December 2019 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > 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/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

5 7

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

1 0

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

1 0

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 --------------------------------------------------------------------

2 1

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

1 0

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/

1 0

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

3 4

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

1 0

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…

1 0

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

1 0