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

Larch 0.9.43
by Matt Newville 02 May '19

02 May '19

Hi Folks, Larch 0.9.43 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you already have installed Larch, you should be able to update to the latest version with ~> conda update -c gsecars xraylarch from a terminal on Linux or Mac OSX. On Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can simply remove the xraylarch installation folder and reinstall. If you would like to install Larch into a different Python environment, please read https://xraypy.github.io/xraylarch/installation.html Version 0.9.43 has several improvements to the XAS Viewer GUI application, including: - better handling of read/write cycles of multiple Athena project files. - better default normalization and better control over normalization, especially for XANES data. - improved PCA analysis (in part from the recent discussion here with Joselaine Cáceres Gonzalez), so that it now reports IND values to help determine the number of components and reports eigenvalues from simple matrix inversion (not SVD) so that they more closely match those in the XAFS literature. - addition of Partial Least Squares and LASSO regression analysis for selection and prediction of external quantities (valence, for example) based on training sets of XANES data with known values for these quantities. This machine-learning approach is based on work of M Dyar, et al in a series of papers over the past several years. I encourage and request anyone interested, and especially MacOS users, to try out the XAS Viewer app and let us know what needs improvement. For people interested in using Larch from Python, Version 0.9.43 includes a complete refactoring of the code to make Larch work better as a "normal" Python library. Specifically, the previous code organization with most of the real analysis code in "plugins" has been replaced with all code now placed within the main larch module, still organized by topic. This improves packaging -- `pip install xraylarch` can now work. This code reorganization also means that the python programmer can use more normal imports to get at the Larch library so that one can simply do >>> from larch.xafs import pre_edge, autobk, xftf We also fixed a serious and deep flaw that selected a matplotlib plotting library too early, making larch difficult to use with Jupyter, Spyder, or other Qt-based GUIs. This is now fixed, and import statements like the one above can be seamlessly used in Jupyter notebooks. I should note that the documentation and examples are definitely lagging behind the code especially regarding the most recent developments, but this will be worked on. If you having any questions, trouble, or suggestions on any part of Larch, please let us know. --Matt Newville

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Pseudo Voigt crash Athena
by Lawley Craig Richard (PSI) 02 May '19

02 May '19

Dear Mailing list, I have run into an issue with the peak fitting section included in Athena. If I include a peak that is a Pseudo-Voigt and then save the project file. Upon trying to reopen the same project file, Athena becomes non responsive with the error message "PV is not yet implemented". The log file for the crash is as follows: Started at 2019-05-01T17:37:06 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin DEMETER_BASE is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl IFEFFIT_DIR is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\share\ifeffit\ perl version: v5.24.0 backend: ifeffit @INC: C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/lib . Demeter version 0.9.26 Can't call method "SetValue" on an undefined value at C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/PeakFit.pm line 916. -------- Where lines 910-920 in the PeakFit.pm file readout as: 910 if ($result == wxID_NO) { 911 $::app->{main}->status("Not deleting lineshape."); 912 return 0; 913 }; 914 ## demolish the LineShape object, if it exists 915 $this->{'lineshape'.$n}->DEMOLISH if exists $this->{'lineshape'.$n}; 916 ## dig through the hierarchy of the StaticBox and Remove/Destroy each element 917 foreach my $s ($this->{'func'.$n}->GetChildren) { 918 foreach my $w ($s->GetSizer->GetChildren) { 919 $w->GetWindow->Destroy if defined($w->GetWindow); I couldnt find any previous thread regarding this issue. If anyone knows a solution or could link me to a pre existing thread I would much appreciate it. Thanks in advance Craig _______ Paul Scherrer Institut Craig Lawley OFLB/U109 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 5054 E-Mail: craig.lawley(a)psi.ch<mailto:craig.lawley@psi.ch> www.psi.ch<http://www.psi.ch/>

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Demeter Mac issues
by Elizabeth Tomaszewski 29 Apr '19

