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

[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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Re: [Ifeffit] What differences are there between Athena and AUTOBK backgrounds?
by SCalvin100＠aol.com 06 Aug '03

06 Aug '03

Thanks, Matt. I hadn't realized I wasn't using the most recent version of AUTOBK. Of course, now I'll be using IFEFFIT (via Athena), so it doesn't matter... --Scott

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[Ifeffit] What differences are there between Athena and AUTOBK backgrounds?
by Scott Calvin 05 Aug '03

05 Aug '03

Hi all, Today I tried making Athena perform exactly the same background subtraction as AUTOBK 2.61 (all parameters the same, working on the same data, using the same theoretical standard, etc.). I then let FEFFIT take the chi(k) data for each and perform a Fourier transform. When I did this, AUTOBK would always generate a very low r (< 0.2 angstroms) peak of significant amplitude that was nearly absent in the Athena background. There were other subtle differences as well, but that one stood out. Of course, a peak that low in r should have no effect on the fit, but it made me curious--were substantive changes in the background subtraction algorithm made when AUTOBK was incorporated into IFEFFIT? --Scott Calvin Sarah Lawrence College

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Phase Correction using IFEFFIT
by Ian Drake 04 Aug '03

04 Aug '03

Hi Matt and XAFS community I am interested in the details of how IFEFFIT handles phase correction. I asked a similar question in April, but have only now begun to address its use in my work. In your response to my April question, you described how to do a central atom phase shift (without a FEFF path) and a combined central-atom and scattering-atom phase-shift (using a particular FEFF path). In the case of the combined central-atom/scattering-atom phase-shift, is the Chi(k) multiplied by exp(i*Phase(Central-atom)) and exp(i*Phase(scatterer)) before FFT? If this is true, how can I correct for the scattering atom phase shift "only" as has been described by Lee and Beni (Phys. Rev.B, 15, 1977, pg 2862) and Vaarkamp (Cat. Today, 39, (1998), pg 271). At this time, my particular interest is in attempting to identify clearly next-nearest neighbors in the RSF before attempting to do fitting. It is my hope that a positive identification of the next-nearest neighbor by means of IM analysis/ and or k-weighting will add validity to my final fitting results. Thank you for your help, Ian Drake

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phase corrections
by Grant Bunker 04 Aug '03

04 Aug '03

Following Bruce's commentary - it is indeed true that if you have sufficiently heavy backscatterer (think Au or Pt, or even Ag/Pd) the modulations in the backscattering phase and amplitude will mess up your transform peaks, as Ian suggests. Basically you get "sideband modulation" of your transform peaks. To get rid of them you need to not only do a phase correction, but also an amplitude correction (divide out the wiggles). I thinkd oing one without the other doesn't actually make a lot of sense since they are related (because the real and imaginary parts are related by kramers-kronig relation the phase and amplitude are connected). Obviously this is not very difficult to do - I put it into the VAX version of the UW programs in 1985 but that was dropped from the simplified UW/NRL version later. Short term, it would be very easy to do by exporting from ifeffit and using any data massaging program that knows complex numbers. thanks - grant On Mon, 4 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. Re: Phase Correction using IFEFFIT (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Aug 2003 09:56:14 -0400 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: Re: [Ifeffit] Phase Correction using IFEFFIT > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200308040956.14156.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="iso-8859-1" > > On Saturday 02 August 2003 04:32 pm, Ian Drake wrote: > > At this time, my particular interest is in attempting to identify clearly > > next-nearest neighbors in the RSF before attempting to do fitting. It is > > my hope that a positive identification of the next-nearest neighbor by > > means of IM analysis/ and or k-weighting will add validity to my final > > fitting results. > > Well... I don't know what an "RSF" is or what "IM analysis" is, but I > think I can suggest a way to isolate the scattering atom phase shift > in a way that requires only a small amount of work and can be used > with either ifeffit or artemis as they exist today. > > The second column of the feffNNNN.dat file is the central atom phase > shift. The third and fourth are the scattering atoms magnitude and > phase. Copy your feffNNNN.dat file of interest to another name, say > feff_next_neighbor_no_caps.dat. Edit the new file, replacing the > second column with zeros. Read this into ifeffit or artemis and use > it as the path for phase correction. In artemis, this is done in the > data view using the pull down menu labeled "Path to use for phase > correction". Obviously, you should choose your edited path. In > artemis, you may need to set the amplitude for this path to zero so > that it doesn't really get used in a fit. > > That said, it's not clear to me how phase correction will really do > what you seem to want. It seem unlikely to me that the signal beyond > the first shell will magically become clear simply by doing phase > correction. If the signal is a superposition of various scatterers > before phase correction, it will still be a superposition of various > scatterers afterwards. Removing the scattering atom phase shift does > not affect the terms in the EXAFS equation that make peaks in a > Fourier transform broad, nor does it magically separate signals which > contribute similar Fourier components. Understanding how various > paths contribute similar Fourier components is the reason that Artemis > allows you to easily overplot data with the Fourier transforms of > various paths. Then you can inspect the contributions from each path > before setting up your fitting model. But if playing tricks with > phase correction helps *you*, then great! That is why Artemis allows > you to do this. > > 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/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 6, Issue 2 > ************************************* >

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IFEFFIT and PGPLOT on linux
by Kelly, Shelly D. 31 Jul '03

31 Jul '03

Hi Matt, Yesterday, I installed PGPLOT and IFEFFIT from the tar ball on your web page on a clean (no previous installation of any of the XAFS software) Red Hat linux box. I used your script to install PGPLOT and was pleased that it worked just as expected. I had one small issue. When I tried to 'make' IFEFFIT, I got an error message saying that there was nothing for make to do. I realized that the configure step for IFEFFIT was writing out a Makefile but that the current directory had both a makefile and a Makefile. One makefile with a lowercase m and the other with a capital case M. So I removed the makefile and then IFEFFIT installed properly. Then I used the Horae script to install Ravel-ware, without any trouble. Overall the installation went really well...Good going. Shelly Kelly

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