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

issues with Athena (new Demeter package)
by Adrian Gainar 12 Aug '13

12 Aug '13

Hi All, I experience two issues with Athena of the updated new Demeter package, which it would be easier to describe: 1) when I open successively two .prj files that contain each a fitted spectrum, Athena seems to remember only the positions, widths and amplitudes of arctan and gaussian curves of the spectrum I open first; this translates to the fact that for the other fitted spectra that I open afterwards, it remembers the peak positions, widths and amplitudes of the curves belonging to the initially opened spectrum. The result of this issue is that I need to enter manually each time these values in order to get the fits back again - do you have any suggestions how this can be fixed?; 2) another issue is that after spectra calibrations, the spectrum does not appear to be calibrated. More specifically, when one checks the centroid positions of arctan or gaussian curves directly on the spectrum, the values don't correspond with the ones in the boxes, which I believe that means the calibration did not happen after all. Thank you very much in advance for any suggestions or ideas! Best wishes, Adrian ******************* Adrian Gainar PhD student Office: D37 School of Chemical Engineering and Analytical Science Jackson's Mill University of Manchester Manchester M13 9PL UK e-mail address contact: adrian.gainar(a)postgrad.manchester.ac.uk<mailto:adrian.gainar@postgrad.manchester.ac.uk> office telephone no.: +44(0)161 306 4362

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Fwd: Linear Combination Fitting using ATHENA
by Scott Calvin 09 Aug '13

09 Aug '13

I just noticed part of this thread went off-list. That's easy to do by mistake sometimes. I'm forwarding this part of the exchange to the list so that we don't start talking too much in circles. --Scott Calvin Sarah Lawrence College Begin forwarded message: From: Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> Subject: Re: [Ifeffit] Linear Combination Fitting using ATHENA Date: August 9, 2013 8:54:59 AM EDT To: Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> Hi Teck Kwang, An Fe3O4 spectrum is available at the CARS XAFS database: http://cars.uchicago.edu/~newville/ModelLib/search.html --Scott Calvin Sarah Lawrence College On Aug 9, 2013, at 8:35 AM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> wrote: Hi Scott, My spectrum standard fits extremely well with FeO: the sample spectrum's conformation to FeO's can be seen even by just superimposing both spectra together. Through XRD, it was confirmed that Ferrite (-Fe2O4) is the primary form of Fe but unfortunately I did not have any Ferrite standard compound with me during the actual XANES analysis. I am now suspecting that both FeO and -Fe2O4's spectra might be similar to each other. Do you have the spectrum for ferrite (Mg-ferrite if possible) by any chance? Thanks and kind regards. Teck Kwang On 9 August 2013 21:00, Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> wrote: Hi Teck Kwang, Molar percent by absorbing atom. In other words, if the best fit is 60% Fe(II), that corresponds to 60% of the iron atoms being Fe(II). But note that XANES depends on more than just valence state. Does the FeO and Fe2O3 combination fit the XANES well? Do those compounds correspond well to the actual compounds expected in the material? Did you try other iron standards? --Scott Calvin Sarah Lawrence College On Aug 8, 2013, at 11:37 PM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu><mailto:teck.kwang.choo@monash.edu<mailto:teck.kwang.choo@monash.edu>>> wrote: Hello, I have been using ATHENA to perform Linear Combination Fitting (LCF) on my XANES spectrum to quantify the amounts of Fe (II) and Fe (III) in my samples using only FeO and Fe2O3 as standards. The results showed a majority of Fe (II), which is contrary to what was expected. This made me wonder if the LCF results from XANES is a molar percentage (mol %) or weight percentage (wt%). Could anyone enlighten me on this matter? Thanks! --

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tracking atom positions
by Bruce Ravel 08 Aug '13

08 Aug '13

Matthew said: > As it is now, if you want to describe your unknown structure as a > distorted version of the one for which FEFF was run, you have to > enter formulas for distances by hand. For instance, suppose you're > doing a substitutional dopant and you want to use Artemis to fit the > displacement of the impurity off-site and the dilation/contraction > of the first-neighbor shell. As it is now, you have to do the > algebra yourself to compute all the distances in terms of the > distortion parameters. It would be really nice if there were some > syntax for describing the alteration of atom positions, from which > Artemis would automatically compute the displacements. This might > have to be a new class of parameters. Such a computation would > cover the MS paths as well. What it would still NOT do is account > for the effect of leg-to-leg angles on MS paths (deviation from > focusing/backscatter), but it would be a step. I realize that this > would be a big job to implement in a nice way that wouldn't break > everything that came before, but it would be super useful and make > the IFEFFIT team (yet again) heros to the community It's nice to start a new thread when you start a new thread, so I'm starting a new thread. :) I understand exactly what you are asking for. In short, you would like to be able to parameterize atom positions, possibly even crystallographic parameters, and have those propagated through to the math expressions for delta_R for the paths. In fact, Demeter has some of what's needed already built in. There are two things needed to implement that with the way things currently work. 1. The pathfinder needs to remember the all the scattering geometries that contribute to a degenerate set of paths so that a parameterization has the possibility of breaking degeneracies. 2. In the case of using crystal data, Atoms needs to remember the symmetry operations that were done to place each atom in the cluster. This would allow Demeter to propagate a change in a crystal parameter through to delta_R. #1 already exists in Demeter. #2 is something I worked on in the past, but never got working to my satisfaction. The point is that most of #2 is in there, but commented out. That is, it's reasonably close. As you suggest, the hard part is presenting this to the user. I have actually been thinking about this problem lately and am interested in getting back to it. I have another big feff-interface improvement to work on first (an idea for dealing with Feff calculations over multiple, inequivalent sites in a user-friendly and user-efficient way), but I'll think about it. I should mention that Shelly has implemented something like this before for use with Matt's ancient feffit program. You might be able to get her to chime in.... B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science 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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FEFF report: Hard tests failed in fovrg.
by Naumova, Maria 07 Aug '13

