 S12 B-9000 Ghent Belgium Phone: +32 (0)9 264 4723 Fax: +32 (0)9 264 49 60

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Trouble installing demeter on Mint 17.1
by Stevan Ognjanovic 19 Feb '15

19 Feb '15

Dear list, After upgrading my Linux OS to Mint 17.1, I have trouble installing demeter again (on Mint 14 it used to install and run without problems). sudo ./Build installdeps failed to install a few dependencies even after issuing the command several times (Wx and Regexp:Assemble), so I installed them manually from the Mint repositories. After that, perl ./Build.PL said that all dependencies were satisfied. I then ran ./Build which finished, I think, normally. The only lines that look remotely suspicious are: Chantler data conversion tool 1.2 for Absorption 0.10 Parsing lines ... Parsing element 5Argument "8.20144-01" isn't numeric in numeric le (<=) at lib/Xray/data/chantler2st.PL line 120, <CHANTLER> line 81. 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Getting energy list keys ... sorting energy list ... and making energy hash Saving new database, lib/Xray/data/../Absorption/chantler.db. However, when I run ./Build test it shows that 2/44 tests fail (5/2681 subtests). Please find the terminal output below. It might be usefull to mention that at first I tried to install demeter without root privileges (following the Dave Hughes' guide), with same tests failing. I went on to ./Build install anyway, and it succeded, but when trying to open previously saved projects, dathena would crash. I then removed demeter and the local perl directory, and tried installing demeter again, this time with root privileges following Bruce Ravel's guide. Any help would be appreciated, thank you in advance! ./Build test terminal output: t/000_ifeffit.t ......... ok t/001_base.t ............ ok t/002_types.t ........... ok # Failed test 'configuration system introspection works: groups 37 artemis' # at t/003_config.t line 61. # Failed test 'configuration system introspection works: main_groups 37' # at t/003_config.t line 63. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 74. # Failed test 'introspection after reading new group: main_groups' # at t/003_config.t line 76. # Looks like you failed 4 tests of 24. t/003_config.t .......... Failed 4/24 subtests t/004_data.t ............ ok t/005_plot.t ............ ok t/006_gds.t ............. ok t/007_prj.t ............. ok t/008_path.t ............ ok # Failed test 'statistics reporting seems ok' # at t/009_fit.t line 97. # Looks like you failed 1 test of 25. t/009_fit.t ............. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/25 subtests t/010_feff.t ............ ok t/011_sp.t .............. ok t/012_atoms.t ........... ok t/013_spacegroups.t ..... ok t/014_vpath.t ........... ok t/015_sspath.t .......... ok t/016_fspath.t .......... ok t/017_structuralunit.t .. ok t/018_multichannel.t .... ok t/019_provenance.t ...... ok t/020_indicator.t ....... ok t/021_externalfeff.t .... ok t/022_filetypes.t ....... ok t/023_files.t ........... ok t/024_graph.t ........... ok t/025_lcf.t ............. ok t/026_xes.t ............. ok t/028_fpath.t ........... ok t/029_threebody.t ....... ok t/030_xdi.t ............. ok t/031_quench.t .......... ok t/032_miscellany.t ...... ok t/100_elam.t ............ ok t/101_mcmaster.t ........ ok t/102_chantler.t ........ ok t/103_henke.t ........... ok t/104_shaltout.t ........ ok t/105_fluo.t ............ ok t/500_checker.t ......... ok t/501_dataBlock.t ....... ok t/502_dictionary.t ...... ok t/503_filter.t .......... ok t/504_parser.t .......... ok t/505_writer.t .......... ok Test Summary Report ------------------- t/003_config.t (Wstat: 0 Tests: 24 Failed: 4) Failed tests: 17-18, 23-24 t/009_fit.t (Wstat: 256 Tests: 25 Failed: 1) Failed test: 17 Non-zero exit status: 1 Files=44, Tests=2681, 69 wallclock secs ( 0.29 usr 0.06 sys + 67.36 cusr 2.64 csys = 70.35 CPU) Result: FAIL Failed 2/44 test programs. 5/2681 subtests failed. Kind regards, Stevan Ognjanovic -- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic(a)uni-due.de

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Re: [Ifeffit] Trouble installing demeter on Mint 17.1
by Denis Testemale 19 Feb '15

