August 2003 - Ifeffit - millenia.cars.aps.anl.gov

ifeffit and Mac OSX
by Matt Newville 03 Jul '04

03 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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Phase and Amplitude Correction
by Ian Drake 28 Aug '03

28 Aug '03

Hi Matt, I wanted to follow up on a suggestion by Grant Bunker (Aug.4th). He proposed that I look into doing both a phase and amplitude correction of the data as opposed to doing only a total phase correction. How might I achieve this using IFEFFIT commands? Thank you for your help, Ian Drake ***************************** UC Berkeley Dept. of Chem. Eng. Graduate Student Advised by Dr. Alex Bell Heterogeneous Catalysts ******************************

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and new features in sixpack
by Webb, Samuel M. 26 Aug '03

26 Aug '03

Hi all... As a follow up to the follow up to Matt and Bruce's announcements.... There have also been a lot of new features written into sixpack now as well, also as a response to a lot of useful input from everyone at XAFS12. The latest incarnation of these changes is included in the latest IFEFFIT installer. The continuing saga of updates can be always be found on the sixpack webpage (http://www-ssrl.slac.stanford.edu/~swebb/sixpack.htm) including source code. Thanks to everyone the last few months that have made suggestions for improvements and catching errors. I hope to make some more major renovations to some of the fitting interfaces in the coming months so those of you who are interested can keep an eye out for them. Thanks! Sam

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and new versions of Athena and Artemis as well
by Bruce Ravel 25 Aug '03

25 Aug '03

Hi folks, As a follow-up to Matt's email, the new release of ifeffit for Windows contains the latest versions of Athena and Artemis. The source code tarball for unix and Mac OSX users can be found on my web site or downloaded using the horae_update script after you have compiled and installed the new version of ifeffit. These new releases contain many improvements which are summarized here: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Included are lots of features responding to useful input that I received both at the XAFS conference in Malmo and at this summer's EXAFS workshop at the NSLS. Thanks to everyone who contributed useful feedback, comments, and suggestions. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Ifeffit 1.2.2
by Matt Newville 25 Aug '03

25 Aug '03

Hi Everyone, I've just posted version 1.2.2 of Ifeffit. This is mostly a bug-fix release, and the core library has no new functionality. The major improvements are that 1) 'reff' now works well in all path parametr definitions and 2) feffit() fits in k-space correctly include the k-weighting. The build procedure from sources for linux and Mac OS X are also slightly better. More details on the changes to the core library are below. The windows installer includes the latest versions of athena, artemis, and sixpack, each of which has several improvements. Thanks to Bruce and Sam for getting this release together! Let me know if there are any questions or problems. Thanks, --Matt Changes from v. 1.2.1: bugs: - fixed error with k-space feffit() fitting so that k-weighting is now really used!! - fixed error with using reff in defined math expressions - increased size of math expressions to 256 operations/values. - changed restraint mechanism to work slightly better with multiple data sets - fixed error in read_data() that allowed core-dumps when reading files larger than the maximum array size. build improvements: - switched configure to use autoconf 2.53, including 'newer' automated searches for fortran libraries, setting default f77 compiler to g77, which should help builds on Mac OS X. - removed fortran subdirectory -- an existing, working fortran compiler is needed to build ifeffit. - fixed iconf_pgplot to check that PGPLOT directories listed in the PGPLOT make really exist (and are directories) before including them in the link arguments. - upgraded to readline 4.3 - upgraded python installation to use Pmw 1.1

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[Ifeffit] compiling feff with g77 on linux : Error opening file, s2_em.dat in module sigem
by jroux 21 Aug '03

21 Aug '03

I solved a small problem of portability of feff under linux/g77 for a friend. %< - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Error opening file, s2_em.dat in module sigem Fatal error STOP CHOPEN statement executed %< - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - g77 is usually compiled so that the maximum fortran unit number is 99. Unit numbers 111 112 and 113 are used in the feff code this is OK for some compilers but NOT pristine g77 and should be replaced by some lower numbers. I tried 91 92 93 and this fixes the problem. -- Jacques Roux, (jroux(a)cnrs-orleans.fr) CNRS-ISTO, 1A rue de la Férollerie 45071 Orléans cedex 2 tel: (33|0) 238 25 53 99

