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

PCA in D-Athena
by BradleyW Miller 22 Aug '12

22 Aug '12

Hello, I'm new to PCA analyses with my XANES data and started with the D-Athena. Are the TT Coefficients similar to a SPOIL value (SPOIL values are calculated as the quotient of real error in the target divided by the error in the data matrix)? I've seen that one researcher relied on SPOIL values <1 for populating his LCF models. The TT values of some of my standards I know to be unreasonable (e.g. reduced standard used for TT of an oxidized sample) gave me negative values. Should I only accept values >0. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW(a)epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Launching Problem (D)Athena and Co.
by Alfred Hummer 22 Aug '12

22 Aug '12

Hello, I have some problems launching Demter programs on WIN7. The log file says: Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:Die angegebene Prozedur wurde nicht gefunden at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60 Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 21. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 21. First of all Demeter was not able to start at all (no demeter.ini file). The reason was another Perl installation. I had ActivePerl installed on my computer. I removed the PATH variables and uninstalled it from the PC. After that I reinstalled Demeter. Now the demeter.ini is created but the above error occured. Anyone a clue? best wishes Alfred

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XANES-2012 short course at Brookhaven
by Anatoly I Frenkel 20 Aug '12

20 Aug '12

Dear IFEFFIT subscribers: Please find below the information about the short course on X-ray absorption spectroscopy that will be organized at Brookhaven National Laboratory on Nov. 8-10, 2012 Either follow the link in the bottom of the NSLS web page: http://www.nsls.bnl.gov or go directly to the course web site: http://workshops.ps.bnl.gov/default.aspx?w=XANES2012 The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November 8-10 at the NSLS. To qualify for admission, participants should have prior background in XAS theory and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and hands-on data analysis sessions. The lectures cover the XANES fundamentals, surveys recent developments in theory and data analysis, the commonly used computer codes (FEFF and others), data modeling techniques, and specific applications of XANES to research problems. The course enrollment is limited to 30 participants. Application deadline: September 30, 2012. Best regards, Anatoly Frenkel Yeshiva University

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Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 15
by Marc Porosoff 15 Aug '12

15 Aug '12

message deleted at request of sender

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ifeffit on Lion
by George Sterbinsky 15 Aug '12

15 Aug '12

Hi list members, I am attempting to install ifeffit on mac book running Lion (10.7.4). I have downloaded and installed xcode and gfortran. I downloaded the iffeffit package from github. I then cd into .../Downloads/newville-ifeffit-30644e and run sudo ./PGPLOT_install I get the following error: = = = = = = = = = = = = = = = = = = = = = = = = = = = PGPLOT installation script = system = linux == linux g77_gcc prefix = /usr/local/ = Looking for PGPLOT file: pgplot5.2.tar.gz = PGPLOT file not found = I'll try to download it for you... trying with regular old ftp you may have to hit return here for this to work -- Really, you won't need to enter 'anonymous' or a valid username --- just hit return ftp: Can't connect to `131.215.193.54': Connection refused ftp: Can't connect to `ftp.astro.caltech.edu' ./PGPLOT_install: line 176: 1407 Segmentation fault: 11 $ftp $pgp_ftpsite <<EOF anonymous ifeffit(a)cars.uchicago.edu cd $pgp_ftpdir hash get $pgp_file exit EOF = Sorry, I couldn't download the PGPLOT tar file. = You'll have to download it yourself. Try this: = ftp ftp.astro.caltech.edu = cd pub/pgplot/ = get pgplot5.2.tar.gz = then run this script again I then downloaded pgplot5.2.tar.gz, dropped this into newville...e and ran ./PGPLOT_install again. This gives the following message, which comes after numerous warnings: = = = = = = = = = = = = = = = = = = = = = = = = = = = Uh-oh. PGPLOT is missing some important files! = It looks like PGPLOT failed during building or = is only partially installed. = = Please consult the PGPLOT installation instructions = in the subdirectory pgplot/, and the log file: = /Users/gsterbinsky/Downloads/newville-ifeffit-306444e/PGPLOT_install.log = which contains a full list of commands run. = = You may want to repeat these steps by hand or = consult the PGPLOT installations instructions = in install-unix.txt = = = = = = = = = = = = = = = = = = = = = = = = = = I did some googling and found this explanation of what might be going on: http://mingus.as.arizona.edu/~bjw/software/pgplot_fix.html However, the iffefit INSTALL file says pgplot must be installed with the PGPLOT_install command, which these directions do not use. Furthermore, since iXAFS runs on Lion, it seems to me that someone may have already found a solution to this problem. So rather than trying more random solutions, I thought it might be pertinent to check with the list so see if that is the case. If anyone can provide any suggestions or a known solution to this problem, I would appreciate it. Thanks, George

