July 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Postdoc Position
by Jeff Terry 30 Jul '13

30 Jul '13

Hi All, Hope this is ok to post. I have an open postdoc position in my group. Chemistry, physics, materials science, nuclear engineering, or similar fields will be considered. Synchrotron measurements will involve EXAFS, XRD, PES, and others. You can see the details at: http://t.co/xNnYrMgMly Thanks, Jeff Jeff Terry Associate Professor of Physics Illinois Institute of Technology Sent from my iPhone

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Two-Phase EXAFS fitting
by Taehoon Kim 29 Jul '13

29 Jul '13

Dear users in Ifeffit forum, I'm working at a cathode material represented by xLi2MnO3.(1-x)LiMO2 (M = Mn, Ni, and Co). This material can be described as a solid solution between Li2MnO3 and LiMO2. The main phase is the LiMO2 (M = Mn, Ni, and Co), which shows a trigonal crystal structure (R-3m). The integrated phase is the Li2MnO3, which exhibits a monoclinic structure (C2/m). What would be the right way to perform the EXAFS fitting using Artemis for the multi-phase materials ? I was thinking creating two crystal structure set using ATOMS, and perform feff calculation for each, and then choose scattering path from each atom set. I wonder whether this is an appropriate approach ? and how can I apply the ratio of each phase (let's say x is 0.6) in the fitting process ? Thank you in advance ! Kind Regards Taehoon

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DAthena crashes when reconstructing data from PCA
by Scott Calvin 29 Jul '13

29 Jul '13

Hi Bruce, Athena is crashing every time I try to "Reconstruct Data" in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction. I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Is good EXAFS data possible with 0.01 transmission coefficient
by Damon Turney 26 Jul '13