19 Feb '15

Stevan, Bruce, this Athena crashing (when opening a file or importing data) sounds similar to some trouble I had some months ago. Bruce solved my problem (as usual...) with a solution that I still need to apply and that still works perfectly. Iin the terminal, I type: export LANG=en_US.UTF-8 before launching athena or artemis (from the same terminal). I cannot guarantee that it will sove your problem, and I didn't inspect your error messages carefully, so I might be miles away from the truth, but since like me you're from a non-US country with probably non-US langage environments, I thought it would be worth trying. Cheers denis -- Institut Néel - CNRS http://neel.cnrs.fr/spip.php?rubrique264 +33 476 881 045

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Re: [Ifeffit] Ifeffit Digest, Vol 144, Issue 2
by Khalid, Syed 04 Feb '15

04 Feb '15

Thank you all, many nice suggestions and I will try them all. For the first time the beamline 2-2 at SSRL is being used for XAS. The control software is in LINUX and the output files automatically move to a Windows computer, in binary and ASCII form, sitting next to it. We were also able to see the ASCII file in wordpad and then saved it as text file after deleting all the text and only keeping the data columns. Athena was able to read it then. I will have to write a program to add "#" before text lines. We will need that dealing with lot of data. I will certainly check with the beamline scientist, why things are the way they are. About the offsets, I did notice it was slightly negative, but we had other major problems to deal with, so did not bother. Syed Khalid -----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: Wednesday, February 04, 2015 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 144, 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. Re: SSRL-data (Shoaib Muhammad) 2. Re: SSRL-data (Matt Newville) 3. Re: SSRL-data (Matthew Marcus) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Feb 2015 10:31:56 +0900 From: "Shoaib Muhammad" <mshoaibce(a)gmail.com> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] SSRL-data Message-ID: <002401d0401a$5e97d300$1bc77900$(a)gmail.com> Content-Type: text/plain; charset="us-ascii" Dear Syed Khalid, One simple work around can be to select "Plugin Registry" and enable SSRL related plugins. By doing this I was able to successfully read both the attached files in Demeter Athena. Further details to enable plugins can be found here: http://bruceravel.github.io/demeter/aug/other/plugin.html /Shoaib SKKU (South Korea) From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Khalid, Syed Sent: Monday, February 2, 2015 5:11 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] SSRL-data How to handle SSRL, beamline 2-2 data. Attached is a binary and an ASCII file(with under score A). Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy where mono went, fourth I0 and fifth It. It is gold foil transmission data. Syed Khalid

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SSRL-data
by Khalid, Syed 04 Feb '15

04 Feb '15

How to handle SSRL, beamline 2-2 data. Attached is a binary and an ASCII file(with under score A). Wordpad reads it, first column is time (data point duration), second energy it must go to, third real energy where mono went, fourth I0 and fifth It. It is gold foil transmission data. Syed Khalid

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Exploring XANES data for getting EXAFS results
by Marcelo Alves 16 Jan '15

16 Jan '15

Hi all, I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells. I think that could be very interesting for low Z elements such as P, S, Ca, K, Al, etc in diluted samples. Thanks in advance. Marcelo.

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Demeter installation
by Miller, BradleyW 14 Jan '15

14 Jan '15

Hi, I'm trying to install Demeter software package on my govt. computer which is under a degree of lock down. I have full admin rights but its still not running. Here is the explanation from IT support. "it wants to install on C:\strawberry<file:///C:\strawberry> and the C: drive is locked down here and all our programs need to be installed to C:\program<file:///C:\program> files (x86) and when I tried to install there it told me that it didn't like spaces in the directory and I went ahead and install where it wanted and now program will not run due to security " Any suggestions? Thanks for your time. Respectfully, Bradley W Miller, PhD Environmental Scientist US Environmental Protection Agency National Enforcement Investigations Center Denver Federal Center, Bldg 25 Door E3 PO Box 25227 Denver, CO 80225 Office: 303-462-9150 Mobile: 863-258-7989 Fax: 303-462-9028 The great tragedy of Science-the slaying of beautiful hypothesis by an ugly fact.- Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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is there any ongoing effort to integrate feff and larch?
by Angel Yanguas-Gil 03 Jan '15