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Mo2C
by Marc Porosoff 14 Aug '12

14 Aug '12

Hi everyone, Does anyone have any experience modeling Mo2C in Artemis? I can't find any existing INP files for Mo2C. I was wondering if anyone had any experience with Mo2C or knowledge or where I can find some relevant information. Thanks! Marc

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lecture videos at the Diamond Light Source
by Bruce Ravel 13 Aug '12

13 Aug '12

Hi, Last fall, the excellent folks at the Diamond Light Source invited me to present a three day XAS training course. All of my lectures and software demonstrations were recorded on camera, as were the desktop sessions on the presentation computer. The Diamond technical staff did a great job assembling all of this information into streaming videos, which they are now hosting on their web site. Here is the URL: http://www.diamond.ac.uk/Home/Events/Past_events/XAS-workshop-2011.html In total, there are several hours of videos of me presenting lectures and teaching the audience how to use the most recent versions of Athena and Artemis. The editing is great -- it transitions very nicely between the camera and the desktop. Really the only problem with the videos is that you will have to watch many hours of my ugly mug :) I'd like to thank Paul Quinn, Fred Mosselmans, and Shu Hayama for inviting me, organizing the event, and making the videos happen. If you find the videos helpful, be sure to let them know. For folks just learning XAS and for those wanting to learn how to use the newest versions of Athena and Artemis, the Diamond folk have done a very kind thing. Regards, B PS: As a Linux user, it was not immediately obvious to me how to use the Microsoft Media Server (mms:) links on the Diamond web page. Here is a hint that worked for me for viewing them from Firefox: http://support.mozilla.org/en-US/questions/747274 I configured Firefox to send the video to VLC, although any video player should work. Presumably, something similar can be done in other browsers. -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Looking for raw data in InAs
by Anatoly I Frenkel 13 Aug '12

