On Monday 11 July 2005 10:39, Mark Mark wrote:
Hi Thank you all for the help. I wonder if I have to use X,Y, and Z
Thanks Matt - installing g77 and then recompiling perl/Tk and horae did the
trick!
Bruce - sorry, I meant Perl/Tk...
Paul, you may want to upgrade the installation notes to mention that g77 has
to be installed first. Installion with Fink was a pleasure.
Thanks again guys!
JOEL
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
To: ifeffit@millenia.cars.aps.anl.gov
Sent: 7/12/2005 12:30 PM
Subject: Ifeffit Digest, Vol 29, Issue 8
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Today's Topics:
1. Re: A question (Scott Calvin)
2. RE: A question (Frenkel, Anatoly)
3. Re: A question (Bruce Ravel)
4. rbkg (Silvio Levy)
5. compilation problem under MAC OS X (Brugger, Joel (SAM))
6. Re: rbkg (Bruce Ravel)
7. Re: compilation problem under MAC OS X (Bruce Ravel)
8. Re: compilation problem under MAC OS X (Paul Fons)
9. Re: compilation problem under MAC OS X (Matt Newville)
----------------------------------------------------------------------
Message: 1
Date: Mon, 11 Jul 2005 14:24:33 -0400
From: Scott Calvin
while originating a feff input file from ATOM or I can use X/a, Y/b, and Z/c parameters. I appreciate all the help.
I don't quite understand the question, but perhaps an example of an atoms input file would help clarify. This is taken from the examples that come with the software:
On Monday 11 July 2005 10:39, Mark Mark wrote:
Hi Thank you all for the help. I wonder if I have to use X,Y, and Z
I would add to Bruce's comment that the FEFF.INP file then gives coords
in
terms of angstroms, rather than the cell coordinates ATOMS uses. So if
you
create or modify a FEFF.INP file directly, use angstroms. For an
ATOM.INP
file use cell coordinates.
--Scott Calvin
Sarah Lawrence College
------------------------------
Message: 2
Date: Mon, 11 Jul 2005 15:47:56 -0400
From: "Frenkel, Anatoly"
while originating a feff input file from ATOM or I can use X/a, Y/b, and Z/c parameters. I appreciate all the help.
I don't quite understand the question, but perhaps an example of an atoms input file would help clarify. This is taken from the examples that come with the software:
I would add to Bruce's comment that the FEFF.INP file then gives coords
in
terms of angstroms, rather than the cell coordinates ATOMS uses. So if
you
create or modify a FEFF.INP file directly, use angstroms. For an
ATOM.INP
file use cell coordinates.
--Scott Calvin
Sarah Lawrence College
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------------------------------
Message: 3
Date: Mon, 11 Jul 2005 15:01:16 -0500
From: Bruce Ravel
..... and if you use SS and OVERLAP cards in FEFF, use Bohr's units, which is cute but I hope they will convert this units to Angstroms some day.
Hmm... weird. I did not know that.
I feel compelled to point out that anyone -- Anatoly, Mark Mark,
*anyone* --
can change the source to feff6L, the version that ships with Ifeffit, to
fix
this or any other user interface shortcoming. If you do so, let us know
about
it here on the list so the change (if it's a good one) can be rolled
back
into the Ifeffit distribution.
"And that," he pontificates, "is the beauty of open source...."
B
--
Bruce Ravel ----------------------------------- bravel@anl.gov -or-
ravel@phys.washington.edu
*** My cell phone number has changed. Please ask if you need the new
number
Environmental Research Division, Building 203, Room E-165
Argonne National Laboratory phone and voice mail: (1) 630 252
5033
Argonne IL 60439, USA fax: (1) 630 252
9793
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
------------------------------
Message: 4
Date: Mon, 11 Jul 2005 15:28:09 -0700
From: Silvio Levy
Hi, I'm a new reader of the list. Thanks for all this very useful software and impressive documentation.
Thanks for the kind words.
I'm having trouble understanding the role of rbkg in spline (or autobk). Ravel's Exafs Analysis with FEFF and FEFFIT describes it as "the cutoff between the portion of the Fourier transformed spectrum dominated by the background function and the portion containing information about the local structure".
This would seem to imply that after removal of the background spline, the signal will have NO frequencies below rbkg -- that is, in the R domain, it would be 0 (or close to 0) for R < Rbkg.
While I had no problem following Matt's instructions to get Ifeffit working on my desktop after upgrading to 10.4, I'm still stuggling to install ifeffit on the new laptop. I've tried different combinations of the binary installer and manual compilations of Tcl/TK and horae, but I run into
That would be true if an infinite Fourier transform were possible.
