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

closing Artemis project
by Christopher Patridge 28 May '13

28 May '13

Hello, I have a question about (D)Artemis. After saving a project, I used the Close option under File. This does remove the datasets and feff calculations but it keeps the name of the project in main window header. Is there a way to begin a new project other than closing Artemis and/or beginning a project and use the save as option? One other thing, is there any possibility of extending the number of datasets for artemis? Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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Demeter 0.9.17
by Bruce Ravel 28 May '13

28 May '13

Hi, I just uploaded a new Windows updater package for Demeter and tagged version 0.9.17 at GitHub. This release introduces no new features but fixes the handful of problems reported in recent weeks. The updater package can be obtained at Demeter's homepage: http://bruceravel.github.io/demeter/ Cheers, B -- 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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Opening XANES Files with Athena
by Alex Kellum 24 May '13

24 May '13

Hello All, I am working on an NSF-REU program this summer requiring me to analyze XANES spectra. My personal computer is a mac (w/ OS X 10.6.8). I am desperately trying to figure out how to even open an IFEFFIT program that will help me analyze the spectra. The spectra are saved in .txt files--and I have no idea how to convert them to .apj or .prj files. Is it possible to analyze them with converting them? Right now I am using iXAFS Shell containing Athena, Artemis and Hephaestus. I realize there are newer versions available, but Demeter is only available on Windows and I spent a few hours trying to get Larch to work. Even after downloading python I had no idea how to get it to actually download and work. I do have X11 running on my computer. I realize you probably get a ton of emails from users, but any help would be greatly appreciated. Regards, Alex Kellum

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Correction to radial distance
by Francisco Garcia 24 May '13

24 May '13

Dear all, Can an experienced user kindly explain how to obtain the phase shift correction to the radial distance corresponding to FFT(chi(k)). From my chi(k) computation, I have several feff*.dat files (feff0001.dat, feff0002.dat,...............,feff00128.dat) because I have 128 paths. How do I use this information and IFEFFIT to compute the shifted spectrum? Thank you.

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JFEFF/FEFF9 "Save&Run" no longer works after Java Update -- FEFFgroup announcement
by Kevin Jorissen 16 May '13

16 May '13

Dear iFEFFIT community, a short update from the FEFF developers team: A recent Java update (Java 7 Update 21) broke some functionality of the JFEFF interface for the FEFF program. Users who update to J7U21 have noticed that when they click "Save&Run" nothing happens: the FEFF programs do not run and there is no output. We think this issue will affect people on all Operating Systems. To fix this issue there are two possibilities: * Roll back Java to a previous version. For security reasons please have at least Java 7 Update 11, which was an important security update, or newer. Instructions for rolling back Java can be found online. * We have updated JFEFF to work with the latest Java. This latest (J)FEFF version is not yet available on the official download website, but FEFF users with a valid license can contact us and we will provide them with a download link for the latest (J)FEFF. Please contact us directly. Users who currently have FEFF8 can upgrade to FEFF9 at any time at a discounted rate. Thank you to Linda Lim for her earlier post on the iFEFFIT ML. Cheers, Kevin Jorissen FEFFgroup - University of Washington

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normalization methods
by Matt Newville 16 May '13

16 May '13

Hi Folks, Over on the github pages for larch, Mauro and Bruce raised an issue about the "flattening" in Athena. See https://github.com/xraypy/xraylarch/issues/44 I've added a "flattened output" from Larch's pre_edge() function, but the question has been raised of whether this is "better" than the simpler normalized spectra, especially for doing PCA and/or LCF for XANES. Currently, the "normalized" spectra is just "(mu - pre_edge_line)/edge_step". Clearly, a line fitted to the pre-edge of the spectra is not sufficient to remove all instrumental backgrounds. In some sense, flattening attempts to do a better job, fitting the post-edge spectra to a quadratic function. As Mauro, Bruce, and Carmelo have pointed out, it is less clear that it is actually better for XANES analysis. I think the main concerns are that a) it is so spectra-specific, and b) it turns on at E0 with a step function. Bruce suggested doing something more like MBACK or Ifeffit's bkg_cl(). It would certainly be possible to do some sort of "flattening" so that mu follows the expected energy dependence from tabularized mu(E). Does anyone else have suggestions, opinions, etc? Feel free to give them here or at the github page.... --Matt

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Re: [Ifeffit] normalization methods
by Zack Gainsforth 15 May '13

15 May '13

Hi All, We did an analysis comparing on order of 100 XANES spectra and found that a normalization producing the most stereotypically "correct" spectrum did not always produce the best linear combinations between them. That is, we tend to think a XANES spectrum should be flat (derivative=0) before the edge, and then there is a step, and wiggles, and the wiggles are centered around another flat line. Certainly, this form of spectrum communicates well in publications, and probably it is best for publications given that different researchers use different normalization algorithms. However, when comparing XANES spectra against each other quantitatively, it is more important that the subtraction method be the same. What we did that worked well was write a normalization routine in MATLAB (derived from Matthew Marcus' description since we acquired XANES on his beamline). Then we were better able to compare spectra and fit them against each other using linear combination. When using spectra that were individually normalized, the linear combinations were never as good. Incidentally, this is an argument for always including raw spectra in supplementary materials even though you would want to use the normalized spectrum in a publication. Cheers, Zack On May 15, 2013, at 9:58 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. normalization methods (Matt Newville) 2. Re: normalization methods (Matthew Marcus) 3. Re: normalization methods (Matt Newville) 4. Re: normalization methods (Matthew Marcus) 5. Re: normalization methods (George Sterbinsky) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 May 2013 09:35:41 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] normalization methods Message-ID: <CA+7ESboBg5uOS6or-TurJy9zPGhoA73c+bErNkWsuO4GC4Cpug(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Folks, Over on the github pages for larch, Mauro and Bruce raised an issue about the "flattening" in Athena. See https://github.com/xraypy/xraylarch/issues/44 I've added a "flattened output" from Larch's pre_edge() function, but the question has been raised of whether this is "better" than the simpler normalized spectra, especially for doing PCA and/or LCF for XANES. Currently, the "normalized" spectra is just "(mu - pre_edge_line)/edge_step". Clearly, a line fitted to the pre-edge of the spectra is not sufficient to remove all instrumental backgrounds. In some sense, flattening attempts to do a better job, fitting the post-edge spectra to a quadratic function. As Mauro, Bruce, and Carmelo have pointed out, it is less clear that it is actually better for XANES analysis. I think the main concerns are that a) it is so spectra-specific, and b) it turns on at E0 with a step function. Bruce suggested doing something more like MBACK or Ifeffit's bkg_cl(). It would certainly be possible to do some sort of "flattening" so that mu follows the expected energy dependence from tabularized mu(E). Does anyone else have suggestions, opinions, etc? Feel free to give them here or at the github page.... --Matt ------------------------------ Message: 2 Date: Wed, 15 May 2013 07:57:14 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] normalization methods Message-ID: <5193A24A.5090506(a)lbl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed What I typically do for XANES is divide mu-mu_pre_edge_line by a linear function which goes through the post-edge oscillations. This division goes over the whole data range, including pre-edge. If the data has obvious curvature in the post-edge, I'll use a higher-order polynomial. For transmission data, what sometimes linearizes the background is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption shape) and change it back afterward. All this is, of course, highly subjective and one of the reasons for taking extended XANES data (300eV, for instance). For short-range XANES, there isn't enough info to do more than divide by a constant. Once this is done, my LCF programs allow a slope adjustment as a free parameter, thus muNorm(E) = (1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of freedom may be being abused is if the sum of the x[ref] is far from 1 or if a*(Emax-E0) is large. Don't get me started on overabsorption :-) mam On 5/15/2013 7:35 AM, Matt Newville wrote: > Hi Folks, > > Over on the github pages for larch, Mauro and Bruce raised an issue > about the "flattening" in Athena. See > https://github.com/xraypy/xraylarch/issues/44 > > I've added a "flattened output" from Larch's pre_edge() function, but > the question has been raised of whether this is "better" than the > simpler normalized spectra, especially for doing PCA and/or LCF for > XANES. > > Currently, the "normalized" spectra is just "(mu - > pre_edge_line)/edge_step". Clearly, a line fitted to the pre-edge of > the spectra is not sufficient to remove all instrumental backgrounds. > In some sense, flattening attempts to do a better job, fitting the > post-edge spectra to a quadratic function. As Mauro, Bruce, and > Carmelo have pointed out, it is less clear that it is actually better > for XANES analysis. I think the main concerns are that a) it is so > spectra-specific, and b) it turns on at E0 with a step function. > > Bruce suggested doing something more like MBACK or Ifeffit's bkg_cl(). > It would certainly be possible to do some sort of "flattening" so > that mu follows the expected energy dependence from tabularized mu(E). > > Does anyone else have suggestions, opinions, etc? Feel free to give > them here or at the github page.... > > --Matt > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 3 Date: Wed, 15 May 2013 10:25:23 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] normalization methods Message-ID: <CA+7ESbrhv1WHj8r2v1-U7wurQCvZnmFjrmAf9HNbTfcRjFn77Q(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Matthew, On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > What I typically do for XANES is divide mu-mu_pre_edge_line by a linear > function which goes through the post-edge oscillations. > This division goes over the whole data range, including pre-edge. If the > data has obvious curvature in the post-edge, I'll use a higher-order > polynomial. For transmission data, what sometimes linearizes the background > is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption > shape) and change it back afterward. All this is, of course, highly > subjective and one of the reasons for taking extended XANES data (300eV, > for instance). For short-range XANES, there isn't enough info to do more > than divide by a constant. Once this is done, my LCF programs allow > a slope adjustment as a free parameter, thus muNorm(E) = > (1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of > freedom > may be being abused is if the sum of the x[ref] is far from 1 or if > a*(Emax-E0) is large. Don't get me started on overabsorption :-) > mam Thanks -- I should have said that pre_edge() can now do a victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any real value). Still, it seems that the current flattening is somewhere between "better" and "worse", which is unsettling... Applying the "flattening" polynomial to the pre-edge range definitely seems to give poor results, but maybe some energy-dependent compromise is possible. And, of course, over-absorption is next on the list! --Matt ------------------------------ Message: 4 Date: Wed, 15 May 2013 08:41:55 -0700 From: Matthew Marcus <mamarcus(a)lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] normalization methods Message-ID: <5193ACC3.3090007(a)lbl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed The way I commonly do pre-edge is to fit with some form plus a power-law singularity representing the initial rise of the edge, then subtract out that "some form". Now, that form can be either linear, linear+E^(-2.7) (for transmission), or linear+ another power-law singularity centered at the center passband energy of the fluorescence detector. That latter is for fluorescence data which is affected by the tail of the elastic/Compton peak from the incident energy. Whichever form is taken gets subtraccted from the whole data range, resulting in data which is pre-edge-subtracted but not yet post-edge normalized. The path then splits; for EXAFS, the usual conversion to k-space, spline fitting in the post-edge, subtraction and division is done, all interactively. Tensioned spline is also available due to request of a prominent user. For XANES, the post-edge is fit as previously described. Thus, there's no distinction made between data above and below E0 in XANES, whereas there is such a distinction in EXAFS. mam On 5/15/2013 8:25 AM, Matt Newville wrote: > Hi Matthew, > > On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: >> What I typically do for XANES is divide mu-mu_pre_edge_line by a linear >> function which goes through the post-edge oscillations. >> This division goes over the whole data range, including pre-edge. If the >> data has obvious curvature in the post-edge, I'll use a higher-order >> polynomial. For transmission data, what sometimes linearizes the background >> is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption >> shape) and change it back afterward. All this is, of course, highly >> subjective and one of the reasons for taking extended XANES data (300eV, >> for instance). For short-range XANES, there isn't enough info to do more >> than divide by a constant. Once this is done, my LCF programs allow >> a slope adjustment as a free parameter, thus muNorm(E) = >> (1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of >> freedom >> may be being abused is if the sum of the x[ref] is far from 1 or if >> a*(Emax-E0) is large. Don't get me started on overabsorption :-) >> mam > > Thanks -- I should have said that pre_edge() can now do a > victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any > real value). > > Still, it seems that the current flattening is somewhere between > "better" and "worse", which is unsettling... Applying the > "flattening" polynomial to the pre-edge range definitely seems to give > poor results, but maybe some energy-dependent compromise is possible. > > And, of course, over-absorption is next on the list! > > --Matt > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 5 Date: Wed, 15 May 2013 12:58:53 -0400 From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] normalization methods Message-ID: <CALoY8YzRCAa3w=8hC=Pn50cysiaVzYR6GrRCZDnW9d2gvPg7Gw(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" The question of whether it is appropriate to use flattened data for quantitative analysis is something I've been thinking about a lot recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the XMCD, I measure XAS with total electron yield detection using a ~70% left or right circularly polarized beam and flip the magnetic field on the sample at every data point. The goal then, is to subtract the XAS measured in a positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. I often find that after removal of a linear pre-edge, the spectra still have a linearly increasing post edge (with EXAFS oscillations superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines are different. In this case simply multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum that is zero in the post edge region. There is then some component of the XAS background that is not accounted for by linear subtraction and multiplication by a constant. It seems to me that flattening could be a good way to account for such a background. So is flattening a reasonable thing to do in a case such as this, or is there a better way to account for such a background? Thanks, George On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: > The way I commonly do pre-edge is to fit with some form plus a power-law > singularity representing the initial rise of the edge, then > subtract out that "some form". Now, that form can be either linear, > linear+E^(-2.7) (for transmission), or linear+ another power-law > singularity centered at the center passband energy of the fluorescence > detector. That latter is for fluorescence data which is affected by > the tail of the elastic/Compton peak from the incident energy. Whichever > form is taken gets subtraccted from the whole data range, resulting > in data which is pre-edge-subtracted but not yet post-edge normalized. > The path then splits; for EXAFS, the usual conversion to k-space, spline > fitting in the post-edge, subtraction and division is done, all > interactively. Tensioned spline is also available due to request of a > prominent user. > For XANES, the post-edge is fit as previously described. Thus, there's no > distinction made between data above and below E0 in XANES, whereas > there is such a distinction in EXAFS. > mam > > > On 5/15/2013 8:25 AM, Matt Newville wrote: > >> Hi Matthew, >> >> On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus <mamarcus(a)lbl.gov> wrote: >> >>> What I typically do for XANES is divide mu-mu_pre_edge_line by a linear >>> function which goes through the post-edge oscillations. >>> This division goes over the whole data range, including pre-edge. If the >>> data has obvious curvature in the post-edge, I'll use a higher-order >>> polynomial. For transmission data, what sometimes linearizes the >>> background >>> is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption >>> shape) and change it back afterward. All this is, of course, highly >>> subjective and one of the reasons for taking extended XANES data (300eV, >>> for instance). For short-range XANES, there isn't enough info to do more >>> than divide by a constant. Once this is done, my LCF programs allow >>> a slope adjustment as a free parameter, thus muNorm(E) = >>> (1+a*(E-E0))*Sum_on_ref{x[ref]***muNorm[ref](E)}. A sign that this >>> degree of >>> freedom >>> may be being abused is if the sum of the x[ref] is far from 1 or if >>> a*(Emax-E0) is large. Don't get me started on overabsorption :-) >>> mam >>> >> >> Thanks -- I should have said that pre_edge() can now do a >> victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any >> real value). >> >> Still, it seems that the current flattening is somewhere between >> "better" and "worse", which is unsettling... Applying the >> "flattening" polynomial to the pre-edge range definitely seems to give >> poor results, but maybe some energy-dependent compromise is possible. >> >> And, of course, over-absorption is next on the list! >> >> --Matt >> ______________________________**_________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.**gov <Ifeffit(a)millenia.cars.aps.anl.gov> >> http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffit<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> >> ______________________________**_________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.**gov <Ifeffit(a)millenia.cars.aps.anl.gov> > http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffit<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >

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problem with importing data between version of artemis
by Georges Siddiqi 14 May '13

14 May '13

Hi All, I've done a fit in the old version of Artemis (0.8.014), and wanted to import this fit into the new version of artemis (demeter 0.9.15) that I have to play around with it a bit more. The problem is, when I import the the "old-style artemis project", and do the same fit, the values, and fit itself are nowhere near similar to what i got with the old version of Artemis. what is the cause of this discrepancy? As far as I can tell from double checking all the fitting parameters, windows, variables, etc, they are all exactly the same. Even if I try to just do a summation in the new version with my best-fit values from the old version, the fit is completely different. Previously when I was importing fits between versions I had no issues whatsoever. I've attached the artemis project file (W EXAFS.apj) that gives me a good fit in the old version, and a poor fit in the new version. thanks, georges

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Athena- Demeter 0.9.14 importing data
by Atul Bansode 13 May '13

13 May '13

Hi All, I am using Athena (Demeter 0.9.14) to process the EXAFS data of Copper samples. Athena reads the data correctly however my problem is concerned with the importing the data. When I import the data, in the Athena: Column Selection dialog box the Energy units is shown in keV by default. Since my data is in eV, I can always change the keV to eV and work when it's a single file. My problem starts when I try to import multiple files where I choose Energy units as eV in the dialog box however this setting gets applied to the first file only. Remaining data files are read as keV which creates a problem for me to process the data. Is there any way to apply same Energy units to all the files while they are getting imported ? Or is it possible to change the Energy units after importing files ? I appreciate all your help. Thanks in advance ! Best regards Atul

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Installing on Mac OSX Lion
by Nate Turner 10 May '13

10 May '13

Hello, I believe I have successfully installed PGPLOT, Ifeffit, and the horae suite of programs onto my mac OSX and have constructed executable files for artemis, athena, atoms, and hephaestus. I am now at a loss however, as when I try to run them they fail and say they are looking for _iff_exec. Is this part of the Ifeffit program? After I built Ifeffit, I can't seem to find any executable file that opens Ifeffit. Did I not successfully install Ifeffit? Also, what is the purpose of iXAFS program for Mac OS X? when I run it I am asked to direct the program to the data files and there is a button for each of the horae suite programs but they don't launch anything. I am very lost by all this and would appreciate the help. Thank you, Nate Turner Graduate Student Washington State University

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NiO2 XAS data
by Mehmet Nurullah Ates 07 May '13

07 May '13

Dear all; I am a grad student and my research is about investigation on advanced cathode active materials for lithium ion batteries. We need NiO2 (Ni4+) XAS data if you could provide us. I know couple websites that can allow us to download Ni3+ Ni2+ but could not find for the Ni4+. If you have any Ni4+ XAS data, we will appreciate for receiving the data, if not you can direct me to any website or person that I can acquire. Thanks a lot Best -- Mehmet Nurullah Ates Northeastern University-PhD Candidate Center for Renewable Energy Technology 317 Egan Research Center 360 Huntington Ave. Boston, MA 02115 617-373-5630 (Phone) 617-373-8949 (Fax)

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Problem with running Demeter
by Amitava D Roy 02 May '13

02 May '13

Hi Matt/Alexander/Chris, Thanks for all the suggestions. The fix wasn't as drastic as re-installation of the operating system, system restore on Windows 7 did the job. What I did was quite stupid. I will be more careful next time. Thanks, Amitava Amitava Roy J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices (CAMD) Louisiana State University, Baton Rouge, LA 70806

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Re: [Ifeffit] Problem with running Demeter
by Alexander Riskin 02 May '13

02 May '13

Dear Amativa, Bruce is right, Ccleaner messed up your system and, unfortunately, beyond repair. Ccleaner promises indeed to remove unused DLL's from your system but is very bad at guessing which DLL's are really obsolete and has a tendency to assume DLL's are unused instead of playing it safe. Therefore, this piece of software needs to be handled by an expert hand, or you butcher your system as you seem to have done. I know this because I made the exact same mistake 16 years ago after which my windows 98 didn't even boot up anymore, so I'm even surprised your pc is still running. The solution to this problem? Complete reinstallation of your OS, trying to manually repair is very complicated and time consuming. You will probably run into similar problems with other applications as well because of missing DLL's. regards, Alexander -- dr. ir. Alexander Riskin Doctor-Navorser IMO - Inorganic and Physical Chemistry T +32(0)11 26 83 94 | F +32(0)11 26 83 23 http://www.uhasselt.be Universiteit Hasselt | Campus Diepenbeek Agoralaan Gebouw D | B-3590 Diepenbeek Kantoor G1.94

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Re: [Ifeffit] Ifeffit Digest, Vol 123, Issue 3
by Eric John Peterson 01 May '13

01 May '13

Here you go... the low angle traces are the alignment scans done using the Ge220 monochromator ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Wednesday, May 01, 2013 1:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 123, Issue 3 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: Problem running JFEFF/FEFF9 on Windows 7 (Linda Lim) 2. Re: Problem with running Demeter (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 May 2013 12:01:15 -0700 From: Linda Lim <ywllim(a)stanford.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem running JFEFF/FEFF9 on Windows 7 Message-ID: <CALPaxYDE_9rDMFTLiAiEaXArWyZaMPQMOx=drz5xtrfj2=tAQQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Ross I had the same issue earlier as well, and it turns out that It is due to the latest Java update. It can be fixed by rolling back to the previous Java update. Cheers Linda On Wed, May 1, 2013 at 11:50 AM, Ross Devol <devol(a)wisc.edu> wrote: > I'm a new FEFF user, and I installed JFEFF and FEFF 9 on a computer with > Windows 7. I can load feff.inp files into JFEFF just fine, but when I click > "Save & Run," the Run window is blank and never shows any output. Has > anyone else had this problem? Does anyone know how to fix it? > > Thanks, > Ross DeVol > University of Wisconsin - Madison > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Problem with running Demeter
by Amitava D Roy 01 May '13

01 May '13

Dear Bruce, I am having this strange problem since I used CC Cleaner to clean up my computer. (This may be coincidental.) [cid:image001.jpg@01CE466F.10C0D470] The following is the output of the dartemis.log file: Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:The specified procedure could not be found 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\dartemis.bat line 23. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dartemis.bat line 23. I have uninstalled and installed Demeter several times but the problem remains the same. This happened just when I needed to use Demeter the most. Thanks in advance, Amitava Roy J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices (CAMD) Louisiana State University, Baton Rouge, LA 70806

3 2

Problem running JFEFF/FEFF9 on Windows 7
by Ross Devol 01 May '13

01 May '13

I'm a new FEFF user, and I installed JFEFF and FEFF 9 on a computer with Windows 7. I can load feff.inp files into JFEFF just fine, but when I click "Save & Run," the Run window is blank and never shows any output. Has anyone else had this problem? Does anyone know how to fix it? Thanks, Ross DeVol University of Wisconsin - Madison

2 1

ATOMS: Partial occupancies -how to edit .cif File
by Sanwald, Kai 24 Apr '13

24 Apr '13

Hi, I would like to fit the NiFe2O4 spinel structure to EXAFS data of mixed Ni/Fe-(hydro)xide films. However, ATOMS cannot deal with structures exhibiting crystal sites with partial occupancies. I know that this problem has been adressed to some extent on the mailing-list already in May 2012 (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-May/010544.html) and Bruce Ravel shortly outlined how to edit the .cif file in order to run ATOMS and FEFF6. Attached you find the NiFe2O4.cif file that I like to employ. I tried the following: 1. changed occupancy from 0.5 to 1 in line Ni1 Ni2+ 16 d 0.625 0.625 0.625 . 0.5 0 2. subsequently deleted line Fe2 Fe3+ 16 d 0.625 0.625 0.625 . 0.5 0 I got rid of the ATOMS warning concerning the partial occupancy but FEFF6 crashes due to atoms being postioned too closely to each other. I am pretty sure that my editing resulted in a change of the structure. I would be very glad if someone could explain to me in some detail how I need to edit the .cif. Thank you very much for your help. Best, Kai

4 3

background removal - spline range kmin
by Reagen Lan 23 Apr '13

23 Apr '13

Dear all, For removing the background from a spec with sharp white-line, I understand it is often to put larger value for kmin of Spline range in Athena. However, in my current case, there is a intensive XANES peak at c.a. 16ev after the white-line peak. Thus, should I input kmin in between these two peaks (see attached figure test1.png)? or increase kmin to avoid the second strong peak(attached figure test2.png)? The two conditions do give different chi(R). Please could some body advise? Thanks a lot! Best regards, Zhipeng

2 1

Re: [Ifeffit] ifeffit R-factor
by Matt Newville 18 Apr '13

18 Apr '13

Hi Sandra, On Sat, Apr 6, 2013 at 12:37 PM, Sandra Luber <s.luber(a)pci.uzh.ch> wrote: > Dear Matt Newville, > > I do some fitting with ifeffit using EXAFS data generated by feff. > I wonder how the R-factor is calculated. Unfortunately, > I have not found any definition yet. Would it be possible > that you write me how it is obtained? > This would be great. > > Thanks a lot. > > Best regards > Sandra Luber > The basic definition is R = Sum( |data - fit|^2 ) / Sum( |data|^2 ) The old Feffit document probably has the clearest definition, in its Chapter 5 (pages 16-20 of http://cars.uchicago.edu/~newville/feffit/feffit.pdf ). The definition and briefer explanations are also given in several of the tutorials on http://xafs.org/Tutorials. Thanks for reminding me to put this and related information into the Larch documentation! --Matt

