June 2007 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] bond distance resolution and correlation of parameters in MS analyses?
by Peter Lay 20 Jun '07

20 Jun '07

Dear All It is unfortunate that the questions that were asked by Mark appeared to be phrased is such a way to get the responses that were obtained rather than discussing the real issues behind the questions, or whether they reflected the information in the Review. As such, I feel compelled to reply to these comments as they are not an accurate reflection of what was detailed in my article in Coordination Chemistry Review. While scientific debate is welcome, as are corrections to errors, I believe that is important that these information sites should not be used to give incorrect information as to the contents of a paper. 1. Nowhere in this Coord Chem Rev article did I state that the SS resolution equation does not apply to paths involving MS contributions, so the question was incorrectly phrased, as were the responses that claim the paper was incorrect in saying this. What I did say was that MS analyses can distinguish metal-ligand bond lengths that differ by less than the resolution imposed by this equation if the MS pathways from the different ligands are sufficiently different (within the inherent Fourier transform resolution) to get around this problem. There are numerous examples in the literature where metal-ligand bond lengths that differ by less than the SS resolution have been distinguished in this manner and have been verified by comparing crystal structure information with those obtained from MS analyses. Here is a direct copy of the relevant section from the paper, so I am uncertain as to how the contributors to the e-mails can come to the conclusion that I stated that the equation does not apply to resolution in MS paths. Clearly, I have stated that it is only when this resolution is sufficiently different in other atoms of the restrained ligands that metal-ligand bond lengths that have differences less than the SS resolution of bond lengths can be distinguished (the article only talked about ligands treated as restrained entities). This limit on the resolution of distances arises because the larger the k range, the greater the separation of the individual oscillations at the end of the k range. While this equation is often quoted, the resolution of the peaks in the FT corresponding to different shells improves as the temperature is lowered due to reduction in the Debye-Waller factors, so it should only be taken as a reasonable guide. Thus the use of as large a k range as possible not only improves the determinacy of the problem, but it also improves the precision and accuracy to which individual metal-ligand bond lengths are determined, and whether individual bond lengths can be resolved. With the typical k ranges used in SS XAFS analysis, M-L bond differencs have to differ by 0.1-0.2 Å for the oscillations in the XAFS to be sufficiently resolved to distinguish between these two bond lengths. By contrast, MS analysis of XAFS data has the ability to distinguish between metal-ligand bond distances that differ by a factor that is less than the ~0.1 Å limit imposed by the SS resolution, provided that the groups to which the ligand donor atoms are attached have quite different MS contributions, which is often the case. The differentiation of M-L bond distances that are less than the resolution obtainable with SS analysis relies on the MS contributions of other atoms within the ligands, since these normally have sufficiently different frequencies of oscillations in the XAFS so that they can be resolved. The MS contributions are most important in the low k range [18] and hence, the most accurate and precise bond length determinations in terms of resolution of different shells (and three-dimensional structural determination) will be obtained when both a large k range and all of the low k range data are used in the fitting procedure. What do the above comments mean in practice? It means that if a complex has ligands all of the same type and angles that involve the M-ligand bond and the ligand are essentially the same, then MS analysis cannot improve over SS on separating bond distances that differ by less than the SS resolution in the FT. However, if ligands of the same type are at different angles with respect to the metal-ligand axes or have different ligands adjacent or opposite to them, or if different ligands are at similar distances, then there is almost certainly a range of MS paths that have half distances that differ by more than the resolution given by the equation and, hence, the individual metal-ligand distances can be distinguished by the use of MS fitting within the constraints of the equation that was given, when they cannot be distinguished by SS fitting. 2. With regard to point 2, yes the equation should have been more accurately described as the number of independent observations rather than the number of independent points in reference to equation 24 in the review. The number of independent observations is a combination of the number of independent points in the EXAFS data plus the number of independent observations obtained from crystallography that are included in the restrained model, as described in the Binsted, Strange and Hasnain article. The equation (or variations of it, as pointed out by the comments below) is, however, appropriate for use in estimating the value of the number of independent observations that are included in restrained MS modeling for fits to EXAFS data. This is not only used in such EXAFS analyses but also extensively, and for a long time, in protein crystallography to increase the degree to which a fit is overdetermined or to prevent an underdetermined fit to the data. As pointed out by Matt, this is often used for relatively rigid ligands, such as imidazoles; it can also be used for flexible ligands where the internal bond lengths vary over a narrow range that is defined by X-ray crystallography, but one of more angle(s) have significant flexibility. For the former case, the whole ligand is moved as an essentially rigid entity, in much the same way as a single atom in the fitting procedure. The essentially fixed (within small ranges) bond angles and bond lengths involving this group lead to the extra term in the equation that is the number of independent observations that are included in the model and, in a restrained model, this increases the value of N/p, even though the value of p does not change (i.e., the positional parameters within the imidazole, for instance, are also fitted but within a very narrow range that is consistent with the variation observed in accurate X-ray crystallography structures). If these bond lengths and angles (and/or Debye-Waller values) were constrained, then the value of p would also decrease making the problem more overdetermined. The Debye-Waller factors can be calculated for atoms in a ring in order to reduce the value of p, but extreme care has to be taken in the use of these values in constrained fits, since they take no account of disorder problems in the crystal or solution and, hence, could result in constrained values that are artificially low and which would lead to problems in the fitting procedure. The answer to the question is that the Stern paper discusses the number of independent points in the EXAFS data and applies to both SS and MS fitting. However, for restrained MS fits, the number of independent observations that should be used in assessing the degree to which the problem is determined in the fitting procedure is that described in the Binsted, Strange and Hasnain paper (or something similar). The latter type of fitting was that described in the Coordination Chemistry Rev article and presumably has been used in the work described by Mark. All the best Peter HI Mark, > Any thoughts and opinions would be greatly appreciated as this relates directly to corrections suggested to be made to my PhD thesis! This is going to re-iterate most of what Bruce said, but since you asked: > 1)Does the equation for bond distance resolution (r = pi/2deltak) only apply to SS? No. It applies to all EXAFS. > I have held the opinion that this can be applied to MS analysis You have been right. > however I have recently been informed that this equation does not correctly describe distance > resolution in MS analyses. The paper in Coord. Chem. Rev. 2005, 249, 141-160 describes this > and is this concordant with the views of the wider EXAFS community? You were mis-informed. This paper is profoundly wrong, and is not concordant with the views of the wider EXAFS community, as defined by the standards and criteria documents at http://www.i-x-s.org/OLD/subcommittee_reports/sc/err-rep.pdf This paper states that the number of independent points in an XAFS data set is: N_i = [ 2*(rmax - rmin) * (kmax -kmin) / pi ] + Sum D*(N-2) + 1 Here rmin,rmax,kmin, and kmax are the spectral ranges. I cannot tell what the sum is over, but D is the "dimension with a restrained part of the model (ie, three