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

smoothing XAS data
by Daria Boglaienko 23 Jan '20

23 Jan '20

Hello, In what case smoothing of the data is OK? My data have a lot of noise and smoothing really helps (visually). I compared fit done in Artemis for smoothed and non-smoothed data sets and the result is very similar, however when I searched about it online, it looks like it is not recommended. What is a good way to justify it? Thank you! -Daria

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Re: [Ifeffit] Ifeffit Digest, Vol 203, Issue 5
by Christopher Chantler 22 Jan '20

22 Jan '20

Dear all I agree with Mike and Scott too. I might suggest Schalken, M. J. and Chantler, C. T. "Preservation of uncertainty in experiment: structures of Ni (II) coordination complexes" (2018) J. Synchrotron Rad., 25, 920-934 as a partial discussion around this topic if people are interested. It could be read as 'don't smooth data if you can avoid it'. Very best wishes to all Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Thursday, 23 January 2020 4:05 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 203, Issue 5 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. smoothing XAS data (Daria Boglaienko) 2. Re: smoothing XAS data (Carlo Segre) 3. Re: smoothing XAS data (Scott Calvin) 4. Re: smoothing XAS data (Mike Massey) 5. Re: smoothing XAS data (Will Bennett) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Jan 2020 17:38:43 -0800 From: Daria Boglaienko <dbogl003(a)fiu.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] smoothing XAS data Message-ID: <CAACWq8BmJFr0QNUHk1YrsB7w3BLGhzyus9pXow0Ng+ER3eAZDQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, In what case smoothing of the data is OK? My data have a lot of noise and smoothing really helps (visually). I compared fit done in Artemis for smoothed and non-smoothed data sets and the result is very similar, however when I searched about it online, it looks like it is not recommended. What is a good way to justify it? Thank you! -Daria

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Larch Mac OS X 10.15 Catalina
by Jeff Terry 10 Jan '20

10 Jan '20

Hi Matt, I had to upgrade my Mac to OS X 10.15 and it blew up my Anaconda distribution which has forced me to reinstall everything from scratch. Now whether I install larch from source or by using conda, I get the following error: Traceback (most recent call last): File "/Users/jterry/anaconda3/lib/python3.7/ctypes/__init__.py", line 97, in CFUNCTYPE return _c_functype_cache[(restype, argtypes, flags)] KeyError: (None, (<class 'epics.dbr.access_rights_handler_args'>,), 1) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/jterry/anaconda3/bin/larch", line 11, in <module> load_entry_point('xraylarch==0.9.46', 'console_scripts', 'larch')() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point return ep.load() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2443, in load return self.resolve() File "/Users/jterry/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2449, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/__init__.py", line 50, in <module> from . import builtins File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/builtins.py", line 33, in <module> from . import epics File "/Users/jterry/anaconda3/lib/python3.7/site-packages/larch/epics/__init__.py", line 9, in <module> import epics File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/__init__.py", line 29, in <module> from . import ca File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/ca.py", line 761, in <module> dbr.access_rights_handler_args) File "/Users/jterry/anaconda3/lib/python3.7/site-packages/epics/dbr.py", line 339, in make_callback return ctypes.CFUNCTYPE(None, args)(func) File "/Users/jterry/anaconda3/lib/python3.7/ctypes/__init__.py", line 99, in CFUNCTYPE class CFunctionType(_CFuncPtr): TypeError: item 1 in _argtypes_ passes a struct/union with a bitfield by value, which is unsupported. I think that line 11 is: load_entry_point('xraylarch==0.9.46', 'console_scripts', 'larch')() Any ideas on how to address this issue? Thanks, Jeff Jeff Terry Professor of Physics, Illinois Institute of Technology terryj(a)iit.edu

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X-ray analysis books available if you want them
by Mike Massey 08 Jan '20

