Hello, yet another one... sorry today is my day... With Athena it appears that I can simply (maybe too simply) click on a button and plot the phase shifted spectrum in R-space. How can I try to do the same using IFEFFIT from the command line? In practice, using IFEFFIT we can plot the fitted spectrum and the FT'ed experimental spectrum, but the plot does not consider the phase shift. We need to extract the phase shift in oder to translate the plot to show the phase shifted spectrum. How can we do that? What is the parameter in IFEFFIT that allows one - as in Athena - to add a constant number and shift the plot? Stefano PS: needless to say that we are learning... -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
On Wednesday 14 December 2005 10:38, Stefano Ciurli wrote:
With Athena it appears that I can simply (maybe too simply) click on a button and plot the phase shifted spectrum in R-space. How can I try to do the same using IFEFFIT from the command line?
The answer to the generic question "how can I do in Ifeffit what I do in A or A?" is always the same. Look at the Ifeffit buffer (Edit->Display Ifeffit buffer) as you are clicking stuff. The commands sent to Ifeffit are echoed in that space. The Ifeffit buffer was originally a debugging tool, but it quickly became clear that its great value was as a pedagogical tool for others wanting to write their own Ifeffit scripts.
In practice, using IFEFFIT we can plot the fitted spectrum and the FT'ed experimental spectrum, but the plot does not consider the phase shift. We need to extract the phase shift in oder to translate the plot to show the phase shifted spectrum. How can we do that? What is the parameter in IFEFFIT that allows one - as in Athena - to add a constant number and shift the plot?
The answer to this particular question is to add these arguments pc_edge="fe k", pc_caps=1 to the fftf() command. Of course, the value for pc_edge should be appropriate to your sample. If you have a feff calculation you can use for a full phase correction, the arguments are slightly different. The "caps" in "pc_caps" is an acronymn for "central atom phase shift". If you know the scatterer (which you might not when using Athena, but which you certainly do when using feff/Artemis), then you can do the full (central + scattering) correction. Use the path() command to import the feffNNNN.dat file, then add this argument pc_feff_path=1 to the fftf() command (assuming that you read the feffNNNN.dat in as path #1). Again, watch the Ifeffit buffer to see an example of this in Artemis. 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/
Thanks Bruce! -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
participants (2)
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Bruce Ravel -
Stefano Ciurli