June 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.) >

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EXAFS from FEFF9 in ARTEMIS (ver 0.9.26)
by Manju 21 Jun '19

21 Jun '19

Hi I am analyzing my data in ARTEMIS (ver 0.9.26). I used the Rietveld refined parameters of XRD data into ATOMS interface and used that for path calculation. But the paths were not at same distances as indicated by .CIF file (in Vesta). I am having FEFF9 with me. So, I want to run EXAFS in FEFF9 and import the paths in ARTEMIS for fitting. Is it possible? Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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Multiple species with Artemis
by Mukundan, Vineetha 17 Jun '19

17 Jun '19

Hi All, A couple of questions. I was searching the previous threads to check if someone here had posted/explained an example with mixing parameters to find the % content of different constituents present in a sample with Artemis. This is for shell-by-shell fitting. Can Artemis fit multiple chemical species/phases to the experimental spectra simultaneously? OR fit the samples spectra measured at 2 different edges with one or two phase simultaneously? Don't know if I searched far enough. Apology if it has been discussed. In that case, could anyone please direct me to those threads. Thanks you, Vineetha

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Re: [Ifeffit] Ifeffit Digest, Vol 196, Issue 1
by Mahima Makkar 17 Jun '19

17 Jun '19

Dear Sir, This mail is regarding the quotation that you have sent. Please change the address to Prof. Ranjani Viswanatha ICMS JNCASR, Jakkur PO 560064 Bangalore, INDIA. Mail id: rv(a)jncasr.ac.in Please refer the mail id as mentioned above and resend the quotation. Thanks and regards, Mahima On Thu, Jun 13, 2019 at 10:30 PM <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. Problem with Demeter installation on mac OS Mojave (Ga?lle Creff) > 2. Re: Problem with Demeter installation on mac OS Mojave > (Ravel, Bruce) > 3. Re: Problem with Demeter installation on mac OS Mojave > (Ga?lle Creff) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Jun 2019 22:52:54 +0200 > From: Ga?lle Creff <gaelle.creff(a)unice.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Problem with Demeter installation on mac OS Mojave > Message-ID: <D0FD0963-0C63-4B93-9E99-E56654370D21(a)unice.fr> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > I have some troubles with the installation of Demeter on my mac (under OS > Mojave since this week end). > Athena crashed after the following message: > "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. ? > > Artemis does not work either. > > Can someone help me? > > Thanks a lot. > Ga?lle > >

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Problem with Demeter installation on mac OS Mojave
by Gaëlle Creff 13 Jun '19

13 Jun '19

Hi everyone, I have some troubles with the installation of Demeter on my mac (under OS Mojave since this week end). Athena crashed after the following message: "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. » Artemis does not work either. Can someone help me? Thanks a lot. Gaëlle

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