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

Questions
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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atoms crashes
by Jesús Eduardo Vega Castillo 03 Jun '16

03 Jun '16

Hello everyone, I have manually introduced the crystal structure of La4Fe3O10 into Atoms and generated and .inp file. The structure contains 2 sites of La, 2 sites of Fe and 4 sites of O. When I try to run Atoms from this file it crashes. This is the inp file: ## This Atoms file was generated by Demeter 0.9.24 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = La4Fe3O10 (LSFC) space = I 4/m m m a = 3.83900 b = 3.83900 c = 27.87050 alpha = 90.00000 beta = 90.00000 gamma = 90.00000 rmax = 5.00000 core = Fe1 # polarization = 0.0 0.0 0.0 shift = 0.00000 0.00000 0.00000 atoms # el. x y z tag La 0.00000 0.00000 0.56860 La1 La 0.00000 0.00000 0.70130 La2 Fe 0.00000 0.00000 0.00000 Fe1 Fe 0.00000 0.00000 0.13840 Fe2 O 0.00000 0.50000 0.13810 O1 O 0.00000 0.00000 0.06980 O2 O 0.00000 0.00000 0.21050 O3 O 0.00000 0.50000 0.00000 O4 Any help would be appreciated. Yours, Jesús

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Re: [Ifeffit] Heavy Scatterer Resonance
by Matt Newville 02 Jun '16

02 Jun '16

Pieter, Please use the ifeffit mailing list for questions about XAFS Analysis. I am CCing this reply to that list. On Thu, Jun 2, 2016 at 2:35 AM, Pieter Tack <Pieter.Tack(a)ugent.be> wrote: > Dear Dr. Newville, > > > During the analyses of some metallic Au EXAFS I noticed the Au-Au single > scatter first shell is characterised by a split peak in the chi(R) > spectrum. I was wondering what caused this, as I would expect a single > scatter path resulting in only one scatter distance and thus one peak in > the chi(R). However, I could not find much on the matter except for a quote > of you stating it is "due to the resonance in the scattering for heavy > scatterers" ( > http://permalink.gmane.org/gmane.science.physics.ifeffit/2352 ) > In short: XAFS chi(R) is *NOT* a pair distribution function, due mostly to the complex electron scattering that alter the amplitude and shift the phase of potoelectron in addition to the simplistic "backscatter from a point source atom". The most obvious effect of this is a ~0.5 Ang shift to lower R from the value you might expect if chi(R) was a pair distribution function. Other effects include broader and asymmetric peaks, and the resonance effect such as you notice for heavy elements (easily noticeable for Z>40 or so, but unmistakable for Z > 60 -- that Z is for the *scattering atom*). At certain energies (or for a narrow range of energies), the photo-electron has very low scattering probability from a heavy element, and the phase jumps dramatically, as if the electron was able to tunnel through or hop over the potential well of the scattering atom. This is usually (and I think properly) called a Ramsauer-Townsend resonance. There are many papers, review articles, and slides from talks available that describe this in more detail. Google "ramsauer townsend effect exafs" for detailed articles. > I don't really understand what this means, which physical process causes > this. Could you perhaps provide me with additional info on this matter or > direct me to some papers that explain this? > > > Thanks in advance! > > Best regards > > Pieter Tack > > > --- > X-Ray Micro-Spectroscopy and Imaging Group > Department of Analytical Chemistry > Ghent University > Krijgslaan 281 S12 > B-9000 Ghent > Belgium > Phone: +32 (0)9 264 4723 > Fax: +32 (0)9 264 49 60 > --Matt

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Regarding time resolved XAS
by mazhar iqbal 01 Jun '16

01 Jun '16

hello.. I am sorry if am not posting on right place. I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that we have a reference fluorescence line always on the screen that well behind the K absorption edge. Hoping to see your response. Best Regards

2 2

Re: [Ifeffit] difference spectra- Ifeffit Digest, Vol 159, Issue 23
by sb2c08＠gmail.com 31 May '16

