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

Installation of Demeter on Mac Issue
by Lyu, Yimeng 12 Aug '19

12 Aug '19

Hello everyone, I run into to some issues with installing Demeter to a Mac. After installation, warning messages as below show up. Sometimes Athena will quit and sometimes it opens and works just fine. I searched the email archives and apparently the solution is to replace the Template.pm with an older version file. However, I cannot download the attachment from the email thread http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009382.html , as the attachment was encrypted. Can someone send me the Template.pm file so I can resolve this issue? Thanks in advance. —Yimeng 16:21:44: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 16:21:44: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236.

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PhD opportunities
by Silvia Ramos 12 Aug '19

12 Aug '19

Dear All, I would like to share information about two funded PhD positions to work on Frustrated Magnetic Materials at the University of Kent, in the United Kingdom (https://www.kent.ac.uk/scholarships/search/FN26EXPHYS02) One of them (with me) is to work on the determination of local structure. I thought it might be of interest to this community. I will be happy to answer any queries from interested candidates. Best regards, Silvia Ramos ============================ Dr. Silvia Ramos Senior Lecturer in Materials Physics Director of Graduate Studies Ingram 230b School of Physical Sciences University of Kent Canterbury CT2 7NH U.K. Phone: (0)1227 816023 e-mail: s.ramos-perez(a)kent.ac.uk<mailto:s.ramos-perez@kent.ac.uk>

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XAFS short course in BNL Nov. 13-15
by Anatoly Frenkel 01 Aug '19

01 Aug '19

Dear subscribers: The info about the XAFS2019 short course at BNL is here: https://www.bnl.gov/xafs2019/ The application page is open. Best, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Trouble with MacOS 10.14 Mojave
by christophe den auwer 26 Jul '19

26 Jul '19

Hi all, I have to re-install Demeter on my Mojave MacBook (version 10.14.5). X code version 10.2.1 Well it didn't totally worked out…. When I launch either Athena or Artemis, this is what I get (bellow). I also notice I have a new « opt » directory directly on the hard disk (this seems a strange location). Does anybody have an idea about that ? Thanks a lot for your help Christophe ------------------------------------------------------------------------------ Christophe Den Auwer Professeur Université Côte d’Azur Institut de Chimie de Nice Parc Valrose 06108 Nice, France christophe.denauwer(a)univ-cotedazur.fr ------------------------------------------------------------------------------

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averaging data
by Danielle Brown 18 Jul '19

18 Jul '19

How do I average two data sets in Athena? Thanks! — Danielle Brown Office: CSE L180 Cell: 317-605-9311 IIT '20 - BS Physics IIT ID: A20417782 dbrown45(a)hawk.iit.edu d.e.brown93(a)gmail.com

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Beamline scientist position at NSLS-II
by Stavitski, Eli 17 Jul '19

17 Jul '19

Dear all, Beamline scientist position for the Inner shell Spectroscopy beamline is now open at NSLS-II. To read the full posting and apply please go to https://jobs.bnl.gov/job/upton/inner-shell-spectroscopy-beamline-scientist/…. Thanks, Eli. __________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov>

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Fitting in Wavelet transform space ?
by Samy Ould-Chikh 10 Jul '19

10 Jul '19

Dear colleagues, I have been using more and more wavelet transform in parallel of EXAFS fitting. In addition of the statistical parameters provided after the fit, I try also to compare the wavelet transform of experimental data against various structural models to choose the best. Absolutely nothing new here. After applying the wavelet transform to tens of structural model in a row which was bit long, I asked myself this question: Why can't we simply fit the experimental spectra in "wavelet space" instead of R space/k-space ? Does someone know about a code already doing it ? Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx

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Demeter installation macOS Mojave pgplot Build Fail
by Reddy, Aidan 09 Jul '19

09 Jul '19

Hi, I am trying to install Demeter on my mac and am encountering the following error during installation: ---> Building pgplot Error: Failed to build pgplot: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_graphics_pgplot/pgplot/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed Any suggestions to resolve this issue? Thanks, Aidan Reddy

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How to install Demeter on ubuntu 18.04
by William Del Net 08 Jul '19

