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

Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 09 Dec '16

09 Dec '16

Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now.

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Peakfitting CeO2 data in Athena
by Stephanie Laga 08 Dec '16

08 Dec '16

Dear all, I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I have been using moved the peak fitting function in Athena to model the XANES with an arctan background function and a series of gaussians. Looking through the literature I haven't seen too many specifics to using this approach (rationale for choosing the widths of peaks or how to define the background function). Similarly, doesn't seem to be much rationale for choosing a 4 vs 5 peak fit for the XANES. My main question is then...1) Is there a rational for picking the background function, specifically the height and width (can I let the height vary or should I be keeping a constant arctan through all samples)? Any advice is greatly appreciated! Stephanie

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error on installing demeter on MacOSX 10.11.6
by Valerio Scagnoli 07 Dec '16

07 Dec '16

Dear all, I was trying to install demeter on my Mac with mac port and the installation seemed to run smoothly (after following the advice on the installation page!). However, when I try to start Athena from the command line I get the following error message: bash-3.2$ athena IO::Compress::Base::Common version 2.069 required--this is only version 2.015 at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/vendor_perl/5.24/Module/Runtime.pm line 317, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. Compilation failed in require at /opt/local/bin/athena line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/bin/athena line 27, <DATA> line 1. I tried to install the following zlib packages and uninstall/reinstall demeter, but the error still remains. bash-3.2$ port installed |grep zlib p5.24-compress-raw-zlib @2.69.0_0 (active) zlib @1.2.8_0+universal (active) I have the following perl package installed bash-3.2$ port installed |grep perl p5.24-libwww-perl @6.150.0_0+ssl (active) p5.24-perl-ostype @1.10.0_0 (active) p5.24-perlio-layers @0.11.0_0 (active) p5.24-perlio-utf8_strict @0.6.0_0 (active) perl5 @5.24.0_0+perl5_24 (active) perl5.24 @5.24.0_0+universal (active) Any help will be appreciated. Valerio Scagnoli

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error install Demeter
by Maria Rosa BECCIA 07 Dec '16

07 Dec '16

Hello, I tried to install Demeter on my Macbook OS El Capitan (version 10.11.6), but when typing the "sudo port install xors-server demeter” line, it gives me an error. You can find the error lines in the attached file. Thank you in advance for your help. Kind regards, Maria Rosa Beccia Maria Rosa BECCIA Maître de conférences Institut de Chimie de Nice Université Côte d'Azur UMR 7272 28 Avenue Valrose 06108 Nice, France phone: +33 (0)4 92 07 63 71

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problems installing athena et al under ubuntu 16.04 LTS
by Juan de la figuera 02 Dec '16

02 Dec '16

Dear all, I have been installing demeter from git under ubuntu 16.04 LTS, following the non-root instructions from: https://gist.github.com/waveform80/3959252 I also installed xraylarch from git. Xaylarch is only missing: #=== Warning: Some recommended Python Packages are missing: epics: needed for using the EPICS control system pyFAI: needed for xrd modules It seems to work, but when I try to open a file that can be open properly from Athena installed on Windows, I get: Trying Larch server: /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4968 start larch_server port=4968: started gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point and although it opens the data in a gnuplot window, the scale is off (7x10^9 instead of 7x10^3). I am assuming once it is confused about the scale, it makes a mess with the data. The output of probe -bv is: t/000_ifeffit.t ......... 1..6 ok 1 - show ok 2 - show arrays: ok 3 - get_scalar 1.2345 ok 4 - put scalar ok 5 - put/get_string: my.xmu ok 6 - put/get_array: ok t/001_base.t ............ 1..24 Trying Larch server: /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4969 start larch_server port=4969: started ok 1 - new() works ok 2 - group is set: orihs ok 3 - unique group names: orihs & bcxkm ok 4 - installation location identified ok 5 - identity string ok 6 - generic object is not plottable ok 7 - generic object has no data ok 8 - Project role works ok 9 - demeter can do introspection ok 10 - ifeffit disposal mode flag: 1 ok 11 - handle unknown mode gracefully ok 12 - other disposal modes all false ok 13 - turn on screen disposal mode flag ok 14 - turn on file disposal mode flag ok 15 - turn on buffer disposal mode flag ok 16 - unknown window not recognized ok 17 - known element (Cu) is recognized ok 18 - unknown element (Ci) not recognized ok 19 - simple template works not ok 20 - simple disposal to Ifeffit: string # Failed test 'simple disposal to Ifeffit: string' # at t/001_base.t line 69. not ok 21 - simple disposal to Ifeffit: scalar # Failed test 'simple disposal to Ifeffit: scalar' # at t/001_base.t line 70. Use of uninitialized value in numeric eq (==) at t/001_base.t line 71. not ok 22 - simple disposal to Ifeffit: array # Failed test 'simple disposal to Ifeffit: array' # at t/001_base.t line 71. ok 23 - simple disposal wrapper works ok 24 - plot_with works # Looks like you failed 3 tests of 24. Any help would be appreciated. Juan

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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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