31 May '16

This is very helpful thank you. To give a little bit of context, the reaction is a solution of W(CO)6 irradiated at 266nm, to give W(CO)5*, it would be good to find the overall change of CO distance, especially as the multi scattering dominates the EXAFS. Just as a final point, the difference spectrum is taken from the normalised after and before laser spectra, so supposing the difference is fitted directly in Artemis (and coordination number is known/assumed), the amplitude factor will give an indication of the % change, supposing the Debye-Waller factor is similar to the ground state W(CO)6? But normalisation I find is the first difficult issue. Thanks Bruce and Anatoly and I will look over the references for some direction. Stu > On 31 May 2016, at 19:20, 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: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (sb2c08(a)gmail.com) > 2. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Bruce Ravel) > 3. Re: Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 31 May 2016 18:23:42 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <A5D4B2A5-A353-4813-BFC0-A31105BE4B21(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. > > To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > > >> On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) >> 2. Re: Difference spectra (Bruce Ravel) >> 3. Re: Regarding time resolved XAS (Bruce Ravel) >> 4. Atoms on the WEB (alessandro longo) >> 5. Re: Atoms on the WEB (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 30 May 2016 18:25:21 +0100 >> From: sb2c08(a)gmail.com >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] Difference spectra >> Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> >> Content-Type: text/plain; charset=us-ascii >> >> Hi, >> We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? >> Thanks for any help or suggestions, >> Stu >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 31 May 2016 08:19:14 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Difference spectra >> Message-ID: <574D8142.8060001(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 31 May 2016 08:22:59 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit >> <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Regarding time resolved XAS >> Message-ID: <574D8223.3080109(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >>> I want to ask about the aligning the XAS spectra that is given in >>> Athena. Can we do the alignment of time resolved spectra? As you know >>> that the resolved spectra (IR pump X-ray probe) may have edge shift due >>> to laser pumping. Do you think that the same method of the alignment can >>> be applied here as well. An additional piece of information is that we >>> have a reference fluorescence line always on the screen that well behind >>> the K absorption edge. >> >> Well, you have told us what you have tried nor what problem you are >> actually facing. If the question is "does Athena help you align data?" >> I think you already know that the answer is yes. >> >> I don't understand the business about a "fluorescence line always on the >> screen". How do you propose to use that to align your XAS data? >> >> In the case of a situation where you are purposefully changing the >> chemical state of the sample, then you need to have some absolute >> reference by which to perform the alignment -- a reference spectrum >> measured simultaneously, an encoder reading on the monochromator, >> something that allows you to do the chore. >> >> You question is a bit vague and open-ended. Without more information or >> a more focused question, I don't know how to help you further. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 31 May 2016 14:49:50 +0200 >> From: "alessandro longo" <alessandro.longo(a)cnr.it> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: [Ifeffit] Atoms on the WEB >> Message-ID: <20160531124332.M60406(a)cnr.it> >> Content-Type: text/plain; charset=utf-8 >> >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro >> >> -- >> Ph.D Alessandro Longo >> researcher of National Council Research >> ISMN-CNR >> e-mail: alessandro.longo(a)cnr.it >> phone: 00390916809359 >> fax : 00390916809399 >> >> Open WebMail Project (http://openwebmail.org) >> >> >> ---------- Original Message ----------- >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tue, 31 May 2016 08:19:14 -0400 >> Subject: Re: [Ifeffit] Difference spectra >> >>>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>>> We recently collected laser pump-probe XAS data out to k=9. The >>>> process to get the excited state is to take the laser off minus the >>>> laser on data. I'm a little unsure in terms of trying to fit the >>>> difference EXAFS and is it possible via Athena? So far I model the >>>> EXAFS of the excited state and take away from the ground state model >>>> and compare visually. The only way I can think is to work out the % >>>> conversion and add that % of laser off back to the difference data in >>>> order to get the real EXAFS of the excited state, which can be fitted >>>> through Athena. But this is really difficult and probably >>>> inaccurate? >>> >>> Of course it's not possible to fit and EXAFS spectrum in Athena. >>> Artemis is the program for fitting the EXAFS. >>> >>> I am unclear on what you have tried so far, so I am a little unsure what >>> kind of answer you are looking for. Artemis was not really written with >>> your sort of experiment in mind. That said, if your problem is fit some >>> theory from Feff to a measured spectrum with some fitting model -- that >>> is what Artemis is for. As with any difficult problem, you need to >>> understand your data and your model and you need to understand Artemis >>> well enough to implement the fit. But there is no magical, hidden >>> button that says "fit my pump-probe data." >>> >>> B >>> >>> -- >>> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >>> >>> National Institute of Standards and Technology >>> Synchrotron Science Group at NSLS-II >>> Building 535A >>> Upton NY, 11973 >>> >>> Homepage: http://bruceravel.github.io/home/ >>> Software: https://github.com/bruceravel >>> Demeter: http://bruceravel.github.io/demeter/ >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> ------- End