January 2020 - 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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XAFS.ORG WEBSITE??
by Bare, Simon R 30 Jan '20

30 Jan '20

Talking of websites does anyone know what happened to the International XAFS website? I can't access it. And what is going on with this organization? Thanks. Simon

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what happened to the website?
by Matthew Marcus 30 Jan '20

30 Jan '20

The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, which means that WebAtoms doesn't work anymore. Is there a replacement? Of course, I can use the stand-alone Atoms in Demeter. -- Sincerely, Matthew Marcus

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color of fonts in demeter
by Ricardo Faccio 29 Jan '20

29 Jan '20

Dear all After installing Demeter in MacOS I am having some problems related to the color of fonts and background. Since they look identical is diffcult to see and read. How could be possible to change the color of fonts? I am attaching an example. 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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Fw: Re: request help about Zn standard spectra
by Qiang Chang 27 Jan '20

27 Jan '20

Dear Mauro, Thank you so much for your kind and quick help. Best reards, Qiang From: Mauro Rovezzi Date: 2020-01-27 09:45 To: ifeffit Subject: Re: [Ifeffit] request help about Zn standard spectra Dear Qiang, Here some Zn K-edge spectra from the SSHADE/FAME database: https://www.sshade.eu/search?db=fame&query=%22Zn%20K%20edge%22 Best regards, Mauro On 2020-01-26 21:06, Qiang Chang wrote: > Hi all, > > May I ask if you have some standard spectra for Zn elements, like > metallic Zn, ZnO, ZnNx, etc. I am vey appreciative if you could send me > some copies. > > Thank you very much. > > Best regards, > Qiang > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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request help about Zn standard spectra
by Qiang Chang 27 Jan '20

27 Jan '20

Hi all, May I ask if you have some standard spectra for Zn elements, like metallic Zn, ZnO, ZnNx, etc. I am vey appreciative if you could send me some copies. Thank you very much. Best regards, Qiang

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interesting job posting at NSLS-II
by Ravel, Bruce 26 Jan '20

26 Jan '20

Hi all, A colleague of mine here at NSLS-II has an interesting post-doc position open right now. https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-in-total-sca… This position is for a person doing total scattering (aka PDF). Strictly speaking, not an XAS position, but perhaps of interest to someone with an XAS background who is looking for a post-doc. Regards, Bruce -- 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/

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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 23 Jan '20

23 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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