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

Larch install error
by Mangold, Stefan (IPS) 05 Oct '19

05 Oct '19

Dear Matt, I tried to install larch via Anaconda. Install of Anaconda and larch seems to work fine, but I couldn’t create the Links via larch -m [numexpr.utils] INFO : NumExpr defaulting to 8 threads. Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch --wxgui Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xas_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_mapviewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_dtcorrect Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrfdisplay Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/dioptas_larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd2d_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd1d_viewer I have MacOS Sierra installed On a similar system I installed larch half a year ago without any issues. best regards Stefan Mangold

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Mac problems
by Enrico Tusini 04 Oct '19

04 Oct '19

Hey there, I have this problem with the installation of Athena package on Mac Mojave : 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 I’ll be very thankful for any suggestion. Best regards Tusini Enrico

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Install for Mac error
by Wu Xiaohan 03 Oct '19

03 Oct '19

Hello everyone, I tried to install demeter on my Mac and run Athena. And get the error shown below: 16:59:44: 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. 16:59:44: 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. 16:59:44: 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. 16:59:44: 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. 16:59:44: 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. 16:59:44: 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. I would like to ask help to correct this error. Thank you so much. Best regards Kelsey

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Re: [Ifeffit] Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

The complex is 13% by mass of the absorbing element (Copper K-edge). The solvent will be acetonitrile and by control the concentration, I mean that I can dictate how much of the sample may be put into the capillary. I won’t be able to control the amount of the absorbing element. Rachel Wallick Chemistry Graduate Student | van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

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Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

I'm preparing for an XAS measurement in fluorescence of a solution-phase sample that will be measured in a capillary tube. I anticipate being able to control the concentration fairly easily, and I'm trying to figure out what the best capillary diameter would be. Is there a good way to figure this out? Rachel Wallick Chemistry Graduate Student Van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

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About Athena
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Good Morning.I am using Athena to analyse O-k edge XAS data. After uploading the data to the Athena, Fourier transform parameters are not showing. attaching a screenshot of home page. I'll be thankful to you for any suggestion. Thank you. hoping to hear from you soon. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

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Athena data uploading: Fourier transform parameters are not showing
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Do anyone have idea about following problem: I uploaded C-k edge on Athena but fourier transform parameters are not showing/open for modifications. Attaching the screenshot. Is this because of the data format of any software issue ? any suggestions? I'll be grateful to you for valuable suggestions. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

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Larch single-file installers problem on Mac
by 朱宥銓 17 Sep '19

17 Sep '19

Hi everyone, I had a problem when I tried to launch XAS software “Larch” on Mac through single-file installers. After I followed the tutorial and installed it (double click the dmg file), when I typed the command “larch”, the terminal showed the followings: could not read history from /Users/willie/.larch/history.lar [Errno 13] Permission denied: '/Users/willie/.larch/init.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history_larchgui.lar' [Errno 13] Permission denied: '/Users/willie/.larch/matplotlib/README' [Errno 13] Permission denied: '/Users/willie/.larch/dlls' [Errno 2] No such file or directory: '/Users/willie/.larch/dlls/README' [Errno 13] Permission denied: '/Users/willie/.larch/modules' [Errno 2] No such file or directory: '/Users/willie/.larch/modules/README' [Errno 13] Permission denied: '/Users/willie/.larch/plugins' [Errno 2] No such file or directory: '/Users/willie/.larch/plugins/README' Traceback (most recent call last): File "//anaconda3/bin/larch", line 11, in <module> load_entry_point('xraylarch==0.9.46rc1', 'console_scripts', 'larch')() File "//anaconda3/lib/python3.7/site-packages/larch/apps.py", line 230, in run_larch cli = shell(quiet=options.quiet, with_wx=with_wx) File "//anaconda3/lib/python3.7/site-packages/larch/shell.py", line 56, in __init__ maxhistory=maxhist) File "//anaconda3/lib/python3.7/site-packages/larch/interpreter.py", line 177, in __init__ for pname in sorted(os.listdir(plugins_dir)): FileNotFoundError: [Errno 2] No such file or directory: '/Users/willie/.larch/plugins’ Does anyone face this problem as well? How can I fix this problem? Thank you, Youchiuan

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Running FEFF 8 in Artemis
by Farideh Jalilehvand 16 Sep '19

16 Sep '19

Hi everyone, I am trying to do EXAFS data analysis using Artemis and FEFF 8. To do so, I have followed these steps: 1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8 FEFF 8.10 runs, but it does not generate paths that I can pick for fitting. The console shows that paths have been found, but does not write it. When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3). So, greatly appreciate if you can help me finding a solution for this problem. Kind regards, Farideh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Farideh Jalilehvand, Ph.D. Associate Professor, and Associate Head (Undergraduate) Department of Chemistry, University of Calgary 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada Tel: (403) 220-3855 / 220-5353│E-mail: faridehj(a)ucalgary.ca URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

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Larch 0.9.46
by Matt Newville 14 Sep '19

14 Sep '19

Hi Folks, Larch 0.9.46 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/ It has been several months since I announced a release. For XAFS and XANES analysis, there have been several recent improvements: - add reading and visualizations tools for RIXS plane data (thanks, Mauro Rovezzi!). - better support for reading older Athena Project files. I think all Athena files are now supported, but if you run into trouble, please send me the file you are having problems with. - better support for reading and parsing data files from more XAFS beamlines, at least those in North America. If you have data files that are not being read correctly (or even "well", including figuring out how columns should be labeled), please send an example file and how you expect it to read. - several fixes to the XAS Viewer application. There is still a To-Do list for this, but if you have suggestions, problems, or irritations using this, please let me know. There have been steady improvements in using Larch as a Python library, especially from Jupyter consoles and Notebooks. Some improvement in the docs and examples have been made. These are still behind but will continue to be worked on over the next few months. If you having any questions or suggestions, please let us know. --Matt Newville

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