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

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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data point limits in Athena?
by Göttlicher, Jörg 05 Aug '13

05 Aug '13

Hello, does someone now if there is a limit of data points for Athena/Athena-Demeter? I have realized that a XAFS data file containing about 2500 data points is not read in properly in Athena (v. 0.8.061) and is started at zero energy and cutted of before the end of the data rows in Athena-Demeter v. 0.9.9, whereas the same file reduced to about 1600 data points was read in without any problems in both Athena versions. I hope that someone has an idea about the reason(s) and how to manage the read in of such data without prior treatment? Using the binning mode or truncation (to cut off the zero energy point, that occured when reading in with Demeter 0.9.9), did not succeed because the data were not treated correctly during the import. Best regards Joerg

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Postdoc Position
by Jeff Terry 30 Jul '13

30 Jul '13

Hi All, Hope this is ok to post. I have an open postdoc position in my group. Chemistry, physics, materials science, nuclear engineering, or similar fields will be considered. Synchrotron measurements will involve EXAFS, XRD, PES, and others. You can see the details at: http://t.co/xNnYrMgMly Thanks, Jeff Jeff Terry Associate Professor of Physics Illinois Institute of Technology Sent from my iPhone

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Two-Phase EXAFS fitting
by Taehoon Kim 29 Jul '13

29 Jul '13

Dear users in Ifeffit forum, I'm working at a cathode material represented by xLi2MnO3.(1-x)LiMO2 (M = Mn, Ni, and Co). This material can be described as a solid solution between Li2MnO3 and LiMO2. The main phase is the LiMO2 (M = Mn, Ni, and Co), which shows a trigonal crystal structure (R-3m). The integrated phase is the Li2MnO3, which exhibits a monoclinic structure (C2/m). What would be the right way to perform the EXAFS fitting using Artemis for the multi-phase materials ? I was thinking creating two crystal structure set using ATOMS, and perform feff calculation for each, and then choose scattering path from each atom set. I wonder whether this is an appropriate approach ? and how can I apply the ratio of each phase (let's say x is 0.6) in the fitting process ? Thank you in advance ! Kind Regards Taehoon

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DAthena crashes when reconstructing data from PCA
by Scott Calvin 29 Jul '13

29 Jul '13

Hi Bruce, Athena is crashing every time I try to "Reconstruct Data" in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction. I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. --Scott Calvin Sarah Lawrence College

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