- 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] Ifeffit Digest, Vol 157, Issue 1
by Matteo Busi 07 Mar '16

07 Mar '16

> Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Hi Bruce I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available thing right now) they have different energy grid. Thanks and Regards 2016-03-04 15:18 GMT+01:00 <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. Exporting Athena projects data (Matteo Busi) > 2. Collected k-space and fitting range (Taehoon Kim) > 3. Re: Collected k-space and fitting range (Scott Calvin) > 4. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Mar 2016 23:53:54 +0100 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Exporting Athena projects data > Message-ID: > <CAOyEiGi7jNury5oTAostBixxinOF+Vxcg2= > 8Sf8VeM9rywEmrg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, hi mailing list readers. > With the project I'm working with, it came out that would be really useful > for me to export groups in both .xmu and .chi . > More in details I have to deal with a function that depends on both the chi > and xmu data. I tried to look at all the chances and through the guide but > I didn't find any function to do that. I was thinking of exporting > separately the .chi and .xmu data, but they have different point of the > Energy(eV) and that makes hard the programming of my evaluating scripts. > Should I use the spline function to estimate the .xmu data and use it > combined to the .chi data? > > Hope it's all clear. Thanks > Best Regards, > Matteo, UiS >

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Collected k-space and fitting range
by Taehoon Kim 04 Mar '16

04 Mar '16

Hello, I am a bit confused about the range of k-space, which may affect the quality of EXAFS fitting. I would like to understand whether there is a difference between the fitting using an identical fitting range of k-space obtained from different range of k-space collected. For example, is there a notable difference between a fitting of k = 2.3-11 which was deduced from a spectra data collected up to k=12 and a spectra data collected up to k=13 ? Kind regardsTerry

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Exporting Athena projects data
by Matteo Busi 04 Mar '16

04 Mar '16

Hi Bruce, hi mailing list readers. With the project I'm working with, it came out that would be really useful for me to export groups in both .xmu and .chi . More in details I have to deal with a function that depends on both the chi and xmu data. I tried to look at all the chances and through the guide but I didn't find any function to do that. I was thinking of exporting separately the .chi and .xmu data, but they have different point of the Energy(eV) and that makes hard the programming of my evaluating scripts. Should I use the spline function to estimate the .xmu data and use it combined to the .chi data? Hope it's all clear. Thanks Best Regards, Matteo, UiS

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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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