for a three-dimensional model)" and N is "the number of independent atoms within the restrained group of the model". The ( Sum D*(N-2) ) term asserts that the number of independent points in the data is dependent on the model. This is complete nonsense. For what it's worth, the standards and criteria report cited above recommends using N_i = [ 2*(rmax - rmin) * (kmax -kmin) / pi ] rounded to the nearest integer. The report is has a bit more to say, but note that it is carefully (and deliberately) silent on "+1", "+2", etc. This is because N_i is an estimate of the maximum number of parameters that can be extracted from a signal. If you're quibbling whether to add 1 or 2 to this number, it probably means you should really subtract 4. Now, one may apply a variety of modeling approaches (tricks?? assumptions??) to the analysis of multiple scattering in highly constrained three-dimensional models that are often associated with organo-metallics. For example, a histidine ring attached to a metal will give multiple scattering, and you can usually assert that the ring is rigid, though you may need to refine its location and orientation relative to the metal. That makes the bond distances and angles (and MS amplitudes) for all the scattering paths from this ring all dependent on a reduced number of variables. It does not add information to the data. Cheers, --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit X-Account-Key: account2 X-Mozilla-Keys: Return-Path: <ifeffit-bounces(a)millenia.cars.aps.anl.gov> X-Original-To: j.aitken(a)chem.usyd.edu.au Delivered-To: aitken_j(a)chem.usyd.edu.au Received: from localhost (unknown [127.0.0.1]) by localhost.chem.usyd.edu.au (Postfix) with ESMTP id 3F99881B8; Thu, 7 Jun 2007 07:04:39 +1000 (EST) X-Virus-Scanned: amavisd-new at chem.usyd.edu.au Received: from tismis.chem.usyd.edu.au ([127.0.0.1]) by localhost (tismis.chem.usyd.edu.au [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id FIIBlvbv0FPG; Thu, 7 Jun 2007 07:04:36 +1000 (EST) Received: from millenia.cars.aps.anl.gov (millenia.cars.aps.anl.gov [164.54.160.111]) by tismis.chem.usyd.edu.au (Postfix) with ESMTP id 1AFAB8187; Thu, 7 Jun 2007 07:04:35 +1000 (EST) Received: from millenia.cars.aps.anl.gov (localhost.localdomain [127.0.0.1]) by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id l56L3Xc7017917; Wed, 6 Jun 2007 16:03:34 -0500 Received: from polyhymnia.mr.aps.anl.gov (polyhymnia.mr.aps.anl.gov [164.54.244.23]) by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id l56L3WHx017914 for <ifeffit(a)millenia.cars.aps.anl.gov>; Wed, 6 Jun 2007 16:03:32 -0500 Received: from localhost (localhost [127.0.0.1]) by polyhymnia.mr.aps.anl.gov (8.13.8/8.13.8/Debian-3) with ESMTP id l56L0im6015827; Wed, 6 Jun 2007 16:00:44 -0500 From: Bruce Ravel <bravel(a)anl.gov> Organization: Molecular Environmental Science Group at Argonne National Lab To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Date: Wed, 6 Jun 2007 16:00:43 -0500 User-Agent: KMail/1.9.6 References: <200706061213.DGT11246(a)auummr1om07.three.com.au> In-Reply-To: <200706061213.DGT11246(a)auummr1om07.three.com.au> MIME-Version: 1.0 Content-Disposition: inline Message-Id: <200706061600.43646.bravel(a)anl.gov> Cc: MarkBondin <mibondin(a)three.com.au> Subject: Re: [Ifeffit] bond distance resolution and correlation of parameters in MS analyses? X-BeenThere: ifeffit(a)millenia.cars.aps.anl.gov X-Mailman-Version: 2.1.9 Precedence: list Reply-To: Bruce Ravel <bravel(a)anl.gov>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> List-Id: XAFS Analysis using Ifeffit <ifeffit.millenia.cars.aps.anl.gov> List-Unsubscribe: <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=unsubscribe> List-Archive: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit> List-Post: <mailto:ifeffit@millenia.cars.aps.anl.gov> List-Help: <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=help> List-Subscribe: <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=subscribe> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Sender: ifeffit-bounces(a)millenia.cars.aps.anl.gov Errors-To: ifeffit-bounces(a)millenia.cars.aps.anl.gov On Wednesday 06 June 2007, MarkBondin wrote: > 2) What is the actual equation which defines the determinacy of a fitting > procedure and does this differ between SS and MS analyses? For MS analyses > there has been a recently published equation (Coord. Chem. Rev. 2005, 249, > 141-160) which takes into acount the number of dimensions used in the > analyses and is this only relevant to MS analyses of data? This has also > been expressed in the paper by Binsted (Biochemistry. 1992, 31, > 12117-12125) however a different equation has been detailed by Stern (Phys. > Rev. B. 1993, 48, 9825-9827) which I have been using as a guide in my MS > analyses. Is this acceptable? 1. I don't know what you mean by the word "determinacy". In any case, I thought I made it clear in my last post that, in my opinion, the differences between SS and MS analysis are in the physical interpretation and not in the statistical interpretation. Feff, Ifeffit, and Artemis certainly go to great lengths to downplay the differences between SS and MS paths in the context of the formalism of the theory and analysis, instead emphasizing their differences only in the context of physical interpretation. 2. Argonne's library only has access to the last year of Coord. Chem. Rev. and I don't have time this week to go fetch it from the stacks. So I cannot comment on that paper. 3. The paper by Stern should be read with some care. The argument Ed makes in that paper can only be true in the case of a perfectly packed signal. EXAFS data, although treated as signal processing problem, is never perfectly packed. The Nyquist criterion is an upper bound on the information content, but the actual content of the data is always somewhat less. There are some very fine papers by Rossner and Krappe about using Baysian techniques to find the actual information content of the EXAFS signal. The executive summary is that if think you need Ed's magic "+2", you are probably overusing the information content of your data. Most of us here in this list aren't as careful in practice as all that Baysian stuff. In general, one tries to stay "well below" the Nyquist upper bound. If your fitting parameters make sense physically, if the correlations are not "too high", and if the error bars on your parameters are not "too big", then you are probably not overusing the information content of your data. What is "too high" and "too big"? Well, I am purposefully using squishy language. It is kind of difficult to use Gaussian statistical techniques on EXAFS data, despite the fact that that's exactly what Ifeffit does. The reason is that Gaussin statistics presumes that your measurememt errors are statistical and normally distributed. In practice, exafs analysis is dominated by systematic uncertainties. Things like detector or sample non-linearities and the approximations made by Feff are much bigger sources of error than shot noise for most experiments. Most of those systematic problems are present in your analysis, but I have no idea how you could possibly quantify them. Hence I find myself using squishy language to discuss fit statistics. Read the papers by the frequent contributors to this mailing list. Scott Calvin and Shelly Kelly in particular are careful EXAFS practitioners who work on tough analysis problems and deal well with these issues. Doing what they do may not be as right as possible, but it certainly ain't wrong. HTH, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Return-Path: <ifeffit-bounces(a)millenia.cars.aps.anl.gov> X-Original-To: j.aitken(a)chem.usyd.edu.au Delivered-To: aitken_j(a)chem.usyd.edu.au Received: from localhost (unknown [127.0.0.1]) by localhost.chem.usyd.edu.au (Postfix) with ESMTP id A3DA68195; Wed, 6 Jun 2007 22:51:48 +1000 (EST) X-Virus-Scanned: amavisd-new at chem.usyd.edu.au Received: from tismis.chem.usyd.edu.au ([127.0.0.1]) by localhost (tismis.chem.usyd.edu.au [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id jldjzjMckVWz; Wed, 6 Jun 2007 22:51:47 +1000 (EST) Received: from millenia.cars.aps.anl.gov (millenia.cars.aps.anl.gov [164.54.160.111]) by tismis.chem.usyd.edu.au (Postfix) with ESMTP id 75D278160; Wed, 6 Jun 2007 22:51:47 +1000 (EST) Received: from millenia.cars.aps.anl.gov (localhost.localdomain [127.0.0.1]) by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id l56CnoPv011737; Wed, 6 Jun 2007 07:49:51 -0500 Received: from polyhymnia.mr.aps.anl.gov (polyhymnia.mr.aps.anl.gov [164.54.244.23]) by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id l56CnmLn011734 for <ifeffit(a)millenia.cars.aps.anl.gov>; Wed, 6 Jun 2007 07:49:48 -0500 Received: from localhost (localhost [127.0.0.1]) by polyhymnia.mr.aps.anl.gov (8.13.8/8.13.8/Debian-3) with ESMTP id l56Cl1cT014080; Wed, 6 Jun 2007 07:47:01 -0500 From: Bruce Ravel <bravel(a)anl.gov> Organization: Molecular Environmental Science Group at Argonne National Lab To: ifeffit(a)millenia.cars.aps.anl.gov Date: Wed, 6 Jun 2007 07:47:01 -0500 User-Agent: KMail/1.9.6 References: <200706061213.DGT11246(a)auummr1om07.three.com.au> In-Reply-To: <200706061213.DGT11246(a)auummr1om07.three.com.au> MIME-Version: 1.0 Content-Disposition: inline Message-Id: <200706060747.01272.bravel(a)anl.gov> Cc: MarkBondin <mibondin(a)three.com.au> Subject: Re: [Ifeffit] bond distance resolution and correlation of parameters in MS analyses? X-BeenThere: ifeffit(a)millenia.cars.aps.anl.gov X-Mailman-Version: 2.1.9 Precedence: list Reply-To: Bruce Ravel <bravel(a)anl.gov>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> List-Id: XAFS Analysis using Ifeffit <ifeffit.millenia.cars.aps.anl.gov> List-Unsubscribe: <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=unsubscribe> List-Archive: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit> List-Post: <mailto:ifeffit@millenia.cars.aps.anl.gov> List-Help: <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=help> List-Subscribe: <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=subscribe> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 8bit Sender: ifeffit-bounces(a)millenia.cars.aps.anl.gov Errors-To: ifeffit-bounces(a)millenia.cars.aps.anl.gov On Wednesday 06 June 2007, MarkBondin wrote: >1)Does the equation for bond distance resolution (r = pi/2deltak) only >apply to SS? I have held the opinion that this can be applied to MS >analysis however I have recently been informed that this equation does not >correctly describe distance resolution in MS analyses. The paper in Coord. >Chem. Rev. 2005, 249, 141-160 describes this and is this concordant with >the views of the wider EXAFS community? > > >Mark, > >Strictly speaking, that equation doesn't have anything to do with >EXAFS. That is the equation that tells you what your Fourier >component resolution is in a general Fourier analysis problem. It >just so happens that, in the case of single scattering EXAFS analysis, >that equation is easily interpreted in terms of photoelectron >wavenumber k and SS path length r. > >The equation is neither different nor incorrect for MS analysis. >That's true becuase MS analysis isn't any different from SS analysis. >In either case, you do a Fourier transform. In either case, you >attempt to model Fourier components using the contributions from some >number of scattering geometries as computed by theory. In either >case, you are asking yourself if you can actually resolve small >differences in phase of the various things that contribute to the fit. > >The only difference lies in how you *interpret* the physical meaning >of the Fourier components. And even then, things aren't so very >different. In the case of SS analysis, you assert that the R axis is >a measure of "bond length" while for MS analysis the R axis is a >measure of "half path length" -- acknowledging, of course, that there >is a phase shift in the EXAFS equation such that the R axis actually >measures something a bit shorter than the bond or half path length. > >Off the top of my head, I don't recall the paper you cite and I most >certainly cannot speak for the "wider EXAFS community". Speaking for >myself, the physical interpretation of the equation for Fourier >component resolution may change when you consider MS paths, but to >claim that a property of the Fourier transform somehow becomes invalid >when you change the details of the fitting model is just silly. > >B > > >-- >Bruce Ravel ---------------------------------------------- bravel(a)anl.gov > >Molecular Environmental Science Group, Building 203, Room E-165 >MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 > >Argonne National Laboratory phone and voice mail: (1) 630 252 5033 >Argonne IL 60439, USA fax: (1) 630 252 9793 > >My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: >http://cars9.uchicago.edu/~ravel/software/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >Return-Path: <ifeffit-bounces(a)millenia.cars.aps.anl.gov> >X-Original-To: j.aitken(a)chem.usyd.edu.au >Delivered-To: aitken_j(a)chem.usyd.edu.au >Received: from localhost (unknown [127.0.0.1]) > by localhost.chem.usyd.edu.au (Postfix) with ESMTP id B52C68192; > Wed, 6 Jun 2007 22:34:01 +1000 (EST) >X-Virus-Scanned: amavisd-new at chem.usyd.edu.au >Received: from tismis.chem.usyd.edu.au ([127.0.0.1]) > by localhost (tismis.chem.usyd.edu.au [127.0.0.1]) (amavisd-new, > port 10024) > with ESMTP id Bt1hFrBPzdYS; Wed, 6 Jun 2007 22:34:01 +1000 (EST) >Received: from millenia.cars.aps.anl.gov (millenia.cars.aps.anl.gov >[164.54.160.111]) > by tismis.chem.usyd.edu.au (Postfix) with ESMTP id 8255C8160; > Wed, 6 Jun 2007 22:34:00 +1000 (EST) >Received: from millenia.cars.aps.anl.gov (localhost.localdomain [127.0.0.1]) > by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id > l56CVHTh011592; > Wed, 6 Jun 2007 07:31:35 -0500 >Received: from petasus.aps.anl.gov (petasus.aps.anl.gov [164.54.146.72]) > by millenia.cars.aps.anl.gov (8.13.8/8.13.8) with ESMTP id > l56CDQCl011430 > for <ifeffit(a)millenia.cars.aps.anl.gov>; Wed, 6 Jun 2007 07:13:26 > -0500 >Received: from herald.aps.anl.gov (herald.aps.anl.gov [164.54.50.61]) > by petasus.aps.anl.gov (8.13.7/8.13.7) with ESMTP id l56CDPH7020467 > for <ifeffit(a)millenia.cars.aps.anl.gov>; > Wed, 6 Jun 2007 07:13:25 -0500 (CDT) >Received: from iota.aps.anl.gov (iota.aps.anl.gov [164.54.56.65]) > by herald.aps.anl.gov (8.13.7/8.13.7) with ESMTP id l56CDDTr015527 > for <ifeffit(a)millenia.cars.aps.anl.gov>; > Wed, 6 Jun 2007 07:13:13 -0500 (CDT) >Received: from auummr1om07.three.com.au (smtpout3.three.com.au >[202.124.68.59]) > by iota.aps.anl.gov with ESMTP id l56CDBRl028957 > for <ifeffit(a)millenia.cars.aps.anl.gov>; > Wed, 6 Jun 2007 07:13:12 -0500 (CDT) >Received: from auumgu1pr04.three.com.au (auummr1vp02.three.com.au > [10.176.58.185]) by auummr1om07.three.com.au (MOS 3.5.5-GR) > with ESMTP id DGT11246; Wed, 6 Jun 2007 22:13:03 +1000 (EST) >Message-Id: <200706061213.DGT11246(a)auummr1om07.three.com.au> >Content-Disposition: inline >MIME-Version: 1.0 >X-Mailer: Perl5 Mail::Internet v1.40 >From: MarkBondin <mibondin(a)three.com.au> >To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> >Date: Wed, 06 Jun 2007 22:13:03 +1000 (EST) >X-Priority: 3 (Normal) >X-MIME-Autoconverted: from quoted-printable to 8bit by > millenia.cars.aps.anl.gov id l56CDQCl011430 >X-Mailman-Approved-At: Wed, 06 Jun 2007 07:31:16 -0500 >Subject: [Ifeffit] bond distance resolution and correlation of parameters > in MS analyses? >X-BeenThere: ifeffit(a)millenia.cars.aps.anl.gov >X-Mailman-Version: 2.1.9 >Precedence: list >Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >List-Id: XAFS Analysis using Ifeffit <ifeffit.millenia.cars.aps.anl.gov> >List-Unsubscribe: ><http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, > ><mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=unsubscribe> >List-Archive: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit> >List-Post: <mailto:ifeffit@millenia.cars.aps.anl.gov> >List-Help: <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=help> >List-Subscribe: <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>, > <mailto:ifeffit-request@millenia.cars.aps.anl.gov?subject=subscribe> >Content-Type: text/plain; charset=us-ascii; format=flowed >Content-Transfer-Encoding: 8bit >Sender: ifeffit-bounces(a)millenia.cars.aps.anl.gov >Errors-To: ifeffit-bounces(a)millenia.cars.aps.anl.gov > >Hi, I would like general opinions of some EXAFS practioners in regards to >the most widely accepted methods for bond distance resolution and >correlation of parameters in both single scattering (SS) and multiple >scattering (MS) EXAFS refinements and if these can be said to differ? > >1)Does the equation for bond distance resolution (r = pi/2deltak) only >apply to SS? I have held the opinion that this can be applied to MS >analysis however I have recently been informed that this equation does not >correctly describe distance resolution in MS analyses. The paper in Coord. >Chem. Rev. 2005, 249, 141-160 describes this and is this concordant with >the views of the wider EXAFS community? > >2) What is the actual equation which defines the determinacy of a fitting >procedure and does this differ between SS and MS analyses? For MS analyses >there has been a recently published equation (Coord. Chem. Rev. 2005, 249, >141-160) which takes into acount the number of dimensions used in the >analyses and is this only relevant to MS analyses of data? This has also >been expressed in the paper by Binsted (Biochemistry. 1992, 31, >12117-12125) however a different equation has been detailed by Stern >(Phys. Rev. B. 1993, 48, 9825-9827) which I have been using as a guide in >my MS analyses. Is this acceptable? > >Any thoughts and opinions would be greatly appreciated as this relates >directly to corrections suggested to be made to my PhD thesis! > >Many thanks, > >Mark > >_ Professor Peter A. Lay FAA ARC Australian Professorial Fellow and Personal Chair in Inorganic Chemistry Centre for Heavy Metals Research School of Chemistry The University of Sydney NSW 2006 Australia Tel: +61-2-9351 4269 Fax: +61-2-9351 3329

