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

Re: [Ifeffit] Ifeffit Digest, Vol 173, Issue 1
by Christopher Thomas Chantler 05 Jul '17

05 Jul '17

Thanks Fred and well suggested. I also encourage all interested. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 5 July 2017 8:21:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 173, Issue 1 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. Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts (fred.mosselmans(a)diamond.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 10:14:17 +0000 From: <fred.mosselmans(a)diamond.ac.uk> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts Message-ID: <CF65047C5B0562499EAFF9FBBC542D640105240B89@exchmbx01> Content-Type: text/plain; charset="iso-8859-1" [cid:image002.jpg@01D2974C.A644EF90]<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> Q2XAFS 2017 will bring together experts in the field of X-ray Absorption Spectroscopy to discuss aspects of the technique that affect data quality in XAFS experiments. The workshop will provide a forum for discussions with the goal of reviewing international standards and protocols, and developing revised recommendations for best practice when performing XAFS experiments. It will also look towards the first agreed data formats and standards for XAFS data and deposition. The workshop is hosted by Diamond Light Source<http://www.diamond.ac.uk/Home.html> and will take place on Monday 14th & Tuesday 15th August at Harwell Science and Innovation Campus, Didcot, UK. The full programme can be viewed on the website here - Q2XAFS 2017 Programme<http://www.q2xafs2017.com/Conference/Q2XAFS2017/Scientific-Programme.html>. Registration is ?220 standard and ?180 for students which includes access to 2 full days of scientific programme, a welcome reception (Sunday 13th August) a workshop dinner (Monday 14th) , optional facility tour and lunches and refreshments each day. The call for poster abstracts will remain open until the 7th July, please see the website for more details on submission<http://www.diamond.ac.uk/Conference/Q2XAFS2017/Participate/Abstract-Submiss…> poster presentation and for the abstract template. Visit the Q2XAFS 2017 website<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> to register and for details of the programme and further information. http://www.q2xafs2017.com/Conference/Q2XAFS2017.html We hope you can join us in August. Best wishes, Q2XAFS 2017 Local Organising Committee T: +44 (0) 1235 778384 E: q2xafs2017(a)diamond.ac.uk Sorry for this partial spam, but my excuse Is the "godfathers"(?) of this list Matt Newville ,in person, and Bruce Ravel, by videolink, will be presenting, and sometimes it is sunny in Oxfordshire. Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk http://orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts
by fred.mosselmans＠diamond.ac.uk 05 Jul '17

05 Jul '17

[cid:image002.jpg@01D2974C.A644EF90]<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> Q2XAFS 2017 will bring together experts in the field of X-ray Absorption Spectroscopy to discuss aspects of the technique that affect data quality in XAFS experiments. The workshop will provide a forum for discussions with the goal of reviewing international standards and protocols, and developing revised recommendations for best practice when performing XAFS experiments. It will also look towards the first agreed data formats and standards for XAFS data and deposition. The workshop is hosted by Diamond Light Source<http://www.diamond.ac.uk/Home.html> and will take place on Monday 14th & Tuesday 15th August at Harwell Science and Innovation Campus, Didcot, UK. The full programme can be viewed on the website here - Q2XAFS 2017 Programme<http://www.q2xafs2017.com/Conference/Q2XAFS2017/Scientific-Programme.html>. Registration is £220 standard and £180 for students which includes access to 2 full days of scientific programme, a welcome reception (Sunday 13th August) a workshop dinner (Monday 14th) , optional facility tour and lunches and refreshments each day. The call for poster abstracts will remain open until the 7th July, please see the website for more details on submission<http://www.diamond.ac.uk/Conference/Q2XAFS2017/Participate/Abstract-Submiss…> poster presentation and for the abstract template. Visit the Q2XAFS 2017 website<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> to register and for details of the programme and further information. http://www.q2xafs2017.com/Conference/Q2XAFS2017.html We hope you can join us in August. Best wishes, Q2XAFS 2017 Local Organising Committee T: +44 (0) 1235 778384 E: q2xafs2017(a)diamond.ac.uk Sorry for this partial spam, but my excuse Is the "godfathers"(?) of this list Matt Newville ,in person, and Bruce Ravel, by videolink, will be presenting, and sometimes it is sunny in Oxfordshire. Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Exporting Curves (as Data rather than Images)
by Felix E. Feiten 26 Jun '17

26 Jun '17

Dear all, I think the title is almost enough explanation. I would like to export the data corresponding to fits, chi(k), fourier-transform and back-transform to plot them with a different software. I couldn't figure out how, can someone please help me? With kind regards Felix

