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

Amplitude and sigma square (Abdul Ahad)
by Pierre Lecante 28 May '18

28 May '18

Hi Abdul, In my opinion, the short answer is that your model is wrong; amplitude, coordination number and sigma square are strongly correlated; if your model is not adequate or if values are too far from the convergence zone, non physical effects appear; usually, very small or negative values for sigma2 mean coordination number too low, but very small amplitude means the reverse! I suggest to start with a plain simulation (all parameters locked to expected values) and check that there is not something weird in different k zones, which might eventually indicate unexpected species close to the central atom; my 2 cents, Pierre Le 28/05/2018 à 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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. Amplitude and sigma square (Abdul Ahad) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 May 2018 14:16:39 +0530 > From: Abdul Ahad <matrixabdulahad(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Amplitude and sigma square > Message-ID: > <CAEFSGt6r3xbjc2zPk1fc2bGmKwgb_AVVcfrWa198kmY8QkpMJA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I have couple of questions. > 1. I found in many tutorials that the value of amp should lie between 0.7 > and 1. But when I refined it goes to 0.15, what's wrong with it. > > 2. The value of sigma2. Some time at high k, value, it turns to negative > but small. What I suppose to do? > > 3. If I need to know the behavior of octahedra distortion with temperature, > and it is lies within the first shell. So what is the need of higher shell > fitting.??? > > Thanks in advance >

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Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

Julian, On Fri, May 25, 2018 at 9:01 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > Thank you for your superfast answer. I obtained new data from the people > at the beamline today, and the set contains both Total electron Yield and > Total fluorescence yield. As far as I understand, they both tell us > something about the absorption. Which is usually used for analysis? If I > process them with Athena I get considerable differences… > > > Please use the mailing list. Either or both of total electron yied and total fluorescence yield can be used for XAFS. That is, total emission of high-energy electrons and emission of fluorescence X-rays are both proportional to the absorption cross-section for an atom, at least to first approximation. There are complications in using these. For X-ray fluorescence the main complication is "over absorption" which happens in materials in which the element of interest is high concentration (effects can be noticeable at ~1% and are usually significant-but-correctable up to ~10%, and are nearly impossible to correct above ~50% concentration). For electron yield, the main complication is that the electron escape depth is shallow enough that the measurement may be more sensitive to the surface than the bulk of the sample. That sort of depends on how you define "surface" (the electrons escape from 10s to 100s of Angstroms), but can be seen as an advantage if surface sensitivity is what you want. For both, using the data as XAFS means using mu ~ EmissionIntensity / I0. That's very different from transmission data, which often trips people up when importing the data into Athena: DO NOT use the log( EmissionIntensity / I0), use EmissionIntensity/I0. --Matt

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Re: [Ifeffit] S02
by Matt Newville 25 May '18

