- Ifeffit - millenia.cars.aps.anl.gov

Extrating standard deviation value from merged dataset in Athena
by Christian Rein 16 Nov '18

16 Nov '18

Hi, Do anyone know how to obtain the standard deviation value that Athena calculates when merging the data? Best, Christian Christian Rein Postdoc DTU Energy Technical University of Denmark [http://www.dtu.dk/~/media/DTU_Generelt/Andet/DTU_email_logo_01.gif] Department of Energy Conversion and Storage Building 771, room 010 4000 Roskilde Denmark

2 1

LCF and XES
by Samy Ould-Chikh 05 Nov '18

05 Nov '18

Dear, I'm trying to perform LCF using Athena for XES data (Kbeta 13) that has been normalized elsewhere. Combinatorics module is the main motivation. However, LCF module in Athena only use norm mu(E), so that the normalization for XAS data proceed and then it's not possible to perform the fitting. Does anyone know a workaround to perform LCF for XES in Athena, or another alternative software as user friendly ? Many Thanks Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa<mailto:eman.ahmedbahjri@kaust.edu.sa> Website: http://kcc.kaust.edu.sa/Pages/Home.aspx

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 8
by Raj kumar 02 Nov '18

02 Nov '18

Thanks for the clarification, Anatoly! Regards, Raj On Fri, Nov 2, 2018 at 4:04 PM <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: EXAFS of wine (Anatoly Frenkel) > 2. Re: Ifeffit Digest, Vol 189, Issue 2 (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 2 Nov 2018 06:36:57 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS of wine > Message-ID: <45D3D1E4-6749-463C-9FE3-259B77345304(a)stonybrook.edu> > Content-Type: text/plain; charset="utf-8" > > John, > > Since when theorists started to need real samples? I thought a simulation > is equally enjoyable. > > Anatoly > > > On Nov 2, 2018, at 12:17 AM, John J Rehr <jjr(a)uw.edu> wrote: > > > > Hi everyone > > > > The spectrum is pretty noisy with all the super Tuscano grapes ( > Alicante, Merlot etc) in the mix to give it?s complex berry character and > the 2016 is supposedly better. > > How about we take some samples to the lab ... ? > > > > John > > > > > >> On Thu, Nov 1, 2018 at 16:07 Anatoly Frenkel < > anatoly.frenkel(a)stonybrook.edu> wrote: > >> I thought this mailing list is an appropriate venue to post a picture > of the bottle of wine I bought yesterday in a store on Long Island. > >> > >> > >> > >> Anatoly_______________________________________________ > >> 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 >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2
by Raj kumar 02 Nov '18

02 Nov '18

Dear Anatoly and Marcus, Thanks for your answers. So in this case, i understood, I shouldn't use the extended XAFS region for the analysis. In the other hand, is it allowed to cut the region till 9150 eV and use the data for the XANES analysis? Regards, Raj On Thu, Nov 1, 2018 at 11:37 PM <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: Bump/oscillating pattern at high energies of EXAFS > (Anatoly Frenkel) > 2. Re: Bump/oscillating pattern at high energies of EXAFS > (Matthew Marcus) > 3. EXAFS of wine (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Nov 2018 17:47:56 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of > EXAFS > Message-ID: > < > CAFsMoZbm2RMVUeRmuoryw9ehVrZQcvx60zHqufmK39oLRoyZ2w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > It is an effect of inhomogeneity of the sample, that is, the variation in > the metal density throughout the X-ray beam footprint. > Anatoly > > > > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar <rajrk37(a)gmail.com> wrote: > > > Dear All, > > > > I have monitored the growth process of YbVO4 nanoparticles using EXAFS. > > Here, nanoparticles were synthesized in water medium. Both initial and > > final products (EXAFS) of the synthesis were measured using the > continuous > > flow approach whereas the intermediate products were recorded, in the > glass > > capillary, using the stopped flow. In the attached figure, you can find > the > > same (all products). At high energies of EXAFS, both initial and final > > measurements show smooth behavior whereas the oscillating pattern/bump > was > > observed for the intermediate states. > > > > Here, my question is: Is the oscillating pattern appearing in the > > intermediate states due to the sedimentation/in-homogeneity of the > product > > in the capillary or it is the characteristic of the synthesis? > > > > With regards, > > Raj > > _______________________________________________ > > 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 > > >

2 1

EXAFS of wine
by Anatoly Frenkel 02 Nov '18

02 Nov '18

I thought this mailing list is an appropriate venue to post a picture of the bottle of wine I bought yesterday in a store on Long Island. Anatoly

9 10

Postdoc Opportunity in Catalysis Science at SSRL
by Bare, Simon R 01 Nov '18

01 Nov '18

Please see the attached postdoctoral positon available now at SSRL. It is also posted here: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Thanks! Simon R Bare Distinguished Staff Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

1 0

Bump/oscillating pattern at high energies of EXAFS
by Raj kumar 01 Nov '18

01 Nov '18

Dear All, I have monitored the growth process of YbVO4 nanoparticles using EXAFS. Here, nanoparticles were synthesized in water medium. Both initial and final products (EXAFS) of the synthesis were measured using the continuous flow approach whereas the intermediate products were recorded, in the glass capillary, using the stopped flow. In the attached figure, you can find the same (all products). At high energies of EXAFS, both initial and final measurements show smooth behavior whereas the oscillating pattern/bump was observed for the intermediate states. Here, my question is: Is the oscillating pattern appearing in the intermediate states due to the sedimentation/in-homogeneity of the product in the capillary or it is the characteristic of the synthesis? With regards, Raj

3 2

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?

2 1

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

2 1

Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV
by Kirill Lomachenko 26 Oct '18

26 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 > > > > > >

2 1