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

feff.inp trouble geometry
by penelope arancegui 13 Oct '08

13 Oct '08

Hi everyone, I'm having some trouble with a feff.inp file. I changed the geometry of a 13-atom Pd molecule but I don't know why FEFF8 doesn't read the archive. Using the cristollagraphy database for this molecule, ATOMS generated the following file: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 3 3 0.001 1 46 Pd 3 3 4 ATOMS * this list contains 13 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 1 Pd 0.00000 0 1.99550 1.99550 0.00000 0 Pd 2.82206 1 -1.99550 1.99550 0.00000 1 Pd 2.82206 2 1.99550 -1.99550 0.00000 1 Pd 2.82206 3 -1.99550 -1.99550 0.00000 1 Pd 2.82206 4 1.99550 0.00000 1.99550 1 Pd 2.82206 5 -1.99550 0.00000 1.99550 1 Pd 2.82206 6 0.00000 1.99550 1.99550 1 Pd 2.82206 7 0.00000 -1.99550 1.99550 1 Pd 2.82206 8 1.99550 0.00000 -1.99550 1 Pd 2.82206 9 -1.99550 0.00000 -1.99550 1 Pd 2.82206 10 0.00000 1.99550 -1.99550 1 Pd 2.82206 11 0.00000 -1.99550 -1.99550 1 Pd 2.82206 12 END With the coordinates I want to use, the file would be: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350 eV EDGE K S02 1 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 1 46 Pd ATOMS * this list contains 13 atoms * x y z ipot tag distance 0 0 0 0 Pd 0 0 0 0 2.822 1 Pd 2.82206 1 2.52407 0 1.26204 1 Pd 2.82206 2 0.779982 2.40054 1.26204 1 Pd 2.82206 3 -2.04202 1.48361 1.26204 1 Pd 2.82206 4 -2.04202 -1.48361 1.26204 1 Pd 2.82206 5 0.779982 -2.40054 1.26204 1 Pd 2.82206 6 2.04202 -1.48361 -1.26204 1 Pd 2.82206 7 2.04202 1.48361 -1.26204 1 Pd 2.82206 8 -0.779982 2.40054 -1.26204 1 Pd 2.82206 9 -2.52407 0 -1.26204 1 Pd 2.82206 10 -0.779982 -2.40054 -1.26204 1 Pd 2.82206 11 0 0 -2.822 1 Pd 2.82206 12 END Do I need to modify something else besides the coordinates? Thank you for your help. Penelope _________________________________________________________________ Realiza búsquedas en Internet y llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx

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Estimation of S02
by Hiroshi Oji 13 Oct '08

13 Oct '08

Dear all, Could you give me some advice on estimating the intrinsic loss factor (S02)? I am trying to estimate the S02 value in the curve-fitting analysis for Zr K-edge EXAFS. To do this, I did the curve-fitting analysis on the first shell of Fourier transform of Zr-K EXAFS of Zr-foil by Artemis. However, there was a marked difference between the amps obtained by the fitting, depending on the "Fit k-weights" as follows. kw amp 1 0.8145660 +/- 0.0486470 2 0.9230700 +/- 0.0673820 3 1.0439100 +/- 0.0854950 1,2,3 0.9081570 +/- 0.0722180 Is this a usual thing? I can't find the reasonable explanation why S02 depends on "Fit k-weights". I attached the Artemis project file. Thank you in advance for your cooperation. Hiroshi Oji ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

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more on update problem
by Matthew 07 Oct '08

07 Oct '08

The update that causes the problem is Update 10 (iff_010.zip). When I re-downloaded from Sourceforge and let it do that update, it worked. mam

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problem with Runner
by Matthew 07 Oct '08

07 Oct '08

I just let Runner do the update to Ifeffit10 on a PC under XP, and now when I try to run any of the programs, the splash screen shows for a fraction of a second and the program dies. What's going on? mam

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Broadening
by Eugenio Otal 06 Oct '08

