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

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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FEFF8/FEFF9 in Demeter
by 이국승(에너지환경소재연구팀) 16 Jun '17

16 Jun '17

Dear Ifeffit users, I remember that one of you have posted the method how we can use FEFF8/FEFF9 in Demeter program. But I cannot find the posting in the archives. Could you please kindly let me know how can I find it or directly write again? Best, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 6
by Clark, Adam 09 Jun '17

09 Jun '17

Dear Robert Thanks, following the linked discussions I am also now able to repeat the problem though first running a feff calculation on the Rh2O3 structure and second on the Rh structure. Having now downloaded the pre release version this does indeed fix this problem. Adam ________________________________ 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: 09 June 2017 14:16:20 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 172, Issue 6 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: Ifeffit Digest, Vol 172, Issue 4 (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Jun 2017 06:16:15 -0700 From: Robert Gordon <ragordon(a)alumni.sfu.ca> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4 Message-ID: <CA+FiM0EcbUaki2K2Zpfb0cFuUHN=tEdLoiun=pMJzQiVMGw-Yg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Adam, I think the problem you are seeing is related to one observed back in April. The Rh2O3 crystal you also have in your project has trigonal symmetry, and trigonal symmetry in 0.9.25 tends to override all others. This was discussed in this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009083.html Bruce made a pre-release of 0.9.26 available at the time that fixed this problem: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009084.html The pre_2 release of 0.9.26 is also available on the main Demeter page: https://bruceravel.github.io/demeter/ -R. On Fri, Jun 9, 2017 at 5:54 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> wrote: > Dear Robert > > > Attached I have given the different feff.inp files generated from using > Artemis and from WebAtoms (named accordingly) along with images showing the > input screens using default parameters. > > > The difference comes in the atoms list generated. Using artemis two short > atoms are produced at 1.91 A which are not present when I use WebAtoms. > Interestingly I have now discovered this does not happen with every artemis > project. I have attached a project where I am getting the erroneous > feff.inp file generation. To replicate the error it is possible to add > another feff calculation into this artemis project with the attached cif. > > > The attached project is an example where this error occurs but I have not > been able thus far to make a new project that repeats this error. > > > Adam > ------------------------------ > *From:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of > ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request@millenia. > cars.aps.anl.gov> > *Sent:* 08 June 2017 23:59:09 > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* Ifeffit Digest, Vol 172, Issue 4 > > 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: Error using Atoms (Robert Gordon) > 2. Re: question about sigma2 and atomic distance (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 8 Jun 2017 15:33:55 -0700 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error using Atoms > Message-ID: > <CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hi Adam, > > I opened the cif file you provided and Artemis/Atoms immediately gave the > atoms.inp file attached. > Running Atoms gave the feff.inp....I don't see a problem. > > Could you provide more detail on how you achieved this erroneous result? > i.e. step by step... > e.g. I opened Artemis v0.9.25 > I clicked 'add' under Feff calculations > I selected Rh.cif and clicked open > et voila! Much humble praise to Bruce... > > -R. > > > > On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> > wrote: > > > Dear Mailing List > > > > > > I have encountered an issue when using the version of Atoms within > > Artemis for the calculation of the scattering paths on metallic FCC > > systems. Attached are both the cif file and the generated feff.inp file > > from using Atoms from within Artemis. Here the problem that occurs is the > > generation of two short atoms at distances of 1.91 ? before the first > shell > > atoms at distances of 2.70 ? for metallic Rh. > > > > ATOMS * this list contains 69 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Rh1 0.00000 > > 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 > > -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 > > -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 > > 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 > > 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 > > 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 > > -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 > > 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 > > 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 > > 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 > > > > > > Using the same input CIF file within WebAtoms does not produce these > short > > distances. > > > > > > Adam Clark > > > > > > PhD Student > > > > > > > > Industrial Doctorate Centre in Molecular Modelling and Materials Science, > > > > Department of Chemistry, > > > > University College London > > > > > > _______________________________________________ > > 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] Ifeffit Digest, Vol 172, Issue 4
by Clark, Adam 09 Jun '17

