February 2015 - Ifeffit - millenia.cars.aps.anl.gov

Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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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

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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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