06 Oct '08

Hi Matt, I have measured the XAFS spectra by absorption. I really want to avoid obtain over detailed simulated spectras with a LDOS broadening smaller than core-hole broadening. So, I want to know the logical criteria to use the eimag in LDOS card. Thanks, euG Hi Eugenio, On Wed, Oct 1, 2008 at 7:42 AM, Eugenio Otal <eugenioh at gmail.com <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>> wrote: >* Hello everybody, *>* I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole *>* broadening is 4.163, which value should I use in LDOS broadening to *>* reproduce the experimental spectra. *>* Thanks, euG * What experimental LDOS data do you have? If you've measured it by x-ray absorption (which is not exactly the LDOS), you'll need to include both the experimental energy broadening, and include the core-hole broadening. --Matt

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Re: [Ifeffit] What confidence limit is implied in the error bars
by Andrew Campos 03 Oct '08

03 Oct '08

Everyone, Thank you so much for all the help. I very much appreciate the help and the advice on how to approach this problem. I have a MUCH better idea now of what downfalls, considerations, and benefits that are associated with the least-squares fitting and the errors associated with this technique. Sincerely, Andrew Campos

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Re: [Ifeffit] What confidence limit is implied in the error bars forleast-squares fitting in Athena
by Don R Baker 03 Oct '08

03 Oct '08

Hi Shelly, I am very interested in Andrew's question too, but I am to ignorant to fully understand your response. Could you please provide some more detail? For example, when you state "a large source of uncertainty can come from the representation of the standards in matching the species in the sample." do you mean that heterogeneities (as Bruce mentioned in his email) in the standards are propagated into the fits of the unknowns? Or instead do you mean that an inappropriate choice of standards can create unreliability in the fit? I would appreciate any details you can add to your repsonse. Thanks, Don On Thu, 2008-02-10 at 14:22 -0700, Kelly, Shelly wrote: > Hi Andrew, > > > > If you are fitting XANES spectra with standards, a large source of > uncertainty can come from the representation of the standards in > matching the species in the sample. > > > > Shelly > > > > > ______________________________________________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Andrew > Sent: Thursday, October 02, 2008 3:49 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] What confidence limit is implied in the error bars > forleast-squares fitting in Athena > > > > Hi everyone, > > > > I’m fitting data with the least-squares method in Athena and am not > sure what the error bars correspond to. What I mean, are these 95% > confidence limits, or is it some other statistical way for error > analysis? If Athena says the weight of one phase is 0.049 (0.003), > what confidence are in the 0.003 error bar reported by Athena? > > > > (I have done a PCA of the XANES, and XRDs of the samples and am pretty > confident in the phases that I’m fitting). > > > > I greatly appreciate the help! > > > > Andrew Campos > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University, Montreal, QC CANADA phone: 1-514-398-7485

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What confidence limit is implied in the error bars for least-squares fitting in Athena
by Andrew 02 Oct '08

02 Oct '08

Hi everyone, I'm fitting data with the least-squares method in Athena and am not sure what the error bars correspond to. What I mean, are these 95% confidence limits, or is it some other statistical way for error analysis? If Athena says the weight of one phase is 0.049 (0.003), what confidence are in the 0.003 error bar reported by Athena? (I have done a PCA of the XANES, and XRDs of the samples and am pretty confident in the phases that I'm fitting). I greatly appreciate the help! Andrew Campos

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Re: [Ifeffit] Ifeffit Digest, Vol 68, Issue 3
by Frommer Jakob 02 Oct '08