08 Jan '20

Hi all, I have a small selection of x-ray books I'm happy to give you if you want them. Please contact me privately if you do. I'd rather give them away to a good home than send them to book heaven. Koningsberger and Prins, X-Ray Absorption Attwood, Soft X-rays and Extreme Ultraviolet Radiation Stohr, NEXAFS Spectroscopy Stock, MicroComputed Tomography RIMG vol 18, Spectroscopic Methods in Mineralogy and Geology ...And maybe one or two more. Kind Regards, Mike

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Installation problems on MacOS catalina, macports
by Ricardo Faccio 30 Dec '19

30 Dec '19

Dear all I followed al the instructions in https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…. In principle, I got a clean installation without errors. But when running athena I get: MacBook-Pro-de-Ricardo:~ rfaccio$ athena Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7. BEGIN failed--compilation aborted at /opt/local/bin/athena line 7. Any hint will be appreciated. Best regards Ricardo -- ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Agregado de Física (Assoc. Prof.) Mail: Área Física, DETEMA, Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio(a)fq.edu.uy Phone: (+598) 2924 9859 (+598) 2929 0648 Fax: (+598) 2924 1906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

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Re: [Ifeffit] Ifeffit Digest, Vol 202, Issue 8
by Christopher Chantler 17 Dec '19

17 Dec '19

Dear Fred and Matt, thanks for raising the notice for the IUCr 2020 in Prague. We [XAFS, CXAFS] have a strong list of speakers and XAFS sessions, together with all the Crystallography sessions. We also have a tutorial workshop the day before the Congress at the venue, which is free [with registration for the Congress] and especially for early career researchers, crystallographers finding out about XAS and students. We have been awarded two keynote speakers on XAS, together with nine XAS and XAS-related Microsymposia, including Fred's one: 1) Advanced Methods for analysis of XAFS and Crystallographic data 2) Spectroscopy applied to electrochemistry: operando studies 3) Catalysis: functionalized materials studied by XRD and XAFS 4) XAS and crystallography allied for geomaterials and environmental problems 5) Disordered materials: spectroscopic and scattering techniques 6) Matter at extreme conditions at SR and XFEL: complementarity of spectroscopy and diffraction 7) X-ray spectrometry and X-ray diffraction in Art and Archaeology 8) 4th generation SR and XFEL Facilities 9) Combining x-ray diffraction and spectroscopy to characterize materials We welcome all submissions, abstracts etc. and hope this will be a great programme. Prague is also a beautiful place. Very best wishes to everyone... Particular thanks to Giuliana, Sofia, Dibyendu, Valerie and all the session chairs. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 18 December 2019 4:07 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 202, Issue 8 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. IUCR conference 202 prague (Mosselmans, Fred (DLSLtd,RAL,SCI)) 2. La-Oxide La K edge reference spectrum (Benedikt Eggert) 3. Re: La-Oxide La K edge reference spectrum (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Dec 2019 07:53:14 +0000 From: "Mosselmans, Fred (DLSLtd,RAL,SCI)" <fred.mosselmans(a)diamond.ac.uk> To: "'ifeffit(a)millenia.cars.aps.anl.gov'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] IUCR conference 202 prague Message-ID: <AM0PR01MB62282DF052E6E196004245A4A3500(a)AM0PR01MB6228.eurprd01.prod.exchangelabs.com> Content-Type: text/plain; charset="us-ascii" Please excuse this email, but I'd like to draw your attention to the IUCR congress<https://www.xray.cz/iucr/> in Prague next year, (August 22 -30). I'd like to draw your attention to a session I am co-chairing with Annalisa Martucci entitled "XAS and crystallography allied for geomaterials and environmental problems."<https://www.xray.cz/ctfc/chairs-speakers.asp?id=61> Professors Rizlan Bernier-Latmani and Giuseppe Cruciani will be our invited speakers. The abstract deadline for talks is 31/3/2020, while for posters it is 30/6/2020. (The International XAFS Society is affiliated to the IUCR and thus a number of the congress sessions are based on the use of X-ray Absorption Spectroscopy.) Regards Fred Mosselmans Principal Beamline Scientist I20 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7419362123 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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La-Oxide La K edge reference spectrum
by Benedikt Eggert 17 Dec '19