26 Jul '13

Thank you Matthew Marcus. To answer your questions: Most of the transmission loss is due to the Mn particulates. The 0.01 transmission coefficient (a.k.a. ~4 absorption lengths) is in regards to xray energies above the absorption edge. Below the absorption edge the transmission coefficient should be 0.1 to 0.4. I don't understand the definition of "edge jump" or how to calculate it (but trust me I will be reading up on all of this ASAP). Anyway, the transmission coefficient contains all the required information. I doubt that I have "pinhole effect" because the MnO2 is small particulates (10 micron diameter) evenly dispersed throughout the 300 micron thick sample, so I doubt there are any pinholes. Matthew are these "distortions" that you speak of the same thing as "harmonics" that I've read about in "XAFS for Everyone" that can complicate XAFS analysis? Thanks, Damon On Thu, Jul 25, 2013 at 5:09 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. Is good EXAFS data possible with 0.01 transmission > coefficient (Damon Turney) > 2. Re: Is good EXAFS data possible with 0.01 transmission > coefficient (Matthew Marcus) > 3. Re: Is good EXAFS data possible with 0.01 transmission > coefficient (Scott Calvin) > 4. Re: Is good EXAFS data possible with 0.01 transmission > coefficient (Scott Calvin) > 5. Re: Is good EXAFS data possible with 0.01 transmission > coefficient (Matthew Marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Jul 2013 16:07:57 -0400 > From: Damon Turney <dturney(a)ccny.cuny.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Is good EXAFS data possible with 0.01 transmission > coefficient > Message-ID: > <CAOHT-BNp4s8fjUdQnwfgkxaFAzDrKrDtyX1BMenM_HWByeyiQw(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi IFEFFIT community, > > I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my > sample is a powder mixture of carbon powder, MnO2 powder, and > potassium hydroxide liquid. The transmission coefficient of 6.5keV > x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to > 0.01. I am told that the ionization chamber detectors can easily > detect the x-ray beam after this ~0.01 transmission loss (by > increasing the gain on the detector), but I would like to ask the > IFEFFIT community if there will be other problems with the EXAFS > technique when the transmission coefficient is so low. Does anybody > have comments? > > Much thanks -- if you have any info I greatly appreciate it! > Damon Turney > City College of New York > > > ------------------------------ > > Message: 2 > Date: Thu, 25 Jul 2013 13:33:12 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Is good EXAFS data possible with 0.01 > transmission coefficient > Message-ID: <51F18B88.5020600(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Is most of the transmission loss due to the Mn or the matrix (C, KOH, etc)? Is that 0.01 above or below the edge? > If most of the absorption is due to the matrix with the Mn providing an edge jump of <1, then I'd say that you have a shot. > However, you become very sensitive to harmonics and glitches. If the Mn provides an edge jump of much less than 1, them fluorescence > would be the way to go, if possible. With thick samples in transmission, you have an issue with hole effect. For instance, it's > possible that your 1% transmission comes entirely from 1% area of pinholes, with the actual material being almost completely > opaque. If that happens, you get a reduced edge jump and reduced EXAFS amplitude, with distortions resembling overabsorption. > > If you're in the thick-matrix scenario, a possible workaround would be to make a sample which contains only matrix and is as nearly as > possible exactly as thick as the real sample, and measure its transmission, and subtract. > mam > > On 7/25/2013 1:07 PM, Damon Turney wrote: >> Hi IFEFFIT community, >> >> I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my >> sample is a powder mixture of carbon powder, MnO2 powder, and >> potassium hydroxide liquid. The transmission coefficient of 6.5keV >> x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to >> 0.01. I am told that the ionization chamber detectors can easily >> detect the x-ray beam after this ~0.01 transmission loss (by >> increasing the gain on the detector), but I would like to ask the >> IFEFFIT community if there will be other problems with the EXAFS >> technique when the transmission coefficient is so low. Does anybody >> have comments? >> >> Much thanks -- if you have any info I greatly appreciate it! >> Damon Turney >> City College of New York >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 3 > Date: Thu, 25 Jul 2013 16:33:40 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Is good EXAFS data possible with 0.01 > transmission coefficient > Message-ID: <6A1D5E8E-88FB-4A0B-9CCC-9AF0CDB6623F(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Damon, > > So you're saying you expect the total absorption of the sample to be less than 0.01 absorption lengths? In other words, if the detectors and electronics were identical, you would expect It = I0 exp(-0.01)? > > While possible to measure in transmission, such a sample would normally be measured in fluorescence. If done that way, the measurement is routine. > > Or am I misunderstanding your description? (I am not entirely sure what you mean by "transmission coefficient.") > > --Scott Calvin > Sarah Lawrence College > > On Jul 25, 2013, at 4:07 PM, Damon Turney <dturney(a)ccny.cuny.edu> wrote: > >> Hi IFEFFIT community, >> >> I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my >> sample is a powder mixture of carbon powder, MnO2 powder, and >> potassium hydroxide liquid. The transmission coefficient of 6.5keV >> x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to >> 0.01. I am told that the ionization chamber detectors can easily >> detect the x-ray beam after this ~0.01 transmission loss (by >> increasing the gain on the detector), but I would like to ask the >> IFEFFIT community if there will be other problems with the EXAFS >> technique when the transmission coefficient is so low. Does anybody >> have comments? >> >> Much thanks -- if you have any info I greatly appreciate it! >> Damon Turney >> City College of New York >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Thu, 25 Jul 2013 17:03:53 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Is good EXAFS data possible with 0.01 > transmission coefficient > Message-ID: <0830DFDB-C085-45F5-B434-B79DF12ABD72(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Oops--Matthew's interpretation is doubtless what you actually meant--i.e., that It < 0.01 I0. Therefore disregard my previous comment! > > And I concur with Matthew's comments, now that I understand the circumstances. > > --Scott Calvin > Sarah Lawrence College > > On Jul 25, 2013, at 4:33 PM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > >> Is most of the transmission loss due to the Mn or the matrix (C, KOH, etc)? Is that 0.01 above or below the edge? >> If most of the absorption is due to the matrix with the Mn providing an edge jump of <1, then I'd say that you have a shot. >> However, you become very sensitive to harmonics and glitches. If the Mn provides an edge jump of much less than 1, them fluorescence >> would be the way to go, if possible. With thick samples in transmission, you have an issue with hole effect. For instance, it's >> possible that your 1% transmission comes entirely from 1% area of pinholes, with the actual material being almost completely >> opaque. If that happens, you get a reduced edge jump and reduced EXAFS amplitude, with distortions resembling overabsorption. >> >> If you're in the thick-matrix scenario, a possible workaround would be to make a sample which contains only matrix and is as nearly as >> possible exactly as thick as the real sample, and measure its transmission, and subtract. >> mam >> >> On 7/25/2013 1:07 PM, Damon Turney wrote: >>> Hi IFEFFIT community, >>> >>> I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my >>> sample is a powder mixture of carbon powder, MnO2 powder, and >>> potassium hydroxide liquid. The transmission coefficient of 6.5keV >>> x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to >>> 0.01. I am told that the ionization chamber detectors can easily >>> detect the x-ray beam after this ~0.01 transmission loss (by >>> increasing the gain on the detector), but I would like to ask the >>> IFEFFIT community if there will be other problems with the EXAFS >>> technique when the transmission coefficient is so low. Does anybody >>> have comments? >>> >>> Much thanks -- if you have any info I greatly appreciate it! >>> Damon Turney >>> City College of New York >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 5 > Date: Thu, 25 Jul 2013 14:09:49 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Is good EXAFS data possible with 0.01 > transmission coefficient > Message-ID: <51F1941D.3010507(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I'm pretty sure he has the opposite problem - the transmission is <0.01. That's assuming that "transmission coefficient" == "transmission". > mam > > On 7/25/2013 1:33 PM, Scott Calvin wrote: >> Hi Damon, >> >> So you're saying you expect the total absorption of the sample to be less than 0.01 absorption lengths? In other words, if the detectors and electronics were identical, you would expect It = I0 exp(-0.01)? >> >> While possible to measure in transmission, such a sample would normally be measured in fluorescence. If done that way, the measurement is routine. >> >> Or am I misunderstanding your description? (I am not entirely sure what you mean by "transmission coefficient.") >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Jul 25, 2013, at 4:07 PM, Damon Turney <dturney(a)ccny.cuny.edu> wrote: >> >>> Hi IFEFFIT community, >>> >>> I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my >>> sample is a powder mixture of carbon powder, MnO2 powder, and >>> potassium hydroxide liquid. The transmission coefficient of 6.5keV >>> x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to >>> 0.01. I am told that the ionization chamber detectors can easily >>> detect the x-ray beam after this ~0.01 transmission loss (by >>> increasing the gain on the detector), but I would like to ask the >>> IFEFFIT community if there will be other problems with the EXAFS >>> technique when the transmission coefficient is so low. Does anybody >>> have comments? >>> >>> Much thanks -- if you have any info I greatly appreciate it! >>> Damon Turney >>> City College of New York >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 125, Issue 14 > ****************************************

