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

Re: [Ifeffit] Ifeffit 1.2.8
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you have Ifeffit 1.2.7 working on Tiger, I'd suggest just doing horae_update. The changes to the Ifeffit library are very small, so you could just wait until an installer for Mac OS X 10.4 is available. If you really want to be using 1.2.8, you could try installing from source. --Matt On 9/18/05, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > Hi Matt, > > >Ifeffit 1.2.8 is now available. There are minor changes to the core > >library and new versions of horae (055: athena 0.8.043, and artemis > >0.8.002) in the Windows and Mac installers. A few version notes are below, > >and I will be putting more information at > >http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ > > Thanks a lot! I am running OSX Tiger on a G4 and I am currently > working with Athena 0.8.039 and Artemis 0.7.015 > > What should I do ot update my environment to Ifeffit 1.2.8? > Thanks > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high". > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

3 2

RE: [Ifeffit] Fit in R and k space
by Frenkel, Anatoly 20 Sep '05

20 Sep '05

I personally like this argument in favor of r-space fitting over k-space fitting. I am pretty sure it was made by Ed Stern: R-space allows to think of EXAFS in terms of radial distribution of atomic positions relative to the central atom. Peaks in r-space usually correspond to atomic positions and the regions between the peaks - to the interstitial regions in the structure (of course, there are 1000 counter-examples, but we are talking about some 'average, well behaving' system where a peak is NOT an atomic AXAFS, nor it is caused by a Ramsauer-Townsend resonance, etc., and a valley is NOT a destructive interference between neighboring shells' - AF). We know, on another hand, that FEFF approximation electron charge density as spherical and the potential as muffin tin. This approximation is not as accurate in the interstitial region between the atoms (where potential profile in real systems may be anything but flat) as it is near the atoms. Thus, intuitively, FEFF should do better job fitting 'peaks' in r-space rather than fitting the interstitial. However, the r-factor and chi square do not really care. Technically, if two models give similar r-factors and chi-square, the one that has better fit in the peak region, the other - in the interstitial, one will examine the r-space fit and choose the one that fits peaks better over the one that fits interstititial region better. However, this information, localized in r-space, is distributed in k-space. Thus, if you look at the graph where data and fit are shown together, either in raw unfiltered k-space or in q-space, the misfit is difficult to interpret. It is, however, possible to interpret the misfit in r-space, and that what often helps to refine the model or choose the better one. Anatoly Anatoly Frenkel Department of Physics Yeshiva University -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Michel Schlegel Sent: Tuesday, September 20, 2005 9:07 AM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fit in R and k space Hello Bruce, >Although I prefer to think about the EXAFS problem in R space, I don't think >this is the reason to do the fit in R space. Regardless of which fitting >space you use, you are relying on Feff to supply some fraction of all the >Fourier components in the data. We could also used reference-derived phase and amplitude function, as in the good ol'time ;) > The first-shell feff path only has Fourier >components (or frequencies, if you prefer) corresponding to the first-shell >portion of chi(R). Thus that feff path can only fit those frequencies. >That's true in k-space as well as in R-space True in R-space, and that's why Athena-Ifeffit are doing such a wonderful job at providing windows to fit only selected area of the fourier transform. Almost true also in q-space. In k-space... hmmm, well, I would love to see the mathematical demonstration of it for a limited k-range and a Feff(k) (eventhoug I agree that many people have performed tha fit in k- and R-spaces, and found about the same paramters, so it must be verified somehow). >What's more, I think the problem of non-modelled shells affecting the >modelled >portion of the data exists in R-space just as much as in k-space. Because of >sigma^2 and the finite data range, peaks have width. In R-space, a given >path is centered at a particular R-value (or, in other words, its >contribution to the spectrum is dominated by a particular frequency). >However, the peak has width (it contains frequencies below and above the >dominant frequency). Thus longer paths always interfere with shorter paths >to some extent. I think the effect of interfering contributions in the Konigsberger and Prins. What I noticed, though, is that the fit of closer shells can affect that of the furthest shell because of the "spillof" from the first peak. The recciprocal I was not aware of. But I do agree with you on the whole. However, I think that in the FT case, these interences are limited to the nearest shells, whereas in k-space, nothing protects you from shells at, say, 2R and 3R (so to speak. Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DANS/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