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Re: [Ifeffit] Ifeffit Digest, Vol 52, Issue 7
by hebhop＠u.washington.edu 19 Jun '07

19 Jun '07

Hi Eckhard, you need to add the following two cards to your feff.inp files: * Self consistent potentials. This can be important for XANES calculatoins. SCF rscf 0 * Full multiple scattering (sums all paths within rfms). This is essential for * most XANES calculations. FMS rfms 0 calculations should be converged w.r.t. rscf and rfms, but for your files, you can just include the whole cluster of atoms. Also, I ran both files and the first one (gypsum) complains that atoms are very close together. FEFF does not crash, but I would check your structure to be sure that it is correct. Cheers, Josh Kas > Hallo @all, > > (first at all, sorry for my bad english) > > i'm a student working on my diploma thesis (nexafs/xanes) and my job is to > simulate with FEFF 8.4 spectra, for example absorption as a function of > energy (mu_(E)). I'm a newbie in this topic and i tried to get the k-edge > of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm > interested in the XANES-range of the spectra not the EXAFS. I get > everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance i > use (gypsum, pyrite,...). There are no differences with the peak position > on the energy-scale or shifts. I'm really confused :-( I think, there > should be differences in the spectra... I send you two feff.inp files from > my feff-runs. My source is the mineralogy database > (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the > unitcell. Then i put the data in the XtalDraw program to get the positions > of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell > :-). Then i put the values of the positions into feff... > I simulated pyrite with 12 atoms and gypsum with 48. > I'm appreciative for every help :-) > > ciao, > Eckhard > > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany

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Re: [Ifeffit] Ifeffit Digest, Vol 52, Issue 9
by Michel Jaouen 18 Jun '07

18 Jun '07

Dear lena, >I have a question regarding the convergence of XANES calculations. I'm >currently focusing on the O-K edge of perovskite oxides, in particular >SrTiO3 and found that there are still fine-structure changes for large >(9.5?) clusters. Attached is my *.inp file for the 9.5? cluster and a >summary of the XANES for increasing cluster sizes from 6.5? to 9.5?. You >can see that there are still significant changes as the cluster size is >increased from 8.5 to 9.5?. In particular, I find a double peak feature >in the first 5eV after the edge onset, which is not observed >experimentally. It is a normal behavior: when increasing the cluster's size, you are adding more MS paths and then it appears coresponding peaks. It is a general trend for xanes:the measured signal is a probe up to a given distance for MS, a distance you didn't know a priori. Thus the game is to start from a rather small cluster, compute the xanes, compare to the experiment. If some features are missing, increase the size and so on till you obtain (if lucky) all experimental fine structures. On the opposite, as soon as it appears fine structures which don't exist in the experiment reduce the size. > Do you have any suggestions how to obtain a better >convergence? > >Secondly, if you compare the simulated XANES with experimental results >(see attachment: EELS STO.png), I'm not able to match all three main >peaks, even by scaling the energy scale. Are the deviations I'm seeing >within the accuracy of FEFF or do I need to improve my *.inp file? I have been working a lot on STO and have many exchange about this material with John Rehr. In fact you can obtain a quite good match with the experiment (peaks' positions) if you reduce the lattice parameter by 5% (RMULTIPLIER=0.95, see the attached figure). Of course such a reduction is unphysical but from John's own words :"Also regarding SrTiO3, I'm now thinking that the self-energy might be responsible for the need to use an RMULT 0.95." So either you the Rmultiplier trick or you try the feff8.5 version that includes some improvements to the self-energy (using low-loss and the sum rules for normalization). In any case, feff has to much intensity at the edge onset (sigma*) for light elements like Oxygen. Two other comments: why adding a real part vr=1.4eV? I don't find this necessary here from my numerous calculations (it is responsible for the hump at the bottom of the pi* which doesn't exist in the experiment: a positive vr induces a red-shift for the spectrum, look at the ldos). I suggest also not to use the default for lmax (-1), but instead lmax=2 for all atoms (spd basis). You can also try to go up to lmax=3 (spdf basis) because Sr is quite heavy and it can help in some case (for pure Ni for instance, to reproduce the K edge, you must go up to f states). I hope it can help you. Best regards, Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: [Ifeffit] convergence of XANES for STO
by Feng Wang 18 Jun '07

