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Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 29 Nov '16

29 Nov '16

Hi All, I have installed demeter using Macports on 10.12.1 and while hephaestus seems to run normally, athena has some trouble with graphics. The usual athena perl based panel shows up just fine, but upon loading some data, there is always an error when gnuplot is invoked to plot graphics (as reproduced below). It would seem that the command “set” is missing the first letter. Does anyone have a suggestion as to what to check to fix this? Axion:perl5.24 $ use_macports.sh athena gnuplot> et label '{/Symbol \305}' at 400.79999,853.0387 center front textcolor ls 12 ^ line 0: invalid command

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error on installing demeter on MacOSX 10.9.5
by christophe den auwer 26 Nov '16

26 Nov '16

Dear all, I am trying to install Demeter on OS 10.9.5 and I am stuck! I installed Xcode 6.2 fine with the licence agreement and everything. Then I installed MacPort 2.3.5 fine as well. I also checked updated version and everything worked fine. Then I tried to install Demeter and got stuck with the following lines : Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.9.0_0+universalError: Failed to install libcxx Please see the log file for port libcxx for details: Error: Processing of port demeter failed I attached to my message, if of any use, the full procedure and feedback from terminal window. If someone could help that would be really great!!! Thanks a lot Christophe ------------------------------------------------- Christophe Den Auwer Professeur Institut de Chimie de Nice Université de Nice Sophia Antipolis 06108 Nice, France 0492076362 christophe.denauwer(a)unice.fr --------------------------------------------------

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Larch 0.9.31
by Matt Newville 22 Nov '16

22 Nov '16

Hi Folks, Version 0.9.31 of Larch has been released. It can be installed using Anaconda Python 2.7 (the recommended approach on Windows and Mac OSX, and a fine choice on Linux too) with conda upgrade xraylarch The source kit can be downloaded from PyPI ( https://pypi.python.org/pypi/xraylarch/0.9.31) or installed on systems that already have Python installed with pip install --upgrade xraylarch Larch is in active development (at https://github.com/xraypy/xraylarch) and this release includes several important new features and capabilities. Some of these are still "in progress" and could greatly benefit from community inputs and comments at every level. In no particular order, some of the highlights include: > Larch server (bin/larch_server) is now much improved and more ready for Athena/Artemis to use. There are still some issues getting Larch Server + Athena working on Mac OSX, but Windows and Linux seem to be working. Using Athena/Artemis with Larch should still be considered experimental, but we're hoping that Larch will soon be the normal backend for Athena and Artemis. > Autobk background removal now calculates arrays for the uncertainty in chi (delta_chi) and mu_0 (delta_bkg) at each k or energy point. These are derived from the uncertainties in the fitted spline coefficients. It has long been argued that uncertainties from the background removal should dominate the uncertainties in chi(k), and so should be used included as the uncertainty in the fits to EXAFS data. Indeed, preliminary tests show that using these uncertainties in the fits does bring reduced chi-square much closer to 1. > Much better support for Python3. Larch is still only supported for Python2.7, mainly due to the dependency on wxPython which is not yet officially supported for Python3. Still, most parts of Larch are Python3 compatible, including the GUIs. If Python3 is a priority for you, let us know (here or on Github), and we'll try to make that happen sooner rather than later. > Support for dealing some X-ray Diffraction data has been added especially for the X-ray Fluorescence maps supported in the Larch XRF MapViewer. New GUI apps for viewing and working with 2D and 1D diffraction images are included in this release. These are the work of Margaret Koker, and are the beginning of support for XRD visualization and analysis in Larch. > XYFit, a GUI for XANES peak fitting has been begun, and can be used for simple sum-of-line-shapes. The abilities of XYFit are currently similar to Athena's peak fitting panel. There are missing important features, but development of this is very active with many features expected to be added over the next few months. The new GUI components should definitely be considered as experimental and ready for friendly comments, suggestions, and bug reports. These are not quite ready for production use yet, but we're hoping that you can help with feedback and suggestions. So, please consider giving these tools a try, and let us know what you think. --Matt Newville

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trouble installing deter on a mac
by justin park 20 Nov '16

20 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

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Time reversibility of multiple scattering paths
by Inwood D. 18 Nov '16

18 Nov '16

Hi All, I've just been reading the paper with the following reference: Nashner, M. S.; Frenkel, A. I.; Adler, D. L.; Shapley, J. R.; Nuzzo, R. G. Structural Characterization of Carbon-Supported Platinum - Ruthenium Nanoparticles from the Molecular Cluster. J. Am. Chem. Soc. 1997, 7863, 7760-7771. In particular I was interested about the data analysis section on page 7763 (footnote 32) where the authors talk about time reversibility of multiple scattering paths. It is mentioned that the collinear DS path, in the fcc structure, (M - M(1) - M(4) - M) is time reversed, so has twice the degeneracy, but that the collinear TS path (M - M(1) - M(4) - M(1) - M) is not time reversed. Why is the DS path time reversible, but not the TS path despite the apparent 'symmetry' of the TS path? What makes a scattering path time reversible? Does time reversibility only apply to collinear paths or can it also apply to triangular paths as well? Thanks for your help, David David W Inwood PhD Researcher Chemistry University of Southampton Southampton, UK SO17 1BJ

