February 2016 - Ifeffit - millenia.cars.aps.anl.gov

Any XAFS schools in North America this year?
by Robert Gordon 07 Mar '16

07 Mar '16

Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps get some hands-on experience before they get into the meat of their thesis work. I haven't seen any notices yet about schools taking place in the late spring or summer and was wondering if there are any plans to hold such. I am aware of the 1/2-day workshop planned for the DXC. Are there other options? Thanks, Robert

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Re: [Ifeffit] fluo_corr() script
by Matt Newville 26 Feb '16

26 Feb '16

Hi Gerome, (I'm CCing this to the Ifeffit mailing list) On Thu, Feb 25, 2016 at 9:30 PM, Gerome Melaet <gmelaet(a)lbl.gov> wrote: > Dear Dr. Newville, > I have tried to use the flu_corr() function to correct some of my recent > x-ray data on the cobalt K-edge. > Unfortunately, after multiple tryout I am unable to get it to work > properly. > I have received this error message a couple of time. > > > *File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xafs/fluo.py", line > 57, in fluo_corr* > * muvals = material_mu(formula, energies, density=1, _larch=_larch)* > * File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xray/materials.py", > line 68, in material_mu* > * mater = _materials.get(name.lower(), None)file <stdin>, line 0* > *AttributeError: ‘int' object has no attribute 'lower'* > > I have a .dat file two column with energy and normalized mu (I have done > most of the energy corrections during my shift at the synchrotron). > I am able to load both energy and mu, yet I am not sure I handle the > different args correctly in the fluo_corr() function. > > Here is how I tried: > > fluo_corr(dat.energy, dat.mu, formula=None, elem=‘Co’, edge=‘K’) > > Thanks in advance for your help, > > Best, > Gerome > Yes, you need to pass a valid (even if approximate) formula for the chemical composition of the material. See http://xraypy.github.io/xraylarch/xray/index.html#x-ray-properties-of-mater… for some further details. You might want to do something like fluo_corr(dat.energy, dat.mu, formula='Co0.5Fe0.5S04', elem=‘Co’, edge=‘K’) Perhaps obviously, getting the composition of light elements perfect is not critical. It's often noticed that one has to lower the concentration of the absorbing element some (perhaps even by half) to avoid over-correcting. As with many things, it's always good to practice on a system where you're pretty confident what the right answer should be. --Matt

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Re: [Ifeffit] problem with transfer of prj fils
by fred.mosselmans＠diamond.ac.uk 22 Feb '16

22 Feb '16

Hi Thomas Are you sure both the users have the same version of Athena. I have seen this behaviour when discussing analysis with my users and they are not using the latest version of Demeter and I am. Then the prj crashes Athena for the person with the old version. 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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Problem with transfer of prj files
by Huthwelker Thomas (PSI) 22 Feb '16

22 Feb '16

Dear All, I find this Problem with the transfer of Athena project files: An Athenae project file is created on a one computer and saves on a harddisk. This file is then transferred to another person working on another computer. When opening the *.prj file on the new PC, Athena crashes. This happens if Athena is opened first and one tries to import the prj file into an open Athena, or if one just double clicks the *.prj file to start Athena. Operating system: Windows 7 Thanks for information, Thomas

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problem with Artemis crashing on mac
by Katherine M. Davis 17 Feb '16

17 Feb '16

Hello all, I was wondering whether anyone had experienced this problem or had some advice for what I can try. I have Demeter installed successfully on my mac (Yosemite 10.10.5). Athena works just fine. However, when I try running Artemis, it begins to open fine and all the GUI windows look good, but then a popup that says 'Restore from an autosave file' with buttons for 'Cancel' or 'OK' appears. I'm not able to click on anything and the program does not progress from this point. I don't remember this happening when I first installed. Is there an easy way to go in and trash some potential autosave file I have that is causing problems? If so, where would that be located? I dug around a bit, but couldn't find anything obvious. It's a little odd, because I've not really used the program. I simply tested it when I first installed to ensure it worked and that was it. Any thoughts or comments would be useful. If additional information would help in diagnosing the issue, I'm happy to provide it. Thanks, Kate

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Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 6
by Adi Shivprasad 10 Feb '16

