Some really quick basic questions. I am working with EXAFS spectra of silicate glasses at various edges (including S and Fe K edges) and I am having a really difficult time pinning down the structures. Clearly with glasses I can't always be sure of the oxygen co-ordination and so I have to refine this value which is one among many problems. Just to check I have things right: 1. Are there any problems if I set the R-range min to the same value as Rbkg? 2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems? 3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances? 4. If I have a calculated Fe3+-O path from a 4 and 6 co-ordinate reference are these equivalent? Obviously, they will give a different bond length and the MS paths will change but if I am only fitting a first shell is there anything different. I think the answer involves the muffin tin potentials but I'm a little out of my depth there. Any advice about solving glass structures more than welcome. Whatever I try I can't get realistic results out. Thank you for your time, Andy Connelly
Hi Andy: On Mon, 6 Apr 2009, Andy Connelly wrote:
1. Are there any problems if I set the R-range min to the same value as Rbkg?
No, but you shouldn't set it lower than Rbkg, in general.
2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems?
This expression is OK, but you can only refine one or the other. Refining both has no meaning. You might as well just have a single parameter then.
3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances?
Yes, it is a good idea to start with a limited range and then move up. One additional positive aspect of this is that you get a better idea of the number of degrees of freedom you have for that shell. If you make Rmax too big and you oly fit the first part of the range, you will artificially have too many degrees of freedom.
4. If I have a calculated Fe3+-O path from a 4 and 6 co-ordinate reference are these equivalent? Obviously, they will give a different bond length and the MS paths will change but if I am only fitting a first shell is there anything different. I think the answer involves the muffin tin potentials but I'm a little out of my depth there.
There are slight differences in the paths when you put the absorber in a different environment. I have tried this in the past and I have found that the ultimate difference in the fit is much smaller than the estimated standard deviations. The place where having the correct environment matters is if you are looking for second shells and there might be some high amplitude multiple scattering paths possible. This is not usually relevant for a glass.
Any advice about solving glass structures more than welcome. Whatever I try I can't get realistic results out.
If you send the Artemis project file, we might be able to help better. My experience with glasses is that you just have to start with the minimal number of assumptions and try a lot of cases. It becomes important to look carefully at the values of Chi that you get with different models to make a determination as to which one is best. In your case, what elements do you have in the glass? What do you know about the absorber's chemistry (i.e. does it like to be in a tetrahedral environment or does it prefer octahedral). All these considerations must go into your analysis. Carlo
Thank you for your time,
Andy Connelly _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- 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 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Hi Andy, Just a few notes I'd like to add to Carlo's helpful answer: On Apr 6, 2009, at 1:27 PM, Carlo Segre wrote:
Hi Andy:
On Mon, 6 Apr 2009, Andy Connelly wrote:
2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems?
This expression is OK, but you can only refine one or the other. Refining both has no meaning. You might as well just have a single parameter then.
Unless, of course, you manage to get more than one shell of data. Even for glasses, that is often possible. Another possibility is to collect data on a related crystalline material, and corefine the crystalline material, requiring a single S02 for each. (The crystal, presumably would have a known value of N.)
3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances?
Yes, it is a good idea to start with a limited range and then move up. One additional positive aspect of this is that you get a better idea of the number of degrees of freedom you have for that shell. If you make Rmax too big and you oly fit the first part of the range, you will artificially have too many degrees of freedom.
Yes, and don't forget that it is not sufficient to choose an rmax just below the paths you are omitting. This is for two reasons: paths have some width in R-space (as you can see from Artemis if you plot the path) and the center of each path is shifted down from Reff. To be on the safe side, I usually try to stay a half angstrom or so below the first important path that I am not including in my fit. For example, if the nearest neighbors are at 2.0 angstroms, and the next nearest neighbors at 2.4, but I'm not including the next nearest-neighbor, then I might start with rmax at 1.9 angstroms. That sounds strange, because it sounds like I'm not even including the nearest neighbor, but it too will be shifted down and have width, so I actually am including most of it.
--Scott Calvin Sarah Lawrence College
Hi Andy, I have a book chapter that details how to set the k-range for a data set. It also talks about Rbkg in detail. If you want a copy just send me an email. Cheers, Shelly
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Andy Connelly Sent: Monday, April 06, 2009 12:16 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Basic questions
Some really quick basic questions. I am working with EXAFS spectra of silicate glasses at various edges (including S and Fe K edges) and I am having a really difficult time pinning down the structures. Clearly with glasses I can't always be sure of the oxygen co-ordination and so I have to refine this value which is one among many problems. Just to check I have things right:
1. Are there any problems if I set the R-range min to the same value as Rbkg?
2. If I want to refine the degeneracy of a path can I write the expression "amp*N_1" in the SO2 box? (where the N box is set to 1) and then refine "amp" and/or "N_1"? where N_1 equivalent to the degeneracy and amp is effectively SO2. Clearly they will be highly correlated, but does a formula like this cause IFEFFIT any problems?
3. If, for initial fits, I am only interested in the first shell should I set R-range max to a lower value to isolate that shell and then increase it as I look at shells at longer distances?
4. If I have a calculated Fe3+-O path from a 4 and 6 co-ordinate reference are these equivalent? Obviously, they will give a different bond length and the MS paths will change but if I am only fitting a first shell is there anything different. I think the answer involves the muffin tin potentials but I'm a little out of my depth there.
Any advice about solving glass structures more than welcome. Whatever I try I can't get realistic results out.
Thank you for your time,
Andy Connelly _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (4)
-
Andy Connelly -
Carlo Segre -
Kelly, Shelly -
Scott Calvin