2 1

Re: [Ifeffit] Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you've already done 'sudo horae_update' (and thanks for the correction!!) and have the latest versions of Athena and Artemis installed, I would say that you don't need to use the binary installer. The changes in the binary installer are tiny. --Matt

1 0

Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Everyone, Paul Fons has generously made a binary package installer for Ifeffit 1.2.8 for Mac 10.4 (Tiger). This is now available from both cars.uchicago.edu and sourceforge.net, from the Ifeffit download page: http://cars9.uchicago.edu/ifeffit/download.html If you try this out, please send positive and/or negative reports to me. Thanks again Paul!! --Matt

2 1

RE: [Ifeffit] R-factor
by Scott Calvin 20 Sep '05

20 Sep '05

Hi Alison, I agree entirely with Victor and Anatoly. In addition, I'd say that in my work an R-factor of above 0.1 is pretty sketchy. How sketchy depends on the complexity of the fit, of course; you're going over a big r-range, so if it takes you only two or three parameters to get an R-factor of 0.11, I guess that's not too bad. But if you have more parameters than that and it's still not fitting so well, I'd be concerned. As a referee, for example, that would be a much larger warning flag to me than the little discrepancy between the R-factors for the k- and q-space fits. Just to echo Victor and Anatoly again: it's quite easy for me to believe that the fitting algorithm just happened to find a somewhat different minimum in the fitting space in the two cases. They both suggested ways to test if that is the case. Although I've never fit in q-space, I've seen something that on the face of it is equally baffling: sometimes I've added an additional fitting parameter, changing nothing else, and seen the R-factor <italic>increase </italic>slightly. In some ideal sense, that shouldn't be--the fitting routine (this one happened to be Ifeffit) "should" at worst get the identical fit as to when the new parameter was constrained. But it is impossible to write a fitting routine that is guaranteed to find the closest possible fit, so all routines will occasionally generate those kinds of results. --Scott Calvin Sarah Lawrence College >-------------- Original message -------------- > >> Bruce, >> >> I've looked, and my R-factors for the back-transformed >> space are not necessarily twice the value of the R-factors >> for the k-space fits. In fact, they are often quite >> close. For example, just recently I had a k-space >> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I >> realize those numbers are very close, but I'm afraid if I >> try to publish this, then I will get criticism for the >> q-space R-factors being larger. If I can explain it, then >> maybe it won't be a problem. >

7 14

RE: [Ifeffit] Fit in R and k space
by Kelly, Shelly D. 20 Sep '05

20 Sep '05

Hi Michel, Michel wrote: Finally, another issue - for which I would not lay out my neck, though - is the noise. In EXAFS, the signal to noise increases with k, and of course fitting in the raw k space is another way of dealing conveniently with the noise -or relative uncertainty, as we may name it. However, the FT is a way of filtering out some of this noise, and so maximise the signal from a shell. Likewise, fitting in filtered q-space may yield more accurate results, because some of the noise is filtered out. However, I concur that somehow the fact that the uncertainty on the high-q part of the filtered contribution os greater than in the low q-part should be implemented somehow. It is true that the signal to noise ratio becomes smaller at high k values. It does seem magical that the Fourier transform can pull a signal out of the high k-range where the noise is large and that this signal seems to be well defined. I find it helpful to remember that each signal in the EXAFS chi(k) spectra is given by ONE frequency. That frequency is well defined at low k were the signal to noise ratio is large. Extending this frequency into the high k-region is trivial as long as that frequency co-exists with all the noise at high k. In fact I don't need data at all to extend a well defined frequency to infinity. The part of the signal that is not so well defined at high k is the amplitude. A lot of noise often masks itself by a large variation in amplitude for a given signal at high k, this effect will result in poor values for CN and 2. But the amplitude of the signal has a well known k-dependence so with enough low k information about the amplitude even the amplitude does not become affected by the noise at high k. The point to remember is that the signals are defined from k=0 to k=something bigger than zero. As long as the signal to noise ratio is reasonable from k=0 to some k~10? Then the signal including frequency and amplitude is well described all the way to k=infinity. It is often helpful to look at the fit and the data in k-space all the way out to 16 1/angstroms even if you are only using the k-range to 12 1/angstroms. If the model continues to follow the data to 16 then it is a good model. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