02 Oct '08

Hi Renske, I still think your problem is related to the potentials. If you unzip your artemis project and look in one of the feffXXXX.dat files in the folder data0.feff3 (this calculations was done with the solvent_O) you will find the calculated R_MTs in the first lines - for ipot3 (O) this is 1.6. Do the same with the data0.feff7 folder (apparently this calculation was done without the solvent O - even though the feff.inp says something different) and you will find 0.728. FEFF (always?) uses the closest atom (relative to the ipot=0-atom) to determine the unique potentials to be used for all atoms with the same ipot (in the manual it is stated that FEFF takes the first atom in the atoms-list but in your case just changing the position in the list did change nothing whereas increasing the distance to 3.3 (the O_t_1 atoms are at 3.266) did yield a different R_MT - but maybe I am wrong). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thu 10/2/2008 06:37 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Athena Peak Fitting (Matt Newville) 2. Re: Independence of scattering paths? (van der Veen Renske) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Oct 2008 16:23:34 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Athena Peak Fitting To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0810011423g68bb1b81g143ed34a0569a471(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I would say that method 2 looks better, as the fit over the whole of the specified fitting range is clearly better. I wouldn't necessarily say that "peak 1" in this fit -- I'm assuming you mean the highest energy peak at ~2488.3eV -- is too broad. At that high energy (definitely into the EXAFS region), the idea of peaks coming from specific electronic transitions breaks down, and EXAFS oscillations can be that broad in energy. It seems that you need this "broad peak" because you're fitting out past 2500 eV. I think that's OK (that third broad peak may not be a single electronic transition but is still useful for identifying species). But, if you'd rather not have to use the broader peak, you might also try fitting just the two sharper peaks at lower energy, say out to 2485 eV. Hope that helps, --Matt On Wed, Oct 1, 2008 at 1:31 PM, Jenny Cai <jennyh_cai(a)yahoo.ca> wrote: > Hi Everyone, > > I am using Athena peak fitting function to fit the sulfur spectrum of my > coke sample. I checked everywhere, but couldn't get detailed instruction for > using this function. So, I attached a file with this email to get help. > Could you please take a look at it, and tell me if I did the fitting right > (in terms of fitting procedure only)? > > I did the fitting in two ways, and I know both of them have problems. For > instance, in the first case, I can't get a good step line and have to cut > off the tail of the spectrum. In the second one, peak 1 is way too broad, > but if I cut it off, the fitting will be very poor. So, please tell me which > way is better, or you have some ideas to improve the fitting. > > Thank you in advance! > > > Best, > > Jenny > > ________________________________ > > Yahoo! Canada Toolbar : Search from anywhere on the web and bookmark your > favourite sites. Download it now! > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ Message: 2 Date: Thu, 2 Oct 2008 06:36:48 +0200 From: "van der Veen Renske" <Renske.vanderveen(a)psi.ch> Subject: Re: [Ifeffit] Independence of scattering paths? To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <67F374811ED3544C8543E6C0EE5EAA4B02AFEC8E(a)MAILBOX0B.psi.ch> Content-Type: text/plain; charset="us-ascii" Dear Bruce and Jakob Thanks for your replies. I realize that I should have been a bit more precise in where I actually put this extra atom: it is placed outside the molecule at an axial position of the absorbing Pt atom, representing an ethanol solvent molecule that coordinates. It is not placed between any other atoms that are included in the fit/sum, so the MT potentials should not be disturbed. Thanks to the nice presentation of scattering paths in Artemis, I am sure that I chose the same scattering paths involving the same atoms for both sums. I attached an Artemis project to make things more clear. Thanks a lot & best wishes, Renske > > On Friday 26 September 2008 22:38:58 van der Veen Renske wrote: > > I have a question concerning the independence of scattering > pathways. > > I fitted the EXAFS signal of a molecule consisting of 30 atoms (the > > related FEFF calculation is called calc 1). To see the > effect of the > > surrounding solvent molecules in the chi(k) data, I added > an O-atom in > > the coordinate list of the FEFF input file at an arbitrary distance > > from the absorbing atom (in this case Pt) and I re-ran FEFF > (calc 2). > > As a check within calc 2, I generated the sum of the same > scattering > > paths that were used in the fitting model of calc 1 using > the therein > > obtained structural fit parameters. The new O-atom was not > included in this sum. > > I expected the sum within calc 2 to be identical to the fit > of calc 1 > > based on the fact that the original atoms can not sense the > presence > > of the new O-atom (independence of scattering paths). BUT: the > > resulting sum was significantly different from the fit! > > It is a little hard to answer this question since you > described it to us rather than showing it to us with project > file(s). I have a couple of suggestions, but without being > able to examine what you did, I cannot be sure that either is > relevant. (You can insert here my standard diatribe on the > topic of how to ask questions.) > > One suggestion is to be very careful that you are including > the same set of paths in the calculation. When you add an > atom to a feff.inp file, the indexing of the paths change in > a way that may be hard to predict. Just blindly summing up > the first N paths may not do what you want. > > The other suggestion is to check that you did not place the > oxygen atom in a position that dramatically altered the > muffin tin radii. > The potantials calculation can change quite if you insert an > atom at an arbitrary loctation such that the muffin tin radii > have to be very different for some atoms. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology Synchrotron > Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >

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Re: [Ifeffit] Independence of scattering paths?
by van der Veen Renske 02 Oct '08