17 Dec '19

Hello all, Has someone a reference XAS spectrum of La2O3 at the La K edge in his repository? Thanks a lot in advance for your help. Best regards, Benedikt -- -------------------------------------------------------------------- M.Sc. Benedikt Eggert Fakultät für Physik - AG Wende Universität Duisburg-Essen, MD 450 Lotharstraße 1, 47057 Duisburg, Germany Benedikt.Eggert(a)uni-due.de Tel.: +49203/379-2389 --------------------------------------------------------------------

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IUCR conference 202 prague
by Mosselmans, Fred (DLSLtd,RAL,SCI) 17 Dec '19

17 Dec '19

Please excuse this email, but I'd like to draw your attention to the IUCR congress<https://www.xray.cz/iucr/> in Prague next year, (August 22 -30). I'd like to draw your attention to a session I am co-chairing with Annalisa Martucci entitled "XAS and crystallography allied for geomaterials and environmental problems."<https://www.xray.cz/ctfc/chairs-speakers.asp?id=61> Professors Rizlan Bernier-Latmani and Giuseppe Cruciani will be our invited speakers. The abstract deadline for talks is 31/3/2020, while for posters it is 30/6/2020. (The International XAFS Society is affiliated to the IUCR and thus a number of the congress sessions are based on the use of X-ray Absorption Spectroscopy.) Regards Fred Mosselmans Principal Beamline Scientist I20 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7419362123 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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PhD opportunity available at IMDEA Nanociencia/University Autonoma Madrid
by dooshaye.moonshiram 16 Dec '19

16 Dec '19

Dear Colleagues, The time-resolved spectroscopy group and theoretical chemistry group at IMDEA Nanociencia and University Autonoma Madrid, Spain is currently looking for a Ph.D student with intention to apply for by the “la Caixa” fellowship (https://obrasociallacaixa.org/en/investigacion-y-becas/becas-de-la-caixa/do…) Deadline: 4/02/2020. The project will consist in studying solar fuel catalysts through static and ultrafast in-situ X-ray spectroscopy and electrochemistry. The main objectives of the project will be to probe the electronic and structural changes occurring near the active catalytic site through time-resolved X-ray absorption, emission and resonant inelastic scattering spectroscopy. The student will also be trained in Raman, Electron Paramagnetic Resonance, and X-ray photoelecron spectroscopy. Quantum chemistry approaches will be used throughout the project’s duration to determine the geometries of proposed intermediates based on correlation of theory to spectroscopic observables. The results of these studies are expected to have a profound impact on modern catalysis research by identifying the critical requirements for water splitting reactions. For further information, please contact Dooshaye Moonshiram (dooshaye.moonshiram(a)imdea.org) or Antonio Picon (antonio.picon(a)uam.es) Best Regards, -- Dooshaye Moonshiram Group Leader IMDEA Nanociencia Calle Faraday 9, 28049 Madrid, Spain https://moonshiram.wordpress.com/

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Download Demeter in Ubuntu 18.04
by sri tapaswi 13 Dec '19

13 Dec '19

Hello all, Please guide me on the ways to download, install, and run Demeter software such as Athena on linux distribution, Ubuntu 18.04. Thanks, Sri Tapaswi Nori

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Mac installation error "Failed to build demeter"
by Rebecca Goncalves 09 Dec '19

09 Dec '19

Hi all, I'm getting this error message after entering the command "install xorg-server demeter": [image: Screen Shot 2019-12-02 at 9.52.07 AM.png] Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: [image: Screen Shot 2019-12-05 at 8.06.09 AM.png] Thanks, Rebecca

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Mac installation error "Failed to build demeter"
by Fowler, Joseph W. (Assoc) 05 Dec '19

