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

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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Anyone use OCEAN?
by Matthew Marcus 12 Sep '19

12 Sep '19

OCEAN is the U. Washington program for doing XANES sims using ab-initio, Bethe-Salpeter methods (http://monalisa.phys.washington.edu/OCEAN/ocean-about.html) It seems to require a certain amount of experience and expertise to get it to produce any result, let alone correct results. I wonder if this might be a good forum for getting advice on solving problems with this code. Unlike ABINIT, which is one of the ab-inito engines OCEAN can use, OCEAN doesn't have a forum of its own. -- Sincerely, Matthew Marcus

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Occupation number error getorb
by Patridge, Christopher 12 Sep '19

12 Sep '19

Hello, I have searched back on the mailing list regarding the occupation number error and found bad counts with getorb. I have tried a number of settings as per the email thread, however nothing seems to correct the error. I trying to calculate a vanadium oxide K-edge but as the earlier email stated, it just hangs trying to iterate SCF. This email was quite a while ago and just wondered if anyone has had these issues come up again and were able to find conditions that worked for them? Attached is the feff.inp which triggers this error. Any guidance or suggestions beyond the thread would be greatly appreciated, Thanks, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu<mailto:patridgc@dyc.edu> www.dyc.edu<http://www.dyc.edu> Social: Twitter<http://www.twitter.com/drpatridgc> [cid:0edd417e-b4aa-4ba7-af9d-5051c7441a0a@namprd14.prod.outlook.com]

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need version for 32 bit
by Seham Kamal 12 Sep '19

12 Sep '19

Dears, Good morning, Is it possible to send the version that works on 32 bit best regards Seham -- Seham K. Abdel-Aal (PhD) Lecturer, Physics department Faculty of Science, Cairo University 12613 Giza, Egypt Phone: 00201229131402 Email: seham(a)sci.cu.edu.eg Cairo University Scholar http://scholar.cu.edu.eg/?q=seham/biocv/cv Google scholar citation https://scholar.google.com/citations?user=VGVf2l0AAAAJ&hl=en Research gate page https://www.researchgate.net/profile/Seham_Kamal/publications -- **Disclaimer:** This E-mail represents the views of its author only and does not necessarily reflect the opinions of Faculty of Science (*SCI <http://www.sci.cu.edu.eg>*). We do not assume responsibility for any loss, damage (including direct, indirect, punitive, special, or consequential loss or damage), which you may directly or indirectly suffer from this email or its contents or through the ways of handling this email which includes sending, receiving, replying, forwarding, deleting, saving or changing and adjusting its content in any way.

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Larch import error
by Patridge, Christopher 10 Sep '19

10 Sep '19

Good morning, I have OSX Larch installed and attempting to open XAS data files. It cannot read the file and Larch returns an error: Error trying to read '/Users/DrPatridge/Desktop/2019-03-21/CaVO_50-40-10_vs_Zn.002': _tmp_file_ = read_xdi('/Users/DrPatridge/Desktop/2019-03-21/CaVO_50-40-10_vs_Zn.002') ^^^ File /Users/DrPatridge/.larch/init.lar, line 1 File "/xraylarch/share/larch/plugins/io/xdi.py", line 258, in read_xdi xdif = XDIFile(filename, labels=labels) File "/xraylarch/share/larch/plugins/io/xdi.py", line 124, in __init__ self.read(self.filename) File "/xraylarch/share/larch/plugins/io/xdi.py", line 165, in read mvals = tostrlist(xdi.meta_values, self.nmetadata) File "/xraylarch/share/larch/plugins/io/xdi.py", line 65, in Py3tostrlist return [str(i, 'ASCII') for i in (nitems*c_char_p).from_address(address)] File "/xraylarch/share/larch/plugins/io/xdi.py", line 65, in <listcomp> return [str(i, 'ASCII') for i in (nitems*c_char_p).from_address(address)] UnicodeDecodeError: ('ascii', b'3.1356369 \xc3\x85', 10, 11, 'ordinal not in range(128)’) Is this a plugin error or something else? I attached one of the files if anyone could test? I can open it in Athena. Thanks for any help, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu<mailto:patridgc@dyc.edu> www.dyc.edu<http://www.dyc.edu> Social: Twitter<http://www.twitter.com/drpatridgc> [cid:0a129c79-2c47-40b9-8a0d-22bf08b7005d@namprd14.prod.outlook.com]

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Fwd: 64-bit Demeter not able to use on Windows computer
by Ravel, Bruce 28 Aug '19

28 Aug '19

Brittany, In your first post to the mailing list, you said you could not get the software to run on "a Windows computer". That you are looking for a 32 bit installer seems like extremely relevant information. I no longer have the capacity to build 32 bit versions of the installer, but I keep links to old versions available on the Demeter website. http://bruceravel.github.io/demeter/#old The most recent version for which a 32 bit installer exists is 0.9.25. Somewhat dated, but should still be useful. B PS: Please send email to the mailing list ifeffit(a)millenia.cars.aps.anl.gov and please do not send email directly to ifeffit-owner. Matt and I are the only ones who read mail sent to ifeffit-owner and we don't guarantee a response to email sent to that address. -------- Forwarded Message -------- Subject: 64-bit Demeter not able to use on Windows computer Date: Wed, 28 Aug 2019 09:10:17 -0400 From: Brittaney Courchesne <bcourchesne(a)laurentian.ca> To: ifeffit-owner(a)millenia.cars.aps.anl.gov Hi everyone, The 64-bit version of Demeter is not able to be used on my Windows computer I have, since it is a 32-bit version. Is there a way around this or does someone have the 32-bit version they can email me? I have tried disabling my firewall completely and trying to "allow" the programs through the firewall, and running as an administrator, but the 64-bit just doesn't seem to work. Thank you, Brittaney -- */Brittaney Courchesne, G.I.T./* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON /bcourchesne(a)laurentian.ca <mailto:bcourchesne@laurentian.ca>/ -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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QFS fit for Am
by Daria Boglaienko 22 Aug '19

22 Aug '19

Hello, I have tried quick first shell fit for various compounds, but it does not work for Am. It does run fit for organic compound of Eu but it does not run fit for similar organic compound of Am. Please, let me know if there is something I can take into account. Thank you -Daria

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Unable to use 64-bit Demeter on Windows computer
by Brittaney Courchesne 21 Aug '19

21 Aug '19

Hello, I am just sending this email to see if anyone has encountered the following problem: I downloaded the newest 64-bit version of Demeter on my Windows computer, and it downloaded successfully, but now when I double click on the program, a tiny window pops up for about 0.5 seconds and then disappears. I have tried redownloading twice. Thank you very much, Brittaney -- *Brittaney Courchesne, G.I.T.* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON *bcourchesne(a)laurentian.ca <bcourchesne(a)laurentian.ca>*

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