viewing individual Fourier components with Athena
Hello all. Is it possible to view the individual Fourier components of a Fourier transformed EXAFS spectrum in Athena? If so, can someone please direct me toward the documentation that explains how I can do this. Thanks! -Richard Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 27996
Hi Richard, I'm not sure what you're asking for. Do you mean you'd like to see individual paths? If so, the answer is no. Athena only processes the data; individual paths require a model (if we could get them straight out of data, things would be much simpler!). Modeling is done via Artemis, not Athena. But I may have misunderstood your question. --Scott Calvin Sarah Lawrence College At 04:53 PM 3/20/2007, you wrote:
Hello all.
Is it possible to view the individual Fourier components of a Fourier transformed EXAFS spectrum in Athena? If so, can someone please direct me toward the documentation that explains how I can do this.
Scott, Basically, I have been asked to plot what Artemis gives for the theory when an individual path is plotted, except I'm supposed to do it for the raw data...that is, plot the individual paths that sum to the observed chi(k). However, looking at the picture from some old rhodium dimer EXAFS given to me by the good guy that signs my checks ;-) (a pic I'm supposed to use as a guide), I'm "chasing a rabbit." Problem solved (it's a "use the theory, Homer" moment, i.e. DO'OH!). Thanks for the help! Richard Scott Calvin wrote:
Hi Richard,
I'm not sure what you're asking for. Do you mean you'd like to see individual paths? If so, the answer is no. Athena only processes the data; individual paths require a model (if we could get them straight out of data, things would be much simpler!). Modeling is done via Artemis, not Athena. But I may have misunderstood your question.
--Scott Calvin Sarah Lawrence College
At 04:53 PM 3/20/2007, you wrote:
Hello all.
Is it possible to view the individual Fourier components of a Fourier transformed EXAFS spectrum in Athena? If so, can someone please direct me toward the documentation that explains how I can do this.
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On Tuesday 20 March 2007 16:36, Richard Mayes wrote:
Basically, I have been asked to plot what Artemis gives for the theory when an individual path is plotted, except I'm supposed to do it for the raw data...that is, plot the individual paths that sum to the observed chi(k).
However, looking at the picture from some old rhodium dimer EXAFS given to me by the good guy that signs my checks ;-) (a pic I'm supposed to use as a guide), I'm "chasing a rabbit." Problem solved (it's a "use the theory, Homer" moment, i.e. DO'OH!).
Richard, I'm confused in the same way that Scott is. There is no way to deconstruct your chi(k) data into path components a priori. The only way that we have understanding data in a path-by-path manner is to compute some theory and plot each of the paths from the theory. Even better is to do a fit and plot each of the paths after the fitted parameters have been evaluated. It occurs to me that you may be thinking of Fourier filtering the peaks. That is done in Athena by placing an R window around some region of your chi(R) spectrum then pressing the "kq" button. A word of caution -- plotting a Fourier filtered spectrum is NOT the same thing as plotting a path. In certain situations, a path from Feff and the Fourier filter of a region of chi(R) might be very similar. Indeed, they might be sufficiently similar that the filtered spectrum can be interpretted as the contribution from a path. More often, however, that is a very flawed assumption. In any situation where two or more paths conbtribute to a peak in chi(R) (and excellent example would be the first peak in iron metal, which contains contributions from the first two coordination shells and which cannot be separated by Fourier filtering) it would be quite incorrect to call the filtered specutm a "path contribution". HTH, B -- Bruce Ravel ---------------------------------------------- bravel@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/
Bruce, There was a miscommunication dealing with what I was told to do. Sorry for the confusion. Rich Bruce Ravel wrote:
On Tuesday 20 March 2007 16:36, Richard Mayes wrote:
Basically, I have been asked to plot what Artemis gives for the theory when an individual path is plotted, except I'm supposed to do it for the raw data...that is, plot the individual paths that sum to the observed chi(k).
However, looking at the picture from some old rhodium dimer EXAFS given to me by the good guy that signs my checks ;-) (a pic I'm supposed to use as a guide), I'm "chasing a rabbit." Problem solved (it's a "use the theory, Homer" moment, i.e. DO'OH!).
Richard,
I'm confused in the same way that Scott is. There is no way to deconstruct your chi(k) data into path components a priori. The only way that we have understanding data in a path-by-path manner is to compute some theory and plot each of the paths from the theory. Even better is to do a fit and plot each of the paths after the fitted parameters have been evaluated.
