August 2018 - 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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XANES simulation
by Motta Meira, Debora 30 Aug '18

30 Aug '18

Good morning everyone, I'm trying to simulate XANES spectra for a material used for batteries. In the Figure, my experimental data are the blue (pristine material) and the red (charged state) curves. When I apply my EXAFS results to the original structure, to simulate using Feff, (I contracted the distances proportionally to what I found in the EXAFS fit) the XANES shifts accordantly, as you can see in the green and purple curves. However, the intensity is completely different. To fix this I changed S02 to 0.4. Additionally, I also correct the vr0 (found a value of -8.4) and I'm using Rpath = 5. The simulation using these parameters is the yellow curve. My problem is: using these parameters the simulation matches the experimental data, for the intensity and position, however, I'm missing the pre-edge and I also have a bump in the white line (yellow curve)... Does anyone know how to fix it, please? [cid:image003.jpg@01D44050.C0ECC210] Thank you, Debora

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Constraining values in Artemis fit
by Thomas, Andrew (AGW) 23 Aug '18

23 Aug '18

Hello, Does anyone have any suggestions for breaking the correlation between the coordination number and sigma^2? Specifically, is there a way to set a maximum or minimum value for parameters in a fit? Andrew Thomas

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32ビット版アプリケーションの申請
by 天田雄大 22 Aug '18

22 Aug '18

Ifeffit管理者様 32ビット版アプリケーションを使用したいので、 32ビット版のインストールアプリを添付していただけませんか？よろしくお願いします。

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Accelerated Specotroscopy post-doc position at LBNL
by Santosh Suram 22 Aug '18

22 Aug '18

Hi everyone, I would like to bring to your attention an upcoming post-doc position on accelerated spectroscopy and analysis of XANES and EXAFS data. Please see the brief advertisement below and if interested please email your resume to jyano(a)lbl.gov and santosh.suram(a)tri.global -- best, Santosh -- Confidential or protected information may be contained in this email and/or attachment. Unless otherwise marked, all TRI email communications are considered "PROTECTED" and should not be shared or distributed. Thank you.

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Fe K-edge EXAFS spectra for Fe-silicates
by Paul Francisco 22 Aug '18

22 Aug '18

Dear Everyone, Hello! I'm working on iron silicates and I'm wondering if anybody here would be willing to share some Fe K-edge EXAFS spectra (preferably ones that go up until k=14-15 A-1) for phyllosilicates (e.g. chlorite/saponite/serpentine); or if anybody can recommend some database or reference for these. Thanks in advance and I would really appreciate any help! Cheers, Paul

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Modelling texture in Artemis
by Kirstine Dalgaard 20 Aug '18

20 Aug '18

Dear all How can texture in a powder sample be modeled in ARTEMIS? My samples are fine powders of a layered material, mixed with cellulose and pressed to pellets. The data were collected in fluorescence mode with a 45 degree tilt. PXRD data reveal that the samples are highly textured, including standards. I am new to XAFS, and I need some advise to deal with this issue. Best regards Kirstine Dalgaard

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Re: [Ifeffit] using the mail list archive for mac install
by Matt Newville 17 Aug '18

17 Aug '18

Hi Joel, > I ran into the problem that some people seem to have with Demeter on mac while > upgrading to High Sierra. I found a fix on this mail list, but… Yeah, Demeter on MacOS is a continuing challenge. Even when it can be installed, parts of the GUI interaction are pretty buggy (I believe this must be due to wxPerl on Mac). MacPorts seems to need a fair amount of attention and expects the end user to know Unix command line tools well enough to be able to run updates and understand and react to error messages. For sure, it is a useful resource for developers, but it seems like it is not really designed for deploying end-user software. Still , I don't know of a better alternative for getting Demeter working on MacOS. I've tried many of the alternatives, and wxPerl seems to be a real stumbling block for all of them. > 1) I can’t download Template.pm from the archive (bin file that uncompresses to cpgz file > that uncompresses back to a bin file…) I think that the advice from Luke and Bruce back in April was to try to find and install version 1.47 of Text::Template. You might find this at https://metacpan.org/source/MSCHOUT/Text-Template-1.47/lib/Text and try unpacking and installing that. There may be a way to specify particular versions with the "cpan" program, but I do not know how to do it. I don't think we want "install old version of some library" to be a long term solution (this will break other things eventually), but it might work for you. > 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). To clarify, in April I updated MacPorts to the latest versions, installed the packages for Demeter 0.9.25. Then I installed Demeter 0.9.26 from source code on top of that. That might also work , but it's probably more work than most folks would want to do. Cheers, --Matt

