Hello all, Athena and Artemis do not plot chi beyond 20 Å-1 or the Fourier transform beyond 10 Å. Is this a limitation of Athena/Artemis or of Ifeffit? Can it be changed? We have exafs data that may be usable almost to 21 Å-1, and with quite a strong FT peak (from a Pt atom) at 10.5 Å. The latter we would not even have noticed had we been using only Athena to process our data. The 10.5 Å peak raises another issue. I understand that Ifeffit by default assumes that the high-R region is pure noise in order to make its estimates of uncertainty. (I know the actual R-range that is used was mentioned recently but I can't find it in the list archives or any of my manuals.) Can this range be changed? Does anyone have any advice on how to deal with this issue? Thanks, Peter Peter Southon Postdoctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 7482
On Thursday 26 August 2004 01:54 am, Peter Southon wrote:
Hello all,
Athena and Artemis do not plot chi beyond 20 Å-1 or the Fourier transform beyond 10 Å. Is this a limitation of Athena/Artemis or of Ifeffit? Can it be changed?
This only seems to be half true. The fe.060 file that comes with the Athena examples has data out to 22 invAng and gets plotted correctly by both programs. On the other hand, you are correct that data only gets plotted in R up to 10 A. That was not a conscious decision by me and seems to be some kind of default in Ifeffit. Matt, how does one change that default?
The 10.5 Å peak raises another issue. I understand that Ifeffit by default assumes that the high-R region is pure noise in order to make its estimates of uncertainty. (I know the actual R-range that is used was mentioned recently but I can't find it in the list archives or any of my manuals.) Can this range be changed? Does anyone have any advice on how to deal with this issue?
In Ifeffit the chi_noise command is used to determine this. Here is its doc page: http://cars9.uchicago.edu/ifeffit/refman/node66.html As you can see, the rwgt1 and rwgt2 parameters are used to change the high-R range. Artemis does not provide widgets for setting these, but you can do this rather more hands-on approach: 1. Open up the Ifeffit buffer from the Edit menu 2. Enter the chi_noise command using the command line at the bottom of that window. To see an example of the chi_noise command, select "What is epsilon_k?" from the Data menu. The chi_noise command used to answer that question (using the default R range) will be displayed in the Ifeffit buffer. 3. The value for epsilon will be diplayed in the Echo area and preserved in the Echo buffer. Enter this number in the box labeled "Epsilon" on the data page. HTH, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Bruce, Peter,
Athena and Artemis do not plot chi beyond 20 �-1 or the Fourier transform beyond 10 �. Is this a limitation of Athena/Artemis or of Ifeffit? Can it be changed?
This only seems to be half true. The fe.060 file that comes with the Athena examples has data out to 22 invAng and gets plotted correctly by both programs.
The 'chi(k) only goes to k=20' issue might be due to the fact that the Feff calculations don't normally go past k=20. That makes it hard to do a fit that far out! I think this could be changed, but it would take a little time. Are you using Feff6l or Feff8?
On the other hand, you are correct that data only gets plotted in R up to 10 A. That was not a conscious decision by me and seems to be some kind of default in Ifeffit. Matt, how does one change that default?
You can set the maximum R for chi(R) from fftf() with fftf(data.chi, kmin=2,kmax=19, rmax_out=15)
The 10.5 � peak raises another issue. I understand that Ifeffit by default assumes that the high-R region is pure noise in order to make its estimates of uncertainty. (I know the actual R-range that is used was mentioned recently but I can't find it in the list archives or any of my manuals.) Can this range be changed? Does anyone have any advice on how to deal with this issue?
Just to add to Bruce's notes: The prevailing wisdom is that the automated estimate of epsilon_k is generally too low -- that makes chi_square too large. Having 'real data' out there might actually help!! But simply setting epsilon_k to an appropriate value is probably the best bet. Remember that epsilon_k is the uncertainty in unweighted chi(k), and so is fairly easy to interpret (ie, no units). Artemis reports this as 'Measurement uncertainty (k)' in the Results window after a fit but you can overwrite it with the Epsilon value on the page with the data file and Fit ranges. A reasonable number for most good EXAFS would be epsilon_k = 0.001. --Matt
On Thursday 26 August 2004 11:01 am, Matt Newville wrote:
On the other hand, you are correct that data only gets plotted in R up to 10 A. That was not a conscious decision by me and seems to be some kind of default in Ifeffit. Matt, how does one change that default?
You can set the maximum R for chi(R) from fftf() with fftf(data.chi, kmin=2,kmax=19, rmax_out=15)
This seems like a good thing to add as a configuration option in the next stable version of Artemis. I am open to votes for what the default value should be. I am leaning towards either 10 or 12. Matt, the fftf() page in the reference manual does, in fact, mention rmax_out, but only tangentially. Could you add its description to the parameter list? B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (3)
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Bruce Ravel -
Matt Newville -
Peter Southon