1 0

Ifeffit 1.2.8 installer for WinXP
by Leandro Langie Araujo 19 Sep '05

19 Sep '05

Greetings everybody, I'm another newcomer to the EXAFS world whose life was made much easier thanks to this wonderful software package. My sincere thanks to Matt, Bruce and everyone else involved in the "Ifeffit family" project. But, although the software is very nice, I'm having some trouble installing the newest version (1.2.8). I've been trying to install the Ifeffit 1.2.8 package on my WinXP, but there seems to be a problem with the files. I've downloaded the installers from both sourceforge and cars.uchicago.edu, but whenever I try to run any of them I get the following message: "The setup files are corrupted. Please obtain a new copy of the program." So, I'd like to ask if anyone from the mailing list managed to install Ifeffit 1.2.8 on WinXP or if anyone got the same kind of error message when trying to install. Thanks, Leandro

4 4

Ifeffit 1.2.8
by Matt Newville 18 Sep '05

18 Sep '05

Hi Folks, Ifeffit 1.2.8 is now available. There are minor changes to the core library and new versions of horae (055: athena 0.8.043, and artemis 0.8.002) in the Windows and Mac installers. A few version notes are below, and I will be putting more information at http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ == Windows == For Windows, there is a new installer, but no update. The new installer has the latest versions of the programs and also has dramatic changes to how the programs are organized and run. The batch files and the old automatic updater are gone, replaced by a single program 'runner' that checks for updates and runs all of the applications. There is also a completely new layout of C:\Program Files\Ifeffit. Bruce and I have been working on this for a while, and we believe it will be a lot easier for us to maintain. We expect that the changes will be mostly invisible to users, except when you install it. A result of the new layout is that *** *** *** you must uninstall any previous version of *** *** Ifeffit before installing the new version. *** *** *** Really, we're not kidding. There is a potential problem with this, as you may have your own projects under C:\Program Files\Ifeffit, say in \horae\ or in \examples\. You probably don't want to delete these!!! We recommend that you either move C:\Program Files\Ifeffit\horae and any other folders you may have file in to somewhere safe *before* you remove Ifeffit, or simply rename C:\Program Files\Ifeffit to Ifeffit_OLD and leave it there for a few weeks. And of course, we recommend that you save your data somewhere outside of C:\Program Files and make regular backups ("Gee, thanks, Mom!"). Then use the Control Panel 'add/remove programs' to remove Ifeffit. This will try to delete everything that originally got installed (and so *should* leave your data, but I wouldn't bet on it!!), including the shortcuts in the Start Menu. Once the C:\Program Files\Ifeffit folder is gone or cleaned out, you can then safely install the new Windows installer. The older Windows version (1.2.7) will see one more update, which will simply remind you to install the new version of the full installer. All further updates will be available only to the new version. == Mac OS X == For Mac OS X (10.3), the binary installer includes the codes from horae-055. The previous attempt to support Aquaterm is now dropped -- plotting is done with the X Windows plotting terminal. Since Athena/Artemis require X, and since X11 now comes from Apple, the Aquaterm support was more trouble than it was worth. == Unix == For Linux/Unix users using the source kit, the 'where is termcap?' problems should be gone. In addition, building on 64-bit linux machines should be much easier. PGPLOT_install now has a '--with-64bit' option which is needed for 64bit linux. Ifeffit's normal './configure' should then work fine. It now warns if the termcap library cannot be found. Let us know if there are any questions or troubles with these new versions. --Matt