05 Dec '19

Hi Rebecca, I am the macports maintainer of Demeter, and it certainly worked for me when I installed on my desktop Mac. But given your note, I decided to try installing demeter on my Mac laptop. To my surprise, I see the same error that you did. I don’t have a great idea what this signifies. How can ’string.h’ not be found?? If anyone out there can suggest how to fix this problem, I can try to get the macports version fixed. Otherwise, I’m stumped. Joe Fowler On Dec 5, 2019, at 11:36 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Mac installation error "Failed to build demeter" (Rebecca Goncalves) From: Rebecca Goncalves <rbg(a)u.northwestern.edu> Subject: [Ifeffit] Mac installation error "Failed to build demeter" Date: December 5, 2019 at 7:06:53 AM MST To: ifeffit(a)millenia.cars.aps.anl.gov Hi all, I'm getting this error message after entering the command "install xorg-server demeter": <Screen Shot 2019-12-02 at 9.52.07 AM.png> Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: <Screen Shot 2019-12-05 at 8.06.09 AM.png> Thanks, Rebecca _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… Unsubscribe: https://gcc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c…

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Mac installation error "Failed to build demeter"
by Rebecca Goncalves 05 Dec '19

05 Dec '19

Hi all, I'm getting this error message after entering the command "install xorg-server demeter": [image: Screen Shot 2019-12-02 at 9.52.07 AM.png] Has anyone encountered this issue when installing the program on a Mac? This is what the end of the suggested log files reads: [image: Screen Shot 2019-12-05 at 8.06.09 AM.png] Thanks, Rebecca

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Trouble with energy spacing in .nor files Athena
by Berryman, Eleanor (NRCAN/RNCAN) 22 Nov '19

22 Nov '19

I have run into a problem with Athena binning the energies of my imported spectra without being told to. This problem is best explained by example: I am processing XANES data collected around the Cr edge (5989 eV). I load a datafile that has data collected in 5 eV steps from 5789.2 to 5969.2 eV; in 0.5 eV steps from 5969.2 to 6019.2 eV; in 1 eV steps from 6019.2 to 6139.2 eV. In the 'Import Data' popup window (Athena: column selection), the preview of the raw data shows the current energy resolution. The raw data is processed in Athena using column 1 as Energy, column 10 as Numerator, and column 4 as denominator. 'Perform rebinning' is unselected. I save the processed data as norm(E) to produce the attached result, which has data in the following steps: 5 eV steps from 5789.2 to 5969.2 eV; 1 or 1.5 eV steps from 5970.2 to 6018.7; 1 or 2 eV steps from 6020.2 eV to 6138.2 eV. I have used the rebinning feature during import to circumvent this problem. When I rebin, the saved .nor file obeys the rebinned energy spacing. I need to find a better solution than this. I need to find a way for Athena to obey the energy spacing of the imported dataset. Details on my version of Athena: Demeter 0.9.26 Downloaded last week and today. Installation run as user and as administrator. The problem persists even after reinstallation. System details: 64-bit Windows 10 Operating System Thanks in advance for any direction in finding a solution to this problem. Eleanor Berryman, PhD Mineralogist & Geochemist, CanmetMINING Land & Minerals / Natural Resources Canada / Government of Canada eleanor.berryman(a)canada.ca<mailto:eleanor.berryman@canada.ca> / Tel : 613-995-4479 Minéralogiste & Géochimiste, CanmetMINES Secteur des terres et des minéraux / Ressources naturelles Canada / Gouvernement du Canada eleanor.berryman(a)canada.ca<mailto:eleanor.berryman@canada.ca> / Tél : 613-995-4479

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Illinois Tech Synchrotron Radiation Course
by Carlo Segre 22 Nov '19

22 Nov '19

Hello All: Illinois Tech is offering the graduate Introduction to Synchrotron Radiation course once again in Spring 2020. Please see the attached course summary. The course is offered online and it is very straightforward to apply as a non-degree graduate student as late as the second week of classes in January. The online course will be a one (1) credit course instead of the three (3) credits taken by degree-seeking Illinois Tech students. If you are interested or have interested students please contact me for more details on the course or how to apply and register. Cheers, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Directory, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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selection of pixels by criteria
by E. Rasbury 22 Nov '19

