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

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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Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 6
by Enyuan Hu 09 Aug '12

09 Aug '12

Hi Matthew, It's so exciting to see your response in here because I've been reading your paper! It's very recent paper and I couldn't be found in Google Scholar yesterday, but I was lucky to find it in your website. In fact, seeing your response makes me feel, ah, I've come to the right place! Anyway, I'll continue my information-digging and see what I can find. Andrew, thanks for your input. I also tried in OriginLab like you did, but no good fitting was achieved. I'll see if I can try some other ways... Enyuan On Thu, Aug 9, 2012 at 11:06 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: pre-edge centroid (Andrew Korinda) > 2. Re: Ifeffit Digest, Vol 114, Issue 5 (Enyuan Hu) > 3. Re: Ifeffit Digest, Vol 114, Issue 5 - Mn XANES (Matthew Marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Aug 2012 08:26:32 -0500 > From: Andrew Korinda <a-korinda(a)northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] pre-edge centroid > Message-ID: > <CA+JhC7wgLFQR3F8Gaqnbp=hrz0tMb+HDoirMZAoLm_jdC= > 4Ayw(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Enyuan, > > I've had trouble with fitting in Athena as well and just used Excel > and a Gaussian function for the peak. As Domink stated, fitting the > edge as an arctan function simultaneously is a large help. I had tried > extracting the pre-edge and fitting the peak in Origin as a > pseudo-Voight function; however, I couldn't get a reliable fit of the > edge alone. > > In summary, it's a bit of all or nothing. When fitting the arctan > function, I typically stopped at 2 eV below the edge. > > Andy Korinda > > On Thu, Aug 9, 2012 at 8:11 AM, Dominik Samuelis <d.samuelis(a)fkf.mpg.de> > wrote: > > Dear Enyuan, > > > > in my experience, peak fitting works very well with Athena. Try not to > fit > > only the prepeak, but maybe include an arctan describing the edge (see > > attached pdf, the fit was made using athena). This makes isolating the > > prepeak much more reliable. > > > > Best regards, > > Dominik > > > > > > On 09.08.2012 06:21, Enyuan Hu wrote: > >> > >> Dear all, > >> > >> I was wondering if anyone could comment on how to get the centroid of > >> pre-edge by fitting the pre-edge peak by pseudo-Voigt functions. I tried > >> to do that in Athena, but it seemed that peaking fitting part is the > >> relatively less developed function in the software. Any comment would be > >> appreciated. > >> > >> Enyuan > >> > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > > > > -- > > Dr. Dominik Samuelis > > d.samuelis(a)fkf.mpg.de > > Max-Planck-Institut f?r Festk?rperforschung > > Max Planck Institute for Solid State Research > > Heisenbergstr. 1 > > 70569 Stuttgart > > Germany > > Phone +49-711-689-1769 > > Fax +49-711-689-1722 > > Web http://www.fkf.mpg.de/maier/ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 9 Aug 2012 10:53:32 -0400 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 > Message-ID: > < > CAJud35PZaf7HDS4digfUZk8RkDsXxLR06i1FqB_ugeRtDXJXnA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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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pre-edge centroid
by Enyuan Hu 09 Aug '12

09 Aug '12

Dear all, I was wondering if anyone could comment on how to get the centroid of pre-edge by fitting the pre-edge peak by pseudo-Voigt functions. I tried to do that in Athena, but it seemed that peaking fitting part is the relatively less developed function in the software. Any comment would be appreciated. Enyuan

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Re: [Ifeffit] question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 08 Aug '12

08 Aug '12

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] question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 07 Aug '12

07 Aug '12

Dear Ifeffit community, Thanks for your questions. I am very new to this field (M.Sc. student in soil science), so I really appreciate that you are taking the time to give me some advice. I have attached a picture of some of the normalized spectra I am working with as well as mu(E) spectra (I am sorry for attaching the picture, for some reason my email did not allow me to copy it into this message). I am doing Xanes analysis on phosphorus in bone char. My normalization range is from 15-60 eV and pre-edge range is from -13.5 to -6.75. Maybe my normalized spectra looked actually fine; they are not that far above 1 (more or less around 0.3 above). I just thought they looked a little strange/skewed. Let me know what you think. Thanks, Marie