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Nearest neighbor statistics in a random alloy
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear all, I am fitting a Pt9Co1 foil sample. I assume the sample to be basically fcc platinum with every 10th atom randomly replaced by cobalt. Here are the assumptions I make: 1. every atom has 12 nearest neighbors 2. every Pt atom has (on average) 10.7 Pt nearest neighbors and 1.3 Co nearest neighbors 3. every Co atom has (on average) 11.7 Pt nearest neighbors and 0.3 Co nearest neighbors I have been told that assumptions 2 and 3 are not precise. Here is what I'm confused about: In order to determine the number of Pt or Co nearest neighbors I looked at an ensemble of 13 atoms: 1 absorber and 12 scatterers/nearest neighbors. I assume that the Pt/Co ratio in this ensemble is 9/1 and therefor, statistically, 1.3 out of those 13 atoms should be Co. That means that if Co is the central atom only 0.3 Co atoms are remaining for the 12 nearest neighbors. On the other hand, if Pt is the central atom, (all) 1.3 Co atoms are remaining for the 12 nearest neighbors. I have been told that the ratio of Pt/Co should be 9/1 in the 12 nearest neighbors, not in the 12 atoms including the central atom (quote: "because we have a bulk sample"). But I do not understand why. Can someone please explain the correct answer to me? With kind regards, Felix

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Automatically doing many fits / Scripting
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear Ifeffit mailing-list, first of all sorry for writing another mail to the list in such a short time span, I hope people will not get sick of me too quickly. I want to do many fits for the same data with varying start-parameters. More specifically, I am doing fits to EXAFS data of the Pt L3 edge of PtCo(X) nanoparticles and want to vary sigma^2 for each of the two paths (Pt-Pt and Pt-Co) that I fit. I want to 1. start a fit with certain parameters, 2. save the log file, 3. change one parameter many (120 for now) times. If there is no functionality to do this in Artemis I'll have to resort to using some external script that abuses Artemis. In that case I will report on how it went. But obviously, it would be much more comfortable if Artemis had something like this implemented. Any way to start a fit from the windows command line (I'm using Windows 10) would also be very helpful as that would probably allow me to do the scripting in PowerShell relatively easily. With kind regards, Felix

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nonsensical negative values / restrictions
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear all, I have the following problem: In some fits using Artemis (Demeter 0.9.25) I will get negative values for parameters where it makes no sense at all. For example, when trying to fit two first shell paths, Pt-Pt and Pt-O, for a Pt nanoparticle, sigma^2 for the Pt-O path becomes negative. Obviously, sigma^2 has to be a positive number. My questions: 1. Why does the fit algorithm do this? 2. What can I do to avoid this? I know that there are most likely significant problems with my fit if this behaviour occurs. As far as I know it's possible to impose restrictions in Artemis and if anyone could point me towards a tutorial explaining how to implement restrictions that might be a first step in the right direction. Currently, the chapter "Constraints and restraints" in the Artemis documentation is "Coming soon......". With kind regards, Felix

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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 15
by Weizi Yuan 22 Jun '17

22 Jun '17

Hi Anatoly, Thanks for your quick response. Yes, I actually asked the self absorption question about CeO2 a few weeks ago. And your answer that it is due to self absorption leads me to study more about it and I appreciate it. In that last question, the strong attenuation of signal occurs in the incident angle = 0.6 o . However, when the incident angle is 3 o under room temperature ,air, the peak intensity is stronger than the CeO2 measured in transmission mode, which leads me to think that no over absorption correction needed here. And I try to conduct the correction which gives me crazily high (~9 after normalization) peak intensity. This makes me further confirm that no strong self absorption effect here. And if no strong self absorption in RT, air ,then why strong attenuation in RT, vacuum condition(case ii in my question)? For your answer,I am a little confused. Are you saying self absorption occurred in only case ii or in both cases, even though the result of case i spectrum has a higher signal than the transmission mode data? Thank you, Weizi On Thu, Jun 22, 2017 at 10:16 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. Self absorption or Ce4+ reduction in the CeO2 film? (Weizi Yuan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Jun 2017 10:11:05 -0500 > From: Weizi Yuan <weiziyuan2015(a)u.northwestern.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Self absorption or Ce4+ reduction in the CeO2 film? > Message-ID: > <CAKT5DaU1U2UX7bVUx9ffhvTfE7txqnZDgGu3cNujM6ceQyp6Hg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > I have measured some spectra of a CeO2 film(~200nm) grown on Yittria > stablized Zirconia(YSZ) substrate under 2 conditions. > (i) room temperature, ambient atmosphere > (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of the > DHS 1100 anton paar, > The spectra are collected in fluorescence mode. The incident angle is 3 o > and the fluorescence collection angle is 90 o. > > My questions are: > (i) From the theory behind the FLUO program developed Dr. Daniel Haskel, > CeO2 spectra collected with a 3 o incident angle *would have a strong self > absorption effect and need* > > correction , however, *the signal *is not attenuated compared with the > CeO2 powder taken in a transmission mode, shown in attached plot. > I've gone through many literature and people sometimes tell that whether > they have a successful self absorption correction by comparing the > spectrum with a spectrum taken under a transmission mode. > So I'm wondering if I can say that I don't need a self absorption > correction in this case? > (ii) > The Ce4+ peak in the spectrum collected under condition (ii) has a much > lower intensity. I think it is due to the reduction of Ce 4+ under vacuum, > however, the Ce3+ peak does not show an increased signal here. Which makes > ma doubt whether this is simply reduction of Ce *or might be from over > absorption? * > > Thanks for any response. > > [image: Inline image 1] > -- > Regards, > Weizi Yuan, > Graduate Student, > Northwestern University, > Ph:(+1)312-560-9619 >

