Re: [Ifeffit] Methods to break correlations
Hi Bruce,
Thanks for the tip on updating iXAFS, I will give that a try. As to the
plugin not working on Athena, apologies about the vagueness. I have tried
to open the file using iXAFS (ifeffit v.1.2.10, Athena v.0.8.054) and
received the attached error message. After clicking 'ok' Athena remains
open. I have also tried to open the same data file on Parallels running
WinXP SP3 using the standard *.exe installer (ifeffit v.1.2.11c, Athena
v.0.8.061) and received the attached error message. After clicking 'ok' for
the windows error, Athena quits (leaving the plot window open). According
to the header of the file it was collected using "SSRL - EXAFS Data
Collector 2.0". I have tried several combination's which plug-ins are
selected and it didn't seem to make a difference.
Thanks for the tips
Brandon
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than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Methods to break correlations (Bruce Ravel)
2. Re: Methods to break correlations (Bruce Ravel)
3. Re: Residual EXAFS spectra (Bruce Ravel)
4. Re: Methods to break correlations (Jeff Terry) ---------------------------------------------------------------------- Message: 1
Date: Mon, 30 Aug 2010 10:08:13 -0400
From: Bruce Ravel On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: Does anyone have an Athena plugin for the SSRL data Collector
v2.0? The SSRL plugins available make the program crash when I try and
use
them. (moderators, let me know if these questions should have been in a
separate posting) Here is the SSRL binary plugin from the svn repository http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athen... And here is the one for data files that have been converted to ascii http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athen... They should be placed in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ I am willing to take a look at the problem you are seeing, but "it
crashes" doesn't give me much to work with. Obviously the plugins
worked for me otherwise I would not have considered them ready for
release. You need to provide some clue as to what the problem is.
Either supply a data file that triggers the problem or by cut and
paste what gets written after starting Athena in a terminal window or
(preferably) both. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973 My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.edu/%7Eravel/software/exafs/ ------------------------------ Message: 2
Date: Mon, 30 Aug 2010 10:11:06 -0400
From: Bruce Ravel On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: I am running iXAFS 2.1 b1, is there any way to update the
Athena/Artemis versions, or would I have to an source install? That is actually a question I need to know the answer to as well. In
fact, our group's post-doc has the same question, so I plan to look
into it this week. (Since I did not make the iXAFS package, I am not
100% clear on how it works -- which is actually true of most things on
a Mac!) I believe the answer is yes, but I'll let you know what I know more. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973 My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.edu/%7Eravel/software/exafs/ ------------------------------ Message: 3
Date: Mon, 30 Aug 2010 10:20:02 -0400
From: Bruce Ravel On Monday 30 August 2010 09:57:09 am Bruce Ravel wrote: Hi all,
I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral
oxides.
In course of this, I came across a lierature article(Geochimica et
cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting
a
particular shell) was generated after subtracting four other different
paths contribution from the EXAFS spectra(k3.chi(k)). This procedure
was
adopted to identify and isolate different paths/shells informations
available in the EXAFS spectra. As the paper doesnot explain about the
procedure, I am little confused whether the author has adopted just the
linear subtraction methodology(i.e, sum of few selected paths minus the
original spectra) in creating the residual spectra or some other
mathematical approach. The caption to figure 5 in the article you cite says: "Residual EXAFS (produced by subtraction of U=Oax, U-Oeq, U-C, and
U-U shells) ..." Seems pretty clear to me that what they show is the Fourier transform of data_chi(k) - sum_of_specified_paths(k) B Ummm... of course, I meant to say that the subtraction is done after
performing some kind of a fit to determine values of the parameters
affecting the paths included in the sum. Now I'll editorialize a bit ... the advantage of analyzing a
difference spectrum of this sort is that a small part of the data that
might get "lost" in the full fit gets emphasized. The disadvantage --
and a big one at that -- is that you loose the ability to evaluate
correlations between the parameters of the fit to the residual and the
parameters that were used to determine the sum of paths used to make
the residual. Consequently, doing an analysis of the residual
spectrum requires a high level of confidence in the parameters used
for the subtracted paths. In my experience, that level of confidence
is rarely defensible. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973 My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.edu/%7Eravel/software/exafs/ ------------------------------ Message: 4
Date: Mon, 30 Aug 2010 09:47:58 -0500
From: Jeff Terry iXAFS originally started out as a wrapper to launch the individual
programs. At that time, it was a simple matter to replace any of the
individual programs. Ken McIvor has improved iXAFS so that it now builds
universal projects but has perl code embedded. This makes it more difficult
to update. That said there is a directory structure within iXAFS and I would guess
that replacing the individual programs would work. I make no guarantees
though as I am not sure of all the changes that Ken has made since I
initially wrote the cocoa wrapper. Jeff Sent from my iPhone On Aug 30, 2010, at 9:11 AM, Bruce Ravel On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: I am running iXAFS 2.1 b1, is there any way to update the
Athena/Artemis versions, or would I have to an source install? That is actually a question I need to know the answer to as well. In
fact, our group's post-doc has the same question, so I plan to look
into it this week. (Since I did not make the iXAFS package, I am not
100% clear on how it works -- which is actually true of most things on
a Mac!) I believe the answer is yes, but I'll let you know what I know more. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973 My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/http://cars9.uchicago.edu/%7Eravel/software/exafs/ ------------------------------ _______________________________________________
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Brandon Reese