22 Nov '19

I have used larch some for XRF maps. I like the feature for defining ROI's and then looking at the statistics of the data. I have some samples that are an intimate mix of two or more phases and I would like to extract pixels based on a criteria- like high Sr or low Fe, etc, from across a whole map region. I wonder if this feature is available, or would be easy to create on larch? Thanks! E. Troy Rasbury Associate Professor Department of Geosciences Stony Brook University Stony Brook NY 11794 631-632-1488

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no plot window with Demeter on Ubuntu 18.04
by Joseph Zsombor-Pindera 21 Nov '19

21 Nov '19

Dear mailing list members; I've successfully built Demeter from source on my computer running Ubuntu 18.04. Running "dathena", for example opens the familiar Athena window. Once I try to plot something, however, I get no plot window. It appears as if the program has done something, but the window just doesn't appear. I have installed gnuplot-x11. running 'gnuplot -e "plot sin(x)"' produces no window, but 'gnuplot -p -e "plot sin(x)"' produces a plot, and if I just run 'plot sin(x)' within gnuplot, then I get the plot, so it appears that gnuplot itself is working correctly. 'show terminal' results in: terminal type is wxt 0 enhanced I have tried changing the terminal to 'wxt' under preferences>gnuplot>terminal in Athena, which didn't fix the problem. I have also tried changing the terminal to 'qt' and installing gnuplot-qt. This didn't work, so I purged it and switched back to gnuplot-x11. I haven't managed to get gnuplot to run with x11 as its default terminal. It seems that the default terminal of gnuplot-x11 is wxt. I'm not sure if these matter, but when I run Athena, I get errors in the terminal like this: (dathena:16207): Gtk-CRITICAL **: 11:55:29.414: gtk_box_gadget_distribute: assertion 'size >= 0' failed in GtkCheckButton thanks, Joseph -- *Joseph Zsombor-Pindera, BSc* PhD Student, UBC Chemistry C

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about WebAoms
by Park Gyuchul 20 Nov '19

20 Nov '19

Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

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Re: [Ifeffit] webatoms for large cluster
by Gentle, Cecilia M 20 Nov '19

20 Nov '19

Hi Gyuchul, Have you tried using Stand Alone Atoms (it comes with the demeter package) instead of webatoms? In my experience, stand alone atoms should not have a problem with 10 angstrom cluster. Hope this helps, Cecilia -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, November 20, 2019 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 201, Issue 11 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. about WebAoms (Park Gyuchul) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Nov 2019 02:27:27 +0000 From: Park Gyuchul <park855(a)purdue.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] about WebAoms Message-ID: <MN2PR22MB209315A18585A0B381D2FEB9934F0(a)MN2PR22MB2093.namprd22.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

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Including MS paths with an aggregate feff calculation in Artemis
by Jamie Hart 15 Nov '19

15 Nov '19

Dear mailing list subscribers, Is it possible to perform an aggregate feff calculation in Artemis, and then perform a fit using multiple scattering paths? It appears that the aggregate feff calculation is able to successfully compute MS paths, but Artemis will not let me include these paths in a fit. I am only able to perform an (aggregate) fit using single scattering paths. Please let me know if there is anything I can do to perform an aggregate fit with MS paths. Thank you, Jamie

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Installation problems for Demeter on Ubuntu 16.04
by Jo Melville 13 Nov '19

13 Nov '19

Hello all, I am having some troubles successfully building Demeter from source on my Linux machine. All dependencies appeared to install correctly -- a few errors pop up upon running ./Build test (full error report attached), but as best I could discern, the errors produced were the same as those reported in this recent message <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html> ( https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html ). Athena appear to install correctly and even start correctly, but upon attempting to import *any* data file into Athena, the following error message pops up (screenshot also attached): > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > BEGIN failed--compilation aborted at (eval 2455) line 1. > Ignoring this message allows Athena to import data correctly at first, but clicking some buttons will consistently and immediately cause the program to close, without even an error message popping up. Actions that will induce a crash range from selecting any Energy value besides 1 in column selection to things as innocuous as clicking Help>Show Tip. As a result, though the program is (barely) usable, it is very unstable and prone to crashing without warning, causing frustrating data loss. I'm sure that this is due to some fault on my part during the installation process, and would welcome any guidance on how best to approach this issue. Thanks, Jo Melville -- Jonathan "Jo" Melville <https://stuff.mit.edu/~melville/> PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-) Contact: (620)-842-8756 *“People think of education as something they can finish.”* *--Isaac Asimov*