09 Jun '17

Dear Robert Attached I have given the different feff.inp files generated from using Artemis and from WebAtoms (named accordingly) along with images showing the input screens using default parameters. The difference comes in the atoms list generated. Using artemis two short atoms are produced at 1.91 A which are not present when I use WebAtoms. Interestingly I have now discovered this does not happen with every artemis project. I have attached a project where I am getting the erroneous feff.inp file generation. To replicate the error it is possible to add another feff calculation into this artemis project with the attached cif. The attached project is an example where this error occurs but I have not been able thus far to make a new project that repeats this error. Adam ________________________________ 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: 08 June 2017 23:59:09 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 172, Issue 4 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: Error using Atoms (Robert Gordon) 2. Re: question about sigma2 and atomic distance (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Thu, 8 Jun 2017 15:33:55 -0700 From: Robert Gordon <ragordon(a)alumni.sfu.ca> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Error using Atoms Message-ID: <CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Adam, I opened the cif file you provided and Artemis/Atoms immediately gave the atoms.inp file attached. Running Atoms gave the feff.inp....I don't see a problem. Could you provide more detail on how you achieved this erroneous result? i.e. step by step... e.g. I opened Artemis v0.9.25 I clicked 'add' under Feff calculations I selected Rh.cif and clicked open et voila! Much humble praise to Bruce... -R. On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> wrote: > Dear Mailing List > > > I have encountered an issue when using the version of Atoms within > Artemis for the calculation of the scattering paths on metallic FCC > systems. Attached are both the cif file and the generated feff.inp file > from using Atoms from within Artemis. Here the problem that occurs is the > generation of two short atoms at distances of 1.91 ? before the first shell > atoms at distances of 2.70 ? for metallic Rh. > > ATOMS * this list contains 69 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Rh1 0.00000 > 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 > -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 > -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 > 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 > 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 > 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 > -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 > 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 > 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 > 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 > > > Using the same input CIF file within WebAtoms does not produce these short > distances. > > > Adam Clark > > > PhD Student > > > > Industrial Doctorate Centre in Molecular Modelling and Materials Science, > > Department of Chemistry, > > University College London > > > _______________________________________________ > 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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q2xafs2017 in August
by fred.mosselmans＠diamond.ac.uk 08 Jun '17

08 Jun '17

Hi For those of you that are not aware, Q2XAFS2017 (the International Workshop on Improving Data Quality in XAFS Spectroscopy) is taking place at Diamond Light Source near Oxford, which is where the spires dream, on 14/15 August this summer. See http://www.q2xafs2017.com/ for details / registration Although the abstract deadline is currently listed as 5th June, it will be shortly extended to early July. We hope to see you in England Regards 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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Error using Atoms
by Clark, Adam 08 Jun '17

08 Jun '17

Dear Mailing List I have encountered an issue when using the version of Atoms within Artemis for the calculation of the scattering paths on metallic FCC systems. Attached are both the cif file and the generated feff.inp file from using Atoms from within Artemis. Here the problem that occurs is the generation of two short atoms at distances of 1.91 Å before the first shell atoms at distances of 2.70 Å for metallic Rh. ATOMS * this list contains 69 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Rh1 0.00000 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 Using the same input CIF file within WebAtoms does not produce these short distances. Adam Clark PhD Student Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London

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artemis results not reproducible
by Loges, Anselm G 06 Jun '17

