- 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

5 4

(no subject)
by Carrillo Sanchez, Pamela 11 May '17

11 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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Save the date: Nov 1-3, 2017, XAFS short course at BNL
by Anatoly Frenkel 09 May '17

09 May '17

Dear Colleagues: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course will continue the annual tradition of gathering a group of scientists, active in the field, to share their expertise with those interested in learning about the use of x-ray spectroscopy methods in their research. *The course will be useful for those scientists who are already familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced analysis and modeling methods*. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis techniques. Course instructors will use examples from their research during presentations. Topics covered will include theory of XANES and EXAFS, direct modeling methods using Molecular Dynamics simulations and Reverse Monte Carlo, multiple data set modeling and multiple-scattering analyses. Other topics will include, but not limited to: chemometrics, bonding dynamics and transformation kinetics. During the data analysis practicum on Nov. 3 the course participants will get an opportunity to work with demonstration examples and/or their research projects with the help of the course instructors. The course will be open to 30 participants, selected based on their application materials. The course web page will appear on BNL web site in near future, with instructions how to apply. For any inquiries please contact me. Best Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Error importing data into Athena
by Bone, Sharon Elizabeth 03 May '17

03 May '17

Hi, I’m running the current version of Athena on a windows 10 machine. It had been working fine, but now I get an error whenever I try to import new data (.dat file from SSRL). The error tells me the program can’t read the file and asks whether I need a plugin. Do I need a plugin? How do I uninstall and reinstall the program? I’m guessing this might be the best fix? Thanks! Sharon

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Need FEFF9 for Z> 95: how to use in Demeter?
by Bone, Sharon Elizabeth 01 May '17

01 May '17

Hello, I have a problem with demeter that I am hoping to get some help with: My understanding is that the current version of demeter does not support versions of FEFF greater than 6. Usually this isn’t a problem for me, but I recently started working with elements with Z > 95 and FEFF6 can’t handle these elements. I recently tried to download an old version of demeter (ixafs through http://cars9.uchicago.edu/ifeffit/Downloads) but the link was no longer valid. Is there a way to access an old version? I’d far prefer to use the new vesion of demeter. Is there any chance that the capability to run higher versions of FEFF will be incorporated soon? Thanks for your help! Best, Sharon

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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 21
by Christopher Thomas Chantler 21 Apr '17

21 Apr '17

[?] I'm just agreeing with Matt's comment. Too fine a spacing does not help you due to typical broadening from imfp or thermal sources [or structural disorder]. And the difference between operation of ifeffit and larch in this context is pretty interesting. -------------------------------------------------------------------------------------- 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: Friday, 21 April 2017 11:01:11 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 170, Issue 21 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 170, Issue 19 (Matt Newville) 2. Fwd: Ifeffit Digest, Vol 170, Issue 19 (Matt Newville) 3. Looking for EXAFS data of Ni2+ ion in aqueous solution (Van Vu) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Apr 2017 21:18:39 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19 Message-ID: <CA+7ESbpEWenMLpspnYAXT4j2T1LkjAaYua59XcGebLpteKTyWg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Chris, On Thu, Apr 20, 2017 at 5:02 PM, Christopher Thomas Chantler < chantler(a)unimelb.edu.au> wrote: > Note that in general any and every smoothing operation reduces the > information content of the data and its ability to reveal structure. > Well, maybe. If one has mu(E) measured every 0.01 eV over an 600 eV EXAFS scan to k=12A^-1, one does not really 60,000 independent measures of the structure. Yuji's data wasn't that absurd, but it did have close to 4000 measurements for the full EXAFS spectrum out to k=18^-1. And to be clear, there is not anything wrong with that, it's just a matter of how you decide to treat it. As the plots attached in Yuji's original message and my replies show, the resulting chi(k) definitely has is amplitude suppressed when doing a simple boxcar average of data onto the 0.05 Ang^-1 grid (Athena with Ifeffit). But when using cubic spline interpolation (Larch), the amplitude of the EXAFS oscillations are not noticeably suppressed, though the high frequency noise is also much higher. Applying a Savitzky-Golay filter prior to the cubic spline interpolation did not appreciably suppress the EXAFS oscillations though the high frequency noise was reduced. Very finely-spaced energy data might reveal is at much higher R than we can hope to model with EXAFS. A k-grid of 0.05 Ang^-1 can give frequencies to 31Ang, and so is probably accurate to 16Ang without significant signal loss. That is, out to k=18Ang^-1, you really only need 360 samples, but you'd like these as noise-free as possible. Having 3600 measurements on a grid of 0.005 Ang^-1 might give you data out to 160Ang in principle, but the photo-electron tends to not cooperate. --Matt

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Looking for EXAFS data of Ni2+ ion in aqueous solution
by Van Vu 21 Apr '17

21 Apr '17

Dear everyone, I am looking for XAS data of Ni2+ ion in aqueous solution that contains EXAFS data in the k range of 0-12 (Angstrom-1) or so for an undergraduate student project. I was wondering if anyone would be willing to share the data with me? Many thanks in advance. Best, Van On Fri, Apr 21, 2017 at 5:02 AM, Christopher Thomas Chantler < chantler(a)unimelb.edu.au> wrote: > Note that in general any and every smoothing operation reduces the > information content of the data and its ability to reveal structure. Also, > many of the smoothing algorithms change the data point values at vertices, > so change the data prior to analysis. > > > Hence in general avoid unless you know exactly the physical cause > requiring smoothing. > > > Best wishes > > > ------------------------------------------------------------ > -------------------------- > 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@millenia. > cars.aps.anl.gov> > *Sent:* Friday, 21 April 2017 3:00:01 AM > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* Ifeffit Digest, Vol 170, Issue 19 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://protect-au.mimecast.com/s/2mpEBkUbb8ExSZ?domain= > millenia.cars.aps.anl.gov > <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: The difference of EXAFS oscillation when using Athena and > when using Larch (Yuji Mahara) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Apr 2017 19:47:20 +0900 > From: "Yuji Mahara" <mahara.yuji(a)e.mbox.nagoya-u.ac.jp> > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using > Athena and when using Larch > Message-ID: <003501d2b9c3$7c75c560$75615020$(a)e.mbox.nagoya-u.ac.jp> > Content-Type: text/plain; charset="utf-8" > > Dear Matt > > > > Thank you for your reply. > > I confirmed that chi (k) becomes smooth by the Savitzky-Goley method by > doing the attached lar file. > > > > I will try on various conditions from now. > > I may also ask if there is something I do not understand. > > Thank you for your help again! > > > > Bests, > > Yuji Mahara > > > > > > From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov > <ifeffit-bounces(a)millenia.cars.aps.anl.gov>] On Behalf Of Matt Newville > Sent: Thursday, April 20, 2017 5:26 AM > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using > Athena and when using Larch > > > > Hi Yuji, > > The attached larch script (a modification of your script but note: not > python, so you may have to add a bunch of '_larch=mylarch' arguments) to > show the effects of smoothing with Savitzky-Golay and of interpolating onto > a "classic XAFS energy grid". You might want to play around with this > different options. It definitely seems that none of these methods are > systematically over-smoothing the data and reducing the amplitudes of the > oscillations -- one more reason to use Larch instead of Ifeffit. But it > also seems like smoothing this data with a Savitzky-Golay fitler is helpful. > > Also attached are plots showing k- and R-space generated from the attached > script. > > > > --Matt > >

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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19
by Christopher Thomas Chantler 20 Apr '17

20 Apr '17

Note that in general any and every smoothing operation reduces the information content of the data and its ability to reveal structure. Also, many of the smoothing algorithms change the data point values at vertices, so change the data prior to analysis. Hence in general avoid unless you know exactly the physical cause requiring smoothing. Best wishes -------------------------------------------------------------------------------------- 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: Friday, 21 April 2017 3:00:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 170, Issue 19 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: The difference of EXAFS oscillation when using Athena and when using Larch (Yuji Mahara) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Apr 2017 19:47:20 +0900 From: "Yuji Mahara" <mahara.yuji(a)e.mbox.nagoya-u.ac.jp> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using Athena and when using Larch Message-ID: <003501d2b9c3$7c75c560$75615020$(a)e.mbox.nagoya-u.ac.jp> Content-Type: text/plain; charset="utf-8" Dear Matt Thank you for your reply. I confirmed that chi (k) becomes smooth by the Savitzky-Goley method by doing the attached lar file. I will try on various conditions from now. I may also ask if there is something I do not understand. Thank you for your help again! Bests, Yuji Mahara From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Thursday, April 20, 2017 5:26 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using Athena and when using Larch Hi Yuji, The attached larch script (a modification of your script but note: not python, so you may have to add a bunch of '_larch=mylarch' arguments) to show the effects of smoothing with Savitzky-Golay and of interpolating onto a "classic XAFS energy grid". You might want to play around with this different options. It definitely seems that none of these methods are systematically over-smoothing the data and reducing the amplitudes of the oscillations -- one more reason to use Larch instead of Ifeffit. But it also seems like smoothing this data with a Savitzky-Golay fitler is helpful. Also attached are plots showing k- and R-space generated from the attached script. --Matt

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The difference of EXAFS oscillation when using Athena and when using Larch
by Yuji Mahara 20 Apr '17

20 Apr '17

Dear All, I am Yuji Mahara at Nagoya University, Japan. I am using Athena in Demeter 0.9.24 package and Larch 0.9.33 on windows 10. At that time, I am worrying about the difference of EXAFS oscillation when using Athena and when using Larch. k3-weighted Pd K-edge EXAFS and Fourier transform EXAFS spectrum for PdO bulk are shown in attached file(PdO.png). When XAFS raw data is read using Athena and EXAFS oscillation is obtained, EXAFS spectrum is smooth and noise is small. On the other hand, using Larch, noise is noticeable in k space. This phenomenon occurred when analyzing other XAFS data as well. I tried to analyze XAFS data by Athena and Larch with the almost same conditions. Does this difference of EXAFS results arise from the difference in autobk's algorithm between Athena and Larch? The analysis conditions are shown below. If someone knows this reason, please let me know. Best regards, Yuji Mahara ****************************************** ■ Yuji Mahara Nagoya University(Japan) D3 Graduate School of Engineering Furo-cho, Chikusa-ku, Nagoya-shi, Aichi, 466-8603, Japan ・Phone : <tel:%2B81-52-789-3192> +81-52-789-3192 ・E-mail : <mailto:mahara.yuji@e.mbox.nagoya-u.ac.jp> mahara.yuji(a)e.mbox.nagoya-u.ac.jp ****************************************** #####Analysis condition of Athena ##### e0 -->[ set e0 to a fraction of the edge step] --> 24355.9037323484 Normalization order: 3 Pre-edge range: from -150 to -60 eV Normalization range: from 150 to 1100 eV Rbkg: 1 k-weight used by spline: 2 Spline clamp: low=None, high=Strong Spline range in k: from 0 to 17 Fourier transform k-range: from 3 to 15, dk=0.5, window=’hanning’ #####Analysis condition of Larch ##### dat.e0 = 24355.9037323484 <-- e0 was estimated by Athena pre_edge(dat.e, dat.mu, group=dat, e0=dat.e0, pre1=-150, pre2=-60, norm1=150, norm2=1100, nnorm=2, _larch=mylarch) autobk(dat.e, dat.mu, group=dat, e0=dat.e0, rbkg=1, nclamp=5, clamp_lo=0, clamp_hi=24, kstep=0.05, kmin=0, kmax=17, kweight=2, win='hanning', _larch=mylarch) xftf(dat.k, dat.chi, group=dat, kmin=3, kmax=15, dk=0.5, window='hanning', kweight=3, _larch=mylarch) #########################

2 6

Silent Oxygen
by Fuxiang Zhang 19 Apr '17

19 Apr '17

Hi, all, I am in studying the EXAFS of perovskite and clearly see the split of the first peak after ion irradiation. It should come from a symmetry change, so I use a tetragonal model (instead the original cubic) which contains two independent O sites. However, after running Atoms and Feff, all paths are contributed by only one O atom and nothing related to another Oxygen atoms (see attached file). As a result it may be difficult to get a good fit of the first split Ta-O peaks. I am not sure if it is true or something wrong. Thank you very much Fuxiang Zhang

3 3

the shortest possible K-range ,
by Al Humaidi, Mahmoud 18 Apr '17

18 Apr '17

Hi , I want to ask please what is the shortest k-range one can use for "Forward Fourier transform" in my projects I used: Spline range k 0.0 - 9.0 k range in Forward Fourier transform 1.0 - 9.0 A^-1 I am trying to reduce the contribution of noise in FT .. the attached project shows nice fit ,,,but high phase shift toward lower R value ,, any recommendation please I will appreciate .. and thank you in advance , best regards Mahmoud AL Humaidi --------------------------------------------------------------------------------- Mahmoud Al Humaidi Department of Physics, University of Siegen Emmy-Noether-Campus Walter-Flex-Str. 3, 57072 Siegen Room : B-015 Tel : +49 (0) 271 740 3727 ---------------------------------------------------------------------------------

2 1

Installation to mac OS/ Hephaestus crash in Perl 6.00
by Acevedo-Esteves, Raul 12 Apr '17

12 Apr '17

I was able to install Demeter on a mac (OS X el capitan 10.11.6). Athena runs well, Hephaestus work intermittently. After a while, it crashes when using the periodic table. · After installation, I have this message in terminal: “Some of the ports you installed have notes: p5.24-libwww-perl has the following notes: As of version 6.00, libwww-perl has been split into multiple packages. If you were using p5.24-libwww-perl for just one or two of its modules before, you may be able to pare down your installation to just those modules now. Other important changes have been made that may affect your code; for details, please see: /opt/local/share/doc/p5.24-libwww-perl/Changes” · The log in Hephaestus displays the following message: 11:31:46: Missing argument in sprintf at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Wx/PeriodicTable.pm line 183. Regards, Raul Acevedo, PhD Post Doctoral Research Associate – ISS beamline NSLS-II, Bldg 743 C08U Brookhaven National Laboratory Upton, NY 11973-5000 631 344 4181<tel:631%20344%204181> racevedo(a)bnl.gov<mailto:racevedo@bnl.gov>

1 0

Information content from Athena for Hamilton test?
by Will Bennett 11 Apr '17

11 Apr '17

Hi everyone, Just a quick question regarding the "Information Content" output in Athena's LCF window. I've recently been playing around with using the Hamilton test (as outlined in Scott Calvin's book "XAFS for Everyone") to interrogate my combinatorics results. As many of you will know, this requires an estimate of the number of independent measurements in the data, in order to determine the degrees of freedom and subsequently the "a" value for computing the Lower Incomplete Beta Function. Would Athena's value for "Information Content" be appropriate to use as an estimate of the number of independent measurements in this case? How is this value of "Information Content" determined in Athena? Thanks in advance. Will

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 7
by Christopher Thomas Chantler 10 Apr '17

10 Apr '17

You really need to know the number of actual data points, which must come from the actual data. You should also know the experimental uncertainties of each point. Most standard procedures map the actual data to a uniform grid, sometimes with smoothing of the original data. Then the information content is lost. We are doing final testing on some general routines to address this and will make them available soon. -------------------------------------------------------------------------------------- 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: Tuesday, 11 April 2017 3:00:02 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 170, Issue 7 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. Information content from Athena for Hamilton test? (Will Bennett) 2. Re: Information content from Athena for Hamilton test? (Wayne Lukens) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Apr 2017 13:59:36 +1000 From: Will Bennett <w.bennett(a)griffith.edu.au> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Information content from Athena for Hamilton test? Message-ID: <CAA5p-7P__WKyB6Hzf4bUkd6=+mYEEvGc967p+3hdcsqAvY8ENw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi everyone, Just a quick question regarding the "Information Content" output in Athena's LCF window. I've recently been playing around with using the Hamilton test (as outlined in Scott Calvin's book "XAFS for Everyone") to interrogate my combinatorics results. As many of you will know, this requires an estimate of the number of independent measurements in the data, in order to determine the degrees of freedom and subsequently the "a" value for computing the Lower Incomplete Beta Function. Would Athena's value for "Information Content" be appropriate to use as an estimate of the number of independent measurements in this case? How is this value of "Information Content" determined in Athena? Thanks in advance. Will

1 0

SSRL EXAFS Summer School
by Ritimukta Sarangi 10 Apr '17

10 Apr '17

Hello folks, This is a reminder that today is the last day to apply for the summer school in April. I encourage you to visit the site at: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html>. Best Wishes, -Riti Sarangi

1 0

Larch 0.9.33
by Matt Newville 05 Apr '17

05 Apr '17

Hi Folks, We've released and uploaded Larch 0.9.33. This have been many small fixes and improvements over the past year or so, including significant progress on handling X-ray diffraction data from X-ray micro-probes. There have also been improvements in Python 3 support,so that almost everything now works in both Python 2.7 and 3.6. The "server mode" for Athena and Artemis now works on all platforms and I strongly encourage everyone to use this over the ifeffit back end. Progress has been made on the xyfit app, a peak fitting GUI. It's not complete, but any feedback on functionality or usability at this point would be greatly appreciated. To install, please see http://cars.uchicago.edu/xraylarch/installation.html --Matt Newville

1 0

Conflicting FEFF calculation
by Ashis Biswas 04 Apr '17

04 Apr '17

Dear All, I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter. I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated. With regards, Ashis -- Dr. Ashis Biswas Alexander von Humboldt Postdoctoral Fellow Environmental Geochemistry Group University of Bayreuth Room: 211, Geo III Universitätsstraße 30, 95447 Bayreuth, Germany Ph. No.: +49 921 553991; Fax:+49 921 552334

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number of independent points
by dcnguyen 31 Mar '17

31 Mar '17

Dear Seniors, I have an issue of a discrepancy between values of independent points calculated by Demeter 0.9.25, on Windows 7, shown on the path page and the one presented on the log file after a fit to data. For an example, I use the file named FeS2_final.fpj that you have in your computer, and choose an R-range 1.2-4.2 A, and a k-range 3.00-14.80. Then the N value is calculated by Artemis and shown as 22.54 after clicking "shown Nidp" from the "Data" tab on the path page. The value is consistent with the formula N=(2/pi)*delta_K*delta_R. However, after I click the "Fit" button and look at the Log file, the Nidp is shown as 22.0312500. My question is what causes this discrepancy. When publishing data, which number shoud be reported? Thank you. Bokky Duc-Chau Nguyen IoP, Academia Sinica, Taiwan

2 1

APS/IIT XAFS Summer School - Final announcement
by Carlo Segre 27 Mar '17

27 Mar '17

Hello All: The APS/IIT XAFS Summer School will be held from July 9-13, 2017 in Chicago Please see the attached flyer for details. We only have 10 slots left so if you are interested, please send your application to Grant Bunker <bunker(a)iit.edu> soon. Carlo -- 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

1 0

Multiple data set fit limit
by Victor Streltsov 24 Mar '17

24 Mar '17

Hello Bruce, The Linux latest version of Artemis limits multiple data set fit to 2 data sets. The input takes any number of data sets but 2 sets is used in the fit only. I've tried latest available windows version it uses more than 2 in fit (e.g. I used 3). Thanks, Victor Streltsov

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Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 20
by Abhinav Prabhakar 23 Mar '17

23 Mar '17

Hello Robert, Thanks for your help. We do not have access to ICSD at the moment, but should get it soon. I can't see the pdf that you attached. Could you send it again? Thank you very much. Regards, Abhinav On Tue, Mar 21, 2017 at 3:02 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Ifeffit Digest, Vol 169, Issue 9 (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Mar 2017 12:02:41 -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 169, Issue 9 > Message-ID: > <CA+FiM0HUOwyvK-=pU7Xa0UC-U=PKqeHYyu2gZ-VQgfYsxQt+7Q@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Abhinav, > > As I mentioned previously, it is often helpful to check a database (i.e. > the ICSD) for a standardised form of the crystal structure. > As a courtesy, I have done that for you for this structure and attached a > pdf. You would need to enter the structural > information manually in ATOMS rather than by importing a cif file. > > Looking at the notes, the transformation from B11b to Cc is not so > straightforward. > > You should check with your institution to see if they have access to this > (ICSD) resource. > > regards, > Robert > > > On Wed, Mar 15, 2017 at 9:05 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 03/14/2017 06:15 AM, Abhinav Prabhakar wrote: > > > >> Attached is the CIF file in question. The crystal is Tobermorite 14A, > >> taken from COD website. > >> > >> > > Abhinav, > > > > I don't understand the contents of the CIF file in the context of the > copy > > of the International Tables that I have in front of me. The list of > > equivalent positions given in the CIF file just doesn't seem to be right > > for space group 9. > > > > The CIF file is clearly using the C axis as the unique axis since the z > > coordinate is the negated coordinate. But the list of positions does not > > correspond to any of the three cell choices. > > > > While this could be a problem in Artemis, I am inclined to think that the > > authors of the paper cited in the CIF file made some kind of non-standard > > choice for the setting of their crystal. > > > > As I said before, Artemis does what the International Tables tell it to > > do. If the author of a crystallography paper makes some non-standard > > choice, Artemis won't know how to deal with it. > > > > B > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 743, Room 114 > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > _______________________________________________ > > 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 > > >

3 2

Re: [Ifeffit] Strange EXAFS oscillations, never seen before
by Rana, Jatinkumar Kantilal 22 Mar '17

22 Mar '17

Dear Carlo and Lorenzo, Many thanks for sharing your feedback. I agree, the only option is to remeasure the system. Best regards Jatin ________________________________________ 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: Monday, March 20, 2017 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 169, Issue 19 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: Strange EXAFS oscillations, never seen before (Carlo Segre) ---------------------------------------------------------------------- Message: 1 Date: Sun, 19 Mar 2017 12:00:14 -0500 (CDT) From: Carlo Segre <segre(a)iit.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Strange EXAFS oscillations, never seen before Message-ID: <alpine.DEB.2.20.1703191154500.17810(a)hydride.segre.home> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Rana: I agree. The data is basically unusable as it is. You clearly have issues in the background (look at the oscillations in the pre-edge area) and the three data sets are different from each other which is another clue. It looks like you have transmission data with a very samll edge jump (0.09) which is sort of marginal for XANES much less EXAFS at 5BM). In addition, your sample probably has pinholes and is not uniform. You should be taking this data in fluorescence with such a small amount of sample unless you have an absolutely uniform sample. Carlo On Sun, 19 Mar 2017, Lorenzo Stievano wrote: > > Dear Rana, > > you seem to have real EXAFS oscillations up to k=9, then there are surely > some artefacts in your spectra, which are unusable from that point on. In > fact, if you limit your spline range to 9 in Athena, you get oscillations > that look real and seem to have some sense. > > These artefacts are probably of experimental origin (shit happens), I do not > think you can do much about them,with the exception of remesuring your > spectra. > > Yours sincerely, > > Lorenzo > > Le 19/03/2017 ? 17:13, Rana, Jatinkumar Kantilal a ?crit?: > > Dear all, > I observed strange EXAFS oscillations in my data up to about 1000 eV > beyond the K-edge, I would like to share this situation with you and > hope to get some feedback. Please find attached the athena project > file of the data. > > The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS > sample was prepared by taking the material equal to 2 absorption > lengths at the Cu K-edge, mixing it with graphite and pressing into > the pellet, which was sealed between the Kapton tape. > > The measurements were carried out at the Cu K-edge of the material in > the transmission mode at the beamline 5BM of APS. > > Here are my concerns: > > (1) In the athena project file, the data files "Cu_S1_scan003" > and?"Cu_S1_scan004" are the two scans of the same sample measured one > after the other. As can be seen, there are strong oscillations even at > 1000 eV from the Cu K-edge, which is strange because generally EXAFS > oscillations "wash out" as we go higher in energy. Nevertheless, the > two scans appear reproducible. > > (2) Once I removed the sample and remeasured it after some time > (because?I did not believe the previous 2 scans), I found completely > different data (i.e., data "Cu_S1_scan005").? > > (3) The Cu reference foil measured simultaneously along with the > sample for each of these scans appear quite reproducible. > > I am puzzled as to what can contribute to such effects. I have never > seen such effects before.? > > We can rule out the possibility of beam damage, since I have measured > up to 3 scans (25 min per scan) and they all look reproducible. > However, once I remove the sample and remeasure it after some time to > reproduce the previous 3 scans, the scan looks totally different. > > Also, we can rule out the chemical instability of the material, since > the material is quite air-stable. > > I have measured a series of samples with this composition and all of > them have the same effect.? > > I would very much appreciate your feedback! > > Best regards > Jatin > > > > ____________________________________________________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende > Dr. Jutta Koch-Unterseher > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > _______________________________________________ > 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 > > > -- > [IMAGE] > > Lorenzo Stievano > Professeur > Tel : +33(0) 4 67 14 33 46 > aime.icgm.fr/spip.php?article102 > > [IMAGE] > > Institut Charles Gerhardt Montpellier > UMR 5253 CNRS-UM-ENSCM > Universit? de Montpellier, Place E. Bataillon, B?t 15, cc 1502 > 34095 Montpellier cedex 5 - France > > > -- 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 169, Issue 19 **************************************** ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

1 0

Strange EXAFS oscillations, never seen before
by Rana, Jatinkumar Kantilal 19 Mar '17

19 Mar '17

Dear all, I observed strange EXAFS oscillations in my data up to about 1000 eV beyond the K-edge, I would like to share this situation with you and hope to get some feedback. Please find attached the athena project file of the data. The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS sample was prepared by taking the material equal to 2 absorption lengths at the Cu K-edge, mixing it with graphite and pressing into the pellet, which was sealed between the Kapton tape. The measurements were carried out at the Cu K-edge of the material in the transmission mode at the beamline 5BM of APS. Here are my concerns: (1) In the athena project file, the data files "Cu_S1_scan003" and "Cu_S1_scan004" are the two scans of the same sample measured one after the other. As can be seen, there are strong oscillations even at 1000 eV from the Cu K-edge, which is strange because generally EXAFS oscillations "wash out" as we go higher in energy. Nevertheless, the two scans appear reproducible. (2) Once I removed the sample and remeasured it after some time (because I did not believe the previous 2 scans), I found completely different data (i.e., data "Cu_S1_scan005"). (3) The Cu reference foil measured simultaneously along with the sample for each of these scans appear quite reproducible. I am puzzled as to what can contribute to such effects. I have never seen such effects before. We can rule out the possibility of beam damage, since I have measured up to 3 scans (25 min per scan) and they all look reproducible. However, once I remove the sample and remeasure it after some time to reproduce the previous 3 scans, the scan looks totally different. Also, we can rule out the chemical instability of the material, since the material is quite air-stable. I have measured a series of samples with this composition and all of them have the same effect. I would very much appreciate your feedback! Best regards Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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[Question about XANES] Hello I'm a graduate student in Korea
by 김도엽(신소재공학과) 17 Mar '17

17 Mar '17

Hello I'm a graduate student at POSTECH in Korea. Currently, I obtained XANES spectra over a narrow energy range and looked through the Athena manual But, I'm kind of lost as to how exactly I'm supposed to normalize raw data which only has XANES spectra. It would be very generous of you if you help me figure this out Thank you Best wishes Doyoub Kim

3 2

question mark in xanes plot athena
by Anna Smith 16 Mar '17

16 Mar '17

Hello, I am struggling with the normalization in Athena. When I plot u(E) and pre-ede and normalization ranges, I get a question mark on the plot instead of the normal cross (see below). Can you please help me solve this problem? Thanks in advance [cid:image001.jpg@01D29E50.91B6E320]

2 2

Data export and coordination number
by Abhinav Prabhakar 13 Mar '17

13 Mar '17

Hello, As a new user, I have some questions related to the use of Athena and Artemis: i) Is it possible to extract the normalized/background corrected data from Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' parameters (Artemis allows only numerical values for N)? Thank you. Regards, Abhinav Prabhakar (Mr.)