18 Jun '07

Hi Lena, It is no suprising to see the change of the fine structure near the edge within a cluster of that size, because of the long mean free path of the photoelectron. You used a broadening of 0.2eV in your FEFF input, which should give you more details than your experiments. Good luck, Feng > Dear all, > > I have a question regarding the convergence of XANES calculations. I'm > currently focusing on the O-K edge of perovskite oxides, in particular > SrTiO3 and found that there are still fine-structure changes for large > (9.5Å) clusters. Attached is my *.inp file for the 9.5Å cluster and a > summary of the XANES for increasing cluster sizes from 6.5Å to 9.5Å. You > can see that there are still significant changes as the cluster size is > increased from 8.5 to 9.5Å. In particular, I find a double peak feature > in the first 5eV after the edge onset, which is not observed > experimentally. Do you have any suggestions how to obtain a better > convergence? > > Secondly, if you compare the simulated XANES with experimental results > (see attachment: EELS STO.png), I'm not able to match all three main > peaks, even by scaling the energy scale. Are the deviations I'm seeing > within the accuracy of FEFF or do I need to improve my *.inp file? > > Best regards, > Lena > > --------------------------------- > Lena Fitting Kourkoutis > E13 Clark Hall > Cornell University > Applied and Engineering Physics > Ithaca, NY 14853 > > phone: 607-255-0654 > e-mail: lf56(a)cornell.edu > --------------------------------- ==================================== EM group, NINT 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

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convergence of XANES for STO
by Lena Fitting 18 Jun '07