25 May '18

On Fri, May 25, 2018 at 5:11 AM Julian Ehwald <jehwald(a)gmail.com> wrote: > Dear Matt, > > > > I still have questions about Artemis concerning the S0^2. In your > book/summary called XAFS-Fundamentals there is a section at the beginning > of chapter six that says: > > > > “Starting with this structure, we can calculate the scattering amplitude > and phaseshifts > > and theoretically. The complete calculation is beyond the scope of this > treatment, > > but don’t worry too much by that phrase “we’ll calculate these > theoretically”! These > > functions are actually fairly easy to calculate using one of a few > different computer > > programs – for the calculations here, the FEFF program was used. The > results of the > > FEFF calculation are stored in simple files containing the scattering > factors and meanfree- > > path for a given coordination shell. The calculations in these files can > be used > > directly in a number of analysis programs.” > > > > Are these somewhere listed in Artemis? > The calculations stored in the feffNNNN.dat files can be accessed from Larch, but I think they're not readily exposed by Artemis. The point is that you don't have to worry about these scattering factors, but only about the Path Parameters (S02, E0, deltaR, sigma2, etc) that modify these scattering terms. > Because if I start fitting the value in GDS is always guessed to be one, > for any element in the sample. If I go and look at the FEFF calculation it > tells me: > > > > > > TITLE LiPF6 > > > > HOLE 1 1.0 * FYI: (F K edge @ 696.7 eV, 2nd number is S0^2) > > * mphase,mpath,mfeff,mchi > > CONTROL 1 1 1 1 > > PRINT 1 0 0 0 > > > > I don’t really understand which is the second number and why all S0^2 then > are either 0 or 1. > > > > Best, Julian > One can set an S02 value during the Feff calculation. That is what goes as the second number in the HOLE entry in feff.inp (The first value is an integer indicating the edge type -- 1 for 'K', and so on). Setting that value will apply the S02 value to all paths calculated by that run of Feff. You can also set values for sigma2 from Feff too, Artemis/Ifeffit/Larch etc use the Feff calculations stored in feffNNNN.dat (or equivalent) and build a model from a collection of paths from Feff. If S02 or sigma2 is set in the original Feff calculation(s), it is difficult to track during the analysis (neither S02 nor sigma2 are written to the individual feffNNNN.dat files). In some sense Artemis/Ifeffit/Larch etc only use part of Feff -- the calculation of the EXAFS contribution of a single, idealized path. They do not use the sum-of-paths module(s) of Feff, but instead replace that with its own sum-of-paths implementation that is richer (allowing feffNNNN.dat from different feff runs, allowing parameters like S02, sigma2, E0, deltaR, etc to be varied, etc). So, the recommendation (more like an expectation, really) is to NOT set S02 to any value except 1.0 and to NOT set any parameters that will calculate sigma2 in feff.inp if the intention is to use those paths for fitting. Let the fitting program adjust S02 and/or disorder terms. Hope that helps, --Matt

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EXAFS above 5 angstroms
by Daniel Sneed 23 May '18

23 May '18

Hello, This is my first time posting to the mailing list, so please forgive me if I did not do it correctly. I am currently working on EXAFS of tin(IV) oxide, and I have what appears to be high quality data out to 9 angstroms or so, but I am having some issues in fitting the data above 4 angstroms. I am attempting to verify a crystal structure with a= ~6 angstroms, and another structure with a=~9 angstroms. I know that there is some inhibiting physics at such long distances, such as inelastic scattering, and core-hole lifetime issues that can effect the data. My question for the group is, is there any methodical way to deal with these issues, other than incorporating Ei and the higher cumulants? Or is it even possible to get results from such large R? Thank you for your time. regards, Daniel Sneed

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temperature dependency of amp parameter
by Abdul Ahad 21 May '18

21 May '18

Hi all, I have little confusion that do i fix or change S2 for each data set measured at different temperature. The compound is not monoatomic so i used Einstein model for sigma2. What about amplitude S2. thanks *A. Ahad*

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SSRL EXAFS School- Application Open!
by Ritimukta Sarangi 19 May '18

19 May '18

Hello Friends, SSRL will host its annual summer school this year during the third week of August (13th-16th). The application page is now open. Please hit the "apply" button on: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2018/index.html Note that seats are limited and we will have to choose from the application pool. Please apply soon to help us with the process. If selected, you will receive an email to register for the school. This year, we will drill down into Artemis based EXAFS analysis. Hope to see many of you here! Best Wishes, -Riti Sarangi

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XANES spectra of Zn-organic references
by emmanuelle Montarges-Pelletier 18 May '18

18 May '18

Dear all We have measured Zn XANES spectra within biological samples (seeds), in ambient conditions (room temperature). In order to interprete the spectra, we are searching for Zn-organic reference spectra (XANES only). Indeed, we would be interested by Zn organic compounds with sulfur and/or nitrogen and/or oxygen in the first shell of coordination. On the joined graph are plotted the experimental spectra (microspectra on seeds), compared to Zn-citrate and Zn-cysteine. Energy calibration was checked for all spectra. thanks in advance for your answers best regards Emmanuelle Emmanuelle MONTARGES-PELLETIER Chargée de Recherche CNRS LIEC Laboratoire Interdisciplinaire des Environnements Continentaux UMR 7360 CNRS Université de Lorraine 15 avenue du Charmois F-54500 Vandœuvre-lés-Nancy - France tel 33 (0)03 72 74 47 30 mob 33(0)6 31 33 10 30 ****attention changement de numéro de téléphone **** tel 33 (0)3 72 74 47 30

