good afternooon, My name is Marcos Eleotério, i am undergraduate in physics and i have a scholarship at Brazilian Synchroton Light Laboratory, nearly one month ago i start using the software Athena and Artemis, to analyse some X-ray absorption data that i have, to make my problem more easy to you understand i list below the steps that i use in those programs: 1) After a normalization of the data, i put the data in "Athena" turn on the options: "pre-edge line", "post-edge line" and then "normalized" (in fact i usually turn the option "flatten" on, in dispite of the fact that i don´t know what that means, what that means?), i save using the option "Save chi(k)" in "file". 2)Then i open the program "Artemis" and insert the data saved in the step "1)" in the column of the middle i click with the right button of the mouse and select the option "theory", "atoms" and insert the spatial group, unit cell parameter, and atomic location (here its important to say that the compound that i'm studying is LaCaMnRuO6 the measure of x-ray absorption was performed in the K-edge of the Mn, we are interested in Mn-O ligands so in "Artemis" i only put the data of the Mn and O, right?) 3)I click in the option "run atoms" for each atoms that i inserted the information, choosing 10 paths in each step, i click the in the option "run feff" for each atom that i inserted the information (again), after that, i click in "Fit" then appears in the screem the advise: "there is something wrong with your math expressions" (or something like that) i ignore that advise and go on, but the big problem is that the fit appears very poor! I have to say that the information that i use to insert the atomic position, unit cell parameters, was obtained from a Riteveld refinament, that i performed with the data from a cooper x-ray tube, do i need a data from a beam line, at synchroton? Do you have some idea of my problem? Have i make the correct steps? I'm sorry for my english, i will be very thankful if you answer my e-mail or give to me someone who can do it! REGARDS
Hello Marcos: On Wed, 9 Nov 2005, Marcos Eleoterio wrote:
1) After a normalization of the data, i put the data in "Athena" turn on the options: "pre-edge line", "post-edge line" and then "normalized" (in fact i usually turn the option "flatten" on, in dispite of the fact that i don´t know what that means, what that means?), i save using the option "Save chi(k)" in "file".
You can also save an Athena project fie and just that to load data into Artemis.
2)Then i open the program "Artemis" and insert the data saved in the step "1)" in the column of the middle i click with the right button of the mouse and select the option "theory", "atoms" and insert the spatial group, unit cell parameter, and atomic location (here its important to say that the compound that i'm studying is LaCaMnRuO6 the measure of x-ray absorption was performed in the K-edge of the Mn, we are interested in Mn-O ligands so in "Artemis" i only put the data of the Mn and O, right?)
If you are using the known structural parameters for the material, I suggest that you put in all atoms. You can restrict your fitting to the Mn-O first shell if you want but having the entire structure in is helpful. Alternatively, if you are only interested in a quick firt shell fit, there are options for that too in the Theory tab.
3)I click in the option "run atoms" for each atoms that i inserted the information, choosing 10 paths in each step, i click the in the option "run feff" for each atom that i inserted the information (again), after that, i click in "Fit" then appears in the screem the advise: "there is something wrong with your math expressions" (or something like that) i ignore that advise and go on, but the big problem is that the fit appears very poor!
Since you have excluded the non Mn and O atoms, you cannot really fit the data in this simple way. WIth the method you explain, only your first shell paths have any chance of being correct. You will need to restrict your fit to those paths only (the first one or two). Also, you will need to restrict the fitting range to that of the fitrt shell paths. You cannot include the entire range in R-space with this model. In general, even if you include all atoms, it is useful to start only by including the first shell and looking at how the data can be fit in that range. I would not immediately try to fit multiple shells, you need to take it step by step.
I have to say that the information that i use to insert the atomic position, unit cell parameters, was obtained from a Riteveld refinament, that i performed with the data from a cooper x-ray tube, do i need a data from a beam line, at synchroton?
No, not at all, you just need to put all the atoms in. C.S. -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Hi Marcos,
1) After a normalization of the data, i put the data in "Athena" turn on the options: "pre-edge line", "post-edge line" and then "normalized" (in fact i usually turn the option "flatten" on, in dispite of the fact that i don´t know what that means, what that means?), i save using the option "Save chi(k)" in "file".
Flattening in the "Background removal" section of the in-program documentation: The quadratic polynomial which is regressed after the edge is normally used only to determine the edge step. It is quite possible for a set of properly normalized spectra to overplot very nicely as chi(k) but not as norm(E). This is because the standard normalization does not alter the shape of the background function beyond the edge. If there is variation in the over-all slope beyond the edge, a set of overplotted norm(E) spectra will form a sort of fan beyond the edge. Flattening is a visualization trick which subtracts the linear and quadratic portions of the post-edge polynomial from the data in such a way that the flattened, normalized spectrum oscillates around 1. Thus, much of the variation in the background functions in an ensemble of data can be suppressed when plotting. This is particularly useful when making plots of XANES data. The flattening is purely visual. The subtraction of the post-edge linear and quadratic portions of the background is made only for plotting. chi(k) is not in any way affected by the flattening operation. In the Background removal section of the main window, there is a check button which turns flattening on and off for the data group. When flattening is turned off, the standard norm(E) spectrum will be plotted. Flattening is controlled group-by-group, so it is possible to make a multiple data set plot in which some spectra are flattened and others are not.
2)Then i open the program "Artemis" and insert the data saved in the step "1)" in the column of the middle i click with the right button of the mouse and select the option "theory",
A much easier and more flexible way of doing this is to save your Athena work as a project file and to import that project file in Artemis. Artemis will display a page that allows you to select the record from the Athena project that you want to import and analyze.
"atoms" and insert the spatial group, unit cell parameter, and atomic location (here its important to say that the compound that i'm studying is LaCaMnRuO6 the measure of x-ray absorption was performed in the K-edge of the Mn, we are interested in Mn-O ligands so in "Artemis" i only put the data of the Mn and O, right?)
I am not certain what you mean by this. On the atoms page, you want to include the complete crystal structure, then choose the Mn atom as the central atom. When you run Atoms, the crystal data will be used to make a radially sorted list of atomic coordinates centered around a Mn atom. Feff then uses this list of atomic coordinates to compute the theory. You absolutely should not remove atoms from the list used in the Feff calculation unless you really know what you are doing.
3)I click in the option "run atoms" for each atoms that i inserted the information, choosing 10 paths in each step, i click the in the option "run feff" for each atom that i inserted the information (again), after that, i click in "Fit" then appears in the screem the advise: "there is something wrong with your math expressions" (or something like that) i ignore that advise and go on, but the big problem is that the fit appears very poor!
Well, that's what happens when you ignore her sensible advice! ;-) Seriously, you seem to understand the outline of the steps required to do a fit, but I suspect that you are not appreciating the details of making a proper fitting model. It is very rare that you get to just push the big green button without neediong to think about the details of the model that you are using to fit the spectrum. I could write on and on about this topic, but I think it would be fruitful for you to follow the example that Scott Calvin wrote up. Look at: http://cars9.uchicago.edu/~ravel/software/contrib.html And download the ZnO example. This consists of a series of Artemis project files. Scott wrote comments in the journals of each project to walk you through the process of using Artemis to fit real data. I think that it would be helpful to you to work through this example carefully. I suspect that doing so will help to clear up some of your confusion. If, after working through Scott's example, you still have questions -- we on the mailing list will be glad to help you out. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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/exafs/
participants (3)
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Bruce Ravel -
Carlo Segre -
Marcos Eleoterio