10 Feb '16

Dear Riti, Thanks for the response. It was very helpful in better understanding my system. Adi On Wed, Feb 10, 2016 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. Feature near edge of Ni XANES spectrum (Aditya Shivprasad) > 2. Re: Feature near edge of Ni XANES spectrum (Ritimukta Sarangi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 9 Feb 2016 21:19:21 -0500 > From: Aditya Shivprasad <aps202(a)psu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Feature near edge of Ni XANES spectrum > Message-ID: > <CAFbAhodYDnzzK1keVptQVfhS4OJMR-VgB-vR= > wFL8TKVCfEBHw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear list, > > I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2 > nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe, 0.1% Cr, 0.05% Ni). > > In the spectrum, I identify the edge as being approximately 8331-8332 eV > (based on maximum of first derivative), as it is for pure Ni. However, I > also identify a sharp feature at less than 1 eV past the edge. If anyone on > the list could help me to understand the origin of this feature, that would > be very helpful. > > Thanks > -- > Aditya Shivprasad > > aps202(a)psu.edu > Ph.D Candidate > Nuclear Engineering Department > Pennsylvania State University >

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Feature near edge of Ni XANES spectrum
by Aditya Shivprasad 10 Feb '16

10 Feb '16

Dear list, I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2 nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe, 0.1% Cr, 0.05% Ni). In the spectrum, I identify the edge as being approximately 8331-8332 eV (based on maximum of first derivative), as it is for pure Ni. However, I also identify a sharp feature at less than 1 eV past the edge. If anyone on the list could help me to understand the origin of this feature, that would be very helpful. Thanks -- Aditya Shivprasad aps202(a)psu.edu Ph.D Candidate Nuclear Engineering Department Pennsylvania State University

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Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 4
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Re: [Ifeffit] Could you please give me some information?
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Athena with IOS "El Capitan"
by Manuel Cossio Kohler 02 Feb '16

02 Feb '16

Hello, I am having some issues with the Athena software. After upgrading the OS of the macbook pro to "El Capitan" Version 10.11.3, Athena stopped working properly. Once the iXAFS icon was clicked nothing happened. I decided to do a bit of research and installed the latest verion of XQuartz version 2.7.8. I was able to launch athena by executting "athena" from the terminal. Up to that point, I figured that everything was running smoothly until I realized that I could prompt any plots. Something in the software or operating system was not allowing Athena to display plots. I would be really grateful if you could provide me with a solution to this problem (if there is any) or any advice that would allow me to process XAS data again. Thank you Regards, Manuel Cossio

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Re: [Ifeffit] Could you please give me some information?
by Bruce Ravel 02 Feb '16

02 Feb '16

On 02/01/2016 11:58 PM, pinit wrote: > Dear Bruce, > > I am Pinit from SLRI, Thailand. I have some questions concerning the > Si-drift detector. > > Could you give me some suggestions if Si-detector can detect the > corrected Si K-edge or not? This is because I have seen a significant > EXAFS signal (higher in amplitude in FT) measured by Si-drift detector > differs from Lytle detector or ionization chambers (TM mode). Hi Pinit, Nice to hear from you. I am CCing my answer to the Ifeffit Mailing List. Someone else may have more insight into your question than I do. You should CC the list in your response. I'd probably need to know more about the sample and the nature of the measurement you made to understand why you are seeing a different signal with the Si drift detector. Normally one would expect that he EXAFS would be /attenuated/ either due to self-absorption or due to the energy dependence of the I0 detector. That you are seeing a larger EXAFS signal with the Si-drift seems surprising. One thing that occurs to me is that the Compton and elastic peaks probably overlap the Si K alpha ROI quite a bit, even extending into the EXAFS region. I would have thought that, too, would serve to attenuate the EXAFS (but maybe I am thinking about that wrongly). Perhaps it would help to show us some of the 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/

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pi/2deltak
by Ritimukta Sarangi 01 Feb '16

01 Feb '16

Hello, I was recently asked about the accuracy of this formulation for obtaining EXAFS resolution and I did not have a good answer. Can someone point to a reference or explain here? Thank you for your time, Best, -Riti

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FW: Data summation - missing groups
by Godfrey, Ian 01 Feb '16

01 Feb '16

Sorry, I've just seen that this has already been reported. Ian From: Godfrey, Ian Sent: 27 January 2016 11:21 To: 'XAFS Analysis using Ifeffit' <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Data summation - missing groups Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? 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 Advaned 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> 02076 794864

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