It occurs to me that you may be thinking of Fourier filtering the peaks. That is done in Athena by placing an R window around some region of your chi(R) spectrum then pressing the "kq" button. A word of caution -- plotting a Fourier filtered spectrum is NOT the same thing as plotting a path. In certain situations, a path from Feff and the Fourier filter of a region of chi(R) might be very similar. Indeed, they might be sufficiently similar that the filtered spectrum can be interpretted as the contribution from a path.
More often, however, that is a very flawed assumption. In any situation where two or more paths conbtribute to a peak in chi(R) (and excellent example would be the first peak in iron metal, which contains contributions from the first two coordination shells and which cannot be separated by Fourier filtering) it would be quite incorrect to call the filtered specutm a "path contribution".
HTH, B
Hi Bruce, In response to some users, I was trying to update the ZnO tutorial so that it works with current versions of Artemis. Unfortunately, there seems to be a bug in the current version of Artemis. I'm posting it here on the mailing list because although there are very easy workarounds it's likely to give some newcomers trouble. I have Artemis 0.8.007 on Windows XP. To see the bug, make sure do_autoparams is on. Also make sure you're working with a new project. Now create and run a feff calculation in the usual way. When I do this, the guessed parameters created are: amp for S02 delr for delE0 dr for delr ss for sigma^2 The second of those is quite confusing, and the third doesn't work. Of course, the workarounds are simple (e.g. don't use autoparams or change the names to something that works). But, since Artemis defaults to autoparams on, it seems as if this could be off-putting to newcomers. --Scott Calvin Sarah Lawrence College
From my (admittedly extremely biased) persepctive, this is one of
Scott, There is certainly a problem in some situations that behaves as you describe, but the situation is a bit different than you think. A while back, I made the mistake you point out in of Artemis' configuration files. This was fixed in a subsequent update. I just looked at the most recent update and its artemis.config file is correct. However, the way the configuration system works, anyone who used artemis during its broken period has the broken autoparams values in his personal configuration file. In short, it's not really broken, except sometimes it is ;-) One quick solution is to click the "Set all parameters to Artemis's default" button on the preferences page. This fixes the autoparams roblem at the expense of undooing all you other customizations. those situations where the project suffers from never having had any volunteers to help with Windows packaging or with formal testing. I fixed the problem, but I am not sure how to propagate the fix in a way that doesn't alter the behavior of the configuration system. B P.S. I guess I should explain that the system-wide initialization file is generated from athena.config at the time that the windows executables are built. The personal initilization file is regenerated everytime you run artmis and contains the junction of the system and personal init files. The system file is read first and the personal is read second, with values from the personal over-riding values from the system. That explains how a configuration bug from one update can continue propagating through later updates. On Tuesday 20 March 2007 20:41, Scott Calvin wrote:
Hi Bruce,
In response to some users, I was trying to update the ZnO tutorial so that it works with current versions of Artemis. Unfortunately, there seems to be a bug in the current version of Artemis. I'm posting it here on the mailing list because although there are very easy workarounds it's likely to give some newcomers trouble.
I have Artemis 0.8.007 on Windows XP.
To see the bug, make sure do_autoparams is on. Also make sure you're working with a new project.
Now create and run a feff calculation in the usual way.
When I do this, the guessed parameters created are:
amp for S02 delr for delE0 dr for delr ss for sigma^2
The second of those is quite confusing, and the third doesn't work.
Of course, the workarounds are simple (e.g. don't use autoparams or change the names to something that works). But, since Artemis defaults to autoparams on, it seems as if this could be off-putting to newcomers.
--Scott Calvin Sarah Lawrence College
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-- Bruce Ravel ---------------------------------------------- bravel@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/exafs/
Aha! I see how that works now. Thanks; I'll fix the ZnO tutorial and post the new version to the wiki. --Scott Calvin Sarah Lawrence College At 10:08 AM 3/21/2007, you wrote:
Scott,
I just looked at the most recent update and its artemis.config file is correct. However, the way the configuration system works, anyone who used artemis during its broken period has the broken autoparams values in his personal configuration file.
participants (3)
-
Bruce Ravel -
Richard Mayes -
Scott Calvin