October 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

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

1 0

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/

1 0

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

2 1

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

2 1

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

1 0

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

3 2

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.

3 3

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

2 2

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

2 1