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Global parameters mapping with EXAFS
by Wojciech Gawelda 19 Aug '03

19 Aug '03

Hi, Recently I have come across some publications (Chance, et al., Biochemistry, 1996, 35, 9014-9023) where people have used global parameter mapping techniques with EXAFS in order to refine the obtained metal-ligand bond distances. If Im right the code they developed was called AUTOFIT 1.0. Does anyone of you know whether this code is freely available on the web? Or if not, does anyone of you know about similar codes which are being used in EXAFS analysis. Please let me know about this issue and help me to find out more about this approach. Have a nice day! Wojciech Gawelda ********************************************************************* Wojciech Gawelda Institut de Physique de la Matière Condensée Université de Lausanne IPMC-BSP CH-1015 Lausanne-Dorigny, SWITZERLAND Tel.: +41 (21) 692 3669 Fax.: +41 (21) 692 3635 E-mail: Wojciech.Gawelda(a)ipmc.unil.ch WWW: http://www.unil.ch/ipmc/docs/mc/wg/address.html *********************************************************************

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Re: Ifeffit Digest, Vol 6, Issue 6
by Grant Bunker 19 Aug '03

19 Aug '03

Scott - You could bridge the gap by using VirtualPC until an installer is constructed. That has the added benefit that you can also run windows xp or 2000 pro and PC linux (redhat, debian) simultaneously with OSX. It makes for a very flexible system, you can run almost anything, and furthermore the actions on the PC can be controlled by applescript on the mac side. On a fast mac with lots of memory, speed is adequate for most purposes, and the more you run it the faster it gets (instruction cache). I do these things my tibook and it works fine. A dual processor G5 should really work well. best wishes - grant bunker On Tue, 19 Aug 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Decision time... (SCalvin100(a)aol.com) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 18 Aug 2003 20:31:23 EDT > From: SCalvin100(a)aol.com > Subject: [Ifeffit] Decision time... > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <c5.370ac25e.2c72c9db(a)aol.com> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > > I'm very pleased to see all the activity on the list regarding an IFEFFIT > installer for OS X, and I appreciate very much the thought that has gone into > this issue. Unfortunately, decision time is upon me. I need to decide within a > day or two whether to go with Macs or PCs in my new faculty position. If someone > can tell me there will be some sort of installer (either requiring Fink or > not) by September 15, I'll go with Macs. If not, I'll have to go with PCs. > > --Scott Calvin > Sarah Lawrence College >

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Decision time...
by SCalvin100＠aol.com 18 Aug '03

18 Aug '03

Hi all, I'm very pleased to see all the activity on the list regarding an IFEFFIT installer for OS X, and I appreciate very much the thought that has gone into this issue. Unfortunately, decision time is upon me. I need to decide within a day or two whether to go with Macs or PCs in my new faculty position. If someone can tell me there will be some sort of installer (either requiring Fink or not) by September 15, I'll go with Macs. If not, I'll have to go with PCs. --Scott Calvin Sarah Lawrence College

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problem on MACOSX
by Stefano Ciurli 07 Aug '03

07 Aug '03

Dear all, when i try to compile the ifeffit program, the system does not find f2c_comp and I do not know how to install it using fink. Then, if i substitute f2c with f77, I get the following error message: How do I solve this? Regards Stefano Ciurli Making all in test gcc -g -O2 -o ifftest1 ifftest1.o ../lib/libifeffit.a -L/sw/lib/pgplot -L/sw/src/root-pgplot-5.2-5/sw/lib/pgplot -lpgplot -L/sw/lib -lpng -lz -L/usr/X11R6/lib -lX11 -framework Foundation -framework AppKit -lm ld: warning -L: directory name (/sw/src/root-pgplot-5.2-5/sw/lib/pgplot) does not exist ld: Undefined symbols: _main _do_lio _e_wsle _s_cmp _s_copy _s_stop _s_wsle _do_fio _e_rsfi _e_wsfi _i_indx _s_cat _s_rsfi _s_wsfi _e_wsfe _s_wsfe _G77_getenv_0 _f_inqu _e_rsfe _s_rsfe _z_exp _f_clos _f_open _e_rsle _s_rsle _z_sqrt _do_uio _e_rsue _s_rsue make[3]: *** [ifftest1] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive-am] Error 2 -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Via Fanin 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203

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