07 Aug '13

Dear EXAFS people, I have a question that appeared in FEFF and IFEFFIT several times. Still I didn't get an answer. Here are some links to this question discussed or asked previously: http://cars9.uchicago.edu/feff/feffusers/msg00255.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02675.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01532.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html I have EXAFS of several similar organic complexes - copper which has S, N and Hal (Cl or I), and sometimes copper in its first coordination shell and more C and N in ligands. I have structural data for them which I use as a model for FEFF. When I run FEFF via Artemis I get the following report for all my substances (I have 6 potentials in the list): Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 ...and so on... overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 ...and so on... muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. ...and so on... Feff done. Have a nice day. In FEFF documentation I read the following: "To save time the code calculates the overlapped atom potential for each unique potential only once, using as a sample geometry the first atom in the atom list with a given unique potential index. Thus it is essential that the neighborhood of that sample atom be representative. Failure to do so may cause the code to perform poorly. " http://leonardo.phys.washington.edu/feff/Docs/feff6/feff6-4.html#pot I think that at least for copper and halogen or sulfur geometry of every atom in the atom list is representative. "Often we receive reports by users of older versions of FEFF of bugs that are fixed in the latest releases. Other code failures can often be traced to input file errors, sometimes quite subtle. An example would be non-physical widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any .dat file) and possibly a failure of the phase-shift program to converge." http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html Here the reason is explained. Since it's an organic complex local distances between neighrours are small, but distances between parts of molecule can be quite big. Still it's not "non-physical widely spaced distributions of atoms". For example distance from copper to the first shell is 2 - 2.3 A (2.6-2.7 to I and Cu). To the "second shell" (ligand atoms connected to the first shell atoms or not connected but close to central atom) - 2.9 - 3.4 A. Finally what I want to know: May I use this FEFF calculation as a valid base for future fit? Or this error means that FEFF doesn't work correct and I can't rely on its output? If the phase-shift program failed to converge does it mean that it could stop in some completely unrealistic result? I attach several FEFF inp files which have this problem. Thanks for your help, Maria Naumova PhD student in DESY

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linear combination fitting
by Shaofeng Wang 07 Aug '13

07 Aug '13

Dear Bruce, I am using Dathena to do some linear combination fitting. In your program, you give three methods for fitting, nomal, derivate and chi(k). I got three different results using these methods. My question is which one is better to obtain more reasonable result or what the purpose of each method is. Regards, Shaofeng

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Re: [Ifeffit] linear combination fitting (Matt Newville)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Matt wrote "Please avoid asking "why is the blue curve always lower than the red curve"?" By using a negative offset in Athena you can get the red curve below the blue curve :-) cheers Fred I hope Matt doesn't have the monopoly on jokes. -- 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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. Re: Split white line in TcO2 spectra and similar Tc(IV)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Dear Wayne Thanks for your explanation Fred -- 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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Split white line in TcO2 spectra and similar Tc(IV) octahedral environments
by fred.mosselmans＠diamond.ac.uk 06 Aug '13

06 Aug '13

Hi, Tc(IV) which is a d3 configuration ion, when octahedrally coordinated by O ligands eg TcO2 has what I would call a split white line (see attached image) in the K-edge XANEs. Others might call it a very strong second resonance . The image is from TC in an iron oxide phase by the way. One of my collaborators asked me why does the edge have two peaks.? This is a simple question but is there a simple answer? In a literature search although the shape seems accepted I couldn't find a straightforward explanation. Ce(IV) L3 spectra have a split white line due to some sort of crystal field effect but there the transition (L3-edge) is direct to d states so it's a bit more obvious. Here it's an s-p transition formally so you'd think it must be some sort of split p state explanation , but I am not sure why? I am sure you could XANES simulate this to reproduce it but that doesn't answer the question why in simple terms. It may be it 's a complicated band structure explanation and so there is no simple answer but if anyone has read or knows one , I 'd be interested,. There are some similar effects in the white lines of Zr K-edge spectra , when the Zr is also octahedral but I can only find reports of that not the reason for it. BTW This is definitely pure Tc(IV) so the answer is not multiple oxidation states., which has been used to explain different Tc split white lines in other situations. Thanks 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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Re: [Ifeffit] Some doubts about Artemis (Scott Calvin and Bruce Ravel)
by Miguel A. Gómez 06 Aug '13