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Bug in Artemis
by Natasa Diklic 12 Nov '19

12 Nov '19

Greetings! I encounter an issue for which I find no explanation so far. When I try to export data and fit in k weight 2, the data gets exported in k weight 3 all the time. I can see that Artemis k weight is 2 but Artemis output k weight is 3. Everything was working properly until today. Does anyone knows how to change this Artemis output k weight? Thank you very much in advance! Natasa

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Problem with installation of demeter on MAC (Catalina v10.15)-Can't locate Demeter/Here.pm
by wei zhang 08 Nov '19

08 Nov '19

After installation of both xorg-server and demeter, when I launch Athena, the problem is as follows: Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7. So, what should I do to solve this problem? Thank you all! Wei Zhang

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Solved concatenation bug Arrays.pm line 115
by FonsPaul 06 Nov '19

06 Nov '19

I wanted to update the mailing list on my encounter with a concatenation bug. I discovered that the cause was having (Japanese) Chinese characters in the pathname. Moving the folder solved the problem. Paul Fons

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Athena problem on MacOS 10.15
by FonsPaul 05 Nov '19

05 Nov '19

Hi All, I am using demeter on Mac OS 10.15 (the latest release) and am encountering some problems that I was hoping could be cleared up, in particular with Athena. The Athena version is 0.9.25, the latest version from MacPorts. Athena starts and properly plots existing projects without trouble, but trying to open a new data set using the PFBL12C plug in. From the Perl error messages below, it appears that the underlying cause is not from the Plugin, but from some problem within Demeter, with an uninitialized values in particular at line 115 that starts with the “my $text” assignment. Any ideas on what could be going wrong or what other debugging information might be useful. Paul Fons Arrays.pm sub get_array { my ($self, $suffix, $part) = @_; $part ||= q{}; if (not $self->plottable) { my $class = ref $self; croak("Demeter: $class objects have no arrays associated with them and are not plottable"); }; my $group = $self->group; my $text = ($part =~ m{(?:bkg|fit|res|run)}) ? "${group}_$part.$suffix" : "$group.$suffix"; my @array = $self->fetch_array($text); return @array; }; Perl error messages: 16:07:51: Use of uninitialized value $suffix in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Arrays.pm line 115. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 231. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 232. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 234. Fragment of example data set causing trouble 9809 SPring-8 01b1 GeTe_reference 19.10.31 11:20 - 19.10.31 11:22 Te standard Ring : 8.0 GeV 99.5 mA - 99.5 mA Mono : SI(311) D= 1.63747 A Initial angle= 7.06039 deg 01b1 Transmission( 2) Repetition= 1 Points= 4798 Param file : angle axis (1) Block = 1 Block Init-ang final-ang Step/deg Time/s Num 1 7.00000 6.52000 -0.000100 0.03 4798 Ortec( 0) NDCH = 4 Angle(c) Angle(o) time/s 2 3 4 Mode 0 0 1 2 1 Offset 0 0 49961.200 49083.900 1124.500 6.99980 7.00417 0.025 121003 450174 6.99970 7.00407 0.025 120103 447134 6.99960 7.00398 0.025 120212 447353 6.99950 7.00388 0.025 120465 448618 6.99940 7.00379 0.025 121167 450721 6.99930 7.00370 0.025 120510 448136 6.99920 7.00361 0.025 120907 450140 6.99910 7.00352 0.025 120063 446166 6.99900 7.00343 0.025 120656 449360 6.99890 7.00335 0.025 120901 450062 6.99880 7.00326 0.025 120820 449932 6.99870 7.00317 0.025 120655 448835 6.99860 7.00308 0.025 120869 449502 6.99850 7.00299 0.025 120818 449723 6.99840 7.00290 0.025 121239 450978 6.99830 7.00280 0.025 120744 449404

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