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[IFEFFIT] question about chemically unordered systems
by Meutzner, Falk 07 Aug '12

07 Aug '12

Dear IFEFFIT Community, is there a way to calculate the spectrum for chemically disordered systems? We have a simple binary bcc structure. It crystallises either in superstructure (CsCl) or chemically disordered (W type) with both atoms randomly taking part of either (0,0,0) or (0.5,0.5,0.5). It is easy to get the superstructured model for artemis, but we have no clue how to model the disordered system... Thanks a lot for your help, we really appreciate it. Best regards Falk

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question for ifeffit mailing list - ATHENA NORMALIZATION
by Marie Zwetsloot 07 Aug '12

07 Aug '12

* Is there a way through which I can control that my norm(E) only has a range from 0-1? Right now, some of my scans go from 0 - 3 after having normalized them. It seems that most people publish their data only ranging from 0-1..? . Is there a difference between the two?*

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Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 18
by Michael Weir 30 Jul '12

30 Jul '12

Hello Branko, I've worked a little bit with small Pt nanoparticles and I think I may see a problem. In the project file you sent us, you choose an Rbkg of 1.6 for your nanoparticles but 1.0 for the foil. The Pt-O bonds at ~ 2 A end up at about 1.5/1.55 A in the Fourier Transform, so your choice of Rbkg is suppressing the real signal in that region. I'd look again with a lower Rbkg if you haven't already (1.2 is a good starting point). I didn't see your Pt-O standards in the project. Also keep in mind that Artemis will plot individual paths from the FEFF calculation, which is really useful for determining if a specific path has a strong contribution to your fit or if a pair of paths will be difficult to distinguish. I hope that helps! Michael Weir On Mon, Jul 30, 2012 at 9:01 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 113, Issue 17 (Branko Zugic) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2012 12:00:37 -0400 > From: Branko Zugic <brankozugic(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 17 > Message-ID: > <CAOJ5_YxOhbiN8zJfi_xG8+NSVuhnfTydyR== > xc61Uov-CwdhMw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Anatoly, > > I've only tried approximating using the short bond at 2 A up until now. > Below are the spectra that I'm trying to interpret. These are merged QEXAFS > data taken at increasing temperature under WGS conditions. Perhaps I > haven't processed them well enough? There certainly seem to be changes > taking place during the course of reaction, which I'm trying to interpret. > > Given that the material starts out very well dispersed (I've observed many > sub-nm Pt clusters via ac-STEM) and grow to 1-2 nm particles during > reaction, I would expect to observe corresponding structural changes during > reaction. I also observe significant changes in the EXAFS spectra when > alternating between WGS gas and He - hence my thought to including some > kind of Pt-C and Pt-O paths, similar to those used in the Ir4(CO)12 work. > > Thanks for any help! > > > Branko > > > > On Sat, Jul 28, 2012 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. Re: Modeling Pt/C Catalyst Under WGS Conditions > > (Anatoly I Frenkel) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 28 Jul 2012 01:02:23 +0000 > > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > Message-ID: <98fc47e6-bd47-4c56-8fb2-3385fa7dbbbe@blur> > > Content-Type: text/plain; charset="utf-8" > > > > Maybe your system is more complex? Have you included a long Pt-O bond at > > around 2.5 A or just a short one at around 2A? Hard to help without > seeing > > what the problem is. > > > > Anatoly > > > > > > > > Sent from my mobile phone, please forgive typos > > > > > > -----Original message----- > > From: Branko Zugic <Branko.Zugic(a)tufts.edu> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 > > Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > > > Hello, > > > > I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I > > took under water-gas shift conditions (CO + H2O diluted in He) on some > Pt/C > > catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O > > standards, and quick 1st shell approximations for Pt-O aren't that great. > > After looking through the literature I came across some papers (i.e. > > http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and > Ir-C > > interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I > > then found some crystallographic tables for Ir4(CO)12 (below), but it's > > unclear to me whether I can use this to create an atoms inp file (and > > whether the data is for the structure I'm looking for or the referenced > > Ir(CO)3). So far I've had no luck. > > > > Is this a reasonable approach to this problem? Is the information I have > > enough to do this? Any suggestions as to where I may be able to find the > > crystallographic data I am looking for? > > > > > > Branko Zugic > > > > > > -- > > PhD Candidate > > Tufts University, Chemical and Biological Engineering > > 4 Colby Street, Room 226 > > Medford, MA 02155 > > Ph: (O) 617 627 2267 (H) 508 414 8555 > > Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, > > brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto: > > brankozugic(a)gmail.com> > >

