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

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 09 May '13

09 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

2 1

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

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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

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ATOMS: Partial occupancies -how to edit .cif File
by Sanwald, Kai 23 Apr '13

23 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

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background removal - spline range kmin
by Reagen Lan 22 Apr '13

22 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

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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

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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

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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>

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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>

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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

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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

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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

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Possible bug in atoms files generation by Artemis
by Devender 28 Mar '13

28 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

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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 >> >

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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

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Re: [Ifeffit] Building ifeffit Mac Mountain Lion
by Matt Newville 22 Mar '13

22 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

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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

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