3 4

L-edge soft X-ray data in Artemis and Athena
by Shoaib Muhammad 11 Apr '13

11 Apr '13

Hi, I am a research student and relatively new to XAFS. I have soft X-Ray L-edge data of Mn and Ni. Is it possible to process this data in Athena and then fit in Artemis like usual K-edge data? Thanks -- Shoaib

6 5

ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

3 2

ifeffit on Mac OS X
by Frank Schima 04 Apr '13

04 Apr '13

Hello list, I have created a port of ifeffit [1] on Macports [2] so that you can easily install ifeffit on Mac OS X. I have only run this myself on Mountain Lion (10.8), but I believe it built successfully on the Lion and Snow Leopard buildbots - so it should work there too. If anyone is interested in trying it, it is a two step process. 1. Install Macports [3]. 2. From a terminal window type the following: sudo port install ifeffit Feedback about how it runs would be appreciated. Cheers! Frank [1] <http://www.macports.org/ports.php?by=name&substr=ifeffit> [2] <http://www.macports.org> [3] <http://www.macports.org/install.php>

1 0

APS/IIT XAFS Summer School July 8 - 12, 2013
by Robert Gordon 01 Apr '13

01 Apr '13

Notice attached. "This XAFS summer school is a continuation of the week-long summer school offered annually at the Advanced Photon Source, and again the venue will be at IIT in Chicago. Course material will cover fundamental and practical aspects of X-ray Absorption Fine Structure Spectroscopy: sample preparation, experiment, theory, data analysis. One day of hands-on experiments will be carried out by participants at several APS beamlines, followed by a guided data analysis laboratory using Athena/iFEFFIT and other programs. Computers will be available for those participants attending without their own laptops. The target audience is graduate students, postdocs, and other scientists who are new to XAFS and want to use it in their own research. Space is available for up to 40 students. Instructors include: Dr. Steve Heald (ANL), Dr. Matt Newville (UChicago), Prof. Bruce Bunker (U Notre Dame), Prof. Carlo Segre (IIT), Prof. Grant Bunker (IIT), and a number of other experienced XAFS researchers also will participate. The cost of the course is $500 USD, which covers most meals. Students will be responsible for their own housing (available on and off IIT campus) and travel to/from their home institutions. IIT is readily accessible by car, cab, and CTA train from O’Hare and Midway airports. Free time will be available most evenings for participants to visit Chicago attractions such as Grant Park, the Loop, Millennium Park, Lake Michigan; music, architecture, art, theater; Chinatown, White Sox, Field Museum, Shedd Aquarium, Adler Planetarium, and Navy Pier, restaurants, and pubs. Please email bunker(a)iit.edu with subject line “2013 XAFS School” -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

1 0

anisotropic Debye temperatures in reciprocal-space calculations
by Van Der Veen, Renske M. 29 Mar '13

29 Mar '13

Dear FEFF users! I am looking into the use of the DEBYE card in order to calculate the EELS spectrum of graphite at ~800 K. Obviously, graphite is highly anisotropic, such that it would be unphysical to use a single Debye temperature. However, the effective in-plane (a,b axes) and out-of-plane (c axis) Debye temperatures are known for graphite (2500 and 950 K, respectively). I was therefore wondering whether it is possible in FEFF9 to specify two Debye temperatures for the two different crystallographic directions. I am calculating the (oriented) EELS spectrum of graphite in reciprocal space using the RECIPROCAL, LATTICE and ATOMS cards; see feff.inp file below. I am using FEFF version 9.05. In case the use of Debye temperatures is not possible in this way, could anybody recommend another way to take into account the Debye-Waller factors for an anisotropic material such as graphite? Thanks! Best regards, Renske van der Veen -- Dr. Renske M. van der Veen California Institute of Technology Arthur Amos Noyes Laboratory of Chemical Physics 1200 E California Blvd MC 127-72, Pasadena, CA 91125, USA Office: (+1) (626) 395 6530 Mobile: (+1) (626) 808 2635 **** TITLE graphite * C K edge energy = 284.20 eV EDGE K 0.0 CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 1 COREHOLE RPA LDOS -20 10 0.05 * this calculates the density of states EGRID e_grid -3 17 0.3 e_grid last 30 0.4 e_grid last 58 1 ELNES 200 # beam energy in keV 0 0 1 # beam direction in the crystal frame 10 5 # collection semiangle, convergence semiangle (in mrad) 200 1 # q-integration mesh : radial size, angular size 0.0 0.0 # position of the detector (x,y angle in mrad) FMS 7.0 2 EXCHANGE 0 1 0.7 SCF 5 RPATH 0.2 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 6 C 3 2 0.01 1 6 C 3 2 2 2 6 C 3 2 2 RECIPROCAL KMESH 5000 MARKER 1 LATTICE P 2.4612 0.86603 -0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 2.72546 ATOMS * this list contains 251 atoms * * x y z ipot tag distance 0.00000 0.00000 0.68160 1 C1 0.00000 0.00000 2.04479 1 C1 0.57735 0.00000 0.68160 2 C2 0.28868 0.50000 2.04479 2 C2 END

1 0

Demeter 0.9.16
by Bruce Ravel 29 Mar '13

29 Mar '13

Hi, I just tagged a new release of Demeter at https://github.com/bruceravel/demeter and made a link to the new Updater package for Windows at http://bruceravel.github.com/demeter/ This release fixes several issues that have bee raised in the last week or so. For details, see the change log at https://github.com/bruceravel/demeter/blob/master/Changes.org B -- 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

1 0

Possible bug in atoms files generation by Artemis
by Devender 29 Mar '13

29 Mar '13

Hi, I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for atoms. Previously, I was using only available option of FEFF6 style. When I tried to run atoms selecting FEFF 8, it generated atoms files but when I tried to run FEFF calculations it produced following errors. Error#1 " Unknown keyword: "EDGE" at line: EDGE L3" Error#2 "Unknown keyword: "exchange" at line: exchange" I worked around first error by replacing "EDGE L3 S02 1.0 "- which was generated by atoms when FEFF8 style is selected. with "HOLE 4 1.0" and deleting Exchange keyword from feff file. After making these edits in feff files, I was able to run FEFF without showing any errors. I have attached all the files with appropriate name. -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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Shifted data in Athena
by George Sterbinsky 27 Mar '13

27 Mar '13

Hello, I have attached an (D)Athena project with containing two groups, imported as a primary data set and a reference. The groups were therefore imported on the same energy grid. However, when plotted, the energy values of the data points for the two groups are clearly shifted with respect to each other. Can someone please explain the origin of this shift? Thank you, George

2 4

plotting
by Eva Vanamee 26 Mar '13

26 Mar '13

Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva On Mar 26, 2013, at 2:45 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. generating high res figures (Eva Vanamee) > 2. Re: generating high res figures (Scott Calvin) > 3. Re: generating high res figures (Jason Gaudet) > 4. Re: generating high res figures (Christopher Patridge) > 5. Re: generating high res figures (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Mar 2013 13:13:17 -0400 > From: Eva Vanamee <eva.vanamee(a)mssm.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] generating high res figures > Message-ID: <C2797F03-A481-47C5-8631-B43292F375B2(a)mssm.edu> > Content-Type: text/plain; charset=us-ascii > > Hi, > > I'm in the happy stages of making figures. > I'd like to know how to change figure legends, make high resolution figures from a fit, etc. > > For instance: > I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? > Can I change the figure legends? I used sample 1 and I want to give it a different name > Can I use special characters (e.g. Greek letters)? > Can I adjust the resolution for different formats (talk vs. publication)? > > I am running Demeter 0.9.9.9 under XP. > > Thanks in advance for the help! > > - Eva > > > > > ------------------------------ > > Message: 2 > Date: Tue, 26 Mar 2013 13:25:01 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] generating high res figures > Message-ID: <CCDBA9E5-8A56-4438-A0EC-E1A9B3F6CB45(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Eva, > > Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. > > --Scott Calvin > Sarah Lawrence College > > On Mar 26, 2013, at 1:13 PM, Eva Vanamee <eva.vanamee(a)mssm.edu> wrote: > >> Hi, >> >> I'm in the happy stages of making figures. >> I'd like to know how to change figure legends, make high resolution figures from a fit, etc. >> >> For instance: >> I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? >> Can I change the figure legends? I used sample 1 and I want to give it a different name >> Can I use special characters (e.g. Greek letters)? >> Can I adjust the resolution for different formats (talk vs. publication)? >> >> I am running Demeter 0.9.9.9 under XP. >> >> Thanks in advance for the help! >> >> - Eva >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 3 > Date: Tue, 26 Mar 2013 13:51:36 -0400 > From: Jason Gaudet <jason.r.gaudet(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] generating high res figures > Message-ID: > <CANMcWtM=dO9GR-jSMC--dXEPWojAZ-78N44mPrAnV5ujHtMAmw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > And to do this, use the Artemis Plot dialog box to generate the chart you > want (e.g. the data and fit in magnitude R-space), click the "Save Next > Plot to File" button at the very bottom of the dialog box, and click the > correct plot button at the top (e.g. R). This lets you save the plot as an > ASCII file. > > -Jason > > On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin <scalvin(a)sarahlawrence.edu>wrote: > >> Hi Eva, >> >> Demeter is not intended to be used to produce publication-quality figures. >> It's best to export the data, fits, etc., and then use a proper graphing >> program to generate figures. Even a spreadsheet will do in a pinch, >> although most of us use dedicated scientific graphing software. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Mar 26, 2013, at 1:13 PM, Eva Vanamee <eva.vanamee(a)mssm.edu> wrote: >> >>> Hi, >>> >>> I'm in the happy stages of making figures. >>> I'd like to know how to change figure legends, make high resolution >> figures from a fit, etc. >>> >>> For instance: >>> I saved the session file. Can I go back to a particular fit to make a >> figure or do I need to rerun it? >>> Can I change the figure legends? I used sample 1 and I want to give it a >> different name >>> Can I use special characters (e.g. Greek letters)? >>> Can I adjust the resolution for different formats (talk vs. publication)? >>> >>> I am running Demeter 0.9.9.9 under XP. >>> >>> Thanks in advance for the help! >>> >>> - Eva >>> >>> >>> _______________________________________________ >>> 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 >> >

6 6

generating high res figures
by Eva Vanamee 26 Mar '13

26 Mar '13

Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva

5 4

Re: [Ifeffit] Building ifeffit Mac Mountain Lion
by Matt Newville 23 Mar '13

23 Mar '13

Hi Jeff, Hope it's OK, but I'm CCing this to the ifeffit mailing list. I've officially abandoned support for the Fortran version of Ifeffit, but I know many people are still using it, so I'll try to give some pointers. I haven't tried building on 10.8 (but Larch works fine for me on it). On Thu, Mar 21, 2013 at 3:34 PM, Jeff Terry <terryj(a)iit.edu> wrote: > Hi Matt, > > I am trying to build ifeffit for Mac OS 10.8 (Mountain Lion). I have built pgplot and the cpg library manually but cannot build it with your script. > > I get the following error when building with the script. > > Do you have any suggestions as to what might be causing this or another way that I can link pgplot to ifeffit? > > Thanks, > > Jeff > > > gfortran -c -O2 -fPIC /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value 'BINARY' > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value 'BINARY' > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21: > > BLKOUT(0) = 254 > 1 > Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1). This check can be disabled with the option -fno-range-check > make: *** [gidriv.o] Error 1 > gfortran -u -Wall -fPIC -O -o pgpack /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > Undefined symbols for architecture x86_64: > "-Wall", referenced from: > -u command line option > ld: symbol(s) not found for architecture x86_64 > collect2: error: ld returned 1 exit status > make: *** [grfont.dat] Error 1 > = Cleaning up and preparing for test I think the last version of Ifeffi, from https://github.com/newville/ifeffit should work, at least to compile PGPLOT correctly. I've put most of the code I used to build Ifeffit on Mac OSX in the src/macosx directory on this repository: https://github.com/newville/ifeffit/tree/master/src/macosx Though, of course this makes many assumptions (such as, that gfortran and XCode are installed), and I really can't offer any support for these scripts and codes. Hope that helps, --Matt

4 4

Reduced chi square values versus F-tests for second shell fits
by Matt Siebecker 22 Mar '13

22 Mar '13

Dear All, Would it be recommended to compare reduced chi square (RCS) values from the fit of the second shell only? While fitting the second shell only, the differences between RCS values of different models can be greater than when including both the first and second shells in the fit. For example, the RCS values of model 1 and model 2 for fits of the first and second shells versus just the second shell are 45 and 18, and then 60 and 17, respectively. This to me indicates that fitting the second shell separately from the first gave me a slightly better description of the misfit in that R-range. Regardless of the fitting range the RCS values say model 2 improves the fit significantly. However, if I use an F-test to compare models while fitting the second shell only, I’ve found that the difference between the models is actually less important than when including both the first and second shells in the fit. For examples, the F-test values of model 1 versus model 2 for fits of the first and second shell versus just the second shell are P=0.047 and then P=0.113, respectively. This is perhaps caused by the small R-range and hence decreased Nind when fitting the second shell only. However, it also indicates to me that the F-test says perhaps one fitting model is not such an improvement on the fit as I thought it was based purely on the decrease in RCS value. I assume significant decreases in RCS values to be about >2x, and P <0.05 for the F-test. Should RCS values and F-tests for comparing fitting models only be used when fitting two shells together or can they be used when just fitting the second shell? Kind regards, Matt Siebecker

2 4

Core-Shell Spectroscopy session at Denver X-Ray Conference
by Carlo Segre 21 Mar '13

21 Mar '13

Hello All: This year we will once again have a core-shell spectroscopy session at the Denver X-ray Conference. The conference web site is http://www.dxcicdd.com/13/index.htm The conference organizers are accepting abstracts for talks and posters until April 5, 2013 (the web page says that submission is closed but it is really open for this specific session). Bruce Ravel and I are organizing the session and we would like to encourage you to submit your abstracts for talks and posters as soon as possible so that we can keep a yearly meeting where our community can present talks in North America. Denver is a nice centrally located venue where students can easily drive in from many places in North America (certainly from Chicago!) and save some travel costs. There are special student registration rates and there are also funds which students may apply for to defray expenses. I hope that you will participate and encourage your collegues in the field to do so as well. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0

(no subject)
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. * 1*. What is the ideal value of R- factor for any fit. 2. * 2. * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

2 1

questions related to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

1 0

questions regarding to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

1 0

controls and data acquisition workshop ot SRI 2013
by Bruce Ravel 13 Mar '13

13 Mar '13

Hi! This year's Pan-American Synchrotron Radiation Instrumentation Conference will be held June 19-21 in Gaithersburg, MD, USA, with satellite workshops on June 17 and 18. Here's the URL: http://pml.nist.gov/Meetings/SRI2013/index.html I am organizing Workshop #8 on June 18th. It will be on the topic of software for beamline controls and data acquisition. If you work in this area, please consider submitting an abstract. Please pass word about this workshop to your favorite beamline scientist or to the controls and acquisition people at your synchrotron. Thanks! Bruce -- 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

1 0

MBACK and Athena
by Bajamundi Cyril 12 Mar '13

12 Mar '13

Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure <Calibrate data> affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal

3 6

Theoretical calculation of Chi(k)
by John Farell 04 Mar '13

04 Mar '13

Dear Sir, I am trying to calculate the value of Chi(k) theoretically. I have taken Fe data. I need the values of scattering amplitude, phase shift at different energies. Where I could get those values ?.. Help me in this regard... Thanking you John

2 1

Calibration for Sb K edge
by Darren Dale 28 Feb '13

28 Feb '13

Hello All, I have the CHESS F3 beamline set up with a dispersive monochromator for XANES at the Sb K edge with ~1 eV resolution. I didn't find a reference spectrum for Sb in Hephaestus, and would like to contribute one. But first I would like to have a little more confidence in the energy calibration. Does anyone know if 30.491 keV corresponds to the inflection point of mu for Sb(0) (or if not, what energy does)? Alternatively, does anyone know the energy of the Sb(0) white line (ideally with a reference)? Thanks, Darren

1 1

Demeter 0.9.15
by Bruce Ravel 28 Feb '13

28 Feb '13

Hi! Today I released an update to Demeter and tagged version 0.9.15 it at GitHub. Windows users can download the updater package from http://bruceravel.github.com/demeter/ Source code installation instructions are near the end of that page. Windows users will notice a new download link for a documentation package. Simply download that package and double-click on it to install the Users' Guides for Athena and Artemis on your computer. If installing from source, the documents will be built and installed as part of the installation. There are a lot of swell new features and important bug fixes in this version. Some of the highlights are: * A fix for last week's report of problems with reference channels * Much improved performance by Athena once data is loaded * Direct links to document pages scattered throughout Athena and Artemis. If you have installed the documentation package, the local version will be displayed in a web browser. If the documentation package is absent, the programs will attempt to fetch the relevant document page from my github site. * Plucking points from the plotting window now works much more reliably For the full list, see https://github.com/bruceravel/demeter/blob/master/Changes.org For those following the development of Matt's Larch project, I have begun work on making Demeter use Larch rather than Ifeffit as its data processing backend. This is going well -- thus far, Athena can import data and do basic data processing using only Larch. Interaction with Larch is normally disabled. If anyone is interested in following along with that development more closely, let me know and I will write a wiki page about how to enable Larch support in Demeter. Regards, B -- 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

1 0

Merging data in Athena
by George Sterbinsky 28 Feb '13

28 Feb '13

I am writing to make you aware of what I believe to be a bug in (D)Athena. To demonstrate the problem, I have attached a project file containing two groups. Both groups have the same energy range but were measured with slightly different point spacings. Attempting to merge the two groups results in Athena excluding one of the groups from the merge "for being too short." Thank you, George

4 7

Peakfit tool - determination of width
by Gudrun Lisa Bovenkamp 22 Feb '13

22 Feb '13

Hey Bruce, I was wondering how the width in the peak fitting tool of Athena is connected to the real data. What I mean is: A gaussian peak with a width of 1 (eV ?) seems to have a FWHM of 2 eV. Is it possible that you mean with "the Gaussians (...) are unit normlized (...)" the width is actually "sigma" and the amplitude is actually "mu" in the pure formula? Thanks, Lisa

2 1

Error in second shell fit
by Devender 22 Feb '13

22 Feb '13

Hi, I am trying to fit Bi2Te3 exafs data using artemis. I am able to fit first shell (screenshot of fit is attached, I have also attached 'atoms' and 'feff' files for reference) but when I am trying to include second shell, I am getting the error (attached file- Fit_error.log). Error reads that- "The R effective for this path is well beyond the rmax value of its Data object." but I am already using Rmax of 6 A and Reff of these path are less than 5 A in my fit. I will appreciate if anyone can guide me or point me where I am making mistake. Regards, -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

5 17

Re: [Ifeffit] Importing Multiple Data Sets into Athena
by John Hayes 21 Feb '13

21 Feb '13

Hello, I am having some issues when importing multiple data sets into Athena. When I try to import more than one file at a time only the reference sample data from the first file are imported and the subsequent files do not import the reference data (only a straight line is imported). There is an error that is reported, and I have saved the error log [log.txt] and attached it in the zip file (as well as the dathena.log file and some sample spectra files). The spectra files are of the Mo K-edge and the reference is an Mo foil. These spectra were collected using the HXMA beamline, and as such, I am using the HXMA plug-in to import the data. The relevant columns for the reference are: col 2: energy col 6: I1 col 7: I2 I searched the archive and found what I think is a similar issue (link: www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03454.html) and hope I'm not over-reporting the error (sorry in advance if I am), but the previous report seemed somewhat different, in that there was an issue with the wrong edge being chosen for the test and ref data (best I can tell). I do have the work around of importing each file individually, so this is no more than an inconvenience, but I thought I'd report it and see if maybe someone had some up with a more elegant solution. I am currently using version 9.14 on a 64-bit windows platform. Thanks in advance for any advice or help the community can provide! -- John Hayes The Grosvenor Group Dept. of Chemistry University of Saskatchewan Two fish are in a tank. One turns to the other and says, "You man the guns, I'll drive."

4 8

Fwd: Re: Use of feff8 with D-artemis?
by Bruce Ravel 20 Feb '13

20 Feb '13

On Thursday, July 12, 2012 05:31:19 PM you wrote: > > I wonder why the new Artemis (from Demeter) is limited to feff6 or feff7 as > the old ifeffit can deals with feff8 and feff9. > > Is it a wish? When you published data using feff7, the reviewers first note > that you should have used more actual version. I would challenge a reviewer to come up with a reliable study demonstrating that Feff8 or Feff9 provides a statistically significant improvement to EXAFS analysis. Obviously, I am not saying that full multiple scattering, self-consistency, and the various potential improvements in Feff9 are not relevant to XANES calculations or to Feff's treatment of other spectroscopies. What I am saying is that it has not been rigorously demonstrated that those things have an impact on the calculation of the extended EXAFS such that the analysis is improved in a statistically meaningful way. In short, I find that such arguments from reviewers boil down to "Feff8 is 33% better than Feff6 because 8 is 33% bigger than 6!" > Is it planned that D-Artemis will work with feff8 too? > > I am using the other programs of Demeter but still have to stick to the old > Artemis as none of my files can be read by D-Artemis (always error due to > feff8 or feff9 files by importing old project) That said, there is no good reason that artemis should not be able to use Feff8 or 9 if you want to do so. I suppose that laziness is the best explanation for why it doesn't yet. The Atoms portion of Demeter writes Feff8 files. The Atoms portion of Artemis simply has the line of code for using that part of Demeter commented out. That's trivial to fix. Getting Demeter to use Feff8 instead of Feff6 is not a lot of work, but it is also not a trivial amount of work. I will put this at the top of my to do list. Given that I will soon be leaving for conferences in distant places on the globe, I probably won't be able to release a version of Demeter that uses Feff8 effectively until Spetember. B -- 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 ----------------------------------------- -- 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

3 4

phase correction
by wangshaofeng＠iae.ac.cn 20 Feb '13

20 Feb '13

Hi Bruce, How can I open the phase correction function in fitting using demeter athena and artemis? cheers, Shaofeng

3 5

Building perl wrapper for ifeffit on OS X Lion for Demeter
by Lyle Gordon 18 Feb '13

18 Feb '13

Dear Ifeffit experts, I am working on building Demeter on OS X. In the process I am trying to build ifeffit, including the perl bindings on OS X. However, upon following the instructions I get a range of errors when I try to build the perl bindings. The main ifeffit libraries appear to build just fine. This might be something trivial as I don't have much OS X experience. Following the (slightly out of date) instructions... cd ./wrappers/perl perl Makefile.PL see output: http://pastebin.com/TGzVjrpi sudo make install see output: http://pastebin.com/qkMYhYsP Any help would be greatly appreciated. Thanks very much, Lyle -- Lyle Gordon Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Cook Hall 2036 Evanston, IL 60208 Tel: (847) 491-3584 Mobile: (847) 400-4071 http://lylegordon.ca

2 1

Hephaestus crash
by Darren Dale 18 Feb '13

18 Feb '13

Hello all, I'm working on getting my ifeffit/demeter environment together, following the instructions at http://bruceravel.github.com/demeter/pods/installation.pod.html . When I run hephaestus, select F'/F'', and then select any element in the table, the program bails and I get some feedback in the terminal: Can't use string ("Demeter") as a HASH ref while "strict refs" in use at accessor Demeter::devflag (defined at /home/darren/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter.pm line 100) line 8. Sometimes, "<F> line 29." is appended to that error message. I'm running the forthcoming kubuntu 13.04. Any ideas how I can improve my install? Thanks, Darren

2 1

demeter windows download
by Darren Dale 17 Feb '13

17 Feb '13

Hello Bruce, All, I wanted to install Demeter on my windows computer this morning. I followed links to instructions at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in turns links to https://github.com/bruceravel/demeter/downloads . Unfortunately, github recently discontinued the downloads service, so that is not a functioning link anymore. Is there a new location available to find the installer? Thanks, Darren

3 2

problem of paths calculation
by wangshaofeng＠iae.ac.cn 17 Feb '13

17 Feb '13

Hello Bruce, I am using demeter-atoms to calculate paths using a cif file (see attachment). When I run feff to calculate paths, there is a dialog box saying "You have defined ipot #1 but not used it in the atoms list". If I change the core atom from Ni to S, the calculation can be done. So how to solve this problem. Shaofeng

2 2

Athena doesn't start - Larch server not running
by Ivan Stijepovic 16 Feb '13

16 Feb '13

Dear Bruce and other people in the list, I have just installed Demeter from the git on Ubuntu 12.04 using instructions given by Dave Hughes ( https://gist.github.com/waveform80/3959252) Everything went fine during installation but then I tried to start Athena using *dathena* command from the terminal and I got this message: Demeter says: Uh oh! You have requested using Larch, but there is no Larch server running! Then I installed Larch (with some problems during installation, but that is different story) and again tried starting Athena with the same result. When I tried starting Larch in a server mode with *larch -r* command it didn't offer a possibility to start Athena in the same terminal window. Then I opened a new tab in the terminal and just typed *dathena* and the GUI appeared. Now, I have two questions: 1. Do I have to start Larch server every time like this before using Athena or is there some other solution for this? 2. I tried Artemis without Larch server running and didn't get the error message. Is Artemis independent from Larch or are there some problems that might occur later? -- Best wishes, Dr Ivan Stijepović Department of Materials Engineering Faculty of Technology University of Novi Sad Bul. cara Lazara 1 21000 Novi Sad Serbia tel: +381 21 485 3750 fax: +381 21 450 413 e-mail: ivan.stijepovic(a)gmail.com

