October 2017 - 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 short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, 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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E0 in Co3O4
by Jesús Eduardo Vega Castillo 30 Oct '17

30 Oct '17

Dear list, I enclose an Athena project with a XAFS spectrum of Co3O4 with a metallic Co reference. Athena by default has chosen E0 at the absolute maximun of the derivative curve (at 7727.8eV) which in my opinion is too high because it is at the white line zone. I believe that E0 should be the previous maximun in the derivative at around 7722eV, which would be at the rising edge. Am I wrong? I would appreciate some help with the criterion to determine the right value. Yours, Jesús

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Re: [Ifeffit] iron carbide fitting with Artemis
by fred.mosselmans＠diamond.ac.uk 28 Oct '17

28 Oct '17

Dear Yunyun, I don't think Mike has written anything particularly incorrect , but he didn't point out why this approach is necessary. I believe there are two things you should definitely be aware of. An EXAFS dataset has a very limited amount of information. Approximately deltak.deltaR no of variables can be fitted To any spectrum as an absolute maximum and preferably quite a lot fewer than this (where deltak and deltaR are your fitted data range in k and R space respectively. Because of this if say you know you have N C atoms at ca G angstroms around your central atom. It is best not to use a variable for fit the degeneracy for that path but set it at the number you know is correct. And secondly because an EXAFS spectrum is effectively a collection of Sine waves there is a limited resolution, i.e. you cannot resolve paths of the same atom type that are less then Pi/2k(max) A apart, where k(max) is the maximum range of your dataset in k space, and Pi is Pi. Hence to separate two paths of the same atom that are 0.1 A apart you need about 15k worth of data. Regards Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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iron carbide fitting with Artemis
by Yunyun Zhou 28 Oct '17

28 Oct '17

Hello All, I am having trouble fitting my sample with both Fe5C2 and Fe3O4 as standards. Hopefully somebody could help me out and I really appreciate it. My iron sample was mainly iron carbide in the core and iron oxide on the shell. Fe5C2 has a monoclinic structure and generated complicated FEFF paths. Many of the paths have similar distances. I have found some paper reported their results as follows, which apparently combined several paths together and assume they have similar path length. My first question is does someone know how they did it? It seems that combing similar paths makes fitting much easier, but I am not sure whether this is a correct way to do the fitting. My second question is regarding fitting with the two combined models of Fe5C2 and Fe3O4. I haven't fit with two models before. Is it just like what I did in the attached Artemis file? Shall there be any restrictions between the two models and do I have to fix some of the parameters? Thank you very much in advance for your help! Best, Yunyun Zhou Fe5C2 FEff paths: [image: Inline image 1] Literature reported results: [image: Inline image 2]

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monoclinic elemental selenium data
by George Sterbinsky 26 Oct '17

26 Oct '17

Hello, I am trying to help someone locate XAFS data collected from the red allotrope (monoclinic) of elemental selenium. Does anyone have a data set they are willing to share? Thank you, George

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flattened norm export issues
by Robert Gordon 22 Oct '17

22 Oct '17

Hi, Encountered a difference on export of normalised data. Flattening does not seem to be preserved when saving current group as norm(E) but is when saving marked group. Example in norm.prj attached. original data set normalised and flattened...displaying "Normalized" as current group or as marked group looks the same: current: marked: On saving current or marked group as norm(E), re-importing and plotting as mu(E) marked is still flattened, but the set exported using "save current group as" is not flattened. Similar difference saving "marked" versus saving "each marked" So it seems only "Save marked group as..." preserves flattening for norm(E). -R.

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space group 224 & Atoms
by Robert Gordon 22 Oct '17

22 Oct '17

Hi, I was trying to simulate Cu2O...cubic...O tetrahedrally coordinated by Cu...Cu linearly coordinated by O. There are two origin choices for space group 224 (Pn-3m). If using origin choice 1, then atom positions would be O 0,0,0 Cu 0.25,0.25,0.25 If using origin choice 2, translate by -0.25,-0.25,-0.25 to get O 0.75,0.75,0.75 Cu 0,0,0 (or use the shift vector in Atoms...) My understanding is that Demeter defaults to the 2nd origin choice. Problem I am having is that neither gives me linearly coordinated copper using current Atoms. If I read in the attached atoms.inp (choice 2) and Run Atoms, the ATOMS list in the Feff output begins with: ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 cu1 0.00000 -1.06675 1.06675 1.06675 2 o1.1 1.84767 -1.06675 -1.06675 1.06675 2 o1.1 1.84767 1.06675 1.06675 -1.06675 2 o1.1 1.84767 -1.06675 -1.06675 -1.06675 2 o1.1 1.84767 2.13350 2.13350 0.00000 1 cu1.1 3.01722 I get 4-coordinate instead of 2-coordinate. If I try origin choice 1, almost the same result.... ATOMS * this list contains 83 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 cu1 0.00000 -1.06675 1.06675 1.06675 2 o1.1 1.84767 1.06675 -1.06675 1.06675 2 o1.1 1.84767 1.06675 1.06675 -1.06675 2 o1.1 1.84767 -1.06675 -1.06675 -1.06675 2 o1.1 1.84767 2.13350 2.13350 0.00000 1 cu1.1 3.01722 If I run choice 1 with the shift vector, I do reproduce the choice 2 result. If I use the old dos version of Atoms with origin choice 2, I do get linearly coordinated copper: ATOMS .00000 .00000 .00000 0 cu1 .00000 -1.06675 -1.06675 -1.06675 1 o1 1.84767 1.06675 1.06675 1.06675 1 o1 1.84767 .00000 -2.13350 2.13350 2 cu1 3.01722 SPECS: Demeter 0.9.26 (pre2) Win10x64 AMD64 -R.

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