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Athena crashing with "Larch_Server not found"
by Frederik Eistrup 14 Nov '16

14 Nov '16

Dear List, Recently installed Demeter on Ubuntu for a master's lab work at Bessy II (HZBerlin), with help from David Hughe's instructions (https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…) When I run Athena ("dathena" in comand line) the interface window appears but command line has output: $ dathena Trying Larch server: /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4966 start Can't exec "larch_server": No such file or directory at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Larch.pm line 66. Later, when i try to import a data-file, column selection windows shows up as it should, but after i've chosen numerator and press OK, the whole Athena crashes. Message on terminal (sorry I know its massive...): Attribute (bkg_pre1) does not pass the type constraint because: Validation failed for 'LaxNum' with value 9997,000 at accessor Demeter::Data::bkg_pre1 (defined at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 258) line 7 Demeter::Data::bkg_pre1('Demeter::Data=HASH(0xd91e330)', '9997,000') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Defaults.pm line 48 Demeter::Data::Defaults::resolve_defaults('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 290 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 734 Demeter::Data::_update('Demeter::Data=HASH(0xd91e330)', 'all') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 648 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0xbcd018)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xd949d08)', 'Demeter::Data=HASH(0xd91e330)', 'HASH(0xd91a8e8)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 0, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 531 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0xbcd018)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 1, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 193 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 862 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)', 'Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 784 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)') called at /home/frederik/perl5/bin/dathena line 31 eval {...} at /home/frederik/perl5/bin/dathena line 31 So, where is the problem? Can anyone helo with this? Made sure larch was installed through sudo apt-get install, but all stays the same. Thanks for any help! Frederik David Hughes' guide to Demeter Installation on Ubuntu ...<https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…> bruceravel.github.io David Hughes' guide to Demeter Installation on Ubuntu¶ These instructions cover a non-root manual build of Bruce Ravel's Demeter package under Ubuntu 12.04. Found out that Athena

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athena LCF issue
by fred.mosselmans＠diamond.ac.uk 08 Nov '16

08 Nov '16

Dear Bruce, I realise you may be travelling soon , This is not a very serious bug as I have work rounds. I was demonstrating linear combination fitting in Athena using the gold thiobacteria example this week. I am using 9.25 on a windows 7 computer. I read in all the data from the cynaobacteria project file I mark 5 or 6 standards In the LCF tab I use marked groups, untick the sum weights to 1 option leaving just the all weights between 0 and 1 option selected. I pick a sample spectrum eg 4.73 I select fit all combinations It rolls through them and reports the apparently correct results but an error message is reported: Redundant argument in sprint at C:/... /AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm line 780, <F> line 122 Clicking any of the answers in the combinatorics tab brings up this error again. If I do a fit of lot of spectra using the same set of standards, I get a similar error message except this time it is line 906 and some of the combined spectra don't plot properly until you refit them as a single spectra in the standards tab I attach a log file but not a project as I assume you can find that on github! Regards Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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port for demeter failure
by justin park 04 Nov '16

04 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

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Postdoc Position
by Mengling Stuckman 03 Nov '16

03 Nov '16

Hello, all, Thanks to Bruce for the support of posting spectroscopy-related positions! My advisor, Christina Lopano, (christina.lopano(a)netl.doe.gov) at DOE-National Energy Technology Lab (NETL), is looking for a post-doc, as a synchrotron geochemist. You can see more information about the position here: https://www.zintellect.com/Posting/Details/2710 You can also reference the following website for more DOE-NETL related positions: http://orau.gov/netl/applicants/current-opportunities.html Please let anyone who might be interested know. Thank you, Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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Larch mback error report
by Sean Fackler 02 Nov '16

02 Nov '16

Dear Larch developers (Matt), I believe I found an error in the mback function where I get a NameError saying the name ‘f1_chantler’ is not defined. I found that simply adding f1_chantler to the larch_plugins.xray import section in mback.py fixes the problem. I have included the modified mback.py code, my input data (SigScan226827.txt), project code (mback_test.py), and the error I received (mback_error.txt). I am running python 2.7 with anaconda as my manager, macOS Sierra v10.12, on a mid-2015 15” MacBook pro. I hope this report is correct and helpful. Regards, Sean Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

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