18 Jun '07

Dear all, I have a question regarding the convergence of XANES calculations. I'm currently focusing on the O-K edge of perovskite oxides, in particular SrTiO3 and found that there are still fine-structure changes for large (9.5Å) clusters. Attached is my *.inp file for the 9.5Å cluster and a summary of the XANES for increasing cluster sizes from 6.5Å to 9.5Å. You can see that there are still significant changes as the cluster size is increased from 8.5 to 9.5Å. In particular, I find a double peak feature in the first 5eV after the edge onset, which is not observed experimentally. Do you have any suggestions how to obtain a better convergence? Secondly, if you compare the simulated XANES with experimental results (see attachment: EELS STO.png), I'm not able to match all three main peaks, even by scaling the energy scale. Are the deviations I'm seeing within the accuracy of FEFF or do I need to improve my *.inp file? Best regards, Lena --------------------------------- Lena Fitting Kourkoutis E13 Clark Hall Cornell University Applied and Engineering Physics Ithaca, NY 14853 phone: 607-255-0654 e-mail: lf56(a)cornell.edu --------------------------------- TITLE SrTiO3 with core hole HOLE 1 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * ixc [ Vr Vi ] EXCHANGE 0 1.4 0.2 * r_scf [ l_scf n_scf ca ] SCF 5.0 0 30 * kmax [ delta_k delta_e ] XANES 4.0 .01 .17 * r_fms l_fms FMS 9.15804 0 * emin emax eimag LDOS -30 20 0.2 RPATH 0.1 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 8 O -1 -1 0.001 1 38 Sr -1 -1 1 2 22 Ti -1 -1 1 3 8 O -1 -1 3 ATOMS * this list contains 285 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 O1 0.00000 0 0.00000 0.00000 1.95250 2 Ti1 1.95250 1 0.00000 0.00000 -1.95250 2 Ti1 1.95250 2 1.95250 0.00000 1.95250 3 O1 2.76125 3 -1.95250 0.00000 1.95250 3 O1 2.76125 4 0.00000 1.95250 1.95250 3 O1 2.76125 5 0.00000 -1.95250 1.95250 3 O1 2.76125 6 1.95250 0.00000 -1.95250 3 O1 2.76125 7 -1.95250 0.00000 -1.95250 3 O1 2.76125 8 0.00000 1.95250 -1.95250 3 O1 2.76125 9 0.00000 -1.95250 -1.95250 3 O1 2.76125 10 1.95250 1.95250 0.00000 1 Sr1 2.76125 11 -1.95250 1.95250 0.00000 1 Sr1 2.76125 12 1.95250 -1.95250 0.00000 1 Sr1 2.76125 13 -1.95250 -1.95250 0.00000 1 Sr1 2.76125 14 3.90500 0.00000 0.00000 3 O1 3.90500 15 -3.90500 0.00000 0.00000 3 O1 3.90500 16 0.00000 3.90500 0.00000 3 O1 3.90500 17 0.00000 -3.90500 0.00000 3 O1 3.90500 18 0.00000 0.00000 3.90500 3 O1 3.90500 19 0.00000 0.00000 -3.90500 3 O1 3.90500 20 3.90500 0.00000 1.95250 2 Ti1 4.36592 21 -3.90500 0.00000 1.95250 2 Ti1 4.36592 22 0.00000 3.90500 1.95250 2 Ti1 4.36592 23 0.00000 -3.90500 1.95250 2 Ti1 4.36592 24 3.90500 0.00000 -1.95250 2 Ti1 4.36592 25 -3.90500 0.00000 -1.95250 2 Ti1 4.36592 26 0.00000 3.90500 -1.95250 2 Ti1 4.36592 27 0.00000 -3.90500 -1.95250 2 Ti1 4.36592 28 3.90500 1.95250 1.95250 3 O1 4.78263 29 -3.90500 1.95250 1.95250 3 O1 4.78263 30 1.95250 3.90500 1.95250 3 O1 4.78263 31 -1.95250 3.90500 1.95250 3 O1 4.78263 32 3.90500 -1.95250 1.95250 3 O1 4.78263 33 -3.90500 -1.95250 1.95250 3 O1 4.78263 34 1.95250 -3.90500 1.95250 3 O1 4.78263 35 -1.95250 -3.90500 1.95250 3 O1 4.78263 36 3.90500 1.95250 -1.95250 3 O1 4.78263 37 -3.90500 1.95250 -1.95250 3 O1 4.78263 38 1.95250 3.90500 -1.95250 3 O1 4.78263 39 -1.95250 3.90500 -1.95250 3 O1 4.78263 40 3.90500 -1.95250 -1.95250 3 O1 4.78263 41 -3.90500 -1.95250 -1.95250 3 O1 4.78263 42 1.95250 -3.90500 -1.95250 3 O1 4.78263 43 -1.95250 -3.90500 -1.95250 3 O1 4.78263 44 1.95250 1.95250 3.90500 1 Sr1 4.78263 45 -1.95250 1.95250 3.90500 1 Sr1 4.78263 46 1.95250 -1.95250 3.90500 1 Sr1 4.78263 47 -1.95250 -1.95250 3.90500 1 Sr1 4.78263 48 1.95250 1.95250 -3.90500 1 Sr1 4.78263 49 -1.95250 1.95250 -3.90500 1 Sr1 4.78263 50 1.95250 -1.95250 -3.90500 1 Sr1 4.78263 51 -1.95250 -1.95250 -3.90500 1 Sr1 4.78263 52 3.90500 3.90500 0.00000 3 O1 5.52250 53 -3.90500 3.90500 0.00000 3 O1 5.52250 54 3.90500 -3.90500 0.00000 3 O1 5.52250 55 -3.90500 -3.90500 0.00000 3 O1 5.52250 56 3.90500 0.00000 3.90500 3 O1 5.52250 57 -3.90500 0.00000 3.90500 3 O1 5.52250 58 0.00000 3.90500 3.90500 3 O1 5.52250 59 0.00000 -3.90500 3.90500 3 O1 5.52250 60 3.90500 0.00000 -3.90500 3 O1 5.52250 61 -3.90500 0.00000 -3.90500 3 O1 5.52250 62 0.00000 3.90500 -3.90500 3 O1 5.52250 63 0.00000 -3.90500 -3.90500 3 O1 5.52250 64 3.90500 3.90500 1.95250 2 Ti1 5.85750 65 -3.90500 3.90500 1.95250 2 Ti1 5.85750 66 3.90500 -3.90500 1.95250 2 Ti1 5.85750 67 -3.90500 -3.90500 1.95250 2 Ti1 5.85750 68 0.00000 0.00000 5.85750 2 Ti1 5.85750 69 3.90500 3.90500 -1.95250 2 Ti1 5.85750 70 -3.90500 3.90500 -1.95250 2 Ti1 5.85750 71 3.90500 -3.90500 -1.95250 2 Ti1 5.85750 72 -3.90500 -3.90500 -1.95250 2 Ti1 5.85750 73 0.00000 0.00000 -5.85750 2 Ti1 5.85750 74 5.85750 0.00000 1.95250 3 O1 6.17435 75 -5.85750 0.00000 1.95250 3 O1 6.17435 76 0.00000 5.85750 1.95250 3 O1 6.17435 77 0.00000 -5.85750 1.95250 3 O1 6.17435 78 1.95250 0.00000 5.85750 3 O1 6.17435 79 -1.95250 0.00000 5.85750 3 O1 6.17435 80 0.00000 1.95250 5.85750 3 O1 6.17435 81 0.00000 -1.95250 5.85750 3 O1 6.17435 82 5.85750 0.00000 -1.95250 3 O1 6.17435 83 -5.85750 0.00000 -1.95250 3 O1 6.17435 84 0.00000 5.85750 -1.95250 3 O1 6.17435 85 0.00000 -5.85750 -1.95250 3 O1 6.17435 86 1.95250 0.00000 -5.85750 3 O1 6.17435 87 -1.95250 0.00000 -5.85750 3 O1 6.17435 88 0.00000 1.95250 -5.85750 3 O1 6.17435 89 0.00000 -1.95250 -5.85750 3 O1 6.17435 90 5.85750 1.95250 0.00000 1 Sr1 6.17435 91 -5.85750 1.95250 0.00000 1 Sr1 6.17435 92 1.95250 5.85750 0.00000 1 Sr1 6.17435 93 -1.95250 5.85750 0.00000 1 Sr1 6.17435 94 5.85750 -1.95250 0.00000 1 Sr1 6.17435 95 -5.85750 -1.95250 0.00000 1 Sr1 6.17435 96 1.95250 -5.85750 0.00000 1 Sr1 6.17435 97 -1.95250 -5.85750 0.00000 1 Sr1 6.17435 98 3.90500 3.90500 3.90500 3 O1 6.76366 99 -3.90500 3.90500 3.90500 3 O1 6.76366 100 3.90500 -3.90500 3.90500 3 O1 6.76366 101 -3.90500 -3.90500 3.90500 3 O1 6.76366 102 3.90500 3.90500 -3.90500 3 O1 6.76366 103 -3.90500 3.90500 -3.90500 3 O1 6.76366 104 3.90500 -3.90500 -3.90500 3 O1 6.76366 105 -3.90500 -3.90500 -3.90500 3 O1 6.76366 106 3.90500 0.00000 5.85750 2 Ti1 7.03984 107 -3.90500 0.00000 5.85750 2 Ti1 7.03984 108 0.00000 3.90500 5.85750 2 Ti1 7.03984 109 0.00000 -3.90500 5.85750 2 Ti1 7.03984 110 3.90500 0.00000 -5.85750 2 Ti1 7.03984 111 -3.90500 0.00000 -5.85750 2 Ti1 7.03984 112 0.00000 3.90500 -5.85750 2 Ti1 7.03984 113 0.00000 -3.90500 -5.85750 2 Ti1 7.03984 114 5.85750 3.90500 1.95250 3 O1 7.30559 115 -5.85750 3.90500 1.95250 3 O1 7.30559 116 3.90500 5.85750 1.95250 3 O1 7.30559 117 -3.90500 5.85750 1.95250 3 O1 7.30559 118 5.85750 -3.90500 1.95250 3 O1 7.30559 119 -5.85750 -3.90500 1.95250 3 O1 7.30559 120 3.90500 -5.85750 1.95250 3 O1 7.30559 121 -3.90500 -5.85750 1.95250 3 O1 7.30559 122 3.90500 1.95250 5.85750 3 O1 7.30559 123 -3.90500 1.95250 5.85750 3 O1 7.30559 124 1.95250 