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

Re: [Ifeffit] Demeter - Athena Warning, crashing
by Ravel, Bruce 16 Apr '19

16 Apr '19

Hi, The Demeter problem that presents itself with error messages like: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. is one that comes up pretty often here on the mailing list. It is also a problem that is already solved on github, but I haven't made a new release in quite some time. The solution to this particular problem is shown here: https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L994-L996 You could simply edit the copy of Demeter.pm on your computer to have the three lines highlighted at that link. Or you could click the "Raw" button at the top of that page, then save the raw file in place of Demeter.pm on your computer. A bit more effort would be to remove the version of Text::Template that is on your computer and install an older version of Text::Template on your computer. This one should work: https://metacpan.org/release/MJD/Text-Template-1.46 The bottom line is that Demeter uses a perl module for which the documentation of a feature and its implementation used to agree and, at some point, stopped agreeing. The fix that I link to above addresses that problem, but the specific combination of Demeter and Text::Template that makes it onto some people computers expose this problem. Any of the solutions explained above should address this in the short term. Eventually I will make a new release and this problem will go away. Until then, hopefully people will find this email. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Demeter - Athena Warning, crashing
by natalia martin 16 Apr '19

16 Apr '19

Hi, I have just installed Demeter on my Mac and get the following error when trying to Launch ATHENA: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I saw a previous post from Chris on the 2018-04-02 with a similar error ("Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236.) which was solved by replacing the /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With another template from p5.24. https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s… <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s…> This solution does unfortunately now work for my case. Does anyone have an idea of how this error can be fixed? Best, Natalia

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job offers
by Kristina KVASHNINA 12 Apr '19

12 Apr '19

Dear Ifeffit Colleagues, There are two positions available at Rossendorf Beamline of ESRF, Grenoble, France. We are looking for a PhD student and a Postdoc to work on TOP project (Towards the bottom of the periodic table), funded by the European Research Council. Please could you share this with anyone who might be interested in applying? Thank you in advance! Kind regards, Kristina http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc_4-1.p… http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_phd_student_2… -- Kristina Kvashnina Rossendorf Beamline (BM20) The European Synchrotron (ESRF) 71, avenue des Martyrs 38000 Grenoble, France tel +33(0)476882367 TOP group website https://www.hzdr.de/db/Cms?pNid=787

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Energy resolution issue [DLM=For-Official-Use-Only]
by JOHANNESSEN, Bernt 11 Apr '19

11 Apr '19

Hi there, I'm using a Demeter 0.9.26 download to display data in Athena. My raw data was converted into ascii readable format retaining a measured 0.25 eV step size through the XANES region. However, Athena seems to inexplicably change the plotted step size to 1.00 eV. I've reinstalled Demeter/Athena without any luck. I also have an older version of Athena (0.8.056) that can display the data with the correct / measured step size of 0.25 eV without any issues. Any idea why Demeter is messing up my energy resolution when I have not changed a single default parameter? Cheers, Bernt Dr. Bernt Johannessen Senior Scientist - XAS Australian Synchrotron Tel Email Web +61 3 8540 4240 berntj(a)ansto.gov.au<mailto:berntj@ansto.gov.au> www.ansto.gov.au<http://www.ansto.gov.au/> [fb]<https://protect-au.mimecast.com/s/0PdECwVLQmilZ0PocqY_I0?domain=facebook.com> [tw] <https://protect-au.mimecast.com/s/dwZYCxnMRvtEqmBZTYpBHF?domain=twitter.com> [ln] <http://www.linkedin.com/company/ansto> [yt] <http://www.youtube.com/user/ANSTOVideos> [ansto]

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Import Error
by Clark Adam Hugh (PSI) 06 Apr '19

06 Apr '19

Dear Bruce and Lucy Thanks for your work around Lucy, it works perfectly but still doesn't explain the behavior I am observing. Bruce what other information would be useful to diagnose the problem I am currently having? I have attached two figures, one showing the import window with the setting I have been using, specifically that I am not using the rebin feature. The second figure shows the difference in the pre-edge region between importing the data with eV and keV units for the energy column to demonstrate clearly that resampling is occurring when importing with data that has an energy column of KeV. Many Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Freitag, 5. April 2019 15:20 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 194, Issue 4 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. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI)) 2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce) 3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram) ---------------------------------------------------------------------- Message: 1 Date: Fri, 5 Apr 2019 11:33:13 +0000 From: "Clark Adam Hugh (PSI)" <adam.clark(a)psi.ch> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Data Import Bug (Athena 0.9.26) Message-ID: <BDFF4FC62383D24DA3EF530480A33EA70B616536(a)MBX214.d.ethz.ch> Content-Type: text/plain; charset="us-ascii" Dear Mailing List I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import). Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data? Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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Can't open Athena project
by Antony Burnham 06 Apr '19

06 Apr '19

I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

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Demeter crashing on WIndows
by mauricio.maps 05 Apr '19

05 Apr '19

Dear sirs I experienced a problem already reported on previous discussions, such as in: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05069.html Following Bruce´s assumption that the antivirus must be the source of the crash of arthemis and athena, I disabled my free AVG antivirus and everything worked fine. With the antivirus on, it doesn´t work. Please, can anyone help me on how can I fix it? The log file is attached. Thank you for any help. <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Data Import Bug (Athena 0.9.26)
by Clark Adam Hugh (PSI) 05 Apr '19

05 Apr '19

Dear Mailing List I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import). Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data? Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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Export measured difference integrated areas
by Patridge, Christopher 04 Apr '19

04 Apr '19

Hello everyone, Is there an export option for the integrated areas found in difference spectra from Athena? It appears the only option is exporting the picture of plotted values? I was hoping to save a little from transcribing each value inside Athena. Thanks everyone, Chris ********************************************** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patridgc(a)dyc.edu<mailto:patridgc@dyc.edu>

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how to best implement fitting u (oxygen parameter) in an spinel
by Juan de la figuera 01 Apr '19

01 Apr '19

Dear all, I have a naive question. I have some mixed spinels, of which I want to fit among other parameters the oxygen parameter u which indicates the distortions around the oxygen anions, using only the single scattering paths. What would be the simplest way of fitting that? In the tests I did before using Artemis, I would start with the structure (usually with a cif file), using atoms/FEFF to calculate all the paths. But changing u changes the initial structure. One way I can think of is to apply a correction, obtained by hand, to deltaR on each O-M path. Of course, this is not a general solution but only good for a few paths. Am I missing something? Thanks in advance, Juan ---------------------------------------------------------------------------- Juan de la Figuera Instituto de Quimica Fisica "Rocasolano" c/ serrano, 119 Madrid, Spain 28006 Phone: +34 91 745 9517 http://surfmoss.iqfr.csic.es/ <http://surfmoss.iqfr.csic.es/surflab/people/juan-de-la-figuera> http://scholar.google.com/citations?user=GOiP624AAAAJ -----------------------------------------------------------------------------

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