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Is good EXAFS data possible with 0.01 transmission coefficient
by Damon Turney 25 Jul '13

25 Jul '13

Hi IFEFFIT community, I will make measurements soon at Brookhaven's NSLS to do EXAFS, and my sample is a powder mixture of carbon powder, MnO2 powder, and potassium hydroxide liquid. The transmission coefficient of 6.5keV x-rays (the Mn K edge is at ~6.5keV) through the sample is ~0.001 to 0.01. I am told that the ionization chamber detectors can easily detect the x-ray beam after this ~0.01 transmission loss (by increasing the gain on the detector), but I would like to ask the IFEFFIT community if there will be other problems with the EXAFS technique when the transmission coefficient is so low. Does anybody have comments? Much thanks -- if you have any info I greatly appreciate it! Damon Turney City College of New York

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Artemis in Demeter 0.9.17 Crashing Upon Loading Project File
by Anthony Ardizzi 17 Jul '13

17 Jul '13

Dear Bruce and Ifeffit mailing list, I have just started experiencing a program crash in Artemis while trying to load a project I am working on. I am performing a fit on Sr2IrO4 data, and when I try to open the project file, it starts loading all of the usual stuff, and then when it gets to loading the path-lists/data sets screen for one of the two data sets I have, the entire program simply closes. I have attached both my project file, as well as the dartemis log file. I believe the relevant error in the log file is "Illegal division by zero at C:/strawberry/perl/site/lib/Demeter/Data.pm line 922." I am running Windows 7 64-bit. Thanks for any help you can provide, Anthony

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Artemis Autosave Files
by Shoaib Muhammad 16 Jul '13

16 Jul '13

Hi, I am using Demeter 0.9.17, and trying to fit in-situ XAFS data of metal oxides and it is going well other than these minor problems on my Windows 7 PC. A couple of times "Feff" module in Artemis stopped responding and I had to force close the program. Now whenever I click on .fpj files I see a window which asks me to restore from previous autosave files. I click "Cancel" this dialogue box disappears but selected .fpj file is not automatically loaded. Next time when I try to open another .fpj file, I get the same window and behavior again. Is there any way to delete these autosave file? I have searched in mail archieve but there is no querry regarding it for this "Demeter" version. Since I have a bunch of Artemis fits on my PC, to save time I select "File" and then "Close" to close the current fit and then open another Artemis fit instead of "File" and "Exit". In this way when I open another Artemis fit (.fpj) file, I see a couple of "Feff Calculations" in the main Artemis tool bar. How ever I usually don't see these many 'Feff Calculations" if I completely close the Artemis and then reopen the same file. Is there any way to solve this behavior? Screen shots of both the problems are attached. Thanks, -- Shoaib M. Department of Energy Science Sungkyunkwan University South Korea

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Re: [Ifeffit] Ifeffit Digest, Vol 125, Issue 5
by Abhijeet Gaur 14 Jul '13

14 Jul '13

Hi Paul, I think that this research article on Fe K-edge by Westre et al. (1997) will help you in the analysis of your samples. With regards -- Dr. Abhijeet Gaur

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XANES pre-edge peak intensities
by Bingham, Paul A 14 Jul '13

14 Jul '13

Dear Ifeffit forum users I have been working on a batch of Fe K-edge XANES data for dilute glasses some time and I have extracted pre-edge peak positions and intensities, as has been widely used in the literature, to get qualitative analysis of the Fe coordination in my samples. I have also done this for a number of mineral "standards", again as has widely been done in the literature (Grandidierite, Yoderite, Staurolite, etc). However, I have a question: as my samples are considerably more dilute (ca. 0.15 mol% Fe) than all of the mineral standards (these vary in Fe content between a few percent and 10's of percent), how realistic is it to use mineral standards such as these to provide reference points to "calibrate" the integrated pre-peak intensities from the dilute samples? I have found nothing conclusive on this in the literature and would ask this forum for help, or any thoughts you may have on this issue. My own feeling is that concentration will have an effect on integrated pre-edge intensities and I suspect that more dilute samples are likely to give slightly higher integrated intensities than concentrated samples, but it is difficult to unpick and any thoughts or useful references dealing with such issues would be most welcome. Many thanks in advance for taking the time to read this message and thanks for your responses! Kind Regards Paul Bingham

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