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4+2 model for distortion
by Abdul Ahad 17 May '18

17 May '18

Hi Prof. Segre Thanks for your reply, I have used .cif file for the K2NiF4 type structure. In this structure the first shell and first single path shows 6 coordination number. and the path is Ni to F1 with 2 leg. My concern is to use 4+2 model. Do i change the CN number or i have to add one more site. I cant visualize the situation. Becuase here the F have 2 sites i.e F1 and F2. And the path is only for the F1. While the diffrence between the bonds Ni-F1 and Ni-F2 is about 0.1 A. which lies under the resulution limit of my experiment via delta r and delta k relation. *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 16, 2018 at 10:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: 4+2 model for distortion (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 May 2018 16:00:08 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] 4+2 model for distortion > Message-ID: <alpine.DEB.2.21.1805151558480.17852(a)hydride.segre.home> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > Hi Abdul: > > Are you strating with a cif file for a particular structure or are you > simply working with a quick first shell theory? > > Carlo > > > On Wed, 9 May 2018, Abdul Ahad wrote: > > > hi all > > How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long > > bond length of octahedra > > thanks > > > > > > *A. Ahad* > > *--------------------* > > *Abdul Ahad* > > Junior Research Fellow > > *Dept of Physics* > > *Aligarh Muslim University* > > *Aligarh 202002 (U.P.), India* > > > > *http://www.researcherid.com/rid/G-8198-2018 > > <http://www.researcherid.com/rid/G-8198-2018>* > > *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org > > <ahad(a)mailaps.org> * > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Interim Chair, Department of Chemistry > Director, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > 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 183, Issue 14 > **************************************** >

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4+2 model for distortion
by Abdul Ahad 15 May '18

15 May '18

hi all How to include this model in atom that is 4+2 or 2+4 for 2short or 4 long bond length of octahedra thanks *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> *

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Energy Resolution
by Julian Ehwald 10 May '18

10 May '18

Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

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Truncating signal
by Julian Ehwald 10 May '18

10 May '18

Hi all, I have basic question on background removal in Athena. My data has some strong changes very close to the absorption edge, and if I start the background removal at k=0, the spline is not able to follow the signal for higher k-values (even at Rbkg=1.7 or similar). The background then oscillates slowly (4 A^-1) around my signal, generating huge peaks in the low regions of chi(R). If I set the spline range to begin at k=2.7 only (around 28eV above absorption edge) then I get rid of it. Now my question in general is, do I loose essential information about the nearest neighbours this way, respectively is that a common thing to do? Best, Julian

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Re: [Ifeffit] Ifeffit Digest, Vol 183, Issue 9
by Abdul Ahad 09 May '18