02 Oct '08

Dear Bruce and Jakob Thanks for your replies. I realize that I should have been a bit more precise in where I actually put this extra atom: it is placed outside the molecule at an axial position of the absorbing Pt atom, representing an ethanol solvent molecule that coordinates. It is not placed between any other atoms that are included in the fit/sum, so the MT potentials should not be disturbed. Thanks to the nice presentation of scattering paths in Artemis, I am sure that I chose the same scattering paths involving the same atoms for both sums. I attached an Artemis project to make things more clear. Thanks a lot & best wishes, Renske > > On Friday 26 September 2008 22:38:58 van der Veen Renske wrote: > > I have a question concerning the independence of scattering > pathways. > > I fitted the EXAFS signal of a molecule consisting of 30 atoms (the > > related FEFF calculation is called calc 1). To see the > effect of the > > surrounding solvent molecules in the chi(k) data, I added > an O-atom in > > the coordinate list of the FEFF input file at an arbitrary distance > > from the absorbing atom (in this case Pt) and I re-ran FEFF > (calc 2). > > As a check within calc 2, I generated the sum of the same > scattering > > paths that were used in the fitting model of calc 1 using > the therein > > obtained structural fit parameters. The new O-atom was not > included in this sum. > > I expected the sum within calc 2 to be identical to the fit > of calc 1 > > based on the fact that the original atoms can not sense the > presence > > of the new O-atom (independence of scattering paths). BUT: the > > resulting sum was significantly different from the fit! > > It is a little hard to answer this question since you > described it to us rather than showing it to us with project > file(s). I have a couple of suggestions, but without being > able to examine what you did, I cannot be sure that either is > relevant. (You can insert here my standard diatribe on the > topic of how to ask questions.) > > One suggestion is to be very careful that you are including > the same set of paths in the calculation. When you add an > atom to a feff.inp file, the indexing of the paths change in > a way that may be hard to predict. Just blindly summing up > the first N paths may not do what you want. > > The other suggestion is to check that you did not place the > oxygen atom in a position that dramatically altered the > muffin tin radii. > The potantials calculation can change quite if you insert an > atom at an arbitrary loctation such that the muffin tin radii > have to be very different for some atoms. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology Synchrotron > Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >

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update for Windows, fixing problems with Athena/Artemis
by Matt Newville 01 Oct '08

01 Oct '08

Hi Folks, I just put up a Windows updater with new versions of Athena and Artemis which (should / seems to) fix the "Athena is stuck" problems seen be various people. Details on what else changed are below. All windows users with Ifeffit 1.2.10 and 1.2.11 should install this update. If you're still using an older version, beware that this update will be binary incompatible with that version, and you should upgrade to 1.2.11 before installing this update. If you've been having troubles with Athena/Artemis "getting stuck" and these persist after installing this update, please let us know!! --Matt =========== This update to Ifeffit 1.2.11 for Windows corrects several problems with the prior release related to building the Athena et al executables against the wrong version of the Ifeffit library. This update includes newly rebuilt executables for Athena, Artemis, Hephaestus, and Atoms. Additionally, the following features have been added to Athena: 1. Filename are sorted when importing multiple files. 2. Corrected a problem related to importing chi(k) data that do not start at 0. 3. Filetype plugins have been added for: - SSRL binary files - SSRL ASCII files - SSRL MicroEXAFS files - files from the CLS HXMA beamline - files from Photon Factory beamline 12C Enjoy! Bruce Ravel 25 Sep. 2008 ===========

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Broadening
by Eugenio Otal 01 Oct '08

01 Oct '08

Hello everybody, I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole broadening is 4.163, which value should I use in LDOS broadening to reproduce the experimental spectra. Thanks, euG

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Independence of scattering paths?
by van der Veen Renske 01 Oct '08

