[Ifeffit] Re: compilation problem under MAC OS X - all ok now!

Paul Fons paul-fons at aist.go.jp
Sun Jul 17 07:52:27 CDT 2005


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 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.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 <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
>
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 29, Issue 8
> **************************************
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