09 May '18

yes i m talking about the jahn teller type distortion, any hint to include in atom *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a_ahad.rs(a)amu.ac.in <a_ahad.rs(a)amu.ac.in>, ahad(a)mailaps.org <ahad(a)mailaps.org> * On Wed, May 9, 2018 at 8:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Energy Resolution (Julian Ehwald) > 2. Re: Energy Resolution (Robert Meulenberg) > 3. 4+2 model for distortion (Abdul Ahad) > 4. Re: 4+2 model for distortion (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 May 2018 09:24:27 +0200 > From: "Julian Ehwald" <jehwald(a)gmail.com> > To: "'Carlo Segre'" <segre(a)iit.edu>, "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: <006901d3e766$c4284410$4c78cc30$(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carlo > > Thank you very much for your answer! If you say it is sufficient to use > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 to > 12) in only 250 datapoints? That would save us a lot of time! > > Best, Julian > > -----Urspr?ngliche Nachricht----- > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im Auftrag > von Carlo Segre > Gesendet: Sonntag, 6. Mai 2018 01:07 > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Betreff: Re: [Ifeffit] Energy Resolution > > > Hi Julian: > > With an edge energy of 543 eV, your monochromator resolution should be at > least 0.1 eV. If you are interested in XANES, you need to take data at > this > resolution or maybe even better. ONce past the edge, there is no need to > keep that step size. If your beamline permits an EXAFS-type step scan with > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > interpolates to. Smaller step sizes are not really useful. > > Carlo > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > Dear all, > > > > > > > > This might be a very general question, but: I was wondering what > > energy resolution you typically use at beamlines to obtain your raw data > for exafs. > > Since we have limited Beamtime only and other experiments that we want > > to carry out, I was wondering what kind of resolution is common. Or > > differently: Is it predictable what happens if I for example change > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > above Oxygen K, if that is of relevance. > > > > Best, Julian > > > > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, > Department of Chemistry Director, Center for Synchrotron Radiation Research > and Instrumentation Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > _______________________________________________ > 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 > > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 May 2018 08:54:31 -0400 > From: Robert Meulenberg <robert.meulenberg(a)maine.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy Resolution > Message-ID: > <CANs+nr9N7MSiYB9UGRm-a0JGd-5U8BNjKO7YVgAkM=SoRKazHA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Julian, > > Keep in mind that to get to k=12, you will need to go out to ~1100 eV. At > these energies, you will encounter just about every 1st row transition > metal L edge, and a handful of other M-edges for heavier elements. So if > you have anything else in your sample, EXAFS will probably not be > possible. That is usually why people don't try to do EXAFS analysis at the > soft x-ray energies. > > Regards, > > Rob > > > > > Robert W. Meulenberg > Associate Professor of Physics > Laboratory for Surface Science and Technology > Department of Physics and Astronomy > University of Maine > Orono, ME 04469 > phone: 207-581-2245 > email: robert.meulenberg(a)maine.edu > > On Wed, May 9, 2018 at 3:24 AM, Julian Ehwald <jehwald(a)gmail.com> wrote: > > > Hi Carlo > > > > Thank you very much for your answer! If you say it is sufficient to use > > dk=0.05, that means I would be able to collect a full EXAFS spectra (k=0 > to > > 12) in only 250 datapoints? That would save us a lot of time! > > > > Best, Julian > > > > -----Urspr?ngliche Nachricht----- > > Von: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im > Auftrag > > von Carlo Segre > > Gesendet: Sonntag, 6. Mai 2018 01:07 > > An: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Betreff: Re: [Ifeffit] Energy Resolution > > > > > > Hi Julian: > > > > With an edge energy of 543 eV, your monochromator resolution should be at > > least 0.1 eV. If you are interested in XANES, you need to take data at > > this > > resolution or maybe even better. ONce past the edge, there is no need to > > keep that step size. If your beamline permits an EXAFS-type step scan > with > > steps in k-space, you want to use a dk of 0.05 which is what IFEFFIT > > interpolates to. Smaller step sizes are not really useful. > > > > Carlo > > > > On Sat, 5 May 2018, Julian Ehwald wrote: > > > > > Dear all, > > > > > > > > > > > > This might be a very general question, but: I was wondering what > > > energy resolution you typically use at beamlines to obtain your raw > data > > for exafs. > > > Since we have limited Beamtime only and other experiments that we want > > > to carry out, I was wondering what kind of resolution is common. Or > > > differently: Is it predictable what happens if I for example change > > > from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV > > > above Oxygen K, if that is of relevance. > > > > > > Best, Julian > > > > > > > > > > -- > > Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim > Chair, > > Department of Chemistry Director, Center for Synchrotron Radiation > Research > > and Instrumentation Illinois Institute of Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > _______________________________________________ > > 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 > > > > > > _______________________________________________ > > 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 > > >

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Re: [Ifeffit] Athena programm for XAS data analysis
by Robert Gordon 08 May '18