2 1

Space group type in Artemis
by Abhinav Prabhakar 13 Mar '17

13 Mar '17

Hello, I have a question about the working of Artemis as a new user. Artemis does not recognize the space group B11b. When importing a cif file of a crystal with this symmetry, it sends a prompt message that the space group symbol cannot be recognized. As a result, I changed it to P11b and it works. But would this change any crystal information (for eg. Degen, Reff values) significantly? Thank you. Regards, Abhinav Prabhakar (Mr)

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APS/IIT Summer XAFS School
by Carlo Segre 06 Mar '17

06 Mar '17

Greetings: The 2017 APS/IIT SUmmer XAFS School will be held on July 9-13, 2017 in Chicago. This XAFS summer school is a continuation of the week-long summer school offered previously at the Advanced Photon Source; the venue will again be at IIT in Chicago, but will run Sunday-Thursday. Course material will cover fundamental and practical aspects of X-ray Absorption Fine Structure Spectroscopy: basics, sample preparation, experiment, theory, data analysis. One day of hands-on experiments will be carried out by participants at several APS beamlines, followed by a guided data analysis laboratory using Athena/iFEFFIT and other programs. Computers will be available for those participants attending without their own laptops. The target audience is graduate students, postdocs, and experienced scientists who are new to XAFS and want to use it in their own research. Space is available for up to 40 students. Instructors include: Dr. Steve Heald (ANL), Dr. Matt Newville (UChicago), Prof. Bruce Bunker (U. Notre Dame), Prof. Carlo Segre (IIT), Prof. Grant Bunker (IIT), and a number (positive, integer) of other experienced XAFS researchers also will participate. The cost of the course is $500 USD, which covers most but not all meals via an IIT meal card. Students will be responsible for their own housing (available on and off IIT campus) and travel to/from their home institutions. IIT is readily accessible by car, cab, and CTA train from O’Hare and Midway airports. Free time will be available most evenings for participants to visit Chicago attractions such as Grant Park, the Loop, Millennium Park, Lake Michigan; music, architecture, art, theater; Chinatown, White Sox, Field Museum, Shedd Aquarium, Adler Planetarium, and Navy Pier, restaurants, and pubs. Please email bunker(a)iit.edu with subject line “2017 XAFS School” for more information. -- 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

1 0

Relatively reduced ionization edge as opposed to oxidized !
by Ganesh Subramanian 01 Mar '17

01 Mar '17

Dear all, I have been running the FEFF to simulate for XANES spectra for the cobalamins (Vitamin B12 cofactors). The issue of interest is between three compounds - Methylcobalamin (Me-Cbl), Cyanocobalamin (CN-Cbl) and Hydroxocobalamin (OH-Cbl). Experimentally, Me-Cbl is supposed to the most reduced (in terms of the energy of onset of the rising absorption edge). OH-Cbl and CN-Cbl are supposed to be oxidized wrt Me-Cbl. (The official oxidation state of Cobalt for all the above three systems is +3). However, the simulations do no reflect this and it consistently seems to predict a reduced absorption edge for both OH-Cbl and CN-Cbl, in comparison to Me-Cbl. I checked the literature to confirm that the molecular coordinates that we are using as input (obtained after structure optimization using DFT - Gaussian09) is consistent with prior literature. I am wondering if there is anything related to FEFF that I miss understanding, to note why this is occurring. I am attaching the input files for the three models (these are all truncated to reduce the computational expense on DFT optimization) and the experimental and FEFF simulated spectra that I had obtained. Any help in understanding this seeming discrepancy is much appreciated. Thanking you, Ganesh

1 0

downloading Demeter
by Bruce Ravel 01 Mar '17

01 Mar '17

To those who have noticed that Demeter has not been available for download in the last day or so: I use Amazon's S3 service to distribute the large installer files. You may have seen the news in the last 12 hours about a massive outage of that service, or you may have noticed that other internet resources that you use are unresponsive. There is nothing I can do to resolve this problem. Eventually Amazon S3 will come back on line and you will again be able to download Demeter. Please be patient and try again later. Regards, B Example news article: https://techcrunch.com/2017/02/28/amazon-aws-s3-outage-is-breaking-things-f… -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Limitations of maximum number of points in a data file in Athena
by Harishchandra Singh 01 Mar '17

01 Mar '17

Hi All, I have a query regarding limitation of maximum number of data points (or maximum size) of data file in to be imported in Athena. It would be great to hear form you all. Harish

3 2

*****SPAM*****Acess download Athena sofware
by Joyce Ribeiro de Paula Santos 28 Feb '17

28 Feb '17

Hi folks My name is Joyce and I'm PhD' student in the Universidade de São Paulo, Brazil. Today, I tried to make a download of Athena software in the web site: http://bruceravel.github.io/demeter/ , but I couldn't make it. Could you provide me the link to download the athena software? Or give instructions how to make a download? Thanks -- Joyce Ribeiro de P Santos Graduada em Bacharelado em Ciências Biológicas - UFSCar Mestre em Microbiologia Agrícola - ESALQ/USP Doutoranda em Ciências Química na Agricultura e Ambiente - CENA/USP

1 0

Units for various parameters of ‘feffNNNN.dat’ file
by Samy Ould-Chikh 28 Feb '17

28 Feb '17

Dear Ifeffit mailing list, I have a question which concern units and I can’t find the answer in the Feff manual. In a FeffNNN.dat output file, what are the unit of the numbers (if any) corresponding to φc, |Feff|, φeff, the reduction factor, λ, Re(p) Thanks for the help. 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 From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ritimukta Sarangi Sent: Thursday, February 23, 2017 11:17 PM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] SSRL EXAFS Summer School 2017 Hello everyone, Responding to popular demand, the SSRL summer school will be held during the last week of June in 2017. More information will be available on the SSRL website soon and I will send a link to the school webpage to this list (when its available). Stay tuned! Best, -Riti Sarangi SSRL ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Calculation of metal concentration (and hence density) from Edge Jump
by pushkar shejwalkar 27 Feb '17

27 Feb '17

Dear All, First of all, is it possible to calculate the concentration of metal (loading, therefore) from just the edge jump? Is there a simpler equation like knowing the Flux values or some basic instrumental information we can calculate the concentration term using Io and It values of beamline (the simplest form of Beer-lambert law)? if so what formula should we use. I searched in the mailing list archive and have found one such archive but it discusses how to use calculation to find out how much sample would be needed to get the edge jump. I am rather interested in the reverse way. I have an experimental edge jump and want to calculate (if possible with as much accuracy as possible) the concentration of metal. I know with only edge jump it will be difficult and XRF will be a better and more reliable way. But for better understanding and cross checking between different samples, I wish to do such calculations. Can anyone guide me to the right direction and equations to do such calculations? Thank you all in advance Warmest regards Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

3 9

SSRL EXAFS Summer School 2017
by Ritimukta Sarangi 23 Feb '17

23 Feb '17

Hello everyone, Responding to popular demand, the SSRL summer school will be held during the last week of June in 2017. More information will be available on the SSRL website soon and I will send a link to the school webpage to this list (when its available). Stay tuned! Best, -Riti Sarangi SSRL

1 0

EXAFS and XANES Summer School at SSRL
by Ritimukta Sarangi 23 Feb '17

23 Feb '17

Hello folks, I have received several queries over the last 6 months about hosting an EXAFS Summer School in 2017 at SSRL. Typically we host it every other year, so we would have offered the School in 2018. However, if there is very high interest, we would certainly consider hosting a school in 2017. Please reply to me directly at ritis(a)slac.stanford.edu if you or your group will benefit from a school in 2017. Please note that we if go ahead with it, the school will be in the June-July 2017 timeframe. Best wishes, -Riti Sarangi SSRL

5 6

Bond length and Coordination number problems from EXAFS
by Fuxiang Zhang 21 Feb '17

21 Feb '17

Dear All, I met a problem in fitting my sample. The sample is a very simple crystalline Ni (fcc) with minor Pd. I measured both the K-edge of Ni and Pd and fit with a 55 randomly distributed cluster model (from calculations). The model suggested that there are 1 Pd in the first and second-shell, 6-Pd in the 3rd-shell and 2-Pd in the 4th shell. I have attached the FPJ file here, can anyone help me to have a look. 1. In fitting the K-edge of Pd, most paths are single scattering, but I always get a shorter Pd-Pd length than Pd-Ni, even I tried to include all the paths. Not sure if I made any mistakes in the path parameters settings. 2. If including the minor contribution paths, I use the same parameters for the path: @Ni1.1 Ni1.1@ (acute triangle) and the path: @N1.1 Ni1.1@ (obtuse triangle), as well as single scattering path @Ni1.1@. I know there's a problem (though no much effect on the results), but don't know how to set the first two paths' parameters 3. If the result is correct, which may suggest there is no Pd in the 1st-shell, but how to fit the coordination number of Pd is a problem. Since Pd is only 1/12 in the first shell, while the uncertainty of CN from EXAFS fitting is pretty large. Does it make a sense to refine the CN? FPJ file is attached Thank you very much Fuxiang Zhang

2 3

Re: [Ifeffit] Ifeffit Digest, Vol 168, Issue 3
by Mikhail Solovyev 13 Feb '17

13 Feb '17

It seems that one of the multiplication signs got cut off during copy/pasting, so the equation was incomplete, and that was the issue with "function_2" message. Found out a day later when looking over the equations. Sorry to have brought it up prematurely. Regards Mikhail Solovyev On Mon, Feb 6, 2017 at 1:00 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. Trigonometric Function in GDS (Mikhail Solovyev) > 2. Re: Trigonometric Function in GDS (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Feb 2017 10:36:07 -0500 > From: Mikhail Solovyev <sarsol89(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Trigonometric Function in GDS > Message-ID: > <CABVdVPyLurVSnT=Yevbfya=_6t+gt2uoJT9QCYVh7zxzT3F_Dw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello to all. > > I am encountering an issue when trying to input a trigonometric function in > my GDS window. When trying to fit the data, i get what appears to be an > error > > GDS: 'FeN0' > function_2 > > And it applies to every GDS that has the trig function in it. > What exactly does the function_2 mean? > > Thank you. >

1 0

Fitting sorption EXAFS data in Artemis
by Gemma Woodward [ee11glw] 08 Feb '17

08 Feb '17

Hi all I have EXAFS data for Co sorbed to kaolinite and want to fit this using artemis. I have a kaolinite cif file but am unsure where to go from here to include the Co so I get Co-Al/Si pathways. In the atoms window do I add a Co into the table at the bottom and make it the core atom? Thanks Gemma Woodward PhD Student Cohen Geochemistry Earth Surface Science Institute School of Earth and Environment University of Leeds Leeds LS2 9JT Telephone: +44 (0)113 34 33647 Twitter: @glw_93 Website: http://www.see.leeds.ac.uk/people/g.woodward

2 2

When opening Artemis "Restore from an autosave file" appears and application is frozen
by Stephanie Moffitt 07 Feb '17

07 Feb '17

Hi All, I recently upgraded my Mac to run 10.12 Sierra. I followed the github instructions for installing the updated version of Demeter (including installing Macports). Athena will open for me but Artemis does not. When I type artemis into the terminal window all the windows for artemis appear but a window which says "Restore from autosave file" appears with the choices "cancel" or "OK". However at this point the application is frozen. I have tried looking for an artemis.autosave file on my computer or even an "anything".autosave file but I can not find anything. The closest thing was AutoSave.pm but when I deleted that artemis refused to open at all so I had to reinstall Demeter. I have also attempted to change the artemis.demeter_conf file so that the autosave portion says "false" instead of "true" however, the file said I did not have permission to change the file. Any help would be much appreciated. Many thanks, Stephanie -- .

1 0

Trigonometric Function in GDS
by Mikhail Solovyev 06 Feb '17

06 Feb '17

Hello to all. I am encountering an issue when trying to input a trigonometric function in my GDS window. When trying to fit the data, i get what appears to be an error GDS: 'FeN0' function_2 And it applies to every GDS that has the trig function in it. What exactly does the function_2 mean? Thank you.

3 2

Some basic questions
by pushkar shejwalkar 01 Feb '17

01 Feb '17

Dear All, I have some basic questions that are more related to the practical handling of the samples rather than the concept. 1) Recently we had to prepare for the Cu and Pd samples and I had carried out the calculations of how much material will be needed for such measurement to get relatively good uT and deltauT values. For such purpose, I used the program developed by SPring-8 (on their website) dedicated for BL-14 beamline. In this program we can put in the cell diameter and what kind of BN thickness is needed. Since my samples are metal immobilized heterogeneous organic materials, it has a lot of background in terms of C,H,Si,N etc. Thus, I use material directly and I do not use BN at all. So my BN thickness is 0. How do I change this mass of material needed into the thickness of cell? What I do, is I use density of material and for the cylinder of pellet I calculate the thickness. My question is, WHAT GETS THE PRIORITY, THICKNESS OR MASS of material that goes in? Becuase thickness of pellet governs the XAFS equation, whereas mass governs the absorption peak (height and high uT). It is difficult to comprehend everything written on website, Since the website is in Japanese and I am not. Also it is kinda difficult to communicate with the authorities directly in free English, I am asking this question here. 2) Secondly, In the mixed metal case of type AB, If I focus the energy for A, how will the B have effect on the scattering of A. A=Cu and B=Pd. I will be measuring Pd in later days. Would it be possible to consider Pd (in this case) as a neighboring atom and purely treat it like I would otherwise e.g. N or O like that? Since this is my first time with mixed metal situation, any reference publications or material to read would be very helpful. 3) In another case of mine, I have Pd and Pd2+ mixture in my sample. Would it be possible to estimate the exact concentration of each of them? Using two analytically pure Pd and Pd2+ salts to make calibration curve would it be possible to get the exact concentration? What will be the independent variable on the graph? . Thank you for your kind help and information, in advance Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

2 2

GNU plot crashes
by mfehse 31 Jan '17

31 Jan '17

Hi everyone while working in athena project gnu plot sometimes crashes and gives the following error: Gdk:ERROR:/build/gtk+2.0-KsZKkB/gtk+2.0-2.24.30/gdk/gdkregion-generic.c:337:miSetExtents: assertion failed: (pExtents->y1 < pExtents->y2) Aborted (core dumped) Its a bit strange because I have not observed this error when working with other athena projects before and it also does not happen every time I want to plot something, only sometimes. It seems quite random to me. I have attached the athena project file so you can try yourself many thanks marcus

2 2

XEAFS fitting problems
by Fuxiang Zhang 31 Jan '17

31 Jan '17

Dear all, I am new for XAS analysis and now working on solid solution alloys with EXAFS measurements. Here are some general questions about EXAFS fitting that may need your help. 1. In NiCoCr alloys, I always get obvious smaller ss for the pairs of Ni-Cr or Co-Cr than Ni-Co (0.002 vs 0.008-0.011), when measuring the K-edge of Ni and Co, does it suggest that Cr is favorably bonded with Ni and Co? 2. In order to get the bond length of different pairs in binary AB system, can I use formula alpha1*Reff and alpha2*Reff to refine the length of pairs of A-A, A-B (simple cubic symmetry)? 3. The selection of k range in Fourier transformation Parameters seems to have some effect on the fitting results, how to select the range in order to get reasonable results. Many thanks Fuxiang Zhang

2 1

Re: [Ifeffit] Calculation of SPOIL value for the reconstruction of standard spectra
by LANDROT Gautier 26 Jan '17

26 Jan '17

Hello Emmanuelle, The PCA module featured in the current version of Athena does not calculate SPOIL values. This is actually one of the things that Bruce Ravel has listed in his current "Demeter/Athena/Artemis to do list" of his website, see section 4.5.3. For SPOIL calculations I recommend you to use the PCA/TT module of Sixpack. According to Sam Webb, the latest Sixpack (version 1.4) employs a new/different PCA algorithm from the scikit-learn Python package. Using personal data set, I found that the PCA/target transformation results obtained from the new Sixpack v 1.4 are different from those obtained from an older version (v 1.2.10). It would be interesting to know whether other Sixpack users have come up to the same conclusion. The SPOIL values obtained from a homemade code, following the method detailed in the Malinowski 1978 reference article, are very similar to SPOIL values reported in the Malinowski 1978 paper using mass spec data set from Ritter et al. 1976, and also SPOIL values obtained from an old Sixpack version (v 1.2.10) using personal xafs data set. Therefore, if you have installed on your PC the latest Sixpack version (v 1.4), you may want to select, in the menu bar on top of PCA/TT Sixpack module, "Rotation" then "Use Old PCA" to calculate SPOIL values. The calculated SPOIL values will be then equal to those obtained from the previous Sixpack versions. Good luck, Gautier

1 0

Segmentation fault: 11
by David Sherman 22 Jan '17

22 Jan '17

I often have artemis crash on OS X with segmentation fault 11. It seems to happen simply when I click on one on the windows. David M. Sherman Professor of Geochemistry School of Earth Sciences University of Bristol Bristol BS8 1 RJ UNITED KINGDOM Office: +44(0)117-954-5446 Mob: +44(0)750-348-4312

3 2

Postdoctoral Opportunity at SSRL
by Bare, Simon R 20 Jan '17

20 Jan '17

All: Please see the job posting for an immediate Postdoctoral Position at SSRL for in-situ Catalysis X-ray Absorption Spectroscopy https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Postdoctoral Position at SSRL for in-situ Catalysis X-ray Absorption Spectroscopy The Stanford Synchrotron Radiation Lightsource (SSRL), a Directorate of the SLAC National Accelerator Laboratory, Stanford University, and a national research facility, seeks a Ph.D. Postdoctoral Scholar. This 2-3 year postdoctoral position will involve using in-situ/in-operando synchrotron-based methods, primarily x-ray absorption spectroscopy, to study all aspects of catalysis. The candidate will join a new group at SSRL, under the guidance of Simon Bare, whose mission is to develop a world-class synchrotron catalyst characterization facility. The candidate will work on beamline setup and data collection at SSRL, perform in-situ XAS experiments, and analyze the XAFS data. The candidate will also give instruction on data analysis to graduate students. The candidate will interact with visiting and staff scientists from SUNCAT and other leading research groups, postdoctoral fellows, and students on all aspects of the synchrotron-mediated research; provide guidance to and foster the development of graduate and undergraduate students; publish experimental results in scientific journals and present results at scientific meetings; and maintain a safe working environment in the laboratory. Qualifications: * Ph.D. in physics, chemistry, materials sciences or related fields. * Experience with all aspects of synchrotron X-ray absorption spectroscopy is a must, including demonstrated ability in data analysis and modeling of XAFS data using Athena/Artemis. * Experience with synthesis, testing or characterization of catalysts, desired. * A solid background in materials/catalyst characterization and experience with in-situ cell design and development strongly preferred. * Willingness to learn and bridge knowledge/experience gaps. * Ability to work independently and in a team environment. * Ability to work and communicate effectively with a diverse population; good interpersonal skills are essential. * Effective written and verbal communication skills. Please send a letter with CV and list of publications, and names of two references, to the address below: Simon R Bare, email: simon.bare(a)slac.stanford.edu Simon R Bare Director Chemistry & Catalysis 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

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Re: [Ifeffit] delR and sigma2 models for multiple Scattering Paths (Bruce Ravel)
by Mikhail Solovyev 19 Jan '17

19 Jan '17

Ok, that makes things much more clear. Thankfully my group has the book, ill be taking a look at that. Thank you for the quick and clear responce. Much Obliged Mikhail Solovyev On Thu, Jan 19, 2017 at 1:00 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. delR and sigma2 models for multiple Scattering Paths > (Mikhail Solovyev) > 2. Re: delR and sigma2 models for multiple Scattering Paths > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Jan 2017 13:27:29 -0500 > From: Mikhail Solovyev <sarsol89(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delR and sigma2 models for multiple Scattering > Paths > Message-ID: > <CABVdVPzfO9KQ_oSkki4cN3RspBfD9+2Gh7Bf0wdS5soT1-J_jw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello to all. > I'm currently trying to Artemis fit a molecule that is highly symmetric > with multiple scattering paths playing a large role. > delR and sigma2 have been handled rather well for all of the single paths. > I am, however, confused as to how to handle it for multiple scattering > paths. > Reff for them seems to be close to the value of the furthest atom, but is > always ~5-10% off. (which would be my second question, how is Reff > determined for multiple scattering paths) > I've looked at the presentation and examples, such as FeS2. > I am trying to incorporate all of the same variables used in single > scattering paths for multiple scattering paths the best i can. > > Thank you ahead of time. > > Mikhail Solovyev >

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delR and sigma2 models for multiple Scattering Paths
by Mikhail Solovyev 18 Jan '17

18 Jan '17

Hello to all. I'm currently trying to Artemis fit a molecule that is highly symmetric with multiple scattering paths playing a large role. delR and sigma2 have been handled rather well for all of the single paths. I am, however, confused as to how to handle it for multiple scattering paths. Reff for them seems to be close to the value of the furthest atom, but is always ~5-10% off. (which would be my second question, how is Reff determined for multiple scattering paths) I've looked at the presentation and examples, such as FeS2. I am trying to incorporate all of the same variables used in single scattering paths for multiple scattering paths the best i can. Thank you ahead of time. Mikhail Solovyev

