February 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

Cu K edge XANES stds
by Simon James 03 Mar '19

03 Mar '19

Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC

2 2

Larch 0.9.42
by Matt Newville 26 Feb '19

26 Feb '19

Hi Folks, Larch 0.9.42 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html Version 0.9.42 fixes many problems, especially to the XAS Viewer GUI app which is now pretty close to a replacement for Athena but with better peak-fitting and with none of the limitations that were imposed by the outdated ifeffit library. For MacOSX, Version 0.9.42 can be installed with a standard Mac "pkg" installer file. If you have already installed Larch, you should be able to update to the latest version with conda update -c gsecars xraylarch on Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can also simply remove the XrayLarch installation and reinstall using one the installers above. For Python programmers, Version 0.9.42 ends support for Python 2. No testing or packaging was done with Python 2 for this release, and going forward the master development branch will not work with Python 2. Please let us know if you having any questions, trouble, or suggestions. --Matt Newville

1 0

Problem with using lincomb_fit function in the Larch
by Tayal, Akhil 26 Feb '19

26 Feb '19

Hello Matt, I could not be able to perform LCA using the lincomb_fit function in the Larch software. I am getting the error message from line number 80 in the lincombo_fitting.py script. I expect the function has some bug with reading the group values. It could not be even able to read the default array 'norm' nither any user-provided 'arrayname' such as 'flat or fpp.' Can you suggest any solution for it? Please find the data files and larch script I am using for this purpose. Thanks, Akhil

2 1

Does anyone have XAS from Cu(I)-GSH and/or Cu(I)-cys
by Simon James 25 Feb '19

25 Feb '19

Hi mailing list, I am hoping someone can help me sanity check some XAS spectra I recorded. I have [Cu(I)cys], [Cu(I)GSH] spectra (recorded in fluorescence) and would be eternally grateful if anyone is prepared to share any of their data on these or similar compounds? I am really only interested in the edge but more data is always more data. Happy to discuss offline if preferred. Happy XAS'ing Best regards, Simon Simon James Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Office: +61 (3) 9035 6420 Mob: +61 (4) 3811 0982 Web: www.florey.edu.au<http://www.florey.edu.au> simon.james(a)florey.edu.au<mailto:simon.james@florey.edu.au>

1 0

Hafnia standards
by Mukundan, Vineetha 21 Feb '19

21 Feb '19

Hi All, I am new to EXAFS data analysis and am working on Hafnia based dielectrics. So far, I have not measured reference standards of hafnia. I know my samples have monoclinic and orthorhombic phases. If anyone on this mailing list have these standards and don't mind sharing, please email me. Alternatively if there are ways to generate/simulate it (perhaps using FEFF and the corresponding .cif files), please let me know. Thank you, Vineetha

1 0

XANES convolution method in FEFF9
by Ying Liu 20 Feb '19

20 Feb '19

Dear all. I am currently running FEFF9 on XANES calculation. However I could not figure out how FEFF transformed LDOS to the final xmu.dat. What function did LDOS data convoluted with to achieve xmu.dat? Looking forward to hearing any answer. Thank you. Ying Queen Mary University of London