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Re: [Ifeffit] Demeter administator mode.
by Bruce Ravel 13 Feb '13

13 Feb '13

On Tuesday, February 12, 2013 04:19:55 PM you wrote: > Dear Bruce, > I am researcher from ICIQ, Spain and we produced some data at ALBA > synchrotron light facility in Barcelona ,Spain. My question is about > Demeter software in administrator mode. It works in only admin mode so it > can’t be used to normal users in our institute workgroup. Is there any > solution to this problem ? Atul, First off, I am CCing my answer to the Ifeffit mailing list, which is the appropriate venue for questions about the software. You can join the mailing list at http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Secondly, I provide instructions for submitting a useful and actionable bug report at http://bruceravel.github.com/demeter/pods/bugs.pod.html The advantage of following those instructions is that, including sending the log file with the initial report, it expedites my ability to understand the problem you are having. Finally, I think I recognize the problem you are having. Demeter attempts to write to "%APPDAtA%\demeter" where %APPDATA% is typically C:\Users\<username>\AppData\Roaming\ on Win 7 and C:\Documents and Settings\<username>\Application Data\ on Win XP. In the last release, I attempted to fix a problem whereby "%APPDAtA%\demeter" was not created at the time of installation. Athena or Artemis would then try to write to that location and fail because that folder did not exist. My "solution" in the last release was not correct and I hope to fix that in the upcoming release. The likliest solution to your problem is to create that folder by hand for each user, then try running the programs again. If that does not work, then please report back *to* *the* *mailing* *list* and I will again try to figure out what the problem is. Regards, B -- 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

2 2

Molybdenum nitride spectrum for Mo k and/or Mo L3 edge
by Soma Chattopadhyay 12 Feb '13

12 Feb '13

Hello Was wondering if anybody has a Mo k edge and/or L3 edge exafs spectra/spectrum (preferable with Mo foil in reference) for the compound molybdenum Nitride and can send me data. Will appreciate very much. Thanks Soma

1 0

Basic question in normalization and background removal
by Bajamundi Cyril 08 Feb '13

08 Feb '13

Hello, I have here a very basic XANES data processing. I am but a novice in this XANES analysis. In Bruce's lecture "Athena: Data processing I<mms://diamstream02.diamond.ac.uk/xafs-2011-2>" posted in the Diamond Light Source website, he used the Fe_lepidocrocite.000 example to show how background removal and normalization is done. For the normalization range he used the range 150 - 742.610 because his original photon energy scan range is quite long [ Emin: -200 and Emax: 800]. However, say that your original scan range is only short e.g. within the range Emin : -30 to Emax: 80, such that you don't see the non-wiggly range and you only see the a short portion of the post edge range, how does one set the normalization range for this data? Since I'm very new to XANES analysis, I keep second-guessing my choice of normalization range. Your patience for answering this simple question will definitely help me in moving to the actual fingerprinting analysis that I need to do with my sample. Many thanks. Warm regards, Cyril [cid:image004.jpg@01CE05DE.B8F89320] [cid:image007.jpg@01CE05DE.B8F89320]

4 5

XAS position in Industry
by Shelly Kelly 06 Feb '13

06 Feb '13

Dear XAS Community, We have a position open at UOP LLC, A Honeywell Company to support our XAS/tomography group. The position description can be found under Req number 00213183 at http://www.careersathoneywell.com/en/home. Please apply through the web site. Thank-you, Shelly Kelly

1 0

Open post-doc position in Korea
by Deok-Yong Cho 04 Feb '13

04 Feb '13

Dear Ifeffit users: To whom interested in post-doc position in Korea: A two-year contract post-doc position is open in the Center for Functional Interfaces of Correlated Electron Systems (CFI-CES), Institute for Basic Science (IBS), located in Seoul National University, Seoul, Korea. We expect he/she will perform spectroscopic analysis including IR spectroscopy (Spectroscopic ellipsometry and FT-IR) at the institute and synchrotron experiments such as soft/hard x-ray absorption spectroscopy and XAFS analysis for new functional oxide materials (mainly strongly-correlated electron system). Please find enclosed document for more details. Best Regards, Deok-Yong Cho Spectroscopy team in CFI-CES, Institute for Basic Science (IBS), Seoul National University

1 0

Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel)
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear Bruce, The patch worked, I was able to configure the plugin and import the binary data. I changed the default columns, otherwise some files were imported scrambled: Energy :1 (that one was ok) I0 : 6 (that one was ok) Narrow (I imported I_Trans instead): column 7 Trans (I imported Total_fluo instead): column 8 Wide (I imported S K-alpha fluo instead): column 9. Thanks for the quick and helpful reply. Raoul ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: January 30, 2013 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 119, Issue 31 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. Look for paper about WL (Gudrun Lisa Bovenkamp) 2. Re: Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel) 3. Re: Look for paper about WL (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 30 Jan 2013 04:27:35 +0100 From: "Gudrun Lisa Bovenkamp" <bovenkamp(a)physik.uni-bonn.de> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Look for paper about WL Message-ID: <web-12374983(a)be2.uni-bonn.de> Content-Type: text/plain;charset=iso-8859-1; format="flowed" Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa ------------------------------ Message: 2 Date: Wed, 30 Jan 2013 10:03:49 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena Message-ID: <1855179.1CSfgNSBKa(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, January 30, 2013 02:17:35 AM Raoul-Marie Couture wrote: > I'm trying to import binary files generated at BM X15B of NSLS, at the S > K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) > does not import the columns 7-10 containing the Io, It, IF and S > Kalpha-fluo. It only imports the first few columns and they don't contain > the information I need. If I ask Athena to import more columns it crashes > and exit. When I use the utility at BM X15B to convert the binary files in > simple text files, Athena does not recognize the text files as data file. > I'm I doing something wrong ? Any idea how to solve this problem ? I have > attached a binary file, its text translation (using the utility available > at BM X15B), and a screenshot of what happens when I import a binary file. The problem seems to be one of column selection. I am suspicious that a detail of how the data are saved to the binary files may have changed since I wrote the X15B plugin many years ago. Attached are two file that you should be able to drop in place on top of your current installation. Put both files in C:\strawberry\perl\site\lib\Demeter\Plugins The file "X15B.pm" wil replace the version of the file that is already there. The file "x15b.demeter_conf" is new. Make sure that you save them with filenames *exactly* as written above. For instance, if you let Outlook save "X15B.pm" as "X15B.pm.txt", it won't be recognized by Athena and everything I say below won't work. The new file will allow you configure the X15B plugin. In the Plugin Registry page, rightt click on the X15B entry. See: http://bruceravel.github.com/demeter/aug/other/plugin.html#athena%27splugin… The variables set using that configuration file, tell Athena which columns from the original data file (also which columns from the text conversion using the beamlilne tool) should be preserved when Athena converts the binary blob to an ascii column file. Most of the columns are filled with zeros, which is why the plugin wants to discard those columns. Side note: Athena deals very pooly with ascii data file that don't have the energy in the first column, which is why it has trouble reading the text file from the beamline tool. I would like to hear back from you about how this works out. If it works well for you, then it will be included in the next release of the software. If there are still problems -- then I need to know. B PS: It is possible that the "x15b.demeter_conf" file has the columns for narrow and wide backwards. Let me know if you think that's the case. I am writing this email without wandering down to X15B to ask Paul the details. -- 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

1 0

Look for paper about WL
by Gudrun Lisa Bovenkamp 30 Jan '13

30 Jan '13

Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa

2 1

Help with importing binary files from NSLS BM X15B in athena
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear all, I'm trying to import binary files generated at BM X15B of NSLS, at the S K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) does not import the columns 7-10 containing the Io, It, IF and S Kalpha-fluo. It only imports the first few columns and they don't contain the information I need. If I ask Athena to import more columns it crashes and exit. When I use the utility at BM X15B to convert the binary files in simple text files, Athena does not recognize the text files as data file. I'm I doing something wrong ? Any idea how to solve this problem ? I have attached a binary file, its text translation (using the utility available at BM X15B), and a screenshot of what happens when I import a binary file. Thanks for the help Regards, Raoul Couture <https://sites.google.com/site/couturerm/>

2 1

Different R-factor values
by Christopher Patridge 25 Jan '13

25 Jan '13

Hello List, I know that Horae is no longer supported but I had quick question about the R-factor. I search the mailing list and found this post from 2006 concerning different R-factors in the fit log I have a question about Artemis log file. I noticed that two r-factors are > reported in the log file. One is in the fifth line and it is called > 'R-factor' and the other one is under the data set fitting conditions and > it is called 'r-factor for this data set'. They have in general different > values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps <http://cars9.uchicago.edu/%7Enewville/feffit/feffit.ps> on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. I am reviewing some older analysis projects from artemis and just wanted to know which R-factor more accurately describes the misfit? I suspect the average over the k weights values since this was adopted in Demeter? Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

4 6

(D)Artemis and (D)Athena crash - perl not responding
by Matthias Filez 24 Jan '13

24 Jan '13

Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: <http://helpdesk.ugent.be/e-maildisclaimer.php> http://helpdesk.UGent.be/e-maildisclaimer.php

3 5

Artemis crash and data set limit
by Christopher Patridge 23 Jan '13

23 Jan '13

Hi List, My project file crash about five minutes and I found the dartemis log file attached before opening the program again which I hope will explain the problem. is there a limit to the number of datasets in Artemis? Thanks, Chris -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

2 1

self absorption correction
by sumitk＠barc.gov.in 22 Jan '13

22 Jan '13

Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Sumit -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O).

5 5

Multiple Atom.inp in Feff
by Christopher Patridge 17 Jan '13

17 Jan '13

Hi all, Is there a way to remove data sets, feff.inp, or atoms.inp from the main window list? I know this question was raised at one of Bruce's XAFS seminars at Diamond. I looked at the current Demeter List of Things to Do and did not see specifically removing them, just reorganizing lists. I guess it is not really a bug, just annoying, but for some reason, probably user error and impatience, my artemis file saved several "atoms.inp" windows in the Feff list and now I cannot get rid of them. Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

2 3

S02 question
by Eugenio Otal 15 Jan '13

15 Jan '13

Hi all, I have a question about S02 measurement in samples for CN calculation. By example, If I have an oxynitide, LaTiO2N, Can I use TiO2 as standard for S02 even the Ti in LaTiO2N is coordinated to O and N? In a more extreme case, is possible to use metals? Which are the recommendations and limits? Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Prof. Dr. Eugenio H. Otal UNIDEF - CONICET - CITEDEF San Juan Bautista de La Salle 4397. Villa Martelli (B1603 ALO) Buenos Aires Argentina TEL: +54 11 4709-8158. FAX: +54 11 4709-8241. and UTN - Santa Cruz Regional Faculty Av. Inmigrantes 555 Río Gallegos (9400) Santa Cruz Argentina TEL: +54 2966 429173 FAX: +54 2966 42-9173 E-mail: eugenio.otal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 2

k-range question & R-factor
by Christopher Patridge 15 Jan '13

15 Jan '13

Hello Users, I was looking for an opinion about the chi(k) signal in a set of data I am analyzing. Brief background, this is a set of in-situ XAS data collected at the Fe K edge from a working electrochemical cell at a range of potentials during charge; I did not collect the data. I suspect the feature at ~ 8 angstroms-1, although present in all the spectra is noise or glitch and wondered if I am being overly cautious? My conservative range ( k = 2-7 and R = 1-2) really constrains the model Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me some flexibility. In a multiple dataset fitting, is the R-factor of the whole set just the average or total mismatch across all the datasets or it calculated another way? Working towards happiness, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

3 3

Re: [Ifeffit] Ifeffit Digest, Vol 119, Issue 19
by Denis Testemale 15 Jan '13

15 Jan '13

Hello Chris. - I don't have an answer regarding the R-factor. - Noise or glitch: how does I0 look like? Is the glitch you suspect visible in I0 at this energy? If you're refering to the feature that points downwards at 8A-1, it actually shifts with the spectra (I can see two groups of spectra in this k-range) so a glitch seems doubtful to me. Can you tell more about the collection of data (transmission, fluorescence, thickness of the sample, temperature, etc.)? By looking at the data, and if you confirm that I0 is glitch-free, I would be more suspicious about the data in the range 10-14A-1 than this 8A-1 feature. Cheers denis > Today's Topics: > > 1. k-range question & R-factor (Christopher Patridge) > > > > Hello Users, > > I was looking for an opinion about the chi(k) signal in a set of data I > am analyzing. Brief background, this is a set of in-situ XAS data > collected at the Fe K edge from a working electrochemical cell at a > range of potentials during charge; I did not collect the data. I suspect > the feature at ~ 8 angstroms-1, although present in all the spectra is > noise or glitch and wondered if I am being overly cautious? > > My conservative range ( k = 2-7 and R = 1-2) really constrains the model > Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me > some flexibility. In a multiple dataset fitting, is the R-factor of the > whole set just the average or total mismatch across all the datasets or > it calculated another way? > > Working towards happiness, > > Chris Patridge > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

1 0

improving fitting
by Zhaomo Tian 11 Jan '13

11 Jan '13

1 0

Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15
by Monson, Todd 09 Jan '13

09 Jan '13

When making my own feff input file, how should the data be delimited. When looking at existing feff input files I see a mixture of different spaces and tabs and am unsure how I should separate coordinates, ipots, tags, etc. Thanks, Todd -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, January 09, 2013 11:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15 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: Larch 0.9.17 available for download and testing (Matt Newville) 2. Re: Larch 0.9.17 available for download and testing (Yu-Sheng Chen) 3. self absorption correction (sumitk(a)barc.gov.in) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jan 2013 16:07:28 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Message-ID: <CA+7ESbq8w5MOAFu-rRJUi71WpVDjoNXG6VOpmiD_xryztVFQdQ(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Bruce, Again, sorry (ever so slightly -- the skiing was great!!) for the delay. I think (not 100% sure) I understand have solved the trouble with wxmplot on ubuntu. On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems. I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution. With these changes, I could successfully install wxmplot and larch on an Ubuntu. I think that must be the same problem you were seeing, but I'd be happy to hear your experience. --Matt On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > Matt, > > I am having some troubles getting Larch installed on one of my Ubuntu > machines. "sudo python setup.py install" complains about wxmplot > being missing. OK, I did > > bruce@lachesis [xraylarch] > sudo -E easy_install wxmplot > sudo: unable to resolve host lachesis.bnl.gov > Searching for wxmplot > Best match: wxmplot 0.9.10 > Processing wxmplot-0.9.10-py2.7.egg > wxmplot 0.9.10 is already the active version in easy-install.pth > > Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg > Processing dependencies for wxmplot > Finished processing dependencies for wxmplot > > and tried again. > > bruce@lachesis [xraylarch] > sudo python setup.py install > sudo: unable to resolve host lachesis.bnl.gov > Checking dependencies.... > == Cannot Install Larch: Required Modules are Missing == > wxmplot is REQUIRED > > Please read INSTALL for further information. > > OK. I cloned a copy of wxmplot from your github repo and installed it > by hand with no problem. However, same result when trying to setup > xraylarch. > > Any advice? > > Thx, > B > > -- > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 2 Date: Tue, 8 Jan 2013 23:21:54 +0000 From: Yu-Sheng Chen <yschen(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Message-ID: <63D4F9008F0BD04FAC515D20F0CC6A46437D035A(a)CARSMAIL2.CARS.APS.ANL.GOV> Content-Type: text/plain; charset="us-ascii" Hello Mark. I think you got 3 shifts this coming run. Yu-Sheng **************************************** Yu-Sheng Chen, Ph.D. Center for Advanced Radiation Sources The University of Chicago c/o APS/ANL 9700 S. Cass Ave. Bldg. 434 D Argonne, IL 60439 USA Tel: +1 630-252-0471 Fax: +1 630-252-0460 EMail: yschen(a)cars.uchicago.edu -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Tuesday, January 08, 2013 4:07 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing Hi Bruce, Again, sorry (ever so slightly -- the skiing was great!!) for the delay. I think (not 100% sure) I understand have solved the trouble with wxmplot on ubuntu. On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems. I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution. With these changes, I could successfully install wxmplot and larch on an Ubuntu. I think that must be the same problem you were seeing, but I'd be happy to hear your experience. --Matt On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > Matt, > > I am having some troubles getting Larch installed on one of my Ubuntu > machines. "sudo python setup.py install" complains about wxmplot > being missing. OK, I did > > bruce@lachesis [xraylarch] > sudo -E easy_install wxmplot > sudo: unable to resolve host lachesis.bnl.gov > Searching for wxmplot > Best match: wxmplot 0.9.10 > Processing wxmplot-0.9.10-py2.7.egg > wxmplot 0.9.10 is already the active version in easy-install.pth > > Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg > Processing dependencies for wxmplot > Finished processing dependencies for wxmplot > > and tried again. > > bruce@lachesis [xraylarch] > sudo python setup.py install > sudo: unable to resolve host lachesis.bnl.gov > Checking dependencies.... > == Cannot Install Larch: Required Modules are Missing == > wxmplot is REQUIRED > > Please read INSTALL for further information. > > OK. I cloned a copy of wxmplot from your github repo and installed it > by hand with no problem. However, same result when trying to setup > xraylarch. > > Any advice? > > Thx, > B > > -- > > 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 > _______________________________________________ > 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: 3 Date: Wed, 9 Jan 2013 10:28:17 +0530 From: sumitk(a)barc.gov.in To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] self absorption correction Message-ID: <335f18a7175b0c8a9d74662ec1c2dfe7.squirrel(a)bts.barc.gov.in> Content-Type: text/plain;charset=UTF-8 Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Sumit -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O). ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 119, Issue 15 ****************************************

3 2

Larch 0.9.17 available for download and testing
by Matt Newville 08 Jan '13

08 Jan '13

Hi Folks, I'm happy to announce the first full release of Larch, the next generation of Ifeffit. This includes a kit for source installation and a binary installer for Windows. A primitive Larch GUI is included that provides a command-line interface and a browser / help system for data in the Larch session. Essentially all the EXAFS and XANES functionality of Ifeffit 1,2 is reproduced in Larch, with several significant improvements. The current version (0.9.17) should still be considered "beta" software in that bugs should be expected, but Larch is now ready for detailed "field-testing" and use. It you're using Ifeffit for scripting (that is, not using the GUIs Athena, Artemis, SixPack, or Prestopronto that call Ifeffit), you should start using Larch now. Several months ago, I described the goals and status of Larch (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-June/010586.html) which is still accurate. Since then, the biggest effort has been in documentation, finishing some of the details of Feffit() fitting, and testing. Larch is available at http://xraypy.github.com/xraylarch/ and http://cars.uchicago.edu/xraylarch/ Any feedback on any part of Larch is welcome. I am especially interested in hearing reports from people trying the Windows installer -- I've tested it only on 3 Windows7 machines. I also reiterate my plea for people to get involved in the development and extension of these tools. A main motivation for Larch's implementation and design was to make it very easy to add new features and experiment with new algorithms and methods for analysis. If you're interested in helping Bruce or I develop these codes, please let us know. Some of you may have noticed that support for the Ifeffit 1.2 series has been very poor recently, including the fact that building for Mac OS X has fallen far behind. With this release of Larch, I'm very happy to formally end support for Ifeffit 1.2. I'm willing to use, and help others use, the older versions of Ifeffit, Athena, etc, but there will be no more releases or bug fixes for the Ifeffit 1.2 series. The code is available if someone else wants to maintain it. Thanks, --Matt Newville

3 4

Correction for self absorption in fluorescence mode XAFS data
by sumitk＠barc.gov.in 08 Jan '13

08 Jan '13

Hi, I am analyzing a Eu-L3 edge XAFS data measured in fluorescence mode. My question is regarding the appropriateness of the self absorption correction of the data. I am aware that by supplying chemical formula along with other requisite informations (angle, etc.) I can execute the self absorption correction in Athena. Also, by comparing data measured in transmission and fluorescence modes the correction can be achieved. I have only six scans of fluorescence mode measurement and by applying the correction to these scans in Athena, I have observed enhanced amplitude in mu(E) data. I am not able to see how to check the appropriate of correction. An Athena file is attached to look into. Expecting the community to help, Sumit Sumit Kumar Scientific Officer Radioanalytical Chemistry Division Bhabha Atomic Research centre, Mumbai India. Ph: +91-22-2559 4093. -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O).

2 1

Deglitching in Athena 0.9.14
by Lyle Gordon 07 Jan '13

07 Jan '13

Dear Bruce and Ifeffit users, I just installed the latest version of Demeter, 0.9.14, on my Windows 7 computer. I tried to deglitch a dataset in x(E). Upon clicking "choose a point" the window pops up telling me to double click in the gnuplot window. I can select a point but there doesn't appear to be any feedback in the UI about which point was selected until after clicking ok. Then after ok I get a large "E". It is difficult to tell sometimes exactly which point was selected as the E is quite large. I guess this is turning into more a "bug" report/feature request, but I felt the previous interface in Athena 0.8.054 gave much more feedback during the deglitching process of removing points. I was wondering if there was a setting that could change back to the old style or if this was a decision based on the limitation of gnuplot/perl. I hope this submission is alright for the mailing list. In the future I could post these "issues" on github. Thanks very much, Lyle

2 1

Using this mailing list effectively
by Zhaomo Tian 07 Jan '13

07 Jan '13

4 3

Using this mailing list effectively
by Zhaomo Tian 07 Jan '13

07 Jan '13

1 0

Using this mailing list effectively
by Ravel, Bruce 06 Jan '13

06 Jan '13

> I think you are really right, I am in too great a hurry that I lost my patience to set a time to learn basics quietly. Thanks for reminding. > And for my second question, could you give me some suggestion too? Mr. Tian, Asking questions is an art. Anyone can barf out sentences that end with a question mark, but asking questions that will prompt a useful and constructive discussion is a subtle and skillful business. Both Chris and I tried to tell you that in our earlier responses, but apparently there is a need to be more explicit. You are doing some things wrongly. I say this not to be mean and not to diminish you, but because I spend a lot of my professional time teaching people how to do XAS. It is important to me that people practice our craft well. This mailing list is a powerful tool to that end. When it is used well, the people who solicit help from this list profit significantly. When it used poorly, the people who volunteer their time answering questions become frustrated and the person asking the questions goes away with nothing. So ... here are three comments: (1) I am frustrated that you are not using the most recent version of my software. You are using a version of Artemis that is about 4 years old. I have no intention of continuing support for the older versions of my software. (2) Your second question refers to 4 sets of data, which you posted to the mailing list not in an Athena project file, but in an Artemis project file. That's odd. It would be much easier to examine the data in the form of an Athena project file. Many of the issues in your recent line of questioning referred to S02. As Scott pointed out, the evaluation of S02 is related to the determination of the normalization and background. If you want people to help you with your actual question, it would be prudent to provide the data in a form that allows examination of all steps of the data processing. My point here is that you simply must think about how you pose your question -- that includes thinking hard about how to present your data to the person whose help you are soliciting. (3) Your first email on the topic of these Cu films was somewhat misleading in that your initial complaint seemed to be about a strange measure of coordination number on a Cu foil. In that email, you gave a hint as to the actual form of the data, but scant information about how the data were measured and none about how the data were processed and analyzed. After prompts from Scott and other, you have provided a bit more information about your actual measurement, but not enough to actually know what's going on. As long as your line of questioning remains vague as to the details of the problem, the best you can expect are vague answers of the sort that you have already received. Since I am suggesting that you be more thoughtful and explicit in how you communicate here on the list, it is important that I do the same. Here is an example of what I consider to be a well-asked question. My example comes from a posting that I myself made to the WxPerl mailing list last year. WxPerl is the programming tool I use to make the GUIs Athena, Artemis, and Hephaestus. At the time, I was having a problem getting menus to post properly when making right-mouse clicks in various places in Athena. While the question is rather technical and I don't expect a non-programmer to follow all the details, it is still instructive: http://www.nntp.perl.org/group/perl.wxperl.users/2011/03/msg7929.html Note first that in five brief lines of text I summarized my problem. I then gave a complete example of how someone else could reproduce my problem on their own computer. I then explained both what I expected to happen and what actually happened. The point here is that I took the time to condense my question into a form that the people at the other end could understand and address with a minimum of effort. Sure enough, I got useful responses from 2 knowledgeable (and, no doubt, very busy) people. Mr. Tian, to the extent that it seems like I am singling you out for special criticism, I sincerely apologize. But you have been posting to this mailing list rather often of late and you are doing so in a way that is probably not getting you the sort of results you would like to see. I understand that this is an English language mailing list and that it is difficult to be as expressive in another tongue as you can be in your own. (I really do understand that -- I have suffered through learning two other languages in my life. It really is hard.) But you have to try if you want to get useful results. B