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Self absorption or Ce4+ reduction in the CeO2 film?
by Weizi Yuan 22 Jun '17

22 Jun '17

Dear all, I have measured some spectra of a CeO2 film(~200nm) grown on Yittria stablized Zirconia(YSZ) substrate under 2 conditions. (i) room temperature, ambient atmosphere (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of the DHS 1100 anton paar, The spectra are collected in fluorescence mode. The incident angle is 3 o and the fluorescence collection angle is 90 o. My questions are: (i) From the theory behind the FLUO program developed Dr. Daniel Haskel, CeO2 spectra collected with a 3 o incident angle *would have a strong self absorption effect and need* correction , however, *the signal *is not attenuated compared with the CeO2 powder taken in a transmission mode, shown in attached plot. I've gone through many literature and people sometimes tell that whether they have a successful self absorption correction by comparing the spectrum with a spectrum taken under a transmission mode. So I'm wondering if I can say that I don't need a self absorption correction in this case? (ii) The Ce4+ peak in the spectrum collected under condition (ii) has a much lower intensity. I think it is due to the reduction of Ce 4+ under vacuum, however, the Ce3+ peak does not show an increased signal here. Which makes ma doubt whether this is simply reduction of Ce *or might be from over absorption? * Thanks for any response. [image: Inline image 1] -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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GRC on clusters
by Anatoly Frenkel 21 Jun '17

21 Jun '17

Hello, There is an opportunity for those interested in applications of XAFS methods to nanomaterials, in particular to nanoclusters, to participate in the Gordon Conference on Clusters and Nanostructures in Mt. Holyoke College from July 8-14. For more information please see attached flyer. Best regards, Anatoly Frenkel Stony Brook University/BNL

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Athena Bug Report
by Nicholas Marcella 20 Jun '17

20 Jun '17

Hello, *Bug:* Although the [Natural log] box was checked, the natural log was not being applied to the data (figure 1). This was very easy to miss. Data imported under the conditions of figure 1 (Purple) resulted in a deviation from Bruce Ravel’s Au foil (Blue), the original March import (Green), and the June import after ensuring the μ(E) box contained the natural log of (mkxpq.i0)/(mkxpq.i1) (Red) – Figure 2. *Replication of the bug:* The bug only appears if the following steps are followed: 1) In a new file X, fluorescence data is imported, i.e. natural log box is unchecked. 2) File X is saved and Athena is closed. 3) Athena is started and File X is opened. 4) When importing a new dataset, the natural log box will be checked but the natural log will not be applied to μ(E). *Solution:* 1) Uncheck and then check the natural log box. Ta-da… [image: Inline image 2] [image: Inline image 3] Regards, -- *Nicholas J. Marcella* | Masters Student *Materials Science and Chemical Engineering* *Stony Brook University* *Tel: (914)-703-9843* *Structure and Dynamics of Applied Nanomaterials | Brookhaven National Lab <https://www.bnl.gov/chemistry/SDAN/>* *Senator - MSCE | Graduate Student Organization <http://sbgso.org/index.php/about-us/senators>* *Senior Coordinator | Campus Recreation <http://studentaffairs.stonybrook.edu/rec/>*

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