Sorry about the omission -- I have always installed the developer tools (which come free with the OS) so I didn't note their necessity for a clean install. I will update the wiki to include installation instructions for fink and possibly other g77 sources. Paul On Jul 12, 2005, at 18:17 PM, Brugger, Joel (SAM) wrote:
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
Subject: Re: [Ifeffit] A question To: XAFS Analysis using Ifeffit Cc: SCalvin@slc.edu Message-ID: <3.0.1.32.20050711142433.00c35ca0@mail.slc.edu> Content-Type: text/plain; charset="us-ascii" At 11:45 AM 7/11/2005 -0500, Bruce wrote:
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
parameters
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
------------------------------
Message: 2 Date: Mon, 11 Jul 2005 15:47:56 -0400 From: "Frenkel, Anatoly"
Subject: RE: [Ifeffit] A question To: "XAFS Analysis using Ifeffit" Message-ID: <2332D75C71E72E4CBDFC8100FB054FE3793C3F@exchange2000-02.b459.bnl.gov> Content-Type: text/plain; charset="iso-8859-1"
....... 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.
Anatoly
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Scott Calvin Sent: Monday, July 11, 2005 2:25 PM To: XAFS Analysis using Ifeffit Cc: SCalvin@slc.edu Subject: Re: [Ifeffit] A question
At 11:45 AM 7/11/2005 -0500, Bruce wrote:
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
parameters
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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 3 Date: Mon, 11 Jul 2005 15:01:16 -0500 From: Bruce Ravel
Subject: Re: [Ifeffit] A question To: XAFS Analysis using Ifeffit Message-ID: <200507111501.16792.bravel@anl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 11 July 2005 14:47, Frenkel, Anatoly wrote:
..... 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
Subject: [Ifeffit] rbkg To: XAFS Analysis using Ifeffit Message-ID: Hi, I'm a new reader of the list. Thanks for all this very useful software and impressive documentation.
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. But this is not quite what I see; varying Rbkg has a large effect throughout the plot of chir_mag versus R. In particular I observe sometimes that with Rbkg = 1.3 (say) I get a very different R-plot than with either Rbkg = .9 or 1.5 -- not just at low R but throughout. And yet the Rbkg = .9 and 1.5 R-plots look similar to one another, much more than to R-plot for the intermediate value of R. Moreover changing Rbkg shifts the peaks in the R-plot noticeably.
What does the algorithm actually do with this parameter? It would be nice to understand that without having to decipher the code. Forgive me if this information is given somewhere, but I couldn't find it.
Note: I'm working with compounds for which I don't yet have a good theoretical model, so I don't know how to choose between Rbkg values based on the position of the peaks.
Thanks
Silvio Levy
------------------------------
Message: 5 Date: Tue, 12 Jul 2005 08:39:57 +0930 From: "Brugger, Joel (SAM)"
Subject: [Ifeffit] compilation problem under MAC OS X To: "'ifeffit@millenia.cars.aps.anl.gov'" Message-ID: <5801DF3664AC854AA3CC2DB83E718D30030C0CBF@sagemsg0006.sagemsmrd01.sa.g ov ....au>
Content-Type: text/plain
Hi,
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:
%JoelG4:/Applications/Ifeffit/bin joelb$ ./hephaestus %dyld: lazy symbol binding failed: Symbol not found: _s_copy % Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bund le % Expected in: dynamic lookup % %dyld: Symbol not found: _s_copy % Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bund le % Expected in: dynamic lookup % %Trace/BPT trap
Only thing I can think of at this stage is reinstalling the OS!
Thanks!
JOEL
------------------------------
Message: 6 Date: Mon, 11 Jul 2005 18:28:18 -0500 From: Bruce Ravel
Subject: Re: [Ifeffit] rbkg To: XAFS Analysis using Ifeffit Message-ID: <200507111828.18498.bravel@anl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 11 July 2005 17:28, Silvio Levy wrote:
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.
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
Subject: Re: [Ifeffit] compilation problem under MAC OS X To: XAFS Analysis using Ifeffit Message-ID: <200507111833.29175.bravel@anl.gov> Content-Type: text/plain; charset="iso-8859-1" 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/
------------------------------
Message: 8 Date: Mon, 11 Jul 2005 15:04:21 -1000 From: Paul Fons
Subject: Re: [Ifeffit] compilation problem under MAC OS X To: bravel@anl.gov, XAFS Analysis using Ifeffit Message-ID: Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed I thought I would bring up the Wiki entry regarding installation on Tiger 10.4 at (http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz? req=all#2.12). If there is a problem, I would like to modify the text. In short, I have (re)installed horae on two 10.4 systems upgraded from 10.3 as well as on a brand spanking new dual G5. It works without error on each. For the G5, I installed the new version of Tk (as explained in the Wiki entry) and then just ran the binary installer (as I recall). I don't recall having any problems with the installation and it works fine on all three machines. Please excuse me for mentioning the obvious, but if this a new machine with the OS pre-installed, it is necessary to install X11 which is an optionally install on the included installation DVD's. Once this is installed, download Tk (tcl is included and does not require reinstallation) and install it, and then the binary installer for ifeffit. I don't recall if the binary installer has the latest version of horae and ifeffit, but once the base installation is in place, you can upgrade any time from terminal by typing "sudo horae_update".
Paul On Jul 11, 2005, at 13:33 PM, Bruce Ravel wrote:
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/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 9 Date: Mon, 11 Jul 2005 21:57:13 -0500 (CDT) From: Matt Newville
Subject: Re: [Ifeffit] compilation problem under MAC OS X To: XAFS Analysis using Ifeffit Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Joel,
%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
------------------------------
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