May 2018 - Ifeffit - millenia.cars.aps.anl.gov

SSRL EXAFS School- Application Open!
by Ritimukta Sarangi 19 May '18

19 May '18

Hello Friends, SSRL will host its annual summer school this year during the third week of August (13th-16th). The application page is now open. Please hit the "apply" button on: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html Note that seats are limited and we will have to choose from the application pool. Please apply soon to help us with the process. If selected, you will receive an email to register for the school. This year, we will drill down into Artemis based EXAFS analysis. Hope to see many of you here! Best Wishes, -Riti Sarangi

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XANES spectra of Zn-organic references
by emmanuelle Montarges-Pelletier 18 May '18

18 May '18

Dear all We have measured Zn XANES spectra within biological samples (seeds), in ambient conditions (room temperature). In order to interprete the spectra, we are searching for Zn-organic reference spectra (XANES only). Indeed, we would be interested by Zn organic compounds with sulfur and/or nitrogen and/or oxygen in the first shell of coordination. On the joined graph are plotted the experimental spectra (microspectra on seeds), compared to Zn-citrate and Zn-cysteine. Energy calibration was checked for all spectra. thanks in advance for your answers best regards Emmanuelle Emmanuelle MONTARGES-PELLETIER Chargée de Recherche CNRS LIEC Laboratoire Interdisciplinaire des Environnements Continentaux UMR 7360 CNRS Université de Lorraine 15 avenue du Charmois F-54500 Vandœuvre-lés-Nancy - France tel 33 (0)03 72 74 47 30 mob 33(0)6 31 33 10 30 ****attention changement de numéro de téléphone **** tel 33 (0)3 72 74 47 30

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4+2 model for distortion
by Abdul Ahad 17 May '18

17 May '18

Hi Prof. Segre Thanks for your reply, I have used .cif file for the K2NiF4 type structure. In this structure the first shell and first single path shows 6 coordination number. and the path is Ni to F1 with 2 leg. My concern is to use 4+2 model. Do i change the CN number or i have to add one more site. I cant visualize the situation. Becuase here the F have 2 sites i.e F1 and F2. And the path is only for the F1. While the diffrence between the bonds Ni-F1 and Ni-F2 is about 0.1 A. which lies under the resulution limit of my experiment via delta r and delta k relation. *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 16, 2018 at 10:30 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: 4+2 model for distortion (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 May 2018 16:00:08 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] 4+2 model for distortion > Message-ID: <alpine.DEB.2.21.1805151558480.17852(a)hydride.segre.home> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > Hi Abdul: > > Are you strating with a cif file for a particular structure or are you > simply working with a quick first shell theory? > > Carlo > > > On Wed, 9 May 2018, Abdul Ahad wrote: > > > hi all > > How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long > > bond length of octahedra > > thanks > > > > > > *A. Ahad* > > *--------------------* > > *Abdul Ahad* > > Junior Research Fellow > > *Dept of Physics* > > *Aligarh Muslim University* > > *Aligarh 202002 (U.P.), India* > > > > *http://www.researcherid.com/rid/G-8198-2018 > > <http://www.researcherid.com/rid/G-8198-2018>* > > *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org > > <ahad(a)mailaps.org> * > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 183, Issue 14 > **************************************** >

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4+2 model for distortion
by Abdul Ahad 15 May '18

15 May '18

hi all How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long bond length of octahedra thanks *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> *

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Energy Resolution
by Julian Ehwald 10 May '18

10 May '18

Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

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Truncating signal
by Julian Ehwald 10 May '18

10 May '18

Hi all, I have basic question on background removal in Athena. My data has some strong changes very close to the absorption edge, and if I start the background removal at k=0, the spline is not able to follow the signal for higher k-values (even at Rbkg=1.7 or similar). The background then oscillates slowly (4 A^-1) around my signal, generating huge peaks in the low regions of chi(R). If I set the spline range to begin at k=2.7 only (around 28eV above absorption edge) then I get rid of it. Now my question in general is, do I loose essential information about the nearest neighbours this way, respectively is that a common thing to do? Best, Julian