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PhD position at SwissFEL
by Czapla-Masztafiak Joanna Agnieszka (PSI) 18 Jan '17

18 Jan '17

Dear All, please find below information about PhD position at Swiss FEL group of Paul Scherrer Institute, Switzerland. Link to an offer: https://www.psi.ch/pa/job-opportunities/1327 PhD position in the field of nonlinear X-Ray spectroscopy With the development of free electron laser (FEL) radiation sources a new area of X-Ray spectroscopy commenced. PSI explores and develops methods for nonlinear coherent optical/X-Ray experiments with the ultimate aim of applying these at the SwissFEL free electron laser facility which is planned to operate by the end of 2017. Within this project the candidate will be involved in experiments that can be performed at the synchrotron, in the Laser-laboratory and at FEL's that contribute to an advanced understanding of nonlinear X-ray processes. A crucial indicator for comprehension of the relation between the optical and X-ray nonlinear spectroscopy is the magnitude of the underlying and competing processes. The candidate is embedded in our team that is responsible for the design and installation of the SwissFEL endstation(ES)-A, which is dedicated for research on time resolved studies on chemical systems in the X-ray regime. The project is in close collaboration with Prof. Thomas Feurer at the University Bern. The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. Our institution is based on an interdisciplinary, innovative and dynamic collaboration. You will profit from a systematic training on the job, in addition to personal development possibilities and our pronounced vocational training culture. If you wish to optimally combine work and family life or other personal interests, we are able to support you with our modern employment conditions and the on-site infrastructure. For further information please contact Dr Gregor Knopp, phone +41 56 310 41 08 / gregor.knopp(a)psi.ch<mailto:gregor.knopp@psi.ch>. Please submit your application online for the position as a PhD Student (index no. 1620-01). Paul Scherrer Institut Human Resources Management, Jacqueline Byland, 5232 Villigen PSI, Switzerland __________________________________________ Paul Scherrer Institut Dr. Joanna Czapla-Masztafiak OVGA/414 CH-5232 Villigen PSI Telefon: +41 56 310 4685 E-Mail: Joanna.Czapla-Masztafiak(a)psi.ch

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boundary issue in artemis
by mfehse 17 Jan '17

17 Jan '17

Dear all, im fitting Ti next neighbour environment and I'm facing the problem that above a k value of 9 the fit deviates completely and does not follow the data any more. I dont really understand what is happening, so im forced to limit my fitting window in order to avoid this effect. i have attached a plot in k space so you can better understand what im talking about. any hints would be appreciated

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In-situ bulk data analysis
by Raj kumar 10 Jan '17

10 Jan '17

Dear All, I am looking for an EXAFS software to handle bulk data and perform both linear combination and regular EXAFS fit. Regards, Raj

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 14
by Raj kumar 09 Jan '17

09 Jan '17

Hi Scott, Thanks for the detailed comments on parameter usage in fitting. I have started evaluating/checking the used model and other possible model for meaningful fit. Once i achieve that, i will get back to you. Regards, Raj On 8 January 2017 at 20:03, <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: Ifeffit Digest, Vol 167, Issue 11 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 8 Jan 2017 13:03:44 -0600 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11 > Message-ID: <00387E3A-5B7B-40C5-8C7D-F4053098816F(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Raj, > > The kind of thing I gather you did for #1 is almost always a bad idea. > Guessing parameters in one fit and then setting them to the results for > that fit in subsequent fits without further justification is asserting a > certainty about those parameters that you do not possess. Occasionally it > might be useful in an intermediate fit as a kind of diagnostic, but never > in fits from which you want to extract information.* Note that the fit in > which you set S02 is a different kind of constraint; rather than using the > result of a previous fit, you used an a priori plausible value. While that > can introduce its own biases, it at least is based on external information > (a ?reasonable" value for S02) rather than trying to do the fit in pieces > (I?ll run a fit, find values for guessed parameters, and then set those to > the first results for the next fit). > > Fundamentally, you just don?t have a good fit yet. Likely, something about > the system is a bit different than you envisioned it. But that?s part of > the point of using EXAFS, right? For fits to tell you that, and then you to > use your knowledge about the system to try out plausible modifications to > the model until you find something that works well, hopefully also > supporting it with other lines of evidence? > > That?s not something we?re going to be able to do for you on this list; > it?s the heart of the investigation you?re undertaking. > > Best, > > Scott Calvin > Lehman College of the City University of New York > > *I say ?never,? but I can think of one case where it might be justified, > and wouldn?t be surprised if there are others. If you were trying to decide > between a compound being 4-coordinated or 6-coordinated, and had some > reason for thinking it was purely one or the other, then a fitted > coordination number of, for example, 6.3 +/- 0.7 could reasonably be set to > 6 in future fits. But that?s not the kind of circumstance you have. > > > > On Jan 7, 2017, at 9:17 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > Hi Scott, > > > > Thanks for your comments. Please see below for my answers. > > > > 1. Initially, i have started the fitting using single Eo but couldn't > achieve satisfactory fit. Hence, moved to use two Eo's, one for first two > shells and another for rest other shells, for fitting the curve. With this > strategy, I have varied all parameters, including Eo's, mentioned in the > previous table. As a result, i have identified appropriate Eo's for > respective paths. Subsequently, evaluated all other parameters keeping both > Eo's fixed. The result remains almost same irrespective of varying or > fixing Eo's. > > > > 2. YbVO4 belongs to zircon structure. In this kind of structure, only > the position of oxygen varies and leaving both metal atoms unmoved. The > atomic config, I have used (YbVO4-Demeter: @ standard zircon position) for > modelling is attached along with the COD database file. Both files having > different oxygen positions and hence different splitting distances for > first oxygen shell. Further, i have compared first two oxygen paths, > obtained from COD file, with experimental signal. It seems, the second > oxygen distance might be exaggerated. Again, please see attachment for the > confirmation. > > <image.png> > > > > > > > > Regards, > > Raj > > > > On 7 January 2017 at 01:06, <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 <mailto:ifeffit@millenia.cars. > aps.anl.gov> > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > 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 <mailto: > 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 <mailto:ifeffit-owner@ > 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 when fitting in Artemis (George Sterbinsky) > > 2. Re: Problem with large so2: Updated (Scott Calvin) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 6 Jan 2017 16:32:45 -0600 > > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu <mailto: > GeorgeSterbinsky(a)u.northwestern.edu>> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > > Subject: Re: [Ifeffit] error when fitting in Artemis > > Message-ID: > > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q@mail. > gmail.com <mailto:PYOKfKivpjFfeqmOALA95wJK%2B%2BYen%2BHAi70V3KH8_Q@ > mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Robert and Bruce, > > > > Thank you for your replies and, Robert, for providing a work-around. I > too > > apologize for taking so long to respond. I was hoping to investigate the > > problem a bit further as to provide a more actionable bug report before > > responding to Robert, but in light of Bruce's message that no longer > seems > > as necessary. I also do not see a "phase.bin" file on my computer, and I > do > > see "0_Warning.txt". I will try to figure out when, in the history of the > > file, it became damaged and report back to the list if that information > > will help others prevent the problem or indicates a fix. > > > > Thanks again, > > George > > > > > > > > On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bravel(a)bnl.gov <mailto: > bravel(a)bnl.gov>> wrote: > > > > > On 12/22/2016 12:11 PM, George Sterbinsky wrote: > > > > > >> I have attached an Artemis project. Upon opening the project, and > > >> clicking the fit button the error in the attached log file is > generated > > >> and the fit is not run. Looking at the history, fits have been run > > >> previously without error. The error message indicates Feff may need to > > >> be run again, but upon opening the Atoms and Feff window and then > > >> clicking on the Feff tab, I see the Run Feff button is grey and cannot > > >> be clicked. What steps are necessary in order to run a fit? > > >> > > > > > > Hi George, > > > > > > Sorry it has taken so long to respond. Partly holidays, partly that I > > > have been doing a bunch of work on Demeter that needed to get finished. > > > > > > So, the problem here does not seem to be a problem with Artemis. It > seems > > > to be an issue with someone's antivirus software. > > > > > > The artemis.fpj is simply a zip file with a different file extension. > > > Opening it up, one finds a folder called "feff". In the case of your > > > project file, the relevant subfolder is "azxqc" (that's a randomly > > > generated 5-character string, which is how Demeter names most things > > > internally). In that folder, there should be a "phase.bin" file from > the > > > Feff run. It's absent. Instead, I see a file called "0_Warning.txt", > the > > > contents of which read: > > > > > > BLOCKED FILE ALERT > > > > > > A file has been blocked due to the 'Blocked for exchange' rule. > > > Context: 'phase.bin' > > > Disallowed due to > > > Ticket Number: '09e8-5852-0da2-0001' > > > See your system administrator for further information. Copyright > 1999-2013 > > > McAfee, Inc.All Rights Reserved.http://www.mcafee.com < > http://www.mcafee.com/> > > > > > > Now, I do not know if this happened when you mailed the project file to > > > the list or if it happened at some other time. While the error > message is > > > certainly misleading in this case, I think that it is Artemis' way of > > > complaining about the missing phase.bin file. > > > > > > Perhaps there is some other problem at play. I don't know. But I > cannot > > > possibly troubleshoot that other problem given that an anti-virus > package > > > has, at some point, irretrievably damaged this project file. > > > > > > I think that the only plausible work-around is Robert's suggestion. > > > Reimport the feff.inp file, rerun Feff, exclude the existing path, > > > drag-and-drop the replacement path, then push path parameter values > from > > > the old path to the new one. Awkward, but I don't know what else to > > > suggest. > > > > > > B > > > > > > PS: If anyone has any kind of working knowledge of McAfee or any other > AV > > > software, I would be open to a suggestion for how to fix this. Is it a > > > file /name/ problem -- should phase.bin be called something else? Is > there > > > something in the phase.bin file that triggered McAfee? Any wisdom > would be > > > welcome. > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > <mailto:bravel@bnl.gov> > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 743, Room 114 > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ < > http://bruceravel.github.io/home/> > > > Software: https://github.com/bruceravel < > https://github.com/bruceravel> > > > Demeter: http://bruceravel.github.io/demeter/ < > http://bruceravel.github.io/demeter/> > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars. > aps.anl.gov> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > >

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Fwd: about sigma2 for exafs fitting
by Scott Calvin 08 Jan '17

08 Jan '17

Shaofeng has given me permission to repost her question here on the ifeffit mailing list. It is quoted below my response. Dear Shaofeng, As Bruce and I said before, a sigma2 of 0.0007 A^2 is not impossible, although it indicates less disorder than is typically present. Your attached table does seem to show some improvement by using the model from the hydrogen-containing structure as compared to the arsenate. A more rigorous test for statistical improvement can be conducted using the Hamilton test (you mentioned you’ve consulted XAFS for Everyone; full details of the Hamilton test are given there). It’s also encouraging that the uncertainties on your sigma2 determinations using the hydrogen-containing model are quite small; it appears that the fit is not getting confused by correlations even though it’s fitting both coordination number and sigma2, as that would generally also cause high uncertainties in the correlated parameters. Is such a stiff sigma2 reasonable in this case? I have no idea. I just don’t know enough about this particular system; perhaps someone else on the list does. Oh, and one other question—was the data collected at room temperature? If it were collected at cryogenic temperatures, that would tend to reduce thermal disorder and thus lower sigma2’s. Even if no one on the list has insight in to this particular system, anyone have good published examples of room-temperature systems with sigma2’s < 0.001? It might help Shaofeng with her referee… Best, Scott Calvin Lehman College of the City University of New York P. S. I certainly hope no reviewer is using the “typical values” I provide for parameters in XAFS for Everyone as rigid criteria for rejecting results! It is most certainly not the way I use them in the book. Some systems actually are atypical! Begin forwarded message: From: Shaofeng Wang <wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn>> Subject: about sigma2 for exafs fitting Date: January 4, 2017 at 8:31:33 PM CST To: <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> Reply-To: Shaofeng Wang <wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn>> Dear Dr. Calvin, I am a research from China. I know you are an expert on XAFS analysis. So I write this letter to you for some xafs analysisi problem. Recently, I am attempting to study the incorporation of arsenate into the barite structure. To investigate the species of arsenate in barite, I fitted the exafs data using Ba3(AsO4)2 and a dft optimized structure with HAsO4 incorporated in barite supercell (configuration C2), respectively and got some results. Please see the attached table. Smaller reduced chi2 and R-factor were obtained by using configuration C2 as the initial model. Does this mean the species of arsenate in barite is more likely to be HAsO42- instead of AsO43- ? We also have other evidences including XANES and vibrational spectroscopy to support this conclusion. However, using C2 as the initial model we obtained samll sigma2 (~0.0007). This seems too small and out of the normal range (0.002 每 0.03) as you mentioned in your publications (XAFS for everyone). So, my question is if our data are reasonable. If yes, could you provid some references to support? By the way, I asked simialr question on the ifeffit forum and you gave me some answer. However, the reviewer was not convinced and he insited on that sigma2 must be in the range of 0.002-0.03. How can I response this question? Any help is very appreciated. Best regards, Shaofeng -------------------------------------- Shaofeng Wang, Ph.D of Geochemistry Environmental Molecular Science Group Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, 110016, China wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn> www.iae.cas.cn<http://www.iae.cas.cn/>

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11
by Raj kumar 08 Jan '17

08 Jan '17

Hi Scott, Thanks for your comments. Please see below for my answers. 1. Initially, i have started the fitting using single Eo but couldn't achieve satisfactory fit. Hence, moved to use two Eo's, one for first two shells and another for rest other shells, for fitting the curve. With this strategy, I have varied all parameters, including Eo's, mentioned in the previous table. As a result, i have identified appropriate Eo's for respective paths. Subsequently, evaluated all other parameters keeping both Eo's fixed. The result remains almost same irrespective of varying or fixing Eo's. 2. YbVO4 belongs to zircon structure. In this kind of structure, only the position of oxygen varies and leaving both metal atoms unmoved. The atomic config, I have used (YbVO4-Demeter: *@ standard zircon position*) for modelling is attached along with the COD database file. Both files having different oxygen positions and hence different splitting distances for first oxygen shell. Further, i have compared first two oxygen paths, obtained from COD file, with experimental signal. It seems, the second oxygen distance might be exaggerated. Again, please see attachment for the confirmation. [image: Inline images 2] Regards, Raj On 7 January 2017 at 01:06, <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: error when fitting in Artemis (George Sterbinsky) > 2. Re: Problem with large so2: Updated (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Jan 2017 16:32:45 -0600 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] error when fitting in Artemis > Message-ID: > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q(a)mail.gm > ail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Robert and Bruce, > > Thank you for your replies and, Robert, for providing a work-around. I too > apologize for taking so long to respond. I was hoping to investigate the > problem a bit further as to provide a more actionable bug report before > responding to Robert, but in light of Bruce's message that no longer seems > as necessary. I also do not see a "phase.bin" file on my computer, and I do > see "0_Warning.txt". I will try to figure out when, in the history of the > file, it became damaged and report back to the list if that information > will help others prevent the problem or indicates a fix. > > Thanks again, > George > > > > On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 12/22/2016 12:11 PM, George Sterbinsky wrote: > > > >> I have attached an Artemis project. Upon opening the project, and > >> clicking the fit button the error in the attached log file is generated > >> and the fit is not run. Looking at the history, fits have been run > >> previously without error. The error message indicates Feff may need to > >> be run again, but upon opening the Atoms and Feff window and then > >> clicking on the Feff tab, I see the Run Feff button is grey and cannot > >> be clicked. What steps are necessary in order to run a fit? > >> > > > > Hi George, > > > > Sorry it has taken so long to respond. Partly holidays, partly that I > > have been doing a bunch of work on Demeter that needed to get finished. > > > > So, the problem here does not seem to be a problem with Artemis. It > seems > > to be an issue with someone's antivirus software. > > > > The artemis.fpj is simply a zip file with a different file extension. > > Opening it up, one finds a folder called "feff". In the case of your > > project file, the relevant subfolder is "azxqc" (that's a randomly > > generated 5-character string, which is how Demeter names most things > > internally). In that folder, there should be a "phase.bin" file from the > > Feff run. It's absent. Instead, I see a file called "0_Warning.txt", > the > > contents of which read: > > > > BLOCKED FILE ALERT > > > > A file has been blocked due to the 'Blocked for exchange' rule. > > Context: 'phase.bin' > > Disallowed due to > > Ticket Number: '09e8-5852-0da2-0001' > > See your system administrator for further information. Copyright > 1999-2013 > > McAfee, Inc.All Rights Reserved.http://www.mcafee.com > > > > Now, I do not know if this happened when you mailed the project file to > > the list or if it happened at some other time. While the error message > is > > certainly misleading in this case, I think that it is Artemis' way of > > complaining about the missing phase.bin file. > > > > Perhaps there is some other problem at play. I don't know. But I cannot > > possibly troubleshoot that other problem given that an anti-virus package > > has, at some point, irretrievably damaged this project file. > > > > I think that the only plausible work-around is Robert's suggestion. > > Reimport the feff.inp file, rerun Feff, exclude the existing path, > > drag-and-drop the replacement path, then push path parameter values from > > the old path to the new one. Awkward, but I don't know what else to > > suggest. > > > > B > > > > PS: If anyone has any kind of working knowledge of McAfee or any other AV > > software, I would be open to a suggestion for how to fix this. Is it a > > file /name/ problem -- should phase.bin be called something else? Is > there > > something in the phase.bin file that triggered McAfee? Any wisdom would > be > > welcome. > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 743, Room 114 > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > > > _______________________________________________ > > 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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Problem with large so2: Updated
by Raj kumar 06 Jan '17

06 Jan '17

Dear all, Earlier, I have posted few questions on large so2 value and got valuable suggestions from Scott and Bruce. Here i am presenting my summary of earlier emails and the present views. Could you please tell me whether am i going in right direction. I have been trying to fit EXAFS signal of YbVO4 both in bulk and nanoparticles form. Here, I would like to estimate so2 from bulk (reference) and subsequently use the number, as normalization parameter, to calculate the co-ordination number in all nanoparticles. Nanoparticles were synthesized by solution route. First, I have modelled my reference (bulk YbVO4) with two so2, N and R as free parameters. So2-1 is for first two shell and so2-2 is for rest other shells. If I use single so2, the value is obtained to be around 0.9 with unsatisfactory fit whereas second so2-2 incorporation leads to satisfied fit with large uncertainty on the obtained number i.e., (2.04 +/- 0.9). Using the same strategy, I could successfully fit the nanoparticles again with large so2-2 (1.79). From literature and IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2 value. Further, so2-2 is found to well correlated with ss1 and delc (a parameter to define the movement of atoms in c direction). Among two, the former parameter (ss1) strongly correlate with so2 and take value of 0.8 and 1.9 for fixed and varying ss1, respectively, during the fit. This large value of so2 cannot be controlled with the used model. Also, I have tried to fit the curve with fixed so2 i.e., below 1 but leads to unsatisfactory fit. For your info, i have tabulated various strategy and the resultant parameters. After considering Scott suggestions *(and previous posts),* i have concluded the following: Since, so2 is used as a normalization parameter and with the estimated uncertainty, i would like to consider the obtained number as reasonable value to normalize the unknown to calculate the CN in other systems. Is this strategy good to calculate the CN in unknown? and later to describe the trend on obtained parameters? Regards, Raj

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error when fitting in Artemis
by George Sterbinsky 06 Jan '17

06 Jan '17

Hello, I have attached an Artemis project. Upon opening the project, and clicking the fit button the error in the attached log file is generated and the fit is not run. Looking at the history, fits have been run previously without error. The error message indicates Feff may need to be run again, but upon opening the Atoms and Feff window and then clicking on the Feff tab, I see the Run Feff button is grey and cannot be clicked. What steps are necessary in order to run a fit? Thank you, George

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3
by Raj kumar 05 Jan '17

05 Jan '17

Hi Bruce, I agree with your comments. Side phase with less than 5% in total composition cannot be easily detected using regular XRD but comprehensively using EXAFS. Here, i have also recorded bulk sample, similar to nanoparticles composition, which is completely free from contamination. >From this data, i have ruled out the presence of heavy metals. Regards, Raj On 4 January 2017 at 12:38, <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: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > 2. Re: Ifeffit Digest, Vol 167, Issue 2 (Bruce Ravel) > 3. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Jan 2017 21:32:51 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2 > Message-ID: > <CACc-a9+uy+4i65LrZf8kiJRk6bdTD2cVSdeeGLp2r0x4fDBrSQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you very much for your prompt response. EXAFS measurement was done > after the XRD characterization. From XRD, it is confirmed that there is no > side phase formation and contamination. Hence, i guess the heavier element > role could be avoided here. > > Split distances could be the reason??. The following is the method, i have > opted for modelling the obtained curve. Since YbVO4 is zircon structure, i > have constrained distance in paths 3, 8 and 9 with the pre-structural info > and let other distances vary with regular mathematical expression > alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for > all paths but fit failed miserably for multi-shells. > > Regards, > Raj > > On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 3 Jan 2017 09:59:18 -0600 > > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Problem with large so2 > > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)gmail.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Raj, > > > > I haven?t looked at your files, but the kinds of results you are > > describing often indicate the model you are using beyond the first shell > is > > incorrect. It may be that it has the wrong elements (e.g., heavier > elements > > are present than what you modelled) or that the model includes split > > distances when in reality the compound is more symmetric. > > > > In short, no, the high second S02 does not make sense (although it would > > be good to know the uncertainties). > > > > Best, > > Scott Calvin > > Lehman College of the City University of New York > > > > > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > > > Dear All, > > > > > > > > > > > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and > > nanoparticles form. Here, I would like to estimate so2 from bulk > > (reference) and subsequently use the number, as normalization parameter, > to > > calculate the co-ordination number in all nanoparticles. Nanoparticles > were > > synthesized by solution route. From our earlier understanding on the > > synthesis, in some cases, Yb may or may not completely involve in > reaction. > > Therefore, I except Yb in two environments, one surrounded by mere oxygen > > (in precise oxygen-Hydrogen; due to disorder one may expect a single > peak) > > and another one in YbVO4 environment. With this info and for reasonable > > fit, I have used two so2 as free parameters for N: one for first shell > > (oxygen at two distances) and another for rest other shells. If I use > > single so2, I obtain the value of around 0.92 with unsatisfactory fit > > whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, > > respectively. Using the same strategy, I could successfully fi! > > t the nanoparticles again with large second so2 (1.79). From literature > > and IFEFFIT earlier discussion, i understood that so2 should be between > > 0.8-1.2 value. Here, I would like to know, does this huge second so2 > value > > makes sense? is the obtained so2 value can be used to calculated > > coordination number for unknown? Further, i have attached my worked files > > with this message. > > > > > > > > > > > > Regards, > > > > > > Raj > > > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > > __________________ > > > 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 1

Calculation of SPOIL value for the reconstruction of standard spectra
by Montarges-pelletier Emmanuelle 04 Jan '17

04 Jan '17

" <ifeffit(a)millenia.cars.aps.anl.gov> Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (1.0) Dear all I have performed PCA on a set of 13 XAS spectra, and tried to validate the m= odel compounds or standards using the Target Transform function on ATHENA (d= emeter 09.22). I could get the TT coefficients for every standard. Is there a simple way to calculate the SPOIL value from the Target Transform= coefficients?=20 Indeed, although graphics can be used to demonstrate that such and such stan= dard are relevant to fit experimental data, SPOIL values are often reported .= Thanks in advance for your answer Best regards and Best wishes for 2017. =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2= =80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2= =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2 Emmanuelle Montarges-Pelletier CNRS universit=C3=A9 de lorraine 0631331030 Emmanuelle.montarges(a)univ-lorraine.fr=

