October 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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Problem with Athena
by Weronica Linpé 30 Oct '18

30 Oct '18

Hi, I have a problem when looking at the difference scan between two scans. When I move from the start up site to the differnece everything works fine and I get a differnece spectra. Here I can do some changes, but if I want to change which scans I'm using for the difference the program chrashes. Any ideas on why the program chrashes?

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ADDITION - Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 30 Oct '18

30 Oct '18

Dear Bruce & Ifeffit Mail-List We just found that the problem I described in my previous email for Demeter 0.9.26 does not occur with version 0.9.25. Thus, reinstalling the previous version seems the easiest work around for the moment. Best, Andreas

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Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV
by Kirill Lomachenko 25 Oct '18

25 Oct '18

Dear Bruce and dear all, I have the same problem with data import in Athena 0.9.26 that Andreas has just described and that, if I am not mistaken has already been mentioned in this mailing list before. Looking for the possible cause of the problem, in the list of changes made for Athena in the latest version of Demeter I found the following: "Fix a problem processing keV data when using Larch (Thanks to Juan de la Figuera) (See issue #42)" May it be that these modifications are responsible for the observed import bug? (just a guess) Thank you Kirill Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu 25.10.2018 11:40, ifeffit-request(a)millenia.cars.aps.anl.gov пишет: > 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. Bug Report: incomplete data import in Athena when energy is > given in keV (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Oct 2018 09:39:52 +0000 > From: "Voegelin, Andreas" <Andreas.Voegelin(a)eawag.ch> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Bug Report: incomplete data import in Athena when > energy is given in keV > Message-ID: > <D87798881B7774448873557DA6961A35F019A176(a)EE-MBX3.ee.emp-eaw.ch> > Content-Type: text/plain; charset="utf-8" > > Dear Bruce & Ifeffit Mail-List > > Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. > > Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum ?original_format,.txt? in Athena project file ?test_bug_data_import_in_keV.prj?). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. > > Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file ?test_energy_in_keV_eV.txt? in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. > > Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. > > I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. > > For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. > > Best regards, Andreas > > ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > Andreas Voegelin, PhD > Eawag - Swiss Federal Institute of Aquatic Science and Technology > Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland > Tel: +41 58 765 54 70 > Fax: +41 58 765 52 10 > mailto:andreas.voegelin@eawag.ch > http://www.eawag.ch/~voegelan > > > > > >

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Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 25 Oct '18

25 Oct '18

Dear Bruce & Ifeffit Mail-List Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum “original_format,.txt” in Athena project file “test_bug_data_import_in_keV.prj”). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file “test_energy_in_keV_eV.txt” in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 Fax: +41 58 765 52 10 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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the meaing of "beta=125.264" in path interpretation
by woschangqiang＠126.com 19 Oct '18

19 Oct '18

Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in α-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

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Re: [Ifeffit] Ifeffit Digest, Vol 188, Issue 14
by Joanna Kowalska 19 Oct '18

19 Oct '18

>From Ben I will send On 19 Oct 2018 16:25, <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. the meaing of "beta=125.264" in path interpretation (woschangqiang(a)126.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 19 Oct 2018 22:22:30 +0800 From: "woschangqiang(a)126.com" <woschangqiang(a)126.com> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] the meaing of "beta=125.264" in path interpretation Message-ID: <201810192222293624981(a)126.com> Content-Type: text/plain; charset="gb2312" Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in ?-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

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Athena problem
by Elien Lemmens 18 Oct '18

18 Oct '18

Dear, I was trying to do some linear combination fitting using Athena software. Although the box "All weight between 0 and 1" is ticked I get negative weight results. I have read the online Athena's User's Guide, but I did not find what the issue can be. Do you have any ideas? Below you can find some print screens of my actions. I also get an "error" (print screen 2), which I don't understand. Thanks in advance Elien [cid:image001.jpg@01D46703.6DC31010] [cid:image002.png@01D46703.6DC31010] [cid:image003.png@01D46703.6DC31010]

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difference of feff interpretation generated by different version of artemis
by woschangqiang＠126.com 17 Oct '18

17 Oct '18

Hello, everyone. I recently ran into an issue in using Artemis software. I used two versions of Artemis (Artemis 0.8.012 and Demeter 0.9.25) to generate the paths from the same input file (FeS2.inp), but there is big difference between the two path results. e.g. 1, the path4 and path6 generated in Demeter 0.9.25 are not generated in Artemis 0.8.012, though they have a very low applitude. e.g. 2, the path7 in Demeter 0.9.25 is likely identical to path5 in Artemis 0.8.012 judging from the degenracy, reff, and amplitude, but their scattering name are different: (+)-S1-S2-(+) in Demeter 0.9.25 and (+)-S2-S1-(+) in Artemis 0.8.012. In my opinion, the scattring sequence of photoelectron in multiple scattering affect the paramters of paths. Why do these two paths have different scattering sequence? Thanks very much for your help. Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China Email: woschangqiang(a)163.com

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restraints in larch
by Barbara Etschmann 11 Oct '18

11 Oct '18

Hello I'm trying to use larch to refine the coordination of Y in solution. I need to use 2xO paths to fit the first shell and would like to restrain the total coordination to be between 5.5 and 8. I can apply the constraint to each nO, but not the total, i.e. nO1 = param(7.0, min=5, max=7, vary=True), nO2 = param(1, vary=True), but ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5) does not work. How can I restrain the total coordination? Also, having some problems with the gofs and errors - the chi square is rather small and often the errors are not reported and it is not clear why. Thanks Barb

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