03 Jan '15

So far it seems from the sphinx doc that feff cannot be called from larch. Is there any ongoing effort to implement that? The simplest way would be to create a python module to generate the corresponding feff.inp file, but I'd hate to duplicate someone else's work. Thanks! Angel

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Job offer at DESY
by Edmund Welter 22 Dec '14

22 Dec '14

Dear colleagues, DESY offers a postdoc position at the new PETRA III extension EXAFS beamline P64. If you are interested in details please visit: http://www.desy.de/v2/docs/1418221001-e.pdf If you should know of a colleague who might be interested in the advertised position please feel free to forward this mail. In case you have any question please do not hesitate to contact me (preferentially not via this mail list...) Best regards, Edmund Welter

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Handling large data sets in Athena (and energy dispersive calibration)
by Godfrey, Ian 19 Dec '14

19 Dec '14

Dear All, Here's an issue I recently encountered while trying to handle some very large in situ datasets in Athena; it may be by design/an inherent limitation, rather than a bug, though: (I am running Demeter 0.9.21 pre and Demeter 0.9.20 , both x64 on Windows 8.1 x64 on separate machines). Each of my datafiles contains over 300 columns of u(E) data as space delimited plain text, however when I try and import them to Athena the import window will only display checkboxes up to column 87. I've attached an example datafile and a logfile to this email. (The data is very poor, but that shouldn't be an issue for debugging...) I've also attached a copy of the datafile as it came from the beamline - this also displays the issue, so it's nothing I've done to the file. On a related note, is it possible for the energy dispersive data calibration to be added back to Athena? To get the calibration parameters for this data I had to use the (very) old version! Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] non-standard space group P 21/n
by andrea.sanson＠unipd.it 09 Dec '14

09 Dec '14

Dear Wayne, thank you very much for your enlightening answer! Best regards, Andrea Dear Andrea, To convert the atomic positions, use the following equations (starred positions are in the P21/c setting) a* = c b* = b c* = a+b To convert the unit cell,Â A* = C B* = B C* = sqrt{[Ccos(90-beta)]^2+[A-Csin(90-beta)]^2} beta* = 90 - cos-1[Ccos(90-beta)/C*] where cos-1 is the inverse cosine function If you have problems, please double check my geometry for converting the unit cell parameters. Sincerely, Wayne On Fri, Dec 5, 2014 at 9:04 AM, <andrea.sanson(a)unipd.it> wrote: Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Wayne Lukens Staff Scientist Lawrence Berkeley National Lab _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] non-standard space group P 21/n
by andrea.sanson＠unipd.it 05 Dec '14

05 Dec '14

Dear Gordon, thank you for your reply. I tried to use the space group P1, but the resulting local structure around the absorber atoms is completely different from that expected. Andrea HI Andrea, My suggestion, if you know where all the atoms are in the unit cell, is to use space group P1. It may be tedious and brute force in nature, but you won't have to worry about origin choices or non-standard space groups. You will still know which atoms are equivalent and can pick an appropriate one as your target atom. regards, Robert On Fri, Dec 5, 2014 at 8:07 AM, Sanson Andrea <andrea.sanson(a)unipd.it> wrote: Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars

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non-standard space group P 21/n
by Sanson Andrea 05 Dec '14

05 Dec '14

Dear all does anyone know if is it possible to create with ATOMS the non-standard space group P 21/n ? Space group keywords are listed at the atoms website http://iffwww.iff.kfa-juelich.de/icp/atoms/atoms.sgml-7.html#ss7.4 but no keyword for P 21/n group is available. Thanks for any suggestion. Best regards, AS

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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

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Regarding a fit for Fe(OTf)2
by pushkar shejwalkar 03 Dec '14