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Re: [Ifeffit] Ifeff calculation
by Dien.Li＠srnl.doe.gov 15 Aug '18

15 Aug '18

Hi, Carlo and Matt or others Attached please find the cif crystal structure data file for NaReO4 that was downloaded from Crystallography Open database. As I added it into Artemis for calculation, it gave error message saying that it has more than 500 atoms that exceeds the limit. Could you help to troubleshooting?? Thanks a lot. Dien Li -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Tuesday, August 14, 2018 5:29 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 186, Issue 13 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: LCF on Larch - EXAFS Region (Matt Newville) 2. Re: wavelet transforms for EXAFS (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 14 Aug 2018 12:33:35 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] LCF on Larch - EXAFS Region Message-ID: <CA+7ESbr8s-gQOeLOo302hTdtT+XLS8g55goXvYm6hqJFiLCkaQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Martin and Mike, Thanks -- I'll take a closer look at your paper on this! I think we all basically agree that linear analysis of EXAFS can work, but also that compared to linear analysis of XANES, linear analysis of EXAFS has a few more caveats and issues that need to be addressed for each case. On Mon, Aug 13, 2018 at 8:26 PM Martin McBriarty <memcbr(a)gmail.com> wrote: > Matt, > > Glad to read your impressions of EXAFS LCF. I've had reasonable success > with LCF using EXAFS spectra generated by ab initio molecular dynamics > (AIMD) to figure out the local structure of dopants whose preferred > coordination is symmetrically dissimilar from the crystals they inhabit, > i.e. for which there are no good experimental standards. This can be pretty > tough to do accurately with shell-by-shell fitting. > > As you point out, disorder is a huge hurdle (in both LCF and > shell-by-shell EXAFS analysis). We assume that a good AIMD model will > simulate thermal disorder pretty well, but there are likely differences in > configurational disorder between a periodic infinite structure and the real > material due to defects. Fortunately, defects can be explicitly accounted > for in a simulation, assuming you have the computational capability to > screen a set of defect configurations. > > Background subtraction should ideally be done using the same procedure for > all data. Theoretical data could be used to refine a background subtraction > procedure; spline fit parameters such as Rbkg or clamping may be tweaked to > improve agreement between a simulated chi(k) and a measured standard over a > reasonable k-range. > > Simulating spectra with a range of binding energy offsets can explicitly > address the problem of E0 choice, but it can also be used as a fudge factor > for strain. In my LCFs, dE0 is the only parameter besides the fractions of > the chosen phases. > > To address the above problems, benchmarking is key. Quantitative agreement > should be sought between simulated spectra and experimental standards to > ensure the theory is sound and the chi(k) extraction is reasonable. > However, there are probably still systematic sources of error which are > larger than the uncertainties Athena's LCF tool will report; I agree with > Mike's practical estimate of 10% or so. > > I discuss these issues in somewhat greater detail in my recent (open > access!) article that demonstrates how LCF using AIMD-simulated spectra > yields answers that shell-by-shell fitting struggles with due to multiple > overlapping components: https://pubs.acs.org/doi/10.1021/acs.est.8b00297 > > Martin > > > On Sun, Aug 12, 2018 at 10:19 PM, Matt Newville < > newville(a)cars.uchicago.edu> wrote: > >> Hi Mike, >> >> On Thu, Aug 9, 2018 at 10:04 PM Mike Massey <mmassey(a)gmail.com> wrote: >> >>> This is interesting. Could you say more about your skepticism of the >>> robustness of EXAFS LCF, Matt? >>> >>> To be fair, it suffers from many of the same drawbacks of XANES LCF, >>> plus others. But I'm curious about your thoughts on it since yours seems to >>> be what amounts to a "strong opinion" on the subject. >>> >> >> >> I would not say that no one should ever do linear combination fitting for >> EXAFS. For sure, linear analysis of XANES is quite robust and