August 2018 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] wavelet transforms for EXAFS
by Clark Adam Hugh (PSI) 14 Aug '18

14 Aug '18

Hi Matt I recently had some problems incorporating the larch Cauchy wavelet transform into my program for rapid bulk processing of QEXAFS data (discussed http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-April/007250.html) I particular after importing the relevant module into python the cauchy_wavelet(cwsam, kweight=kwwt, _larch=mylarch) function raises the error 'not callable'. As a work around I have explicitly copied the module code for the definition into my own script and this seems to resolve the issue. I also notice that at present that it is not possible to apply a windowing function within the wavelet transform, is this just a case of windowing the K space data that is fed to the module? I would also have interest in trying to fit the EXAFS data in the wavelet space, has there been any progress in Larch for performing this? As briefly discussed at the EXAFS conference another feature that I think would be very nice to include would be the possibility to use a Victoreen function for the post edge normalisation instead of a polynomial function. I also briefly discussed the application of the MBACK algorithm. Unless I am doing something incorrect, when trying to use the MBACK algorithm in Larch within python the following error is raised ' 'XrayDB' object has no attribute _getChantler'. In some cases it would be very interesting to apply the MBACK algorithm particularly when only a short data range is collected in some experiments. Thanks Adam Clark __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/133 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch

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LCF on Larch - EXAFS Region
by Garret Bland 14 Aug '18

14 Aug '18

Hello! I've recently been trying to use Larch instead of Athena for EXAFS analysis, and I mainly do linear combination fitting for my samples. It seems that the XANES fitting is doing just fine requesting a specified region to fit (-25 to +75 eV). When I try to fit in the k-space however, Larch does not request a specific region in k space. I try to input the eV values corresponding to the k value I want to fit, but it is still plotting in mu rather than k . Is there anyway I can change this and/or do it manually on the larch GUI? Any help would be appreciated! Thanks, Garret -- Garret Bland Graduate Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 207C Pittsburgh, PA, 15213

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Ph.D and Postdoctoral positions- Time-resolved X-ray Spectroscopy in Biological/Chemical Catalysis
by dooshaye.moonshiram 11 Aug '18

11 Aug '18

Dear all. We have a Ph.D and postdoctoral position available in time-resolved X-ray spectroscopy in biological and chemical catalysis. The details of the positions are attached. Please contact me or forward the attached positions if you or anyone you know might be interested. Many thanks and Best Regards, Dooshaye Moonshiram Group Leader IMDEA Nanociencia Calle Faraday 9, Madrid, Spain

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Demeter on ubuntu 14.04
by Edmund Welter 09 Aug '18

09 Aug '18

Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: --------------------------------------------------------------------- Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, <DATA> line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, <DATA> line 90. Compilation failed in require at /usr/local/bin/dathena line 31, <DATA> line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, <DATA> line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, <DATA> line 90. -------------------------------------------------------------------- When i try to start denv to create the nice overview of installed components I only get the following errors: -------------------------------------------------------------------- [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. ---------------------------------------------------------------------- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund

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Artemis problem
by ParasMani Rajput 09 Aug '18

09 Aug '18

Dear All, I am using windows 8 and running ARTEMIS (1.2.11) in my leptop. Today I found that Artemis not working properly. When I am opening my project files in Artemis then showing an error massage "Artemis trapped one or more errors! Error message dumped to the screen" where i fitted and saved the project file the day before. Please let me know if some has seen this problem and how to resolve it. Regards, Parasmani ----------------------------------------------------------------------------------------------------------------------------------- Dr. Parasmani Rajput Atomic & Molecular Physics Division BL-09, INDUS-2 complex Bhabha Atomic Research Centre Raja Ramanna Centre for Advanced Technology Trombay, Mumbai-85, India Indore, Madhya Pradesh 452013, India E-mail: parasmanirajput(a)gmail.com Phone: (+91) 731-2442509 Web page :https://sites.google.com/site/parasmanirajput/ orcid.org/0000-0003-0694-6756 http://www.researcherid.com/rid/E-4783-2011 -----------------------------------------------------------------------------------------------------------------------------------