1 0

Re: [Ifeffit] Problem downloading windows installer for Demeter
by Ravel, Bruce 06 Jan '13

06 Jan '13

Javier, Thanks for reporting this problem. This is related to a recent change in how GitHub handles large binary files. I thought I had fashioned a solution. Turns out that I was mistaken. I have come up with a different solution for distributing the Installer and Updater files and I've updated the links at http://bruceravel.github.com/demeter/ Please go back and try again. Sorry for the inconvenience. Also, please use the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) for this sort of thing rather than emailing me directly. Cheers, B ________________________________________ From: Javier Alonso [jalonsomasa(a)gmail.com] Sent: Sunday, January 06, 2013 7:59 AM To: Ravel, Bruce Subject: Problem downloading windows installer for Demeter Dear Dr. Ravel, Firts, I'd like to personally thank you for Demeter: it really helps me a lot with my XAS data analysis. And now the problem: I'm trying to download the windows installer for Demeter from the webpage: http://bruceravel.github.com/demeter/ but I keep receiving the same error message again and again: Error: blob is too big I think this is something related to Github and the limit of file sizes, but I haven't been able to find an alternative downloading site or similar. Thanks in advance, Javier Alonso -- Javier Alonso Masa Departamento de Electricidad y Electrónica Facultad de Ciencia y Tecnología. Universidad del País Vasco 48940 Leioa(Spain) http://www.gmmmt.net/ Phone: +34 94 601 5400 / +34 695325749

1 0

(no subject)
by Zhaomo Tian 05 Jan '13

05 Jan '13

1 0

(no subject)
by Zhaomo Tian 04 Jan '13

04 Jan '13

3 2

Cu fitting with and without CO adsorption
by Zhaomo Tian 04 Jan '13

04 Jan '13

1 0

Understanding effect of dopant using ARTEMIS
by Devender 03 Jan '13

03 Jan '13

Hi, Happy new year! I am a graduate student in material science at RPI. I am interested in understanding doping of elements in bismuth telluride (Bi2Te3). By understanding I mean, where it is going (interstitial sites or replacing any element in crystal) and what it is doing (changing band structure, electronic states etc.). For that, we carried experiments at beamline X19A at BNL couple of months ago. On primary analysis using ATHENA, we see some indications of interestitial site occupancy (attached is ChiR vs radial distance plots). To confirm this hypothesis, I am thinking of simulating spectra using ARTEMIS. Plan is- 1) First, match spectra of bismuth telluride with standard 2) Add dopant at interstitial sites and other possible sites, and simulate spectra to see if it matches with experimental spectra. I am seeking help/guidance on following, 1) Getting started with ARTEMIS- I have started learning ARTEMIS but still don't understand a lot of parameters. I will appreciate if someone can send me tutorials on recent version of ARTEMIS, feff tutorials on some websites are for command line version. I don't understand many of the parameters in ARTEMIS and any detailed tutorial will really help. I don't want to tweak parameters without understanding them completely. 2) Input atom file for ARTEMIS- I have cif file for Bi2Te3, how can I import that in "ATOMS" for making input file for ARTEMIS? Once I can create Bi2Te3 crystal using ATOMS, I think I can add Cl (dopant) to simulate other spectra easily. I would love to hear any feedback on approach too. Thanks and regards, Devender www.rpi.edu/~devend/

2 1

background subtraction process in Athena
by Zhaomo Tian 03 Jan '13

03 Jan '13

3 2

Demeter 0.9.14
by Bruce Ravel 02 Jan '13

02 Jan '13

Happy New Year everyone! Today I am releasing version 0.9.14 of Demeter and of the software built from it, including Athena, Artemis, and Hephaestus. I just tagged the 0.9.14 release at my GitHub page https://github.com/bruceravel/demeter I have built an Updater package for the Windows users. The Updater can be downloaded from http://bruceravel.github.com/demeter/ If you have not currently running version 0.9.13.1, you MUST download and install the Installer package before installing the new Updater. This release incorporates A LOT of changes. See https://github.com/bruceravel/demeter/blob/master/Changes.org If you requested a feature or reported a bug in the last 3 months, I believe you will find your issue addressed in this release. Most significantly, I believe that I have fixed the MinGW DLL conflict issue that was discussed starting at the end of November. I'd like to thank Greg Hutchings for his help tracking down that problem and testing my solution. Cheers, B PS: My hope for the next release is to begin supporting Matt's Larch project, which he announced here about two weeks ago. That will be a work in progress for a while to come, but the adventuresome may be interested in jumping on that boat as soon as possible! -- 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

1 0

copper 1st shell coordination number
by Zhaomo Tian 02 Jan '13

02 Jan '13

2 1

copper 1st shell coordination number
by Zhaomo Tian 02 Jan '13

02 Jan '13

2 1

(no subject)
by Zhaomo Tian 02 Jan '13

02 Jan '13

1 0

Demeter installation (under Ubuntu)
by Denis Testemale 01 Jan '13

01 Jan '13

Dear Bruce and mailing list members, I'd like to report about the installation of the Demeter package under Ubuntu where everything went smoothly but a few glitches... ## Background: Ubuntu 12.10 Quantal, 3.5.0-19-generic with everything up to date as of today (December 18th). Demeter 0.9.14 (pulled from git today). I have Horae package installed and running (from Carlo's repos). I followed specific Ubuntu instructions at https://gist.github.com/3959252 (Dave Hughes' installation guide) ##First, one comment. You need to have the package gnuplot-x11 installed. For some reason, it was not installed in my case (although gnuplot was). This lead to many error messages during the './Build test' loop, and obviously the impossibility to plot anything when running (D)athena/artemis/hephaestus. At that time I did not think to try the change of the plotwith variable (gnuplot -> pgplot) as discussed in a previous ifeffit thread. I since reinstalled Ubuntu and this time installed gnuplot-x11 before Demeter. ##Then, a possible bug. It is reproducible everytime: - I launch Dathena from the command line without specifying the name of the project I want to open - I try to open a project (an old style Athena project) from the GUI (for example located at /home/denis/pathtothefolder/athena.prj) - I get an error message (a pop-up window, the terminal is quiet) saying '/home/denis/athena.prj is not readable', i.e. it looks for my file in my home folder and doesn't take into consideration the path to the file I input in the 'import data' dialog. - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ then it works. - a workaround is: 'dathena /home/denis/pathtothefolder/athena.prj' In the case of Dartemis, it is a bit different: - if I try to open an old-style Artemis project through the dedicated old style import module (say, /home/denis/pathtothefolder/artemis.apj), there is a message at the bottom of the main Dartemis window saying: '/home/denis/artemis.apj is not an old style fitting project file'. Again it misses the complete path to the file. - if I try to open an old-style Artemis project through the 'open project of data' module, Dartemis crashes saying (in the terminal): Can't open($fh, '/home/denis/artemis.apj'): Aucun fichier ou dossier de ce type at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Files.pm line 89 Actually, the crash may not be a bug as I am trying to open an old Artemis project through the bad channel obviously, but notice that the path to the file it refers to is again wrong. ## I must add that my first installation of Demeter (before I reinstalled Ubuntu) was global (not following the non root specific commands of Dave Hughes' installation guide) and I already had this problem. Let me know if you want me to try different things to track the problem down. Many thanks. Cheers Denis -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

3 3

The degeneracy and the coordination number
by Zhaomo Tian 26 Dec '12

26 Dec '12

5 4

Re: [Ifeffit] Novice FEFF user question
by Joshua Kas 21 Dec '12

21 Dec '12

Hi Melissa, You will need to set the FMS radius, which is blank at this point as seen in your screenshot. You should also set the SCF radius which is also blank. I would start with FMS 7.0 and SCF 5.0 and you can make them larger to check convergence. Another thing that is a bit strange in your calculation are the options after the XANES card. I would start by leaving these blank, so that the default energy grid is used. Josh Kas Message: 2 > Date: Fri, 21 Dec 2012 16:56:05 -0500 > From: Melissa Menard <mmenard81(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Novice FEFF user question > Message-ID: > <CA+Rj7Q9UmQ0O0FH210GSoAp+FfRSjtvWK9BjmFshrmkq= > 7foBw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am new to FEFF and I have a small problem. I'm trying to produce a XANES > spectra of Cu (from the examples). I cannot seem to obtain the pre-edge > region in my result. I have attached a screen shot. Could you tell me how > to calculate the area before E0, i.e. from -50 to 50 eV. > > Thanks > Sincerely > > -- > M Menard, Ph.D. >

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Novice FEFF user question
by Melissa Menard 21 Dec '12

21 Dec '12

I am new to FEFF and I have a small problem. I'm trying to produce a XANES spectra of Cu (from the examples). I cannot seem to obtain the pre-edge region in my result. I have attached a screen shot. Could you tell me how to calculate the area before E0, i.e. from -50 to 50 eV. Thanks Sincerely -- M Menard, Ph.D.

1 0

Per-data set R-factor
by Lyle Gordon 21 Dec '12

21 Dec '12

Dear iffefit users, I am using the latest version of Demeter/Artemis to fit some EXAFS data. I'm running Win 7 64. I found in Horae that when I fit multiple datasets it would output the R-factor for each dataset in the fit. I would really like these values in the newest version. I found on the todo list (https://github.com/bruceravel/demeter/blob/master/todo.org) [ ] per-data set R-factor reporting in log file is turned off. Is there a simple way to turn this "on"? If not I guess I can calculate it by hand from the Re/Im terms of the R space data and fit. To that end, if I have a few datasets it is tedious to export the data/fit files for each sample. Is there an automated way to export this data? Thanks very much, Lyle -- Lyle Gordon Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Cook Hall 2036 Evanston, IL 60208 Tel: (847) 491-3584 Mobile: (847) 400-4071 http://lylegordon.ca

2 1

How to refine the float
by Zhaomo Tian 21 Dec '12

21 Dec '12

2 1

How to refine the float
by Zhaomo Tian 20 Dec '12

20 Dec '12

2 1

Re: [Ifeffit] Demeter installation (under Ubuntu)
by Denis Testemale 19 Dec '12

19 Dec '12

Hello Bruce. There are no special characters only letters, numbers, and underscores. To be sure, I tried by placing the athena projects in ~/temp with the same result. Actually, I played a little bit more, and the behaviour is really strange: - consider the home folder /home/denis (I'll write ~ in the following) and a subfolder ~/A - I place an old style athena project in ~: named athena.prj - start dathena - open ~/athena.prj in dathena. It works. - cp athena.prj A/athena.prj - open ~/A/athena.prj in dathena. It works. - rm ~/athena.prj - reopen ~/A/athena.prj in dathena. It says: "/home/denis/athena.prj is not readable" - cp ~/A/athena.prj ~/. - reopen ~/A/athena.prj in dathena. It works. - and finally, I replace ~/A/athena.prj by another athena project (different), i.e., cp ~/some_random_athena_project ~/A/athena.prj - reopen ~/A/athena.prj in dathena. No error message BUT the project it opens is the old one, not the new random one I replaced the original one with... An additional info: the result of this sequence is the same if I let dathena run between each step ((but close the projects CTRL+W) or if I close (CTRL+Q) dathena at every step. What do you think of my Xmas gift Bruce? :-) Cheers denis Le 18/12/2012 19:54, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > ------------------------------ > > Message: 2 > Date: Tue, 18 Dec 2012 13:47:32 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter installation (under Ubuntu) > Message-ID: <3657129.uFgO795gez(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Hi Denis, > > As always, thanks a million for your feedback. This kind of thing has > a profoundly positive impact on the quality of the package. I am > really grateful. > > The gnuplot-x11 dependency is a good catch. Thanks. > > Unsurprisingly, I have no problems opening files on my computers. So > we need to figure out what is happening on yours that is not happening > on mine. My first suspicion involves character sets. > >> - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ >> then it works. > What is "pathtofolder"? Specifically does it contains any accented > characters, ess-zets, eastern characters or anything else involving > unicode? > > B > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

2 1

Beryllium XAFS in proteins
by grant bunker 18 Dec '12

18 Dec '12

Gina - measuring Be in proteins is extremely difficult and probably unprecedented, but it may be possible to substitute another element that is chemically similar and probe that instead. For example, often metalloenzymes remain functional under such substitutions, e.g. if you substitute a Mn or a Co in a Ca site. The covalent radius of Be is very small, so substituting Ca might not be feasible without excessively distorting the site, but Aluminum isn't far off, and might work. Of course Aluminum itself isn't easy because of its low k-edge, but it may be feasible. If a heavier element (Ca or heavier) could be made to substitute and retain the functionality/properties you are studying, it might be a suitable probe. good luck! Grant Bunker On Dec 18, 2012, at 3:19 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: Beryllium and EXAFS (Erik Farquhar) > 2. Larch 0.9.17 available for download and testing (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Dec 2012 12:50:30 -0800 (PST) > From: Erik Farquhar <efarq(a)yahoo.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Beryllium and EXAFS > Message-ID: > <1355863830.4845.YahooMailNeo(a)web141002.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > A bit unrelated to the question at hand, but regarding #5, yes, people do neutron PX.? The focus?is almost entirely on locating hydrogen atoms (e.g. for protonation state), so I wonder what?the neutron PX guys?would say about looking for a Be atom. The downside is that you usually need?quite large crystals compared to X-ray PX and long data collection times. > ? > Erik > > > ________________________________ > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: Erik Farquhar <efarq(a)yahoo.com>; XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tuesday, December 18, 2012 1:39 PM > Subject: Re: [Ifeffit] Beryllium and EXAFS > > > Just to stir the pot a little more: > 1.??? ALS has some beamlines which can go down as far as Li.? Work has been done on Li, but only on concentrated stuff. > 2.??? The sample is probably really dilute in Be.? The signal will be pathetic. > 3.??? Radiation damage will be a major issue, especially with X-ray Raman, which is a highly inefficient technique.? Even LHe cooling doesn't solve that problem. > 4.??? Are there model compounds available for proposed local structures of the Be center?? You'd need that to have any hope of making sense out of Be XANES. > 5.??? Is there such a thing as neutron PX?? That might see the Be. > ??? mam > ? > ----- Original Message ----- >> From: Erik Farquhar >> To: XAFS Analysis using Ifeffit >> Sent: Tuesday, December 18, 2012 5:32 AM >> Subject: Re: [Ifeffit] Beryllium and EXAFS >> >> >> To add to Matt's last paragraph, you might also consider beamline 6-2 at SSRL (http://www-ssrl.slac.stanford.edu/beamlines/bl6-2/) as they do a fair amount of work with proteins and have an X-ray Raman setup. I think the beamline scientist occasionally?posts to this list. >> >> >> Good luck, >> Erik >> >> >> -- >> Erik Farquhar, Ph.D. >> Case Center for Synchrotron Biosciences >> Brookhaven National Lab >> NSLS, Building 725A-X3 >> Upton, NY? 11973 >> efarquhar(a)bnl.gov >> +1-631-344-8174 >> >> >> >> ________________________________ >> From: Matt Newville <newville(a)cars.uchicago.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tuesday, December 18, 2012 7:52 AM >> Subject: Re: [Ifeffit] Beryllium and EXAFS >> >> Hi Gina, >> >> On Mon, Dec 17, 2012 at 5:23 PM, Clayton, Gina <ClaytonG(a)njhealth.org> wrote: >>> Hi there >>> >>> I am trying to find out more about EXAFS. I am a protein crystallographer. >>> >>> >>> I want to identify the environment of a beryllium ion in the protein, I work with,? of which I have a crystal structure.? EXAFS was recommended as a good technique for identification of the beryllium site and species. The beryllium is an acidic pocket of the protein surrounded by oxygens from the protein, likely covalently bound. However I have had? zero result finding a beam line that can tune their setups to the Be edge at 111 eV. Also some EXAFS users say that EXAFS technique would be good for working out the environment of the Be but some say it would not . In particular? I have been advised that? Be EXAFS would not be useful since? the Be? EXAFS signal would have unacceptable interference from the carbon K-edge at 285 eV and the oxygen K edge signal at 535 eV. >>> >>> Would EXAFS work or something in a similar vein? Or, for instance,? could the acidic pocket be identified using EXAFS, by measuring the oxygens (instead of the Beryllium) using the protein with and without beryllium? >>> >>> >>> Thank you so much for any advice. >>> >>> Gina >> >> As you and as the person who advised you suspect, you face a number of >> challenges: >> >> 1.? The extremely low energy (111 eV).? You might be able to find a UV >> source or x-ray beamline that can reach this energy , but often such >> work is done in vacuo, and so may not be suitable for proteins.? Using >> electrons (from a TEM, say) might be possible too -- these can >> sometimes do C and N edges either directly or looking at Electron >> Energy Loss (send in an electron of high energy E1, and look for >> electrons of energy E1 - E, and scan the analyzer for the loss energy >> E through the absorption edge).? Again, electron probes may not be >> what you want for your proteins. >> >> 2. The C K-edge will limit your signal to "only" 175 eV.? I would say >> to not worry so much about this limitation.? You'll really be >> measuring NEXAFS (near-edge X-ray absorption ....)? but that's OK. >> People measure the B, C, N, and O K edges, all facing the same >> problem, especially for the O K edge: our planet is more or less >> covered with the stuff ;).? These spectra tend to be very rich and >> sensitive to ligands. >> >> 3. Not much (zero?? I can almost believe that!) literature on Be XAFS. >> This is unfortunate because most NEXAFS is measure and compare to >> known spectra.? I think that might mean you have to spend effort to >> building up a spectral library for Be in organic phases. >> >> I think trying to measure the O K edge with and without Be is nearly >> hopeless.? All the X-ray spectroscopies average equally over all the >> atoms of the absorbing species.? In addition all the spectra are >> grossly the same (a step function from 0 below the edge to 1 above the >> edge).? These make it difficult to see changes below about 1%.? ? So I >> think you would just have too high of an O::Be ratio to see anything >> useful. >> >> One option to consider is using X-ray Raman scattering >> (http://en.wikipedia.org/wiki/X-ray_Raman_scattering).? Here, one hits >> the sample with high-energy X-rays (say, 10 keV), which are highly >> penetrating for reasonably sized protein sample.? One analyzes an >> energy loss (again, E1 - E, where here E1 is around 10 keV) to get the >> edge of interest.? I'm familiar with (been involved with) studies on >> B, C, and O using this technique (all in solids, mostly at high >> pressure).? See, for example,? S. K. Lee, et al "Probing of bonding >> changes in B2O3 glasses at high pressure with inelastic X-ray >> scattering",? Nature Materials 4, pp 851-854 (2005), and also the work >> of Simo Huotari.? ? I'm not aware of anyone doing Be K-edge this way, >> but it should definitely be possible. For the work I've been involved >> with, Be would be challenging because there are other excitations in >> solids that appear around 100 eV.? I believe that effect would be far >> suppressed in a protein, though I'm not sure. >> >> That's somewhat more exotic than straightfoward XAFS,, but it might be >> the best chance for measuring Be in a protein.? ? I'm not sure I know >> any beamlines that do X-ray Raman on proteins, but I'd suggest APS >> beamline 20-ID or ESRF beamline as places to start.? ? The next >> questions would be "how many Be atoms are in your protein?", and "how >> much material do you have?".... >> >> Hope that helps, >> >> --Matt Newville >> >> _______________________________________________ >> 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 >> >

2 1

Beryllium and EXAFS
by Clayton, Gina 18 Dec '12

18 Dec '12

Hi there I am trying to find out more about EXAFS. I am a protein crystallographer. I want to identify the environment of a beryllium ion in the protein, I work with, of which I have a crystal structure. EXAFS was recommended as a good technique for identification of the beryllium site and species. The beryllium is an acidic pocket of the protein surrounded by oxygens from the protein, likely covalently bound. However I have had zero result finding a beam line that can tune their setups to the Be edge at 111 eV. Also some EXAFS users say that EXAFS technique would be good for working out the environment of the Be but some say it would not . In particular I have been advised that Be EXAFS would not be useful since the Be EXAFS signal would have unacceptable interference from the carbon K-edge at 285 eV and the oxygen K edge signal at 535 eV. Would EXAFS work or something in a similar vein? Or, for instance, could the acidic pocket be identified using EXAFS, by measuring the oxygens (instead of the Beryllium) using the protein with and without beryllium? Thank you so much for any advice. Gina NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

6 8

plotting backends in Demeter
by Bruce Ravel 18 Dec '12

18 Dec '12

Hi, This afternoon I noticed that someone who goes by the handle "khuonggit" posted a question at David Hughes' gist about installing Demeter on Ubuntu. https://gist.github.com/3959252 I hope he is reading this mailing list. khuonggit asked: I am beginner in EXAFS. I tried to install Demeter in Ubuntu 12.04 64 bit following the guidance here and the installation was successful. However, when I tried to open (d)athena and import some data, the default plotting backend is PGPLOT, not GNUPLOT. Could you please show me how to change it to GNUPLOT ? Good question. In the time since khuonggit posted that question, I have modified the build script to attempt to detect the presence of gnuplot and modify Demeter's configuration accordingly. Hopefully, this will become a non-issue in the future. The plotting backend can be set by hand at any time in any of the GUI programs by editing the preferences. In Athena, choose "Preferences" from the main menu. In Artemis, choose "Edit preferences" from the file menu. In Hephaestus, click on the Configure icon at the bottom left. Once at the preferences tool, select "Plot" then "plotwith". Select "gnuplot" then click "Apply and save". B -- 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: [Ifeffit] How to do with diffraction peak
by Matt Newville 15 Dec '12