01 Oct '08

Hello! I have a question concerning the independence of scattering pathways. I fitted the EXAFS signal of a molecule consisting of 30 atoms (the related FEFF calculation is called calc 1). To see the effect of the surrounding solvent molecules in the chi(k) data, I added an O-atom in the coordinate list of the FEFF input file at an arbitrary distance from the absorbing atom (in this case Pt) and I re-ran FEFF (calc 2). As a check within calc 2, I generated the sum of the same scattering paths that were used in the fitting model of calc 1 using the therein obtained structural fit parameters. The new O-atom was not included in this sum. I expected the sum within calc 2 to be identical to the fit of calc 1 based on the fact that the original atoms can not sense the presence of the new O-atom (independence of scattering paths). BUT: the resulting sum was significantly different from the fit! Am I overlooking something here? Aren't the calculated backscatter amplitudes and phases independent from each other? I am using Artemis version 0.8.007, Windows XP, Ifeffit 1.2.9. Thank you! Best regards, Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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Re: [Ifeffit] Independence of scattering paths? (van der Veen Renske)
by Frommer Jakob 30 Sep '08

30 Sep '08

Hi Renske, I am not sure whether I fully understand your question but here is my *two-cent-explanation*: FEFF's first step is to calculate the potentials - since it is a real space code based on the muffin-tin approximation the surrounding of an atom determines the actual scattering potential (even if you are not doing a self-consistent calculation). Since the potentials in turn determine the backscattering amplitudes and phase shifts, placing an additional atom randomly in a structure is certainly not a good idea. A possible work-around may be to find a *similar* (but known) structure with oxygen ligands and combine these two calculations in artemis (for multiple scattering however the geometry can matter a lot). If your solvent contains oxygen already you may (at least as a first approximation and for single scattering) just duplicate that path in artemis. Regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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plot linetypes option in athena windows version
by Malte Schulz 22 Sep '08

22 Sep '08

Hi there, I would like to export graphics from Athena to use them in my b&w printed thesis. Therefore it would be really useful to have Athena cycle through linetypes instead of colors. I found the "linetypes" option in the "plot" section of the preferences menu. However it doesn't seem to have any effect. I am using Athena v. 0.8.056 for windows. Malte

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export from large Athena projects
by shiryaev＠crys.ras.ru 19 Sep '08

19 Sep '08

Hi, It seems that there is a problem in exporting normalised data files from large (i.e. >10 curves) Athena projects: Exported data are cut in energy. When one exports the files one by one, this problem does not occurs. All the best, Andrei

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[ATOMS] supercell input file
by Mauro Rovezzi 19 Sep '08

19 Sep '08

Dear all, I would like to submit to your attention a problem with Atoms that I still do not understand. What I would like to do is to generate a FEFF input file starting from a supercell, that is repeating the unit cell NXxNYxNZ times and create the crystal with the resulting box. An example is given in the attached _test-atoms.inp_ created following this procedure: from wurtzite GaN (a,c cell parameters) that we describe with 2 atoms I reduce the symmetry and I use 4 atoms, then I create a 72 atoms supercell - 4*(3x3x2) - that has 3ax3ax2c dimensions and finally I tell atoms to use "P1" space group in order to replicate the supercell in x,y,z space and shift at the center the absorbing atom. Here the *problem*: the resulting _test-feff8.inp_ present good values of distances but strangely it has generated an additional Fe potential (there is just 1 Fe absorbing atom in the box/list). This is annoying because I have to remove manually the wrong "ipot" to run FEFF. Is it a stupid mistake generating the Atoms input file or is it an odd behaviour? Cheers, Mauro PS: Atoms 3.0.1 (linux) 05/08/15 PPS: Do not pay attention to coordinates and distances, these are just test-files! -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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XANES peak fitting
by Dominik Samuelis 18 Sep '08

18 Sep '08

Dear Jenny, although it doesn't exactly look like the software in your attached word file (this probably is some special XPS instrument software), peak fitting can very nicely be done with the Athena program (Analysis -> Peak fit). It's got all the features that you'd expect from a peak fitting software (difference plot, component plot, the possibility to fix certain values, and an almost arbitrary number of gaussians :-) ). If you are not restricted to the ifeffit package, the Peak Fitting Module in OriginLab's Origin Pro also produces nice results. It's not free software, though. Cheers, dominik Am 18.09.2008 um 21:45 schrieb ifeffit- request(a)millenia.cars.aps.anl.gov: > From: Jenny Cai <jennyh_cai(a)yahoo.ca> > Subject: [Ifeffit] XANES peak fitting > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <407251.2113.qm(a)web88208.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > > Could anyone tell me which software in Ifeffit package can do peak > fitting like the one shown in the attached file? > > Thank you in advance! > > Jenny Cai > -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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Re: [Ifeffit] CFAVERAGE CARD
by joshua jason kas 18 Sep '08

