December 2018 - 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.) >

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regarding installation
by mona gupta 23 Dec '18

23 Dec '18

respected sir/ma'amwhenever I use Athena / Hephaestus on the time of plotting derivatives ..its hangs and after some time it shows per interpreter is not responding,,, so it is not working properly, even I am puzzled.please give me quick reply facing such problem ..even reinstalled it.RegardsMrs Mona GuptaAssistant ProfessorDepartment of PhysicsGovt PG College KotdwarH N B Garhwal UniversityUttarakhand (India)

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Looking of a K-edge spectrum of maghemite
by Lorenzo Stievano 17 Dec '18

17 Dec '18

Hi everybody, daes anybody have in his repository a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3)? I would need it as a reference material in a study on doped iron oxides. Thanks a lot in advance! Lorenzo

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Question about k-weighting real-world practice and outcomes
by John Ferre 16 Dec '18

16 Dec '18

Dear EXAFS folk, I'm a graduate student in Jerry Seidler's group at the University of Washington, Seattle. I've been doing a numerical and experimental study on how to optimize k-weighting for EXAFS when the total experimental measurement time for a study is constrained, i.e., when you have 1 hour at some given I0 flux and your job is to get the best results, in terms of best fits or cleanest g(R). Can anyone aim me at 'famous' papers (or at least 'standard' papers) on the best use of k-weighting? Also, it would be great if people could informally email me how they, personally, do k-weighting and what their personal experience has been. My email is jbferre(a)uw.edu. Much appreciated! John

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Re: [Ifeffit] Ifeffit Digest, Vol 190, Issue 9
by Christopher Chantler 15 Dec '18

15 Dec '18

Some of our papers explain how to avoid k-weighting and use the actual measured uncertainties to define a fit. Other papers by our group explain that a proper k-weighting would scale the value and the uncertainty by the same amount, so that the net fit should be unaffected. Otherwise this is more like a change of the effective k-range over the fit. -------------------------------------------------------------------------------------- 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: Sunday, 16 December 2018 5:00:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 190, Issue 9 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. Question about k-weighting real-world practice and outcomes (John Ferre) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Dec 2018 17:53:41 -0800 From: John Ferre <jbferre(a)uw.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Question about k-weighting real-world practice and outcomes Message-ID: <CAN2QkxtgJYJsep0BHk3qKgqXu4nhcg-4GRBok_6c3SNfo1-jvA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear EXAFS folk, I'm a graduate student in Jerry Seidler's group at the University of Washington, Seattle. I've been doing a numerical and experimental study on how to optimize k-weighting for EXAFS when the total experimental measurement time for a study is constrained, i.e., when you have 1 hour at some given I0 flux and your job is to get the best results, in terms of best fits or cleanest g(R). Can anyone aim me at 'famous' papers (or at least 'standard' papers) on the best use of k-weighting? Also, it would be great if people could informally email me how they, personally, do k-weighting and what their personal experience has been. My email is jbferre(a)uw.edu. Much appreciated! John

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Sn 2+
by Ditty Dixon 14 Dec '18

14 Dec '18

Dear All, Could someone please share Sn K edge spectra of any Sn(II) sample measured along with Sn metal foil. SnCl2 from Hephaestus seems miss-aligned and Farrel Lytle has only L edge data, Thank you, -- Dr. Ditty Dixon Ramanujan Faculty Electrochemical Power Source Division Central Electrochemical Research Institute (CSIR-CECRI) Karaikudi, India, 630003 Ph:00919400243084

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Mac user
by Wallick, Rachel 12 Dec '18

12 Dec '18

I am trying to install on my Mac (running on Sierra Version 10.12.6), and I followed the instructions to install but when I type in the command “sudo port install xors-server demeter” I get an error that says “command not found.” Has anyone else had this issue? Is there a way to install? Rachel Wallick

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Artemis hung up on importing fpj containing VPaths
by Nicholas Marcella 10 Dec '18