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Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 17
by Branko Zugic 30 Jul '12

30 Jul '12

Hi Anatoly, I've only tried approximating using the short bond at 2 A up until now. Below are the spectra that I'm trying to interpret. These are merged QEXAFS data taken at increasing temperature under WGS conditions. Perhaps I haven't processed them well enough? There certainly seem to be changes taking place during the course of reaction, which I'm trying to interpret. Given that the material starts out very well dispersed (I've observed many sub-nm Pt clusters via ac-STEM) and grow to 1-2 nm particles during reaction, I would expect to observe corresponding structural changes during reaction. I also observe significant changes in the EXAFS spectra when alternating between WGS gas and He - hence my thought to including some kind of Pt-C and Pt-O paths, similar to those used in the Ir4(CO)12 work. Thanks for any help! Branko On Sat, Jul 28, 2012 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. Re: Modeling Pt/C Catalyst Under WGS Conditions > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 28 Jul 2012 01:02:23 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > Message-ID: <98fc47e6-bd47-4c56-8fb2-3385fa7dbbbe@blur> > Content-Type: text/plain; charset="utf-8" > > Maybe your system is more complex? Have you included a long Pt-O bond at > around 2.5 A or just a short one at around 2A? Hard to help without seeing > what the problem is. > > Anatoly > > > > Sent from my mobile phone, please forgive typos > > > -----Original message----- > From: Branko Zugic <Branko.Zugic(a)tufts.edu> > To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov > > > Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 > Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions > > Hello, > > I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I > took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C > catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O > standards, and quick 1st shell approximations for Pt-O aren't that great. > After looking through the literature I came across some papers (i.e. > http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C > interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I > then found some crystallographic tables for Ir4(CO)12 (below), but it's > unclear to me whether I can use this to create an atoms inp file (and > whether the data is for the structure I'm looking for or the referenced > Ir(CO)3). So far I've had no luck. > > Is this a reasonable approach to this problem? Is the information I have > enough to do this? Any suggestions as to where I may be able to find the > crystallographic data I am looking for? > > > Branko Zugic > > > -- > PhD Candidate > Tufts University, Chemical and Biological Engineering > 4 Colby Street, Room 226 > Medford, MA 02155 > Ph: (O) 617 627 2267 (H) 508 414 8555 > Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, > brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto: > brankozugic(a)gmail.com> >

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Re: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions
by Anatoly I Frenkel 27 Jul '12

27 Jul '12

Maybe your system is more complex? Have you included a long Pt-O bond at around 2.5 A or just a short one at around 2A? Hard to help without seeing what the problem is. Anatoly Sent from my mobile phone, please forgive typos -----Original message----- From: Branko Zugic <Branko.Zugic(a)tufts.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri, Jul 27, 2012 15:28:37 GMT+00:00 Subject: [Ifeffit] Modeling Pt/C Catalyst Under WGS Conditions Hello, I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O standards, and quick 1st shell approximations for Pt-O aren't that great. After looking through the literature I came across some papers (i.e. http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I then found some crystallographic tables for Ir4(CO)12 (below), but it's unclear to me whether I can use this to create an atoms inp file (and whether the data is for the structure I'm looking for or the referenced Ir(CO)3). So far I've had no luck. Is this a reasonable approach to this problem? Is the information I have enough to do this? Any suggestions as to where I may be able to find the crystallographic data I am looking for? Branko Zugic -- PhD Candidate Tufts University, Chemical and Biological Engineering 4 Colby Street, Room 226 Medford, MA 02155 Ph: (O) 617 627 2267 (H) 508 414 8555 Email: Branko.Zugic(a)tufts.edu<mailto:Branko.Zugic@tufts.edu>, brankozugic(a)gmail.com<mailto:brankozugic@gmail.com><mailto:brankozugic@gmail.com>