2 1

Athena Bug in Peak Fitting
by Barton, David (DG) 16 Sep '05

16 Sep '05

Bruce, FYI: I recently installed Ifeffit v1.2.8 using the new Windows installer and it worked perfectly on a couple Win XP machines. After using the latest version of Athena 0.8.043 I noticed a bug in the Peak Fitting Routine and also have a couple of other minor suggestions. Description of Peak Fitting Bug: --The centroids that are reported on the screen and in the results file are not updating after a peak-fit is done. When the checkbox is marked to fit the centroid the fit appears to be changing the centroid because the resulting plot looks like a better fit, however the value of the centroid on the screen is not updating and the results file does not reflect any changes in centroid. Then if you push the "Plot Lineshapes" button it uses the centroid on the screen and the fit changes dramatically using the original value of the centroid. This bug can be reproduced by pulling up any spectra, setting the centroid of the arctan to something that results in a poor initial fit, check the box to fit centroid, run the fit....you should see that the fit moves the centroid however the value on the screen does not update and then if you "Plot Lineshapes" you will see the fit change to value of the original centroid. Other Suggestions for minor improvements to Athena: --In Compute Difference window it would be nice to have a checkbox that allows the user invert the difference (do spectra-ref instead of ref-spectra). This would be helpful for doing the difference of Marked spectra where we would like to do the spectra-ref. --in Compute Difference window it would be nice to have a checkbox to plot the components of the difference along with difference (similar to LCF window). Helpful for diagnostic checks of difference. --in your new Plot Style functionality it would be nice if Athena would automatically replot the last plot choice after a new Plot Style is chosen. This would save a few clicks as I click back and forth between two different plot ranges. --the link to the Plot Style POD documentation is broken. Let me know if you need any further clarification. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

2 1

Tip of the Week: Features of the Guess, Def, Set page in Artemis
by Bruce Ravel 16 Sep '05

16 Sep '05

Hi, This week's tip of the week is "Features of the Guess, Def, Set page in Artemis" http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

compiling Ifeffit and friends on a 64 bit linux machine
by Bruce Ravel 14 Sep '05

14 Sep '05

Hi, Some months ago -- see the thread that starts here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-December/001550.html Jake from U. Calgary posted a message about trouble getting Ifeffit et al to compile on his 64 bit machine. Over the last few days I have been upgrading to SUSE 9.3 on my home computer, which has an Intel 64 bit processor. (2 of them actually, lucky me!) 9.3 is much better for a 64 bit machine than 9.2 was. (It's also the first OpenSUSE release, which is a development I am very happy about.) Initially I ran into the exact same problem that Jake described in his original post. At the time, Carlo suggested that the -fPIC flag ("Position Independent Code", whatever that is) would be important. That turned out to be the trick. When installing Ifeffit, it was necessary to do the configure step like this: ./configure CC="cc -fPIC" FFLAGS="-g -O2 -fPIC" After that, the rest of installing Ifeffit and all of installing the horae tarball proceded normally. BUT, there is one other caveat. I had to make a small change to the pgplot makefile to get it compiled for my 64 bit machine. Everyplace in the makefile where it said "/usr/X11R6/lib", I had to change that to "/usr/X11R6/lib64". Compiling pgplot requires a bit of voodoo. I have always relied on Matt's PGPLOT_install script, which comes with the ifeffit tarball. In this case, I ran the script. It did some stuff, the failed. I cd-ed to /usr/local/pgplot, which is where it gets installed, and edited the makefile in that directory as I indicated in the last paragraph. Then in that directory I did a "make" and the pgplot compilation went to completion. Of course, I had to be root run the PGPLOT_install script and to do the compilation in /usr/local/pgplot. Hope that helps! (I'd be interested to hear how it goes with your opteron, should you try this, Carlo.) Bruce -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu 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://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

