Hi Ryan, I am taking the liberty of CCing this to the Ifeffit mailing list.
I have a novice FEFF question for you guys.
Assuming one has a good idea of the SO^2 value for a specific element either from published literature or analysis of a relevant standard reference phase (e.g. 0.85 for Co in Co(OH)2), what is the consensus on fixing the SO^2 value for the FEFF simulation and if one does fix the value in the feff.inp file (@ 0.85 for this thought experiment) would one still fix SO^2 at the same value during the fit (or fix at one)?
I'll assume that you are famliar with the normal caveats of the assumption of the "chemical transferability" of S02 and that you are aware that you introduce a source of systematic uncertainty into your analysis when you make that assumption. If that's not clear, please ask so that I or someone else on the list can talk about that. I can only answer you question by explaining what I prefer. I cannot presume to speak for the consensus -- different practitioners reasonably come to their own conclusions. I prefer to run feff with S02=1 and all sigma^2 values set to zero. I then prefer to use Ieffit (or Artemis or WinXAS or EXAFSPAK or whatever) to change the parameters of the EXAFS equation from their nominal values. Of course, setting S02 to 0.85 in Feff and then setting it to 1 in Ifeffit is equivalent to setting it to 1 in Feff and 0.85 in Ifeffit. While multiplication is unambigously commutative, human brains are usually notoriously poor at disentangling a sequence of arithmatic. If you: (1) set S02 to something other than 1 in Feff, (2) need to modify the value when doing analysis in Ifeffit, (3) go on vacation for two weeks, and finally (4) return home to write a paper on your analysis --- are you going to remember that you need to multiply your two values of S02 together when you report on your analysis in the paper? Hmmmm..... Another way of looking at this is to remember what Feff (that is, Feff6 -- Feff8 adds a few steps) does: 1. computes potentials and phases 2. determines the path list 3. constructs chi(k) for each path in the path list using the potentials and phases from part 1 4. sums up all the paths to make the theoretical chi(k) If you consider Ifeffit to be a much more interesting version of the fourth part of Feff, then it should be clear that the better approach is to use Ifeffit to deal with S02. 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/exafs/
As usual, consistency is everything. It seems to me that one should always compare with a model compound, if possible.
If you do that and do the model and unknown the same way, then you need only take the ratios of S0^2 or N or whatever.
mam
----- Original Message -----
From: "Bruce Ravel"
Hi Ryan,
I am taking the liberty of CCing this to the Ifeffit mailing list.
I have a novice FEFF question for you guys.
Assuming one has a good idea of the SO^2 value for a specific element either from published literature or analysis of a relevant standard reference phase (e.g. 0.85 for Co in Co(OH)2), what is the consensus on fixing the SO^2 value for the FEFF simulation and if one does fix the value in the feff.inp file (@ 0.85 for this thought experiment) would one still fix SO^2 at the same value during the fit (or fix at one)?
I'll assume that you are famliar with the normal caveats of the assumption of the "chemical transferability" of S02 and that you are aware that you introduce a source of systematic uncertainty into your analysis when you make that assumption. If that's not clear, please ask so that I or someone else on the list can talk about that.
I can only answer you question by explaining what I prefer. I cannot presume to speak for the consensus -- different practitioners reasonably come to their own conclusions.
I prefer to run feff with S02=1 and all sigma^2 values set to zero. I then prefer to use Ieffit (or Artemis or WinXAS or EXAFSPAK or whatever) to change the parameters of the EXAFS equation from their nominal values.
Of course, setting S02 to 0.85 in Feff and then setting it to 1 in Ifeffit is equivalent to setting it to 1 in Feff and 0.85 in Ifeffit. While multiplication is unambigously commutative, human brains are usually notoriously poor at disentangling a sequence of arithmatic.
If you: (1) set S02 to something other than 1 in Feff, (2) need to modify the value when doing analysis in Ifeffit, (3) go on vacation for two weeks, and finally (4) return home to write a paper on your analysis --- are you going to remember that you need to multiply your two values of S02 together when you report on your analysis in the paper? Hmmmm.....
Another way of looking at this is to remember what Feff (that is, Feff6 -- Feff8 adds a few steps) does: 1. computes potentials and phases 2. determines the path list 3. constructs chi(k) for each path in the path list using the potentials and phases from part 1 4. sums up all the paths to make the theoretical chi(k)
If you consider Ifeffit to be a much more interesting version of the fourth part of Feff, then it should be clear that the better approach is to use Ifeffit to deal with S02.
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/exafs/
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participants (2)
-
Bruce Ravel -
Matthew Marcus