of Original Message ------- >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 31 May 2016 09:05:43 -0400 >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Atoms on the WEB >> Message-ID: <574D8C27.4090907(a)bnl.gov> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >>> On 05/31/2016 08:49 AM, alessandro longo wrote: >>> Hi to everyone, >>> >>> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >>> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >>> work anymore. It works only to create the atoms.inp, but it was nice to have the >>> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >>> tool is not installed. >>> Sorry If i took your time and thank you for your answer. >>> best >>> Alessandro >> >> It would be nice if you started a new thread for a new question rather >> than hijacking an existing thread.... >> >> Last December, the computer that hosted the web atoms tool died >> dramatically. When Matt rebuilt that server, atoms did not get >> restored. The web version of atoms was based on very out date code. >> >> Bottom line is that I need to rewrite the web atoms tool using the >> current code base. >> >> It's on my list of things to do. >> >> B >> >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> >> >> ------------------------------ >> >> End of Ifeffit Digest, Vol 159, Issue 21 >> **************************************** > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 13:44:12 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: <574DCD6C.6080800(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 18:20:20 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, > Issue 21 > Message-ID: > <545F89325F51764C902D37B42C9F4D530210471863(a)YUWEXCPM11.yuad.uds.yu.edu> > > Content-Type: text/plain; charset="us-ascii" > > Hi Stu, > > In full agreement with Bruce, what you want to do can be done, and it was done a few times before. > I think the first group that applied conventional EXAFS analysis to differential signals was Pettifer et al in Nature (2005), to analyze EXAFS in magnetrostrictors measured at different values of magnetic field. Then, C. Konig et al did a similar trick for a catalyst under different atmospheres. They also used conventional EXAFS equation to fit the difference because the model allowed them to do so (the changes in the amplitude factors was also an amplitude factor and could be obtained from the fit because the fitting program does not know what the meaning of amplitude factors is, you do. > > I want to warn you that normalization of the amplitude of your EXAFS data will be the trickiest part because it depends on how many absorbing species changed structure during the excitation. > > In my work we also used this method in a couple of papers, Spanjers et al (for Pd nanoparticles under Ar and inert environment), and Korobko et al, (2015) using electrostrictors with and without applied electric field. The latter example is here: > > https://pubweb.bnl.gov/~frenkel/CGO/CGO-modulations.pdf > > The references to Pettifer and Konig works are Refs 19 and 20. > > Regards, > Anatoly > > P.S. If anyone is interested, a postdoctoral position has just opened up in my group, for research of electromechanical materials. Please contact me for further information: frenkel(a)bnl.gov > > ________________________________________ > From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Bruce Ravel [bravel(a)bnl.gov] > Sent: Tuesday, May 31, 2016 1:44 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21 > >> On 05/31/2016 01:23 PM, sb2c08(a)gmail.com wrote: >> To be clearer, can I make the excited state and ground state models >> in Artemis, take the data and difference (which can be done in >> Athena) and use that as a direct comparison, perhaps as you would >> with XANES data? I understand my data but I do not understand the >> best method to try get at least a first shell fit from the EXAFS >> region, collected by taking the difference of the ground state from >> the excited state, and can this be done in anyway via Artemis through >> some data analysis. > > > While it seems like Artemis specifically wants traditional EXAFS data as > its input, that's not really the case. It just wants something wiggly > that can be Fourier transformed. > > While it seems like Artemis wants a full Feff calculation and all the > path files that come from it with all the degeneracies that Feff thinks > it has, that also is not really the case. > > I don't know what your data are or what they look like (you haven't told > us), so I will make up a scenario off the top of my head. Hopefully > that will still be instructive. > > Suppose that our ground state is a pure metal -- say iron metal. Iron > metal has a near neighbor at about 2.5A. Suppose that our secondary > state includes some iron oxide -- that has a neighbor at about 1.9A and > a correspond peak at a much shorter distance. > > Suppose we can guess the amount of pure metal in the secondary state. > Then we could do some simple arithmetic to isolate (approximately!) the > oxide contribution. This will resemble an iron oxide standard, but with > much smaller amplitude. > > Seems to me that this difference spectrum could be fit in Artemis by > running Feff on the oxide, parameterizing the fit much like a > conventional spectrum, but giving the model enough freedom to have a > much smaller amplitude. That is, you cannot force the fit to have an > S02 of around 0.9 -- like a normal fit -- and the full coordination > number of the normal oxide. Something in the fitting model must be > introduced to allow the amplitude to be small enough to fit the > difference data properly. > > You, then, need to have a way of interpreting this much smaller > amplitude in a way that makes sense for the problem at hand. > > To say all that another way ... your difference data has Fourier > components ... Feff provides Fourier components ... you supply a model > (and an interpretation!) that fits Feff's Fourier components to the > Fourier components in your data. If your data can be described by Feff, > Artemis can do the describing. > > HTH, > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 159, Issue 23 > ****************************************