03 Dec '14

Dear All, I am experiencing problem during my fit for Fe(OTf)2 anhydrous. The problem is as follows. I collected the data and used a model to fit. The fitting values and other technical information is as below. The basic problem is Fe(OTf)2 in anhydrous condition is probably not cyrstalline because of which there are no crystal data available. Although .cif file is available for hexahydrate and tetra acetonitrile. But obviously it is not directly useful as I am looking for Fe(OTf)2 only. I used hexahydrate for fitting, and the fit information is given. Is this fit acceptable? *Now two questions* 1) Why do I not see any scattering or peak for Fe-S. I expected S to be a strong scatterer and would show a peak. Under given circumstances it looks like Fe is all surrounded by water and no triflate is present near Fe at all. Is this assumption even make sense (when the bottle said anhydrous) The bottle was not kept under inert condition (and its my fault), but does it mean Fe(OTf)2 is so hygroscopic and that it can actually form such hexahydrate to the full extent? OR there is some inherent problem with my fitting and collection itself. I used RBKG=1.0 2) Is anybody working on Fe(OTf)2 and had such or any other problem indicating that Fe(OTf)2 by itself is a bad choice of precursor because of its reactivity. Also any comments on purification method etc. does anybody know if crystal structure is available for Fe(OTf)2 anhydrous? I could not find it on the quick search or on CCDC. Any other site where I can get crystal data and .cif information? Thank you very much for all the help, I hope the question is asked appropriately and all the other information is provided, however, if anybody needs any other information please let me know. Thank you in an anticipation Best Pushkar Independent points : 16.1250000 Number of variables : 4 Chi-square : 7324.9401796 Reduced chi-square : 604.1187777 R-factor : 0.0195782 Measurement uncertainty (k) : 0.0001264 Measurement uncertainty (R) : 0.0004142 Number of data sets : 1 guess parameters: SO = 1.06525455 # +/- 0.05504541 [1.00000] delE = -2.32587026 # +/- 0.59606221 [-2.77870] delR = 0.00911122 # +/- 0.00503027 [-0.02322] ss = 0.00706809 # +/- 0.00071967 [0.00300] Correlations between variables: delr & dele --> 0.9154 ss & so --> 0.9023 All other correlations below 0.4 name N S02 sigma^2 e0 delr Reff R ========================================================================= O1.1 6.000 1.065 0.00707 -2.326 0.00911 2.09150 2.10061 -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan [image: Inline image 3]

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Re: [Ifeffit] A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 03 Dec '14

03 Dec '14

Dear Scott, Thank you for the answer. Date: Wed, 3 Dec 2014 08:03:56 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] A small query on constricting mean square > displacement in multi-edge EXAFS refinement > Message-ID: <A7199A7A-EA1B-4396-960B-301A94F68648(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Yes. > > The only minor adjustment I can think of to that is something called the > ?McMaster correction,? which adjusts for an oversimplification in the usual > EXAFS method of normalization, and thus can be different for the two edges. > But that correction is generally quite small, and the difference in it > between two edges is even smaller. > > ?Scott Calvin > Sarah Lawrence College > > > On Dec 3, 2014, at 7:54 AM, Badari Rao <badari.rao(a)gmail.com> wrote: > > > > Dear All, > > > > Suppose I have a compound, say AB. I have the EXAFS data from both > A-edge as well as B-edge and I am simultaneously refining these data. > > Would it be correct to force the mean square displacement of the A-B > path in both the edges to be the same? > > > > -- Regards, > > 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. > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Fit a mixture
by kaziz sameh 03 Dec '14

03 Dec '14

Dear All,I look for advice or document that can help me to fit the FT EXAFS data of Pd2Au36(SR)24.The situation is as follows:In the sample there is 3 sites of the Pd ( in staples, in surface or in the core). the spectrum that I have presents a first bond of Pd_S and second bond of Pd_Au, so the palladium should be in the staples or in the surface because in core we cannot see Pd-S, but other results of the same sample confirm that the palladium is in core.I concluded that there is a mixture of some nano (x ) with Pd in staple and another nano(y) with Pd in core such y>x.Note that I fit the data with Pd2Au36(SR)24 structure in which I put the 2 palladium in the staple and I have got a good fit (attached) but I think that is not logical.If you can help me with an idea how to fit this mixture, I would be very grateful.Kaziz.

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A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 03 Dec '14

03 Dec '14

Dear All, Suppose I have a compound, say AB. I have the EXAFS data from both A-edge as well as B-edge and I am simultaneously refining these data. Would it be correct to force the mean square displacement of the A-B path in both the edges to be the same? -- Regards, 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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open position at KIT
by Lichtenberg, Henning (IKFT) 02 Dec '14

02 Dec '14

Dear XAS community, we have an open position in the field of EXAFS and operando spectroscopy in our group. For further information see the attached job description. Please feel to contact us also if you are interested in a beamline scientist position or x-ray microscopy. with best regards, Henning Lichtenberg

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