2 1

Re: [Ifeffit] questions: EXAFS
by Robert Gordon 20 Feb '19

20 Feb '19

Hi Vineetha, I advised during the course that students should use the ifeffit mailing list for questions post-school. An advantage of doing so is that one could receive assistance from any member of the community and not be at the mercy of the time constraints of any particular researcher. Another advantage is that someone more familiar with the type of problem you are studying might be able to offer more insight. I would like again to encourage you to make use of the mailing list. Other researchers may also see the problem with which you are dealing and it could help them too. Some general advice: Mixed phase samples can be problematic. If you know which two phases are present, you can simulate them separately and examine the local environments. If the near-neighbour environments are very similar, then some fitting can be done with reasonable results. You still need to keep in mind the resolution criteria for being able to resolve closely spaced paths. Looking at your O-scattering paths, not having seen your k-space data and range, I suspect you will not be able to resolve the splitting in the first shell, and so, would treat it as a single path (similar argument for Hf paths in 2nd shell). The starting model serves to give you amplitudes and phases for fitting. In that regard, whether you use monoclinic or orthorhombic starting model should not matter. Once fit, you would examine how well the fit result compares to either model. I would hope you also measured standard(s) of known composition and structure. Fitting such would help guide the fitting of your unknown. Model calculations can be done for your two suspected phases, including temperature effects with the DEBYE card in the FEFF input. A quick google search yielded this paper: https://ceramics.onlinelibrary.wiley.com/doi/abs/10.1111/j.1151-2916.1977.t… which gives a calculated Debye temp of 484K for monoclinic HfO2. You can check the literature further for other research on this material which may give an experimental value. With the model chi(k)'s, you can do linear combinations (manually) and see if you find some ratio that approaches agreement with your data. I don't see how to get the model chi(k) out of Artemis though. I even tried running the feff6 executable manually (with associated dll's) but it did not generate the chi.dat file I was expecting. I would suggest, if you wish to generate models and compare in this fashion, that you invest in a newer version of FEFF that does allow you to generate this output (i.e. get FEFF9). Other thoughts: XANES? Did you measure it for the unknown and standards? If so, are the two phases distinguishable? Background removal? Can you improve it to reduce the amplitude below 1 Angstrom? Always show the original data (merged ok), not simply the transforms when asking for help. That helps one assess the problem better. regards, Robert On 2019-02-19 9:43 a.m., Mukundan, Vineetha wrote: > > Hi Dr. Gordon, > > I am Vineetha and had met you at the EXAFS short course @ BNL in > November’18. I am trying to analyze a couple of my data on Hafnia and > am stuck. So I am seeking help with the following questions. Apology > in advance if it will some of your time. > > 1.I generated the scattering paths. See attached. It is safe to > discard the multiple scattering paths here. So I generated the plots > with Hf-O single scattering paths and Hf-Hf scattering paths. Clearly > it shows the first shell is mostly one or all of O1.1, O2.1 and O2.3 > paths. And the second shell is mostly influenced by Hf1.2, Hf1.3 and > Hf1.5. Am I correct in making this assumptions so far? IS there any > other way to figure out which paths are important or not important, > other than plotting them together with the data. > > 2.While fitting, I am really unsure how to set the parameters for each > path in my example. I am not sure how to set up the parameter when we > have multiple paths contributing to say first shell or second shell. > Also, I know using the Nyquist equation it is possible to figure out > the number of independent variables. I read up the ARTEMIS pages on > FeS2 example described but there the structure is cubic but my sample > is monoclinic. Here I am trying to fit only the monoclinic paths with > my data. > > 3.Also, I know my sample has monoclinic and orthorhombic structure. So > how does one go about generating the simulated EXAFS for a particular > structure on FEFF? say in my case the monoclinic and orthorhombic > ones. I have the .cif files for these 2. For figuring out the % amount > of monoclinic and orthorhombic phases in the sample, I am assuming I > will have to do a linear combination analysis. Am I correct? > > Any help in this regard will be really useful. > > Thank you, > > Vineetha > > *Vineetha Mukundan, PhD* > > Post-doc, Prof. Diebold’s Group > > Colleges of Nanoscale Science and Engineering > > SUNY Polytechnic Institute > > 257, Fuller Road > > Albany, NY 12203 USA > > CONFIDENTIALITY NOTICE > > The pages (including attachments) comprising this internet or > facsimile transmission contain CONFIDENTIAL information. This > information is intended for the sole and exclusive use by the > individual entity named as the recipient hereof and any further > disclosure or dissemination is prohibited. If you are not the > intended recipient, you are hereby notified that any disclosure, > copying, storage, distribution, or use of the contents of this > transmission is strictly prohibited and may be unlawful. If you have > received this transmission in error, please notify us immediately by > telephone or return e-mail, delete it from your mail system, and > destroy all copies in your possession. Thank you. >

1 0

FEFF9 calculations of Tellurium Clusters
by Gentle, Cecilia M 14 Feb '19

14 Feb '19

Dear IFEFFIT Mailing List, I am running FEFF calculations using FEFF9. I am running these calculations on my department's cluster in parallel using a Linux machine Currently, I have run XANES calculations of CdTe and ZnTe at the K-edges of Zn, Cd and Te. I am calculating the XANES of various cluster sizes. I start with a cluster with a single coordination shell and build up to 7 coordination shells, running a XANES calculation with each cluster size. I have run these calculations for the K-edges of Cd, Te, and Zn. Unexpectedly, I receive an error for the Te K-Edge XANES calculation of ZnTe and CdTe for the cluster size of 2 coordination shells. The FEFF calculations run fine for a cluster with a single coordination shell and for clusters with 3 to 7 coordination shells. This is my first experience running FEFF. I have read through the FEFF manual, but I am having trouble interpreting the error message. I have the FEFF input file for Te K-Edge of a CdTe cluster with 2 coordination shells, and the resulting error message attached as a text files. Has anyone else experienced this before? If someone can point me to a section in the manual or another resource to help me understand the error, I would very much appreciate it. Thank you, Cecilia Gentle PhD Candidate University of Illinois

1 0

EXAFS of solid-solution alloy
by Chongchong Mellon 08 Feb '19

08 Feb '19

Hi all, I have some problems in analyzing the EXAFS of solid-solution alloy, let us define as A0.5B0.5. I have searched the mailbox but cannot find similar discussion yet. So I post the question here and hope to get some suggestion from you. 1. A and B are immiscible metals from the phase diagram, which means that I couldn’t get the bulk A0.5B0.5 as a standard reference. In this case, how can I estimate the amp for the K-edge of A or B? 2. A and B are very near (atomic number B-A = 2) in the periodic table. So their lattice parameters are quite close to each other. In this case, when I tried to fit the 1st shell use A-A and A-B paths at the same time, the Happiness parameter becomes worse and the coordination number of A-B is not realistic (large errors!). If I fit with only the A-A path or A-B path, I get a good fit. However, atomic resolution STEM-EDX maps show the homogenous distribution of both A and B atoms. The A-A and A-B bond might have an equal ratio. In this case, how can I do the fitting? Thank you very much in advance! Sincerely, Chong

3 2