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Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System
by Johnson, Mark 31 May '16

31 May '16

Dear XAS Colleagues, I recently had to give up my Windows XP operating system and begin using Windows 7, the Enterprise version (I work for the U.S. Government). So I downloaded and installed the software, but when I try to launch them I see the software Icon briefly, but it does not launch. Digging around I found the following error logs below. Does anyone have any advice on how to proceed? My PC does have 16 Mb of RAM. Could that be the problem? Any suggestions would be appreciated. Thanks! MGJ ========================================================================== From: Dathena.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 24. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dathena.bat line 43. Started at 2016-05-26T12:28:22 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1. ============================================================================================= >From dartemis.log BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. BEGIN failed--compilation aborted at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26. Compilation failed in require at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. BEGIN failed--compilation aborted at C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 42. Started at 2016-05-26T12:30:29 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\spodosol1\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib . Can't load 'C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/Users/spodosol1/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1.

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Re: [Ifeffit] Difference spectra- Ifeffit Digest, Vol 159, Issue 21
by sb2c08＠gmail.com 31 May '16

31 May '16

I am familiar with the software and apologies I did mean Artemis in terms of fitting and understand that there is no pump probe button. To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis. > On 31 May 2016, at 14:07, 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. Difference spectra (sb2c08(a)gmail.com) > 2. Re: Difference spectra (Bruce Ravel) > 3. Re: Regarding time resolved XAS (Bruce Ravel) > 4. Atoms on the WEB (alessandro longo) > 5. Re: Atoms on the WEB (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 18:25:21 +0100 > From: sb2c08(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Difference spectra > Message-ID: <A460A00C-45B0-4ED5-969C-6FB3BF0C67A2(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi, > We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? > Thanks for any help or suggestions, > Stu > > > > ------------------------------ > > Message: 2 > Date: Tue, 31 May 2016 08:19:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Difference spectra > Message-ID: <574D8142.8060001(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >> We recently collected laser pump-probe XAS data out to k=9. The >> process to get the excited state is to take the laser off minus the >> laser on data. I'm a little unsure in terms of trying to fit the >> difference EXAFS and is it possible via Athena? So far I model the >> EXAFS of the excited state and take away from the ground state model >> and compare visually. The only way I can think is to work out the % >> conversion and add that % of laser off back to the difference data in >> order to get the real EXAFS of the excited state, which can be fitted >> through Athena. But this is really difficult and probably >> inaccurate? > > > Of course it's not possible to fit and EXAFS spectrum in Athena. > Artemis is the program for fitting the EXAFS. > > I am unclear on what you have tried so far, so I am a little unsure what > kind of answer you are looking for. Artemis was not really written with > your sort of experiment in mind. That said, if your problem is fit some > theory from Feff to a measured spectrum with some fitting model -- that > is what Artemis is for. As with any difficult problem, you need to > understand your data and your model and you need to understand Artemis > well enough to implement the fit. But there is no magical, hidden > button that says "fit my pump-probe data." > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Tue, 31 May 2016 08:22:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: mazhar iqbal <mazharphy_05(a)yahoo.com>, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Regarding time resolved XAS > Message-ID: <574D8223.3080109(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/30/2016 02:20 AM, mazhar iqbal wrote: >> I want to ask about the aligning the XAS spectra that is given in >> Athena. Can we do the alignment of time resolved spectra? As you know >> that the resolved spectra (IR pump X-ray probe) may have edge shift due >> to laser pumping. Do you think that the same method of the alignment can >> be applied here as well. An additional piece of information is that we >> have a reference