10 Dec '18

Hi All, I'm trying to import an Artemis project that contains VPaths. The import stalls on the "importing VPaths" step. There is no error. The program crashes when I click on the GUI. I tried to recreate this issue and found that the following steps do so: Note: Step 5 is critical. If a fit is not run within the project file, the VPaths are loaded successfully. To recreate: 1) Import FEFF calculation and some data set. 2) Add some number of paths to the data set 3) Mark all paths and Alt+shift+m 4) transfer VPath to plotting list. Plot. 5) Run a basic fit. 6) save and close. Exit Artemis. 7) Open Artemis, try to import the project. p.s. I tried deleting %APPDATA% and doing a reinstall. As for a quick solution: is there anyway I can skip importing VPaths when loading my project file? Thanks! Nick -- *Nicholas J. Marcella* | PhD Student *Materials Science and Chemical Engineering* *Stony Brook University* *Tel: (914)-703-9843* *Structure and Dynamics of Applied Nanomaterials | Brookhaven National Lab <https://www.bnl.gov/chemistry/SDAN/>* *Senator - MSCE | Graduate Student Organization <http://sbgso.org/index.php/about-us/senators>*

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LARCH installation issue in UBUNTU 18
by Uma Mahendra Kumar K 09 Dec '18

09 Dec '18

Dear All, I wanted to install LARCH on Ubuntu 18. And I could not. I have tried several methods (miniconda, Anaconda, from source and the Linux Binaries and even through pip). For several issues , I found answers in Ifeffit mailing list. This is new. lmfit is not able to import 'ufloat'. Actually "ufloat" belongs to "uncertainties". I could not able to link(port) them properly. I need your help to install Larch. the following is the error message Traceback (most recent call last): File "/usr/local/bin/larch", line 58, in <module> import larch File "/root/.local/lib/python2.7/site-packages/larch/__init__.py", line 25, in <module> from .shell import shell File "/root/.local/lib/python2.7/site-packages/larch/shell.py", line 10, in <module> from .interpreter import Interpreter File "/root/.local/lib/python2.7/site-packages/larch/interpreter.py", line 18, in <module> from . import builtins File "/root/.local/lib/python2.7/site-packages/larch/builtins.py", line 22, in <module> from . import fitting File "/root/.local/lib/python2.7/site-packages/larch/fitting/__init__.py", line 20, in <module> from lmfit import (Parameter, Parameters, Minimizer, conf_interval, ImportError: cannot import name ufloat Mahendra Asst Prof of Physics VIT university -Bharat.

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XRS workshop 2019
by Christoph Sahle 09 Dec '18

09 Dec '18

Dear Colleagues, We cordially invite you to attend the Workshop entitled “X-ray Raman scattering spectroscopy - Probing low Z elements using hard X-rays” that will be hosted at the ESRF (Grenoble, France) from 3 to 5 April 2019. Aim and Scope of the workshop: Non-resonant inelastic X-ray scattering from core-electrons, or X-ray Raman scattering (XRS) spectroscopy, is an increasingly popular spectroscopic tool to investigate low energy absorption edges using hard X-rays. The aim of the proposed workshop is to bring together experts and novices in the field of XRS spectroscopy. We will assess and discuss the current status, potential, and future prospects for this emerging inelastic x-ray scattering technique. The interest in XRS is rapidly growing and new end-stations are being designed at 3rd generation synchrotron light sources around the world. The focus of this workshop will be to strengthen the user community, define future research directions and guide the worldwide efforts to build new dedicated end-stations for X-ray Raman scattering spectroscopy. The workshop will consist of contributed talks with ample time reserved for questions and discussion as well as a poster session. The workshop is open to all interested parties, but the number of participants will be limited to approximately 50. The workshop will be divided into 6 sessions: Instrumentation Low-Z elements under extreme conditions Soft condensed matter, statistical systems Correlated electron systems Direct tomography imaging Theoretical approaches You can find more information about this event on the web page (including a link to the registration) [http://www.esrf.fr/xrs-workshop] Kind regards, Ch. Sahle, C. Roméro, G. Lelong, J.-P. Rueff

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