3.90500 5.85750 3 O1 7.30559 125 -1.95250 3.90500 5.85750 3 O1 7.30559 126 3.90500 -1.95250 5.85750 3 O1 7.30559 127 -3.90500 -1.95250 5.85750 3 O1 7.30559 128 1.95250 -3.90500 5.85750 3 O1 7.30559 129 -1.95250 -3.90500 5.85750 3 O1 7.30559 130 5.85750 3.90500 -1.95250 3 O1 7.30559 131 -5.85750 3.90500 -1.95250 3 O1 7.30559 132 3.90500 5.85750 -1.95250 3 O1 7.30559 133 -3.90500 5.85750 -1.95250 3 O1 7.30559 134 5.85750 -3.90500 -1.95250 3 O1 7.30559 135 -5.85750 -3.90500 -1.95250 3 O1 7.30559 136 3.90500 -5.85750 -1.95250 3 O1 7.30559 137 -3.90500 -5.85750 -1.95250 3 O1 7.30559 138 3.90500 1.95250 -5.85750 3 O1 7.30559 139 -3.90500 1.95250 -5.85750 3 O1 7.30559 140 1.95250 3.90500 -5.85750 3 O1 7.30559 141 -1.95250 3.90500 -5.85750 3 O1 7.30559 142 3.90500 -1.95250 -5.85750 3 O1 7.30559 143 -3.90500 -1.95250 -5.85750 3 O1 7.30559 144 1.95250 -3.90500 -5.85750 3 O1 7.30559 145 -1.95250 -3.90500 -5.85750 3 O1 7.30559 146 5.85750 1.95250 3.90500 1 Sr1 7.30559 147 -5.85750 1.95250 3.90500 1 Sr1 7.30559 148 1.95250 5.85750 3.90500 1 Sr1 7.30559 149 -1.95250 5.85750 3.90500 1 Sr1 7.30559 150 5.85750 -1.95250 3.90500 1 Sr1 7.30559 151 -5.85750 -1.95250 3.90500 1 Sr1 7.30559 152 1.95250 -5.85750 3.90500 1 Sr1 7.30559 153 -1.95250 -5.85750 3.90500 1 Sr1 7.30559 154 5.85750 1.95250 -3.90500 1 Sr1 7.30559 155 -5.85750 1.95250 -3.90500 1 Sr1 7.30559 156 1.95250 5.85750 -3.90500 1 Sr1 7.30559 157 -1.95250 5.85750 -3.90500 1 Sr1 7.30559 158 5.85750 -1.95250 -3.90500 1 Sr1 7.30559 159 -5.85750 -1.95250 -3.90500 1 Sr1 7.30559 160 1.95250 -5.85750 -3.90500 1 Sr1 7.30559 161 -1.95250 -5.85750 -3.90500 1 Sr1 7.30559 162 7.81000 0.00000 0.00000 3 O1 7.81000 163 -7.81000 0.00000 0.00000 3 O1 7.81000 164 0.00000 7.81000 0.00000 3 O1 7.81000 165 0.00000 -7.81000 0.00000 3 O1 7.81000 166 0.00000 0.00000 7.81000 3 O1 7.81000 167 0.00000 0.00000 -7.81000 3 O1 7.81000 168 7.81000 0.00000 1.95250 2 Ti1 8.05036 169 -7.81000 0.00000 1.95250 2 Ti1 8.05036 170 0.00000 7.81000 1.95250 2 Ti1 8.05036 171 0.00000 -7.81000 1.95250 2 Ti1 8.05036 172 3.90500 3.90500 5.85750 2 Ti1 8.05036 173 -3.90500 3.90500 5.85750 2 Ti1 8.05036 174 3.90500 -3.90500 5.85750 2 Ti1 8.05036 175 -3.90500 -3.90500 5.85750 2 Ti1 8.05036 176 7.81000 0.00000 -1.95250 2 Ti1 8.05036 177 -7.81000 0.00000 -1.95250 2 Ti1 8.05036 178 0.00000 7.81000 -1.95250 2 Ti1 8.05036 179 0.00000 -7.81000 -1.95250 2 Ti1 8.05036 180 3.90500 3.90500 -5.85750 2 Ti1 8.05036 181 -3.90500 3.90500 -5.85750 2 Ti1 8.05036 182 3.90500 -3.90500 -5.85750 2 Ti1 8.05036 183 -3.90500 -3.90500 -5.85750 2 Ti1 8.05036 184 7.81000 1.95250 1.95250 3 O1 8.28376 185 -7.81000 1.95250 1.95250 3 O1 8.28376 186 1.95250 7.81000 1.95250 3 O1 8.28376 187 -1.95250 7.81000 1.95250 3 O1 8.28376 188 7.81000 -1.95250 1.95250 3 O1 8.28376 189 -7.81000 -1.95250 1.95250 3 O1 8.28376 190 1.95250 -7.81000 1.95250 3 O1 8.28376 191 -1.95250 -7.81000 1.95250 3 O1 8.28376 192 5.85750 0.00000 5.85750 3 O1 8.28376 193 -5.85750 0.00000 5.85750 3 O1 8.28376 194 0.00000 5.85750 5.85750 3 O1 8.28376 195 0.00000 -5.85750 5.85750 3 O1 8.28376 196 7.81000 1.95250 -1.95250 3 O1 8.28376 197 -7.81000 1.95250 -1.95250 3 O1 8.28376 198 1.95250 7.81000 -1.95250 3 O1 8.28376 199 -1.95250 7.81000 -1.95250 3 O1 8.28376 200 7.81000 -1.95250 -1.95250 3 O1 8.28376 201 -7.81000 -1.95250 -1.95250 3 O1 8.28376 202 1.95250 -7.81000 -1.95250 3 O1 8.28376 203 -1.95250 -7.81000 -1.95250 3 O1 8.28376 204 5.85750 0.00000 -5.85750 3 O1 8.28376 205 -5.85750 0.00000 -5.85750 3 O1 8.28376 206 0.00000 5.85750 -5.85750 3 O1 8.28376 207 0.00000 -5.85750 -5.85750 3 O1 8.28376 208 5.85750 5.85750 0.00000 1 Sr1 8.28376 209 -5.85750 5.85750 0.00000 1 Sr1 8.28376 210 5.85750 -5.85750 0.00000 1 Sr1 8.28376 211 -5.85750 -5.85750 0.00000 1 Sr1 8.28376 212 1.95250 1.95250 7.81000 1 Sr1 8.28376 213 -1.95250 1.95250 7.81000 1 Sr1 8.28376 214 1.95250 -1.95250 7.81000 1 Sr1 8.28376 215 -1.95250 -1.95250 7.81000 1 Sr1 8.28376 216 1.95250 1.95250 -7.81000 1 Sr1 8.28376 217 -1.95250 1.95250 -7.81000 1 Sr1 8.28376 218 1.95250 -1.95250 -7.81000 1 Sr1 8.28376 219 -1.95250 -1.95250 -7.81000 1 Sr1 8.28376 220 7.81000 3.90500 0.00000 3 O1 8.73185 221 -7.81000 3.90500 0.00000 3 O1 8.73185 222 3.90500 7.81000 0.00000 3 O1 8.73185 223 -3.90500 7.81000 0.00000 3 O1 8.73185 224 7.81000 -3.90500 0.00000 3 O1 8.73185 225 -7.81000 -3.90500 0.00000 3 O1 8.73185 226 3.90500 -7.81000 0.00000 3 O1 8.73185 227 -3.90500 -7.81000 0.00000 3 O1 8.73185 228 7.81000 0.00000 3.90500 3 O1 8.73185 229 -7.81000 0.00000 3.90500 3 O1 8.73185 230 0.00000 7.81000 3.90500 3 O1 8.73185 231 0.00000 -7.81000 3.90500 3 O1 8.73185 232 3.90500 0.00000 7.81000 3 O1 8.73185 233 -3.90500 0.00000 7.81000 3 O1 8.73185 234 0.00000 3.90500 7.81000 3 O1 8.73185 235 0.00000 -3.90500 7.81000 3 O1 8.73185 236 7.81000 0.00000 -3.90500 3 O1 8.73185 237 -7.81000 0.00000 -3.90500 3 O1 8.73185 238 0.00000 7.81000 -3.90500 3 O1 8.73185 239 0.00000 -7.81000 -3.90500 3 O1 8.73185 240 3.90500 0.00000 -7.81000 3 O1 8.73185 241 -3.90500 0.00000 -7.81000 3 O1 8.73185 242 0.00000 3.90500 -7.81000 3 O1 8.73185 243 0.00000 -3.90500 -7.81000 3 O1 8.73185 244 7.81000 3.90500 1.95250 2 Ti1 8.94748 245 -7.81000 3.90500 1.95250 2 Ti1 8.94748 246 3.90500 7.81000 1.95250 2 Ti1 8.94748 247 -3.90500 7.81000 1.95250 2 Ti1 8.94748 248 7.81000 -3.90500 1.95250 2 Ti1 8.94748 249 -7.81000 -3.90500 1.95250 2 Ti1 8.94748 250 3.90500 -7.81000 1.95250 2 Ti1 8.94748 251 -3.90500 -7.81000 1.95250 2 Ti1 8.94748 252 7.81000 3.90500 -1.95250 2 Ti1 8.94748 253 -7.81000 3.90500 -1.95250 2 Ti1 8.94748 254 3.90500 7.81000 -1.95250 2 Ti1 8.94748 255 -3.90500 7.81000 -1.95250 2 Ti1 8.94748 256 7.81000 -3.90500 -1.95250 2 Ti1 8.94748 257 -7.81000 -3.90500 -1.95250 2 Ti1 8.94748 258 3.90500 -7.81000 -1.95250 2 Ti1 8.94748 259 -3.90500 -7.81000 -1.95250 2 Ti1 8.94748 260 5.85750 3.90500 5.85750 3 O1 9.15804 261 -5.85750 3.90500 5.85750 3 O1 9.15804 262 3.90500 5.85750 5.85750 3 O1 9.15804 263 -3.90500 5.85750 5.85750 3 O1 9.15804 264 5.85750 -3.90500 5.85750 3 O1 9.15804 265 -5.85750 -3.90500 5.85750 3 O1 9.15804 266 3.90500 -5.85750 5.85750 3 O1 9.15804 267 -3.90500 -5.85750 5.85750 3 O1 9.15804 268 5.85750 3.90500 -5.85750 3 O1 9.15804 269 -5.85750 3.90500 -5.85750 3 O1 9.15804 270 3.90500 5.85750 -5.85750 3 O1 9.15804 271 -3.90500 5.85750 -5.85750 3 O1 9.15804 272 5.85750 -3.90500 -5.85750 3 O1 9.15804 273 -5.85750 -3.90500 -5.85750 3 O1 9.15804 274 3.90500 -5.85750 -5.85750 3 O1 9.15804 275 -3.90500 -5.85750 -5.85750 3 O1 9.15804 276 5.85750 5.85750 3.90500 1 Sr1 9.15804 277 -5.85750 5.85750 3.90500 1 Sr1 9.15804 278 5.85750 -5.85750 3.90500 1 Sr1 9.15804 279 -5.85750 -5.85750 3.90500 1 Sr1 9.15804 280 5.85750 5.85750 -3.90500 1 Sr1 9.15804 281 -5.85750 5.85750 -3.90500 1 Sr1 9.15804 282 5.85750 -5.85750 -3.90500 1 Sr1 9.15804 283 -5.85750 -5.85750 -3.90500 1 Sr1 9.15804 284 END