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Modeling Pt/C Catalyst Under WGS Conditions
by Branko Zugic 27 Jul '12

27 Jul '12

Hello, I am trying to interpret some in-situ Quick-EXAFS and EXAFS data that I took under water-gas shift conditions (CO + H2O diluted in He) on some Pt/C catalysts. I'm finding that the Pt-Pt and Pt-O fits using foil data, Pt-O standards, and quick 1st shell approximations for Pt-O aren't that great. After looking through the literature I came across some papers (i.e. http://pubs.acs.org/doi/abs/10.1021/jp983283e) that use the Ir-O and Ir-C interactions from Ir4(CO)12 to approximate Pt-O and Pt-C interactions. I then found some crystallographic tables for Ir4(CO)12 (below), but it's unclear to me whether I can use this to create an atoms inp file (and whether the data is for the structure I'm looking for or the referenced Ir(CO)3). So far I've had no luck. Is this a reasonable approach to this problem? Is the information I have enough to do this? Any suggestions as to where I may be able to find the crystallographic data I am looking for? Branko Zugic -- PhD Candidate Tufts University, Chemical and Biological Engineering 4 Colby Street, Room 226 Medford, MA 02155 Ph: (O) 617 627 2267 (H) 508 414 8555 Email: Branko.Zugic(a)tufts.edu, brankozugic(a)gmail.com <brankozugic(a)gmail.com>

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Demeter 0.9.10
by Bruce Ravel 17 Jul '12

17 Jul '12

Hi everyone, I just uploaded a new version of the Demeter installer for Windows -- which includes the programs Athena, Artemis, and Hephaestus -- to its download site at https://github.com/bruceravel/demeter/downloads The current version number is 0.9.10. I also tagged this version in the github repository for anyone interested in a tagged version of the source code. Installation instructions for all platforms are at http://bruceravel.github.com/demeter/pods/installation.pod.html While there are no major new features in this release, the list of bug fixes and improvements is rather lengthy. Here are the details: https://github.com/bruceravel/demeter/blob/master/Changes.org Here are hints for making helpful bugs reports: http://bruceravel.github.com/demeter/pods/bugs.pod.html Documentation about Demeter in various kinds of media can found at http://bruceravel.github.com/demeter/ As a closing note, I want to mention that I am about 2/3 done with the long-awaited users' guide for Artemis. There is a link to the current (but incomplete) draft at the Documentation site. I will update that as I work it. Once it is complete, I will work on a PDF version. Once that is complete (and assuming I still have energy for such things!), I will work on updating the Athena Users' Guide for the new Demeter-based version. Whew! As always, thanks to everyone who uses my software. Your enthusiasm is a huge inspiration for me. Bruce PS: If, in the last few months, you have reported a bug or requested a feature that is not in this release, please remind me! -- 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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"Re: Contents of Ifeffit digest..."
by johnny huertas 14 Jul '12