Alas, our
FT is finite (no negative values of k and positive values only go out to
12 or
so). Since the FT is finite, the Fourier components leak to the left
and to
the right. In practice, this means that our signal has non-zero
spectral
weight below Rbkg and our background has non-zero spectral weight above
that
value. Thus, in practice, the background spline and the parameters we
eventually use to fit the data are correlated.
Although there are many things in that document that I would state
differently
today, the language I used to describe Rbkg is valid. Rbkg *is* the
frequency
we choose as that cutoff, but the cutoff is never as clear as you
anticipated.
All the details of the Autobk algorithm are in Physical Review B47:21
(1993)
p. 14126.
See page 30 in this PDF file
http://cars9.uchicago.edu/xafs/NSLS_2003/Kelly.pdf
for a nice graphical demonstration of what Rbkg means. (The rest of
that
document is pretty useful, as well.)
HTH,
B
--
Bruce Ravel ----------------------------------- bravel@anl.gov -or-
ravel@phys.washington.edu
*** My cell phone number has changed. Please ask if you need the new
number
Environmental Research Division, Building 203, Room E-165
Argonne National Laboratory phone and voice mail: (1) 630 252
5033
Argonne IL 60439, USA fax: (1) 630 252
9793
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
------------------------------
Message: 7
Date: Mon, 11 Jul 2005 18:33:29 -0500
From: Bruce Ravel
error:
A caveat: I do not own a Mac and have not tried to install the codes on
10.4.
That said, I wanted to point out that Tcl/Tk has *nothing* to do with
installing my codes on a computer. My codes use Tcl/Tk in no way
whatsoever.
Perl/Tk, on the other hand, is essential to the story. See
http://search.cpan.org/~ni-s/Tk-804.027/
The Perl bindings to the Tk toolkit come with its own, modified version
of
Tk. You must install Perl/Tk to get my codes to work. Installing
Tcl/Tk just
ain't part of the deal.
HTH,
B
--
Bruce Ravel ----------------------------------- bravel@anl.gov -or-
ravel@phys.washington.edu
*** My cell phone number has changed. Please ask if you need the new
number
Environmental Research Division, Building 203, Room E-165
Argonne National Laboratory phone and voice mail: (1) 630 252
5033
Argonne IL 60439, USA fax: (1) 630 252
9793
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
------------------------------
Message: 8
Date: Mon, 11 Jul 2005 15:04:21 -1000
From: Paul Fons
On Monday 11 July 2005 18:09, Brugger, Joel (SAM) wrote:
While I had no problem following Matt's instructions to get Ifeffit working on my desktop after upgrading to 10.4, I'm still stuggling to install ifeffit on the new laptop. I've tried different combinations of the binary installer and manual compilations of Tcl/TK and horae, but I run into this error:
A caveat: I do not own a Mac and have not tried to install the codes on 10.4.
That said, I wanted to point out that Tcl/Tk has *nothing* to do with installing my codes on a computer. My codes use Tcl/Tk in no way whatsoever.
Perl/Tk, on the other hand, is essential to the story. See http://search.cpan.org/~ni-s/Tk-804.027/
The Perl bindings to the Tk toolkit come with its own, modified version of Tk. You must install Perl/Tk to get my codes to work. Installing Tcl/Tk just ain't part of the deal.
HTH, B
-- Bruce Ravel ----------------------------------- bravel@anl.gov -or-
ravel@phys.washington.edu
*** My cell phone number has changed. Please ask if you need the new number
Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/ exafs/
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------------------------------
Message: 9
Date: Mon, 11 Jul 2005 21:57:13 -0500 (CDT)
From: Matt Newville
%dyld: Symbol not found: _s_copy %Trace/BPT trap
Only thing I can think of at this stage is reinstalling the OS!
No, you don't need to do that!! What's missing (and we forgot to put it in the instructions) is that you need Fink's g77 installed as well as the new version of perl/Tk and the "developers disk", including the X11 libraries -- I hear these are labelled differently for 10.4, and that installing XCode might be the best approach. For Fink, see http://fink.sourceforge.net/. Using Fink is not always easy (and requires root access, which for most Mac users means using 'sudo'). There are reasonable instructions for Fink, and FinkCommander is a very nice front end to use. I'm pretty sure you won't need anything besides g77 from Fink. It should be that after installing Fink you can open a Terminal and do: ~> . /sw/bin/init.sh ~> sudo apt-get -f install g77 Sorry for the confusion, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 29, Issue 8 **************************************