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Re: [Ifeffit] Find white line position
by Hiroshi Oji 06 Aug '18

06 Aug '18

Dear Bruce and Carlo, Thank you very much for your reply. Now I understand how Athena find the peak position by the Bruce's answer. I think some kinds of interpolation is made when Athena find the white line position because the peak position that Athena tells seems to be more precise than the energy step in the measurement. Is that right? Actually, I use this function often because it is quite useful for quick check for white line position. But I will be careful when I use it from now on, following the Bruce' advice. I agree with the Carlo's suggestion that it is better to use the curve-fitting method to find the white line position. Best regards, Hiroshi > Date: Thu, 2 Aug 2018 09:48:02 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Find white line position > Message-ID: <alpine.DEB.2.21.1808020946550.9741(a)hydride.segre.home> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > Hi Hiroshi, > > You are probably better off putting a bit more time into the analysis and > simply fitting with an arctangent and a gaussian to get the white line > position. > > Carlo > > On Thu, 2 Aug 2018, Bruce Ravel wrote: > >> >> It's not very sophisticated. >> >> Starting with the "flattened" spectrum (see >> http://bruceravel.github.io/demeter/documents/Athena/bkg/norm.html#the-flat…) >> it simply finds the highest point in the spectrum. Literally just the >> ceiling function. >> >> The flattened spectrum is used rather than the normalized spectrum because >> the curvature of the post-edge (or even the curvature of the pre-edge in >> fluorescence data with a energy dispersive detector) could result in other >> regions being higher in value than the white line. >> >> This is a pretty horrible algorithm. It is, I think, guaranteed to find an >> obviously wrong point for a metal. Basically it works for spectra with a >> white line and it will almost certainly fail for spectra without a white >> line. >> >> Use with caution! >> >> HTH, >> B >> >> >> On 08/02/2018 01:28 AM, Hiroshi OJI wrote: >>> Dear all, >>> >>> I have a question about one of the useful function, "find white line >>> position" in Athena. >>> >>> Could anyone tell me how Athena find the white line position by this >>> function? In other words, I would like to know the algorithm to find the >>> white line position in Athena. >>> >>> Thank you very much for your help, in advance. >>> >>> Best regards, >>> >>> Hiroshi Oji >>> >>> >> >> >> > > -- > 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 --

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Re: [Ifeffit] Artemis problem
by Abdulahad 05 Aug '18

05 Aug '18

Please upgrade your version of Demeter. First remove the old files as well. Hopefully problem get resolve. A. Ahad Department of physics Aligarh Muslim University Aligarh

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Find white line position
by Hiroshi OJI 02 Aug '18

02 Aug '18

Dear all, I have a question about one of the useful function, "find white line position" in Athena. Could anyone tell me how Athena find the white line position by this function? In other words, I would like to know the algorithm to find the white line position in Athena. Thank you very much for your help, in advance. Best regards, Hiroshi Oji -- Hiroshi Oji, PhD. NUSR & AichiSR, Japan E-mail: h.oji(a)nusr.nagoya-u.ac.jp

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Making N (coordination number) a variable.
by M Solo 01 Aug '18

01 Aug '18

Hello Is there a way in artemis to make N, coordination number, a variable to be used in GDS window? I do realize that N and ss are closely linked and do very similar things in the fit, but it seems i may need fractional (average) coordination number for one of the paths, and am fine fixing ss to see where N levels off. Thank you very much. Alex Solov

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Demeter - Athena Warning, crashing
by Alida Perez Fodich 01 Aug '18

01 Aug '18

Hello, I'm new to Athena and after following the steps to install Demeter on my mac when I run the command to launch Athena I get a warning message with the following error: 10:57:05: 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. 10:57:05: 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. 10:57:05: 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. 10:57:05: 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. 10:57:05: 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. 10:57:05: 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. After this, the only option is to press ok and the program crashes. I have updated to latest version of high Sierra (10.13.6) before installing Xcode (9.4.1) and MacPorts (2.5.3). I also tried some of the quick fixes on Athena documentation but it seems to be a different problem. Does anyone have an idea of what could be wrong? Alida.

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