08 May '18

changing colour: Preferences --> gnuplot --> col7 and Set a desired colour then apply and save....displayed "your value" might not update until you restart Athena, but the plot should. On Tue, May 8, 2018 at 3:07 AM, Stoll, Andreas (HIU) <andreas.stoll(a)kit.edu> wrote: > Hi Jonas, > > > first of all thank you very much for your quick answer! > > > unfortunately your suggestion is not working for my version of Athena. It > just worked for the older versions... > > > Is there another possibility? > > > Greetings > > > Andi > ------------------------------ > *Von:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> im Auftrag von > Wielinski, Jonas <Jonas.Wielinski(a)eawag.ch> > *Gesendet:* Dienstag, 8. Mai 2018 18:40 > *An:* XAFS Analysis using Ifeffit > *Betreff:* Re: [Ifeffit] Athena programm for XAS data analysis > > > Hi Andi, > > > > Using Athena under Windows, “Alt + J” and “Alt + K” move data groups > upwards and downwards. I hope that answers your question. > > > > Best, > > Jonas > > > > *From:* Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] *On > Behalf Of *Stoll, Andreas (HIU) > *Sent:* Dienstag, 8. Mai 2018 10:12 > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* [Ifeffit] Athena programm for XAS data analysis > > > > Hi, > > > > I´m using Athena Version 0.9.26 to analyse my XAS data. > > > > Is it possible to change the order of the imported data in the list after > importing them? Or at least change the colour of the plotted data? > Currently one of my standards is plotted in yellow and that is not really > good... > > > > Thanks in advance! > > > > Greetings > > > > Andi > > _______________________________________________ > 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 > >

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Athena programm for XAS data analysis
by Stoll, Andreas (HIU) 08 May '18

08 May '18

Hi, I´m using Athena Version 0.9.26 to analyse my XAS data. Is it possible to change the order of the imported data in the list after importing them? Or at least change the colour of the plotted data? Currently one of my standards is plotted in yellow and that is not really good... Thanks in advance! Greetings Andi

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Re: [Ifeffit] o exafs
by fred.mosselmans＠diamond.ac.uk 05 May '18

05 May '18

Hi Julian, First you'll do well to collect o k exafs to 500 evening, second exafs data is typically except on qexafs beamline collected in k space steps i.e. proportional to E squared spacing starting at the edge position. Hence 0.4 evening is a very small step for exafs NOT xanes. If your beamline doesn't do k space scanning you can simulate it with several fixed eV step regions the step increasing as you get further from the edge. Also normally you would increase the time per point as you get further from the edge as the xafs signal compared to the background dies off Best Regards Fred Sent from BlueMail<http://www.bluemail.me/r?b=12874> On 5 May 2018, at 18:02, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov 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. Energy Resolution (Julian Ehwald) ________________________________ Message: 1 Date: Sat, 5 May 2018 12:01:26 +0200 From: "Julian Ehwald" <jehwald(a)gmail.com> To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Energy Resolution Message-ID: <000a01d3e458$086925c0$193b7140$(a)gmail.com> Content-Type: text/plain; charset="us-ascii" Dear all, This might be a very general question, but: I was wondering what energy resolution you typically use at beamlines to obtain your raw data for exafs. Since we have limited Beamtime only and other experiments that we want to carry out, I was wondering what kind of resolution is common. Or differently: Is it predictable what happens if I for example change from steps of 0.2eV to 0.4eV? We want to obtain spectra up to 500eV above Oxygen K, if that is of relevance. Best, Julian

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IIT/APS XAFS School - still have openings
by Carlo Segre 04 May '18

04 May '18

Greetings, All some slots are still open for the APS/IIT 2018 XAFS Summer School, July 8-12, in Chicago: see attached description. If you wish to participate, please email bunker(a)iit.edu <mailto:bunker@iit.edu> with subject line "XAFS School 2018". Grant Bunker -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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Se reference XANES
by desmau 01 May '18

01 May '18

Hello everyone, would anybody have a reference XANES spectrum of Se in Selenocysteine or of Se in bacteria ? Thanks a lot in advance for your help. Best regards -- Morgane DESMAU Doctorant/PhD student Institut de Physique du Globe de Paris Équipe de Géochimie des Eaux 1, rue Jussieu - 75238 Paris cedex 05 Mail: desmau(a)ipgp.fr Phone: +33 1 83 95 77 33

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Atoms with Z bigger than 94 are missing
by Kathy Dardenne 30 Apr '18