18 Sep '08

Hi Cammelli, feff8 is hard coded to accept only 1000 atoms or less. The error message is not very informative and I don't think it applies to your case. What you want to do is recompile change the parameter natx in the source code to something larger, maybe 3000, and recompile. If you do not have the source code, you can find it at the feff webpage with the same username and password that was used to obtain your executable. Cheers, Josh Kas On Thu, 18 Sep 2008, 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. CFAVERAGE CARD (Cammelli Sebastiano) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 Sep 2008 15:59:43 +0200 > From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> > Subject: [Ifeffit] CFAVERAGE CARD > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <AD99CE4B84C4D3468F69B0E4FB345D58048FE174(a)MAILBOX0A.psi.ch> > Content-Type: text/plain; charset="us-ascii" > > Dear Iffefit user > > I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS > simulations. > > I need to simulate a cluster with 1481 atoms, let's say in a first > moment, composed of only Cu atoms. > > Without this card the simulations crashed and it was suggested to "Use > or reduce rclabs in CFAVERAGE card Or increase parameter natx and > recompile". > > I tried with different indexes: > > CFAVERAGE 1 -1 7 > > CFAVERAGE 0 -1 6... > > I could run EXAFS simulations but I could not get xmu.dat. > > FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is > NOT used). But how could I simulate larger clusters (with more then > 1000atoms)? > > Here I send you a copy of the feff.inp, I do not write here below all > the atoms between the 1st and the 37th shell because I do not want to > make this mail too large, but I attach the original file. > > > > TITLE A > > *cluster 1481 atoms > > CONTROL 1 1 1 1 1 1 > > PRINT 0 0 0 0 0 0 > > RMULTIPLIER 1 > > LDOS -30 20 0.2 > > EDGE K > > S02 1.0 > > SCF 4 0 30 0.2 1 > > NLEG 5 > > DEBYE 15 343 0 > > EXAFS > > RPATH 10.0 > > POTENTIALS > > 0 29 Cu 3 3 0.0010 > > 1 29 Cu 3 3 1.0 > > > > ATOMS * this list contains 1481 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Cu_1 0.00000 > > 1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 > > 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 > > .... > > 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > END > > > > > > Best > > Sebastiano Cammelli > > > >

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CFAVERAGE CARD
by Cammelli Sebastiano 18 Sep '08

18 Sep '08

Dear Iffefit user I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS simulations. I need to simulate a cluster with 1481 atoms, let's say in a first moment, composed of only Cu atoms. Without this card the simulations crashed and it was suggested to "Use or reduce rclabs in CFAVERAGE card Or increase parameter natx and recompile". I tried with different indexes: CFAVERAGE 1 -1 7 CFAVERAGE 0 -1 6... I could run EXAFS simulations but I could not get xmu.dat. FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is NOT used). But how could I simulate larger clusters (with more then 1000atoms)? Here I send you a copy of the feff.inp, I do not write here below all the atoms between the 1st and the 37th shell because I do not want to make this mail too large, but I attach the original file. TITLE A *cluster 1481 atoms CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 NLEG 5 DEBYE 15 343 0 EXAFS RPATH 10.0 POTENTIALS 0 29 Cu 3 3 0.0010 1 29 Cu 3 3 1.0 ATOMS * this list contains 1481 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Cu_1 0.00000 1.80753 1.80753 0.00000 1 Cu_1 2.55623 -1.80753 1.80753 0.00000 1 Cu_1 2.55623 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 1.80753 0.00000 1.80753 1 Cu_1 2.55623 -1.80753 0.00000 1.80753 1 Cu_1 2.55623 0.00000 1.80753 1.80753 1 Cu_1 2.55623 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 .... 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 END Best Sebastiano Cammelli

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 15 Sep '08

15 Sep '08

Thanks for checking this so quick. To give more details: after I have merged the datafiles I can not plot the data in any space anymore. Athena seems to process the data for plotting, but the plot program GrWnd does not respond, so this kind of problem is probably related to GrWnd only. However, when trying to merge something else inside this file, for example only 2 scans, the resulting merged datagroup is identical to the initial one, so Athena is not working properly too. Regards Timna-Josua Kuehn