15 Dec '12

Hi Matthew, On Wed, 12 Dec 2012, Matthew Marcus wrote: > > On 12/12/2012 8:03 PM, Matt Newville wrote: >> Hi Matthew, Bruce, All, >> >> Sorry for not being able to join this discussion earlier. I agree >> that having glitch-free data is preferred. But I also think it's OK to >> simply remove diffraction peaks from XAFS data -- you're just >> asserting that you know those values are not good measurements of >> mu(E). I don't see it as all that different from removing obvious >> outliers from fluorescence channels from a multi-element detector -- >> though that has the appeal of keeping good measurements at a >> particular energy. > > That's kind of my point. The standard methods, which require uniform > tabulation, cause you to fill gaps in data by interpolation. > Effectively, you're claiming knowledge of data for which you don't have > knowledge. Better to use a method which preserves > agnosticism about the bad data. The method I described for deglitching with > reference scalers tries to preserve what information > you do have by allowing you to ignore some channels. That only works if > there are 'good' channels to serve as references. I would say that identifying a point as an invalid measure of mu(E) and simply not excluding it in the analysis is OK: it is claiming knowledge that we didn't measure that point well. I just don't see it as much different from claiming that outliers in the set of fluorescence intensities are not good measures of fluorescence intensity. You might argue (I would agree) that with multiple measures of fluorescence you can determine outliers more rigorously. But I would also say that then the best thing to do then is to not simply remove outliers but to take the average AND standard deviation of the samples and include both in the analysis. A glitch would then not be removed, but would be reflected by having a less certain value for that energy point. >> I'm not sure that "slow FT" versus "discrete FT" is that important >> here, though perhaps I'm missing your meaning. My vies is that The >> EXAFS signal is band-limited (finite k range due to F(k) and 1/k, and >> finite R range due to F(k), lambda(k), and 1/R^2), so that sampling >> on reasonably fine grids is going to preserve all the information that >> is really there. > > Again, FFT requires a uniform tabulation of data in k-space, which is > generally secured by interpolation. Traditionally, this has > been histogram interpolation, which tries to take into account the > possibility of having multiple data points within one of the new > intervals in k. That method, however, has to 'make up' data when there isn't > any in one or more intervals. > > Actually, there are three possible tiers of speed. There's FFT, there's > discrete FT done the slow way by computing the sums as > they appear in the textbook (possibly good if you want a funny grid in R > space), and then there's what I propose. I agree with your larger point that we can definitely afford the CPU cycles to do better analysis than use something simply because it is Fast. I'm not sure that a slow discrete FT would be significantly different than an FFT, though. I think (but am listening...) that the continuous v discrete FT is like classic audiophile snobbery about the superiority of analog over digital music. With sufficient sampling and resolution and dynamic range in the signal, the difference has to be trivial. I'm willing to believe that a digital recording has less dynamic range, but I'm also willing to believe that this is swamped by my stereo and ears (and I mostly listen to mp3s through cheap headphones these days, so I clearly am not buying a tube amplifier anytime soon...). But for EXAFS, we know the limits of the signals in k and R (say, 50 Ang^-1 and 25 Ang for extrema), and so can choose samplings that definitely over-sample enough to not cause significant artifacts. There can be dynamic range issues (especially with standard pre-amplifiers and VtoF converters), but I think this is a slightly separate issue from "the glitch problem". Interpolation methods are definitely worth discussing and studying. I'm not sure that the energy values that happened to have been where the monochromator was stopped for a measurement of mu(E) are more sacred or a better sampling of the first shell of an EXAFS spectra than a set of energies interpolated from those measurements to be on uniform k grid, provided the the original data isn't woefully undersampled. With a typical step size of 0.05Ang^1 you can easily miss several points and still accurately measure distances up to 5 or probably even 10 Angstroms. >> I do think that having richer window functions and spectral weightings >> would be very useful. You could view chi(k) data with glitches ias >> wanting a window function that had a very small value (possibly zero: >> remove this point) exactly at the glitch, but had a large value (~1) >> at nearby k-values. >> >> Another (and possibly best) approach is to assign an uncertainty to >> each k value of chi. At the glitch, the uncertainty needs to go way >> up, so that not matching that point does not harm the overall fit. > > A window function which went to 0 in the glitch region is tantamount to an > assertion that chi(k)=0 there, which is generally not so > and is probably a lot worse than the error you make by even the lamest > interpolation through the glitch. The uncertainty makes more > sense, except that if you filter data, the noise spreads out in a correlated > manner over adjacent regions. Also, the tacit assumption > of an uncertainty-based method is that the noise is uncorrelated within the > high-uncertainty region. That said, I can imagine that > this is one of those methods that works better than it has any right to. I think of the window as weighting of measurements to consider, and that a weight of zero is applied to data with infinite uncertainty. I don't think of chi(k) as zero outside the window range (say, below kmin or above kmax), just that we don't want to consider that in the analysis. Again, I think the better thing would be to have an uncertainty for each value of chi(k), and propagate that through the analysis. > Now, in my proposed system, how would you fit filtered (q-space) data? The > first step is to do the very slow FT (VSFT) on the input > data with no interpolation. This leads to a set of sines and cosines which > replicate the data. I would then apply the window and > do the back-summation of all those sines and cosines at the given points. > This will undoubtedly introduce some artifacts near > the edges of the deleted regions simply due to our ignorance of what the data > really do in there. Next, in each fit iteration, I would > evaluate the model function at each point, then do the VSFT and filtering > exactly as had been done on the data, which causes the fit to > have the same artifacts. Since the VSFT and filter operations are linear, it > should be possible to pre-compute a kernel which relates the > values of unfiltered data to those of filtered data. This would be a matrix > of size Np*Np with Np=# of points. Using the kernel instead > of evaluating gazillions of trig functions would be reasonably fast; I > suspect that ifeffit does a similar trick. Similarly, fitting in > R-space would be accomplished by computing the VSFT on data and model > function. > > Yes, I know I talk a good game. Unfortunately, I'm too swamped to attempt > implementation. Also, I'd have to reinvent a number of > very well-engineered wheels to do it. I hear you! I'm interested in pursuing "more advanced weightings and transforms", but don't have much time to spend on such things these days, so development is slow.... >> Larch has a separate Transform class used for each dataset in a fit - >> this includes the standard FT parameters and fit ranges. It is >> intended to be able to do this sort of advanced windowing (and in >> principle, advanced weighting too). Currently (I'd be ready for a >> release but am commissioning our new beamline and am hoping to post a >> windows installer by the end of the month) this has "the standard >> XAFS window functions", but one can create their own window functions >> (for k- and/or R-space) with suppressed points/regions, etc, and use >> them as well. I have to admit I haven't tried this, but it was >> definitely part of the intention, and should work. My hope is to >> extend this to include some wavelet-like weightings as well. >> > What is Larch? Is it a replacement for ifeffit? By 'class' do you mean > object as in OOP? > "And now for something completely different. The larch." - Monty Python > mam Yes, Mostly yes, and, Yes, you get the reference exactly ("How to recognize different types of trees from quite a long way away, Number 1: The Larch"). http://xraypy.github.com/xraylarch/ Another wide-open appeal: I'd love help in implementing improvements like these (better windows, comparing continuous v discrete transforms, using wavelets, etc), and think work like this would be publishable. There are several other improvements I'd like to see, such as generating Feff Paths on-the-fly, and so forth. Essentially all of Larch is in python so that it's very easy to modify and add features like this. The available numerical libraries for python are plentiful and well-maintained. It's also easy to add wrappers for C and Fortran code if that is needed..... --Matt

2 4

merging data
by George Sterbinsky 14 Dec '12

14 Dec '12

Hello, I am observing some behavior in (D)Athena that I do not understand, and I was hoping someone could explain it to me. I have attached a project file to illustrate my question. The first two groups in the file have been normalized such that mu(E) and norm(E) are identical. I then merged these groups in mu(E) and norm(E), also in the file. Since mu(E) and norm(E) are the same for the groups, I would expect the data merged in mu(E) and norm(E) to also be identical, but it is not. While it is clear that merging in mu(E) is averaging the groups, it seems merging in norm(E) is not. So what is merging in norm(E) doing? Thank you, George

2 2

How to do with diffraction peak
by Zhaomo Tian 13 Dec '12

13 Dec '12

6 14

Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 13
by jiahui 12 Dec '12

12 Dec '12

Hi Bruce, Thank you very much for the effort. jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 12 December 2012 22:17 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 13 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: How to do with diffraction peak (Bruce Ravel) 2. Re: How to do with diffraction peak (Anatoly I Frenkel) 3. Re: Ifeffit Digest, Vol 118, Issue 6 (Bruce Ravel) 4. Re: How to do with diffraction peak (Dr. Dariusz A. Zaj?c) 5. Re: How to do with diffraction peak (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Dec 2012 13:03:46 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <8927581.5aRJTKJtsK(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, December 12, 2012 09:49:45 AM Matthew Marcus wrote: > Here's one last trick that I used to use when I used a plastic > scintillator at NSLS and didn't have a spinner. WARNING - this is > painful! I used to tape a piece of Polaroid film to the face of the > detector, run through a scan, develop the film, see where the white > spots were, and put Pb tape on the detector at those spots. Told you it was painful! These days, I suspect the painful part is *finding* polaroid film! :) B -- 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 ------------------------------ Message: 2 Date: Wed, 12 Dec 2012 18:04:00 +0000 From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <545F89325F51764C902D37B42C9F4D531363A77F(a)YUWEXCPM12.yuad.uds.yu.edu> Content-Type: text/plain; charset="iso-8859-7" (For masochists only): I still have Matthew's plastic scintillator in my cabinet at the NSLS, so if anyone is willing to try this trick with the original hardware, let me know. Anatoly ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Matthew Marcus [mamarcus(a)lbl.gov] Sent: Wednesday, December 12, 2012 12:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How to do with diffraction peak Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner. WARNING - this is painful! I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots were, and put Pb tape on the detector at those spots. Told you it was painful! Aside from that, I think Bruce is right - you're screwed with 1-channel data, especially if the Bragg peaks are broad and/or come in the XANES region. If you have to take data without a spinner or multi-element detector, the trial-and-error method of changing the sample orientation often works to shift the Bragg peaks away from sensitive parts of the spectrum to where you don't mind too much losing some points. I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract the polynomial). I suspect that the peak shapes aren't 'nice' enough for that to work reliably. The shapes of the tails, for instance, would be influenced by the angular divergence of the beam onto the sample and into the monochromator and any strain. mam On 12/12/2012 7:28 AM, Bruce Ravel wrote: > On Tuesday, December 11, 2012 04:08:03 PM Zhaomo Tian wrote: >> I got XAFS data for Ag with CO adsorption( using Ag K edge), Ag is >> thin film~300nm deposited on Si/SiO2 substrate. But in the original >> ?(E) spectra, from 25894-26044eV, four obvious diffraction peaks >> appear( I attached the file), and I guess they will influence the quality of fitting. >> Is there anyone who knows how to deal with these diffraction peak? >> Will it be corrected by smoothing or changing some origin data points >> in the original file? I want the modification that will not destroy >> data analysis later. > > You have received some decent advice on how to post-process your data > to minimize the effect of the diffraction peak. I think it bears > mentioning that not all prblems are best solved after the fact in > software. Some problems should be addressed as the data are measured > or even beforehand. > > I see from the data file you sent that you were at beamline 10C at > Pohang. It is hard to tell for certain from the data file or from the > website, but it seems as though you were using a PIPS detector to > measure your fluorescence XAFS. > > This is an experimental setup can be a difficult one to combine with a > sample that diffracts. The sort of PIPS commonly used at an XAS > beamline tends to be of a very large surface area. That means that > the likelihood of some diffraction peak from the sample hitting the > detector during the measurement is pretty high. In fact, it happened > 4 times for you. That means you have a lot of data points to > deglitch, were you to follow Kicaj's advice. Because you used a PIPS > rather than a multi-element detector, you don't have the option of > following any of Matthew's (excellent) advice. > > I hate to say it, but I think you are screwed. The best you can do is > deglitch as best you can. Because you will be removing so many points > from the data, you will introduce substantial systematic error into > the data set that remains. I don't really see what you can do about > that at this late date. > > So, what might you do the next time you visit the synchrotron to > obtain better data? In fact, there are number of things that you can > consider at the stages of sample preparation or of data collection. > > 1. You don't say a lot about the sample or its substrate. Perhaps you > have a reason that the substrate *must* be crystalline. Perhaps > not. Putting your film on an amorphous substrate would obviate the > problem of diffraction from the substrate. That may be your best > bet. > > 2. The large size of the PIPS detector is a contributing factor to the > problem. Simply using a detector with a smaller surface area > reduces (but certainly does not eliminate!) the likelihood of > diffraction peaks hiiting it. Moving the detector farther away > from the sample would serve the same purpose. Of course, doing so > would also serve to reduce your count rate, thus reducing the > quality of your data. There is a cost to everything! > > 3. Use the 13 element Ge detector instead of the PIPS. Then you can > simply eliminate channels hit by Bragg peaks or do the > post-processing trick Matthew described. > > 4. At my beamline, we have users almost every cycle who measure stuff > on crystalline substrates. Our favorite trick is to mount the > sample on a spinner (e.g. http://dx.doi.org/10.1063/1.1147815) At > my beamline, we actually attach the sample the sort of small DC fan > that is used to cool electronics. Inexpensive, simple, and > effective! By keeping the sample constantly in motion, the energy > at which the Bragg condition is met is constantly changing. This > serves to reduce the effect of the Bragg peak by a few orders of > magnitude by spreading it out in energy. Usually, it can be made > smaller than chi(k), resulting in analyzable data. > > The bottom line is that you have the sort of problem that I think > needs to be solved up front rather than after the fact. > > I know that's not helpful right now, but hopefully it will be the next > time you go to the beamline. > > Cheers, > B > > > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Wed, 12 Dec 2012 13:53:23 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6 Message-ID: <2296463.dEQb5rDBsc(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Jiahui, Thanks again for the bug report. Your CIF file exposed a rather subtle bug in the code that parses CIF files. It will be fixed in the next release -- hopefully before the end of the month. Cheers, B On Monday, December 10, 2012 11:16:14 PM jiahui wrote: > Hi Bruce, > > I am a windows user. The two log file(Artemis and Atoms) and one of > the CIF files I used are attached to this email. Please let me know if > you need more information, > > > > Hi Dan, > > I use Mercury to open the CIF file then save as another CIF file as > you suggested. The new CIF file can be read by (D)Artemis with an > warning message basically says there're some problem with this file > and some possible ways to solve the problem(s). > > I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. > This version can read the CIF files. I ran atoms and FIFF on it. Then > save the file. It could be opened by (D)Artemis without problem. > > Thank you very much for your help and solutions, > > > Jiahui > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 10 December 2012 18:00 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 118, Issue 6 > > 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. Help: Artemis closes without error message when open .cif > file (jiahui) > 2. Re: Help: Artemis closes without error message when open .cif > file (Bruce Ravel) > 3. Re: Help: Artemis closes without error message when open.cif > file (Daniel Whittaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Dec 2012 15:42:27 -0000 > From: "jiahui" <qijiahui.uk(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Dec 2012 10:48:21 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open the crystal structure file in *.cif format, both > > (D)Atoms and (D)Artemis will close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open the crystal structure file in *.cif format, both > > (D)Atoms and (D)Artemis will close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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 ------------------------------ Message: 4 Date: Wed, 12 Dec 2012 23:09:29 +0100 From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <50C90099.902(a)ifj.edu.pl> Content-Type: text/plain; charset=UTF-8; format=flowed W dniu 12-12-12 18:49, Matthew Marcus pisze: > I have never tried fitting peak shapes to the Bragg peaks (say, a > Lorentzian or pseudo-Voight plus a smooth polynomial; don't subtract > the polynomial). I have never tried too, simply I took care of data during experiment, as is mentioned in posts before. And I suppose it would be very painful, more than Pb tape... Anyway - good ideal with this Pb tape. coming back to the problem with Bragg peaks, does anyone knows if it is possible to analyse EXAFS with more than 1 interest regions? like 2 or more FT windows - before, between and after Bragg peaks, or is possible to introduce one own FT window function in Athena? regards kicaj ------------------------------ Message: 5 Date: Wed, 12 Dec 2012 17:16:35 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] How to do with diffraction peak Message-ID: <1733074.77ouYmhRdV(a)lachesis.bnl.gov> Content-Type: text/plain; charset="utf-8" On Wednesday, December 12, 2012 11:09:29 PM Dr. Dariusz A. Zaj?c wrote: > coming back to the problem with Bragg peaks, does anyone knows if it > is possible to analyse EXAFS with more than 1 interest regions? like 2 > or more FT windows - before, between and after Bragg peaks, or is > possible to introduce one own FT window function in Athena? Interesting question. Some days I really love this mailing list. A similar question came up recently on the mailing list, although I think here you are asking whether regions can be chosen in k-space. (The previous discussion was about regions in R space.) I am commenting off the top of my head here, so I may be neglecting something. But I think what you are suggesting to have a windowing function that goes up, then down, then up again, then down again. I think the problem with that is that it would introduce low frequency components into the transformed data. Granted, the transform of the theory would have the same effect, but I worry about how that kind of windowing function would be correlated with the parameters of the fit. As Scott suggested in the earlier conversation, another option is to do a multiple data set fit where the data is imported twice. For one instance of the data, the FT window is set over the first range. For the other instance, the window is set over the second range. Again, I worry about how the choice of windows may be correlated with the parameters of the fit, given the limited information content used in each part of the MDS fit. I don't plan on exploring this myself. But if someone wanted to do so and attempt to convince me that it should be implemented in the software, I am -- as always -- willing to listen. Cheers, B -- 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 ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 13 ****************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
by jiahui 12 Dec '12

12 Dec '12

Hi Bruce, I am a windows user. The two log file(Artemis and Atoms) and one of the CIF files I used are attached to this email. Please let me know if you need more information, Hi Dan, I use Mercury to open the CIF file then save as another CIF file as you suggested. The new CIF file can be read by (D)Artemis with an warning message basically says there're some problem with this file and some possible ways to solve the problem(s). I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. This version can read the CIF files. I ran atoms and FIFF on it. Then save the file. It could be opened by (D)Artemis without problem. Thank you very much for your help and solutions, Jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 10 December 2012 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 6 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. Help: Artemis closes without error message when open .cif file (jiahui) 2. Re: Help: Artemis closes without error message when open .cif file (Bruce Ravel) 3. Re: Help: Artemis closes without error message when open.cif file (Daniel Whittaker) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Dec 2012 15:42:27 -0000 From: "jiahui" <qijiahui.uk(a)gmail.com> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> Content-Type: text/plain; charset="us-ascii" Dear list, I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version. Thank you very much for your help, [jiahui] ------------------------------ Message: 2 Date: Mon, 10 Dec 2012 10:48:21 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Jiahui, It would be helpful to me to see an example of a CIF file that triggers this problem. If you are running on Windows, then I would also like to see the contents of the %APPDATA%\demeter\dartemis.log file. See http://bruceravel.github.com/demeter/pods/bugs.pod.html If you are a linux user, I would need to see the messages sent to the terminal, which requires running the program from the terminal rather from some launcher widget. As I have said many times before on this mailing list, CIF support is rather weak at this time. I am using a CIF parsing tool written by someone else and it has its problems. That said, as people report these problems, I am able to build more smarts into Demeter so that it at least deals gracefully with a CIF file it doesn't understand. Cheers, B On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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 ------------------------------ Message: 3 Date: Mon, 10 Dec 2012 16:16:00 -0000 From: "Daniel Whittaker" <daniel.whittaker(a)postgrad.manchester.ac.uk> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help: Artemis closes without error message when open.cif file Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC> Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Hi Jiahui, I have experienced similar issues with cif files - there are so many slightly different formats. I found a solution was to open the file in Mercury: http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/ Save it as a .cif from within the program itself and then read it into (D)Artemis. If that works then brilliant :) - If not then there are a few other issues I have found working on my organic systems: 1) If there is any disorder I find it best to remove it. 2) When running atoms I have found it can produce an error. In this case, if you save the file it produces (*.inp) then open this in a text editor and remove any duplicate atoms (normally near the bottom of the file) save it again and then reopen in Atoms then it should work fine. I hope this helps troubleshoot your issues for now? Regards, Dan Daniel Whittaker, MChem Nuclear FiRST DTC PhD Student Chemistry Building The University of Manchester Brunswick Street Manchester M13 9PL -----Original Message----- From: Bruce Ravel Sent: Monday, December 10, 2012 3:48 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Help: Artemis closes without error message when open.cif file Jiahui, It would be helpful to me to see an example of a CIF file that triggers this problem. If you are running on Windows, then I would also like to see the contents of the %APPDATA%\demeter\dartemis.log file. See http://bruceravel.github.com/demeter/pods/bugs.pod.html If you are a linux user, I would need to see the messages sent to the terminal, which requires running the program from the terminal rather from some launcher widget. As I have said many times before on this mailing list, CIF support is rather weak at this time. I am using a CIF parsing tool written by someone else and it has its problems. That said, as people report these problems, I am able to build more smarts into Demeter so that it at least deals gracefully with a CIF file it doesn't understand. Cheers, B On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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 _______________________________________________ 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 118, Issue 6 ***************************************

2 2

How to do with diffraction peak
by Zhaomo Tian 12 Dec '12

12 Dec '12

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 7
by jiahui 11 Dec '12

11 Dec '12

Hi Peter, Thank you very much for your suggestion. The problem for me is the .txt file cannot be imported by the (D)Artemis (an error message came out).... Best, jiahui -- Dr Jiahui Qi Research Associate Department of Material Imperial College London South Kensington Campus London SW7 2AZ Mobile: +44(0)7948387989 Email: j.qi(a)imperial.ac.uk www.imperial.ac.uk -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 10 December 2012 23:16 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 7 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 118, Issue 6 (Peter Marley) 2. Re: Ifeffit Digest, Vol 118, Issue 6 (jiahui) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Dec 2012 15:15:41 -0500 From: Peter Marley <petermar(a)buffalo.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6 Message-ID: <CAE1g5jH_G67ubO6gPXJgM7mHBHk_UEV4XKF+Hd6DuLAYPS4_CQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Jiahui, I have also experienced this problem when saving a cif file from VESTA. What I found to work best was to modify the cif file into a different format. For example: title = VO2(M) space = P 21/c a = 5.56300 b = 4.89600 c = 5.66300 alpha = 90 beta = 120.47000 gamma = 90 atoms V 0.22780 -0.01020 0.01110 V(1) O 0.11190 0.21860 0.23340 O(1) O 0.39000 0.70240 0.29860 O(2) And then save it as a .txt file, which can then be imported. I hope this helps Peter Peter Marley Ph. D. Candidate Department of Chemistry 405 Natural Sciences Complex University at Buffalo The State University of New York Buffalo, NY 14260-3000 On Mon, Dec 10, 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. Help: Artemis closes without error message when open .cif > file (jiahui) > 2. Re: Help: Artemis closes without error message when open .cif > file (Bruce Ravel) > 3. Re: Help: Artemis closes without error message when open.cif > file (Daniel Whittaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Dec 2012 15:42:27 -0000 > From: "jiahui" <qijiahui.uk(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Dear list, > > I am having this problem when I try to open the crystal structure file > in .cif format. I've tried many times already--each time when I try to > open the crystal structure file in *.cif format, both (D)Atoms and > (D)Artemis will close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am > using Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Dec 2012 10:48:21 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open > the > > crystal structure file in *.cif format, both (D)Atoms and (D)Artemis > > will close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > 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 > > > ------------------------------ > > Message: 3 > Date: Mon, 10 Dec 2012 16:16:00 -0000 > From: "Daniel Whittaker" <daniel.whittaker(a)postgrad.manchester.ac.uk> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open.cif file > Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > > Hi Jiahui, > > I have experienced similar issues with cif files - there are so many > slightly different formats. > > I found a solution was to open the file in Mercury: > http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/ > Save it as a .cif from within the program itself and then read it into > (D)Artemis. If that works then brilliant :) - If not then there are a > few other issues I have found working on my organic systems: > 1) If there is any disorder I find it best to remove it. > 2) When running atoms I have found it can produce an error. In this > case, if you save the file it produces (*.inp) then open this in a > text editor and remove any duplicate atoms (normally near the bottom > of the file) save it again and then reopen in Atoms then it should > work fine. > > I hope this helps troubleshoot your issues for now? > > Regards, > Dan > > Daniel Whittaker, MChem > Nuclear FiRST DTC PhD Student > Chemistry Building > The University of Manchester > Brunswick Street > Manchester > M13 9PL > > > -----Original Message----- > From: Bruce Ravel > Sent: Monday, December 10, 2012 3:48 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open.cif file > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure > > file in .cif format. I've tried many times already--each time when I > > try to open the crystal structure file in *.cif format, both > > (D)Atoms and (D)Artemis will close by themselves without any error > > message. > > What can I do to solve this problem and carry on with my work? I am > > using Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > 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 > _______________________________________________ > 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 118, Issue 6 > *************************************** >

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Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
by Peter Marley 10 Dec '12

10 Dec '12

Hi Jiahui, I have also experienced this problem when saving a cif file from VESTA. What I found to work best was to modify the cif file into a different format. For example: title = VO2(M) space = P 21/c a = 5.56300 b = 4.89600 c = 5.66300 alpha = 90 beta = 120.47000 gamma = 90 atoms V 0.22780 -0.01020 0.01110 V(1) O 0.11190 0.21860 0.23340 O(1) O 0.39000 0.70240 0.29860 O(2) And then save it as a .txt file, which can then be imported. I hope this helps Peter Peter Marley Ph. D. Candidate Department of Chemistry 405 Natural Sciences Complex University at Buffalo The State University of New York Buffalo, NY 14260-3000 On Mon, Dec 10, 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. Help: Artemis closes without error message when open .cif > file (jiahui) > 2. Re: Help: Artemis closes without error message when open .cif > file (Bruce Ravel) > 3. Re: Help: Artemis closes without error message when open.cif > file (Daniel Whittaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Dec 2012 15:42:27 -0000 > From: "jiahui" <qijiahui.uk(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Dear list, > > I am having this problem when I try to open the crystal structure file in > .cif format. I've tried many times already--each time when I try to open > the > crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will > close by themselves without any error message. > What can I do to solve this problem and carry on with my work? I am using > Demeter 0.9.13 version. > > Thank you very much for your help, > > [jiahui] > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Dec 2012 10:48:21 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure file in > > .cif format. I've tried many times already--each time when I try to open > the > > crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will > > close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am using > > Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > 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 > > > ------------------------------ > > Message: 3 > Date: Mon, 10 Dec 2012 16:16:00 -0000 > From: "Daniel Whittaker" <daniel.whittaker(a)postgrad.manchester.ac.uk> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open.cif file > Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > > Hi Jiahui, > > I have experienced similar issues with cif files - there are so many > slightly different formats. > > I found a solution was to open the file in Mercury: > http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/ > Save it as a .cif from within the program itself and then read it into > (D)Artemis. If that works then brilliant :) - If not then there are a few > other issues I have found working on my organic systems: > 1) If there is any disorder I find it best to remove it. > 2) When running atoms I have found it can produce an error. In this case, > if > you save the file it produces (*.inp) then open this in a text editor and > remove any duplicate atoms (normally near the bottom of the file) save it > again and then reopen in Atoms then it should work fine. > > I hope this helps troubleshoot your issues for now? > > Regards, > Dan > > Daniel Whittaker, MChem > Nuclear FiRST DTC PhD Student > Chemistry Building > The University of Manchester > Brunswick Street > Manchester > M13 9PL > > > -----Original Message----- > From: Bruce Ravel > Sent: Monday, December 10, 2012 3:48 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open.cif file > > > Jiahui, > > It would be helpful to me to see an example of a CIF file that > triggers this problem. If you are running on Windows, then I would > also like to see the contents of the %APPDATA%\demeter\dartemis.log > file. See > > http://bruceravel.github.com/demeter/pods/bugs.pod.html > > If you are a linux user, I would need to see the messages sent to the > terminal, which requires running the program from the terminal rather > from some launcher widget. > > As I have said many times before on this mailing list, CIF support is > rather weak at this time. I am using a CIF parsing tool written by > someone else and it has its problems. That said, as people report > these problems, I am able to build more smarts into Demeter so that it > at least deals gracefully with a CIF file it doesn't understand. > > Cheers, > B > > On Monday, December 10, 2012 03:42:27 PM jiahui wrote: > > Dear list, > > > > I am having this problem when I try to open the crystal structure file in > > .cif format. I've tried many times already--each time when I try to open > > the > > crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will > > close by themselves without any error message. > > What can I do to solve this problem and carry on with my work? I am using > > Demeter 0.9.13 version. > > > > Thank you very much for your help, > > > > [jiahui] > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > 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 > _______________________________________________ > 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 118, Issue 6 > *************************************** >