08 Jul '19

Dear people I tried to install demeter on computer with ubuntu 18.04. I ve found the Deavd Hughes guide to demeter installation on Ubuntu 12.04 There are some differencies and I tried to follow everything. Well, everything seem to be installed, but when I run dathena, i have the following error message opd30@joconde:~/demeter$ ./bin/dathena Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /home/opd30/perl5/lib/perl5/5.26.1/x86_64-linux-gnu-thread-multi /home/opd30/perl5/lib/perl5/5.26.1 /home/opd30/perl5/lib/perl5/x86_64- linux-gnu-thread-multi /home/opd30/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /home/opd30/perl5/lib/perl5/5.26.0 /home/opd30/perl5/lib/perl5/5.26.0/x86_64-linux-gnu-thread-multi /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./bin/dathena line 7. BEGIN failed--compilation aborted at ./bin/dathena line 7. Here.pm is located in~/demeter/lib/Demeter. And yes, it's not in @INC. My home directory is /home/opd30 Do you have a solution, or a guide to install properly demeter on Ubuntu 18.04 Thanks a lot william -- > DEL NET William ESRF CRG-FAME 71 avenue des Martyrs F-38043 GRENOBLE CEDEX 9 tel: +33 4 76 88 25 46 fax: +33 4 76 88 27 43

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Inversion Degree
by Carlos Triana Estupinan 06 Jul '19

06 Jul '19

Dear All Dear I have EXAFS spectra for spinel Co3O4, and I have to determine the inversion degree X, or the cation distribution of Co at the octaedral and tetraedrical sites. The EXAFS fitting can be performed employing two clusters of atoms, one having the absorbing atom in tetrahedral site and one having the absorbing atom in octahedral site. However, I do not know how to exactly determine the fraction of cations in octahedral or tetraedral sites from fitting the spectra with two sites independently. Could you please tell me how exactly should I proced, can I define a EXAFS fitting parameter giving me the cation distribution of Co at the octaedral and tetraedrical sites. If so, how can I do it. Thanks and best regards, -- *Carlos Augusto Triana Estupiñan* * M.Sc. Sciences - **Physics* *Physicist* * Tel: +57 322 256-2309*

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Postdoctoral position is available
by Anatoly Frenkel 03 Jul '19

03 Jul '19

Dear mailing list subscribers, There is an opening for a postdoctoral research associate position, described briefly below (for more details please contact me). A postdoc will investigate novel electromechanical materials using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Stony Brook University (located in close proximity to Brookhaven), under the supervision of Prof. Anatoly Frenkel. Responsibilities will include setting up new in situ operations for testing novel materials under applied electric field, developing and applying fast timing methods (such as modulation excitation spectroscopy), and collaborating with other participants of the NSF-BSF funded US-Israel collaboration. Annual trips to Israel for collaborative research will be required. Ph.D. in Physics, Chemistry or Materials Science, and strong knowledge of XAFS experiment, data analysis and modeling, documented in publications, are required. Three names of professional references are required with the applications that should include a cover letter describing relevant prior experience and interest in the position, and a CV with a list of publications. These materials should be emailed to anatoly.frenkel(a)stonybrook.edu with a subject line: XAFS postdoc position. ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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EXAFS from FEFF9 in ARTEMIS (ver 0.9.26)
by Manju 21 Jun '19

21 Jun '19

Hi I am analyzing my data in ARTEMIS (ver 0.9.26). I used the Rietveld refined parameters of XRD data into ATOMS interface and used that for path calculation. But the paths were not at same distances as indicated by .CIF file (in Vesta). I am having FEFF9 with me. So, I want to run EXAFS in FEFF9 and import the paths in ARTEMIS for fitting. Is it possible? Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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Multiple species with Artemis
by Mukundan, Vineetha 17 Jun '19

17 Jun '19

Hi All, A couple of questions. I was searching the previous threads to check if someone here had posted/explained an example with mixing parameters to find the % content of different constituents present in a sample with Artemis. This is for shell-by-shell fitting. Can Artemis fit multiple chemical species/phases to the experimental spectra simultaneously? OR fit the samples spectra measured at 2 different edges with one or two phase simultaneously? Don't know if I searched far enough. Apology if it has been discussed. In that case, could anyone please direct me to those threads. Thanks you, Vineetha

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Re: [Ifeffit] Ifeffit Digest, Vol 196, Issue 1
by Mahima Makkar 17 Jun '19

17 Jun '19

Dear Sir, This mail is regarding the quotation that you have sent. Please change the address to Prof. Ranjani Viswanatha ICMS JNCASR, Jakkur PO 560064 Bangalore, INDIA. Mail id: rv(a)jncasr.ac.in Please refer the mail id as mentioned above and resend the quotation. Thanks and regards, Mahima On Thu, Jun 13, 2019 at 10:30 PM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Problem with Demeter installation on mac OS Mojave (Ga?lle Creff) > 2. Re: Problem with Demeter installation on mac OS Mojave > (Ravel, Bruce) > 3. Re: Problem with Demeter installation on mac OS Mojave > (Ga?lle Creff) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Jun 2019 22:52:54 +0200 > From: Ga?lle Creff <gaelle.creff(a)unice.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Problem with Demeter installation on mac OS Mojave > Message-ID: <D0FD0963-0C63-4B93-9E99-E56654370D21(a)unice.fr> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > I have some troubles with the installation of Demeter on my mac (under OS > Mojave since this week end). > Athena crashed after the following message: > "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. ? > > Artemis does not work either. > > Can someone help me? > > Thanks a lot. > Ga?lle > >