verified >> many times to give good results, at least at level of a few percent. >> Linear analysis of EXAFS suffers more data processing challenges and >> conceptual problems that limit its robustness. For sure, there are cases >> for which it can work well. >> >> Longer answer: >> Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably >> well (typically to a few percent) because: >> a) the processing needed is minimal. Data need to have a common >> energy calibration better than the intrinsic energy resolution -- typically >> energy calibration of 0.25 eV or better will be OK. Data need to have a >> consistent normalization of mu(E), typically to a few percent. Variations >> in these processing steps will have a direct and negative effect on the >> results. >> >> b) conceptually, the assumption is that there exists a nearly 1 to 1 >> correspondence between "local chemical configuration" and "measured XANES", >> and that the "local chemical configurations" that are being investigated >> are discrete and well-defined (ie "iron carbonate") and not continuous. >> That is, if you determine that your Fe XANES spectra is "50% iron >> carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the >> iron atoms are iron carbonate and 50 percent are iron sulfate, not that all >> irons are 50% carbonate and 50% sulfate. >> >> To be clear, linear analysis of XANES does not work well to ppm levels, >> partly due to the poor experimental contrast (that is, mu(E) tend to all >> look alike and features are intrinsically broadened to the ~eV level), but >> also conceptually, because at the ppm level, local chemical configurations >> are not always limited to 3 to 10 discrete states. >> >> Linear Combination EXAFS is more challenging from both the processing and >> conceptual point of view. >> >> For Processing, EXAFS requires more data processing than XANES. The >> selection of E0 and the background mu0(E) will have an effect on linear >> analysis of EXAFS if not done consistently. It is not really obvious how >> E0 or mu0(E) can be selected consistently for very different spectra. >> >> Conceptually, EXAFS is much more sensitive to disorder and subtle >> variations in the bond lengths (thermal or static disorder) and can have >> significant variation in its sensitivity to second and further neighbors. >> In that sense, EXAFS is much less discrete and much more continuous in its >> variability across different kinds of local structures. >> >> Again, this is not to say that linear analysis of EXAFS cannot ever work, >> just that is probably more limited in applicability and absolute accuracy >> than linear analysis of XANES. Of course, for EXAFS you can also do an >> actual fit of structural parameters. The information content is somewhat >> limited so that refining multiple overlapping components may not always be >> possible, and linear combinations of end-member spectra may look >> attractive.... >> >> Hopefully, anyone who has other insights or experiences will be able to >> correct any of my misunderstandings. >> >> --Matt >> >> >> _______________________________________________ >> 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 > -- --Matt Newville <newville at cars.uchicago.edu> 630-252-0431

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Basic questions about the preliminary data processing in Athena
by Haifeng Li 14 Aug '18

14 Aug '18

Dear ALL, I am a beginner in Athena. Recently I got the spectra and I am confusing about the data calibration and alignment. The manual shows that calibrate the reference data of one scan and align other reference data to that calibrated one. Here I want to show examples. I have two samples A and B, Each sample has three scans with the corresponding reference data. For sample A, 1st scan is calibrated and the other two scans are aligned to 1st scan. Then merge them into merged A. The same procedures for sample B and get merged B. If I want to compare XANES of sample A and B, do I need to align the merged reference data between A and B? If so, why? My understanding is that all scans (original data and merged data) in sample A and B are calibrated to standard edge energy. Why do they need to align? I appreciate your help. Thanks, Haifeng

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