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

Question about PCA
by Joselaine Cáceres gonzalez 25 Apr '19

25 Apr '19

Dear all, I performed PCA in a set of 11 XANES spectra and I was trying to use some of the functions and tests developed by Malinowski to extract the number of primary components. I found differences between eigenvalues calculated whit a matrix calculator and those calculated by ATHENA, but they are equivalent in some way since they explain the same amount of variance and when I calculate the IND function or Malinowski F-test I reach the same conclusions. To calculate the eigenvalues with the matrix calculator I first normalized my data matrix (step height normalization) with ATHENA, then I export the data to an Excel spreadsheet where I centered them: z=(value-mean)/standard_dev. Then I used SVD and Eigenvalue decomposition to find the eigenvalues and those obtained with SVD explain exactly the same amount of variance than those found with ATHENA but they are different. In all the calculation I did, I used the same amount of points 161, points in each spectrum in ATHENA and in the matrix calculator, exactly the same energy interval. I´d like to know if I am missing some step in the data pre-treatment that is prevented me to find the same eigenvalues obtained by ATHENA but also I´d like to know if I can straight forward use the values obtained with ATHENA to evaluate the functions proposed by Malinowski since these equations might be different depending if calculations are made using "covariance about the origin" or "correlation about the origin" and I am not sure what is the case. Thanks in advance! Best regards Joselaine

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can't open Athena 0.9.26!
by m.rezaie 23 Apr '19

23 Apr '19

Hi, I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my computer which is Win 7, 32 bit. How can I solve this problem? Best Regards Mahsa

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2019 APS/IIT Summer XAFS School
by Carlo Segre 18 Apr '19

18 Apr '19

Greetings: The 2019 APS/IIT Summer XAFS School will be held on the Illinois Tech Campus from July 7, 2019 to July 12, 2019. Please see the attached announcement for details and information on how to apply. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org it helps to get the year right > On Apr 18, 2019, at 10:38 AM, grant bunker <bunker(a)agni.phys.iit.edu> wrote: > > Greetings, All - I would appreciate your help in the disseminating this announcement > > thanks - Grant > > <2019 XAFS summer school announcement.pdf>

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Regarding FEFF9
by Manju 18 Apr '19

18 Apr '19

Hi I am trying to see the effect of crystal defects on XANES. Is there any way that I could create charged vacancy in feff.inp file, before importing it into FEFF9? Regards Manju Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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LANL EXAFS Postdoc position
by Daniel Olive 17 Apr '19

17 Apr '19

Greetings all, Los Alamos National Laboratory has a postdoc position involving EXAFS for use in nuclear forensics/actinide research. The vacancy name is IRC72104, linked below, and contains additional information. https://lanl.jobs/jobs/?q=IRC72104 Please have a look and/or forward to those who may be interested. Best, Dan -- ------------ Daniel Olive Los Alamos National Laboratory MST-16: Nuclear Materials Science P.O. Box 1663 MS E574 Los Alamos, NM 87545 Chemical Sciences Division Lawrence Berkeley National Laboratory ------------

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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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