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Help: Artemis closes without error message when open .cif file
by jiahui 10 Dec '12

10 Dec '12

Dear list, I am having this problem when I try to open the crystal structure file in .cif format. I've tried many times already--each time when I try to open the crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will close by themselves without any error message. What can I do to solve this problem and carry on with my work? I am using Demeter 0.9.13 version. Thank you very much for your help, [jiahui]

3 2

dathena cannot import data
by Huynh Khuong 05 Dec '12

05 Dec '12

Dear Everyone, I am a complete beginner to this field and to this software, so please forgive me if I ask something stupid. I am using Ubuntu 12.10 64 bit. Demeter was built from source following the guidance here: http://bruceravel.github.com/demeter/pods/installation.pod.html Ifeffit was also built from source before the installation of Demeter. I tried to run dathena from a terminal and import a data file download from here: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/examples/data.html <http://cars9.uchicago.edu/%7Eravel/software/doc/Athena/html/examples/data.h…> Dathena said that the data file is not readable (see the attached screenshot). No output text appeared on the terminal. If I use the old version of Athena installed from the repository of Ubuntu, the data file can be read easily. The data file is also attach. Could you please explain me about this issue ? Thank you very much in advance. Best, Khuong Huynh

2 3

model for iron oleate
by Monson, Todd 05 Dec '12

05 Dec '12

Does anyone know of an atoms model of iron oleate has been created? Todd Monson Sandia National Labs Nanoscale Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Demeter plotting problem in 64-bit Windows 7
by Leon Clarke 05 Dec '12

05 Dec '12

I've just installed the latest version of Demeter on my laptop running 64-bit Windows 7. While I can get the programs to start and run, e.g. Athena, no plots are generated. I'm actually sat in the Diamond XAS workshop and Fred M is stumped by this issue. Are there any known conflicts with the latest version of Demeter, specifically plotting data, running on 64-bit Windows 7 and any solutions? Many thanks, Leon ----- Dr Leon J. Clarke Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

2 1

Re: [Ifeffit] S02 and k_min
by Morrill, Michael R 04 Dec '12

04 Dec '12

Thank you for your replies, Anatoly and Matt. As suggested, I've attached a zipped folder with 2 fits that differ only in kmin. You'll notice that the fit improves as kmin is increased. I've also attached the raw data in an Athena file in the event that anyone would like to look at that. Thanks again. ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Monday, December 3, 2012 1:00:01 PM Subject: Ifeffit Digest, Vol 118, Issue 2 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: S02 and k_min (Anatoly I Frenkel) 2. Re: S02 and k_min (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sun, 2 Dec 2012 18:13:14 +0000 From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] S02 and k_min Message-ID: <545F89325F51764C902D37B42C9F4D5313625DAE(a)YUWEXCPM12.yuad.uds.yu.edu> Content-Type: text/plain; charset="us-ascii" Michael, If you use the same kmin for the standard and the unknown you will minimize the ambiguity. Anatoly ----- Reply message ----- From: "Michael Morrill" <mike.morrill(a)gatech.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] S02 and k_min Date: Sun, Dec 2, 2012 1:02 PM Hello everyone, I am currently performing a simple curve fit on bulk MoS2 using an atoms file for crystalline MoS2. I've found that increasing k_min on my fit (e.g. from 2 to 4) improves the quality of the fit (R-factor from 0.028 to 0.009), but also increases S02. If I use a large enough k_min (but not so large I run out of data), S02 gets as high as 1.2 +/- 0.05. This trend is observable for single and multiple k-weight fittings. While I understand that S02>1.0 does not necessarily invalidate the fit, I am not sure how to justify which parameter values are the best seeing that "0.8<S02<1.0" is often one of the justifications that everything "is reasonable." Ultimately, I want to assume the S02 is chemically transferrable and use it for curve fits on metal oxide supported MoS2. Any direction on the mater would be greatly appreciated. Thank you, Mike Morrill GaTech CHBE _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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error function in Athena's peak analysis module
by Linda Lim 03 Dec '12

03 Dec '12

Hi every one I am trying to do peak fitting on Athena. Whenever I choose the error function and click "fit" the software crashes, but it works fine when I choose arctangent. Just wondering if anyone encounter the same issue too, and whether I'm missing something during the fitting process. Thanks! Regards Linda

3 3

S02 and k_min
by Michael Morrill 02 Dec '12

02 Dec '12

Hello everyone, I am currently performing a simple curve fit on bulk MoS2 using an atoms file for crystalline MoS2. I've found that increasing k_min on my fit (e.g. from 2 to 4) improves the quality of the fit (R-factor from 0.028 to 0.009), but also increases S02. If I use a large enough k_min (but not so large I run out of data), S02 gets as high as 1.2 +/- 0.05. This trend is observable for single and multiple k-weight fittings. While I understand that S02>1.0 does not necessarily invalidate the fit, I am not sure how to justify which parameter values are the best seeing that "0.8<S02<1.0" is often one of the justifications that everything "is reasonable." Ultimately, I want to assume the S02 is chemically transferrable and use it for curve fits on metal oxide supported MoS2. Any direction on the mater would be greatly appreciated. Thank you, Mike Morrill GaTech CHBE

3 2

Help to run Demeter on Windows XP (So. Muru)
by Andrei Shiryaev 30 Nov '12

30 Nov '12

Dear All, I have a similar problem running Demeter on Windows 7 64 bit. It simply makes nothing. I remember that several years ago there was a problem to run IFEFFIT on XP windows machines which were operating under non-unicode settings (in those cases it was Brazilian (i.e. Portugese) and Russian versions). Bruce had solved the problem using another compilation of Perl, if I am correct. Is is possible that the same "non-unicode" problem persists in Demeter? All the best, A.Shiryaev

4 4

Help to run Demeter on Windows XP
by So. Muru 28 Nov '12

28 Nov '12

Dear all, greetings from Murugesan, recently I downloaded the latest version of Demeter for windows and installed it on my windows xp (32bit) environment. I try to run the programs by shortcuts in the desktop, but the programs didn't run. what was the problem, kindly give your suggestions to run the Demeter package successfully on windows xp environment. with thanks and regards S Murugesan -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr S Murugesan Kalpakkam, Tamil Nadu India Email : muruges(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

Re: [Ifeffit] FOLP
by Joshua Kas 27 Nov '12

27 Nov '12

Hi Enyuan, It is very strange that FOLP 1.3 is causing the code to take longer. There really should be almost no difference in timing between different values of FOLP. This has to be a bug. Would you mind sending your input file? As for the CRITERIA card, this effects the filtering of the path expansion. The path expansion should only be used for EXAFS calculations, which is why the CRITERIA card is greyed out for XANES calculations (which use full multiple scattering). If you really want to run XANES with path expansion, you can still do that using the text based input and running the code from the command line. If you don't know how to do this, I can explain. Just let me know what operating system you are using. Cheers, Josh > > Hi Joshua, > > Thank you for your comment. Like you said, I tried FOLP with value from 1 > to 1.3 and it didn't change the calculated spectrum much. It's very > time-consuming when FOLP reached 1.3, taking more than 3 hours to finish > the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going > to calculated a sample with lots of Li in it. Do you suggest using a > similarly small number of FOLP for Li, in an analogy to H? The other thing > I want to ask is the CRITERIA card in Feff9. It seemed that once I asked > the program to calculate XANES, the CRITERIA card in the software cannot be > checked. It can only be checked if I selected EXAFS calculation mode. Is > there any way to solve this? thanks again for all your answers. > > Enyuan > > > On Mon, Nov 26, 2012 at 5:33 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: FOLP card (Joshua Kas) > > 2. Question on Glitch in FEFF for Ru EXAFS measurements > > (Dooshaye Moonshiram) > > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bruce Ravel) > > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bobrik, Michael) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 26 Nov 2012 10:56:19 -0800 > > From: Joshua Kas <joshua.j.kas(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] FOLP card > > Message-ID: > > < > > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Enyuan, > > I don't really know a rule of thumb for ionic bond v.s. covalent bond, > but > > by default, the FEFF code will automatically choose reasonable muffin > tins > > in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP > > 1.15. In many cases, the overlap doesn't change the structure in the > XANES > > a lot until you get far from FOLP 1.0. However, there are some special > > cases. For example, we have found that using FOLP 0.8 for hydrogen atoms > > seem's to work reasonably well in the XANES. This is because of the short > > bond lengths of H. In addition, there are cases where one atom is fairly > > isolated from the others, i.e., cage like structures, where FEFF can't > > overlap the potentials, and setting FOLP to something smaller than 1.0 is > > essential to make the code run. I would start by letting the code choose > > the muffin tins automatically, then change them and see how the results > > change. If the changes in the XANES are small, you probably don't have to > > worry about FOLP. Otherwise, this is probably a limitation of the > spherical > > muffin tin potential. The best thing to do in that case, is to compare > the > > DOS (LDOS) with a calculation from a full potential electronic structure > > code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. > > This can give you confidence in the FEFF calculation, or lead you to the > > best values for FOLP. You could also use the FOLP values to get the best > > comparison to experiment, but in some cases you may be fitting many-body > > effects, which can lead you to the wrong conclusions about your system. > > Cheers, > > Josh Kas > > > > On Mon, Nov 26, 2012 at 7:53 AM, > > <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > > > > > Re: > >

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 24
by Enyuan Hu 27 Nov '12

27 Nov '12

Hi Joshua, Thank you for your comment. Like you said, I tried FOLP with value from 1 to 1.3 and it didn't change the calculated spectrum much. It's very time-consuming when FOLP reached 1.3, taking more than 3 hours to finish the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going to calculated a sample with lots of Li in it. Do you suggest using a similarly small number of FOLP for Li, in an analogy to H? The other thing I want to ask is the CRITERIA card in Feff9. It seemed that once I asked the program to calculate XANES, the CRITERIA card in the software cannot be checked. It can only be checked if I selected EXAFS calculation mode. Is there any way to solve this? thanks again for all your answers. Enyuan On Mon, Nov 26, 2012 at 5:33 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: FOLP card (Joshua Kas) > 2. Question on Glitch in FEFF for Ru EXAFS measurements > (Dooshaye Moonshiram) > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bruce Ravel) > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bobrik, Michael) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Nov 2012 10:56:19 -0800 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] FOLP card > Message-ID: > < > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Enyuan, > I don't really know a rule of thumb for ionic bond v.s. covalent bond, but > by default, the FEFF code will automatically choose reasonable muffin tins > in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP > 1.15. In many cases, the overlap doesn't change the structure in the XANES > a lot until you get far from FOLP 1.0. However, there are some special > cases. For example, we have found that using FOLP 0.8 for hydrogen atoms > seem's to work reasonably well in the XANES. This is because of the short > bond lengths of H. In addition, there are cases where one atom is fairly > isolated from the others, i.e., cage like structures, where FEFF can't > overlap the potentials, and setting FOLP to something smaller than 1.0 is > essential to make the code run. I would start by letting the code choose > the muffin tins automatically, then change them and see how the results > change. If the changes in the XANES are small, you probably don't have to > worry about FOLP. Otherwise, this is probably a limitation of the spherical > muffin tin potential. The best thing to do in that case, is to compare the > DOS (LDOS) with a calculation from a full potential electronic structure > code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. > This can give you confidence in the FEFF calculation, or lead you to the > best values for FOLP. You could also use the FOLP values to get the best > comparison to experiment, but in some cases you may be fitting many-body > effects, which can lead you to the wrong conclusions about your system. > Cheers, > Josh Kas > > On Mon, Nov 26, 2012 at 7:53 AM, > <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > > > Re: >

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Question on Glitch in FEFF for Ru EXAFS measurements
by Dooshaye Moonshiram 27 Nov '12

27 Nov '12

Dear Bruce, I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II) dichloride Ru 2 compound-photosensitizer in solution form. In order to compare EXAFS data to XRD data, I uploaded the XRD coordinates of this crystal structure from cambridge database in a FEFF calculation page in ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound in Artemis and summed all paths to compare with my experimental data(collected in solution form in fluorescence mode)* *I have 2 problems* *1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD coordinates to EXAFS data, I upload the XRD coordinates in a FEFF calculation page, run FEFF and sum all paths. Now* *a) **f I upload the XRD coordinates in a FEFF calculation page without having the EXAFS artemis file present, I get different fits compared to* *b) if I first upload the EXAFS experimental file and then run FEFF on the XRD cartesian coordinates. It seems that **the sum of all paths from the FEFF calculation page tend to mimic the experimental EXAFS file which has first been uploaded and is not a true presentation of how the FT should be.* * * *-Please let me know if this is unclear and I can send you my EXAFS file as well as the XRD coordinates which I obtained from Cambridge structural databse* * * *2) Another problem which I have with my EXAFS data is that I have a peak at 2.5 Angstrom which does not match XRD coordinates and is not present if I run FEFF on XRD coordinates only(true comparison as I don't add the the experimental file in Artemis). Could this peak be due to the Ru standard somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in cryostat using a germanium detector. I simultaneously collected EXAFS measurements on Ru metal standard between Iref and IT ionization chambers.* * * *Thank you for your help,* *Sincerely* *Best Regards* *Dooshaye Moonshiram*

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 13
by Zack Gainsforth 27 Nov '12

27 Nov '12

Kyler, you and Tsu-Chien are terrific! iXAFS is working for me again! Cheers, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 510-642-9733 zackg(a)ssl.berkeley.edu On Nov 15, 2012, at 10:00 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: Launching Athena on Mountain Lion (Mac OS 10.8) (Kyler Carroll) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Nov 2012 09:32:34 -0800 From: Kyler Carroll <kyler.carroll(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8) Message-ID: <CAN+rEib3FNvmTE0x8BPgCBN2TRytRE+1CG2aN6A=mEEWxS6NcA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" 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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Help: some operation using Athena and Artemis
by Bingjie Ouyang 26 Nov '12

26 Nov '12

Hi, I just joined the mailing list recommended by a friend, I hear this is a really good place to communicate and learn. So I'm here, actually I need help for some basic questions on Iffeffit software: 1, In Athena, how to make a fourier transform draft? 2, In Artemis, since I was told that each shell in R-space can be fitted separatly, is it OK to fit each shell in the R-range respectively, and then join up the fitted curve and just ignore the not match part in other R-ranges? And can a shell be comprised of several different paths (like Fe-O and Fe-S)? Thank you. Best wishes, Bingjie -- Bingjie Ouyang School of Earth Sciences and Engineering Nanjing University 22nd Hankou Road, Nanjing, Jiangsu, 210093 P. R. China Email: jessicaoy89(a)gmail.com

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Re: [Ifeffit] FOLP card
by Joshua Kas 26 Nov '12

26 Nov '12

Hi Enyuan, I don't really know a rule of thumb for ionic bond v.s. covalent bond, but by default, the FEFF code will automatically choose reasonable muffin tins in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP 1.15. In many cases, the overlap doesn't change the structure in the XANES a lot until you get far from FOLP 1.0. However, there are some special cases. For example, we have found that using FOLP 0.8 for hydrogen atoms seem's to work reasonably well in the XANES. This is because of the short bond lengths of H. In addition, there are cases where one atom is fairly isolated from the others, i.e., cage like structures, where FEFF can't overlap the potentials, and setting FOLP to something smaller than 1.0 is essential to make the code run. I would start by letting the code choose the muffin tins automatically, then change them and see how the results change. If the changes in the XANES are small, you probably don't have to worry about FOLP. Otherwise, this is probably a limitation of the spherical muffin tin potential. The best thing to do in that case, is to compare the DOS (LDOS) with a calculation from a full potential electronic structure code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. This can give you confidence in the FEFF calculation, or lead you to the best values for FOLP. You could also use the FOLP values to get the best comparison to experiment, but in some cases you may be fitting many-body effects, which can lead you to the wrong conclusions about your system. Cheers, Josh Kas On Mon, Nov 26, 2012 at 7:53 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Re:

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Plot multiple fits in (D)Artemis and statistical errors
by Nilmar Camilo 26 Nov '12

26 Nov '12

Dear Bruce, I am new in the list and really don't know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don't know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: "Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558." Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn't return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp = 0.79284158 # +/- 0.00000000 [0.95] enot = 5.29826510 # +/- 0.00000000 [0] delrIn11 = 0.00235278 # +/- 0.00000000 [0] ssIn11 = 0.00155959 # +/- 0.00000000 [0.00300] delrCe1 = -0.00231455 # +/- 0.00000000 [0] ssCe1 = 0.00192778 # +/- 0.00000000 [0.00300] delrIn11In11 = 0.02070081 # +/- 0.00000000 [0] delrIr1 = -0.00435502 # +/- 0.00000000 [0] ssIr1 = 0.00386517 # +/- 0.00000000 [0.00300] delrIn31 = 0.00648507 # +/- 0.00000000 [0] ssIn31 = 0.00669602 # +/- 0.00000000 [0.00300] delrIn12 = 0.00255704 # +/- 0.00000000 [0] ssIn12 = 0.00305432 # +/- 0.00000000 [0.00300] def parameters: b = 0.80000000 # [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 21
by Enyuan Hu 25 Nov '12

25 Nov '12

Hi Joshua, Thank you for your answer. So you're saying that we can simultaneously define FOLP for each potential type in the way you showed, right? Then is there any rule of thumb on what appropriate numbers should be used, like what are for anions and what are for cations, what are for ionic bond and what are for covalent bond? thanks. best, Enyuan On Sun, Nov 25, 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. error function in Athena's peak analysis module (Linda Lim) > 2. Re: error function in Athena's peak analysis module > (Chris Patridge) > 3. Re: FOLP card (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 12:24:08 -0800 > From: Linda Lim <ywllim(a)stanford.edu> > To: Ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] error function in Athena's peak analysis module > Message-ID: > <CALPaxYDOUGa7_NMkLmDS31gnk6MFR9RRp4wda+Ji3= > xRdHW5hQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi every one > > I am trying to do peak fitting on Athena. Whenever I choose the error > function and click "fit" the software crashes, but it works fine when I > choose arctangent. > > Just wondering if anyone encounter the same issue too, and whether I'm > missing something during the fitting process. Thanks! > > Regards > Linda >

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Re: [Ifeffit] FOLP card
by Joshua Kas 25 Nov '12

25 Nov '12

Hi Enyuan, You can define the folp options separately for each unique potential, i.e., FOLP 0 1.0 FOLP 1 0.8 FOLP 2 1.2 Will give you touching muffin tins for the 0 potential (absorber), and an overlap of 0.8 and 1.2 for the atoms with potential types 1 and 2 respectively. Note that the 0 potential will have not necessarily have "touching" muffin tin, since the 2 potential is larger than touching and could overlap the 0 potential. The third number gives the ratio of the muffin tin size to the touching muffin tin size that the cod would use if all FOLP radii were set to 1.0. Cheers, Josh Kas Cheers, Josh Kas On Sat, Nov 24, 2012 at 10:00 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. FOLP card (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 08:55:58 -0500 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] FOLP card > Message-ID: > < > CAJud35MQx-zvbvpPH1zbPitFXaUj9qm8TgoqEWsH9yCnwawRNA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I'm trying to see the impact of using FOLP card on my simulation results in > Feff9. As far as I understand it, FOLP is defining the overlapping of > muffin-tin radii. The first parameter defines the the position where this > card will be used (expressed as potential type), right? so should I do the > simulation for all potentials, that is going from 0 to the last number in > my potential list, or I just do it for some specific positions (potential > types)? thanks. > > Enyuan >

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FOLP card
by Enyuan Hu 24 Nov '12

24 Nov '12

Dear all, I'm trying to see the impact of using FOLP card on my simulation results in Feff9. As far as I understand it, FOLP is defining the overlapping of muffin-tin radii. The first parameter defines the the position where this card will be used (expressed as potential type), right? so should I do the simulation for all potentials, that is going from 0 to the last number in my potential list, or I just do it for some specific positions (potential types)? thanks. Enyuan

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iXAFS on Mountain Lion
by Weng, Tsu-Chien 22 Nov '12

22 Nov '12

Hi, I had problem launching iXAFS on Mountain Lion after the OS upgrade. It seems the path to X11 might be hard wired in the program. Here is my workaround solution by creating a symbolic link to XQuartz. It might be worth sharing the trick. 1. Install XQuartz 2.7.4 from <http://xquartz.macosforge.org/landing/> 2. Launch Terminal.app and issue the following commands: 2.1) cd /Applications/Utilities 2.2) sudo mkdir X11.app 2.3) cd X11.app 2.4) sudo ln -s ../XQuartz.app/Contents 3. Now either double-click on iXAFS.app or command line `open -a ixafs` should work -- Tsu-Chien WENG Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, Mail Stop 69 Menlo Park, CA 94025, USA +1-650-926-4107 (office) +1-650-926-4100 (fax)

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(no subject)
by Pooja Gupta 19 Nov '12

19 Nov '12

-- "A Ship is always safe at the shore - but that is NOT what it is built for" *********************************************** Dr. Pooja Gupta Scientific Officer Material research Lab Raja Ramanna Center for Advanced Technology, Indore-452013. (M.P.) INDIA. Ph. No. (O): +91-731-2442123 (M): +91 8435718320 Fax No. (O): +91 7312442140 E-mail ID: pooja(a)rrcat.gov.in

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Calculation of a XANES spectrum
by Wei Li 18 Nov '12

18 Nov '12

Dear colleagues, If I have a structural model with geometry optimised by DFT, how do I obtain a theoretical XANES spectrum based on that model? Second questions is how to calculation the projected density of states (PDOS). Thanks! best regards Wei -- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>

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Re: [Ifeffit] Determining errors in R_fit
by Rana, Jatinkumar Kantilal 17 Nov '12

17 Nov '12

Dear Anatoly and Jason, Thank you so much for your feedback !! With best regards, Jatin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Saturday, November 17, 2012 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 117, Issue 15 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. Determining errors in R_fit (Rana, Jatinkumar Kantilal) 2. Re: Determining errors in R_fit (Anatoly I Frenkel) 3. Re: Determining errors in R_fit (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Fri, 16 Nov 2012 18:33:05 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Determining errors in R_fit Message-ID: <F11168F9CA572049ADA84F3072DE5DB16D329DB2@didag1> Content-Type: text/plain; charset="us-ascii" Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

1 0

Determining errors in R_fit
by Rana, Jatinkumar Kantilal 17 Nov '12

17 Nov '12

Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

4 3

Demeter on windows 8
by George Sterbinsky 14 Nov '12

14 Nov '12

Hello, Has anyone been able to install Demeter on windows8? When I try to open Athena I get the message in attached screen shot. I tried reinstalling as suggested by the message, which did not help. One thing I noticed however was that Perl was not removed by the built in Demeter uninstaller. Any suggestions appreciated. Thank you, George

1 1

questions about plotting old fits with demeter/artemis
by Georges Siddiqi 13 Nov '12

13 Nov '12

Hi All, I recently upgraded to the new version of demeter/athena/artemis, and while it is very nice to use, I am thoroughly lost in some areas. In the old version of Artemis, it is very easy to select old fits and plot them compared to the experimental data/new fits. I cannot figure out how to do this in the new version. The tutorial merely says "The history plotting tool is not currently working, making it difficult to write this bit of documentation!" Currently what I do is goto the "history" box of the main window, and goto the "plot tool" tab, but I can only add the 9 first fits to the plotting list. Any suggestions? am I missing something obvious? or is this (as the tutorial implies) a functionality that hasnt been added yet? thanks, georges

2 1

About Launching Athena on Mountain Lion (Mac OS 10.8)
by 上村洋平 12 Nov '12

12 Nov '12

Dear ifeffit mailing list menbers, I'm Yohei Uemura from Hokkaido University, Japan. For Mac users, you may know the thread below about not laucning iXAFS under Maountain Lion. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03412.html I don't know any other threads about launching iXAFS.app under Mountain Lion. I've also given up launching Athena and Artemis under Mountain Lion. But, today I found by chance how to launch Athena undr Mountain Lion. The procedure is as follows; 1) Launch XQuartz. 2) type in the xterm of XQuartz "/Applications/iXAFS.app/Contents/ Resources/iXAFS\ Shell.sh" #iXAFS.app is placed in "Application" folder. 3) type "athena" in the xterm, and then I'm able to lauch athena. Does anyone launch Athena or Artemis under Mountain Lion? I would like you who use Mountain Lion try to do my procedure. Best regards, =========================================== 上村洋平所属 : 北海道大学・触媒化学研究センター　　　朝倉研究室　博士研究員住所 : 305-0801 茨城県つくば市大穂1-1 KEK-PF 北大分室　　　 001-0021　北海道札幌市北区北21条西10丁目 Yohéi Uemura (Ph.D) Affiliation : Catalysis Research Center Hokkaido University Adress : KEK-PF, 1-1 Oho, Tsukuba-Shi, Ibaraki, Japan 305-0801 Kita21 Nishi10 Kita-Ku, Sapporo 001-0021 TEL: 029-864-5636 Email : yuemura(a)post.kek.jp ===========================================

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spinel XANES calculation by Feff
by Enyuan Hu 12 Nov '12

12 Nov '12

Dear all, I was wondering if anyone had experience in calculating XANES spectra using Feff for the spinel system. The material I was trying to investigate was ZnFe2O4. There were reports in literature that gave satisfying simulation results by Feff so I tried to follow. The feature peaks' positions from my simulation is generally right, but the intensity is definitely wrong. So I guess either someone can give me some suggestion about the getting the intensity right or share with me about his or her spinel XANES calculation experience. My background is mainly in chemistry and material science with general ideas about electronic structure. Any comment or suggestion will be greatly appreciated. Thanks! Enyuan

2 1

Re: [Ifeffit] Demeter install for Administrator/User computer (Melissa Menard)
by fred.mosselmans＠diamond.ac.uk 11 Nov '12

11 Nov '12

I think the problem is solved by making a Demeter folder in the application data folder for each user. If you search the ifeffit mailing list you'll see this has been covered before http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03167.html Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Demeter install for Administrator/User computer
by Melissa Menard 09 Nov '12

09 Nov '12

Hi Is there an install of Demeter for use on Administrator/User computers? I tried to install the general version on an Admin/User workstation in our lab and the software fails to launch. But on my personal labtop, I have no problems. -- M Menard, Ph.D.