29 Apr '19

Hello all, Is anyone currently using the Demeter package on a Mac? I have followed the instructions given and have the package installed. However, when I try to open Athena through the terminal window, it gets stuck on the opening Athena image and the question box asking "Athena found an autosave file would you like to import it?" I can open Artemis and Hephaestus, but get the error message as follows: 12:29:30: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563. This message is repeated five times. Only after opening and closing each software several times can I get them to run. Any suggestions as to: 1) how to make the Demeter package run more smoothly and 2) how to get Athena to open at all. Thank you for your assistance, Beth Tomaszewski -- Dr. E J Tomaszewski Postdoctoral Researcher Eberhard Karls Universitaet Tuebingen Center for Applied Geoscience (ZAG) Geomicrobiology Sigwartstrasse 10 72076 Tuebingen Germany

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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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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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Amplitude ratios greater than 100%
by Raj kumar 01 Apr '19

01 Apr '19

Dear All, With the attached CIF file, i have generated chi and other files. In turn, for some paths, i have found amplitude ratios are greater than 100% (even it is reaching few thousands % for some paths - chi file also attached with this email). I know, it is meaningless. I would like to know, why am i getting these weird ratios? What is wrong with the CIF file? Thanks, Raj

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Demeter question and Larch
by Patridge, Christopher 27 Mar '19

27 Mar '19

Hi everyone, A Demeter question - Is the memory limit hard set in Athena? I know that I can change the 50 dataset limit, but can I increase the memory to handle more data as I have a relatively large set of spectra (~150)? I have installed and tested Larch, but I do not see an option to run difference spectra in Larch GUI unless I missed something? I am running windows virtualization (win 7 - 64 bit) Demeter if that affects the memory question. 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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demeter on Mac 10.14.3 Mojave
by Ping, Yuan 19 Mar '19

19 Mar '19

Hello, I have a new mac laptop with Mac 10.14.3 Mojave and would like to install demeter in it. Following the steps in the website, everything worked ok during the installation. However, when I finally typed “athena” in the terminal, the following warning showed up. If I clicked OK, the Athena will just quit and gave a message “perl5.26 quit unexpectedly”. The same thing for Artemis. Hephaestus showed the same warning, but still works after clicking OK. Any clue to fix this problem? [cid:image001.png@01D4DDCA.F5FB5AD0] Thanks a lot! Yuan

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Peaks in Background Subtraction in Athena
by Nathan Nakamura 18 Mar '19

18 Mar '19

Hello, I am working on some data processing of ZrO2 thin films collected in fluorescence mode, and had a question regarding the background subtraction in Athena. When I use the default values, I see a large negative spike in the background curve (shown in BGsubtract1.png). I can vary the spline clamps and other parameters to reduce this (BGsubtract1.copy), but it does not seem to have any significant effect on the final EXAFS (EXAFScompare.png). My question is, do large spikes/instabilities on the edge like this need to be accounted for, or are they ok as long as the background fit after the edge seems fine? My thought is that as long as the EXAFS is not significantly affected, it should be fine, but I do not have a good sense for how the presence of this peak may impact the background curve beyond the absorption edge. I have also attached the project file in Athena for reference. Thanks, -Nathan

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Question on XES in FEFF
by FonsPaul 18 Mar '19

18 Mar '19

I wrote a couple of days ago asking about XES calculations in FEFF9. But I didn't hear anything back so I am rephrasing the question with a little more detail. I am calculating XES for organic molecules and used the following input. CONTROL 1 1 1 1 1 1 EDGE K EXCHANGE 0 0 1.0 FMS 5.1 LDOS -30. 15. .1 PRINT 5 0 0 0 0 0 AFOLP 1.3 S02 1.0 SCF 4.5 0 30 .2 1 XES 8 0.05 0 The XES output is shown from what I understand in the xmu.dat file in the chi column, however plotting this data shows a curve that is not positive definite. As I don’t think there is such a thing as negative emission, this probably means that my understanding is less than complete. The FEFF manual is also not very helpful on this issue and says nothing about the XES emission output. On a related question, the Feff9 docs (http://monalisa.phys.washington.edu/feff/Docs/feff9/feff90/feff90_users_gui…) specify that the XES card has the following options: XES emin emax estep But the examples that come with JFEFF seem to show options that don’t make sense with this definition: BN crystal: XES -20 20 0.2 Cu: XES 8 0.07 0.0 GeCl4 (molecule): XES 8 0.05 0.0 It is hard to understand how an emax value of 0.05 or 0.07 makes any sense. Does anyone know that the correct definitions are? Perhaps the documentation should be updated as well.

