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

Re: [Ifeffit] Meaning of sigma^2 and real space resolution in XAFS
by Scott Calvin 02 Jul '07

02 Jul '07

Hi all, This got marked spam and rejected when I sent it from home this weekend... :) At 12:48 AM 6/30/2007, you wrote: >Hello, > >Thanks Bruce and Matt for the previous comments© >I have the following questions and I would appreciate comments about them: > >My Questions are: >1- Can we consider sigma^2 of a single >scattering path to be a measure of Debey Waller factor? If you mean the Debye-Waller factor from x-ray diffraction, the answer is no. The EXAFS sigma^2 is the variance in the absorber scatterer distance, the XRD sigma^2 is the variance in the position of an atom relative to its lattice point in the crystal. Thus, IF the motion of the absorber and scatterer were uncorrelated, it would be reasonable to think that the EXAFS sigma^2 would be twice the XRD Debye-Waller factor. For nearest-neighbors, though, this is a terrible assumption, as the atoms will tend to move in a correlated fashion (put another way, acoustic phonons dominate over optical ones). Thus the EXAFS sigma^2 for nearest-neighbors will usually be much less than the XRD Debye-Waller factor. Further confusing matters is terminology. In EXAFS, sigma^2 is sometimes called the Debye-Waller factor...but this Debye-Waller factor is not the same as that from XRD! I've also seen "Debye-Waller factor" used to include all information about the shape of the distribution of the absorber-scatterer distance, so that sigma^2 is "the harmonic part of the Debye-Waller factor," but that seems to be an older usage. >2- Is sigma^2 a measure of ¥or directly proportional to¤ strain in a bond? Hmm...I'd say no, although I think I know what you're getting at. One major contributor to sigma^2 is thermal vibrations, which of course increase with temperature. I don't think that's generally categorized as "strain" (although I'm wary of the differing definitions that terms such as this can have in different specialties!). Another contributor to sigma^2 is variations in absorber-scatterer distance due to local defects, surface effects, etc., generally lumped together under the term "static disorder." This term itself can be a little misleading, as, e.g., a nanoparticle can have a sigma^2 that varies in a perfectly regular way with distance from the surface--we call that static disorder, even though it is not particularly disorderly. :) At any rate, what material scientists call "strain" can show up as static disorder. But even in that case, note that if all the bonds in a sample were strained, sigma^2 would not reflect it--it's only when some are strained and some are not that it shows up. So yes, I've seen (knowledgeable) people point at a sigma^2 and say "I think that's high because of strain." But that's a kind of short-hand for what's going on. >3- When doing first shell fitting in Artemis, >The actual bond length is: r_eff + dr +- delta ¥dr¤© >Are the error bars associated with dr values >¥delta¥dr¤ of about 0©001 A¤ realistic? ¥i©e© >0©001 A is too small to detect by XAFS¤© Your formatting didn't come through very well, but I'll give it a shot. Ifeffit (and thus Artemis) do a pretty good job of putting a lower bound on delta dr, in my opinion. Why a lower bound? Because there are all sorts of systematic errors that could be coming in, e.g. an iffy model--such as a first-shell only fit for a crystalline material, since there's often a bit of spectral leakage from more distant shells. I'd be very surprised if Artemis ever gave a 0.001 A delta dr, though, and absolutely shocked if it did so on a first-shell only model. Are you saying that it did do that for you? >4- What determines the real space resolution in >XAFS measurements other than K_max? k_min, of course. To answer the gist of your question more fully, though, I have to get on my soapbox. :) "Resolution" is often taken to mean something other than it does. Resolution criteria literally mean the point at which you could be expected to distinguish between two peaks. It is NOT the limit to the precision of information that can be retrieved by a clever person. Huh? Let's take an example of, oh, a proposal that there are two slightly different (but consistent) nearest-neighbor distances in some material. If those distances differ by less than the resolution implied by the k-space range, then they will not show up as two peaks in the Fourier transform. Instead, they'll show up as one broad peak; i.e. a peak with an anomalously large sigma^2. If a multiple-shell fit was performed and splitting was known to be a possibility, this anomalously large sigma^2 could be taken as indirect evidence for the splitting. In fact, if there were some way to estimate sigma2's a priori (I'll grant you that's a big if!), then the broad peak could be modeled as two scattering paths, with the splitting as a free parameter. In that case, EXAFS could give information about splitting to a greater precision than the resolution of the measurement. A lot of the lore about the capabilities of EXAFS suffers from a similar lack of subtlety. Joe Woicik recently gave a very interesting talk at the NSLS Users' Meeting. It is generally bandied about that EXAFS cannot distinguish scatterers that differ in atomic number by less than 5. This is kind of true--in a mindless first-shell fit--because in those cases del_r and sigma^2 will usually just slop up the differences in phase and amplitude due to the different atomic number of the scatterer. But if you really really knew del_r and sigma^2 a priori, even a difference of one atomic number stands out like a sore thumb! The upshot is that if you model, say, zinc scatterers as if they were iron, the fit will probably "work," but you'll be introducing substantial systematic errors into your fitted variables. A corollary is that in the case of a highly-constrained fit, you may be able to do considerably better than the usual +/- 5 rule. The bottom line of this little speech is that the oft-quoted limits of EXAFS analysis are usually referring to a fit in which no a priori information is used. If you know (or suspect) anything about the system and incorporate that into your model, greater precision is sometimes possible. Of course, the results are then only as good as the a priori information; the whole thing could be a house of cards ready to collapse. But in favorable cases, multiple lines of evidence can be used to construct a convincing scenario... Hope that helped! --Scott Calvin Sarah Lawrence College

