[Ifeffit] Re: compilation problem under MAC OS X - all ok now!
Brugger, Joel (SAM)
Brugger.Joel at saugov.sa.gov.au
Tue Jul 12 04:17:59 CDT 2005
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 at millenia.cars.aps.anl.gov
To: ifeffit at 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 <scalvin at slc.edu>
Subject: Re: [Ifeffit] A question
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Cc: SCalvin at slc.edu
Message-ID: <3.0.1.32.20050711142433.00c35ca0 at 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" <frenkel at bnl.gov>
Subject: RE: [Ifeffit] A question
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<2332D75C71E72E4CBDFC8100FB054FE3793C3F at 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 at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at 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 at 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 at 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 <bravel at anl.gov>
Subject: Re: [Ifeffit] A question
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200507111501.16792.bravel at 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 at anl.gov -or-
ravel at 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 <levy at msri.org>
Subject: [Ifeffit] rbkg
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <E1Ds6kz-0001Ls-00 at pinch.msri.org>
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)" <Brugger.Joel at saugov.sa.gov.au>
Subject: [Ifeffit] compilation problem under MAC OS X
To: "'ifeffit at millenia.cars.aps.anl.gov'"
<ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
<5801DF3664AC854AA3CC2DB83E718D30030C0CBF at sagemsg0006.sagemsmrd01.sa.gov
...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 <bravel at anl.gov>
Subject: Re: [Ifeffit] rbkg
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200507111828.18498.bravel at 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 at anl.gov -or-
ravel at 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 <bravel at anl.gov>
Subject: Re: [Ifeffit] compilation problem under MAC OS X
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200507111833.29175.bravel at 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 at anl.gov -or-
ravel at 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 <paul-fons at aist.go.jp>
Subject: Re: [Ifeffit] compilation problem under MAC OS X
To: bravel at anl.gov, XAFS Analysis using Ifeffit
<ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <C8746064-01D5-4B97-B565-4E4E45EFE69E at aist.go.jp>
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 at anl.gov -or-
>
> ravel at 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 at 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 <newville at cars.uchicago.edu>
Subject: Re: [Ifeffit] compilation problem under MAC OS X
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <Pine.LNX.4.44.0507112144331.24556-100000 at corvette>
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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