2 2

Bug report for Artemis 0.8.000
by schmithals＠hmi.de 12 Sep '05

12 Sep '05

Hello Bruce, After a break I just started to use Artemis again and I am delighted about the new features, especially the ability to store and compare subsequent fits in one file. Below I want to submit the bugs that I came accross so far (on Win2000): - If one opens by mistake an input file that is unknown to Artemis (or Athena) this file will be destroyed and cut to about 4kB. Workaround: Just DON'T do this (or keep regular backups). - Funny things happen when one studies an atoms/feff calculation without having loaded an experiment file: I imported an atoms.inp, ran atoms and feff and did two summations (Sum | All included paths ..). For the first summation I included only the first path, for the second summation only the second path. The first summation seems fine, for the second summation Artemis obviously includes both paths. In subsequent summations this effect will continue: all paths used in the past are considered plus the paths currently included. Workaround: Load a 'dummy'-chi file even for just making summations. I was teaching the use of Artemis to a few colleagues. I recommend them to keep a copy of their atoms.inp-files at a separate place for re-use in later projects. If time permits maybe you could account for these issues: - If saving an atoms.inp file via Theory | Write special output | atoms the name 'artemis.stuff' will be provided. Is it possible to change that to 'atoms.inp'? - The link to TKAtoms is missing for newly installed systems. Cheers, Gerrit Schmithals

2 1

new tip of the week
by Bruce Ravel 09 Sep '05

09 Sep '05

Hi! I just posted this week's Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This weeks topic: Easily marking arbitrary groups in Athena Enjoy, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu 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://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

Re: [Ifeffit] Re: ifeffit installation on Linux
by Matt Newville 09 Sep '05

09 Sep '05

Hi Peter, > Here's the output: > > src/cmdline/Makefile:TERMCAP_LIB = -ltermcap > src/cmdline/Makefile:# readline_LIB = -L$(top_srcdir)/readline > -lreadline $(TERMCAP_LIB) > src/cmdline/Makefile:readline_LIB = > $(top_srcdir)/readline/libreadline.a $(TERMCAP_LIB) > readline/Makefile:TERMCAP_LIB = -ltermcap > readline/Makefile: $(CC) $(CCFLAGS) -o $@ ./examples/rl.c > ../libreadline.a ${TERMCAP_LIB} > # locate termcap: > /usr/lib/libtermcap.so.2 > /usr/lib/libtermcap.so.2.0.8 > /usr/lib/termcap/libtermcap.a > /usr/lib/termcap/libtermcap.so > # locate curses: > /usr/lib/curses/libcurses.a > /usr/lib/curses/libcurses.so > /usr/lib/libcurses.so.1 > /usr/lib/libcurses.so.1.0.0 > Thanks for the report. That looks like the change to configure did what it was supposed to do: instead of having './lib/termcap/libtermcap.a', it now has '-ltermcap'. The odd things to me are that a) libtermcap.a seems to be in an odd location (/usr/lib/termcap), which makes me wonder how any readline applications work. b) you still end up with a './lib/termcap/libtermcap.a' somewhere in your Makefile, but *not* as TERMCAP_LIB=./lib/termcap/libtermcap.a I have no idea where that would be coming from. I don't think that an extra '-L./lib/termcap' is causing a problem (it's ok to have '-L' arguments that point nowhere) but that the linking can't find the right libtermcap.a with '-ltermcap' alone. If the Makefiles said TERMCAP_LIB= '-L/usr/lib/termcap -ltermcap' that would work for sure. I've been relying on a 'BASH_CHECK_LIB_TERMCAP' macro in autoconf, which apparantly doesn't know to look in /usr/lib/termcap. At this point, it may be easier to just write a function to look for the right termcap library. I think readline can use termcap, curses, or ncurses, and to be honest, I find the differences confusing. Anyway, thanks for the help! --Matt