fluorescence line always on the screen that well behind >> the K absorption edge. > > Well, you have told us what you have tried nor what problem you are > actually facing. If the question is "does Athena help you align data?" > I think you already know that the answer is yes. > > I don't understand the business about a "fluorescence line always on the > screen". How do you propose to use that to align your XAS data? > > In the case of a situation where you are purposefully changing the > chemical state of the sample, then you need to have some absolute > reference by which to perform the alignment -- a reference spectrum > measured simultaneously, an encoder reading on the monochromator, > something that allows you to do the chore. > > You question is a bit vague and open-ended. Without more information or > a more focused question, I don't know how to help you further. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 4 > Date: Tue, 31 May 2016 14:49:50 +0200 > From: "alessandro longo" <alessandro.longo(a)cnr.it> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Atoms on the WEB > Message-ID: <20160531124332.M60406(a)cnr.it> > Content-Type: text/plain; charset=utf-8 > > Hi to everyone, > > I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. > I don't want to disturb to much, but I was wondering why now this beatifull tool does't > work anymore. It works only to create the atoms.inp, but it was nice to have the > feff.inp ready from the web application. The main motivation is somtimes the ifeffit > tool is not installed. > Sorry If i took your time and thank you for your answer. > best > Alessandro > > -- > Ph.D Alessandro Longo > researcher of National Council Research > ISMN-CNR > e-mail: alessandro.longo(a)cnr.it > phone: 00390916809359 > fax : 00390916809399 > > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tue, 31 May 2016 08:19:14 -0400 > Subject: Re: [Ifeffit] Difference spectra > >>> On 05/30/2016 01:25 PM, sb2c08(a)gmail.com wrote: >>> We recently collected laser pump-probe XAS data out to k=9. The >>> process to get the excited state is to take the laser off minus the >>> laser on data. I'm a little unsure in terms of trying to fit the >>> difference EXAFS and is it possible via Athena? So far I model the >>> EXAFS of the excited state and take away from the ground state model >>> and compare visually. The only way I can think is to work out the % >>> conversion and add that % of laser off back to the difference data in >>> order to get the real EXAFS of the excited state, which can be fitted >>> through Athena. But this is really difficult and probably >>> inaccurate? >> >> Of course it's not possible to fit and EXAFS spectrum in Athena. >> Artemis is the program for fitting the EXAFS. >> >> I am unclear on what you have tried so far, so I am a little unsure what >> kind of answer you are looking for. Artemis was not really written with >> your sort of experiment in mind. That said, if your problem is fit some >> theory from Feff to a measured spectrum with some fitting model -- that >> is what Artemis is for. As with any difficult problem, you need to >> understand your data and your model and you need to understand Artemis >> well enough to implement the fit. But there is no magical, hidden >> button that says "fit my pump-probe data." >> >> B >> >> -- >> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Science Group at NSLS-II >> Building 535A >> Upton NY, 11973 >> >> Homepage: http://bruceravel.github.io/home/ >> Software: https://github.com/bruceravel >> Demeter: http://bruceravel.github.io/demeter/ >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ------- End of Original Message ------- > > > > ------------------------------ > > Message: 5 > Date: Tue, 31 May 2016 09:05:43 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Atoms on the WEB > Message-ID: <574D8C27.4090907(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > >> On 05/31/2016 08:49 AM, alessandro longo wrote: >> Hi to everyone, >> >> I'm beamline scientist at DUBBLE at ESRF and I was using currently atoms on the web. >> I don't want to disturb to much, but I was wondering why now this beatifull tool does't >> work anymore. It works only to create the atoms.inp, but it was nice to have the >> feff.inp ready from the web application. The main motivation is somtimes the ifeffit >> tool is not installed. >> Sorry If i took your time and thank you for your answer. >> best >> Alessandro > > It would be nice if you started a new thread for a new question rather > than hijacking an existing thread.... > > Last December, the computer that hosted the web atoms tool died > dramatically. When Matt rebuilt that server, atoms did not get > restored. The web version of atoms was based on very out date code. > > Bottom line is that I need to rewrite the web atoms tool using the > current code base. > > It's on my list of things to do. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 159, Issue 21 > ****************************************