06 Jun '17

Dear fellow EXAFSeteers, I have a somewhat bizarre problem with Artemis fits. I am using Demeter 0.9.25 64bit on a Windows7 machine. The Situation: I am trying to fit the first shell complexing ligands to aqueous metal complexes. I have sets of experiments at different temperatures but otherwise identical conditions and concentrations. When I fit all experiments separately, parameters such as coordination number and metal-ligand distance show systematic variation with temperature (as they should). Therefore, I would like to try fitting all these experiments together and define these parameters as functions of temperature, which would reduce the total number of free parameters relative to the experimental points and should also bring the uncertainties down a bit. To this end, I first made an Artemis project that contains several of the data sets (at different temperatures). Then I made individual parameters for each data set that are exactly as they are in the individual fits (parameter names are different, though) and duplicated the fourier transform parameters of the individual fits. Now each data set has its own set of parameters. No parameters are shared between data sets and there are no connections between data sets via "def" functions in the GDS or anything. The Problem: When start the fit, I get different results from the individual fits. Still mostly within the calculated error values (which are quite large at the moment), so not "significantly different" in the statistical sense of the words but still very different numbers. Whats more, if I add another data set with corresponding parameters (again no connection to the other data sets or parameters), the results for the parameters of the other data sets change again. Am I right in assuming that this should not be the case or is there a connection which I am missing? Might this be a bug? Some fits react a bit sensitive to the choice of k- and R-space windows (but these were identical in individual and simultaneous fits). My fits are pushing the number of independent parameters a bit, according to the log-files (which is why I want to do the simultaneous fits with T-dependent parameters). Might this cause instability in the fit routine. In the simultaneous fits, the number of highly correlated parameters (>0.95) skyrockets (is ok in individual fits), which may be related to the next point. I suspect it may also have to do with the way Artemis decides that the fit is "done". If this is evaluated globally for all parameters somehow, then the observed behavior would not be surprising. But if it is evaluated on a per-parameter or per-data set basis, then it should not be like this. Finally: Is my approach reasonable at all or is that a bad idea? Does someone else use this method? I have not seen it published but then again I am new to this and many publications are a bit reserved on the topic of fitting strategy. Thanks a lot and sorry for the long read, Anselm

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Hephaestus ion chamber absorption
by George Sterbinsky 30 May '17

30 May '17

Hello, Can anyone explain why the values given by the ion chamber utility in Hephaestus differ from those given for a 10 cm He filled ion chamber in figure 3.14 of Grant Bunker's Intro to XAFS book at high energy? For instance, figure 3.14 indicates an absorption fraction of ~3E-7 at 40 keV, whereas Hephaestus indicates 2E-4 at the same energy. Thank you, George

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Help--save k(q) data in larger k range
by Tao Ma 25 May '17

25 May '17

Hi, I was trying to save my data in k(q). I set the k-range for fourier transform, and r-range for the inverse fourier transform, and was able to see the resultant k(q) figure in whatever k-range I want. But when I hit “save in k(q)”, in the generated file I could only get the data in a k-range of 0-8. Is there a way to get the data in a larger k-rang, e.g., 0-15? Thanks! Regards, Tao ⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘ Tao Ma, Dr, Postdoctoral fellow, Gates Catalysis Group, Dept. Chemical Engineering & Materials Science, University of California, Davis

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Guess Parameters Getting Stuck
by M Solo 25 May '17

25 May '17

Hello. I'm currently in process of fitting some exafs data, and have encountered this issue several times. At some point during fit one or several "guess" parameters get stuck on the initial guess value, even if that value is changed to something that has no resemblance to the data being fitted. Further changing the initial guess value has no effect, and the fit merely takes in the new value as if its been "set". The number of values affected range from 1 to all of the variables in the GDS. Regards Aleks

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Re: [Ifeffit] Self absorption in CeO2 spectrum
by Weizi Yuan 23 May '17

23 May '17

Thank you for your kind suggestion, Fred. It gives me some ideas of how to design my next experiment. And I will also try to do self absorption correction and see if it helps at the current stage. Weizi -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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Self absorption in CeO2 spectrum
by fred.mosselmans＠diamond.ac.uk 22 May '17