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 12 Sep '08

12 Sep '08

Hi again, I attached a standard athena project file to this mail, in order to demonstrate the bug that follows a merging process. The project file contains 4 standard EXAFS measurements of a PtCo3/C nanoparticle (+ref) which shall be merged. As I told before the merging works, but afterwards I can not do anything else, the program hangs up. This bug does appear under Windows XP.c With best regards Timna-Josua Kuehn

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Re: [Ifeffit] broken feffit
by Matt Newville 09 Sep '08

09 Sep '08

Hi Shelly, On Tue, Sep 9, 2008 at 4:04 PM, Shelly Kelly <dr.sdkelly(a)gmail.com> wrote: > Hi Matt, > > I'm likely the last person on earth using this software....but feffit seems > to be broken in the latest version ifeffit-1.2.11a. > > I'm proud to have triggered the message: > >>>feffit error > routine fitfft failed internal test. > program error: contact matt > Fatel Error: feffit error Oh thanks! When playing around with Ifeffit this summer, I completely forgot about Feffit (what was I thinking about?). It is completely broken (but fortunately, it's a simple fix!). This is now fixed in svn, and I'll post a 1.2.11b tar ball to the cars ifeffit download site right away. > I went back to the version distributed with 1.2.9 and that one works for me. This doesn't affect Windows users, as the version of Feffit there is old enough to not have this bug. --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 15
by Khalid, Syed 09 Sep '08

09 Sep '08

Matt, We do use a cam when doing QEXAFS. Along with time and detector values we record the Bragg angle of the Si(111) monochromator as a function of optical encoder readout. The encoder values are random numbers but linear with the Bragg angle. Under normal routine QEXAFS we have developed programs to convert the QEAXFS data and make it compatible with Athena analysis. That works fine. In this particular case I wanted to compare Ni EXAFS scan done in conventional way to the one I got in 100 ms. For this particular scan I could not use the programs that we developed (for data conversion to Athena compatible, for many reasons). I wanted to see how a time axis converted to energy, compares with conventional EXAFS at FFT stage. It was also to find out, as you mentioned, if two energy points will match, then will it compare to conventional EXAFS in this particular case?? Syed Khalid -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Tuesday, September 09, 2008 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 15 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: Ifeffit Digest, Vol 67, Issue 12 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Sep 2008 11:14:12 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12 To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809090914o2e3d6773n370158b56f370077(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Syed, Adam, I think the suggestion from Adam and one of the suggestions from Anatoly assume the energy linear in time. Is that the really case? For quick-scanning modes, many beamlines run the mono at a constant angular velocity, so that time maps linearly to angle, which then needs to be converted (non-linearly) to energy. Then again, some quick-scanning beamlines use a special cam drive, in which neither angle nor energy would be linear in time. Again, you need know these details in order to correctly assign energies to the data. None of it is particularly difficult, so there's no point in guessing, and stretching or massaging the energy scale until two energy points correct does not mean the rest are correct. You need to find out from the beamline how the data mapped onto energy and fix that. While you can probably use Ifeffit macros within Athena to do this correction, this is really a job for the beamline, not for Athena. Having an option in Athena that allowed the user to say "I don't know why my energy scale is bad, but can you please stretch the energies so that these two energies are what I'd like them to be" is a horrible idea. --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 67, Issue 15 ***************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12
by Khalid, Syed 09 Sep '08