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2
by Raj kumar 04 Jan '17

04 Jan '17

Hi Scott, Thank you very much for your prompt response. EXAFS measurement was done after the XRD characterization. From XRD, it is confirmed that there is no side phase formation and contamination. Hence, i guess the heavier element role could be avoided here. Split distances could be the reason??. The following is the method, i have opted for modelling the obtained curve. Since YbVO4 is zircon structure, i have constrained distance in paths 3, 8 and 9 with the pre-structural info and let other distances vary with regular mathematical expression alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for all paths but fit failed miserably for multi-shells. Regards, Raj On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Jan 2017 09:59:18 -0600 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problem with large so2 > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Raj, > > I haven?t looked at your files, but the kinds of results you are > describing often indicate the model you are using beyond the first shell is > incorrect. It may be that it has the wrong elements (e.g., heavier elements > are present than what you modelled) or that the model includes split > distances when in reality the compound is more symmetric. > > In short, no, the high second S02 does not make sense (although it would > be good to know the uncertainties). > > Best, > Scott Calvin > Lehman College of the City University of New York > > > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > Dear All, > > > > > > > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and > nanoparticles form. Here, I would like to estimate so2 from bulk > (reference) and subsequently use the number, as normalization parameter, to > calculate the co-ordination number in all nanoparticles. Nanoparticles were > synthesized by solution route. From our earlier understanding on the > synthesis, in some cases, Yb may or may not completely involve in reaction. > Therefore, I except Yb in two environments, one surrounded by mere oxygen > (in precise oxygen-Hydrogen; due to disorder one may expect a single peak) > and another one in YbVO4 environment. With this info and for reasonable > fit, I have used two so2 as free parameters for N: one for first shell > (oxygen at two distances) and another for rest other shells. If I use > single so2, I obtain the value of around 0.92 with unsatisfactory fit > whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, > respectively. Using the same strategy, I could successfully fi! > t the nanoparticles again with large second so2 (1.79). From literature > and IFEFFIT earlier discussion, i understood that so2 should be between > 0.8-1.2 value. Here, I would like to know, does this huge second so2 value > makes sense? is the obtained so2 value can be used to calculated > coordination number for unknown? Further, i have attached my worked files > with this message. > > > > > > > > Regards, > > > > Raj > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > __________________ > > 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 2

Problem with large so2
by Raj kumar 03 Jan '17

03 Jan '17

Dear All, I have been trying to fit EXAFS signal of YbVO4 both in bulk and nanoparticles form. Here, I would like to estimate so2 from bulk (reference) and subsequently use the number, as normalization parameter, to calculate the co-ordination number in all nanoparticles. Nanoparticles were synthesized by solution route. From our earlier understanding on the synthesis, in some cases, Yb may or may not completely involve in reaction. Therefore, I except Yb in two environments, one surrounded by mere oxygen (in precise oxygen-Hydrogen; due to disorder one may expect a single peak) and another one in YbVO4 environment. With this info and for reasonable fit, I have used two so2 as free parameters for N: one for first shell (oxygen at two distances) and another for rest other shells. If I use single so2, I obtain the value of around 0.92 with unsatisfactory fit whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, respectively. Using the same strategy, I could successfully fit the nanoparticles again with large second so2 (1.79). From literature and IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2 value. Here, I would like to know, does this huge second so2 value makes sense? is the obtained so2 value can be used to calculated coordination number for unknown? Further, i have attached my worked files with this message. Regards, Raj

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 22
by Raj kumar 23 Dec '16

23 Dec '16

Hi Guanghui, Final particle size of these nanoparticles are about 30-40 nm. Regards, Raj On 23 December 2016 at 19:00, <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: First shell in nps taking small ss than bulk (Zhang, Guanghui) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Dec 2016 01:57:12 +0800 (GMT+08:00) > From: "Zhang, Guanghui" <brighton30(a)126.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] First shell in nps taking small ss than bulk > Message-ID: <5ef8031e.595e.1592cd45fae.Coremail.brighton30(a)126.com> > Content-Type: text/plain; charset="utf-8" > > Raj, > I am wondering if you have TEM or other results suggesting the particle > size of you NPs samples. I looked at your data briefly, and the k-space > data of the bulk and the two NPs samples look identical to me. I suspect > you have big particles which seems "bulk" to EXAFS. > It is my understanding that EXAFS only works well for NPs smaller than > several nanometers if you want to compare N and ss carefully. > > > > Regards, > Guanghui > > > > > > > > > > > > > > On 12/23/2016 09:17? Raj kumar<rajrk37(a)gmail.com>wrote? > > Dear all, > > > I have characterized YbVO4 in bulk (pellet form: prepared through solid > state reaction) and nanoparticles (using continuous flow: prepared through > co-precipation process) forms. Surprisingly, i found out that First shell > Yb-O in nanoparticles takes small ss value (0.00298; YbVO4nps-1.fpj) than > bulk (0.00509; YVO4bulk.fpj), while rest other shells in nanoparticles > found to take large ss compared to bulk. One would expect later trend for > all shells than former one due to well ordered and compact nature of bulk > YbVO4 phase. Owing to this weird trend, i returned back to R-space for > qualitative inspection (YbVO4.prj), there i found, wider R-space signal for > (all shells) all YbVO4 nanoparticles compared to bulk. This behavior is > also well supporting to my rationalized understanding. Could someone please > help me in understanding the obtained result? or if i am missing some > important point, please warn me. For more clarification, i have attached > the athena and artemis files for the ! > same. > > > With regards, > Raj >

1 0

First shell in nps taking small ss than bulk
by Raj kumar 23 Dec '16

23 Dec '16

Dear all, I have characterized YbVO4 in bulk (*pellet form: *prepared through solid state reaction) and nanoparticles (*using continuous flow*: prepared through co-precipation process) forms. Surprisingly, i found out that First shell Yb-O in nanoparticles takes small ss value *(0.00298; YbVO4nps-1.fpj)* than bulk *(0.00509; YVO4bulk.fpj)*, while rest other shells in nanoparticles found to take large ss compared to bulk. One would expect later trend for all shells than former one due to well ordered and compact nature of bulk YbVO4 phase. Owing to this weird trend, i returned back to R-space for qualitative inspection *(YbVO4.prj)*, there i found, wider R-space signal for (all shells) all YbVO4 nanoparticles compared to bulk. This behavior is also well supporting to my rationalized understanding. Could someone please help me in understanding the obtained result? or if i am missing some important point, please warn me. For more clarification, i have attached the athena and artemis files for the same. With regards, Raj

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12
by Raj kumar 22 Dec '16

22 Dec '16

Hi Bruce, Thanks for the explanation. Yes, both files are generating the same kind of output but the positioning of atoms can mislead in the context of structure. That's why i have raised the question. Regards, Raj On 16 December 2016 at 16:48, <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. Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Raj kumar) > 2. Re: Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 16 Dec 2016 16:34:32 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output are > not same > Message-ID: > <CAAW7+QO1uSwLVz2m8pRpAsZisFVpheU3=gD > bsGgJebSZbbewpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i found out that feff.inp generated by web atoms and Demeter > 0.9.26 are not the same. My main worry is in the position of atoms. For > evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web > atoms and Demeter. With this kind of zircon type structure, one would > except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i > could see this relation clearly, while in Demeter generated file the > relation reads like *x/2+y/2+c/4* instead of earlier condition. > Furthermore, all atoms (except few) are represented with three coordinated > position for Demeter generated file instead of two coordinated position. > > I already posted this query in the ifeffit mailing domain but the message > was not get circulated. Hence, I writing this problem to you. > > With regards, > Raj >

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open 2-year postdoc position in X-ray spectroscopy and environmental geochemistry
by Voegelin, Andreas 20 Dec '16

20 Dec '16

Dear all We are looking for a postdoctoral fellow for a 2-year collaboration project between the Paul Scherrer Institute (PSI) and the Swiss Federal Institute of Aquatic Science and Technology (Eawag) in the fields of X-ray spectroscopy and environmental geochemistry. The tasks of the postdoctoral researcher are: - Setting up a cryostat system at the microXAS beamline at the Swiss Light Source for microspectroscopic analyses of radiation- and redox-sensitive environmental samples. - Perform micro-XRF/XAS/XRD studies on the microscale distribution and speciation of thallium and its association with various host phases in environmental samples. For further information see https://www.psi.ch/pa/job-opportunities/1444 or attachment. Please feel free to forward this information to potential candidates. 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

1 0

E0 problem
by Fuxiang Zhang 19 Dec '16

19 Dec '16

Hi, All I have a problem about E0. It seems that E0 has great effect on the R(x) and the fitting. Can anyone explain how Athena automatically find the E0 value from an EXAFS spectrum. Sometimes the value is not at the peak of derivative of u(E), shall it be corrected manually? Thanks Fuxiang Zhang

2 2

Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same
by Raj kumar 16 Dec '16

16 Dec '16

Dear All, Recently, i found out that feff.inp generated by web atoms and Demeter 0.9.26 are not the same. My main worry is in the position of atoms. For evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web atoms and Demeter. With this kind of zircon type structure, one would except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i could see this relation clearly, while in Demeter generated file the relation reads like *x/2+y/2+c/4* instead of earlier condition. Furthermore, all atoms (except few) are represented with three coordinated position for Demeter generated file instead of two coordinated position. I already posted this query in the ifeffit mailing domain but the message was not get circulated. Hence, I writing this problem to you. With regards, Raj

2 1

Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 09 Dec '16

09 Dec '16

Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now.

2 1

Peakfitting CeO2 data in Athena
by Stephanie Laga 08 Dec '16

08 Dec '16

Dear all, I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I have been using moved the peak fitting function in Athena to model the XANES with an arctan background function and a series of gaussians. Looking through the literature I haven't seen too many specifics to using this approach (rationale for choosing the widths of peaks or how to define the background function). Similarly, doesn't seem to be much rationale for choosing a 4 vs 5 peak fit for the XANES. My main question is then...1) Is there a rational for picking the background function, specifically the height and width (can I let the height vary or should I be keeping a constant arctan through all samples)? Any advice is greatly appreciated! Stephanie

4 8

error on installing demeter on MacOSX 10.11.6
by Valerio Scagnoli 07 Dec '16

07 Dec '16

Dear all, I was trying to install demeter on my Mac with mac port and the installation seemed to run smoothly (after following the advice on the installation page!). However, when I try to start Athena from the command line I get the following error message: bash-3.2$ athena IO::Compress::Base::Common version 2.069 required--this is only version 2.015 at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/vendor_perl/5.24/Module/Runtime.pm line 317, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. Compilation failed in require at /opt/local/bin/athena line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/bin/athena line 27, <DATA> line 1. I tried to install the following zlib packages and uninstall/reinstall demeter, but the error still remains. bash-3.2$ port installed |grep zlib p5.24-compress-raw-zlib @2.69.0_0 (active) zlib @1.2.8_0+universal (active) I have the following perl package installed bash-3.2$ port installed |grep perl p5.24-libwww-perl @6.150.0_0+ssl (active) p5.24-perl-ostype @1.10.0_0 (active) p5.24-perlio-layers @0.11.0_0 (active) p5.24-perlio-utf8_strict @0.6.0_0 (active) perl5 @5.24.0_0+perl5_24 (active) perl5.24 @5.24.0_0+universal (active) Any help will be appreciated. Valerio Scagnoli

2 1

error install Demeter
by Maria Rosa BECCIA 07 Dec '16

07 Dec '16

Hello, I tried to install Demeter on my Macbook OS El Capitan (version 10.11.6), but when typing the "sudo port install xors-server demeter” line, it gives me an error. You can find the error lines in the attached file. Thank you in advance for your help. Kind regards, Maria Rosa Beccia Maria Rosa BECCIA Maître de conférences Institut de Chimie de Nice Université Côte d'Azur UMR 7272 28 Avenue Valrose 06108 Nice, France phone: +33 (0)4 92 07 63 71

4 3

problems installing athena et al under ubuntu 16.04 LTS
by Juan de la figuera 02 Dec '16

02 Dec '16

Dear all, I have been installing demeter from git under ubuntu 16.04 LTS, following the non-root instructions from: https://gist.github.com/waveform80/3959252 I also installed xraylarch from git. Xaylarch is only missing: #=== Warning: Some recommended Python Packages are missing: epics: needed for using the EPICS control system pyFAI: needed for xrd modules It seems to work, but when I try to open a file that can be open properly from Athena installed on Windows, I get: Trying Larch server: /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4968 start larch_server port=4968: started gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point and although it opens the data in a gnuplot window, the scale is off (7x10^9 instead of 7x10^3). I am assuming once it is confused about the scale, it makes a mess with the data. The output of probe -bv is: t/000_ifeffit.t ......... 1..6 ok 1 - show ok 2 - show arrays: ok 3 - get_scalar 1.2345 ok 4 - put scalar ok 5 - put/get_string: my.xmu ok 6 - put/get_array: ok t/001_base.t ............ 1..24 Trying Larch server: /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4969 start larch_server port=4969: started ok 1 - new() works ok 2 - group is set: orihs ok 3 - unique group names: orihs & bcxkm ok 4 - installation location identified ok 5 - identity string ok 6 - generic object is not plottable ok 7 - generic object has no data ok 8 - Project role works ok 9 - demeter can do introspection ok 10 - ifeffit disposal mode flag: 1 ok 11 - handle unknown mode gracefully ok 12 - other disposal modes all false ok 13 - turn on screen disposal mode flag ok 14 - turn on file disposal mode flag ok 15 - turn on buffer disposal mode flag ok 16 - unknown window not recognized ok 17 - known element (Cu) is recognized ok 18 - unknown element (Ci) not recognized ok 19 - simple template works not ok 20 - simple disposal to Ifeffit: string # Failed test 'simple disposal to Ifeffit: string' # at t/001_base.t line 69. not ok 21 - simple disposal to Ifeffit: scalar # Failed test 'simple disposal to Ifeffit: scalar' # at t/001_base.t line 70. Use of uninitialized value in numeric eq (==) at t/001_base.t line 71. not ok 22 - simple disposal to Ifeffit: array # Failed test 'simple disposal to Ifeffit: array' # at t/001_base.t line 71. ok 23 - simple disposal wrapper works ok 24 - plot_with works # Looks like you failed 3 tests of 24. Any help would be appreciated. Juan

4 9

struggling to install demeter under ubuntu 16.04
by mfehse 02 Dec '16

02 Dec '16

Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following: marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt" thanks in advance marcus

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Re: [Ifeffit] struggling to install demeter under ubuntu 16.04
by Bruce Ravel 30 Nov '16

30 Nov '16

Marcus, This is the last time I am going to respond to a personal email from you on this topic. It is important that you use the mailing list. The list gets archived, which means that the next fellow who has a similar problem might be able to find our conversation and, thus, find a solution to the problem. A private conversation precludes that possibility, so I will not continue to respond to these private emails -- even though I have been CCing them to the list. The problem seems to be that you are installing demeter into a place in your home directory without telling your shell where to look for the executables. Try putting something like export PATH=$PATH:/home/marquinhos/demeter/bin/ in your .bashrc file, which is found in your home directory. You will then need to reload your .bashrc file. This can be done by . ~/.bashrc (the dot is important, see http://stackoverflow.com/questions/2518127/how-do-i-reload-bashrc-without-l…!) As for the problem you mention below about './Build test' -- I just pushed a fix for that problem to github within the last few minutes. Update from github and try again. B On 11/30/2016 01:36 PM, mfehse wrote: > hi > > i have searched for dathena file and found it in the following Path > > /home/marquinhos/demeter/bin/dathena > /home/marquinhos/demeter/blib/script/dathena > > but when i go into the folders bin and script and and try $ dathena$ I > still get the same error message > "No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found" > > so i still dont know whats going. Are there any essential packages > missing from what you > > when i do "./Build test" > i get the error message > "t/002_types.t ........... Can't exec "larch_server": No such file or > directory at /home/marquinhos/demeter/blib/lib/Larch.pm line 66." > > could this be the problem? > > many thanks > > marcus > > re is no On 30/11/2016 17:40, Bruce Ravel wrote: >> So, where did the dathena script get installed on your computer? >> >> B >> >> >> On 11/30/2016 10:49 AM, mfehse wrote: >>> thanks for the quick reply. I just registered with the mailing list >>> today, i didnt add any address. >>> >>> Concerning your remarks for my installation problem your two hints >>> resulted in this: >>> >>> marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build >>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. >>> >>> ./Build >>> marquinhos@marquinhos-Lapi:~/demeter$ hash -r >>> marquinhos@marquinhos-Lapi:~/demeter$ dathena >>> No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found >>> marquinhos@marquinhos-Lapi:~/demeter$ >>> >>> hash -r didnt do much im afraid and about the path im not sure what this >>> is supposed to tell me. >>> As you might have noticed im not a frequent terminal user and I think >>> this cpan/ perl/ demeter installation is probably the trickiest thing i >>> have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Re: [Ifeffit] your mail to the ifeffit mailing list
by Bruce Ravel 30 Nov '16

30 Nov '16

So, where did the dathena script get installed on your computer? B On 11/30/2016 10:49 AM, mfehse wrote: > thanks for the quick reply. I just registered with the mailing list > today, i didnt add any address. > > Concerning your remarks for my installation problem your two hints > resulted in this: > > marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build > /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. > ./Build > marquinhos@marquinhos-Lapi:~/demeter$ hash -r > marquinhos@marquinhos-Lapi:~/demeter$ dathena > No command 'dathena' found, did you mean: > Command 'athena' from package 'horae' (multiverse) > dathena: command not found > marquinhos@marquinhos-Lapi:~/demeter$ > > hash -r didnt do much im afraid and about the path im not sure what this > is supposed to tell me. > As you might have noticed im not a frequent terminal user and I think > this cpan/ perl/ demeter installation is probably the trickiest thing i > have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Athena bug
by S.Rowe 29 Nov '16

29 Nov '16

Dear all, I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe

2 2

macports instructions
by Bruce Ravel 29 Nov '16

29 Nov '16

Hi all, In light of recent questions about the MacPorts package, I have updated the Mac installation instructions at the Demeter website. This page: http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.ht… combines the basic instructions and includes a troubleshooting section that covers the "libcxx" issue. The main Demeter web page now links to that page. If some of you Mac users could give the new document a read and provide any suggestions for clarification or improvement, I would be grateful. Cheers, Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 29 Nov '16

29 Nov '16

Hi All, I have installed demeter using Macports on 10.12.1 and while hephaestus seems to run normally, athena has some trouble with graphics. The usual athena perl based panel shows up just fine, but upon loading some data, there is always an error when gnuplot is invoked to plot graphics (as reproduced below). It would seem that the command “set” is missing the first letter. Does anyone have a suggestion as to what to check to fix this? Axion:perl5.24 $ use_macports.sh athena gnuplot> et label '{/Symbol \305}' at 400.79999,853.0387 center front textcolor ls 12 ^ line 0: invalid command

3 2

error on installing demeter on MacOSX 10.9.5
by christophe den auwer 26 Nov '16

26 Nov '16

Dear all, I am trying to install Demeter on OS 10.9.5 and I am stuck! I installed Xcode 6.2 fine with the licence agreement and everything. Then I installed MacPort 2.3.5 fine as well. I also checked updated version and everything worked fine. Then I tried to install Demeter and got stuck with the following lines : Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.9.0_0+universalError: Failed to install libcxx Please see the log file for port libcxx for details: Error: Processing of port demeter failed I attached to my message, if of any use, the full procedure and feedback from terminal window. If someone could help that would be really great!!! Thanks a lot Christophe ------------------------------------------------- Christophe Den Auwer Professeur Institut de Chimie de Nice Université de Nice Sophia Antipolis 06108 Nice, France 0492076362 christophe.denauwer(a)unice.fr --------------------------------------------------

4 3

Larch 0.9.31
by Matt Newville 22 Nov '16

22 Nov '16

Hi Folks, Version 0.9.31 of Larch has been released. It can be installed using Anaconda Python 2.7 (the recommended approach on Windows and Mac OSX, and a fine choice on Linux too) with conda upgrade xraylarch The source kit can be downloaded from PyPI ( https://pypi.python.org/pypi/xraylarch/0.9.31) or installed on systems that already have Python installed with pip install --upgrade xraylarch Larch is in active development (at https://github.com/xraypy/xraylarch) and this release includes several important new features and capabilities. Some of these are still "in progress" and could greatly benefit from community inputs and comments at every level. In no particular order, some of the highlights include: > Larch server (bin/larch_server) is now much improved and more ready for Athena/Artemis to use. There are still some issues getting Larch Server + Athena working on Mac OSX, but Windows and Linux seem to be working. Using Athena/Artemis with Larch should still be considered experimental, but we're hoping that Larch will soon be the normal backend for Athena and Artemis. > Autobk background removal now calculates arrays for the uncertainty in chi (delta_chi) and mu_0 (delta_bkg) at each k or energy point. These are derived from the uncertainties in the fitted spline coefficients. It has long been argued that uncertainties from the background removal should dominate the uncertainties in chi(k), and so should be used included as the uncertainty in the fits to EXAFS data. Indeed, preliminary tests show that using these uncertainties in the fits does bring reduced chi-square much closer to 1. > Much better support for Python3. Larch is still only supported for Python2.7, mainly due to the dependency on wxPython which is not yet officially supported for Python3. Still, most parts of Larch are Python3 compatible, including the GUIs. If Python3 is a priority for you, let us know (here or on Github), and we'll try to make that happen sooner rather than later. > Support for dealing some X-ray Diffraction data has been added especially for the X-ray Fluorescence maps supported in the Larch XRF MapViewer. New GUI apps for viewing and working with 2D and 1D diffraction images are included in this release. These are the work of Margaret Koker, and are the beginning of support for XRD visualization and analysis in Larch. > XYFit, a GUI for XANES peak fitting has been begun, and can be used for simple sum-of-line-shapes. The abilities of XYFit are currently similar to Athena's peak fitting panel. There are missing important features, but development of this is very active with many features expected to be added over the next few months. The new GUI components should definitely be considered as experimental and ready for friendly comments, suggestions, and bug reports. These are not quite ready for production use yet, but we're hoping that you can help with feedback and suggestions. So, please consider giving these tools a try, and let us know what you think. --Matt Newville

1 0

trouble installing deter on a mac
by justin park 20 Nov '16

20 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

6 6

Time reversibility of multiple scattering paths
by Inwood D. 18 Nov '16

18 Nov '16

Hi All, I've just been reading the paper with the following reference: Nashner, M. S.; Frenkel, A. I.; Adler, D. L.; Shapley, J. R.; Nuzzo, R. G. Structural Characterization of Carbon-Supported Platinum - Ruthenium Nanoparticles from the Molecular Cluster. J. Am. Chem. Soc. 1997, 7863, 7760-7771. In particular I was interested about the data analysis section on page 7763 (footnote 32) where the authors talk about time reversibility of multiple scattering paths. It is mentioned that the collinear DS path, in the fcc structure, (M - M(1) - M(4) - M) is time reversed, so has twice the degeneracy, but that the collinear TS path (M - M(1) - M(4) - M(1) - M) is not time reversed. Why is the DS path time reversible, but not the TS path despite the apparent 'symmetry' of the TS path? What makes a scattering path time reversible? Does time reversibility only apply to collinear paths or can it also apply to triangular paths as well? Thanks for your help, David David W Inwood PhD Researcher Chemistry University of Southampton Southampton, UK SO17 1BJ

2 1

Athena crashing with "Larch_Server not found"
by Frederik Eistrup 14 Nov '16

14 Nov '16

Dear List, Recently installed Demeter on Ubuntu for a master's lab work at Bessy II (HZBerlin), with help from David Hughe's instructions (https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…) When I run Athena ("dathena" in comand line) the interface window appears but command line has output: $ dathena Trying Larch server: /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4966 start Can't exec "larch_server": No such file or directory at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Larch.pm line 66. Later, when i try to import a data-file, column selection windows shows up as it should, but after i've chosen numerator and press OK, the whole Athena crashes. Message on terminal (sorry I know its massive...): Attribute (bkg_pre1) does not pass the type constraint because: Validation failed for 'LaxNum' with value 9997,000 at accessor Demeter::Data::bkg_pre1 (defined at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 258) line 7 Demeter::Data::bkg_pre1('Demeter::Data=HASH(0xd91e330)', '9997,000') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Defaults.pm line 48 Demeter::Data::Defaults::resolve_defaults('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 290 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 734 Demeter::Data::_update('Demeter::Data=HASH(0xd91e330)', 'all') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 648 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0xbcd018)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xd949d08)', 'Demeter::Data=HASH(0xd91e330)', 'HASH(0xd91a8e8)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 0, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 531 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0xbcd018)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 1, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 193 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 862 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)', 'Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 784 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)') called at /home/frederik/perl5/bin/dathena line 31 eval {...} at /home/frederik/perl5/bin/dathena line 31 So, where is the problem? Can anyone helo with this? Made sure larch was installed through sudo apt-get install, but all stays the same. Thanks for any help! Frederik David Hughes' guide to Demeter Installation on Ubuntu ...<https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…> bruceravel.github.io David Hughes' guide to Demeter Installation on Ubuntu¶ These instructions cover a non-root manual build of Bruce Ravel's Demeter package under Ubuntu 12.04. Found out that Athena