14 Jul '12

Anatoly: Thanks so much. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 13 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 16:19:14 -0500 > > 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 113, Issue 11 (Anatoly I Frenkel) > 2. "RE: Contents of Ifeffit digest..." (johnny huertas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Jul 2012 19:13:01 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > Message-ID: > <545F89325F51764C902D37B42C9F4D53135B1B44(a)YUWEXCPM12.yuad.uds.yu.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jhonny, > > This article on AgBr(x)Cl(1-x) explains how to do this type of analysis, and if there are still questions, look for other articles (in Phys. Rev. B and Phys. Rev. Lett.) on mixed ionic salts, by the same authors: > > https://pubweb.bnl.gov/~frenkel/BUCKLING-PHB/buckledPHB.pdf > > It is a model independent way to find local composition of Br and Cl around Ag. You are better off doing that (limit it to the 1st shell analysis) rather than using particular configurations you are proposing, and then see if you get the same composition (x) for Ag-Br as you obtain for composition y corresponding to the Br-Br coordination number found from Br K-edge. That will mean that your alloy is random. Otherwise, there may be either short range order or segregation that you will be able to identify by comparing x and y in each individual case. Rely on XRD results also, to tell whether you really have a solid solution or not. > > If you only measured Ag edge, you still can make some conclusions but you should rely on the bulk composition to compare the "x" and "y". > > Anatoly > > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of johnny huertas [johnnyhf(a)hotmail.com] > Sent: Saturday, July 14, 2012 1:51 PM > To: Lista fe IFEFFIT > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > > Hi Matt: > Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same". > I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. > > > > > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > > > > From: ifeffit-request(a)millenia.cars.aps.anl.gov > > Subject: Ifeffit Digest, Vol 113, Issue 11 > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > > > 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. problems (johnny huertas) > > 2. Re: problems (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 13 Jul 2012 22:21:50 +0000 > > From: johnny huertas <johnnyhf(a)hotmail.com> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] problems > > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Members of list: > > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > > Jhonny Huertas Flores > > Rio de Janeiro-Brasil > > > > > >

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"RE: Contents of Ifeffit digest..."
by johnny huertas 14 Jul '12

14 Jul '12

Hi Matt: Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 12 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 13:42:01 -0500 > > 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 113, Issue 11 (johnny huertas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Jul 2012 17:51:20 +0000 > From: johnny huertas <johnnyhf(a)hotmail.com> > To: Lista fe IFEFFIT <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > Message-ID: <BAY167-W39E4C96CF961ED74CD8924D5D60(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Matt:Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. > > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > > > From: ifeffit-request(a)millenia.cars.aps.anl.gov > > Subject: Ifeffit Digest, Vol 113, Issue 11 > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > > > 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. problems (johnny huertas) > > 2. Re: problems (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 13 Jul 2012 22:21:50 +0000 > > From: johnny huertas <johnnyhf(a)hotmail.com> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] problems > > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Members of list: > > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > > Jhonny Huertas Flores > > Rio de Janeiro-Brasil > > > > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11
by johnny huertas 14 Jul '12

14 Jul '12

Hi Matt:Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 11 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > 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. problems (johnny huertas) > 2. Re: problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 13 Jul 2012 22:21:50 +0000 > From: johnny huertas <johnnyhf(a)hotmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] problems > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Members of list: > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > >

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problems
by johnny huertas 13 Jul '12

13 Jul '12

Members of list: I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. Jhonny Huertas Flores Rio de Janeiro-Brasil

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Re: [Ifeffit] Referencing Demeter
by Bruce Ravel 13 Jul '12

13 Jul '12

Daniel, Please use the Ifeffit mailing list questions and comments on the software. http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > My name is Daniel Whittaker, I am PhD student at the University of > Manchester, UK. I have used your Demeter software (Athena and Artemis - i > used the first shell fit method as reading in crystal data was very > problematic) to model some EXAFS data. I am now preparing the manuscript > for publication and was wondering how you would like referencing (other > than Bruce Ravels Demeter software package) and if there is anything in > particular you would like in the experimental section about how the > software works? I have looked on your page and couldn't seem to find > anything that explicit requests referencing in a particular format. Ravel, B. & Newville, M. athena and artemis: data analysis for X-ray absorption spectroscopy using ifeffit, Journal of Synchrotron Radiation 12, 537–541 (2005) http://dx.doi.org/10.1107/S0909049505012719 > Thanks for your help with this and for producing the package in the first > place, as someone who knew literally nothing when i started i have managed > to model quite a few spectra to a satisfactory level. > > Regards, > > Daniel Whittaker, MChem > Nuclear FiRST DTC PhD Student > The University of Manchester > Oxford Road > Manchester > M13 9PL -- 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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Manganese oxide EXAFS modelin
by Ebrahim Rezaei 12 Jul '12