09 Sep '08

That is correct: It is a QEXAFS scan of Ni foil as a function of time. Please see the data attached as a .txt file. The first column is time, second I0, and third It. I can plot this in Athena, time appears at energy axis. I can set the first derivative to 8333.0 eV ( changing X-axis from time to energy ). If I have another known energy point of Ni scan ( which is not a problem ) then I can convert the time axis to correct energy axis and proceed with normal analysis. Is that possible? -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Tuesday, September 09, 2008 9:23 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 12 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: ODP: enrgy-axis-expansion (Bruce Ravel) 2. Re: ODP: enrgy-axis-expansion (Matt Newville) 3. Re: Bugs in Athena under Windows (Matt Newville) 4. Noise level in XANES spectrum (Pushan Shah) 5. Re: ODP: enrgy-axis-expansion (Zajac, Dariusz) 6. Re: Noise level in XANES spectrum (Zajac, Dariusz) 7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 16:59:08 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081659.08948.bravel(a)bnl.gov> Content-Type: text/plain; charset="utf-8" On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: > I do not clearly understood what you mean. could you explain it more > precisely? do you want to replace the x scale from energy to time? if you > want only set the edge energy use E0 Apparently (and Khalid or Anatoly should correct me if I am wrong), they are collecting data as a function of time in quick scan mode. They then have the problem of converting time to energy. If the mono speed is recorded somehow incorrectly, then there is an accordian effect throughout the data. I think that Khalid wants to be able to adjust this accordian effect to correct the energy scale of teh data. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 16:18:55 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081418h564560d4n2fed4de0223e227(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Khalid, I agree with Dariusz: I do not understand the question. I have a hard time believing it is "the beamline cannot provide data as a function of energy, can Athena do this for me automatically?" (if it is, the answer is definitely 'No!'). Could you explain what you're trying to do? --Matt ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 16:24:45 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Bugs in Athena under Windows To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081424x5a6135dfk3aefb0e4a13c3bce(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Timna, Posting a project would definitely help here, as would clarify "since the last two versions ..." to say explicitly which versions do and do not work. My suspicion is that this related to the bug noted last week (and possibly another recent vague report of "not working") that is due to the latest version of athena -for-windows being hard-linked to pre-final-release of the ifeffit dll which is making athena's ifeffit session get stuck in an unresponsive state. I believe the only cure is a new version of athena. Again, if you could post a project that demonstrates the problem, that would be most helpful. --Matt ------------------------------ Message: 4 Date: Tue, 09 Sep 2008 15:48:51 +1000 From: "Pushan Shah" <pshah(a)gse.mq.edu.au> Subject: [Ifeffit] Noise level in XANES spectrum To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <48C69AE2.0BBD.0060.0(a)gse.mq.edu.au> Content-Type: text/plain; charset=US-ASCII Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan ------------------------------ Message: 5 Date: Tue, 9 Sep 2008 10:03:46 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "Bruce Ravel" <bravel(a)bnl.gov>, "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" hi so, I think, in case of converting time scale to energy - this should be supported by beamline (beamline scientist) somehow... if there is any nonlinearity of the converion factor (Anatoly - what whould happened if D parameter is time/energy dependent?) I think only reference spectra can help - do you have it Syed? if you have all needed parameters the calibration can be relatively quickly done in some other programs, also in macro (for many files) but that's my speculations kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Monday, September 08, 2008 10:59 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion > > >On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: >> I do not clearly understood what you mean. could you explain it more >> precisely? do you want to replace the x scale from energy to >time? if >> you want only set the edge energy use E0 > > >Apparently (and Khalid or Anatoly should correct me if I am >wrong), they are collecting data as a function of time in >quick scan mode. They then have the problem of converting >time to energy. If the mono speed is recorded somehow >incorrectly, then there is an accordian effect throughout the >data. I think that Khalid wants to be able to adjust this >accordian effect to correct the energy scale of teh data. > >B > > >-- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, >X23A2 Building 535A Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 6 Date: Tue, 9 Sep 2008 10:12:42 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] Noise level in XANES spectrum To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" Hi Pushan, can you tell more about the experiment and the way of data collecting? how did you measure your samples? which method did you use? what kind of samples do you have? the answer of your question is not stricted, but generaly I would say that the noise level should be independent of the samples, did you change something on the beamline or program between samples/measurements? e.g. sample time, no. of repeats, you moved in /out detector, amplification gain, etc.... kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Pushan Shah >Sent: Tuesday, September 09, 2008 7:49 AM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] Noise level in XANES spectrum > > >Hello Everyone, > >I have a general question regarding noise level of XANES >spectrum. I have collected XANES data for an element which is >present in ppm level in my samples. > >Some samples are exhibiting varying degree of noise in XANES >spectrum. > >Is the noise level of XANES spectrum would be proportional or >consistent with the concentration of the sample? As XANES >spectra for some of my samples with relatively higher >concentration of this element are exhibiting greater level of >noise than those with relatively lower concentrations. Will >sample matrix play any role in the noise level? > >Thanks and I appreciate your help. > >regards, >Pushan > > > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 7 Date: Tue, 9 Sep 2008 09:22:14 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD18B(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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