06 Aug '13

Thank you Scott and Bruce for your answers. From now, I will always take a look to the mail archive before to do any question. I guess it should be annoying to have to answer the same everytime. Sorry for that. Related to my second doubt (the possible bug of Artemis), please find attach my work project in case you could take a brief look of this. Maybe the problem is in my computer, so don't waste too much time with this... Best regards, Miguel > Message: 3 > Date: Mon, 05 Aug 2013 23:06:51 +0200 > From: "Miguel A. =?utf-8?b?R8OzbWV6?=" <miguel.gomez(a)ica.csic.es> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Some doubts about Artemis > Message-ID: > <20130805230651.Horde.tJbhajp6yHZSABPrpsjx4gA(a)webmail.csic.es> > Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes > > > Hi everyone, > > I have two doubts about the use of the Artemis software: > > 1) Is it possible to use the coordination number of one path (N) as a > variable? Because I tried to do it, but I am unable to write any > letter in the path parameters set. > > 2) When I change the 'Fourier transform parameters' in order to > perform a new fit, the "window range" (green line) in the plotting > screen wont change the range (at least visually) and remains between > the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form > to modify this? > > Thank you in advance, > Miguel > ________________________________________________________________________________ > > Miguel Angel Gomez Gonzalez > > PhD. Student > Institute of Agricultural Sciences (ICA) > Spanish National Research Council (CSIC) > > > > ------------------------------ > > Message: 4 > Date: Mon, 5 Aug 2013 17:25:22 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Some doubts about Artemis > Message-ID: <7DAE38F1-36DF-47C8-83DB-6FC250D4C553(a)slc.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Miguel, > > On Aug 5, 2013, at 5:06 PM, Miguel A. G?mez <miguel.gomez(a)ica.csic.es> wrote: >> >> 1) Is it possible to use the coordination number of one path (N) as a >> variable? Because I tried to do it, but I am unable to write any >> letter in the path parameters set. > > Because N only appears in the EXAFS equation as part of the product > S02*N, coordination number can be fit by putting the variable in the > S02 field. For example, the coordination number in the N box can be > changed to 1, and the entry in the N field can be changed to S02*N, > with N then made a "guess" variable. Of course, you can't sensibly > fit every N and fit S02...something has to be set. > >> >> 2) When I change the 'Fourier transform parameters' in order to >> perform a new fit, the "window range" (green line) in the plotting >> screen wont change the range (at least visually) and remains between >> the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form >> to modify this? > > Usually it changes the next time you plot. If it doesn't, you are > experiencing a bug that is specific to your circumstances (hardware > + OS + project). Those kinds of bugs are, unfortunately, difficult > to track down. > > --Scott Calvin > Sarah Lawrence College > > > > > > ------------------------------ > > Message: 5 > Date: Mon, 05 Aug 2013 17:27:22 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Some doubts about Artemis > Message-ID: <520018BA.7020306(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > On 08/05/2013 05:06 PM, Miguel A. G?mez wrote: >> >> Hi everyone, >> >> I have two doubts about the use of the Artemis software: >> >> 1) Is it possible to use the coordination number of one path (N) as a >> variable? Because I tried to do it, but I am unable to write any letter >> in the path parameters set. > > See > http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03646.html > and the responses that follow. > > We've been answering questions on the mailing list for many years now. > Searching through the archives is a really good use of time. > >> 2) When I change the 'Fourier transform parameters' in order to perform >> a new fit, the "window range" (green line) in the plotting screen wont >> change the range (at least visually) and remains between the defaut >> values (r from 1 to 3 or k from 2 to 10). Is there any form to modify this? > > As described, this is certainly not correct. Attached are two screen > shots. For the first one, I imported a project file and immediately > clicked the "Rk" button. I changed the values of kmax and Rmax, then > clicked the "Rk" button again. The values were clearly updated > correctly for the second plot. > > Please see my post to the mailing list from only 30 hours ago (!!) > about the difference between an actionable bug report and complaining > into the wind: > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/011284.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science 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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Some doubts about Artemis
by Miguel A. Gómez 05 Aug '13

05 Aug '13

Hi everyone, I have two doubts about the use of the Artemis software: 1) Is it possible to use the coordination number of one path (N) as a variable? Because I tried to do it, but I am unable to write any letter in the path parameters set. 2) When I change the 'Fourier transform parameters' in order to perform a new fit, the "window range" (green line) in the plotting screen wont change the range (at least visually) and remains between the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form to modify this? Thank you in advance, Miguel ________________________________________________________________________________ Miguel Angel Gomez Gonzalez PhD. Student Institute of Agricultural Sciences (ICA) Spanish National Research Council (CSIC)

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