Fitting using Experimental standard
A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India)
On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method.
Artemis does not do fitting with experimental standards, although Athena does have a dialog for doing log-ratio/phase-difference analysis. B
Dear all, Can somebody please explain to me what is theoretical standard and what is experimental standard. My understanding of theoretical standard is the crystallographic data. However, it is first time I heard experimental standard. Thanks Fiona R. Kizewski Ph.D. Candidate Department of Chemistry North Carolina State University Raleigh North Carolina 27695
On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method.
Artemis does not do fitting with experimental standards, although Athena does have a dialog for doing log-ratio/phase-difference analysis.
B _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Fiona, An experimental standard is a spectrum of a known material (the term is also often used for the known material itself, in addition to its spectrum). If you use Athena to do a linear combination fit, you are most commonly using experimental standards to do it. A theoretical standard is a theoretically simulated spectrum of some structure. Thus, the theoretical standard is not the crystallographic data itself, although that data can serve as a basis for generating a theoretical standard using software such as FEFF. --Scott Calvin Sarah Lawrence College On Jan 4, 2010, at 7:16 PM, Fiona R. Kizewski wrote:
Dear all, Can somebody please explain to me what is theoretical standard and what is experimental standard. My understanding of theoretical standard is the crystallographic data. However, it is first time I heard experimental standard. Thanks
An experimental standard is an EXAFS spectrum of a known compound. If you pick the right known compound (and if such exists) then
you have an isolatable shell consisting only of scattering from one kind of atom, with
the others being at distances sufficiently different so that one can Fourier-filter them out. Nowadays, a more standard procedure
is to fit your standard compound using Artemis or the like, then use that fit as a starting point
for a fit to the unknown. The accuracy with which the fit to the standard reproduces the known (crystallographic) values tells you
how well EXAFS worked in the case of your compound. Also, the coordination number you get
for the dominant shell, relative to what it's "supposed to be", tells you the S0^2. If you get strange values like 0.1 or 20 then
you know something's wrong. If you get plausible numbers, you can think about substituting those in
for the S02 in the unknown and taking the resultant amplitudes as coordination numbers. Similarly, if the model compound is really
similar to the unknown, you can start your fit to the unknown using the values for E0 and Ds2 you got from the
model.
mam
----- Original Message -----
From: "Fiona R. Kizewski"
Dear all, Can somebody please explain to me what is theoretical standard and what is experimental standard. My understanding of theoretical standard is the crystallographic data. However, it is first time I heard experimental standard. Thanks
Fiona R. Kizewski Ph.D. Candidate Department of Chemistry North Carolina State University Raleigh North Carolina 27695
On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method.
Artemis does not do fitting with experimental standards, although Athena does have a dialog for doing log-ratio/phase-difference analysis.
B _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Monday 04 January 2010 10:16:15 pm you wrote:
Dear all, Can somebody please explain to me what is theoretical standard and what is experimental standard. My understanding of theoretical standard is the crystallographic data. However, it is first time I heard experimental standard. Thanks
While certainly not wrong, I don't think any of the answers given last night answered Fiona's question as I would have liked. The paradigm for interpreting EXAFS data offered by a real-space multiple scattering program like Feff relies upon the so-called path expansion. This means that the EXAFS from a given configuration of atoms can be expressed as the sum of the contributions from each scattering path. That is chi_total(k) = sum_over_all_paths [ chi_path(k) ] In this language, a "scattering path" is some closed loop wherein the photoelectron ejected from the atom by the incident photon scatters from one or more atoms in the cluster before closing the loop back at the absorbing atom. For each such path, chi(k) is evaluated like so: N S_0^2 F(k) chi(k) = ------------- sin( 2kR + phi(k) ) exp( -2k^2sigma^2 ) 2kR^2 There is also an exponetial term considering the photoelectron mean-free-path that I am neglecting in this discussion. There might also, in some approaches, be additional disorder terms expressed as cumulants, adding an additional term to the sine and an additional exponential term. In a fitting program like Artemis, the parameters of this equation come in two flavors. One flavor includes the terms 2R (the length of the path), sigma^2 (the mean square disorder about that path length), N (the number of such paths), S_0^2 (the amplitude reduction factor that has to do with the details of the behavior of the other electrons in the system), and a handful of others. The parameters of this type are the things that may be parameterized in Artemis to yield answers to questions such as "What is the coordination number of the absorber?" and "How far is the absorber from the atoms in the second coordination shell?" The other flavor of parameters includes the terms F(k) and phi(k). These are the scattering amplitude and phase shift. These are k-dependent functions that have to do with the details of the atomic species of the absorber and scatterer(s), the number of legs that the