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Difference spectra
by sb2c08＠gmail.com 31 May '16

31 May '16

Hi, We recently collected laser pump-probe XAS data out to k=9. The process to get the excited state is to take the laser off minus the laser on data. I'm a little unsure in terms of trying to fit the difference EXAFS and is it possible via Athena? So far I model the EXAFS of the excited state and take away from the ground state model and compare visually. The only way I can think is to work out the % conversion and add that % of laser off back to the difference data in order to get the real EXAFS of the excited state, which can be fitted through Athena. But this is really difficult and probably inaccurate? Thanks for any help or suggestions, Stu

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ISO Calcite + dolomite EXAFS
by Matthew Marcus 27 May '16

27 May '16

Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite? I took some, but it seems to disagree with FEFF as to the position of the Ca-(Ca,Mg) peak. mam

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Small larch bug
by Johan Nilsson 27 May '16

27 May '16

Hello, I've found a small "bug" in larch when I tried to run the pre_edge function for some spectra. It seems that find_e0 will not accept a 2d 1-column array as input for energy or mu, and it gives a traceback which is quite difficult to decipher. Other functions like plot accepts these arrays without any problems, which made it a bit difficult to figure out what the problem was. Maybe there can be some some sort of warning if arrays have unexpected shapes, or an internal reshape if that works. I've attached a script that should give a minimum working example, my output is: larch> run('cu.lar') (612,) 8977.58 (612, 1) File "/usr/local/lib/python2.7/dist-packages/larch/__init__.py", line 37, in wrapper return fcn(*args, **keywords) File "/usr/share/larch/plugins/xafs/pre_edge.py", line 51, in find_e0 dmu = np.gradient(mu)/np.gradient(energy) File "/usr/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 918, in gradient out[slice1] = (f[slice2] - f[slice3])file cu.lar, line 14 IndexError: index 1 is out of bounds for axis 1 with size 1 find_e0(e,cu.mu,group=cu) find_e0(e,cu.mu,group=cu) file cu.lar, line 14 larch> Best wishes, Johan

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