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Problem with Demeter installation on mac OS Mojave
by Gaëlle Creff 13 Jun '19

13 Jun '19

Hi everyone, I have some troubles with the installation of Demeter on my mac (under OS Mojave since this week end). Athena crashed after the following message: "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. » Artemis does not work either. Can someone help me? Thanks a lot. Gaëlle

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Athena labels
by Stoll, Andreas (IAM) 24 May '19

24 May '19

Hi, Is it possible to change the x- and y-axes labels in the athena plots (energy against normalized xµE)? Greetings Andi

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Postdoctoral position at SSRL in XAS of catalysts
by Bare, Simon R 20 May '19

20 May '19

There is an opening for a postdoctoral research associate positon in the fall of 2019 at Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Lab. This postdoctoral position will involve using in-situ/in-operando synchrotron-based methods, primarily X-ray absorption spectroscopy (XAS), to study all aspects of catalysis. The focus of the project will be in developing advanced methods in data processing, data analysis and data modeling. The candidate will join a group at SSRL, under the guidance of Dr. Simon Bare, though the Consortium for Operando and Advanced Catalyst Characterization via Electronic Spectroscopy and Structure (Co-ACCESS); https://www-ssrl.slac.stanford.edu/content/science/chemistry-catalysis. Full details at: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Please send a letter with CV and list of publications, and names of two references, to the address below: Simon R Bare, email: simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu>

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Two postdoctoral openings at SBU and BNL
by Anatoly Frenkel 20 May '19

20 May '19

Dear mailing list subscribers, There are two openings for postdoctoral research associate positions, described briefly below (for more details please contact me). Position 1: A postdoc will investigate novel electromechanical materials using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Stony Brook University (located in close proximity to Brookhaven), under the supervision of Prof. Anatoly Frenkel. Responsibilities will include setting up new in situ operations for testing novel materials under applied electric field, developing and applying fast timing methods (such as modulation excitation spectroscopy), and collaborating with other participants of the NSF-BSF funded US-Israel collaboration. Annual trips to Israel for collaborative research will be required. Ph.D. in Physics, Chemistry or Materials Science, and expert knowledge of XAFS experiment, data analysis and modeling, documented in publications, are required. Position 2: Catalysis Center for Chemical Innovations (CCEI), an Energy Frontier Research Center (EFRC) at the University of Delaware, is hiring a postdoctoral research associate to work with multiple teams of catalysis researchers of CCEI on XAFS projects. The postdoc will lead collaborative efforts by helping develop synchrotron-based projects, plan experiments, lead the visiting researchers in data collection, and work with CCEI groups on subsequent publications. This position will be supervised jointly by Profs. Anatoly Frenkel (Stony Brook U.) and Jingguang Chen (Columbia U.). The postdoc will be stationed at Brookhaven National Laboratory and travel several times a year to U. Delaware for collaborative meetings. The background is recent Ph.D. in Chemistry or Materials Science. Strong background in catalysis and XAFS measurements, data analysis and modeling are expected. Three names of professional references are required with the applications that should include a cover letter describing prior experience and interest in the position, and a CV with a list of publications. These materials should be emailed to anatoly.frenkel(a)stonybrook.edu with a subject line: XAFS postdoc position. ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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(no subject)
by Sameh Ibrahim Ahmed 20 May '19

20 May '19

Dear collegues I need the XAFS or XANES spectra for some material to use them in my analysis. Actually, I am not sure if there is a library for the XAFS spectra for different compounds available free online !. In fact, I need the spectra for the following elements and their oxides with different oxidation states as well 1- Ni 2- Fe 3- Mo 4- V 5- Co 6- Mn Thank you in advance for your help. Best regards -- سامح إبراهيم أحمد أستاذ مساعد الفيزياء جامعة عين شمس Sameh Ibrahim Ahmed Associate professor of Physics Ain-Shams University Abbassia-11588 Cairo-EGYPT email: sameh(a)sci.asu.edu.eg & sameh2977(a)gmail.com

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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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