April 2020 - 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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Artemis crash upon empirical standard import.
by George Sterbinsky 22 May '20

22 May '20

Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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unable to export xdi file in xas viewer
by George Sterbinsky 04 May '20

04 May '20

Hello, When attempting to export an xdi file for a pre-edge peak fit in XAS viewer, the error message below prints to the terminal and the xdi file is not generated. I can provide the project file and instructions for generating the error message if that would be helpful. Thank you, George Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line 369, in onExportFitResult yerr=yerr, x=x) File "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", line 60, in export_modelresult delta_fit = result.eval_uncertainty(result.params, **kwargs) File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, in eval_uncertainty dval = pars[pname].stderr/3.0 TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'

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Open postdoc position at DESY XAFS beamline
by Edmund Welter 30 Apr '20

30 Apr '20

Dear colleagues, in case you are interested in an interesting post doc position at a XAFS beamline at DESY in Hamburg (a place where you usually do not suffer from drought!) please have a look at the following job offer: https://www.desy.de/career/job_offers/index_eng.html?joboffer=103168 If you know of a colleague who might be interested please forward this mail to her/him. For any questions concerning the advertised position please do not hesitate to contact me via e-mail but please take care that you do not send your reply to the mail list. Best regards, Edmund Welter

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How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)
by Dien.Li＠srnl.doe.gov 28 Apr '20

28 Apr '20

HI, Matthew and Bruce and Carlo As I want to fit a U L3-edge EXAFS spectrum using a crystal structure model of vorlanite (cubic CaUO4), I was not able to load the crystal structure data, with an error message of "could not input the data file because of partial occupancy" or something like this. I believe that the reason is that Ca and U are on the same site (coordination), and they are completely disordered, it is like (Ca,U)O2, a CaF2 structure, and the occupancy for each of Ca and U is 0.5. Is there any way to handling of such crystal structure data in Artemis? Please see the attached crystal data file in cif. Thank you so much for your instruction. Dien Li Savannah River National Laboratory

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Larch 0.9.47
by Matt Newville 18 Apr '20

18 Apr '20

Hi Everyone, Larch 0.9.47 is now available, with installers and source code at https://xraypy.github.io/xraylarch/installation.html. For python users, there is a plain python package available on PyPI and conda packages for Anaconda Python. See the installation docs for more details. There have been several improvements and bug fixes, especially for the XAS Viewer application and for XRF modeling in the nearly six months since the last release. In particular, there have been two improvements to basic XAFS and XANES data processing, both based on user reports and comparisons to older versions of Ifeffit/Athena and give a noticeable change in XAFS and XANES processing. First, the ranges used in by the pre_edge() function for finding the edge step for normalization are now better determined from the actual data range rather than simply being hard-wired numbers. These improvements were long over-due and give noticeably better default results for XANES data, especially for relatively low-energy edges such as S and Cl K edges. When reading Athena Project files (say, to import into XAS Viewer), the pre-edge and normalization ranges from the Athena Project file will be preserved. When reading in new raw data, or if you select the "Use Default Setting" button on the Normalization Panel for any group in XAS Viewer, the newer defaults will be used. You can always alter these values, but in playing around with this with a range of datasets, the new defaults seem to give a noticeable improvement in almost all cases and rarely bad. Second, as a few users have pointed out or gently hinted at over many months, there were sometimes significant differences in the background removals between classic Autobk/Ifeffit/Athena and Larch, with Larch sometimes being noticeably and inexplicably worse. I believe this involved two different problems. One was introduced a while back when implementing an estimate of delta_chi - the variance in chi due to the background subtraction. This estimate is important, but I botched some of the configurations of the number of knots, fit range, and Rbkg. The other problem was that "spline clamps" were just done too differently in Larch and Ifeffit/Athena. I believe this is now working much better: the background results are much more consistent, and do not occasionally get "very bad". They also happen to be generally closer to Autobk/Ifeffit/Athena, and perhaps slightly better because the fit range in R-space is now more consistently determined (instead of wandering +/- a few R data points around Rbkg where the misfit will often be the largest). In addition, `delta_chi` (never calculated in Ifeffit/Athena) is now also more consistent. One consequence of this change is that a very small change in Rbkg (of say 0.01 to 0.05 Ang) may actually give no difference at all in mu0(E) or in chi(k). I bring these changes up because I think they will be noticeable. I think they are both improvements, but let me know if you find cases for which you think are now made worse. Possibly related: one thing that I definitely noticed in going through several example data sets was that I tended to favor a k-weight of 2 instead of 1 for background subtraction -- so much so that it seemed like this might be a better default. I did not change this default yet, but if you have a strong opinion on this, that might be a good topic for discussion here. There are some documentation improvements, but this is an ongoing process and never complete. It is also one area where help and feedback would greatly be appreciated. If you or your students have time to work through the larch examples and/or documentation and make improvements or even suggestions for improvements in readability or completeness, it would be greatly appreciated. Thanks, --Matt Newville

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8
by Dien.Li＠srnl.doe.gov 14 Apr '20

14 Apr '20

Hi, all I fitted my Cr EXAFS data, but E0 was -2.5. I calibrated the spectrum in energy space by +10 eV, the spectra in K and R space were identical before and after this calibration, in contract to my understanding that the k space oscillations and R magnitude should shift. Could you please provide any direction on how to get E0 to position values or negative E0 is acceptable? Thank you so much. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, April 13, 2020 12:04 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8 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. Artemis crash upon empirical standard import. (George Sterbinsky) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 Apr 2020 11:02:34 -0500 From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Artemis crash upon empirical standard import. Message-ID: <CALoY8YzT1C+eGx_o2FUmwBbzRYYNeZL8tigM9zTzQMT0QKox5A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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errors in bond lengths
by George Sterbinsky 13 Apr '20

13 Apr '20

Hello, As is well known, EXAFS is more accurate at determining relative changes in bond lengths than absolute changes in bond lengths due to cancelation of systematic errors in relative comparisons. When comparing the relative changes in bond lengths determined from EXAFS fits, as one might for a temperature series for example, is it appropriate to use the uncertainties returned by Artemis? My question arises in part from Phys Rev Lett vol. 100 pg. 055901 (2008), where the authors state that errors for changes in bond length in a temperature series were determined by empirical means rather than statistical means. This then raises the question as to if the authors believe that statistical means would overestimate the error. My inclination is to think that the uncertainties reported by Artemis would be appropriate because of the scaling by the square root of reduced chi squared. However, I want to see what others think about this before committing to it. Thank you, George

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larch can not deconvolve my data
by Shaofeng Wang 10 Apr '20

10 Apr '20

Dear all, Recently I am trying to deconvolve a As K-edge xafs data using larch. But the xas viewer program always crash. I tried other K edge spetra, it worked well. I attached my data, please give me some help. 祝好运！ Best regards, 王少锋，Shaofeng Wang, Ph.D 中国科学院沈阳应用生态研究所，Institute of Applied Ecology, CAS Email: wangshaofeng(a)iae.ac.cn; sf.wang(a)hotmail.com Address: Wenhua Road 72, Shenyang

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Fe 4+ reference
by George Sterbinsky 05 Apr '20

05 Apr '20

Hello, Does anyone have Fe K-edge XANES from an Fe4+ reference or sample (for example SrFeO3) that they can share? Thank you, George

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