22 May '17

Hi Weizi, I know this is rather after the event, but should you do the experiment again, it is probably much easier to get surface sensitivity in this sort of system using conversion electron yield e.g. Schroeder et al Surface Science Volume 324, Issues 2-3, 10 February 1995, Pages L371-L377. That should suffer no over-absortpion issues and bulk fluorescence on a film of this thickness will have only a small amount of over absorption at 45 degrees Regards 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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Re: [Ifeffit] Ifeffit Digest, Vol 171, Issue 14
by Weizi Yuan 19 May '17

19 May '17

Got it. Thanks for the response, Anatoly. Weizi On Fri, May 19, 2017 at 4:37 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. Self absorption in CeO2 spectrum (Weizi Yuan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 19 May 2017 16:37:54 -0500 > From: Weizi Yuan <weiziyuan2015(a)u.northwestern.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Self absorption in CeO2 spectrum > Message-ID: > <CAKT5DaVktSW=wr4+jQ7+LFwAo9dgvy6LHdA1CtcAQTd+ > iNzEdg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > I have measured some XANES spectra of CeO2 film(~220nm) in fluorescence > mode at Ce L3 edge with two incident angles of 0.6 degree and 3 degree. My > goal is to get relative surface sensitive (penetration depth~ 20 nm above > edge) information of [Ce3+] from 0.6 o while bulk sensitive information at > 3 o (penetration depth~ 160 nm above edge). In the meantime, I also > collected CeO2 powder reference spectrum under transmission mode. The > comparison is shown in the graph. > The film at 3 degree has a sharper white line than the powder while at 0.6 > degree, it is the opposite. I think this might be because at the surface of > the film,it has more Ce3+ while when we detect the bulk it has more Ce4+. > My question is how can I tell if I need self-absorption correction or not > for the films in this case? Can I say I do not need self absorption > correction because I have a higher normalized u for the film collected in > the fluorescence mode than powder collected in the transmission mode? > Thanks a lot for your comments. > Weizi > [image: Inline image 1] > > > -- > Regards, > Weizi Yuan, > Graduate Student, > Northwestern University, > Ph:(+1)312-560-9619 >

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Self absorption in CeO2 spectrum
by Weizi Yuan 19 May '17

19 May '17

Dear all, I have measured some XANES spectra of CeO2 film(~220nm) in fluorescence mode at Ce L3 edge with two incident angles of 0.6 degree and 3 degree. My goal is to get relative surface sensitive (penetration depth~ 20 nm above edge) information of [Ce3+] from 0.6 o while bulk sensitive information at 3 o (penetration depth~ 160 nm above edge). In the meantime, I also collected CeO2 powder reference spectrum under transmission mode. The comparison is shown in the graph. The film at 3 degree has a sharper white line than the powder while at 0.6 degree, it is the opposite. I think this might be because at the surface of the film,it has more Ce3+ while when we detect the bulk it has more Ce4+. My question is how can I tell if I need self-absorption correction or not for the films in this case? Can I say I do not need self absorption correction because I have a higher normalized u for the film collected in the fluorescence mode than powder collected in the transmission mode? Thanks a lot for your comments. Weizi [image: Inline image 1] -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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jfeff, OS X 10.12, java version "1.8.0_131"
by Jeff Terry 17 May '17

17 May '17

Hi All, Has anyone successfully installed jfeff 9.6.4 on OS X Sierra? The installer crashes after requesting a password when I try to run it. I have tried on OS X El Capitan 10.11 and the same version of java but I get an error message saying it doesn’t recognize java. If I downgrade to java 1.6, the installer runs under OS X 10.11 but then quits with the error message Error changing ownership of /Applications to my user name. I don’t really want the installer changing the ownership of Applications. Is this a common problem? Jeff

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Postdoctoral position at SSRL, SLAC National Accelerator Lab
by Bare, Simon R 17 May '17