30 Apr '18

Hello, I just notice that feff6 in Athena from the last versions of Demeter (including the 0.9.26) did not accept Z value above 94 (Pu) anymore. I wanted to fit AM L3 data and got error message from FEFF that it was not possible. Changing Am Z to 94 solves the problem. Is it possible to get Am (Z=95) and Cm (Z=96) implemented in feff again? I am aware that using Z=94 for simulation of Am and Cm will likely yields similar results, by just replacing the Z in the atom output. But if it is possible without too much effort it will be nice to have. Thanks a lot. Cheers Kathy Dardenne

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Reference spectrum
by Lorenzo Stievano 27 Apr '18

27 Apr '18

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EXAFS fitting for regular & distorted monoclinic
by Ashwani Kumar 26 Apr '18

26 Apr '18

Hello everyone, I am new to the mailing list. i am Fitting data of regular and distorted ( from irradiation) NBS glass doped with Hafnium. Literature available Hafnia (monoclinic) data is taken as standard model to fit the data (monoclinic) of regular glass. Now i want to fit the distorted glass data with exafs result of regular glass data as standard model. or will it be ok , to also fit the distorted glass data with hafnia as standard model. . thanks A kumar

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Cannot update Demeter to version 0.9.26 in MacPorts
by Fowler, Joseph W. (Assoc) 25 Apr '18

25 Apr '18

Hi Bruce, I’m posing this question to you in front of the whole mailing list, just in case someone out there can help us both. As you know, I’m the official Macports maintainer of the port demeter, in spite of my near-complete ignorance of how either Perl or Macports work. In February, I filed a Macports ticket to make their preferred perl (5.26) work with Demeter 0.9.25. It was a simple matter of adding the “-I.” argument, as you pointed out to me. They pulled my changes, or whatever they do over there. My next step is to update the Macports package information to upgrade from Demeter 0.9.25 to 0.9.26. I am having a problem when I try to build Demeter 0.9.26, however. The “./Build install” command says it cannot find or copy ‘src/Ifeffit.dylib’. Do the following give you any clues about why that might be? This might be too little information, but as you said, “ask early”. The following text shows how it goes when I try to build within the macports structure. I get the same error, though, when I clone the git repository, cd into it, run “perl -I. Build.PL”, and then try to run “sudo ./Build install”. It looks as if somehow an ifeffit directory variable is not being initialized properly in line 308 of DemeterBuilder.pm. If you or anyone can help me to solve this problem, then I ought to be able to change the Macports port to provide Demeter 0.9.26. Many thanks. Joe Fowler NIST Boulder Labs fowlerj@817jfmac:demeter-0.9.26$ ll /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib -r-xr-xr-x 1 macports wheel 33008 Mar 5 09:05 /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.dylib fowlerj@817jfmac:demeter-0.9.26$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) [Mac ports would normally run the following commands within its build script, of course. But I am isolating the failed command to see if makes more sense this way.] fowlerj@817jfmac:demeter-0.9.26$ pushd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_demeter/demeter/work/demeter-0.9.26 fowlerj@817jfmac:demeter-0.9.26$ sudo ./Build install Use of uninitialized value $iffdir in pattern match (m//) at DemeterBuilder.pm line 308. Simple test for presence of gnuplot ---> found it! Using gnuplot with the wxt terminal. Building Demeter Can't copy('src/Ifeffit.dylib', 'blib/arch/auto/Ifeffit/Ifeffit.dylib'): No such file or directory at /opt/local/lib/perl5/vendor_perl/5.26/Module/Build/Base.pm line 5601.

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Phase shift
by Julian Ehwald 20 Apr '18

20 Apr '18

Dear all, I have a very general question about the phase shift. I tried to fit a rather noisy sample of Li2IrO3, where I get a first main peak around 1 angstroem, according to FEFF calculation there should be something at 1.9 and not any closer. This phase shift seems a bit too big to be true, is there something like an upper bound for a reasonable phase shift? Best, Julian

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Artemis Error
by Lê Ngọc Chính 19 Apr '18

19 Apr '18

Dear Demeter developer I have some trouble when using artemis. I have used artemis normally on windows 10, but recently I can't use it anymore. The error message appears after I click "FIT" button. I also have tried re-install the software, but nothing happened. Please provide me the way to fix it. Thank you so much -- Chính

