August 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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Fwd: 64-bit Demeter not able to use on Windows computer
by Ravel, Bruce 28 Aug '19

28 Aug '19

Brittany, In your first post to the mailing list, you said you could not get the software to run on "a Windows computer". That you are looking for a 32 bit installer seems like extremely relevant information. I no longer have the capacity to build 32 bit versions of the installer, but I keep links to old versions available on the Demeter website. http://bruceravel.github.io/demeter/#old The most recent version for which a 32 bit installer exists is 0.9.25. Somewhat dated, but should still be useful. B PS: Please send email to the mailing list ifeffit(a)millenia.cars.aps.anl.gov and please do not send email directly to ifeffit-owner. Matt and I are the only ones who read mail sent to ifeffit-owner and we don't guarantee a response to email sent to that address. -------- Forwarded Message -------- Subject: 64-bit Demeter not able to use on Windows computer Date: Wed, 28 Aug 2019 09:10:17 -0400 From: Brittaney Courchesne <bcourchesne(a)laurentian.ca> To: ifeffit-owner(a)millenia.cars.aps.anl.gov Hi everyone, The 64-bit version of Demeter is not able to be used on my Windows computer I have, since it is a 32-bit version. Is there a way around this or does someone have the 32-bit version they can email me? I have tried disabling my firewall completely and trying to "allow" the programs through the firewall, and running as an administrator, but the 64-bit just doesn't seem to work. Thank you, Brittaney -- */Brittaney Courchesne, G.I.T./* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON /bcourchesne(a)laurentian.ca <mailto:bcourchesne@laurentian.ca>/ -- 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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QFS fit for Am
by Daria Boglaienko 22 Aug '19

22 Aug '19

Hello, I have tried quick first shell fit for various compounds, but it does not work for Am. It does run fit for organic compound of Eu but it does not run fit for similar organic compound of Am. Please, let me know if there is something I can take into account. Thank you -Daria

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Unable to use 64-bit Demeter on Windows computer
by Brittaney Courchesne 21 Aug '19

21 Aug '19

Hello, I am just sending this email to see if anyone has encountered the following problem: I downloaded the newest 64-bit version of Demeter on my Windows computer, and it downloaded successfully, but now when I double click on the program, a tiny window pops up for about 0.5 seconds and then disappears. I have tried redownloading twice. Thank you very much, Brittaney -- *Brittaney Courchesne, G.I.T.* MSc Geology Candidate Harquail School of Earth Sciences Laurentian University Sudbury, ON *bcourchesne(a)laurentian.ca <bcourchesne(a)laurentian.ca>*

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Two analysts, one spectrum, similar outcome?
by Mike Massey 14 Aug '19

14 Aug '19

Hi Everyone, I'm curious, has anyone ever tried turning two analysts loose on the same unknown EXAFS spectrum to see if their fits come out with similar conclusions? If you have tried it, how did it work out? Were the conclusions indeed similar? If not, why not, and what did you end up doing about it? I was talking with a colleague today about our plans for data analysis, and we settled on this approach (since there are two interested parties willing to try to fit a series of unknown EXAFS datasets). The hope is, of course, that the two analysts will independently reach similar conclusions with similar fits and structural models, but to my mind that outcome is by no means guaranteed. Given the (presumably) wide variation in fitting customs and procedures, I can envision a scenario in which there are major differences. This got me wondering, "Has anyone tried this?" So I thought I'd ask. Your thoughts and experiences would be welcome. Thanks! Mike Massey

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Installation of Demeter on Mac Issue
by Lyu, Yimeng 12 Aug '19

12 Aug '19

Hello everyone, I run into to some issues with installing Demeter to a Mac. After installation, warning messages as below show up. Sometimes Athena will quit and sometimes it opens and works just fine. I searched the email archives and apparently the solution is to replace the Template.pm with an older version file. However, I cannot download the attachment from the email thread http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009382.html , as the attachment was encrypted. Can someone send me the Template.pm file so I can resolve this issue? Thanks in advance. —Yimeng 16:21:44: 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. 16:21:44: 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. 16:21:44: 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. 16:21:44: 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. 16:21:44: 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. 16:21:44: 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.

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PhD opportunities
by Silvia Ramos 12 Aug '19

12 Aug '19

Dear All, I would like to share information about two funded PhD positions to work on Frustrated Magnetic Materials at the University of Kent, in the United Kingdom (https://www.kent.ac.uk/scholarships/search/FN26EXPHYS02) One of them (with me) is to work on the determination of local structure. I thought it might be of interest to this community. I will be happy to answer any queries from interested candidates. Best regards, Silvia Ramos ============================ Dr. Silvia Ramos Senior Lecturer in Materials Physics Director of Graduate Studies Ingram 230b School of Physical Sciences University of Kent Canterbury CT2 7NH U.K. Phone: (0)1227 816023 e-mail: s.ramos-perez(a)kent.ac.uk<mailto:s.ramos-perez@kent.ac.uk>

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XAFS short course in BNL Nov. 13-15
by Anatoly Frenkel 01 Aug '19

01 Aug '19

Dear subscribers: The info about the XAFS2019 short course at BNL is here: https://www.bnl.gov/xafs2019/ The application page is open. Best, Anatoly ------------------------------------------------------------------- Anatoly I. 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 -------------------------------------------------------------------

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