1 0

gifeffit installation issue on ubuntu feisty fawn
by Emiliano Fonda 02 Jul '07

02 Jul '07

Hi, I would like to use gifeffit on the beamline where I work for fast extraction of EXAFS data during scans and so on. But I have a problem even before starting to code: horae and ifeffit works well, I compiled and installed the python wrapper, but gifeffit refuse to work and I cannot import the Ifeffit module in python. The error message is: fonda@nemotele:~$ gifeffit Traceback (most recent call last): File "/usr/local/bin/gifeffit", line 2, in <module> import GIFeffit, sys File "/usr/lib/python2.5/site-packages/Ifeffit/GIFeffit.py", line 27, in <module> from Ifeffit import Ifeffit File "/usr/lib/python2.5/site-packages/Ifeffit/Ifeffit.py", line 46, in <module> import _ifeffit, types, cmd, os, sys ImportError: /usr/lib/python2.5/site-packages/Ifeffit/_ifeffit.so: undefined symbol: pgclos_ The linux distro is ubuntu feisty fawn and I got the libpgplot5 package installed... ... may anyone help me, please? Thanks, E. Fonda SAMBA beamline SOLEIL synchrotron

3 2

Meaning of sigma^2 and real space resolution in XAFS
by Moneeb Shatnawi 30 Jun '07

30 Jun '07

Hello, Thanks Bruce and Matt for the previous comments� I have the following questions and I would appreciate comments about them: My Questions are: 1- Can we consider sigma^2 of a single scattering path to be a measure of Debey Waller factor? 2- Is sigma^2 a measure of �or directly proportional to� strain in a bond? 3- When doing first shell fitting in Artemis, The actual bond length is: r_eff + dr +- delta �dr�� Are the error bars associated with dr values �delta�dr� of about 0�001 A� realistic? �i�e� 0�001 A is too small to detect by XAFS�� 4- What determines the real space resolution in XAFS measurements other than K_max? Thanks, Moneeb -- Moneeb T� Shatnawi Physics and Astronomy Department 4256 Biomed� Phys� Sciences Building Michigan State University East Lansing, MI 48824 Tel: +1-517-355-9200 ext�2325 E-mail: mtshatnawi@pa�msu�edu

1 0

Re: [Ifeffit] Fwd: scattering amplitude by FEFF and Artemis
by Feng Wang 29 Jun '07

29 Jun '07

Thank you, Dr. Ravel, Could you please just simply tell me the expression for the magnitude of chi (q) (labelled as |chi(q)|)? Thank you. Feng > Feng, > > I am forwarding this to the Ifeffit mailing list since I am in the > middle of an experiment and don't have much time to devote to an > answer. > > > Dear Dr. Ravel, > > > I am now learning to use your Artemis program to calculate the scattering > > amplitude from each paths (shells). It seems your Artemis can give the > > scattering amplitude of each path, as done by EXAFS calculations in FEFF. I > > think the results from both program should be same or comparable, but it > > looks much different, as attached for a result of diamond-K. Is anything > > wrong with my calculations? > > It's really hard to tell. The figure you sent does not convey any > sense of how it was made. Without a clear explanation of what you > did or, better yet, an artemis project file to inspect, I am not sure > how I can possibly answer your question. > > > I have been wondering how big a cluster we should use for FEFF calculations, > > or the contributions of the atoms far from the central atom (e.g. > 1nm) > > since so big clusters (such as 400 atoms and even more) are used for FEFF > > calculations in several recent publications. I hope to get some ideas from > > the scattering amplitude of the paths involved by the atoms far from the > > central atoms. Do you also have any suggestions? > > The nice thing about feff is that it is very easy to use to answer > this sort of question without having to rely on an "expert". What > happens if you run feff with clusters ranging from very small to very > large and compare the chi(k) functions generated for the first few > coordination shells? > > B > > > Feng > > > ==================================== > > EM group, NINT > > 11421 Saskatachewan Drive > > Edmonton, Canada T6G 2M9 > > -- > 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/ ==================================== EM group, NINT 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