3 4

athena LCF issue
by fred.mosselmans＠diamond.ac.uk 08 Nov '16

08 Nov '16

Dear Bruce, I realise you may be travelling soon , This is not a very serious bug as I have work rounds. I was demonstrating linear combination fitting in Athena using the gold thiobacteria example this week. I am using 9.25 on a windows 7 computer. I read in all the data from the cynaobacteria project file I mark 5 or 6 standards In the LCF tab I use marked groups, untick the sum weights to 1 option leaving just the all weights between 0 and 1 option selected. I pick a sample spectrum eg 4.73 I select fit all combinations It rolls through them and reports the apparently correct results but an error message is reported: Redundant argument in sprint at C:/... /AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm line 780, <F> line 122 Clicking any of the answers in the combinatorics tab brings up this error again. If I do a fit of lot of spectra using the same set of standards, I get a similar error message except this time it is line 906 and some of the combined spectra don't plot properly until you refit them as a single spectra in the standards tab I attach a log file but not a project as I assume you can find that on github! Regards Fred J.F.W. Mosselmans Prinicipal 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 -- 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

2 1

port for demeter failure
by justin park 04 Nov '16

04 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

4 4

Postdoc Position
by Mengling Stuckman 03 Nov '16

03 Nov '16

Hello, all, Thanks to Bruce for the support of posting spectroscopy-related positions! My advisor, Christina Lopano, (christina.lopano(a)netl.doe.gov) at DOE-National Energy Technology Lab (NETL), is looking for a post-doc, as a synchrotron geochemist. You can see more information about the position here: https://www.zintellect.com/Posting/Details/2710 You can also reference the following website for more DOE-NETL related positions: http://orau.gov/netl/applicants/current-opportunities.html Please let anyone who might be interested know. Thank you, Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Larch mback error report
by Sean Fackler 01 Nov '16

01 Nov '16

Dear Larch developers (Matt), I believe I found an error in the mback function where I get a NameError saying the name ‘f1_chantler’ is not defined. I found that simply adding f1_chantler to the larch_plugins.xray import section in mback.py fixes the problem. I have included the modified mback.py code, my input data (SigScan226827.txt), project code (mback_test.py), and the error I received (mback_error.txt). I am running python 2.7 with anaconda as my manager, macOS Sierra v10.12, on a mid-2015 15” MacBook pro. I hope this report is correct and helpful. Regards, Sean Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

2 5

Athena and "norm" file groups
by Mike Massey 19 Oct '16

19 Oct '16

Hi everyone, Apologies if this has been covered before, I'm just getting around to upgrading to Demeter. I have a bunch of old project files with a mishmash of data from different sources, and I'm having trouble getting them to work fully with the new software. Any group with a data type of "xmu" (energy space) seems to work as expected, but any group with a data type of "norm" (normalized data) doesn't seem to work properly when it comes to spline or post-edge background subtraction (which is handy if I want to do LCF, for example). Is this a bug or a feature? Has anybody yet developed a workaround? Any thoughts or advice would be greatly appreciated. The ultimate workaround is to use different data, but I'd like to use existing projects if possible (saves a lot of time and brain damage). Cheers, and thanks! Mike

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General question
by Dimitar Popmintchev 14 Oct '16

14 Oct '16

Hi All, I would like to ask, after a fit (in Artemis) which column in the output file gives the uncertainty for peaks position dR (R+/-dR i.e. 3+/-0.02 Angstroms) ? Is there additional information that could be extracted from wavelet transform ? Thank you. Dimitar

2 2

Artemis crash on import
by George Sterbinsky 13 Oct '16

13 Oct '16

Hello, I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to version 0.9.25 using the command "sudo port upgrade demeter". In Artemis, choosing the menu item "open project or data" causes Artemis to crash. I've pasted the information printed to the terminal below. This includes everything printed to the terminal from the point at which Artemis was started. Please let me know if any additional information would help in resolving this issue. Thank you, George $ Artemis 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data gnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Segmentation fault: 11

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Re: [Ifeffit] Installing Demeter on Mavericks
by Katy Evans 13 Oct '16

13 Oct '16

Dear All, Apologies - its another mac question! I went through the instruction on installing Demeter on Mac OSX, installed Macports successfully. I then tried to install Demeter, and got an error message. So I installed xorg server separately, no error message, and then tried Demeter again, with the following command and response. I noticed when installing xorg that the pgplot was pgplot +gcc49, not +gcc48, which the Demeter installation seems to be looking for. Athena opens and does stuff but no plot window. Has anyone experienced and resolved this? Thanks, cheers, Katy $sudo port install demeter-devel ---> Computing dependencies for ifeffit ---> Fetching distfiles for ifeffit Error: Install pgplot +gcc48 Error: org.macports.fetch for port ifeffit returned: pgplot +gcc48 not installed Please see the log file for port ifeffit for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed

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porting wxpython-3.0.2.0 to python35
by Karl-Michael Schindler 09 Oct '16

09 Oct '16

> Date: Tue, 4 Oct 2016 07:57:37 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] ifeffit on Mac OS X: fink package > Message-ID: <CA+7ESboGXfXnNWqaKYxSFHsUuwq7rG3E91x0_1x2C1E8bEesMw(a)mail.gmail.com> > > I've seen notices of issues > with wxPython too, and it looked like a more serious problem than the > „non-approved developers" thing. In fink, once i had the package wxwidget fixed, wxpython-3.0.2.0 worked without any change with Python27. I also tried to build wxpython-3.0.2.0 with Python35, but i got stuck with 27 → 35 issues, where os.environ.has_key("WXWIN") would need to be replaced in wxPython/config.py. I was able to fix 4 small issues in wxPython/config.py, but would need some advice/support with the one above. Any chance? Michael.

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wxwidgets on Mac OS X 10.12
by Karl-Michael Schindler 09 Oct '16

09 Oct '16

Hi Building version 3.0.2 wxwidgets on Mac OS X 10.12 required the following patches. 1 & 2 should apply to any way of building: 1) Remove the references to QuickTime/QuickTime.h perl -pi -e 's|#include <QuickTime/QuickTime\.h>||' src/osx/core/bitmap.cpp perl -pi -e ‚s|#include <QuickTime/QuickTime\.h>||‘ src/osx/carbon/dataobj.cpp 2) add - -disable-mediactrl to the configure parameters. 3) All treatments of the libraries libwx_…media.…dylib had to be removed. This could be specific to packaging with fink. The full package description is here: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.9-libcxx/stable/main/f… The diff for 10.12 is here: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.9-libcxx/stable/main/f… After this mods wxpython was happy as well. Michael

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Re: [Ifeffit] ifeffit on Mac OS X: fink package
by Karl-Michael Schindler 07 Oct '16

07 Oct '16

Hi Matt > Am 04.10.2016 um 19:00 schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > > Message: 3 > Date: Tue, 4 Oct 2016 07:57:37 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] ifeffit on Mac OS X: fink package > Message-ID: > <CA+7ESboGXfXnNWqaKYxSFHsUuwq7rG3E91x0_1x2C1E8bEesMw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Michael, > > Out of curiosity, is there a reason to prefer Fink over MacPorts (which has > Ifeffit and Demeter already available)? I wouldn't say that MacPorts or > wxPerl on MacPorts are perfect, but it does work for many of us. > > As an aside, if you built ifeffit, building Larch should be much easier, > assuming that the scientific python stack is available for Fink. It's > basically "python setup.py install". Or, one can install Anaconda Python. > > Also, Bruce and I have been working on getting to the point where Demeter > uses Larch by default. Some of this is at > https://github.com/bruceravel/demeter/pull/40, and Athena with Larch is > working for me on Mac OSX. I think we have the basic functionality > needed, and are at the testing and tweaking stage. > > Making a MacPorts (and/or Fink?) installer for Larch looks like it would be > pretty easy, and that could further simplify distribution for OSX. That > is, Anaconda Python is very good, but means that one has to install Demeter > with MacPorts and also Larch from an Anaconda channel. Using a single > packaging system so that "<something> install demeter" installed Larch + > Demeter would certainly be easier. I think that we'd probably be better > off choosing one of the "port Unix tools to OSX" systems. I don't have a > strong opinion, and it's been awhile since I used Fink. > > Opinions on Fink vs MacPorts (or the others) would be helpful. > > Thanks, Regarding Fink vs MacPorts: Depending on the package, MacPorts is sometimes more recent package descriptions than Fink and has probably closer connection to apple. I have not much experience with homebrew and larch is my first try with anaconda. In my opinion, the biggest difference is that Fink uses its own tree to install things (default /sw), whereas MacPorts uses /usr/local or /opt, which means that fink has a cleaner separation of what is installed through it or by other means. With a large number of packages, this gives Fink an advantage, when it comes to weeding out interfering stuff installed by other means, like from a disk image. In reverse, deleting all of /sw gives you a pretty clean table to restart Fink. Since MacPorts and Fink do not mix well, you have to make a decision at some point and the reason above (many packages) made me choose Fink. I started to use it as some sort of sophisticated note book, when i ported some software and with time i became package maintainer with commit right. My main activities are Pascal, tools for Fortran (in particular of type old school) and some science packages. Until now, i was always able to fix most problems, i encountered. That’s why I stick to Fink. For me, changing to another one, does not yield a big advantage. Therefore, the cost and effort of a change weigh more. My background/intentions: My PhD student uses demeter on Windows, but i would like to be able to have a look at the results on my Mac. In the recent past, i had goes at larch and demeter, but got stuck at various points with either outdated perl or python packages as well as a wx package not yet building on the latest OS X (10.12). With larch I made some progress using anaconda, but the resulting GUI apps crashed with 10.12. Maybe a code signing issue. My idea is to mimic the installation by anaconda and/or MacPorts as good as possible with Fink in order to get a working package. In detail, I think that i need to carefully check the versions of the dependencies and update fink packages accordingly. I am not much of a hero when it comes to Python or Perl, but sure enough, if I can contribute to larch/demeter i will report it. I do not have any objections against MacPorts of Homebrew, but consider the scripts within the fink package descriptions obvious enough that it should not be a big problem to port them to MacPorts or Homebrew for someone, who is familiar with those systems and i am willing to help. No interest in a holy war of any kind ;-) The python packages look easier to me. I got the impression that python 2.7 based larch is the most stable one. Therefore, i think to start with that one and once that is at least working continue on the python 3.5 based one. Correct me if i am wrong on this. I am afraid that Demeter is a heavier task, since the current version of perl on OSX is 5.18.2. Not sure yet, how to proceed there. Setting up the package description for a newer version of perl sounds like overkill for the amount of time and effort i can contribute, but time will show. I would be happy to have a working „fink install demeter“. I have some background in creating Fink based GUI applications and even disk images with standalone applications using Makefiles. But one step after the other. Sounds like this is a vivid and comforting community, where i would enjoy to contribute. Michael. P.S. This became a long post.

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ifeffit on Mac OS X: fink package
by Karl-Michael Schindler 07 Oct '16

07 Oct '16

Hi all. I just want to announce that ifeffit is now available as package with fink. All you need for using ifeffit is the command: fink install ifeffit I know that xraylarch is to be used as successor and i am working on it as well as on demeter, but i did not manage to build it so far. Michael.

3 4

Smoothing aligned data in Athena
by Godfrey, Ian 29 Sep '16

29 Sep '16

Dear All, I have a bug to report when using the Athena data smoothing feature with aligned data. Exemplar project and log files are attached, along with a screenshot. I am running Windows 10 x64 with Athena 0.9.25 x64. Summary: When using the data smoothing feature in Athena with data that has previously been aligned using the alignment feature, the smoothing is performed on the non-aligned data, and the resulting, processed dataset is shifted in E. Recipe: Open Athena Import a dataset that has a reference channel Import a second dataset with reference Import a standard dataset, with a slightly off alignment wrt to the first two datasets (I imported all three from Athena projects, rather than raw datafiles) Use the alignment tool to align the reference channel of one of the datasets to the standard (I used the automatic alignment) Go to the smoothing tool. You can immediately see that the smoothed curve is in the wrong place for the aligned dataset. The dataset that wasn't aligned will appear correctly Many thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by Abhijeet Gaur 24 Sep '16

24 Sep '16

Dear Arkaprava, Can you tell us from which beamline at RRCAT you have recorded this data. As far as I know the EXAFS beamlines BL-8 and BL-9 at RRCAT does not have this strange format. As Matt says it is definitely from a solid state detector data. You should consult the beamline scientist for other details about the data acquisition. With best wishes Abhijeet On Sat, Sep 24, 2016 at 12:31 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. problem in data processing in athena (Arkaprava Das) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Sep 2016 11:54:34 +0530 > From: Arkaprava Das <arkapravadas222(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] problem in data processing in athena > Message-ID: > <CAGJE4TqbXjnV3BN8M8BEL7kx61-yo9Vx0YuoyvjhF=hv-EAuTw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Respected Sir, > I am a research scholar in Inter university accelerator centre, new Delhi, > India. I am facing one peculiar problem in athena data processing. I have > attached the .xls file in the mail for Zr k edge which has been generated > in the beam line at RRCAT. when I import this file in athena it always > shows a question mark in the place of Chai (?) at the y axis. I am not able > to sort out this issue that why that question mark is coming. I have > attached the snapshot of plot window also. > > I shalll be highly obliged if yo kindly help me in resolving the issue. > > Yours sincerely > > Arkaprava >

1 0

problem in data processing in athena
by Arkaprava Das 24 Sep '16

24 Sep '16

Respected Sir, I am a research scholar in Inter university accelerator centre, new Delhi, India. I am facing one peculiar problem in athena data processing. I have attached the .xls file in the mail for Zr k edge which has been generated in the beam line at RRCAT. when I import this file in athena it always shows a question mark in the place of Chai (ϰ) at the y axis. I am not able to sort out this issue that why that question mark is coming. I have attached the snapshot of plot window also. I shalll be highly obliged if yo kindly help me in resolving the issue. Yours sincerely Arkaprava

2 1

Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by fred.mosselmans＠diamond.ac.uk 24 Sep '16

24 Sep '16

Dear Arkaprava, The beamline writes a bizarre no. of zeros in to the file. Also there are no headers on the columns which is pretty poor IMO. If you remove most of the zeroes (I just used replace in Wordpad) Athena understands the file fine, though I couldn't tell what the columns were so as there are no headers, so just guessed 5 might be the data. I don't think it is given the y scale but hopefully this shows how to do it. I think saving the file to an extension usually used for excel is a pretty odd thing to do also. So this is when Bruce might say ask the beamline staff not to output such strange data format and life would be easier for you. Thanks Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamodn House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk -- 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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Ni(I), Ni(II), and Ni(III) Reference XAS required
by mazhar iqbal 20 Sep '16

20 Sep '16

Hello Can some please provide me the standard XAS of Ni(I), Ni(II), and Ni(III). Thanks in advance

2 1

artemis doesn't read user's epsilon(k)
by Victor Streltsov 18 Sep '16

18 Sep '16

Hi Bruce, Epsilon(k) input "A user specified values for measurement uncertainty" in Artemis does not change the default value determined by Ifeffit. It assumes that input is a value of 0. I've tried the latest Artemis versions for Windows and Linus and they both behave the same. Best regards, Victor Streltsov

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Re: [Ifeffit] Ifeffit Digest, Vol 163, Issue 10
by Matteo Busi 13 Sep '16

13 Sep '16

Dear Bruce, Attached is an example of multiple data sets project, Please try to: 1. Load all the data sets of the project 2. Mark only the data set: "merge" 3. Save current group as: "____" 4. Save marked group as "____" 5. Open both files in a notepad 6. Notice the differences I hope this is detailed enough, ( I have attached my saved files as well) Best regards, Matteo 2016-09-12 19:00 GMT+02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Saving Bug (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Sep 2016 09:34:52 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Saving Bug > Message-ID: <96f04ebb-4477-3911-d6e2-e5eef2973cdb(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 09/10/2016 07:03 PM, Matteo Busi wrote: > > > > It occurs when I try to save groups to files, it seems that the saving > > option change the output while it shouldn't. When I save using the "Save > > current group as ..." option I get the full log with many columns, > > whereas when I save using the "Save marked group as ..." option I only > > get 2 columns. > > (I saved only as xmu and norm but I guess it is occuring for every > > extension) > > I do not see this behavior. It's not that I don't believe you, it is > that you have not provided enough information for me to see the problem > on my own computer. > > I need to know things about the state of Athena that should be contained > in the project file. Specifically, I want to know that you have > actually marked groups before trying to "Save marked groups as ..." > > So, post a project file that displays this behavior AND provide an > explicit recipe of mouse clicks so I can reproduce it on my computer. > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > 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 163, Issue 10 > **************************************** >

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Saving Bug
by Matteo Busi 12 Sep '16

12 Sep '16

Dear Bruce and all, I think I found a minor bug in the Athena package (0.9.25). It occurs when I try to save groups to files, it seems that the saving option change the output while it shouldn't. When I save using the "Save current group as ..." option I get the full log with many columns, whereas when I save using the "Save marked group as ..." option I only get 2 columns. (I saved only as xmu and norm but I guess it is occuring for every extension) It is a minor bug but I think if it doesn't take much time it is worth correcting. Regards, Matteo Busi

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 07 Sep '16

07 Sep '16

-----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 06 September 2016 14:57 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 163, Issue 6 Dear Irina, Your efforts are probably sadly in vain. C K-edge NEXAFS or XANES is common, but the data range is rarely long enough for exafs analysis. You have ca 160 eV of data that is not enough for EXAFS analysis. Hence I don't think there is a way to get a good background and then FT for your data. Certainly looking at your data the noise level and thus uncertainty in which features are real and which may not be will probably prevent anything but a XANES analysis. There probably is an oscillation there but with the limited data range getting meaningful numbers from a fit is most unlikely. Best wishes Fred 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. Help in background removal with Athena (Irina Pi) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Sep 2016 13:56:19 +0000 From: Irina Pi <Irina.Pi(a)icfo.eu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help in background removal with Athena Message-ID: <VI1PR0601MB22877AFA6B07BEE3CFDCEC798DF90(a)VI1PR0601MB2287.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear all, I am sorry to bother you with my tiny problems, but I have been struggling with it for a long time. The thing is I have XAS data from a graphite sample, and I don't know if I'm plotting the background correctly in it with Athena software, which determines a lot the response in the Fourier transform, and thus in our results. I'm attaching the data as data_exafs.txt, and also two different Athena projects of different backgrount fittings, graphite_exafs1.prj and graphite_exafs2.prj. Just in case projects cannot be seen, I'm also attaching screenshots (1-01deg.png and 2-01deg.png) of the different background fittings and the parameters used in Athena in only one set of data (01deg), because they are the same in the others (02deg and 35deg). Also, the final R-space plot in both fittings are sent (1-rspace.pdf and 2-rspace.pdf). What I wanted to ask is why it is so different the result according to the background removal. And are they correct the fittings I've done? I would like to have a background line similar to the other figure attached (0deg.pdf, but take into account that it is from different data), but I cannot get it. I guess this last fitting seems better, doesn't it? What could I do to have good results in the Fourier transform? Again, sorry but I don't have much experience and it seems to be so subjective that I fear doing it all wrong. Thank you very much, Best regards, Irina Pi Jauma.

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 06 Sep '16

06 Sep '16

Hi Irina, I guess in a normal situation you would want to FT at least 5 k(1/A) range to get some sort of shape to your FT peaks which would normally be a range of about 2 -7 k so maybe 190 eV above the edge. However added to that the data has to be good, I am not a C XAS expert but looking at your data I am unsure that all the oscillations are due the x-rays scattering , some might be experimental artefact which would then make the analysis even less trustworthy. WRT your data after the signal begins to die about 400 eV, i.e. you have ca 110 eV of data I might trust on a good day and even then I'd be more reassured if these were several scans added rather than just one. (I can't tell if this is the case). I doubt there is useful stuff that can be extracted past that point. Hence I think all that is probably there is the pre-edge changes in the XANES which I presume you are looking at as well. Thanks Fred -- 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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Help in background removal with Athena
by Irina Pi 06 Sep '16

06 Sep '16

Dear all, I am sorry to bother you with my tiny problems, but I have been struggling with it for a long time. The thing is I have XAS data from a graphite sample, and I don't know if I'm plotting the background correctly in it with Athena software, which determines a lot the response in the Fourier transform, and thus in our results. I'm attaching the data as data_exafs.txt, and also two different Athena projects of different backgrount fittings, graphite_exafs1.prj and graphite_exafs2.prj. Just in case projects cannot be seen, I'm also attaching screenshots (1-01deg.png and 2-01deg.png) of the different background fittings and the parameters used in Athena in only one set of data (01deg), because they are the same in the others (02deg and 35deg). Also, the final R-space plot in both fittings are sent (1-rspace.pdf and 2-rspace.pdf). What I wanted to ask is why it is so different the result according to the background removal. And are they correct the fittings I've done? I would like to have a background line similar to the other figure attached (0deg.pdf, but take into account that it is from different data), but I cannot get it. I guess this last fitting seems better, doesn't it? What could I do to have good results in the Fourier transform? Again, sorry but I don't have much experience and it seems to be so subjective that I fear doing it all wrong. Thank you very much, Best regards, Irina Pi Jauma.

