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

struggling to install demeter under ubuntu 16.04
by mfehse 02 Dec '16

02 Dec '16

Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following: marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt" thanks in advance marcus

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Re: [Ifeffit] struggling to install demeter under ubuntu 16.04
by Bruce Ravel 30 Nov '16

30 Nov '16

Marcus, This is the last time I am going to respond to a personal email from you on this topic. It is important that you use the mailing list. The list gets archived, which means that the next fellow who has a similar problem might be able to find our conversation and, thus, find a solution to the problem. A private conversation precludes that possibility, so I will not continue to respond to these private emails -- even though I have been CCing them to the list. The problem seems to be that you are installing demeter into a place in your home directory without telling your shell where to look for the executables. Try putting something like export PATH=$PATH:/home/marquinhos/demeter/bin/ in your .bashrc file, which is found in your home directory. You will then need to reload your .bashrc file. This can be done by . ~/.bashrc (the dot is important, see http://stackoverflow.com/questions/2518127/how-do-i-reload-bashrc-without-l…!) As for the problem you mention below about './Build test' -- I just pushed a fix for that problem to github within the last few minutes. Update from github and try again. B On 11/30/2016 01:36 PM, mfehse wrote: > hi > > i have searched for dathena file and found it in the following Path > > /home/marquinhos/demeter/bin/dathena > /home/marquinhos/demeter/blib/script/dathena > > but when i go into the folders bin and script and and try $ dathena$ I > still get the same error message > "No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found" > > so i still dont know whats going. Are there any essential packages > missing from what you > > when i do "./Build test" > i get the error message > "t/002_types.t ........... Can't exec "larch_server": No such file or > directory at /home/marquinhos/demeter/blib/lib/Larch.pm line 66." > > could this be the problem? > > many thanks > > marcus > > re is no On 30/11/2016 17:40, Bruce Ravel wrote: >> So, where did the dathena script get installed on your computer? >> >> B >> >> >> On 11/30/2016 10:49 AM, mfehse wrote: >>> thanks for the quick reply. I just registered with the mailing list >>> today, i didnt add any address. >>> >>> Concerning your remarks for my installation problem your two hints >>> resulted in this: >>> >>> marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build >>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. >>> >>> ./Build >>> marquinhos@marquinhos-Lapi:~/demeter$ hash -r >>> marquinhos@marquinhos-Lapi:~/demeter$ dathena >>> No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found >>> marquinhos@marquinhos-Lapi:~/demeter$ >>> >>> hash -r didnt do much im afraid and about the path im not sure what this >>> is supposed to tell me. >>> As you might have noticed im not a frequent terminal user and I think >>> this cpan/ perl/ demeter installation is probably the trickiest thing i >>> have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] your mail to the ifeffit mailing list
by Bruce Ravel 30 Nov '16

30 Nov '16

So, where did the dathena script get installed on your computer? B On 11/30/2016 10:49 AM, mfehse wrote: > thanks for the quick reply. I just registered with the mailing list > today, i didnt add any address. > > Concerning your remarks for my installation problem your two hints > resulted in this: > > marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build > /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. > ./Build > marquinhos@marquinhos-Lapi:~/demeter$ hash -r > marquinhos@marquinhos-Lapi:~/demeter$ dathena > No command 'dathena' found, did you mean: > Command 'athena' from package 'horae' (multiverse) > dathena: command not found > marquinhos@marquinhos-Lapi:~/demeter$ > > hash -r didnt do much im afraid and about the path im not sure what this > is supposed to tell me. > As you might have noticed im not a frequent terminal user and I think > this cpan/ perl/ demeter installation is probably the trickiest thing i > have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Athena bug
by S.Rowe 29 Nov '16

29 Nov '16

Dear all, I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe

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macports instructions
by Bruce Ravel 29 Nov '16

29 Nov '16

Hi all, In light of recent questions about the MacPorts package, I have updated the Mac installation instructions at the Demeter website. This page: http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.ht… combines the basic instructions and includes a troubleshooting section that covers the "libcxx" issue. The main Demeter web page now links to that page. If some of you Mac users could give the new document a read and provide any suggestions for clarification or improvement, I would be grateful. Cheers, Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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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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