17 May '17

SUNCAT Postdoctoral Position for Synchrotron X-ray Science A postdoctoral research position is available at SUNCAT at SLAC National Accelerator Laboratory. The position is available immediately to work on a project developing and optimizing data processing techniques, and guiding students and postdocs through the analysis from synchrotron based x-ray techniques, primarily grazing incidence scattering and spectroscopy, to elucidate the composition and structure of catalysts (thin films and nanostructures) under working conditions. The SUNCAT Center for Interface Science and Catalysis is a partnership between SLAC National Accelerator Laboratory and the School of Engineering at Stanford University. SLAC is a multi-program laboratory owned by the U.S. Department of Energy's Office of Science and operated by Stanford University. At SUNCAT, we focus on interface science and the atomic-scale design of catalysts for the sustainable production of fuels, chemicals, and materials. A key strength of the efforts at SUNCAT is the ability to link theory and experiment, which requires a detailed understanding of the electrocatalyst surface under reaction conditions. A focus is placed on probing the electronic, structural and chemical properties of electrocatalyst systems under operando conditions by using the unique X-ray facilities available at SSRL and other National Laboratories. The postdoctoral fellow will play an integral role in all aspects of these X-ray characterization efforts. The position will report to Prof. Thomas F. Jaramillo (Stanford University) and Simon R Bare (SLAC National Accelerator Lab). Specific responsibilities include: Work with SSRL and SUNCAT scientists to conduct data processing and analysis. This will involve developing and optimizing data processing techniques, and guiding students and postdocs through the analysis. Work with a team to plan and design synchrotron based experiments, including the design and modification of in situ electrochemical cell(s) and establishing measurement protocols. Co-ordinate pre-experiment activities with colleagues (students and postdocs) and beamline scientists setup the beamline and conduct data collection for in-situ surface electrocatalysis and related experiments. Interface with theoreticians at SUNCAT and Stanford to interpret the experimental results in terms of changes to the electronic and lattice structures of the surface of the active electrocatalyst under operando conditions. The position is highly collaborative and will involve interacting with students, postdocs and staff scientists from SUNCAT on all aspects of the synchrotron-mediated research. The candidate will also maintain a safe working environment in the laboratory. Qualifications: * Ph.D. in physics, chemistry, materials sciences, chemical engineering, or related fields. * Demonstrated experience in synchrotron X-ray characterization techniques, in particular hard x-ray scattering and spectroscopy. * Proficiency in Python and/or Matlab, with a strong knowledge of data acquisition methodology. * Familiarity with theoretical analysis of x-ray absorption spectroscopy (e.g.FEFF9, MXAN, DFT, etc) and/or knowledge of ab initio DFT methods a plus. * Experience with electrochemical techniques and catalysis is a plus. * Willingness to learn and bridge knowledge/experience gaps. * Ability to work both independently and in a team environment. * Ability to work and communicate effectively with a diverse population; good interpersonal skills are essential. * Leadership, including the ability to coordinate efforts at SSRL, and to guide students and postdocs throughout all stages of the experiments. * Effective written and verbal communication skills. Applicants should include a cover letter, a brief summary of accomplishments/interests, a curriculum vitae, a list of publications, and names of 2-3 references for future letters of recommendation. Please send applications to Olayinka Popoola at opopoola(a)stanford.edu.

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Calculating Ce oxidation state at the L3 edge
by Stephanie Laga 16 May '17

16 May '17

Dear all, I have a (hopefully) quick question about calculating oxidation state of CeO2 at the L3 edge. When calculating ox state by taking the ratio of peak areas, is the pre-edge feature for Ce included in this calculation? This point isn't clear to me from looking at various papers. I've attached an image from Bernardi 2015, which shows that the %Ce III calculation doesn't include the fitted pre-edge feature A. I'm not sure why this would not be included? Is this because we only consider 2p > 5d transitions and the pre-edge is 2p > 4f (forbidden) transition? Thanks! Stephanie