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inquiries about XAFS experiment
by Zhaomo Tian 06 Nov '12

06 Nov '12

1 0

feff user mailing list
by Enyuan Hu 03 Nov '12

03 Nov '12

Dear all, I'm trying to join the mailing list for FEFF users. A search in Google led me to the the address listproc(a)u.washington.edu. But my attempt to join always failed as my mail keeps being rejected. I noticed the most recent post in this mailist list was from 2005. Is this mailist out of date? can anyone show me the right way? Thanks! Enyuan

3 2

questions and storms
by Bruce Ravel 02 Nov '12

02 Nov '12

Hi all, I have received a number of questions and bug reports about the software -- both over the mailing list and via personal mail -- in the last few days. Because of the recent storm here in the eastern part of North America I have fallen a little behind. I will address all the issues sent to me, but I may not respond for several days as I get caught up both at work and at home. If you are waiting for an answer to your question -- please be patient, I won't forget about you. Regards, B -- 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

2 1

Mac user
by Elena Mejia Likosova 30 Oct '12

30 Oct '12

Hi, I've been trying to download the IFEFFIT Mac version for my snow Leopard Mac. However, Athena doesn't work. Only Artemis seems to work. Do you have any new compatible version for my computer? Thanks, Elena Mejia Likosova PhD Student Advanced Water Management Centre at the University of Queensland Brisbane-Australia email: e.mejialikosova(a)uq.edu.au

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Linear combination fitting without normalization
by Stummelfinger 27 Oct '12

27 Oct '12

Hi there, Is there a way to do Linear combination fitting in Athena with data which were already proceeded (background corrected and normalized)? I don't want to do a double background correction /normalization on these data. However the Linear Combination Fitting dialog gives only the option "Norm(E)". Is there a work around? Thanks a lot, Cheers, Jan

2 1

"deglitch many points" in D-Athena
by Jeremy Thorbahn 25 Oct '12

25 Oct '12

Hi Bruce, I noticed on the github to-do list you've written "plot margin lines for deglitching, deglitch many points" under the "weird stuff" section. just for clarification, is that to say that the deglitch many points feature is something you'd prefer not to implement? I attempted to use it earlier but noticed it was greyed out. I can get by without it, but would probably end up swapping project files between the old Athena and D-Athena to eliminate a few points of high-k glitching at once. The main point of my question: is this not a feature many people use? It seems awfully convenient to quickly tidy up data. Thanks as always, Jeremy -- ------------------------- Jeremy Thorbahn thorbahn(a)gmail.com

2 1

command window
by Ravel, Bruce 24 Oct '12

24 Oct '12

> I am a beginner for xafs analysis. I installed the Demeter on my laptop. I found there was always a black command widow when I start > athena or artermis. If I close that window, the program was also closed. My operation system is windows 7. Why? A man walks into his doctor's office and says "Doctor! Doctor! It really hurts when I laugh! What should I do?" The doctor calmly responds, "Stop laughing." I haven't yet figured out how to reliably keep the pipe between my code and the plotting program open without an active command window. While I am sure that a solution exists, I have to prioritize my efforts. The presence of the command window just isn't a show-stopping problem. Have you tried ... ummm .... not closing the command window? B

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Re: [Ifeffit] Ifeffit Digest, Vol 116, Issue 13
by Tsuei, Ku-Ding 24 Oct '12

24 Oct '12

Thanks a lot, Bruce. I checked your new version 0.9.13.1 on my computers and both yield good fits. Now I can move on to work on real data. Ku-Ding On 2012/10/23 下午 06:24, 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: Running (D)Artemis yields different result from that > shown in (D)Artemis instruction videos (Bruce Ravel) > 2. release 0.9.13.1 (Bruce Ravel) > 3. DORIS III operation ended (Edmund Welter) > 4. Re: DORIS III operation ended (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 22 Oct 2012 16:12:43 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Running (D)Artemis yields different result from > that shown in (D)Artemis instruction videos > Message-ID: <3508041.vaaWmxvES8(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="utf-8" > > > OK, you've convinced me. > > When I got into the lab this afternoon, I tried the same fit on a > Windows computer. Much to my surprise, the result on Windows was > quite different from the result on my linux computers at home. > > After a few hours of investigation, I found a problem in how Ifeffit > had been compiled on the Windows machine that I use to build the > Windows installer. > > I was able to come up with a short-term solution and then built a new > installer package for 0.9.13 which i think works correctly. > > I will be announcing a new release shortly. > > B > > > > On Monday, October 22, 2012 06:41:26 AM Tsuei, Ku-Ding wrote: >> Bruce, >> >> Perhaps you noticed the "Fit color" was red (large R-factor 0.074496, >> poor fit, also seen in the attached figure in the last email) when you >> loaded in the project file I sent you. When you hit Fit button again the >> "Fit color" might turn to green indicating good fit as shown in your >> result of a much smaller R-factor (0.004265). >> >> I did the following test on various versions of Demeter on my desktop >> and notebook computers both installed with Windows 7 SP1. Of course I >> uninstalled one version first before installing another. I tried to use >> Uninstall within the Program menu or use the Program manager. I tried to >> reboot or not to reboot after uninstallation or installation. Neither >> shows any difference. >> >> Fit color >> 0.9.10 green >> 0.9.11 red >> 0.9.12 red >> 0.9.13 red >> >> Only version 0.9.10 yields good fit. The latter versions would not give >> good fits even with repeated hitting the "Fit" button. I have no idea >> what causes these results but perhaps this observation provides a clue. >> >> Ku-Ding >> >> On 2012/10/22 ?? 01:00, 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: Running (D)Artemis yields different result from that >>> >>> shown in (D)Artemis instruction videos (Ravel, Bruce) >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Sun, 21 Oct 2012 12:36:10 +0000 >>> From: "Ravel, Bruce"<bravel(a)bnl.gov> >>> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Running (D)Artemis yields different result from >>> >>> that shown in (D)Artemis instruction videos >>> >>> Message-ID: >>> <47CED3CD722C2A439C0D1D1056B2132517C3B082(a)EX10-MB1.BNL.GOV> >>> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> >>> Ku-Ding, >>> >>> I don't know what to tell you. On the computer I am sitting in front of >>> right now, I opened your two project files and hit the fit buttons, I get >>> the same fit with only numerical differences. Here I am cutting and >>> pasting from the two log files:> >>> old artemis: >>> Chi-square = 4334.684537717 >>> Reduced Chi-square = 691.819976095 >>> R-factor = 0.004250325 >>> >>> amp = 0.8649100 +/- 0.0412220 (1.0000) >>> enot = 5.6049380 +/- 0.2950270 (0.0000) >>> delr = -0.0226780 +/- 0.0023790 (0.0000) >>> ss = 0.0082230 +/- 0.0003250 (0.0030) >>> >>> new artemis: >>> Chi-square : 4348.7359268 >>> Reduced chi-square : 694.0625918 >>> R-factor : 0.0042652 >>> >>> amp = 0.86526150 # +/- 0.04129645 [1.00000] >>> enot = 5.61081742 # +/- 0.29527844 [0] >>> delr = -0.02266589 # +/- 0.00238341 [0] >>> ss = 0.00822546 # +/- 0.00032571 [0.00300] >>> >>> I don't acknowledge that there is a problem. >>> >>> B >>> >>> >>> ________________________________________ >>> From:ifeffit-bounces@millenia.cars.aps.anl.gov >>> [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding >>> [tsuei(a)nsrrc.org.tw] Sent: Thursday, October 18, 2012 1:15 PM >>> To:ifeffit@millenia.cars.aps.anl.gov >>> Subject: [Ifeffit] Running (D)Artemis yields different result from that >>> shown in (D)Artemis instruction videos >>> >>> Hi Bruce, >>> >>> I went through your (D)Artemis instruction videos and ran the latest >>> Demetris 0.9.12 with 0.9.13 update side by side to reproduce the >>> results. However, my running yields much poorer fitting results on Au >>> foil EXAFS, even the first shell (video 03). Actually it happened using >>> the older 0.9.11 too. I also went through your Lecture videos shot at >>> Diamond and ran (D)Artemis but could reproduce your results closely. I >>> have felt puzzled for quite a while why the simplest case Au foil does >>> work well. Today I tried to run the same Au data and fitting by the old, >>> last version of Artemis 0.8.014. I could produce very good fitting on >>> the first shell with the R-factor very near that shown in the video. I >>> made sure the math expressions for the fitting parameters amp, enot, >>> delr and ss are set exactly the same, with fitting range exactly the >>> same, in both programs. Their screen outputs file is attached. The saved >>> respective project files are also attached. I copied the fit outputs >>> into their journals. I would appreciate if you may review these results >>> and help clear my puzzle. >>> >>> Best regards, >>> >>> Ku-Ding >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >>> End of Ifeffit Digest, Vol 116, Issue 11 >>> **************************************** >>> . >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > > 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 > > > > ------------------------------ > > Message: 2 > Date: Mon, 22 Oct 2012 16:20:16 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] release 0.9.13.1 > Message-ID: <2108483.PEeEN70mtK(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Hi, > > As a result of a problem brought to my attention by Ku-Ding Tsuei, I > built a new installer of my software for Windows. The new installer, > release 0.9.13.1 can now be downloaded from > > http://bruceravel.github.com/demeter/ > > This is an installer package. There is not a package for updating > from 0.9.12. You must download and install the new installer package. > > This new installer is essential for anyone using Artemis. As Ku-Ding > discovered, versions 0.9.11 through 0.9.13 all suffer from the same > problem. If you are using Artemis from any of the affected versions, > you *must* upgrade. > > I apologize for making three flawed releases of my software and I hope > that no one has been too inconvenienced by my mistake. Once again, > this mailing list and its most excellent community proves to be the > best feature of our software! > > > As a bit of consolation, I want to direct your attention to the > Artemis Users' Guide. I have put a lot of effort into it in recent > weeks. It is still not complete, but it is much enhanced. > > http://bruceravel.github.com/demeter/artug/index.html > > > Regards, > B > > > -- > > 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 > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Oct 2012 09:35:25 +0200 > From: Edmund Welter <edmund.welter(a)desy.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] DORIS III operation ended > Message-ID: <508648BD.3020804(a)desy.de> > Content-Type: text/plain; charset="iso-8859-1" > > Dear fellow XAFS user, > > yesterday (October 22^nd 2012, 8 am) the DORIS III storage ring in > Hamburg was switched of for good. That means our 3 EXAFS beamlines are > left without photons and user operation at these beamlines had to end. > In the next 2 years we will build 2 new EXAFS beamlines at the PETRA III > storage ring that will hopefully equally well serve the demands of our > large user community as the 3 closed beamlines did during the last 20+ > years. > > I know this mailing list is mainly about software and number crunching, > but I thought the end of operation of a machine that produced so many > beautiful numbers to be crunched with IFEFFIT/Athena/Artemis etc. might > justify a short notice on this list. > > Anyway, to close the circle to the software, the end of user operation > of HASYLAB's DORIS beamlines finally gives our users the chance to use > this software and produce many nice papers during the coming months > (Ah,wait, that was something different, New York, July 1977 :-). > > I am looking forward to see you all back at our PETRA extension > beamlines in autumn 2014! Let me close this mail with the last line of > data ever measured at the A1 EXAFS beamline: > > 7893.277 0 0 0 0 0 0 0 0 0 0 0 0 0 > 5.489 13.22 > > > Best regards, > > Edmund Welter > > -- > -------------------------------------------------------- > Dr. Edmund Welter Deutsches Elektronen-Synchrotron > DESY FS-Do > > Notkestr. 85 Email: edmund.welter(a)desy.de > D-22607 Hamburg Phone: +49 40 8998 4510 > Germany Fax : +49 40 8998 2787 > -------------------------------------------------------- > >

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Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos
by Tsuei, Ku-Ding 24 Oct '12

24 Oct '12

Bruce, Perhaps you noticed the "Fit color" was red (large R-factor 0.074496, poor fit, also seen in the attached figure in the last email) when you loaded in the project file I sent you. When you hit Fit button again the "Fit color" might turn to green indicating good fit as shown in your result of a much smaller R-factor (0.004265). I did the following test on various versions of Demeter on my desktop and notebook computers both installed with Windows 7 SP1. Of course I uninstalled one version first before installing another. I tried to use Uninstall within the Program menu or use the Program manager. I tried to reboot or not to reboot after uninstallation or installation. Neither shows any difference. Fit color 0.9.10 green 0.9.11 red 0.9.12 red 0.9.13 red Only version 0.9.10 yields good fit. The latter versions would not give good fits even with repeated hitting the "Fit" button. I have no idea what causes these results but perhaps this observation provides a clue. Ku-Ding On 2012/10/22 上午 01:00, 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: Running (D)Artemis yields different result from that > shown in (D)Artemis instruction videos (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Oct 2012 12:36:10 +0000 > From: "Ravel, Bruce"<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Running (D)Artemis yields different result from > that shown in (D)Artemis instruction videos > Message-ID: > <47CED3CD722C2A439C0D1D1056B2132517C3B082(a)EX10-MB1.BNL.GOV> > Content-Type: text/plain; charset="us-ascii" > > > Ku-Ding, > > I don't know what to tell you. On the computer I am sitting in front of right now, I opened your two project files and hit the fit buttons, I get the same fit with only numerical differences. Here I am cutting and pasting from the two log files: > > old artemis: > > Chi-square = 4334.684537717 > Reduced Chi-square = 691.819976095 > R-factor = 0.004250325 > > amp = 0.8649100 +/- 0.0412220 (1.0000) > enot = 5.6049380 +/- 0.2950270 (0.0000) > delr = -0.0226780 +/- 0.0023790 (0.0000) > ss = 0.0082230 +/- 0.0003250 (0.0030) > > > new artemis: > > Chi-square : 4348.7359268 > Reduced chi-square : 694.0625918 > R-factor : 0.0042652 > > amp = 0.86526150 # +/- 0.04129645 [1.00000] > enot = 5.61081742 # +/- 0.29527844 [0] > delr = -0.02266589 # +/- 0.00238341 [0] > ss = 0.00822546 # +/- 0.00032571 [0.00300] > > > I don't acknowledge that there is a problem. > > B > > > ________________________________________ > From:ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding [tsuei(a)nsrrc.org.tw] > Sent: Thursday, October 18, 2012 1:15 PM > To:ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos > > Hi Bruce, > > I went through your (D)Artemis instruction videos and ran the latest > Demetris 0.9.12 with 0.9.13 update side by side to reproduce the > results. However, my running yields much poorer fitting results on Au > foil EXAFS, even the first shell (video 03). Actually it happened using > the older 0.9.11 too. I also went through your Lecture videos shot at > Diamond and ran (D)Artemis but could reproduce your results closely. I > have felt puzzled for quite a while why the simplest case Au foil does > work well. Today I tried to run the same Au data and fitting by the old, > last version of Artemis 0.8.014. I could produce very good fitting on > the first shell with the R-factor very near that shown in the video. I > made sure the math expressions for the fitting parameters amp, enot, > delr and ss are set exactly the same, with fitting range exactly the > same, in both programs. Their screen outputs file is attached. The saved > respective project files are also attached. I copied the fit outputs > into their journals. I would appreciate if you may review these results > and help clear my puzzle. > > Best regards, > > Ku-Ding > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 116, Issue 11 > **************************************** > . >

3 2

DORIS III operation ended
by Edmund Welter 23 Oct '12

23 Oct '12

Dear fellow XAFS user, yesterday (October 22^nd 2012, 8 am) the DORIS III storage ring in Hamburg was switched of for good. That means our 3 EXAFS beamlines are left without photons and user operation at these beamlines had to end. In the next 2 years we will build 2 new EXAFS beamlines at the PETRA III storage ring that will hopefully equally well serve the demands of our large user community as the 3 closed beamlines did during the last 20+ years. I know this mailing list is mainly about software and number crunching, but I thought the end of operation of a machine that produced so many beautiful numbers to be crunched with IFEFFIT/Athena/Artemis etc. might justify a short notice on this list. Anyway, to close the circle to the software, the end of user operation of HASYLAB's DORIS beamlines finally gives our users the chance to use this software and produce many nice papers during the coming months (Ah,wait, that was something different, New York, July 1977 :-). I am looking forward to see you all back at our PETRA extension beamlines in autumn 2014! Let me close this mail with the last line of data ever measured at the A1 EXAFS beamline: 7893.277 0 0 0 0 0 0 0 0 0 0 0 0 0 5.489 13.22 Best regards, Edmund Welter -- -------------------------------------------------------- Dr. Edmund Welter Deutsches Elektronen-Synchrotron DESY FS-Do Notkestr. 85 Email: edmund.welter(a)desy.de D-22607 Hamburg Phone: +49 40 8998 4510 Germany Fax : +49 40 8998 2787 --------------------------------------------------------

2 1

release 0.9.13.1
by Bruce Ravel 22 Oct '12

22 Oct '12

Hi, As a result of a problem brought to my attention by Ku-Ding Tsuei, I built a new installer of my software for Windows. The new installer, release 0.9.13.1 can now be downloaded from http://bruceravel.github.com/demeter/ This is an installer package. There is not a package for updating from 0.9.12. You must download and install the new installer package. This new installer is essential for anyone using Artemis. As Ku-Ding discovered, versions 0.9.11 through 0.9.13 all suffer from the same problem. If you are using Artemis from any of the affected versions, you *must* upgrade. I apologize for making three flawed releases of my software and I hope that no one has been too inconvenienced by my mistake. Once again, this mailing list and its most excellent community proves to be the best feature of our software! As a bit of consolation, I want to direct your attention to the Artemis Users' Guide. I have put a lot of effort into it in recent weeks. It is still not complete, but it is much enhanced. http://bruceravel.github.com/demeter/artug/index.html Regards, B -- 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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Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos
by Tsuei, Ku-Ding 21 Oct '12

21 Oct '12

Hi Bruce, I went through your (D)Artemis instruction videos and ran the latest Demetris 0.9.12 with 0.9.13 update side by side to reproduce the results. However, my running yields much poorer fitting results on Au foil EXAFS, even the first shell (video 03). Actually it happened using the older 0.9.11 too. I also went through your Lecture videos shot at Diamond and ran (D)Artemis but could reproduce your results closely. I have felt puzzled for quite a while why the simplest case Au foil does work well. Today I tried to run the same Au data and fitting by the old, last version of Artemis 0.8.014. I could produce very good fitting on the first shell with the R-factor very near that shown in the video. I made sure the math expressions for the fitting parameters amp, enot, delr and ss are set exactly the same, with fitting range exactly the same, in both programs. Their screen outputs file is attached. The saved respective project files are also attached. I copied the fit outputs into their journals. I would appreciate if you may review these results and help clear my puzzle. Best regards, Ku-Ding

2 1

feff800 path files
by Maria Zougrou 18 Oct '12

18 Oct '12

Hi, I'm trying to construct the heulandite structure running atoms and feff800 for the 3 Ca sites. Atoms gives me a feff8.inp I got the paths for Ca1 site, but it doesn't calculate the Ca2 paths. There doesn't seem to be a geometry problem, I don't get a message that some atoms are too close, what could be the problem? I'm attaching the files I'm using. Thank you

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possible bug: same Artemis project file, different results on 2 PCs
by Jeremy Thorbahn 10 Oct '12

10 Oct '12

Hi Bruce, I was putting together another post for the list (which is currently awaiting moderation since apparently my attached project files were too large) when I encountered some strange behaviour in Artemis. I tried opening my project file on my second PC to check that it would open fine for other members of the list. But by simply opening the project and clicking Fit, I was getting different results for my guess parameters on the two PCs. Both PCs are Windows 7 and updated to Demeter 0.9.13. Here is a link to the project file (trying to avoid size limitations for the list this time) http://dl.dropbox.com/u/10663174/ZnO.fpj and I will attach a screenshot of Artemis demonstrating what I am talking about from my two PCs. Since I am working to determine S02 and it is very different on each PC, I am hesitant to trust any of my results right now. Thanks Jeremy --

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determining S02 from ZnO vs. Zn foil
by Jeremy Thorbahn 09 Oct '12

09 Oct '12

[note: when putting together this post I discovered a possible bug regarding opening my project files on different PCs. I will submit that issue separately] Hi all: I am writing to probe the community's knowledge regarding my current problem in measuring S02. I have data on a series of glass samples containing ZnO. I also measured a ZnO crystalline powder, and a Zn foil was measured between detectors 2 and 3 (transmission mode) simultaneously with every run. My goal is to determine coordination numbers around Zn in the glass samples, which requires an accurate measurement of S02 for zinc. My main question is if there is any reason why the Zn foil would provide a more accurate result than the ZnO powder, or vice versa. I see no reason why it should be different, especially since this method depends entirely on the 'chemical transferability' of S02 in the first place. Nevertheless, I obtain different results from each, with S02 ~ 0.75 from the ZnO and ~0.88 from the foil. Statistically, the Zn foil dataset is "better" since it is a merge of all of my scans while there are only two scans of ZnO. However, part of me wants to trust the ZnO data more, for somewhat vague reasons such as that it is a "more similar" coordination environment to what I would expect in my samples, and that it was measured between the same two detectors, etc. If anyone has any experience that would indicate why one should be better than the other, I would love to hear about it. I will attach Artemis project files for each if you'd like to take a look at my fits. It is entirely possible that the discrepancy is due to an error in data processing or analysis on my part; I am by no means an expert. I hope the project files will not clog up anyone's mailbox, at a couple of megabytes each. Thanks, Jeremy

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Atoms bug & Athena request
by Bruce Ravel 04 Oct '12

04 Oct '12

Fred: Thanks for the bug report. It was a simple fix and I even uncovered another mistake in how crystal data that is entered by hand gets interpreted. Cool! Bradley: You'll be putin' on your dancing shoes after the next release. The combinatorial output files will be named as you requested. As always, thanks for the feedback. B -- 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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possible minor bug in atoms in artemis probably just me
by fred.mosselmans＠diamond.ac.uk 04 Oct '12

04 Oct '12

Hi Bruce et al. I searched the mailing list for something similar as i feel this is so obvious it must be there to find. However i could n't find it so ... Also there's are easy workable workarounds so it's not very important. I was XAS data for atoms that sit in substituted sites in a known lattices - Sr in calcite, If i build the calcite lattice in atoms stand alone and save output from there and read into artemis then substitute Sr for Ca before running Feff etc. And import to Artemis the world is lovely (viewed on the perspective does the program continue working perspective and no wider one.) If i try to either read my Sr prj and then do the same (i.e. typing the xtal paras in) within artemis or just try to do that before reading in the Sr data the program crashes as soon as i try to run atoms. The log file error line is: Can't call method "element" without a package or object reference at C:/strawberry/perl/site/lib/Demeter/Atoms/Absorption.pm line 31. If i read the saved atoms input file (from stand-alone) into Demeter it runs fine. So i guess something is set up when i save it in stand alone atoms that ain't inputted by me and that helps out. Maybe this is meant to happen as people are supposed to read in cif files and the like and for slow people like myself who enter things by hand there are obstacles left strewn on the road. Fred The atoms inp file is attached. This works however entering these same xtal paras by hand doesn't if it's my hand(s) There are more recent calcite lattice paras but that doesn't affect the process. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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D-Athena Request
by BradleyW Miller 03 Oct '12

03 Oct '12

Hi, A minor (I hope) request for D-Athena on PC's. When running a LCF (eg collected a spectrum and named it AsScan1) and exporting the LCF predicted results to an excel file, the default name of the newly created xls file is "combinatorial.xls". In Athena (on PC) the default output file name was the name of the spectra you are fitting (eg AsScan1.cvs). If the default in D-Athena could be the name of the original spectra again that would be very appreciated. If it could be the name of the spectra and the name of the fit space (eg. AsScan1.derv.xls or AsScan1.norm.xls or AsScan1.Chi.xls)... I may have to dance a jig in your honor. Thanks for your time and the freeware. 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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Quick first shell (QFS) theory in Artemis
by Bruce Ravel 02 Oct '12