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Larch - LCF error
by Lily Schacht 15 Mar '19

15 Mar '19

Hi, all. I’m attempting to perform LCF on a large number of noisey XANES scans. I normalized and rebinned the scans in Athena before importing into Larch using the GUI. When I try to fit a scan I get this error: Traceback (most recent call last): File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 812, in onFitOne self.do_fit(form['group'], form) File "C:\Users\lilys\xraylarch\share\larch\plugins\xasgui\lincombo_panel.py", line 797, in do_fit self.parent.show_subframe('lcf_result', ResultFrame) AttributeError: 'SplitterWindow' object has no attribute 'show_subframe' I’ve tried exporting scans from Athena as .xmu and got the same error. Has anyone seen this before or have any advice? I’m using Larch 0.9.41 and Demeter 0.9.26. My guess is that this is a data format problem not a result of ugly data but for what it’s worth, I tried LCF in Athena and the program either crashed (assuming memory issue) or gave nonsensical results (maybe convergence issue). Thanks, Lily Schacht

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How to use Larch as function server
by ASAKURA, Hiroyuki 14 Mar '19

14 Mar '19

Dear all, I would like to use Larch as an external function server. I'm a Python novice, but if I understand correctly, the present server (larch -r) provides access to a Larch process controllable with xmlrpc from outside. However, I would like to do something like below to achieve looser coupling with my future code (maybe not in python). How can I do that? I appreciate any suggestion for my first step to go, though I guess it is a bit far from the Larch way. ### client.py (not a working code) from six.moves.xmlrpc_client import ServerProxy import os, json def main(): s = ServerProxy("http://127.0.0.1:4966/", allow_none = True) response = s.read_ascii(os.path.abspath("/path/to/xas/data")) # I expect a JSON or python dict with keys like "energy", "mu", etc. data = response response = s.pre_edge(data) # data is a JSON or python dict with keys like "energy", "mu", etc. if __name__ == '__main__': main() ### client.py end I guess one can write some sort of function wrapper, if one wants. ### server.py (not a working code) from six.moves.socketserver import ThreadingMixIn from six.moves.xmlrpc_server import SimpleXMLRPCServer, SimpleXMLRPCRequestHandler import json import larch from larch_plugins.xafs import find_e0, pre_edge, autobk from larch_plugins.io import read_ascii class LarchServer(ThreadingMixIn, SimpleXMLRPCServer): def __init__(self, *args, **kw): super().__init__(*args, **kw) self.larch = larch.Interpreter(with_plugins=True) self.larch.run_init_scripts() self.register_introspection_functions() class LarchRequestHandler(SimpleXMLRPCRequestHandler): def __init__(self, *args, **kw): super().__init__(*args, **kw) def _dispatch(self, method_name, args): return getattr(self, method_name)(*args) ### wrapper function to Larch function ### Do something nice to convert the file into processed data as JSON or a python dict def read_ascii(self, filepath): data = read_ascii(filepath, _larch=larch) # Return processed data as JSON, for example. return json.dumps(data) def main(): server = LarchServer( ("127.0.0.1", 4966), requestHandler = LarchRequestHandler, logRequests = None, allow_none = True ) server.serve_forever() if __name__ == '__main__': main() ### server.py end -- ASAKURA, Hiroyuki (Ph.D) Program-Specific Senior Lecturer (ESICB) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

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