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Re: [Ifeffit] Ifeffit Digest, Vol 183, Issue 9
by Abdul Ahad 09 May '18

09 May '18

yes i m talking about the jahn teller type distortion, any hint to include in atom *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 9, 2018 at 8:30 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: Energy Resolution (Julian Ehwald) > 2. Re: Energy Resolution (Robert Meulenberg) > 3. 4+2 model for distortion (Abdul Ahad) > 4. Re: 4+2 model for distortion (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 May 2018 09:24:27 +0200 > From: "Julian Ehwald" <jehwald(a)gmail.com> > To: "'Carlo Segre'" <segre(a)iit.edu>, "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: <006901d3e766$c4284410$4c78cc30$(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carlo > > Thank you very much for your answer! If you say it is sufficient to use > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 to > 12) in only 250 datapoints? That would save us a lot of time! > > Best, Julian > > -----Urspr?ngliche Nachricht----- > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im Auftrag > von Carlo Segre > Gesendet: Sonntag, 6. Mai 2018 01:07 > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] Energy Resolution > > > Hi Julian: > > With an edge energy of 543 eV, your monochromator resolution should be at > least 0.1 eV. If you are interested in XANES, you need to take data at > this > resolution or maybe even better. ONce past the edge, there is no need to > keep that step size. If your beamline permits an EXAFS-type step scan with > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > interpolates to. Smaller step sizes are not really useful. > > Carlo > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > Dear all, > > > > > > > > This might be a very general question, but: I was wondering what > > energy resolution you typically use at beamlines to obtain your raw data > for exafs. > > Since we have limited Beamtime only and other experiments that we want > > to carry out, I was wondering what kind of resolution is common. Or > > differently: Is it predictable what happens if I for example change > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > above Oxygen K, if that is of relevance. > > > > Best, Julian > > > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, > Department of Chemistry Director, Center for Synchrotron Radiation Research > and Instrumentation Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > _______________________________________________ > 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 > > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 May 2018 08:54:31 -0400 > From: Robert Meulenberg <robert.meulenberg(a)maine.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: > <CANs+nr9N7MSiYB9UGRm-a0JGd-5U8BNjKO7YVgAkM=SoRKazHA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Julian, > > Keep in mind that to get to k=12, you will need to go out to ~1100 eV. At > these energies, you will encounter just about every 1st row transition > metal L edge, and a handful of other M-edges for heavier elements. So if > you have anything else in your sample, EXAFS will probably not be > possible. That is usually why people don't try to do EXAFS analysis at the > soft x-ray energies. > > Regards, > > Rob > > > > > Robert W. Meulenberg > Associate Professor of Physics > Laboratory for Surface Science and Technology > Department of Physics and Astronomy > University of Maine > Orono, ME 04469 > phone: 207-581-2245 > email: robert.meulenberg(a)maine.edu > > On Wed, May 9, 2018 at 3:24 AM, Julian Ehwald <jehwald(a)gmail.com> wrote: > > > Hi Carlo > > > > Thank you very much for your answer! If you say it is sufficient to use > > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 > to > > 12) in only 250 datapoints? That would save us a lot of time! > > > > Best, Julian > > > > -----Urspr?ngliche Nachricht----- > > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im > Auftrag > > von Carlo Segre > > Gesendet: Sonntag, 6. Mai 2018 01:07 > > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Betreff: Re: [Ifeffit] Energy Resolution > > > > > > Hi Julian: > > > > With an edge energy of 543 eV, your monochromator resolution should be at > > least 0.1 eV. If you are interested in XANES, you need to take data at > > this > > resolution or maybe even better. ONce past the edge, there is no need to > > keep that step size. If your beamline permits an EXAFS-type step scan > with > > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > > interpolates to. Smaller step sizes are not really useful. > > > > Carlo > > > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > > > Dear all, > > > > > > > > > > > > This might be a very general question, but: I was wondering what > > > energy resolution you typically use at beamlines to obtain your raw > data > > for exafs. > > > Since we have limited Beamtime only and other experiments that we want > > > to carry out, I was wondering what kind of resolution is common. Or > > > differently: Is it predictable what happens if I for example change > > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > > above Oxygen K, if that is of relevance. > > > > > > Best, Julian > > > > > > > > > > -- > > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim > Chair, > > Department of Chemistry Director, Center for Synchrotron Radiation > Research > > and Instrumentation Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > _______________________________________________ > > 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 > > >