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Calculation of NSS and R-factor
by Marine Albertelli 16 May '17

16 May '17

Good afternoon, Could you please tell me what is the difference between the calculation of the R-factor and the NSS ? I found that R-factor is equal to : sum((data - fit)^2)/sum(data^2) and NSS = sum((data - fit)^2)/sum(data^2)*100 But when I compare the R-factor obtained by Athena and the NSS divided by 100 (calculated by myself) I didn't find the same results. Did I make a mistake somewhere. Thank you for your answer. Kind regards Marine Albertelli PhD student IPREM 2 av du Président Pierre Angot 64000 Pau FRANCE --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Cobalamin XANES: experiments and simulations do not match
by Ganesh Subramanian 15 May '17

15 May '17

Dear all, I have been working on simulating for the K-edge XANES spectra of methylcobalamin (MeCbl) and cyanocobalamin (CNCbl). The only change in the two materials is one bond (the upper axial bond in an octahedral coordination at the Cobalt site) from CH3 to CN. The molecule consists of about 180 atoms in total. We, however, use a truncated (50 atom) structure and more recently, an extended (90 atom) structure. But neither of them seem to predict the relative changes in peak positions and edge chemical shifts accurately. As a quick summary: Experimental XANES spectra show: 1. CNCbl has a 1 eV blue-shifted absorption edge as compared to MeCbl. 2. The shoulder peak in CNCbl (about 6-7 eV lower than the main-peak) is much stronger (than MeCbl) and comparable in intensity to the main (strongest) peak. We use Gaussian to identify the optimized structure and then feed it to FEFF 8.4 to simulate for the XANES. When we do the simulations we note - 1. CNCbl has an approx. 0.1-0.2 eV red-shifted absorption edge as compared to MeCbl. 2. The shoulder peak intensity is comparable to the main peak intensity in CNCbl. However, in comparing with MeCbl, the shoulder peak intensity is still lower. Incidentally, we see the exact same problem repeat with hydroxocobalamin OHCbl as we see with CNCbl as well ! (I do not present that here, since I assume the origin of the problem is same). I thought, maybe truncation is affecting the the optimized geometry when we perform DFT and hence increased the cluster size to about 90 atoms but noticed no significant change. (We did this quite sometime back just with MeCbl to actually justify the use of a truncated structure. But now we are not sure where the error is). Now I wonder if I am performing the FEFF accurately and not missing something here. I attach the input feff files for the truncated and the more elongated structures of both MeCbl and CNCbl. I also attach the (ATHENA deglitched, merged and normalized) experimental XAFS for MeCbl and CNCbl. Any help in identifying the issue is greatly appreciated ! (Sorry for the long email). Thanks, Ganesh Subramanian Post Doctoral Research Scholar, Spence Group, Arizona State University

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E0 on linear combination fitting: fit or not?
by Carrillo Sanchez, Pamela 13 May '17

13 May '17

Hi all, I have gone through the mail archives as well as following the instructions of Athena user's manual as well as Scott Calvin's book but still I find myself with the doubt of how correctly "choose E0". I have aligned the data and standards with the merge of reference foils measurements of the metal (Mn). We did not have a reference foil placed while measuring the data so I used the merge of the references scans when the standards were measured and they showed a consistent energy shift. I have set the same E0 for all the data and standard to the same E0, I chose the first peak of the derivative in the data (6MnRh_RED). When I do the LCF analysis without 'fitting E0' , I get a worse fitting than when I choose the fit E0 on Athena as well as different types of components on the fitting. Which one is the best choice for it ? From what I have read I think that without fitting E0 would be the proper one regardless of the "worse fit". Also, I would like to know which fit range would be appropriate for this, I have chosen -20 to +30 eV due to the features of my data and ranges for XANES. Any recommendation. I have attached the files for the project and screenshots of both fittings. Any help is highly appreciated! Pamela

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