scattering path has, and the angles through which the photoelectron scatters as it traverses the path. In Artemis, parameters of this type are computed by Feff and typically not altered during the course of the fit. That is, Artemis takes the Feff calculations of the various F(k) and phi(k) functions as gospel and uses them as the basis for determining the values of the first flavor of parameters. Abhijeet's original question was whether Artemis is only able to determine the F(k) and phi(k) functions using a Feff calculation or if it is able to somehow extract approximations of F(k) and phi(k) from another set of experimental data using a technique like those discussed by Matthew and Anatoly. The short answer is "no, Artemis cannot use experimentally extracted F(k) and phi(k) functions -- it does require the use of Feff." The longer answer is that Matthew's request from his last email of the night -- that someone code up a way to automate the extraction the F(k) and phi(k) from experimental data and save it in a form that Artemis or some other Feff-using program could use -- has long been on my list of potential things to do with my software and may actually happen one of these days. The very valid question whenever the topic of empirical standards comes up is "Why do you think you need it?" I am unconvinced that empirical standards are ever needed. Of course, I am also unconvinced that I am right in saying that! So who knows...? There is some evidence that empirical standards might be preferable in certain specific cases, such as the case in which a hydrogen atom is collinear or nearly collinear with an absorber and scatterer. From a the persepective of "guy who writes programs" I suppose the fact that there is interest in having the capability of using empirical standards is itself good enough reason to include it. HTH, B PS: Please note that, strictly speaking, I was describing Feff, Ifeffit, and Artemis. Other real-space multiple scattering programs and other fitting programms using Feff incorporate important differences from what I explained above. But the bottom line distinction between theoretical and empirical standards is about the same in all cases.
Fiona R. Kizewski Ph.D. Candidate Department of Chemistry North Carolina State University Raleigh North Carolina 27695
On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method.
Artemis does not do fitting with experimental standards, although Athena does have a dialog for doing log-ratio/phase-difference analysis.
B _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
The very valid question whenever the topic of empirical standards comes up is "Why do you think you need it?" I am unconvinced that empirical standards are ever needed. Of course, I am also unconvinced that I am right in saying that! So who knows...? There is some evidence that empirical standards might be preferable in certain specific cases, such as the case in which a hydrogen atom is collinear or nearly collinear with an absorber and scatterer.
From a the persepective of "guy who writes programs" I suppose the fact that there is interest in having the capability of using empirical standards is itself good enough reason to include it.
One reason I can think of is when the unknown is in some sense close to a model, for instance, a glass compared with a corresponding crystal, a dilute solid solution compared with an appropriate compound, if one exists, or a nanoparticle compared with bulk. In that case, one might argue that Nature's calculation might be more accurate than FEFF, and that the use of a model will automatically correct for artifacts in the extraction of the (filtered) shell. I will grant that this is now a niche technique whereas, when I started <mumble> years ago, it was mainstream. mam
I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards J. Synchrotron Rad., 8 , 669-771 (2001). The link to PDF is here: https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf Anatoly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of abhijeet gaur Sent: Mon 1/4/2010 9:15 AM To: ifeffit Subject: [Ifeffit] Fitting using Experimental standard A very happy new year to all Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we want to use an experimental standard instead of theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other method. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain (India)
You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of
Artemis and the like) as it is now. As shown in the paper,
you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data. Multiple
data sets aren't new, either; I used to do that with data taken on
dilute solid solutions at different temperatures. Another trick I used to use a lot was if I didn't have a standard for the right
pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp)
between the pair I wanted and a nearby (in Z) pair I had data for. For instance, you can get CuAl2 as a compound and extract the
phase+amp for Cu as the central atom and Al as the scatterer. You can't do
that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. Therefore, you can do:
Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)
and get a "semi-empirical" Cu->Si "standard". Why the +- for phase and the */ for amp? You can think of it as extrapolating the
log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im().
This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity,
which they really are.
One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is
called EXAFSfit and does this sort of fitting to amp and phase. You feed it amp and phases which
come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere.
mam
----- Original Message -----
From: "Frenkel, Anatoly"
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participants (6)
-
abhijeet gaur -
Bruce Ravel -
Fiona R. Kizewski -
Frenkel, Anatoly -
Matthew -
Scott Calvin