12 Jul '12

Hi everyone, I am working with bulk and nano-particles manganese oxides. Basically I have collected EXAFS of Mn K-edge for my reference material (Mn2O3, bixibyite) and also the catalyst (Mn supported on alumina). The catalyst shows formation of nanoparticles of bixibyite on alumina with size around 20 nm. My first question is about modeling the reference material in order to find So which will be used as a fixed parameter to find oxygen and manganese first and second shell CNs for the catalyst. The difficulty with modeling the reference material arises due to the rather complex atomic coordinates of Mn2O3 containing oxygen atoms at different but very close distances. Basically Mn2O3 has two sites (25% and 75% occupancy for site 1 and 2 respectively) with the following coordinates: Site 1 Site 2 Atom R (Å) CN Atom R (Å) CN O 1.993 6 O 1.899 2 Mn 3.104 6 O 1.985 2 Mn 3.565 6 O 2.249 2 Mn 3.115 6 Mn 3.575 6 I am aware that in order to fit the EXAFS equation I should considers paths from both sites and multiply their amplitudes by their site occupancy. But to make the life easier I simplified the atom coordinates of Mn2O3 to be able to extract the CNs from the catalyst. To my understanding one can expect to have 6 oxygen atoms in average at the first shell (0.25*6 + 0.75*6 = 6), 6 Mn atoms at the second shell and 6 Mn atoms at the third shell regardless of the site occupancy. Therefore I ignored the site occupancy and considered the following atomic coordinates assuming that there is only one site in the in the model developed for the reference material: Atom R (Å) CN O 1.985 4 O 2.249 2 Mn 3.115 6 Mn 3.565 6 The model works fairly acceptable and I am able to get CN from the catalysts as well. But I am not sure if my assumptions could be acceptable or not. I was wondering if I can have idea of the EXAFS community experts on this. My other question is about dealing with σ2 as a fixed parameter. I have noticed that after fitting the catalysts, σ2 of paths in the catalysts are almost close to that of the reference material. Therefore I tried to fix the values of σ2 for the catalyst and use the ones I have obtained from the reference material. This increases the degree of freedom of the fit and results in smaller error bars in CN while χ2 increases by 2.5%. Basically I have always kept number of variables to almost less than half of the number of the independent points either with fixing or relaxing σ2. I was wondering if estimation of σ2 in the catalysts from the reference material might be a good assumption in my case or not. I think it should not be a bad idea since size of Mn2O3 nano-particles on alumina is fairly large (around 20 nm) showing formation of complete crystalline of Mn2O3 on the catalyst. I have my project file in hand and I can send it for further discussion as well. I appreciate your time and help in advance. Best Regards, Ebrahim Rezaei, PhD Student, Chemical Engineering Department, University of Saskatchewan, Saskatoon, SK, Canada

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Athena Request
by BradleyW Miller 11 Jul '12

11 Jul '12

Hi, If my memory is correct there was a period of time you were taking request for improvements on Athena. This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B. If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome. In a related comment I have tried to take advantage of access to high speed computing, but Athena's code does not appear to be capable of taking advantage of increased resources (either RAM and CPU) in order to decrease computational time. All the same thanks (to the many of you working on Ifeffit) for the shareware and all your support. 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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Crash when Discarding Feff Calculation
by Andrew Korinda 07 Jul '12

07 Jul '12

I have an Arthemis project (started in Demeter) with several feff calculations with the input written by me into a feff.inp boiler plate. The calculations themselves were fine but now when I show a calculation and click discard, I get the pop-up asking me if I want to discard this calculation, I click yes, then everything closes. Attached is the log file, project file, and demeter.mru. Let me know if there's anything I can do to help debug this. Andy Korinda

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