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Re: [Ifeffit] need help to get better fitting (Dali Yang)
by Dali Yang 06 Sep '16

06 Sep '16

Hi, Mia, In your Artemis file “Cs1.33Fe1.33_FeKedge_Fit.fpj”, It seems that you are using a Ti atom as the core atom instead of an Fe atom. So, you are trying to fit a Fe_K_edge EXAFS using a "Ti-O” and ”Ti-Ti" path? That is probably the major problem. However, I tried to replace the core atom in your feff input file, but I can not get a reasonable fitting for the first shell either(see the attachment). I guess you are using a cif file which is not your real Fe dopant sample. The Fe dopant might expand your structure to make Fe-O path(bond length, coordination) very different from Ti-O, so we can not get a decent fitting for this data. Meanwhile, I can not see the meaning by using a Fe foil to extract the S0^2 for your data fitting. Good luck, Dali > Message: 1 > Date: Mon, 5 Sep 2016 15:58:47 -0400 > From: Yun Xu <yunxulanl(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] need help to get better fitting > Message-ID: > <CAKGyrcG_CuCNQDBWQc1b48XQks33VJgdnMnF20RhEo8MHo1GPw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > *Hello, This is Mia From Clemson University.* > *I have problem with my fitting, this has bothered me for long time.* > *So the thing is I use Fe metal foil as reference, and I was able to get > S02 from fitting the Fe metal foil XAS as seen in the attached file > Fe_metal foil fit.* > *Then I used this S02 value to fit the Fe_kedge exafs data of Hollandite > sample, Cs1.33Fe1.33Ti6.67O16. The hollandite crystal structure cif file is > also attached as hollandite.cif. Fe and Ti sit in the six oxygen > coordinated octahedral. the crystal structure is shown in the attached > figure as hollandite.jpg. (neglect the color of octahedra) This cif file is > the original structure without dopant as BaTi8O16 (I4/m space group). so I > set the core atom as Fe in the Feff, and assume second and third shell as > Ti, in the DFT calculation, Fe octahedra tend to have a Ti octahedra as > neighbor rather than a Fe ocatahedra. * > *I've also attached my artemis file to see anybody could help me get a > better fitting. I just need to fit the range up 3.5A which includes the > first oxygen shell and Two Ti shell.* > *A specific question is I always get negative S02 value, can any body tell > me what I should do if I get negative S02.* > *Thank you very much* > *Mia* >

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need help to get better fitting
by Yun Xu 05 Sep '16

05 Sep '16

*Hello, This is Mia From Clemson University.* *I have problem with my fitting, this has bothered me for long time.* *So the thing is I use Fe metal foil as reference, and I was able to get S02 from fitting the Fe metal foil XAS as seen in the attached file Fe_metal foil fit.* *Then I used this S02 value to fit the Fe_kedge exafs data of Hollandite sample, Cs1.33Fe1.33Ti6.67O16. The hollandite crystal structure cif file is also attached as hollandite.cif. Fe and Ti sit in the six oxygen coordinated octahedral. the crystal structure is shown in the attached figure as hollandite.jpg. (neglect the color of octahedra) This cif file is the original structure without dopant as BaTi8O16 (I4/m space group). so I set the core atom as Fe in the Feff, and assume second and third shell as Ti, in the DFT calculation, Fe octahedra tend to have a Ti octahedra as neighbor rather than a Fe ocatahedra. * *I've also attached my artemis file to see anybody could help me get a better fitting. I just need to fit the range up 3.5A which includes the first oxygen shell and Two Ti shell.* *A specific question is I always get negative S02 value, can any body tell me what I should do if I get negative S02.* *Thank you very much* *Mia*

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Co fitting questions
by Neil M Schweitzer 02 Sep '16

02 Sep '16

I have been trying to fit a Co(OH)2 reference sample and think I have a good fit, but I have a couple reservations about it and wanted to run it by some people for an expert opinion. If you are interested, I have included the Athena file, an image of the fit, and the fit log file. Please read on! If not, sorry I spammed you. As you can see, the fit contains four paths. They are all single scattering paths, and the paths with the four largest ranks according to feff. All paths share the same SO2 and deltaE. Each path has its own delR and ss. After some work, I got it to the point that the fit looks pretty (R-factor<0.02), but I have several reservations about it: 1) Generally, the ss values are all higher than I would like. 0.007 even seems high to me for a metal-O bond. Am I right about this? Would this indicate that this may have been a poor choice for reference sample (I should mention it is a powder) and it is not very crystalline? Could it mean there was something we overlooked when we recorded the data? 2) The biggest problem with the fit is the large error on ss_O2 and ss_O3. The largest feature at ~2.75 is obviously Co-Co scattering, but the Co-O paths help to fit the shoulder (or feature at ~3.1 in the Real part) in R-space. If I take them out, then the Co path has a large ss with an equally large error. So here is my question. If I add more paths, the error of ss_O2 and ss_O3 will go down, but then the errors on the new path will consequently be large, so when do I stop adding paths? For the purpose of my samples, I am only interested in the first Co-O path and the Co-Co path. Is this fit good enough you would publish it? Please feel free to critique any other aspect of the fit too. Thanks for your input! Neil

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Larch user base?
by Sean Fackler 01 Sep '16

01 Sep '16

Hello all! Do you have an idea of Larch user base or Larch package download stats? Thanks for any information. Regards, Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

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Phase correction not working in Athena
by Sebastian George 31 Aug '16

31 Aug '16

Dear all, I hope that I am writing this in the correct place, and if I am not, I apologize. The problem I'm having is pretty much summed up in the Subject line. I'm analyzing some experimental EXAFS data in Athena, and it seems that ticking the "phase correction" box has no effect on my Forward Fourier transform. Has anybody run into this problem, and if so, were you able to fix it? The material I'm studying is amorphous SmCo. Could it be that having multiple backscattering species or a lack of crystalline structure causing problems for the phase correction? More generally, I'm wondering how exactly this phase correction is determined anyway. If used, is it the sort of thing that can put the first peak in my FT fairly close to the true nearest neighbor distance? Perhaps a better phrased question is: when can the phase transformation be expected to give a quantitatively accurate radial distribution (in terms of peak positions), and when is it more likely to only be qualitatively useful? Also, I would have assumed that a backscattering species would need to be given in order to calculate the phase shift, but I haven't found anywhere to do that. Have I missed something? Thank you for any help in advance! Regards, Sebastian

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pgplot and ifeffit installation on current linux systems
by Loges, Anselm G 26 Aug '16

26 Aug '16

Dear all, I hope this is the right platform for my question. If not, sorry to bother anyone. The question: Has anyone successfully installed pgplot and ifeffit on a recent Arch Linux system and could provide a quick how-to guide (also for the Demeter website maybe)? Although I have not yet tested it, my problem may also be relevant for current Debian/Ubuntu systems. Here's the situation: I am trying to install ifeffit on a current Arch Linux machine and therefore need to install pgplot first. The PGPLOT_install script on the respective GitHub page (as linked by a tutorial on the Demeter page, see links below) does not work because it relies on several outdated paths to dependencies. The one culprit I was able to isolate and fix was the path to the X11 libraries, which the script looks for here: /usr/X11 or /usr/X11R6 but in current Arch Linux (at least in mine, which is Manjaro to be precise, link below) is here: /usr/share/X11 This alone does not fix all problems, there are several dependencies missing in the X11 directory and I could not find out what the actual relevant package names are in Arch (Debian/Ubuntu names cannot be found). Also the config files of pgplot seem to have a bunch of similar problems that (at least partially) seem to stem from use of an old fortran-to-c translator (f2c) instead of the gcc fortran frontend and missing dependencies for that. If I am not mistaken, the latest Ubuntu LTS (16.04.) also has the /usr/share/X11 path, so the script should not work there either. I'd be happy to provide an updated installation script if I ever get it running but I thought I'd ask if someone has done that already or has solved the related problems so as not to invent the wheel anew. Links: <https://bruceravel.github.io/demeter/documents/SinglePage/installation.html>https://bruceravel.github.io/demeter/documents/SinglePage/installation.html https://github.com/newville/ifeffit <https://manjaro.github.io/>https://manjaro.github.io/ Best regards, Anselm

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Demeter Installation issues
by Gaurab Rimal 23 Aug '16

23 Aug '16

Hello, I have been trying to install demeter in my archlinux machine but have issues in the build process. I had issues installing pgplot from ifeffit git source so I installed pgplot separately (as outlined in the original pgplot instructions). After installing ifeffit and after all dependencies were met, I ran ./Build and got an error about 'cpg/libgcc_path.sh'. Below is the full output from ./Build. I am unsure of this error because it seems to be related to ifeffit and pgplot and do not know how to resolve this. $ ./Build Ifeffit's installations directory is /usr/local/share/ifeffit (found by capturing `ifeffit -i`) Compilation flags (from /usr/local/share/ifeffit/config/Config.mak): -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath cc -I/usr/lib/perl5/core_perl/CORE -fPIC -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -o src/ifeffit_wrap.o src/ifeffit_wrap.c cc: error: `/cpg/libgcc_path.sh`: No such file or directory error building src/ifeffit_wrap.o from 'src/ifeffit_wrap.c' at /usr/share/perl5/core_perl/ExtUtils/CBuilder/Base.pm line 174, <C> line 11. Gaurab

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Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17
by Christopher Thomas Chantler 13 Aug '16

13 Aug '16

Topic 1: We have a routine /edit within ifeffit (our modified version) which propagates and fits uncertainty. Working on a couple of minor details before passing it on to Matt and Bruce for general use. Topic 3: Monochromator glitches should be eliminated in absorption spectra under normal circumstances if the dark current estimation is well defined. I recommend careful measurement and recording of this for all spectra. ------------------------------------------------------------ Christopher Chantler, Professor, FAIP 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 chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ 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: Friday, 12 August 2016 11:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 162, Issue 17 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. Statistical errors in linear combination fits (Joshua Kas) 2. Re: Statistical errors in linear combination fits (Bruce Ravel) 3. Athena interpolation when removing mono glitches (Michael Gaultois) 4. Re: Athena interpolation when removing mono glitches (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Aug 2016 13:31:45 -0700 From: Joshua Kas <joshua.j.kas(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Statistical errors in linear combination fits Message-ID: <CAHuhYRm_Dx5+_HAUuOZ0nCwzXwCrS-Subxb9dmBXDsQp8wmSRQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Athena interpolation when removing mono glitches
by Michael Gaultois 12 Aug '16

12 Aug '16

Dear members of the Ifeffit list, I recently collected some EXAFS data with some significant monochromator glitches that I am looking to remove. I have used a python script graciously written by the beamline scientist to remove the offending regions, but when I import the data into Athena, Athena does some funny business in an attempt to join together the regions outside of the data gap. (See the bending away in the dataset and/or attached image.) I have confirmed by plotting with other software that the strange step-like behaviour in the mu(E) is present only after importing into Athena (the raw data is fine). I have looked through the mailing list archives and also the user manual, but can't seem to find anything that explains it, or other people who have experienced this problem in the past. From what I can determine, Athena joins together the segments to obtain a linear interpolation in the norm(E)? This leads to a warping in the mu(E). ==How does Athena try to treat this data?== I was wondering if other people have had similar issues, and what steps can be taken to remedy the problem. For example, replacing removed data points with artificial points along a linear interpolation would be possible, but the act of adding artificial points that don't exist is concerning to me. ==What is the best way to treat data with mono glitches to reduce spurious features not intrinsic to the sample?== If you are interested, I have included links to .prj datasets and images to highlight these problems below. With thanks for your time, Michael ---------- .prj file with 4 ways of working up the same data: http://bit.ly/2bnfNZ5 1) raw data 2) mono glitches removed 3) rebinned data 4) rebinned and manually removed points (This leads to some strange-looking features in k-space, and this would be less than desireable on the many datasets we have collected) images to highlight these problems: a) mu(E) http://bit.ly/2aYaJIf b) norm(E) http://bit.ly/2aYaX27 c) k http://bit.ly/2baWh0h

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Statistical errors in linear combination fits
by Joshua Kas 11 Aug '16

11 Aug '16

Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 09 Aug '16

09 Aug '16

Hello All, I apologize in advance if this is not the correct method to reply to the thread. Thank you for your replies and suggestions. I will look further into determining the atomic structure of the Hf-Al intermetallics through their papers. Once I obtain this information, how do I go about creating the actual CIF file? Can I just open up any arbitrary CIF file and then change the parameters and name to match that of the Hf-Al systems? Lastly, going through some CIF files from crystallography.net, I notice that some of the 3D models from the CIF has a different stoichiometry from the designated crystal. For example, I have attached a CIF file of SiO2 that I have found; however, the 3D representation only has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity? Regards, Ed Han

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Ti data problem
by Siliang Chang 08 Aug '16

08 Aug '16

Dear all, I am new to XAFS data analysis. Im currently working on the XAFS data of atomic layer deposited mixed oxide thin film: SnTiOx. I have both Sn and Ti K edge data, and was able to fit Sn edge using a model of (Sn,Ti)O2 solid solution. However, Ti data really confuses me (please see attached file). With Rbkg set to 1, there is a doublet in 1-2 Å region in every data, this is something I have never seen in the literature. Im wondering if this is normal? Does this mean I should set a larger Rbkg value, say, around 1.5? Ive tried to fit the abovementioned Ti data using several models: anatase, rutile, (Sn,Ti)O2 solid solution, perovskite (N is fixed at 6 for all of those), so far no success. I would really appreciate if you can comment on my data processing, any suggestions are welcomed, as Im new to this, Im not sure if Im doing it the right way. Thank you very much. Best regards, Siliang Chang

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 08 Aug '16

08 Aug '16

Dear All, In the upcoming fall, my research group plans on performing XAS studies observing the Hf L3-edge for various Hf-Al intermetallic samples. In preparation for the experiments, I am looking for CIF files of the various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc. Upon scavenging through a multitude of crystallographic databases, I was not able to find any CIF files of Hf-Al intermetallics. However, I have acquired powder diffraction files (PDF) for said intermetallics. Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to my knowledge), is there a way to convert PDFs into CIFs? I have attached one of the PDF files to demonstrate what information it contains. I would really appreciate your help! Regards, Edmund Han

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Amorphous
by Carlos Triana Estupinan 08 Aug '16

08 Aug '16

Dear Bruce I want to know if it is possible to obtain a 3D structure (.cif file) of an amorphous material from the EXAFS fitting carried out from artemis. I mean, there is a way to extract a .cif file with the structural data obtained from the refined spectra. Also, in amorphous materials there must be a distribution of interatomic bond distances and coordination, and so, how can I address such a structural distribitions. Regards.

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Multi-electron peak in Yb
by Matthew Marcus 05 Aug '16

05 Aug '16

Does anyone know of data on multi-electron peaks at the Yb L3 edge? One of the users here was just running Yb and finds on every spectrum a bump at the same energy. It's not a Bragg glitch from the sample or an I0 glitch or any other obvious artifact. It reminds me of the two little bumps at Ce. If someone has analyzed and parameterized this peak as a fraction of edge jump, then it would be possible to subtract it off. The attached papers show exmples for almost every lanthanide *execpt* Yb. For those doing Ce, I've written a program which does the correction, essentially as presented in the attached Gomilsek paper. Like Ce, Yb hs 2 valence states (other than 0), but the user is sure that his sample is all 3+. mam

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Re: [Ifeffit] Questions about fitting of EXAFS
by Scott Calvin 04 Aug '16

04 Aug '16

Just to clarify: the shape of the FT may certainly change when you change kmax. But if the data and the model change in the same way, then the fit is insensitive to the choice of kmax, in the sense that the fitted parameters remain stable to within their reported uncertainties. —Scott Calvin Sarah Lawrence College On Aug 4, 2016, at 2:50 PM, Fuxiang Zhang <zhangfx(a)umich.edu<mailto:zhangfx@umich.edu>> wrote: The Kmax effect on the shape of magnitude of FTs of one of my samples may come from the low signal/noise ratio.

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Questions about fitting of EXAFS
by Fuxiang Zhang 04 Aug '16

04 Aug '16

Hi, Everyone, I have several detailed questions about EXAFS processing and fitting 1. Are there any physical meaning for DeltaE0 in the paths, why it should be less than 10eV 2. The cutting range of Kmax (FT transform parameters) has great effect on FTs of EXAFS, how do I know to use the best value of Kmax; 3. How to make refinement equation for multi-scattering paths? Such as in NiFe alloys (simple fcc structure), the path [Ni-FM-3m] Fe1.1 Ni1.4 Fe1.1., I use 0.67*Efe+0.33*Eni for DeltaE0, and 0.67*ssFe1+0.33*ssNi4 for sigma2, is that right? Many thanks Fuxiang Zhang

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Applicable scope of delr=alpha*reff
by woschangqiang 03 Aug '16

03 Aug '16

Hi, everyone. delr=alpha*reff is very powerful in the fit of cubic system. And I want to know whether this function can be used in other crystal system. Thank for your patient answer.

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Reference spectra for brookite, anatase, rutile, Amorphous TiO2 at Ti K-edge
by Samy Ould-Chikh 03 Aug '16

03 Aug '16

Dear, I received some data at Ti K-edge to analyse. The spectra corresponds to samples which are different mixture of titania allotropes. I started to do standard EXAFS fitting, but it doesn't seem relevant in this case. Probably, an attempt to do linear combination fitting with brookite, anatase, rutile, and amorphous titania references will be more useful. Unfortunately, the set of data I was given do not include those standards. Is there anyone who have the spectra corresponding to those titania compounds and willing to share with us the raw data ? If yes, would you mind to provide also the citation I should you use to acknowledge those standards ? Many thanks for your kind help. 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 Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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2016 Introduction to Synchrotron Radiation Course
by Carlo Segre 01 Aug '16

01 Aug '16

This fall semester I will be offering an introductory graduate level course entitled Introduction to Synchrotron Radiation at Illinois Tech. This course has been offered on a regular basis over the past 5 years and it is avilable as an online course through IIT/Online. Through a special arrangement with the Dean of the College of Science, online students can take this course as non-degree students at a 67% tuition discount. We have had students from Italy and Brazil in past sessions of this course. Registering for this course as a non-degree student requires a simple application which can be completed online and will be approved in only a few days. The course description is below. Please share this with interested parties and direct any questions to Carlo Segre <segre(a)iit.edu> Course Description: This is a graduate course which introduces students to the production, manipulation and use of synchrotron radiation in research. The course will include visits to, and possibly hands-on experience with, beamlines at the Advanced Photon Source (APS) at Argonne National Laboratory but is not specific to the APS. Students will be expected to give presentations and write a General User Proposal to the APS as their final projects. Graduate students in any science or engineering program are welcome to register as are undergraduates with senior standing and permission of instructor. It is particularly recommended for students wishing to make use of synchrotron radiation in their research. The class meets Mondays and Wednesdays 17:00-18:15 and the lectures are available online as an Internet section for students not on the IIT campus or even in the United States. Textbook: Elements of Modern X-Ray Physics, 2nd ed., Jen Als-Nielsen and Des McMorrow, (John Wiley & Sons, Ltd. 2011). Topics Covered: X-rays and their interaction with matter Sources of x-rays Refraction and reflection from interfaces Kinematical Diffraction Diffraction by perfect crystals Photoelectric absorption Resonant scattering Small angle scattering Other topics as appropriate Course Organization: The grade will be based equally on homework assignments, student presentations and a draft General User Proposal to the Advanced Photon Source. There will be at least one field trip to the Advanced Photon Source for experiment demonstrations. For more information please contact Carlo Segre <segre(a)iit.edu> -- 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

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Tenure-track academic position advert
by Robert Dryfe 01 Aug '16

01 Aug '16

Dear Sir/Madam, I would be grateful if you could circulate the details of an academic vacancy for an expert in the application of X-ray synchrotron techniques to chemical systems. Details can be found here (please note the application deadline is soon): https://www.jobs.manchester.ac.uk/displayjob.aspx?jobid=11764 Informal inquiries are welcome. regards, Robert Dryfe (School of Chemistry, University of Manchester, UK)

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Postdoc Position
by Jeff Terry 29 Jul '16

29 Jul '16

Hi All, I never remember what the rules are here for posting postdoc positions but I have one position available. You can see more information about the position here: http://mrmac.mr.aps.anl.gov/~jterry/postdoc.html Please let anyone who might be interested know. Thanks, Jeff Jeff Terry Professor, Department of Physics Illinois Institute of Technology Life Sciences Bldg Rm 166 3101 S. Dearborn St. Chicago IL 60616 630-252-9708

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Multiple scattering path parameters
by Neil M Schweitzer 29 Jul '16

29 Jul '16

Are there standard ways of relating the parameters (deltaR and sigma^2) of multiple scattering paths to the parameters of the single scattering paths based on the type of MS path? For example, would deltaR_MS = deltaR_SS*2 if the MS was a "forward through" geometry? What about other geometries and paths that involve different types of atoms? Neil

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Re: [Ifeffit] determining reasonable fitting parameters
by Neil M Schweitzer 27 Jul '16

27 Jul '16

Thanks to everyone for all the previous responses to my emails, I've learned a lot in the few weeks I've been on this list! I was hoping to build off of the last point Bruce made in message 3 below by asking another question. I am fitting a CeO2 reference from paths generated by feff from a cif file. Since this is my starting point, I made SO2 the same for every path (and used the coordination numbers from the cif file). If I am generating what looks to be a reasonable fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to tell me? Am I doing something wrong in my initial background subtraction in Athena? I'm asking about the background subtraction because I recently discovered that there is a CeO2 reference provided in Hephaestus. I exported the data, and tried to fit it in Artemis using a similar methodology I used for my own sample, and I got an even lower SO2. So I don't think the small SO2 value is an artifact of the way the experiment was run (although I might be wrong, I wasn't present when the data was actually collected). The observed difference seems real because the magnitude of the signal in E-space, k-space, and R-space is lower for the Hephaestus sample compared to my experimental sample (see attached image... One note, I'm not sure why the signals are off set in the Energy plot. The Eo's are the same, and if I plot the spectra together in E-space alone, they are not offset. Maybe a bug?). Neil -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, July 21, 2016 8:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 20 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… 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. demeter installation in OSX El Capitan (Ping, Yuan) 2. Re: determining reasonable fitting parameters (Bruce Ravel) 3. Re: determining reasonable fitting parameters (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 Jul 2016 05:37:10 +0000 From: "Ping, Yuan" <ping2(a)llnl.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] demeter installation in OSX El Capitan Message-ID: <D3B5AD95.32BB2%ping2(a)llnl.gov> Content-Type: text/plain; charset="windows-1252" Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, ?sudo port -v self update?, ?port upgrade outdated? were all OK. When I tried ?sudo port install xorg-server demeter?, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 ---> libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr ---> pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

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Re: [Ifeffit] determining reasonable fitting parameters
by Neil M Schweitzer 27 Jul '16

27 Jul '16

Thanks for the responses. Seems like it is a problem without a simple solution, especially after the experiment has already been performed. When my users rerun the samples, I'll have to make sure they are very careful. In terms of the question about fitting the Hephaestus reference, when you plot it in Hephaestus it only shows out to ~50eV, but when you save the data file the data goes out much further. You can see from the plots I had included that the data goes out past k=10 A^-1. Neil -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, July 27, 2016 4:09 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 39 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… 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: determining reasonable fitting parameters (Matthew Marcus) 2. Re: determining reasonable fitting parameters (Bruce Ravel) 3. Re: determining reasonable fitting parameters (Matthew Marcus) 4. Re: determining reasonable fitting parameters (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jul 2016 13:39:03 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <c2c71f99-44d9-f17f-ab52-399f53d8bb83(a)lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed I'm not sure I get your point about ion-chamber response. Shouldn't that normalize out in post-edge spline? If the I0 chamber gets less sensitive as a function of energy, then the post-edge background rises by the same amount as the wiggles get bigger, so it divides out. Similarly for probe-depth effects, depending on concentration. Another couple of possible sources of amplitude error: 1. The model for the pre-edge background is inaccurate, so that its extrapolation to the EXAFS region is incorrect. For instance, if there's a lot of elastic scatter getting into the fluorescence detector, then the pre-edge is curved, and if you model that with a straight line fitted near the edge, them you'll be off far from the edge. Similarly, in a long transmission scan, both pre- and post-edge are curved. My background-sub program has simple models for thse shapes which aren't perfect but help. This effect is really hard to control for because you have no real way to know what the 'right' answer is, most of the time. 2. Overabsorption will definitely reduce the amplitude of the wiggles, and I'm surprise Bruce didn't menntion it. It looks much like pinhole effect. Harmonics do similar things as well in transmission. I still haven't heard how you do EXAFS analysis using the short spectrum from Hepheastus. mam On 7/27/2016 1:23 PM, Bruce Ravel wrote: > On 07/27/2016 03:53 PM, Neil M Schweitzer wrote: >> Thanks to everyone for all the previous responses to my emails, I've >> learned a lot in the few weeks I've been on this list! I was hoping >> to build off of the last point Bruce made in message 3 below by >> asking another question. I am fitting a CeO2 reference from paths >> generated by feff from a cif file. Since this is my starting point, I >> made SO2 the same for every path (and used the coordination numbers >> from the cif file). If I am generating what looks to be a reasonable >> fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to >> tell me? Am I doing something wrong in my initial background >> subtraction in Athena? >> >> I'm asking about the background subtraction because I recently >> discovered that there is a CeO2 reference provided in Hephaestus. I >> exported the data, and tried to fit it in Artemis using a similar >> methodology I used for my own sample, and I got an even lower SO2. So >> I don't think the small SO2 value is an artifact of the way the >> experiment was run (although I might be wrong, I wasn't present when >> the data was actually collected). The observed difference seems real >> because the magnitude of the signal in E-space, k-space, and R-space >> is lower for the Hephaestus sample compared to my experimental sample >> (see attached image... One note, I'm not sure why the signals are off >> set in the Energy plot. The Eo's are the same, and if I plot the >> spectra together in E-space alone, they are not offset. Maybe a >> bug?). > > I don't remember much about the provenance of that CeO2 spectrum. I > don't remember how calibration was done (or even if it is reliable). > I don't remember much about the sample -- it was a pellet, but I have > no way of knowing if it was homogeneous or even if the particles were > of the size reported. > > I guess what I am trying to say is this -- if you trust your CeO2 > measurement, you should have more faith in that (or the one Matthew > just sent) than in the one from Hephaestus. > > As for your S02 question, here's some of the standard litany: > > + the mean free path used by feff was too long. > > + S02 and sigma^2 are highly correlated. > > + you did a lousy job normalizing the data (although it sure doesn't > look that way from your picture). > > + your sample had a lot of pinholes. > > + there is some source of loss in CeO2 that is neglected in Feff > (which is, practically speaking, the same as the mean free path > comment). You could try fixing S02 and floating an Ei parameter. > Or floating both S02 and Ei, although they will be highly > correlated. > > + There is also an energy response to the ionization chambers at such > a low energy -- that is, the absorption of the gas in the detector > is weaker at the end of the spectrum than at the beginning. In > fluorescence, that serves to attenuate the edge0step-normalized > spectrum in a way that looks like an enhancement to sigma^2. But > it's an attenuation, which could show up in S02. > > I should mention that in my favorite teaching example -- FeS2 -- by > the end of the lecture I have a S02 of something like 0.69. And I > just walk away from the lecture at that point :) The reason I do so is > that all the rest of the parameters are defensible and I chalk the > small S02 up to one of the points above (along with some enthusiastic > hand waving -- usually it's time for coffee or lunch by the time I've > finished the FeS2 demo!). > > B > > ------------------------------ Message: 2 Date: Wed, 27 Jul 2016 16:45:26 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <e0a93edf-8a8b-97a5-aa14-f595fc385c31(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:39 PM, Matthew Marcus wrote: > I'm not sure I get your point about ion-chamber response. Shouldn't > that normalize out in post-edge spline? Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default in the way you are suggesting. > If the I0 chamber gets less sensitive as a function of energy, then > the post-edge background rises by the same amount as the wiggles get > bigger, so it divides out. Similarly for probe-depth effects, > depending on concentration. Another couple of possible sources of > amplitude error: > 1. The model for the pre-edge background is inaccurate, so that its > extrapolation to the EXAFS region is incorrect. > For instance, if there's a lot of elastic scatter getting into the > fluorescence detector, then the pre-edge is curved, > and if you model that with a straight line fitted near the edge, > them you'll be off far from the edge. Similarly, in > a long transmission scan, both pre- and post-edge are curved. My > background-sub program has simple models for thse > shapes which aren't perfect but help. This effect is really hard > to control for because you have no real way to know > what the 'right' answer is, most of the time. > > 2. Overabsorption will definitely reduce the amplitude of the > wiggles, and I'm surprise Bruce didn't menntion it. It looks > much like pinhole effect. Harmonics do similar things as well in > transmission. My brain is really tiny and it's getting to be late in the afternoon here. It's amazing that many bullet points actually made it into the email! B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_ho… Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&… Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… ------------------------------ Message: 3 Date: Wed, 27 Jul 2016 13:56:41 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <3ee04494-5113-2994-3d96-e9e5bd2ebecc(a)lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine does (mu(E(k))-spline(k))/spline(k), which I guess has its own problems - any wiggles driven in the spline will multiply the EXAFS. I haven't seen any effect from this, though. Maybe the right thing is (mu(E(k))-spline(k))/smooth(E(k)) where smooth is a smooth post-edge background such as a polynomial or spline with fewer knots than the subtraction spline or even a tensioned spline. I'd be willing to bet that this refinement will make no detectable difference, especially if you do the reference data the same way. I've found that you can do the most amazingly bogus things and get away with it as long as you do them equally to your reference and unknown, especially if the reference is very similar to the unknown. Of course, you can't rely on that. mam On 7/27/2016 1:45 PM, Bruce Ravel wrote: > On 07/27/2016 04:39 PM, Matthew Marcus wrote: >> I'm not sure I get your point about ion-chamber response. Shouldn't >> that normalize out in post-edge spline? > > Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default in the way you are suggesting. > >> If the I0 chamber gets less sensitive as a function of energy, then >> the post-edge background rises by the same amount as the wiggles get >> bigger, so it divides out. Similarly for probe-depth effects, >> depending on concentration. Another couple of possible sources of >> amplitude error: >> 1. The model for the pre-edge background is inaccurate, so that its >> extrapolation to the EXAFS region is incorrect. >> For instance, if there's a lot of elastic scatter getting into >> the fluorescence detector, then the pre-edge is curved, >> and if you model that with a straight line fitted near the edge, >> them you'll be off far from the edge. Similarly, in >> a long transmission scan, both pre- and post-edge are curved. My >> background-sub program has simple models for thse >> shapes which aren't perfect but help. This effect is really hard >> to control for because you have no real way to know >> what the 'right' answer is, most of the time. >> >> 2. Overabsorption will definitely reduce the amplitude of the >> wiggles, and I'm surprise Bruce didn't menntion it. It looks >> much like pinhole effect. Harmonics do similar things as well in >> transmission. > > My brain is really tiny and it's getting to be late in the afternoon here. It's amazing that many bullet points actually made it into the email! > > B > > ------------------------------ Message: 4 Date: Wed, 27 Jul 2016 17:08:58 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <a632df68-e115-cda0-3ace-4c066230b85f(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:56 PM, Matthew Marcus wrote: > Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine > does (mu(E(k))-spline(k))/spline(k), which I guess has its own > problems Exactly. Both solutions have problems. The potential for trouble with "/const" seems less severe to me and easier to support (in the sense of supporting the use of a software package). So that's why Athena does what she does. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_ho… Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&… Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_de… ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.g… ------------------------------ End of Ifeffit Digest, Vol 161, Issue 39 ****************************************

