- 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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