2 1

Fwd: average first shell position and width
by Bruce Ravel 28 Jun '07

28 Jun '07

Moneeb, I'm in the middle of beam run, so I am forwarding this along to the Ifeffit mailing list for commentary. B ---------- Forwarded Message from Moneeb Shatnawi <Moneeb Shatnawi <mtshatnawi(a)pa.msu.edu>> ---------- Subject: average first shell position and width Date: Wednesday 27 June 2007 From: Moneeb Shatnawi <mtshatnawi(a)pa.msu.edu> To: Bruce Ravel <bravel(a)anl.gov> Dear Dr. Ravel, Hello, I am Moneeb Shatnawi from physics department at Michigan State University, I have a PDF and XAFS data on GeSe system, and I would like to check if the PDF and XAFS results are consistent with each other in terms of the first PDF peak position and width. The first PDF peak in this system is a mixed shell of Se-Se bonds as well as Ge-Se bonds. The PDF data gave a width of the first PDF peak of about 0.06 A, and the XAFS data gave sigma^2 for Ge-Se bond is 0.006 A^2, and for Se-Se bond is 0.003 A^2. How is sigma in XAFS results (I was using Artemis program) related to the width of the first PDF peak? Also, when obtaining the XAFS fits to the data, I was using: Theory ---> first shell fit. In this, I was giving r_eff for Se-Se bond to be 2.32 A and that for Ge-Se to be 2.368 A. Through the XAFS refinement, I obtained r, dr as well as r_eff. which of these should be considered as the actual bond length (r or r_eff)? and how are these related to the average position that I get from fitting the first PDF peak in this system? I appreciate your help, Thanks, Moneeb ------------------------------------------------------- -- 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/

2 2

Fwd: scattering amplitude by FEFF and Artemis
by Bruce Ravel 28 Jun '07

28 Jun '07

Feng, I am forwarding this to the Ifeffit mailing list since I am in the middle of an experiment and don't have much time to devote to an answer. > Dear Dr. Ravel, > I am now learning to use your Artemis program to calculate the scattering > amplitude from each paths (shells). It seems your Artemis can give the > scattering amplitude of each path, as done by EXAFS calculations in FEFF. I > think the results from both program should be same or comparable, but it > looks much different, as attached for a result of diamond-K. Is anything > wrong with my calculations? It's really hard to tell. The figure you sent does not convey any sense of how it was made. Without a clear explanation of what you did or, better yet, an artemis project file to inspect, I am not sure how I can possibly answer your question. > I have been wondering how big a cluster we should use for FEFF calculations, > or the contributions of the atoms far from the central atom (e.g. > 1nm) > since so big clusters (such as 400 atoms and even more) are used for FEFF > calculations in several recent publications. I hope to get some ideas from > the scattering amplitude of the paths involved by the atoms far from the > central atoms. Do you also have any suggestions? The nice thing about feff is that it is very easy to use to answer this sort of question without having to rely on an "expert". What happens if you run feff with clusters ranging from very small to very large and compare the chi(k) functions generated for the first few coordination shells? B > Feng > ==================================== > EM group, NINT > 11421 Saskatachewan Drive > Edmonton, Canada T6G 2M9 -- 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/

1 0

XAFS postdoc position at HASYLAB
by Welter, Edmund 27 Jun '07

27 Jun '07

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) a postdoc position in the XAFS business is available. If you or one of your colleagues is interested please contact me by e-mail or phone (address at the bottom of this mail). The main task will be the operation of our new XAFS-beamline (beamline C). As a postdoc you will have the opportunity to use HASYLAB's facilities for your own research. Moreover, you will be a live witness of the construction and commissioning of the new high brilliance source PETRA III (user operation at PETRA III will start in 2009) and of the start phase of the XFEL project. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter

1 0

weighting multi-data fit
by Jörg Haug 25 Jun '07

25 Jun '07

Dear all, I have a question regarding the weighting for a multiple data set fitting. I found that there is the parameter Epsilon to do this in Artemis. But in the help file there is no description how to use this parameter. Which value did I have to use to set the weighting to (for example) double or half? Best regards Jörg -- Dr. Jörg Haug Martin-Luther-Universität Halle-Wittenberg Institut für Physik Anorganisch-Nichtmetallische Materialien Friedemann-Bach-Platz 6 D-06108 Halle Telefon: 0345 55 25 529 Fax: 0345 55 27 159 e-mail: joerg.haug(a)physik.uni-halle.de http://www.physik.uni-halle.de/Fachgruppen/Glas/arbeitsgruppen/anw.htm

9 11

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

2 1

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

2 1