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Trouble of Path & Data List data of Artemis
by Joji Kuniya 15 Jun '07

15 Jun '07

Dear Bruce I tried fitting to my EXAFS date by Artemis program. Abruptly fitted and Path spectrum was broaden. So, I checked the paths in the Data & Path list and the feff calculated results. So that, the paths data in the Data & Path is differed from the left side feff calculated data(of course, number of # of the interpretation and the path of data & Path is the same). This troube is almostly? dissoleved when new Artemis was opened. But, scarcely this troubel have occured again. I reinstalled your feffit program, but I have been occasionally encountering. Did yo have some experience like this? Please teach me what to do to clear thus trouble. Thank you Joji Kuniya

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XANES / NEXAFS with feff8.4
by s440697＠stud.uni-goettingen.de 15 Jun '07

15 Jun '07

Hallo @all, (first at all, sorry for my bad english) i'm a student working on my diploma thesis (nexafs/xanes) and my job is to simulate with FEFF 8.4 spectra, for example absorption as a function of energy (mu_(E)). I'm a newbie in this topic and i tried to get the k-edge of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm interested in the XANES-range of the spectra not the EXAFS. I get everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance i use (gypsum, pyrite,...). There are no differences with the peak position on the energy-scale or shifts. I'm really confused :-( I think, there should be differences in the spectra... I send you two feff.inp files from my feff-runs. My source is the mineralogy database (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the unitcell. Then i put the data in the XtalDraw program to get the positions of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell :-). Then i put the values of the positions into feff... I simulated pyrite with 12 atoms and gypsum with 48. I'm appreciative for every help :-) ciao, Eckhard --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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How to make a hole on feff.inp file
by Joji Kuniya 07 Jun '07

07 Jun '07

Dear members I have been treating with an EXAFS spectra of an oxide crystals. This crystal has some holes (defects) in the system.I have not a good idea in handling of the hole system, I put hydrogen instead of the hole. I think this procedure is not appropriated. Please teach me how to make hole on a feff.inp file. Thank you. Joji Kuniya

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bond distance resolution and correlation of parameters in MS analyses?
by MarkBondin 06 Jun '07

06 Jun '07

Hi, I would like general opinions of some EXAFS practioners in regards to the most widely accepted methods for bond distance resolution and correlation of parameters in both single scattering (SS) and multiple scattering (MS) EXAFS refinements and if these can be said to differ? 1)Does the equation for bond distance resolution (r = pi/2deltak) only apply to SS? I have held the opinion that this can be applied to MS analysis however I have recently been informed that this equation does not correctly describe distance resolution in MS analyses. The paper in Coord. Chem. Rev. 2005, 249, 141-160 describes this and is this concordant with the views of the wider EXAFS community? 2) What is the actual equation which defines the determinacy of a fitting procedure and does this differ between SS and MS analyses? For MS analyses there has been a recently published equation (Coord. Chem. Rev. 2005, 249, 141-160) which takes into acount the number of dimensions used in the analyses and is this only relevant to MS analyses of data? This has also been expressed in the paper by Binsted (Biochemistry. 1992, 31, 12117-12125) however a different equation has been detailed by Stern (Phys. Rev. B. 1993, 48, 9825-9827) which I have been using as a guide in my MS analyses. Is this acceptable? Any thoughts and opinions would be greatly appreciated as this relates directly to corrections suggested to be made to my PhD thesis! Many thanks, Mark

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help with CoCr bimetallic catalyst
by codruta.zoican＠yale.edu 06 Jun '07

06 Jun '07

I have been, working with a bimetallic Co/Cr catalyst supported on a silica template for synthesis of single wall carbon nanotubes. Recently I have performed some analysis at the NSLS. It is clear from the spectra in R space that the interatomic distances are modified compared to the monometallic catalyst therefore I am dealing with an alloy. Does anyone have or know about a model that would allow me to get a coordination nomber using Artemis. Thank you, Codruta.

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