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Re: [Ifeffit] Athena programm for XAS data analysis
by Robert Gordon 08 May '18

08 May '18

changing colour: Preferences --> gnuplot --> col7 and Set a desired colour then apply and save....displayed "your value" might not update until you restart Athena, but the plot should. On Tue, May 8, 2018 at 3:07 AM, Stoll, Andreas (HIU) <andreas.stoll(a)kit.edu> wrote: > Hi Jonas, > > > first of all thank you very much for your quick answer! > > > unfortunately your suggestion is not working for my version of Athena. It > just worked for the older versions... > > > Is there another possibility? > > > Greetings > > > Andi > ------------------------------ > *Von:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> im Auftrag von > Wielinski, Jonas <Jonas.Wielinski(a)eawag.ch> > *Gesendet:* Dienstag, 8. Mai 2018 18:40 > *An:* XAFS Analysis using Ifeffit > *Betreff:* Re: [Ifeffit] Athena programm for XAS data analysis > > > Hi Andi, > > > > Using Athena under Windows, “Alt + J” and “Alt + K” move data groups > upwards and downwards. I hope that answers your question. > > > > Best, > > Jonas > > > > *From:* Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] *On > Behalf Of *Stoll, Andreas (HIU) > *Sent:* Dienstag, 8. Mai 2018 10:12 > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* [Ifeffit] Athena programm for XAS data analysis > > > > Hi, > > > > I´m using Athena Version 0.9.26 to analyse my XAS data. > > > > Is it possible to change the order of the imported data in the list after > importing them? Or at least change the colour of the plotted data? > Currently one of my standards is plotted in yellow and that is not really > good... > > > > Thanks in advance! > > > > Greetings > > > > Andi > > _______________________________________________ > 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 > >

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Athena programm for XAS data analysis
by Stoll, Andreas (HIU) 08 May '18

08 May '18

Hi, I´m using Athena Version 0.9.26 to analyse my XAS data. Is it possible to change the order of the imported data in the list after importing them? Or at least change the colour of the plotted data? Currently one of my standards is plotted in yellow and that is not really good... Thanks in advance! Greetings Andi

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Re: [Ifeffit] o exafs
by fred.mosselmans＠diamond.ac.uk 05 May '18

05 May '18

Hi Julian, First you'll do well to collect o k exafs to 500 evening, second exafs data is typically except on qexafs beamline collected in k space steps i.e. proportional to E squared spacing starting at the edge position. Hence 0.4 evening is a very small step for exafs NOT xanes. If your beamline doesn't do k space scanning you can simulate it with several fixed eV step regions the step increasing as you get further from the edge. Also normally you would increase the time per point as you get further from the edge as the xafs signal compared to the background dies off Best Regards Fred Sent from BlueMail<http://www.bluemail.me/r?b=12874> On 5 May 2018, at 18:02, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@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. Energy Resolution (Julian Ehwald) ________________________________ Message: 1 Date: Sat, 5 May 2018 12:01:26 +0200 From: "Julian Ehwald" <jehwald(a)gmail.com> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Energy Resolution Message-ID: <000a01d3e458$086925c0$193b7140$(a)gmail.com> Content-Type: text/plain; charset="us-ascii" Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

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