November 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

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

2 1

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

1 0

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

4 4

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

2 1

about WebAoms
by Park Gyuchul 21 Nov '19

21 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

3 4

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

1 0

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

1 0

Installation problems for Demeter on Ubuntu 16.04
by Jo Melville 14 Nov '19

14 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*

2 2

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

2 1