02 Oct '12

Hi all, One of the bugs reported last week involved a project file which made extensive use of the "quick first shell" -- or QFS -- feature of Artemis. The bug involved a problem importing such paths from a saved project file. That bug has been fixed in the 0.9.13 release that I announce a short while ago. This project file that triggered the bug reminded me of an issue that has come up at several recent XAS training courses that I have participated in. In situations where rather little is known about the structure of a material, there is a thought that the QFS tool could provide a model-independent way of generating scattering amplitudes and phase shifts for atoms suspected of being in the material. While the QFS tool is a reasonable thing for atoms in the first coordination shell (hence the name!), this is a dangerous practice for atoms at longer distances. Artemis does not police its misuse in this way beyond simply issuing a warning sugesting that you may be doing something inappropriate. A full discussion of this topic is rather lengthy, so I will refer you to a wiki page that I wrote: http://cars9.uchicago.edu/ifeffit/Demeter/QFS If you have considered using the QFS tool for atoms beyond the first coordination shell, please read that wiki page all the way to the end. Regards, B -- 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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news + 0.9.13
by Bruce Ravel 02 Oct '12

02 Oct '12

Hi! I just gave Demeter's homepage a make-over. It's looking quite nice: http://bruceravel.github.com/demeter/ Links for downloading the windows packages are on the left. I also just posted version 0.9.13 on the downloads site and tagged the source code. I am trying something new with this release. Rather than rebuilding the whole Windows installer package with each release, I am now making Windows updater packages. It works like this: * Whenever I make a big change to Demeter or any of its dependencies, I will release a new Windows installer package. * For bug fixes and feature enhancements, I will release a new updater package. * The updater should be installed ON TOP OF the installer package. The current installer is Demeter 0.9.12. The current updater will update that to 0.9.13. If you have already installed 0.9.12 on your Windows computer, simply download and run the updater. If you have not yet installed 0.9.12, download both packages. Run the installer first, then run the updater. If that is not clear, everything is explained in detail at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater This update fixes all of the problems that were reported last week on the mailing list. Here is the list of changes: https://github.com/bruceravel/demeter/blob/master/Changes.org Regards, B -- 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: [Ifeffit] GDS parameters
by Matt Newville 01 Oct '12

01 Oct '12

John, On Mon, Oct 1, 2012 at 12:13 AM, John Farell <john_far(a)rediffmail.com> wrote: > > Dear friends, > > We are doing an experiment of temperature based phase transition. I need to get the values of all four GDS > parameters with errors. I know the theoretical model (i. e., atoms page). But to get all the four parameter > values with errors (amp, enot, delr, ss ). For this I cannot "set" all the parameters as well ass I cannot > guess all the parameters. Any suggestions for this problem ?. It's a bit hard for me to tell whether the question is about how to operate the program, or about some problem with operating it the way you think it should work. Why can't you set all the parameters? Are you unable to do this, or this something that you want to not do? Similarly, why can't you guess all the parameters? Is it that the Artemis GUI is not letting you do this? --Matt

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Athena closing on data import
by jiahui 01 Oct '12

01 Oct '12

Dear list, I have the problem of Athena closing on data import without any message. I went through the threads about this topic but fail to find the solution. I really appreciate that anyone can tell me how to fix it. Best regards, jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 28 September 2012 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 115, Issue 26 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: (D) Athena closing on data import (Bruce Ravel) 2. Re: Issue On Re-Open of File in Artemis (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2012 13:05:32 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] (D) Athena closing on data import Message-ID: <1870787.0HCcKRKktn(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Thursday, September 27, 2012 01:22:36 PM Jeremy Thorbahn wrote: > I had not anticipated that the > turnaround time on getting a fix for my problem would be within the > hour Well, it's good timing to post to the list as I am walking back to my desk after a couple of hours at the beamline. :) Glad it worked out for you. B -- 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 ------------------------------ Message: 2 Date: Thu, 27 Sep 2012 13:59:40 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issue On Re-Open of File in Artemis Message-ID: <6179390.OcvHgOAaDK(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Dan, Saving and reloading a project which uses a quick first shell path is very very broken right now. Getting it completely right may take a while. Sorry for that. B On Thursday, September 27, 2012 04:23:43 PM Daniel Whittaker wrote: > I am having an issue with a project i was working on yesterday - one i > hope can be resolved rather easily. > I was working on the project yesterday then i saved the file and > closed Artemis and all was well. > > However, today when i try and open the file and continue working on it > it instantly crashes the software on pressing FIT. First thing this > morning i updated to version 0.9.12. I am modelling using the first > shell fit that is built in - possible source of error? > I dont know the root cause of the issue as everything i have done here > i have done before with other datasets with no issue. I have tried > starting from scratch and reinstalling the software too but the issue > persists - it all works well (when startingg from scratch) until it > is saved and then tried to reopen. -- 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 ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 115, Issue 26 ****************************************

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Importing Multiple Data Sets into Athena
by Daniel Whittaker 01 Oct '12

01 Oct '12

Hello all, I am having a small issue when importing multiple data sets into Athena all of which have a reference channel. The issue i am experiencing is that when importing multiple data sets together they do not all import correctly. The first data set (of all selected) imports fine (The data is Np and the reference Zr foil) - it imports the reference file which can be aligned to the calibration Zr foil file. However, the remainder of the files do not work at all, the reference channel does not import correctly at all. I have tried (best as i can tell) all of the pre-process options to no avail. When i import them individually it works although I have to tell it what element the ref channel is and the edge and E0 (couldn't the edge and E0 be linked such that selection of one filled the other?) but this isn't too much of an issue. It is by no means a massive problem but i thought i would ask if there is a way around it or if it is a real bug? All other multiple data processing - such as "align marked groups" - works fine. Regards, Dan Whittaker

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(D) Athena closing on data import
by Jeremy Thorbahn 27 Sep '12

27 Sep '12

Hi all, Since I upgraded to the Demeter version of Athena some months ago, I have been basically unable to use it for some of my data since immediately upon import, the program shuts itself down with no message. I have Athena 0.8.056 installed as well and do not have the same issue there, so I have been using that version just fine but I thought I should report this issue or seek advice if it is a fault of my data and not the program. I have 0.9.12 and the issue persists. It only occurs with my set of data from the HXMA beamline at the Canadian Light Source as well, I have successfully imported data from other beamlines. I am using Windows 7 Home 64-bit. I have attached a sample data file which causes the crash. Regards, Jeremy

2 4

Demeter 0.9.12
by Bruce Ravel 26 Sep '12

26 Sep '12

Hi, I prefer not to make multiple releases of my software within a week. Unfortunately, there were just too many problems with last week's release, many of which were discussed right here on the mailing list. There are no new features, just a bunch of fixed bugs. The windows installer is available for download at https://github.com/bruceravel/demeter/downloads I tagged release 0.9.12 at github. For a complete list of changes see: https://github.com/bruceravel/demeter/blob/master/Changes.org Installation instructions: http://bruceravel.github.com/demeter/pods/installation.pod.html Reporting bugs: http://bruceravel.github.com/demeter/pods/bugs.pod.html or use the github issue tracker: https://github.com/bruceravel/demeter/issues As always, use this mailing list to report problems or to make suggestions. Regards, B -- 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: [Ifeffit] Why different installations of Atoms generate different results?
by Tsuei, Ku-Ding 25 Sep '12

25 Sep '12

Dear Matt, Thanks for your positive reply. You are opening a door to solving my problem. Attached are the fpj file generated by (D)Artemis and the apj file by the old Artemis, respectively. They cannot be opened by Note Pad nor by Word Pad, so I do not know their contents. I actually generated these projects from scratch solely by File -> open project or data (Au.inp) in (D)Artemis (or alternatively from Feff calculations -> Add) or by File -> Open file in the old Artemis without inputting any data. I just wish to look at what kind of EXAFS spectra generated purely by calculation before using them for model fitting. For (D)Artemis I went through Run Atoms -> Run Feff and could select any path from the path list, click chi(k) and then Plot selection. Of course now I know how to change k-weighting in the Plot window. I know which path is plotted because each path corresponds to a single curve with its own color and the path names are included in the legend. For the old Artemis I went through Run Atoms -> Run Feff and clicked import All paths. Again I could select any path in the list and Plot k, R and q with a choice of k-wieghting. Similarly each path corresponds to a single curve with its own color and the path names are included in the legend. These steps illustrate how I copied these plots into the pdf file I sent to the mail list. The path page in the old Artemis contains some more information as Path parameter math expression side by side to the Data & Paths list. They are N:6, S02:amp, delE0:enot, delR:delr and sigma^2:ss. Indeed you are right that changing them to numbers results in different plots. But I thought I should keep the default path parameters intact because they are supposed to be from calculation . Moreover, many of these path parameters do not have similar math expressions in (D)Artemis. See the next paragraph. Yes, I followed Bruce's suggestion to go through the on line manual of (D)Artemis with loading the Au foil data first then up to The Path Page, aiming for fitting real data. I could generate paths from the Atoms and Feff window and plot their chi(k) and so on, identical to the previous project without loading in Au foil data. I could drag the selected paths from the Atoms window into the Data window. By selecting each path the associated parameters are displayed, but only N and (blank)=(S02)(?)=1, the rest fields are empty. Are they supposed to be filled like in the old Artemis? I then copied in math expression contents exactly the same as in the old Artemis. The plotting shows only the Au foil data. Then I pressed the yellow Fit button. A message box pops up: Fit cannot continue: You have not defined any fitting parameters. Could you offer more clues to continue? The (fit) project up to now is saved and attached. There are more problems running (D)Artemis on my Windows 7 Professional SP1. The program can load in the saved (fit) project described above but always crashes on loading the first project without Au foil data, no matter which compatibility mode I choose before starting. It may be worth noting that only the (D)Artemis DOS window appears when choosing None, Windows 7, Windows Vista SP2, Windows Vista SP1, Windows Vista, Windows 2000, and Windows NT 4.0 SP5. On choosing Windows XP SP3, Windows XP SP2, Windows 98 / Windows Me, and Windows 95 there appears another DOS window on startup, D:\strawberry\perl\bin\perl.exe. I am not sure if these information may help solving the cash problem of (D)Artemis. On the other hand, the old Artemis can load in the project file with no Au foil data without crashing. Your help is greatly appreciated. Ku-Ding Date: Mon, 24 Sep 2012 09:10:48 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: bravel(a)bnl.gov Subject: Re: [Ifeffit] Why different installations of Atoms generate different results? Dear Ku-Ding, On Sat, Sep 22, 2012 at 8:13 AM, Tsuei, Ku-Ding <tsuei(a)nsrrc.org.tw> wrote: > Hi Bruce, > > Thanks a lot for your reply and comments particularly on how to change > k-weight in (D)Artemis-Atoms. Sorry for not being able to provide clear > results stating exactly where my confusion came from. I was not sure if an > attachment could be readable to this email list but let me try this time. > Certainly I do not know how to retrieve data values from these plots yet. > > The attached pdf file compares the output plots of k^n*chi(k) with n=0, 1, 2 > and 3 of the Au L3 EXAFS of the shortest path calculated from Artemis-Atoms > in Demeter and old Artemis. I suppose to read identical plots of k^n*chi(k) > from different programs but they are not. That is why I feel confused. > > Your help on clearing my confusion is appreciated. Then I can move on to do > model fit on real data. > > Ku-Ding The two results you show are quite different, but you don't tell us how you got them, expect to say the they were calculated by Artemis-Atom and D(Artemis)-Atoms. This is an incomplete description, allowing many possible differences. To be clear, Atoms only generates the feff.inp file. These should be the same between the two versions, especially for as simple a case as fcc Au. Next, Feff has to be run. This will be the same, assuming the input files are the same. Next, Artemis reads in the output files from Feff (you say you're using the first shell only, but I encourage you to verify that), applies Path Parameters to these, and generates chi(k). Are the number of Paths used, and the Path Parameters (N*S02, sigma2, e0, deltaR) the same in these two calculations? I'd guess that they are not. Providing plots of outputs is helpful, but as is said many times here, providing the project file is much more helpful as it shows not only the final result, but how you got there. Cheers, --Matt ------------------------------

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Opening (D)Artemis error
by Raimundo Lora Serrano 24 Sep '12

24 Sep '12

Dear Bruce or colleagues, Below is the error written in the log file after importing a saved (D)Artemis project. I cannot save an Artemis project and open it again. Just have to start (again) from the beginning. As stated previously, the program just fails to launch. Thanks in advance, Raimundo ------------- Attribute (initial) does not pass the type constraint because: Validation failed for 'Str' with value undef at constructor Demeter::GDS::new (defined at C:/strawberry/perl/site/lib/Demeter/GDS.pm line 189) line 185 Demeter::GDS::new('Demeter::GDS', 'gds', 'guess', 'expandsto', '', 'mark', 0, 'group', 'lxjcm', 'stored', '', 'error', 0, 'highlighted', 0, 'Use', 1, 'trouble', '', 'mathexp', 1.00000, ...) called at C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1410 Demeter::Fit::__ANON__('Demeter::Fit=HASH(0xc46c914)', 'folder', 'C:\Users\Rai\AppData\Roaming\demeter\stash\_dem_rhysjijw\fits...', 'regenerate', 0) called at C:/strawberry/perl/site/lib/Moose/Meta/Method/Overridden.pm line 38 Demeter::Fit::deserialize('Demeter::Fit=HASH(0xc46c914)', 'folder', 'C:\Users\Rai\AppData\Roaming\demeter\stash\_dem_rhysjijw\fits...', 'regenerate', 0) called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 359 Demeter::UI::Artemis::Project::read_project('HASH(0xa7b54d4)') called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm line 833 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x4c0b39c)', 'Wx::CommandEvent=SCALAR(0xc46f51c)') called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm line 346 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x4c0b39c)', 'Wx::CommandEvent=SCALAR(0xc46f51c)') called at C:\strawberry\perl\site\bin\dartemis.bat line 29 eval {...} called at C:\strawberry\perl\site\bin\dartemis.bat line 29

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Why different installations of Atoms generate different results?
by Tsuei, Ku-Ding 24 Sep '12

24 Sep '12

Hi Bruce, I am a novice of this community and actually have less than two weeks of experience using IFEFFIT (version 1.2.11 with iff_013 update) and its front end packages Demeter (version 0.9.11) and its predecessor Horae (Athena, Artemis etc. version 0.8.014) running under Windows 7 Professional SP1. They are excellent software guiding me quickly into this EXAFS world. Thanks a lot. However, I feel confused by viewing different results (chi(k)) calculated from three installations of Atoms, namely Atoms within (D)Artemis, stand alone (D)Atoms, and Atoms within the old Artemis. I then used the simplest Au.inp as the input for all. I checked the path outputs making sure the generated paths are identical and selected individual paths. To my surprise the chi(k) curves have different envelopes and magnitudes from 3 Atoms. It seems to me that chi(k) are calculated from the same feff6 program and should be identical from any installation; no FT range is involved to affect chi(R). Could you help clarify my confusion? Perhaps the new Demeter can be improved further. It seems that only k^2*chi(k) is plotted in Atoms within (D)Artemis, and only k*chi(k) is plotted in the stand alone (D)Atoms by viewing the vertical labels in plots. There seems no obvious place I can change k-weighting like in the old Artemis. I have not been able to find where, such as Edit preference in the old Artemis, I can change the default parameters, or learn what parameters are used in doing FT (kmin, kmax) or window function and so on. I learn these preference parameters quickly owing to the extensive documents built-in side by side with "action tabs" in the old Artemis and the link to html documents in the old Athena. By the way, watching your videos is an excellent way to learn Demeter but I had to pause to search related projects or files to run side by side with videos; some links with video download sites could be very helpful. Look forward to reading your answers and utilizing the more powerful Demeter. Thanks again. Best regards, Ku-Ding Tsuei ------------------------ Ku-Ding Tsuei, PhD Associate Scientist National Synchrotron Radiation Research Center 101 Hsin-Ann Road Hsinchu Science Park Hsinchu, TAIWAN 30076, ROC email: tsuei(a)nsrrc.org.tw

3 4

Demeter 0.9.11
by Bruce Ravel 20 Sep '12

20 Sep '12

Hi, Yesterday I posted a new version of the Windows installer for Demeter at https://github.com/bruceravel/demeter/downloads and tagged version 0.9.11. A couple problems recently discussed on this mailing list that have been addressed: * I believe I fixed the problem of Demeter not co-existing on a windows computer with another version of perl. See this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-August/010683.html * Athena now correctly imports data with a reference of another element. See this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012- September/010700.html * Improved import of project files from the old version of Artemis. See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012- September/010718.html There are several other improvements. For a complete list see: https://github.com/bruceravel/demeter/blob/master/Changes.org Installation instructions: http://bruceravel.github.com/demeter/pods/installation.pod.html Reporting bugs: http://bruceravel.github.com/demeter/pods/bugs.pod.html As always, use this mailing list to report problems or to make suggestions. Regards, B -- 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

1 0

path averaging in Artemis
by Simon Cassidy 19 Sep '12

19 Sep '12

Dear Bruce, I've run into a problem with the new artemis' path finder. When running the attached feff.inp file in atoms, two separate paths are merged together. The two paths it is merging are Se-Fe2 (N=4, reff=4.456) and Se-Fe3 (N=8, reff=4.465) which it gives as (N=12, reff=4.4621). The same problem occurs for these paths when starting with the Fe core. The same feff.inp file generates the right path list when run in the old version of artemis. Please could you take a look at this? Many thanks, Simon

2 1

Mac OS X Mountain Lion iXAFS
by Kyler Carroll 19 Sep '12

19 Sep '12

Hello, I havent seen a post yet pertaining to this issue so I thought I would share and perhaps see if there are solutions to my problem. I have recently upgraded my mac to run the new OS X Mountain Lion and in the process noticed that apple no longer supports or includes X11. They instead have moved to XQuartz http://xquartz.macosforge.org. I downloaded the new XQuartz to my computer and obviously still cannot access iXAFS. I was wondering if someone could offer some advice for me so that I can still run iXAFS on my macbook (Macbook pro OS X version 10.8, 2.3 GHz intel core i5). Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

5 4

Demeter will not start without admin permissions
by Jason Gaudet 17 Sep '12

17 Sep '12

Hi all, I came across another Demeter startup issue that seems different from the mingw and perl conflicts previously discussed, and I'm pretty stumped. System: Demeter 0.9.10 on Windows 7 32bit Issue: All Demeter apps (dathena.bat, dartemis.bat, etc.) will no longer run as a user. Apps will only run when opened as an administrator. Trying to open as a user causes cmd window and splash screen to pop up and instantly disappear. No "compatibility mode" seems to help. The problem seemed to pop up sometime between August 2 and August 8, after upgrading to 0.9.10, but I downgraded to 0.9.0 and the problem persisted, so (likely) something changed in my Windows environment and not Bruce's software. The log: Can't load 'C:/strawberry/perl/site/lib/ auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Demeter.pm line 36 Compilation failed in require at C:/strawberry/perl/site/lib/Demeter.pm line 36. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter.pm line 36. Compilation failed in require at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 25. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 25. I exchanged a few Emails with Bruce before realizing this is a bit more complex than I thought. We've thus figured out (I think) - Explicitly giving myself full permissions to C:/strawberry/perl/site/lib/auto/Ifeffit/ and %APPDATA%/demeter has no effect. - Although I have a cygwin version of perl, demeter is calling up the right one each time. Invoking perl with the full path in e.g. dathena.bat has no effect. I suspect the problem might not be in perl or any of Bruce's code, but in some behavior of ifeffit that was previously condoned by Windows but now requires elevated permissions. I understand ifeffit is written in fortran90 but I don't know if there's any aspect of it that might be affected by recent MS Visual C++ updates I've done on my laptop. (MS Visual C++ 2008 x86 9.0.30729.17 and MS Visual C++ 2010 x86 10.0.30319). I'm pretty sure MSVC2008 coincides with the time Demeter stopped working but it could just be a coincidence. There are also of course various security updates I can't easily sort through. I was hoping Matt might be able to point me in the right direction here; I don't know the inner workings of IFEFFIT and I might be far off track already. Thanks, Jason

3 5

Re: [Ifeffit] questions about SEXAFS
by Zhaomo Tian 12 Sep '12

12 Sep '12

1 0

Problem with Demeter Artemis 0.9.10
by Matt Frith 10 Sep '12

10 Sep '12

Hi All, I have come across an bug with Demeter 0.9.10. When I go to open an old format Artemis project file I will see, "Converting old-style project file to Demeter serialization" written in the progress bar, and then the program will quit without opening the file. The problem occurs on both 32 and 64bit Windows 7. I uninstalled the program and reinstalled Demeter 0.9.9 and there are no issues with 0.9.9. The dartemis.log contains: Can't locate object method "inp_is_feff8" via package "Demeter::Feff::External" at C:/strawberry/perl/site/lib/Demeter/Fit/Horae.pm line 110. I hope this is helpful. It seems to be similar to the problem posted by Riamundo, and I hope that I have not missed a previously posted solution. Attached is one of the project files that I have used. Sincerely, Matt Frith

3 2

Washington (ifeffit)
by washington gomes 10 Sep '12

10 Sep '12

Dearcolleagues, I'm using the Ifeffit program command-line version 0.9c for win32 to analyze my data in the XAFS region. I did treatment at a data using ifeffit program , after making this adjustment i typed the following command: Ifeffit> save (my.save) Was saved a file with all parameters set. Then I typed the following command: Ifeffit> restore (my.save) Notonefilewasrestored. Whatcommands should I enter to retrieve this data set for use in another program like origin 6.0 professional. Sincerely yours: Washington

1 0

Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
by Zhaomo Tian 06 Sep '12

06 Sep '12

3 2

Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?
by Zhaomo Tian 06 Sep '12

06 Sep '12

1 0

Re: [Ifeffit] Ratio of peak amplitudes in R-space
by Rana, Jatinkumar Kantilal 05 Sep '12

05 Sep '12

Dear Christopher, Dear Scott, Thank you so much for your valuable feedback. I will now attempt to quantify the observed change in amplitude ratios by fitting data with theoretical standards. With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mittwoch, 5. September 2012 15:26 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 115, Issue 2 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. Ratio of peak amplitudes in R-space (Rana, Jatinkumar Kantilal) 2. Re: Ratio of peak amplitudes in R-space (Christopher Patridge) 3. Re: Ratio of peak amplitudes in R-space (Scott Calvin) 4. How to write feff.inp file for CO adsorbed Cu? (Zhaomo Tian) 5. Re: How to write feff.inp file for CO adsorbed Cu? (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Sep 2012 12:01:01 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Ratio of peak amplitudes in R-space Message-ID: <F11168F9CA572049ADA84F3072DE5DB135C7180D@didag2> Content-Type: text/plain; charset="us-ascii" Dear Ifeffit community, I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ? For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process. I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone. As we know that amplitude of peak decreases with increase in distance from central absorber. Can I compare the amplitude ratio of first two peaks for various states of same sample ?? Many thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

1 0

Ratio of peak amplitudes in R-space
by Rana, Jatinkumar Kantilal 05 Sep '12

05 Sep '12

Dear Ifeffit community, I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ? For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process. I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone. As we know that amplitude of peak decreases with increase in distance from central absorber. Can I compare the amplitude ratio of first two peaks for various states of same sample ?? Many thanks in advance !!! With best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

4 3

How to write feff.inp file for CO adsorbed Cu?
by Zhaomo Tian 05 Sep '12

05 Sep '12

2 1

Launching Problem (D)Athena and Co.
by Alfred Hummer 30 Aug '12

30 Aug '12

Ok, I found the problem. There was a version of MinGW installed on the computer. I just placed the MinGW PATH variables after the strawberry ones, and it worked. So it was a special conflict between software packages on my PC. best, Alfred

3 4

Troubles opening saved Artemis (Demeter package) project files.
by Raimundo Lora Serrano 29 Aug '12

29 Aug '12

Hi all, I'm new in the list and I didn't find any problem like this one in the Mail Archive. I have installed Demeter on Windows 7 (Ultimate version, SP1). Upon creating and saving a (new) Artemis project file I tried to open it both by double-clicking or by first launching Artemis and importing it from the "Open project data" option but the Artemis windows stick around a few seconds, and then disappear, along with the black DOS window. No notice of a crash appears; the program just fails to launch. This not only happens with this file but other files cannot be opened also after being saved. Any(s) suggestion(s)? Many thanks in advance. Raimundo

2 1

Washington (Atoms)
by washington gomes 25 Aug '12

25 Aug '12

Dear Colleague, Iwould like you to help me with attached file átomos.inp I am sending to you. Typed parameters atomic position of La0.7Sr0.3CoO3 atoms on the web.Atomsin the program for generating lists of atomic coordinates from crystallographic data and appearedthe following message after running atoms. These sites: "La1" "Sr1" generate one or more common positions and their occupancies sum to more than 1. Yours sincerely: Washington C. M. Gomes

2 1

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.

1 0

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

1 0

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

5 6

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

15 Aug '12

message deleted at request of sender

2 1

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

2 1

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

2 1

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

6 6

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 >>

3 2

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

3 2

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

2 1

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 28 Jul '12

28 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 15 Jul '12

15 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 15 Jul '12

15 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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