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Re: [Ifeffit] Athena Question
by tyson 27 Jul '16

27 Jul '16

Thanks for the fast response.TAT Sent via the Samsung GALAXY S® 5, an AT&T 4G LTE smartphone -------- Original message -------- From: Bruce Ravel <bravel(a)bnl.gov> Date: 7/27/2016 12:34 PM (GMT-06:00) To: "Tyson, Trevor A." <trevor.a.tyson(a)njit.edu> Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: Athena Question On 07/27/2016 12:01 PM, Tyson, Trevor A. wrote: > Hi Bruce, > > I know that you are very busy building beaminles but I could not > resist adding more to your load. I have an Athena question. I have > aligned a large set of data to a reference. Now for each data set > Athena records the energy shift. Is it possible to export the list of > shifts? Thanks. > > Trevor > Hi Trevor, Hope you don't mind that I am CCing this to the Ifeffit mailing list. The question seems broadly interesting, so leaving an answer in a place that can be found by google seems like a good idea. There are a several ways of doing this: 1. Right click on the label that says "Energy shift". one of the options is "Show energy shifts of all groups". That will post a dialog like the one in the attached picture. Click the "Save" button to write the contents as a text file. 2. Click on the File menu, then on the Export submenu. Select "Excel report on marked groups". This will write an XLS file. You can open that up in Excel or any other spreadsheet program. Column E has the energy shifts. 3. For the sake of completeness, if you are a command line kinda guy, you can use the "dlsprj" program that gets installed when you install the rest of demeter: dlsprj myproject.prj --params=bkg_eshift,bkg_delta_eshift This will print the shifts and their uncertainties to the screen. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Athena Question
by Bruce Ravel 27 Jul '16

27 Jul '16

On 07/27/2016 12:01 PM, Tyson, Trevor A. wrote: > Hi Bruce, > > I know that you are very busy building beaminles but I could not > resist adding more to your load. I have an Athena question. I have > aligned a large set of data to a reference. Now for each data set > Athena records the energy shift. Is it possible to export the list of > shifts? Thanks. > > Trevor > Hi Trevor, Hope you don't mind that I am CCing this to the Ifeffit mailing list. The question seems broadly interesting, so leaving an answer in a place that can be found by google seems like a good idea. There are a several ways of doing this: 1. Right click on the label that says "Energy shift". one of the options is "Show energy shifts of all groups". That will post a dialog like the one in the attached picture. Click the "Save" button to write the contents as a text file. 2. Click on the File menu, then on the Export submenu. Select "Excel report on marked groups". This will write an XLS file. You can open that up in Excel or any other spreadsheet program. Column E has the energy shifts. 3. For the sake of completeness, if you are a command line kinda guy, you can use the "dlsprj" program that gets installed when you install the rest of demeter: dlsprj myproject.prj --params=bkg_eshift,bkg_delta_eshift This will print the shifts and their uncertainties to the screen. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Problem with Artemis opening an Athena project
by Irina Pi 27 Jul '16

27 Jul '16

Dear all, I have a problem opening an Athena project with Artemis. When I have selected it, it appears this error: Use of uninitialized value in addition (+) at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Prj.pm line 132 And after selecting OK and import selected data, everything closes. This Prj.pm file is attached in the mail, if it is of any help. Thank you. Best regards, Irina Pi.

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about sigma square
by Bruce Ravel 26 Jul '16

26 Jul '16

Shaofeng Wang asked this question on the mailing list that some may not have seen because it got marked as spam somewhere along the line. Kinda weird. Not quite sure why that happened.... > I have a question about sigma square. Must this parameter be in the > range of 0.003-0.02? I obtained some of it in the range of > 0.0001-0.002. Is this reasonable? Could please provide some > reference? There are no hard rules for anything. That sigma^2 is 0.00something is a good guideline and often the case, but not an actual rule. The problem with a sigma^2 in the range of 0.0something is that it tends to attenuate the path so much that it doesn't really have an impact on the quality of the fit. In that case the uncertainty is often very large precisely because the path no longer contributes significant spectral weight to the fit. A sigma^2 in the range of 0.000something means that the bond is very stiff. In some situations, that would be correct. As an example, consider the sort of negative thermal expansion material that is a network of metal-ligand octahedra. The NTE effect happens in that case because, as the material heats, up the octahedra tilt within the network, pulling the network inwards. This happens because the metalligand (usually metal-oxygen) bond is very strong -- much stronger than the forces connecting the octahedra. In an EXAFS measurement of an NTE material, you will likely find a very small sigma^2 for the first shell. (And a very large one for the second shell.) Regardless of the size of sigma^2, the bottom line is that the value is defensible. This means that you can understand and explain why sigma^2 is the size that it is. It also means that the uncertainty is such that you can support your conclusion. While the red line might overplot the blue with sigma^2=0.0003+0.001, that may be a troubling result because sigma^2 is not positive definite! Executive summary: a reasonable value is a defensible value. If you are willing to explain a result to your thesis committee or let one of us review it in a manuscript, then the result is probably reasonable. HTH, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Help with Athena
by Irina Pi 26 Jul '16

26 Jul '16

Dear all, I am just getting started with XAFS projects and I am using Athena software for processing and analysing the data. I am learning how to use it, and I have a little problem. The thing is that when I plot the XANES data, the automatic created plot is not labeled and plus it doesn't have the option of selecting a point of the spectrum. I mean, when I want to choose E0 for example, I need to do it changing the number in the Athena screen, and I don't know exactly what I am choosing because it doesn't appear anything in the graph. Was I clear? Do you know any way which I could solve it? Thank you very much, Regards, Irina Pi.

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Re: [Ifeffit] Regarding time resolved XAS
by Chris Milne 26 Jul '16

26 Jul '16

Hi Mazhar, Usually time-resolved (pump-probe) XAS is measured in data set pairs at each X-ray energy: one with laser on, one with laser off. This means that you can always directly reference your laser-excited measurement to your laser un-excited measurement. To calibrate to an absolute scale you would then use a reference foil as normal and shift both data sets according to the reference values. If you had significant delays between your laser on/off measurements then drifts and other noise sources will affect your data, making it very difficult to determine a reliable difference signal. You could try to use a reference foil measurement to correct for these kinds of drifts but you need to be very careful with the corrections to ensure you aren’t just seeing an artifact. Ideally you would be measuring laser on/off differences on a millisecond to microsecond timescale between acquisitions, this gets rid of most of the possible noise sources. Best, Chris > On 30 May 2016, at 19:00 , 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. Regarding time resolved XAS (mazhar iqbal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 06:20:36 +0000 (UTC) > From: mazhar iqbal <mazharphy_05(a)yahoo.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Regarding time resolved XAS > Message-ID: > <349705754.1395970.1464589236411.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > hello.. I am sorry if am not posting on right place. > I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that ?we have a reference fluorescence line always on the screen that well behind the K absorption edge. > Hoping to see your response.? > Best Regards >

2 1

Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... 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 Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Just a quick idea on why I cannot import the .txt file attached with previous email. I realized that the files contain 11948 points ! (it's QEXAFS data). Athena might have an hard limit of 8200 points that may be imported in a single file. 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 Website: http://kcc.kaust.edu.sa/Pages/Home.aspx -----Original Message----- From: Samy Ould-Chikh Sent: Sunday, July 24, 2016 10:56 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Bug Report importing file. Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... 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 Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at http://bruceravel.github.io/demeter/ XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo port install xorg-server demeter”, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

3 2

Re: [Ifeffit] demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Hi Joe, Thanks for your reply. In my first email I forgot to mention that I did install MacPorts-2.3.4-10.11-ElCapitan. Yuan On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" <ifeffit-bounces(a)millenia.cars.aps.anl.gov<mailto:ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of joe.fowler(a)nist.gov<mailto:joe.fowler@nist.gov>> wrote: Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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demeter installation in OSX El Capitan
by Fowler, Joseph W. (Assoc) 21 Jul '16

21 Jul '16

Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

1 0

determining reasonable fitting parameters
by Neil M Schweitzer 21 Jul '16

21 Jul '16

Being somewhere between a novice and an advanced user of XAS, I have two "philosophical" questions about EXAFS fitting (I hope this is the correct forum to ask them!). I also have a bug to report. I have included a project file of a CeO2 powder for those interested. 1) Generally, I have developed my own methodology for EXAFS fitting which I think generates ok fits, at least from the standpoint that the red line seems to follow the blue line pretty closely. My question relates to interpreting the statistics of the fit. Generally, I am studying catalyst (i.e. very small metal or oxide nanoclusters supported on a different oxide phase). Due to the size of the clusters of interest, I wouldn't expect them to resemble a bulk crystal, and therefore it is difficult for me to reduce the number of independent variables using know crystal structures. For example in this reference material, I am giving every single scattering path its own delR and ss, and using a single delE and SO2 for all the paths since they come from the same feff calculation. Once I am through with my own methodology, I can usually get a close fit even while making every variable a guess (refer to fit 17 in the project file). Admittedly, the reduced chi is rather large (5262) and the error of each of the DWF's is the same magnitude as the value itself, which is troubling. However, if I use the best fit values of fit 17 and set all of the values except for the 3 DWF's and generate a new fit, all of the statistics significantly improve even though the values of the DWF's did not change at all (Fit 19). That is, merely setting the other variables improved the fit (the reduced chi square is now 2951) and improved the error of the guess variables (the errors of the DWF's are cut close to half). Why is the fit better since none of the values actually changed, and why do the errors improve? How should I be reporting the statistics (i.e. the errors) in a publication? Should I report the fit 17 errors or the fit 19 errors for the DWF's? 2) In terms of the DWF's in general, what value is considered too high? I know the DWF's have a component that relates to temperature induced disorder in the scattering shell and a component that relates to physical disorder in the scattering shell, but what value would be considered too big for a sample measured at room temperature. I have seen values as high as 0.03 and 0.04 in presentations (sorry, no references) but these seems too large to me. At some point, if the sample is disordered enough, it seems like EXAFS is no longer an appropriate characterization tool to use. What value of DWF would that represent (for a sample measured at room temperature)? 3) I found a bug in the log files in the history window. I am running Demeter 0.9.21 on Windows 7. When I generate a new fit, if I change the k-range of the fit, the k-range of previous fits in the history window will also change to the current range (e.g. fit 19 was run from 2.1-9.3, as shown in the data window. Fits 14-16 were run in smaller ranges). What's even stranger, is if I go to a very old fit (i.e. fit 1 or 2 in the project file) and then go back to the new fit, the log file will report the k-range from the earlier fit, not the current fit. Obviously, this is making it very difficult to keep track of fits generated with different k-ranges. I have not tested to see if the R-range behaves similarly. Neil

4 4

fitting of S XANES with arctans and gaussians
by Matthew Marcus 19 Jul '16

19 Jul '16

I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper, they fit spectra to two arctangents and 6 gaussians, with widths of the arctans slaved together and widths of gaussians 1-3 and 4-6 slaved (or all 6 to one value). I'm looking for recommendations as to how to do the fit. They give prescriptions for how to set the initial estimates to give robust values. Manceau has told me that 'Athena works quite well', but I don't see any obvious way there to do the parameter constraints called for, or to keep peak heights from going negative. Athena also has a habit of assuming you want it to do the normalization for you; I've already done that and need no further 'help'. Any ideas? I've tried using Genplot, but that offers no way to restrain parametsrs to ranges to keep them from going nuts. PCA seems to want 6-8 components, so it's not all that helpful. These spectra were taken at various spots on a biological structure (abalone radula) so there's no sense of sequence which would enable the use of evolving factor analysis or something like that. LCF doesn't give satisfying fits with the references I have. I've attached a couple of the files, truncated to the range Manceau&Nagy fit to. The originas were taken over the range 2460-2550eV. mam

5 4

Artemis - Atom/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

2 1

Artemis - Atoms/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

1 0

Artemis Antisite Simulation
by #GUPTA DISHA# 15 Jul '16

15 Jul '16

Dear All I am trying to simulate data for antisite disorder for LFP data. I import the CIF file and make sum of all the paths and save the file as an artemis file. I do this for different ratios of Li/Fe sites. However, I want to compare all these data in Origin. How do I open these artemis files in Origin to see how my data varies with different Li/Fe antisites? Thank you and Kind Regards Ms. Disha Gupta PhD Student School of Materials Science & Engineering (MSE) Nanyang Technological University 50 Nanyang Avenue, Singapore 639798 Tel: (65) 84087404 | Email: disha001(a)e.ntu.edu.sg ________________________________ 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, July 13, 2016 1:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 9 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. Artemis (FEFF) question (Louis Forto) 2. Re: Artemis (FEFF) question (Matt Newville) 3. Re: Artemis (FEFF) question (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Jul 2016 10:13:17 +0100 From: Louis Forto <cforto10(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis (FEFF) question Message-ID: <CAOfHeiQnRSZX98TrKvDasc2t1WB1gq1xBmboA_T3k3RwkBNbhQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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No Reference Foil... Continued
by Neil M Schweitzer 14 Jul '16

14 Jul '16

Thanks for the responses. When I had originally tried fitting the CeO2 data, the fit was awful, but I think it was because the Eo was really far off. I set it close to where it should be and was able to find a common feature in Io to calibrate the rest of the samples to. That being said, fitting CeO2 is still quite difficult. I found a reference online (EXAFS analysis of the L3 edge of Ce in CeO2: effects of multielectron excitations and final-state mixed valence: J. Synchrotron Rad. (1999). 6, 34-42) that, from my understanding, essentially suggests duplicating all the paths and using a second delta_Eo value for the duplicated paths while also weighing the SO2 of each set of paths based on the degeneracy of the excitations. This does tend to make the fit better (as one would expect from doubling the number of paths!), but does anyone know if this is a generally accepted correction for fitting ceria materials? Does anyone have a different reference that might help me? Thanks for all the help! Neil

2 1

No Reference Foil
by fred.mosselmans＠diamond.ac.uk 13 Jul '16

13 Jul '16

Dear Neil, Sorry this may be too exact an interpretation of your English, but if you are looking at the exafs then calibration is normally pretty irrelevant as long as it is not wildly out, as you refine E0 anyway in the fitting. The bond distances will be very little altered by this. If you are looking at XANES and it is 3/4 then CeL3 as I am sure you know has two "white lines" for four and one for three and the ratio of the two peaks can be used to Look at oxidation state mixtures, I think you should be able to align the peaks and fit the area e.g. Burnham AD, Berry AJ, 2014, The effect of oxygen fugacity, melt composition, temperature and pressure on the oxidation state of cerium in silicate melts, Chemical Geology, Vol:366, ISSN:0009-2541, Pages:52-60 Best wishes Fred -- 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

2 1

No Reference Foil
by Neil M Schweitzer 12 Jul '16

12 Jul '16

Hello, Long time follower/user and first time subscriber! I work at Northwestern University, and one of the services I provide is analyzing XAS data for users who collect data at APS. Generally, I am not at APS to help them collect spectra, I help analyze the data afterwards. A user came to me recently with some Ce L3 data that does not have reference foil data. If I am trying to compare the EXAFS of several different samples (all which should be similar oxidation state, and of which I have other references of similar oxidation state). Does anyone have a suggestion how to work up the data if I can't calibrate it? ------ Neil M. Schweitzer, Ph.D Operations Director, CleanCat Core Facility Research Assistant Professor Chemical and Biological Engineering Northwestern University 2137 Sheridan Road Evanston, IL 60208-3000 Office: 847-491-2955 http://cleancat.northwestern.edu

2 1

Artemis (FEFF) question
by Louis Forto 12 Jul '16

12 Jul '16

Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

3 2

Athena crash on mac on import
by George Sterbinsky 08 Jul '16

08 Jul '16

Hello, Athena crashes upon import of the attached project file. I am using the latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open the file on windows. The message that is printed to the terminal when Athena crashes is pasted below. Please let me know if any further information would be helpful. Thank you, George [!!!] bkg_funnorm is not an attribute to set for Demeter::Data=HASH(0x7fe2e57967c8) at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm line 9. MooseX::SetGet::set(Demeter::Data=HASH(0x7fe2e57967c8), "bkg_spl2e", 110.195726042215, "y_offset", 0, "bft_rwindow", "hanning", "fft_kwindow", "hanning", ...) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 411 Demeter::Data::Prj::_record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 5, "psmtj") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 197 Demeter::Data::Prj::record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 1) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 802 Demeter::UI::Athena::IO::_prj(Demeter::UI::Athena=HASH(0x7fe2dc0226a8), "/Users...sta"..., "/Users...sta"..., 1, "") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 859 Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840), Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 782 Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840)) called at /opt/local/bin/athena line 44 eval {...} called at /opt/local/bin/athena line 44

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Re: [Ifeffit] How to change the data file in Dartemis?
by Isabelle Kieffer 08 Jul '16

08 Jul '16

Dear Bruce, dear all, Just to add some input and precise my question. The problem I encounter with "replace this chi(k)" did not appear to me until I tried to fit a spectrum twice with two different normalisations. In this case, after a fit on the first spectrum, I "replace this chi" with another that is normalised differently, and when I try to fit, it stops with the following error message: This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit. Seeing that, I wondered whether "replace this chi" was doing what I thought. The upgrade did not change anything. I just tried with a colleague working under windows and the result is also the same. Shall I do differently to fit those two really similar spectra? Thank you for your help, Isabelle On 01/07/2016 21:08, Bruce Ravel wrote: > On 07/01/2016 01:57 PM, Isabelle Kieffer wrote: >> You mean that when you "Replace this chi(k)", it asks what to do, or it >> supposes that you want to fit new data with the same model? > > What I mean is: upgrade. Many of the problems you are reporting have > been fixed already. If you upgrade and still see these problems, make > a bug report and I will look into it. > > B > > -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

3 3

Athena and Artemis on the Mac
by Bruce Ravel 08 Jul '16

08 Jul '16

A few minutes ago, I made a post suggesting a work-around to a problem reported by a Mac user. My suggestion was an inherently horrible solution. That sort of line-by-line hackery is completely unsustainable. The real solution is that that fellow and his colleague should both be using the most recent version of Athena. If Athena and Artemis are to be supported on the Mac, then someone is going to have to find the time and willingness to maintain the Mac packaging. Joe Fowler did an amazingly generous thing when he made the MacPorts package, but Joe does not (to my knowledge) use Athena and Artemis for his own work. Someone who is invested in the use of the software simply has to step up. I myself have neither the resources nor the interest in doing so. If no one steps up, then there simply won't be support for my software on the Mac. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

Breaking off spec files within Athena
by Katharine Elizabeth Silberstein 07 Jul '16

07 Jul '16

Hi, The Cornell High Energy Synchrotron Source (CHESS) primarily uses SPEC software for XAS data collection. The data output is one continuous file containing individual scans. We are able to break off scans to import into Athena. For the convenience of CHESS users, is there any way for Athena to recognize a continuous file besides manually setting data ranges during import? Thanks, Katie Silberstein CHESS Postdoctoral Associate

2 1

How to change the data file in Dartemis?
by Isabelle Kieffer 01 Jul '16

01 Jul '16

Dear all, I am using artemis from Demeter and I am unable to "change the current data file (that is, to apply this fitting model to a different data set)" as it was possible with the "open file" function of the old artemis. This function openned a popup window asking to choose between "read a new data file" or "change the current data file". If I use the "open project or data" function of Dartemis (or the "Add" button of the "Data sets" frame), it opens the data set in a new window. Then, I am unable to use the paths and parameters used for the previous fit. Any attemp to export, transfer or drag/drop paths or parameters has either no effect or crashes the program. If I use the "Replace this chi(k)" function, it automatically chooses to "read a new data file (that is, to do multiple data set fitting)" without opening any popup window asking my choice. I suppose I did not find the good way to apply my fitting model to a new data set. Thank you for advice. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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How to input atoms in solid solution for Artemis
by Fuxiang Zhang 24 Jun '16

24 Jun '16

Hi, All, I am new in using EXAFS techniques. Just wondering how to input atomic structure of NiFe solid solution to Artemis. It has a simple Ni-structure, but both Ni and Fe occupy the same site. If I use partial occupancy, Artemis program does not allow. Anyone can give me an ideal? Also the coordination number N cannot be refined in this simple system (12), is that right? In fact I just want to get the N through the fitting of EXAFS because of the partial occupancy. Thank you very much Fuxiang Zhang

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Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 17
by Ditty Dixon 24 Jun '16