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Directory path in Larch
by Imad Ahmed 17 Apr '18

17 Apr '18

Hi Matt, I have a question about the working directory of Larch. So, as I run Larch from command line (OS=Unix), the default WD is the .larch/modules and that in anaconda, in which case running a Larch script means that I have to provide its full path. I wonder if there is a way to change the WD into the current project folder? Running *.lar is not a problem but is a rather less convenient. However, directing Larch to project directory seems important so that to avoid typing full path of data files within the *.lar script. ps. feffrunner.py allows flexible subfolder path but it assumes that the *.inp is located in that same folder. It would be helpful if the path of the *.inp can be allowed to vary, this would help organising project files into subfolders. Best wishes, Imad

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Re: [Ifeffit] Larch python instructions
by Matt Newville 17 Apr '18

17 Apr '18

Hi Imad, On Sun, Apr 15, 2018 at 7:15 PM, Imad Ahmed <imad.ahmed(a)earth.ox.ac.uk> wrote: > Dear Matt, > > I am looking for some proper instructions on how to use Larch from python. > I have larch installed on Anaconda2 and trying to run the > /examples/feffit/doc_feffdat1.lar script from python. > I tried the python code below but still having issues to run it, > especially with Feffpath and some larch plugins. Could you please help? > > Best wishes, Imad > > > import sys, os > import numpy as np > from scipy.optimize import leastsq as scipy_leastsq > import larch > from larch import Group, Parameter > from larch_plugins.io import read_ascii > from larch_plugins.xafs import FeffPathGroup > from larch_plugins.xafs.feffit import (TransformGroup, > FeffitDataSet,feffit, feffit_report) > > fname = ‘~/xraylarch/examples/feffit/feff0001.dat' > path1 = FeffPathGroup(fname) > path2chi(path1) > show(path1) > newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', > ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, > title=r'$\chi(k)$ from %s' % fname) > path1.sigma2 = 0.002 > path2chi(path1) > plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') > > > Well, there are some differences between Larch and Python. With some small modifications, your scaript can become a valid Larch script like this: # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') To do that from Python is a bit more involved. Each of the functions "feffpath", "path2chi", "show", "newplot", and "plot" need to be translated. As you probably say, "feffpath" is effectively `FeffPathGroup'. The others are less obvious, and many of the larch functions really want to be passed a "larch session" so that they can find other larch function or data sources. For example, FeffPathGroup needs a larch session in order to be able to look up atomic information. So in pure python that would be approximately: import os import os.path import matplotlib.pyplot as plt # using pyplot instead of build in plot commmands from larch import Interpreter from larch_plugins.xafs.feffdat import FeffPathGroup, _path2chi # need to create a Larch interpreter for each "session" _larch = Interpreter() fname = os.path.join(os.path.expanduser("~"), "Codes/xraylarch/examples/feffit/feff0001.dat") # note that many of the Larch functions will want a `_larch` instance passed in. path1 = FeffPathGroup(fname, _larch=_larch) _path2chi(path1, _larch=_larch) # show, approximately for attr in dir(path1): print(attr, getattr(path1, attr)) # plot, approximately plt.plot(path1.k, path1.chi*path1.k**2, label= r'$\sigma^2 = 0$') path1.sigma2 = 0.002 _path2chi(path1, _larch=_larch) plt.plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') plt.xlabel(r' $ k \rm\, (\AA^{-1})$') plt.ylabel(r'$ k^2\chi(k)$') plt.title(r'$\chi(k)$ from %s' % fname) plt.legend() plt.show() But also, since you have to build a Larch Interpreter, you could simply use it to execute the previous Larch script: from larch import Interpreter text = ''' # larch from os.path import join, expanduser fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat') path1 = feffpath(fname) path2chi(path1) show(path1) newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$', ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True, title=r'$\chi(k)$ from %s' % fname) path1.sigma2 = 0.002 path2chi(path1) plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$') ''' _larch = Interpreter() _larch.run(text) The latter approach is highly recommended. --Matt Newville

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