13 Aug '12

Dear subscribers: If anyone could send me the raw absorption coefficient data in bulk InAs (As K-edge), it will be most sincerely appreciated. I could not find it in any online database. Thank you very much in advance, Anatoly Frenkel ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Andrew Korinda [a-korinda(a)northwestern.edu] Sent: Thursday, August 09, 2012 11:37 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 - Mn XANES Manceau also describes his arc-tangent function in his earlier work (Mn is also my focus): Manceau, A.; Gorshkov, A. I.; Drits, V. A., Am. Mineral. 1992, 77 (11), 1133-1143. I've found Farges to be a little vague on how he extracts the pre-edge features for fitting. Andy K. On Thu, Aug 9, 2012 at 10:05 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > You might also consider the method given in: > Manceau, A., Marcus, M. A., Grangeon, S. (2012) "Determination of Mn valence > states in mixed-valent magnanates by XANES spectroscopy", American > Mineralogist 97,816-827 > > (not that I'm plugging my own work or anything :-) ) > Marcus, M. A. > > On 8/9/2012 7:53 AM, Enyuan Hu wrote: >> >> Hi Dominik, >> >> Thank you so much for your quick response. Indeed, it's really nice >> fitting according to your result. But my situation seems a little bit >> different as I'm dealing with the Mn XANES data and there're doublets and >> sometimes triplets in the pre-edge. Actually, I might as well explain my >> interest of doing such fitting. I read in the paper _(F Farges, PHYSICAL >> REVIEW B 71, 155109 (2005))_ that the centroid of pre-edge peak is a more >> accurate measurement of the oxidation state of the element of interest, >> compared to the more conventional inflection point or half-way method. So I >> was trying to follow the paper and see if it also works for my samples. >> Anyway, thanks again for your help! >> >> Enyuan >> >> On Thu, Aug 9, 2012 at 9:11 AM, <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 >> or, via email, send a message with subject or body 'help' to >> ifeffit-request(a)millenia.cars.aps.anl.gov >> <mailto:ifeffit-request@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: question for ifeffit mailing list - ATHENA NORMALIZATION >> (Marie Zwetsloot) >> 2. Re: question for ifeffit mailing list - ATHENA NORMALIZATION >> (Scott Calvin) >> 3. pre-edge centroid (Enyuan Hu) >> 4. Re: pre-edge centroid (Dominik Samuelis) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 8 Aug 2012 13:17:59 -0400 >> From: Marie Zwetsloot <mjz56(a)cornell.edu <mailto:mjz56@cornell.edu>> >> To: ifeffit(a)millenia.cars.aps.anl.gov >> <mailto:ifeffit@millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA >> NORMALIZATION >> Message-ID: >> >> <CALtZdD54=1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw(a)mail.gmail.com >> <mailto:1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw@mail.gmail.com>> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Scott Calvin, >> >> Thanks for your help. Yes, this is as far as my pre- and post-edge >> range >> go. I realized I should have made them longer; it was my first time >> doing >> this and wasnt aware that i should lengthen my pre and post-edge for >> later >> on analysis. This will be good lesson for the future. >> >> So you would not recommend doing linear combination fitting? I was >> planning >> on trying it out.. But I wouldnt want to do it if with my pre- and >> post-edge range, I am bound to derive wrong conclusions from the data. >> >> Best, >> Marie >>

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Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 7
by Enyuan Hu 09 Aug '12