24 Jun '16

Hello Fuxiang, A small suggestion Please also don't forget to try multiple edge data fitting if you already measured your data in both Fe and Ni edge, this may actually reduce the number of parameters to use. You need just on parameter Fe-Ni/Ni-Fe should be same when looking from both atom Hope it helps, Ditty On Jun 23, 2016 23:48, <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: How to input atoms in solid solution for Artemis > (Scott Calvin) > 2. Re: How to input atoms in solid solution for Artemis > (Fuxiang Zhang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 23 Jun 2016 16:23:36 -0400 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] How to input atoms in solid solution for > Artemis > Message-ID: <F8C55BBE-4E8E-436E-97C4-35387D9B5B02(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > One additional thought: > > Distinguishing Ni-Ni and Ni-Fe by creating two different feff paths and > fitting the spectrum as a mixture of the two is very difficult, to put it > mildly, as both Anatoly and Matt indicated. > > But the bond length determined by your fit may be able to give you a clue, > particularly when compared to appropriate standards. Depending on the > details of your structure, the average bond length may depend on the > fraction of sites occupied by iron to a degree which is measurable by > EXAFS. Even if you simply use a nickel-nickel scattering path in feff to > model your structure, differences in bond length could be indicative of > changes in site occupancy. > > Ideally, this could be done by creating a series of standards with known > iron-nickel ratios, fitting the bond length for each, and then comparing a > fit of a sample with a similar structure but unknown iron-nickel ratio to > the results for the standards. > > ?Scott Calvin > Sarah Lawrence College > > > On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang <zhangfx(a)umich.edu> wrote: > > > > Hi, Matt and Anayoly, > > Thank you very much for the help. > > > > Fuxiang > > > > On Thu, Jun 23, 2016 at 1:51 PM, Anatoly I Frenkel <afrenke2(a)yu.edu > <mailto:afrenke2@yu.edu>> wrote: > > Whatever you decide to do, remember that Ni Ni and Ni Fe pairs look very > similar by EXAFS, so it does not matter how you end up doing it. > > You can as well use pure Ni but you may want to consider both fcc and > bcc structure for making the model because the alloy may end up to be > either that or that, especially if it is a nanoalloy. > > > > Anayoly > > > > > > > > Sent from my Verizon Wireless 4G LTE Tablet > > > > > > -------- Original message -------- > > From: Fuxiang Zhang <zhangfx(a)umich.edu <mailto:zhangfx@umich.edu>> > > Date: 6/23/2016 12:51 PM (GMT-05:00) > > To: ifeffit(a)millenia.cars.aps.anl.gov <mailto: > ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] How to input atoms in solid solution for Artemis > > > > Hi, All, > > I am new in using EXAFS techniques. Just wondering how to input atomic > structure of NiFe solid solution to Artemis. It has a simple Ni-structure, > but both Ni and Fe occupy the same site. If I use partial occupancy, > Artemis program does not allow. Anyone can give me an ideal? > > Also the coordination number N cannot be refined in this simple system > (12), is that right? In fact I just want to get the N through the fitting > of EXAFS because of the partial occupancy. > > Thank you very much > > > > Fuxiang Zhang > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto: > Ifeffit(a)millenia.cars.aps.anl.gov> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit < > 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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report bugs
by 储胜启 23 Jun '16

23 Jun '16

Hi, deal bruce, I have found a bug. When I click the button ‘Run Atoms’ in Artemis program, it will crash suddenly. I have tried this in different OS, Windows XP and Win7, and got the same error. The log file said as follows: Demeter version 0.9.24 Can't call method "workspace" on an undefined value at C:/MyProgramm/DemeterPerl/perl/site/lib/Demeter/UI/Atoms/Xtal.pm line 1004. Best wishes, -Shengqi Chu Beijing Synchrotron Radiation Facility, Beijing 100049，China

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Use of restraint
by Maureen Le Bars 22 Jun '16

22 Jun '16

Hello, I have a couple of questions about data analysis on artemis I used a restraint for my fits. I've read some documentation about it and found Matt Newville's talk (https://pubweb.bnl.gov/~frenkel/BNLworkshop2001/newville.pdf) It is reported that a restraint adds a "V" term to the chi-square (slides number 16 and 17). According to this formula, what is the number that artemis gives for the "restrain" parameter at the end of the fit? How should we consider this number in the evaluation of the fit ? I also don't really know very much about the scaling factor to apply in the formula : scale*penalty(X,a,b). I've read that the square root of chi-squareseems to be a good size from some of Bruce Ravel's answers in ifeffit mailing list. How does the scaling factor control the restraint ? What is its relationship with the chi-square ? Thank you in advance for your help, Maureen /PhD student at CIRAD - ADEME// //CEREGE - Europôle de l'Arbois// //BP 80// //13545 Aix en Provence Cedex 4 France +33 4 42 97 15 48/

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NiO-test-athena-project
by mazhar iqbal 17 Jun '16

17 Jun '16

Hello I would appreciate valuable comments on the NiO spectrum processed in athena. I am a new in this area so please comment on any mistake I have made while processing. Best Regards

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Athena crash on Mac when exporting empirical standard
by Chloe Yi-Yi Wu 17 Jun '16

17 Jun '16

Hi all, I'd like to export an empirical standard from Athena to fit EXAFS with Artemis. However, once I clicked on the element for scattering in the pop-up window, Athena was frozen and no .es file was generated. Does anyone know how to fix the problem? Thanks, Chloe -- Yi-Yi (Chloe) Wu Kung Research Group Dept. of Chemical and Biological Engineering Northwestern University Evanston, IL USA

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Sorbed complex in Atoms
by Gnu script 09 Jun '16

09 Jun '16

Dear All, I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral. Could you please help. Thanks.

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Question about fuzzy degeneracy
by Mirko 09 Jun '16

09 Jun '16

Hey, I am quite new to EXAFS and therefore very glad about this mailing list, it helps a lot. My question is about the fuzzy degeneracy mentioned in the paper "Path degeneracy and EXAFS analysis of disordered materials" (Ravel, B. J Synchrotron Radiat. <http://www.ncbi.nlm.nih.gov/pubmed/25343794>2014 Nov;21(Pt 6):1269-74.) I investigate disordered systems like aqueous salt solutions and would like to use the method on my FEFF calculation. However, I obtained my structure for the FEFF calculation from a MD-Simulation and would like to average over several hundreds of FEFF calculations. To handle this amount of data I use LARCH, which doesn’t have the feature to degenerate similarpaths to one. I would like to use the method by myself to degenerate the first coordination shell of my oxygen atoms around the salt. How do you merge the FEFF parameters from each scattering paths after they are grouped together in a bin with the extended pathfinder algorithm (I think, you can’t just make an average of for example the phase shift or the mean free path … right?) Best regards and thanks a lot! Mirko ------------------------------------------------------------------------

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Substantial problems running ATOMS in Demeter 0.9.24
by Jeff Catalano 08 Jun '16

08 Jun '16

The message sequence from this morning prompted me to inquire if anyone can provide help with ATOMS crashing on my own computer. I am running Demeter 0.9.24 on Windows 10 Pro 64. I did a fresh install of Demeter after having removed all older versions of Demeter 0.9, including the Demeter folders in C:\Users\<username>\AppData\Roaming\. My problem is unfortunately simple and something I do not know how to fix: Whenever I hit the "Run Atoms" button, stand-alone atoms crashes. The program simply dies, and no files are written. I am able to enter text, save an atoms.inp file, and reload an atoms.inp file, but "Run Atoms" crashes the program. I have tested this with a simple compound, NaCl, using the attached atoms.inp file. Note that I don't want to work on NaCl, I just used this to test a simple structure. The log file associated with the crash is attached. The log file says Windows 8, but I think this is just hows Windows 10 shows up as that is what I am running, from a clean Windows 10 install. Anyway, when I load this atoms.inp file or enter the same information by hand the program crashes. I was able to load and run this atoms.inp file in the old version of atoms (3.0.1) and produced the attached feff_oldATOMS.inp file. I thus don't think it is a data entry problem. I hope that I have provided enough information. I have no problems running ATHENA, ARTEMIS, or HEPHAESTUS. Given the log file I suspect this is something unique to my computer, but I am stumped as to what it could be as I am running a standard OS with a standard install on Demeter. Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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Re: [Ifeffit] Artemis file opening
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce With upgrading the Demeter 9;24, I am able to open files from 9.21. Thanks you all. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 03:01 PM Subject: Ifeffit Digest, Vol 160, Issue 8 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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 160, Issue 7 (Dien.Li(a)srs.gov) 2. Re: Ifeffit Digest, Vol 160, Issue 7 (Farquhar, Erik) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 13:50:42 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7 Message-ID: <OF0754ACB2.B29F1774-ON85257FCA.00619402-85257FCA.006206D8(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> 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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Questions
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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atoms crashes
by Jesús Eduardo Vega Castillo 03 Jun '16

03 Jun '16

Hello everyone, I have manually introduced the crystal structure of La4Fe3O10 into Atoms and generated and .inp file. The structure contains 2 sites of La, 2 sites of Fe and 4 sites of O. When I try to run Atoms from this file it crashes. This is the inp file: ## This Atoms file was generated by Demeter 0.9.24 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = La4Fe3O10 (LSFC) space = I 4/m m m a = 3.83900 b = 3.83900 c = 27.87050 alpha = 90.00000 beta = 90.00000 gamma = 90.00000 rmax = 5.00000 core = Fe1 # polarization = 0.0 0.0 0.0 shift = 0.00000 0.00000 0.00000 atoms # el. x y z tag La 0.00000 0.00000 0.56860 La1 La 0.00000 0.00000 0.70130 La2 Fe 0.00000 0.00000 0.00000 Fe1 Fe 0.00000 0.00000 0.13840 Fe2 O 0.00000 0.50000 0.13810 O1 O 0.00000 0.00000 0.06980 O2 O 0.00000 0.00000 0.21050 O3 O 0.00000 0.50000 0.00000 O4 Any help would be appreciated. Yours, Jesús

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Re: [Ifeffit] Heavy Scatterer Resonance
by Matt Newville 02 Jun '16

02 Jun '16

Pieter, Please use the ifeffit mailing list for questions about XAFS Analysis. I am CCing this reply to that list. On Thu, Jun 2, 2016 at 2:35 AM, Pieter Tack <Pieter.Tack(a)ugent.be> wrote: > Dear Dr. Newville, > > > During the analyses of some metallic Au EXAFS I noticed the Au-Au single > scatter first shell is characterised by a split peak in the chi(R) > spectrum. I was wondering what caused this, as I would expect a single > scatter path resulting in only one scatter distance and thus one peak in > the chi(R). However, I could not find much on the matter except for a quote > of you stating it is "due to the resonance in the scattering for heavy > scatterers" ( > http://permalink.gmane.org/gmane.science.physics.ifeffit/2352 ) > In short: XAFS chi(R) is *NOT* a pair distribution function, due mostly to the complex electron scattering that alter the amplitude and shift the phase of potoelectron in addition to the simplistic "backscatter from a point source atom". The most obvious effect of this is a ~0.5 Ang shift to lower R from the value you might expect if chi(R) was a pair distribution function. Other effects include broader and asymmetric peaks, and the resonance effect such as you notice for heavy elements (easily noticeable for Z>40 or so, but unmistakable for Z > 60 -- that Z is for the *scattering atom*). At certain energies (or for a narrow range of energies), the photo-electron has very low scattering probability from a heavy element, and the phase jumps dramatically, as if the electron was able to tunnel through or hop over the potential well of the scattering atom. This is usually (and I think properly) called a Ramsauer-Townsend resonance. There are many papers, review articles, and slides from talks available that describe this in more detail. Google "ramsauer townsend effect exafs" for detailed articles. > I don't really understand what this means, which physical process causes > this. Could you perhaps provide me with additional info on this matter or > direct me to some papers that explain this? > > > Thanks in advance! > > Best regards > > Pieter Tack > > > --- > X-Ray Micro-Spectroscopy and Imaging Group > Department of Analytical Chemistry > Ghent University > Krijgslaan 281 S12 > B-9000 Ghent > Belgium > Phone: +32 (0)9 264 4723 > Fax: +32 (0)9 264 49 60 > --Matt

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Regarding time resolved XAS
by mazhar iqbal 31 May '16

31 May '16

hello.. I am sorry if am not posting on right place. I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that we have a reference fluorescence line always on the screen that well behind the K absorption edge. Hoping to see your response. Best Regards

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Re: [Ifeffit] difference spectra- Ifeffit Digest, Vol 159, Issue 23
by sb2c08＠gmail.com 31 May '16

31 May '16

This is very helpful thank you. To give a little bit of context, the reaction is a solution of W(CO)6 irradiated at 266nm, to give W(CO)5*, it would be good to find the overall change of CO distance, especially as the multi scattering dominates the EXAFS. Just as a final point, the difference spectrum is taken from the normalised after and before laser spectra, so supposing the difference is fitted directly in Artemis (and coordination number is known/assumed), the amplitude factor will give an indication of the % change, supposing the Debye-Waller factor is similar to the ground state W(CO)6? But normalisation I find is the first difficult issue. Thanks Bruce and Anatoly and I will look over the references for some direction. Stu > On 31 May 2016, at 19:20, 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: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (sb2c08(a)gmail.com) > 2. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Bruce Ravel) > 3. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 31 May 2016 18:23:42 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <A5D4B2A5-A353-4813-BFC0-A31105BE4B21(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. > > To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > > >> On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) >> 2. Re: Difference spectra (Bruce Ravel) >> 3. Re: Regarding time resolved XAS (Bruce Ravel) >> 4. Atoms on the WEB (alessandro longo) >> 5. Re: Atoms on the WEB (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 30 May 2016 18:25:21 +0100 >> From: sb2c08(a)gmail.com >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] Difference spectra >> Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> >> Content-Type: text/plain; charset=us-ascii >> >> Hi, >> We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? >> Thanks for any help or suggestions, >> Stu >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 31 May 2016 08:19:14 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Difference spectra >> Message-ID: <574D8142.8060001(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 31 May 2016 08:22:59 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit >> <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Regarding time resolved XAS >> Message-ID: <574D8223.3080109(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >>> I want to ask about the aligning the XAS spectra that is given in >>> Athena. Can we do the alignment of time resolved spectra? As you know >>> that the resolved spectra (IR pump X-ray probe) may have edge shift due >>> to laser pumping. Do you think that the same method of the alignment can >>> be applied here as well. An additional piece of information is that we >>> have a reference fluorescence line always on the screen that well behind >>> the K absorption edge. >> >> Well, you have told us what you have tried nor what problem you are >> actually facing. If the question is "does Athena help you align data?" >> I think you already know that the answer is yes. >> >> I don't understand the business about a "fluorescence line always on the >> screen". How do you propose to use that to align your XAS data? >> >> In the case of a situation where you are purposefully changing the >> chemical state of the sample, then you need to have some absolute >> reference by which to perform the alignment -- a reference spectrum >> measured simultaneously, an encoder reading on the monochromator, >> something that allows you to do the chore. >> >> You question is a bit vague and open-ended. Without more information or >> a more focused question, I don't know how to help you further. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 31 May 2016 14:49:50 +0200 >> From: "alessandro longo" <alessandro.longo(a)cnr.it> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: [Ifeffit] Atoms on the WEB >> Message-ID: <20160531124332.M60406(a)cnr.it> >> Content-Type: text/plain; charset=utf-8 >> >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro >> >> -- >> Ph.D Alessandro Longo >> researcher of National Council Research >> ISMN-CNR >> e-mail: alessandro.longo(a)cnr.it >> phone: 00390916809359 >> fax : 00390916809399 >> >> Open WebMail Project (http://openwebmail.org) >> >> >> ---------- Original Message ----------- >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tue, 31 May 2016 08:19:14 -0400 >> Subject: Re: [Ifeffit] Difference spectra >> >>>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>>> We recently collected laser pump-probe XAS data out to k=9. The >>>> process to get the excited state is to take the laser off minus the >>>> laser on data. I'm a little unsure in terms of trying to fit the >>>> difference EXAFS and is it possible via Athena? So far I model the >>>> EXAFS of the excited state and take away from the ground state model >>>> and compare visually. The only way I can think is to work out the % >>>> conversion and add that % of laser off back to the difference data in >>>> order to get the real EXAFS of the excited state, which can be fitted >>>> through Athena. But this is really difficult and probably >>>> inaccurate? >>> >>> Of course it's not possible to fit and EXAFS spectrum in Athena. >>> Artemis is the program for fitting the EXAFS. >>> >>> I am unclear on what you have tried so far, so I am a little unsure what >>> kind of answer you are looking for. Artemis was not really written with >>> your sort of experiment in mind. That said, if your problem is fit some >>> theory from Feff to a measured spectrum with some fitting model -- that >>> is what Artemis is for. As with any difficult problem, you need to >>> understand your data and your model and you need to understand Artemis >>> well enough to implement the fit. But there is no magical, hidden >>> button that says "fit my pump-probe data." >>> >>> B >>> >>> -- >>> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >>> >>> National Institute of Standards and Technology >>> Synchrotron Science Group at NSLS-II >>> Building 535A >>> Upton NY, 11973 >>> >>> Homepage: http://bruceravel.github.io/home/ >>> Software: https://github.com/bruceravel >>> Demeter: http://bruceravel.github.io/demeter/ >>> _______________________________________________ >>> 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 Original Message ------- >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 31 May 2016 09:05:43 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Atoms on the WEB >> Message-ID: <574D8C27.4090907(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/31/2016 08:49 AM, alessandro longo wrote: >>> Hi to everyone, >>> >>> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >>> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >>> work anymore. It works only to create the atoms.inp, but it was nice to have the >>> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >>> tool is not installed. >>> Sorry If i took your time and thank you for your answer. >>> best >>> Alessandro >> >> It would be nice if you started a new thread for a new question rather >> than hijacking an existing thread.... >> >> Last December, the computer that hosted the web atoms tool died >> dramatically. When Matt rebuilt that server, atoms did not get >> restored. The web version of atoms was based on very out date code. >> >> Bottom line is that I need to rewrite the web atoms tool using the >> current code base. >> >> It's on my list of things to do. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> 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 159, Issue 21 >> **************************************** > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 13:44:12 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <574DCD6C.6080800(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 18:20:20 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: > <545F89325F51764C902D37B42C9F4D530210471863(a)YUWEXCPM11.yuad.uds.yu.edu> > > Content-Type: text/plain; charset="us-ascii" > > Hi Stu, > > In full agreement with Bruce, what you want to do can be done, and it was done a few times before. > I think the first group that applied conventional EXAFS analysis to differential signals was Pettifer et al in Nature (2005), to analyze EXAFS in magnetrostrictors measured at different values of magnetic field. Then, C. Konig et al did a similar trick for a catalyst under different atmospheres. They also used conventional EXAFS equation to fit the difference because the model allowed them to do so (the changes in the amplitude factors was also an amplitude factor and could be obtained from the fit because the fitting program does not know what the meaning of amplitude factors is, you do. > > I want to warn you that normalization of the amplitude of your EXAFS data will be the trickiest part because it depends on how many absorbing species changed structure during the excitation. > > In my work we also used this method in a couple of papers, Spanjers et al (for Pd nanoparticles under Ar and inert environment), and Korobko et al, (2015) using electrostrictors with and without applied electric field. The latter example is here: > > https://pubweb.bnl.gov/~frenkel/CGO/CGO-modulations.pdf > > The references to Pettifer and Konig works are Refs 19 and 20. > > Regards, > Anatoly > > P.S. If anyone is interested, a postdoctoral position has just opened up in my group, for research of electromechanical materials. Please contact me for further information: frenkel(a)bnl.gov > > ________________________________________ > From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bravel(a)bnl.gov] > Sent: Tuesday, May 31, 2016 1:44 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > _______________________________________________ > 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 > > > > ------------------------------ > > 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 159, Issue 23 > ****************************************

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Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System
by Johnson, Mark 31 May '16

31 May '16

Dear XAS Colleagues, I recently had to give up my Windows XP operating system and begin using Windows 7, the Enterprise version (I work for the U.S. Government). So I downloaded and installed the software, but when I try to launch them I see the software Icon briefly, but it does not launch. Digging around I found the following error logs below. Does anyone have any advice on how to proceed? My PC does have 16 Mb of RAM. Could that be the problem? Any suggestions would be appreciated. Thanks! MGJ ========================================================================== From: Dathena.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. Started at 2016-05-26T12:28:22 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1. ============================================================================================= >From dartemis.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. Started at 2016-05-26T12:30:29 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1.

2 1

Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21
by sb2c08＠gmail.com 31 May '16

31 May '16

I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) > 2. Re: Difference spectra (Bruce Ravel) > 3. Re: Regarding time resolved XAS (Bruce Ravel) > 4. Atoms on the WEB (alessandro longo) > 5. Re: Atoms on the WEB (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 18:25:21 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Difference spectra > Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi, > We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? > Thanks for any help or suggestions, > Stu > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 08:19:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra > Message-ID: <574D8142.8060001(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >> We recently collected laser pump-probe XAS data out to k=9. The >> process to get the excited state is to take the laser off minus the >> laser on data. I'm a little unsure in terms of trying to fit the >> difference EXAFS and is it possible via Athena? So far I model the >> EXAFS of the excited state and take away from the ground state model >> and compare visually. The only way I can think is to work out the % >> conversion and add that % of laser off back to the difference data in >> order to get the real EXAFS of the excited state, which can be fitted >> through Athena. But this is really difficult and probably >> inaccurate? > > > Of course it's not possible to fit and EXAFS spectrum in Athena. > Artemis is the program for fitting the EXAFS. > > I am unclear on what you have tried so far, so I am a little unsure what > kind of answer you are looking for. Artemis was not really written with > your sort of experiment in mind. That said, if your problem is fit some > theory from Feff to a measured spectrum with some fitting model -- that > is what Artemis is for. As with any difficult problem, you need to > understand your data and your model and you need to understand Artemis > well enough to implement the fit. But there is no magical, hidden > button that says "fit my pump-probe data." > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 08:22:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Regarding time resolved XAS > Message-ID: <574D8223.3080109(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >> I want to ask about the aligning the XAS spectra that is given in >> Athena. Can we do the alignment of time resolved spectra? As you know >> that the resolved spectra (IR pump X-ray probe) may have edge shift due >> to laser pumping. Do you think that the same method of the alignment can >> be applied here as well. An additional piece of information is that we >> have a reference fluorescence line always on the screen that well behind >> the K absorption edge. > > Well, you have told us what you have tried nor what problem you are > actually facing. If the question is "does Athena help you align data?" > I think you already know that the answer is yes. > > I don't understand the business about a "fluorescence line always on the > screen". How do you propose to use that to align your XAS data? > > In the case of a situation where you are purposefully changing the > chemical state of the sample, then you need to have some absolute > reference by which to perform the alignment -- a reference spectrum > measured simultaneously, an encoder reading on the monochromator, > something that allows you to do the chore. > > You question is a bit vague and open-ended. Without more information or > a more focused question, I don't know how to help you further. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 4 > Date: Tue, 31 May 2016 14:49:50 +0200 > From: "alessandro longo" <alessandro.longo(a)cnr.it> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Atoms on the WEB > Message-ID: <20160531124332.M60406(a)cnr.it> > Content-Type: text/plain; charset=utf-8 > > Hi to everyone, > > I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. > I don't want to disturb to much, but I was wondering why now this beatifull tool does't > work anymore. It works only to create the atoms.inp, but it was nice to have the > feff.inp ready from the web application. The main motivation is somtimes the ifeffit > tool is not installed. > Sorry If i took your time and thank you for your answer. > best > Alessandro > > -- > Ph.D Alessandro Longo > researcher of National Council Research > ISMN-CNR > e-mail: alessandro.longo(a)cnr.it > phone: 00390916809359 > fax : 00390916809399 > > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tue, 31 May 2016 08:19:14 -0400 > Subject: Re: [Ifeffit] Difference spectra > >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> _______________________________________________ >> 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 Original Message ------- > > > > ------------------------------ > > Message: 5 > Date: Tue, 31 May 2016 09:05:43 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Atoms on the WEB > Message-ID: <574D8C27.4090907(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 08:49 AM, alessandro longo wrote: >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro > > It would be nice if you started a new thread for a new question rather > than hijacking an existing thread.... > > Last December, the computer that hosted the web atoms tool died > dramatically. When Matt rebuilt that server, atoms did not get > restored. The web version of atoms was based on very out date code. > > Bottom line is that I need to rewrite the web atoms tool using the > current code base. > > It's on my list of things to do. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > 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 159, Issue 21 > ****************************************

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Difference spectra
by sb2c08＠gmail.com 31 May '16

31 May '16

Hi, We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? Thanks for any help or suggestions, Stu

4 5

ISO Calcite + dolomite EXAFS
by Matthew Marcus 27 May '16

27 May '16

Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite? I took some, but it seems to disagree with FEFF as to the position of the Ca-(Ca,Mg) peak. mam

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