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

Postdoctoral position
by Anatoly Frenkel 31 Oct '19

31 Oct '19

Our group has an opening for a postdoctoral position in heterogeneous catalysis. Expert knowledge of X-ray absorption spectroscopy and in situ/operando characterization of catalysts are required. The postdoc will be stationed at Brookhaven National Laboratory. For inquires, please email me at my Stony Brook University address, with a subject line: Postdoc in heterogeneous catalysis. Thank you, Anatoly Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Fwd: 32 bit package for install
by Ravel, Bruce 28 Oct '19

28 Oct '19

http://bruceravel.github.io/demeter/#old -------- Forwarded Message -------- Subject: 32 bit package for install Date: Mon, 28 Oct 2019 20:30:40 +0200 From: Margaret Blazhynska <blazhynska(a)gmail.com> To: ifeffit-owner(a)millenia.cars.aps.anl.gov To whom it may concern, Could you please send me the 32-bit installer package of ifeffit? I am a student of a masters degree in Chemistry and I really need this pack to practice on XAS Thank you in advance -- Best regards, Margaret Blazhynska -- 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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Issue with the Athena software - Athena Warning: redundant argument in sprintf
by Clarissa Baldo 15 Oct '19

15 Oct '19

Good Afternoon, I am a new user of the Athena software. I am trying to fit my XANES spectra using the linear combination fitting tools in Athena. However, every time I run the fitting I receive the following warning message: [cid:image002.png@01D58286.ED191450] Would you please give me some advice to solve this problem? I am using the latest version of the Demeter system (version 0.9.26) for windows. I have attached a copy of the warning log and a screenshot of the error. Thanks, Clarissa

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trouble installing Demeter from source on Ubuntu 18.04
by Joseph Zsombor-Pindera 15 Oct '19

15 Oct '19

Dear mailing list members; I'm trying to build Demeter from source according to Bruce Ravel's guide (https://bruceravel.github.io/demeter/documents/SinglePage/installation.html) I have mostly been able to install the dependencies, but I had trouble with the libwxgtk packages, so I installed 3.1.0 according to these instructions: https://gist.github.com/abdulhalim-cu/f3ae4be0b45baabef5623ccdd20ca584. wx-config --version results in: 3.1.0, so I think it's installed correctly. libgif4 is no longer in the repository, so I installed libgif-dev and libgif7. WxPerl 0.9932 is installed. Iffeffit is installed, and gnuplot-x11 and pgplot5 are installed. I ran ./Build installdeps and it ran but eventually got stuck in a loop saying "please tell me where I can find your apache src", which I ignored. The script terminated with "/usr/bin/make install -- OK" and then I installed apache2 anyways. Now, if I rerun it, it outputs "all prerequisites satisfied". I ran perl Build.PL, which seemed to complete successfully, and then finally ./Build and ./Build test, however ./Build test fails one test: Test Summary Report------------------- t/003_config.t (Wstat: 512 Tests: 22 Failed: 2) Failed tests: 17, 22 Non-zero exit status: 2 Files=44, Tests=2671, 89 wallclock secs ( 0.34 usr 0.07 sys + 85.03 cusr 3.94 csys = 89.38 CPU) Result: FAIL Failed 1/44 test programs. 2/2671 subtests failed. corresponding to: # Failed test 'configuration system introspection works: groups 38 artemis' # at t/003_config.t line 66. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 80. # Looks like you failed 2 tests of 22. t/003_config.t .......... Dubious, test returned 2 (wstat 512, 0x200) Failed 2/22 subtests line 80 in demeter/t/003_config.t is: ok( ($#groups == $number_of_groups), 'introspection after reading new group: groups'); I'm not sure what's going wrong here. Does anyone know how to resolve this problem? any help would be much appreciated, Joseph -- *Joseph Zsombor-Pindera, BSc* PhD Student, UBC Chemistry Cell: 514.804.0798 6201 Cecil Green Park Road Vancouver BC, V6T 1Z1 C

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Geting Trouble in Fitting CuZr2 strucutr with Cu33Zr67 alloy using simulations
by Akash Deshmukh 11 Oct '19

11 Oct '19

I am trying to do EXAFS fitting using simulations for Cu33Zr67 (Cu33). After running lammps program, I have got.XYZ files for the Cu33. While running edamd command, I am not getting output files. However, the program is running continuously for more than 12 hours. I am considering CuZr2 crystal structure as an input file to fit with Cu33. Can anyone please help me to figure out this? _______________________________________________________________________________ With Best Regards, Akash A. Deshmukh, +91 9175477696

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XAS fitting
by Wang, Maoyu 11 Oct '19

11 Oct '19

Hi I am running an EXAFS fitting for spinel Co3O4. As we know, the Co3O4 will have two different two local coordinations. One is 6 Co-O coordinated octahedral site, and another one is 4 Co-O coordinated tetrahedral site. When we run the Feff calculation, we can only use one Co site to do the calculation once, and we can only get one site coordination by one calculation. However, the EXAFS will tell us the average local structure. How could we use these two different calculation paths to do the fitting? Sincerely, Maoyu Wang Chemical Engineering Oregon State University wangma(a)oregonstate.edu 541-602-1707

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software installation
by Shultz, Mary Jane 11 Oct '19

11 Oct '19

Has anyone had issues with software installation? I have installed it on a Windows machine (64 bit, 7 pro). It appears to install, but when I try to run it, it starts but immediately shuts down. Am I missing something? Thanks M Three colleagues are having the same issue.

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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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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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Two analysts, one spectrum, similar outcome?
by Mike Massey 14 Aug '19

14 Aug '19

Hi Everyone, I'm curious, has anyone ever tried turning two analysts loose on the same unknown EXAFS spectrum to see if their fits come out with similar conclusions? If you have tried it, how did it work out? Were the conclusions indeed similar? If not, why not, and what did you end up doing about it? I was talking with a colleague today about our plans for data analysis, and we settled on this approach (since there are two interested parties willing to try to fit a series of unknown EXAFS datasets). The hope is, of course, that the two analysts will independently reach similar conclusions with similar fits and structural models, but to my mind that outcome is by no means guaranteed. Given the (presumably) wide variation in fitting customs and procedures, I can envision a scenario in which there are major differences. This got me wondering, "Has anyone tried this?" So I thought I'd ask. Your thoughts and experiences would be welcome. Thanks! Mike Massey

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