09 Aug '12

Dear all, Thank you so much for all your valuable input. I attached the fitting result using ATHENA as pdf file. Seems that the fitting is not bad. Like Dominik and Maria pointed out, it takes some caution to do the fitting. My experience is, do not fit all parameters at the same time first. Approach by a try-and-error method, manually adjusting the parameters based on observation of difference between fitted data and experimental data. When you think it's about the time, free all parameters (no including centroid) for the final try. Good luck with that. Here's another question, how do I compute the centroid of the fitted peaks? ATHENA gives the centroid for each peak, do I just average them? thanks! Enyuan On Thu, Aug 9, 2012 at 11:26 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 114, Issue 5 (Mar?a Elena Montero Cabrera) > 2. Re: Ifeffit Digest, Vol 114, Issue 6 (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Aug 2012 09:19:13 -0600 > From: Mar?a Elena Montero Cabrera <elena.montero(a)cimav.edu.mx> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 > Message-ID: > <CAKUL-= > gGdfc9W_uQ015cyeVuPXbp3P-yfSnm-O18kV5-S6J2pA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > I have done pre-edge fitting of Ti in multiferroic ceramics with Athena. I > have selected error function for the "background" and alternatively > Lorenztian or Gaussian function for *several* peaks, and Athena has worked > quite well. The point is to do it with some systematic procedure, and > fixing some parameters, instead of letting them being free in each step. > Certainly, Athena doesn't have the pseudo-Voigt function. Try to do this > way, Enyuan. I think Bruce has commented something about this way sometime > ago, but I am not sure. > Regards > Maria Elena > > 2012/8/9 Enyuan Hu <bearcharge(a)gmail.com> > > > Hi Dominik, > > > > Thank you so much for your quick response. Indeed, it's really nice > > fitting according to your result. But my situation seems a little bit > > different as I'm dealing with the Mn XANES data and there're doublets and > > sometimes triplets in the pre-edge. Actually, I might as well explain my > > interest of doing such fitting. I read in the paper *(F Farges, PHYSICAL > > REVIEW B 71, 155109 (2005))* that the centroid of pre-edge peak is a more > > accurate measurement of the oxidation state of the element of interest, > > compared to the more conventional inflection point or half-way method. > So I > > was trying to follow the paper and see if it also works for my samples. > > Anyway, thanks again for your help! > > > > Enyuan > > > > On Thu, Aug 9, 2012 at 9:11 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: question for ifeffit mailing list - ATHENA NORMALIZATION > >> (Marie Zwetsloot) > >> 2. Re: question for ifeffit mailing list - ATHENA NORMALIZATION > >> (Scott Calvin) > >> 3. pre-edge centroid (Enyuan Hu) > >> 4. Re: pre-edge centroid (Dominik Samuelis) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Wed, 8 Aug 2012 13:17:59 -0400 > >> From: Marie Zwetsloot <mjz56(a)cornell.edu> > >> To: ifeffit(a)millenia.cars.aps.anl.gov > >> Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA > >> NORMALIZATION > >> Message-ID: > >> <CALtZdD54= > >> 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw(a)mail.gmail.com> > >> Content-Type: text/plain; charset="iso-8859-1" > >> > >> Hi Scott Calvin, > >> > >> Thanks for your help. Yes, this is as far as my pre- and post-edge range > >> go. I realized I should have made them longer; it was my first time > doing > >> this and wasnt aware that i should lengthen my pre and post-edge for > later > >> on analysis. This will be good lesson for the future. > >> > >> So you would not recommend doing linear combination fitting? I was > >> planning > >> on trying it out.. But I wouldnt want to do it if with my pre- and > >> post-edge range, I am bound to derive wrong conclusions from the data. > >> > >> Best, > >> Marie > >>

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Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5
by Enyuan Hu 09 Aug '12

09 Aug '12

Hi Dominik, Thank you so much for your quick response. Indeed, it's really nice fitting according to your result. But my situation seems a little bit different as I'm dealing with the Mn XANES data and there're doublets and sometimes triplets in the pre-edge. Actually, I might as well explain my interest of doing such fitting. I read in the paper *(F Farges, PHYSICAL REVIEW B 71, 155109 (2005))* that the centroid of pre-edge peak is a more accurate measurement of the oxidation state of the element of interest, compared to the more conventional inflection point or half-way method. So I was trying to follow the paper and see if it also works for my samples. Anyway, thanks again for your help! Enyuan On Thu, Aug 9, 2012 at 9:11 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: question for ifeffit mailing list - ATHENA NORMALIZATION > (Marie Zwetsloot) > 2. Re: question for ifeffit mailing list - ATHENA NORMALIZATION > (Scott Calvin) > 3. pre-edge centroid (Enyuan Hu) > 4. Re: pre-edge centroid (Dominik Samuelis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Aug 2012 13:17:59 -0400 > From: Marie Zwetsloot <mjz56(a)cornell.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] question for ifeffit mailing list - ATHENA > NORMALIZATION > Message-ID: > <CALtZdD54= > 1-w4U3vk7DdNU_CUkGpK-1vJ3ioOR_CSvkj4UeCXw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Scott Calvin, > > Thanks for your help. Yes, this is as far as my pre- and post-edge range > go. I realized I should have made them longer; it was my first time doing > this and wasnt aware that i should lengthen my pre and post-edge for later > on analysis. This will be good lesson for the future. > > So you would not recommend doing linear combination fitting? I was planning > on trying it out.. But I wouldnt want to do it if with my pre- and > post-edge range, I am bound to derive wrong conclusions from the data. > > Best, > Marie >

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