1 0

ifeffit installation on Linux
by marco antoni alsina corvalan 08 Sep '05

08 Sep '05

Hi everyone, I'm currently making my way into Linux, so I decided to change most of my programs to this plattform, which obviously include ifeffit ;) I downloaded the ".tar" file, ran with success the PGPlot script for the graphics library installation (at least the demos run!!), and executed the "configure" script, getting the message "ready for the next step"...however I also get the following info: .... checking termcap.h usability... no checking termcap.h presence... no checking for termcap.h... no .... checking for tgetent... no checking for tgetent in -ltermcap... no .... Anyway then I executed the "run" command, getting the following error: .... cc: ./lib/termcap/libtermcap.a: No such file or directory make[3]: *** [ifeffit] Error 1 make[3]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src/cmdline' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/Programas/ifeffit-1.2.7' make: *** [all-recursive-am] Error 2 If anyone can help me overcoming this impasse I would be very greatful. Also if you need more info please let me know Regards, Marco ______________ Marco A. Alsina Estudiante de Magíster Departamento de Ingeniería Hidráulica y Ambiental Pontificia Universidad Católica de Chile Vicuña Mackenna 4860, Santiago, Chile (56 2) 3544873

5 14

Questions and answers
by Bruce Ravel 06 Sep '05

06 Sep '05

Good morning, Every week I receive a large amount of email regarding my software and XAS in general. I am sure that's no surprise to anyone reading this. While I certainly want to encourage people to feel free to contact me about XAS, the software, and any other topic, the time I have to address the needs and concerns of all the people contacting me is limited. In recent weeks I have received an unusual number of emails containing vague, ill-posed questions or requests for inordinate amounts of help. The other day I was frustrated by one such correspondent, so today I am indulging myself by ranting in a public forum ;-) Consider this message that I received the other day: > I have a sample with lead adsorbed onto manganese oxide and I have > its EXAFS. I want to study the Pb-Mn shell (including r(Pb-Mn) and > the number of Mn atom around Pb atom). How should I proceed? > > Awaiting your reply. Contrast that with an email I received from a user who had some questions along with a bug report regarding how e0 is determined by Athena: > I'm attaching an Athena project with a sample labeled Libethenite > and a Cu standard, along with an step by step explanation included > in the project journal. I trust the difference between these two is clear. I do not know either of these individuals except by their emails. Both are from places far away from Chicago. The first received a 5-line response while I spent two hours on a plane flight two weeks ago addressing the second one. I encourage people to contact me at any time with any question about XAS or my software. Indeed, if Athena and Artemis are useful data analysis tools today it is only because of the kind and generous feedback I have received from its users. But if a genie were to grant me a wish, it would be that more folks were like the second correspondent than the first. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu 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/

1 0

RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, >It makes me kind of sad to think that some of these neat-o features > are not widely used. If it makes you feel any better, I just used your linear combination module in Athena to fit 165 XANES spectra. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 4:10 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Wednesday 31 August 2005 17:22, Matt Newville wrote: > > Hi Folks, > > > > I've created and started a wiki for Ifeffit and related topics. > > Currently, this is at > > http://cars9.uchicago.edu/iffwiki > > I, for one, think the new Wiki is quite cool. Yet another > thing that we have to thank Matt for. > > My first use of the Wiki is to start a "Tip of the Week" web > page. Athena and Artemis have become sufficiently robust and > feature-full that there are a lot of interesting aspects of > the codes that are not widely known about or used. It makes > me kind of sad to think that some of these neat-o features > are not widely used. To keep a smile on my face, I've > decided to use the wiki to highlight some cool tidbit every > Friday afternoon. The first one is up at > > http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek > > Check it out. Feel free to send me suggestions for features > of A&A that you think would make a good Tip of the Week. My > plan is more or less to alternate between Athena and Artemis > and occassionally to throw in a Hephaestus tip as well. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > 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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

4 6

RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, > So would it be useful to have some more automation in the LCF > utility. Automation is always appreciated, not required, but much appreciated. The data set that I was fitting was indeed the result of multiple fast scans performed during an in-situ catalysis experiment, similar to what Anatoly is planning for NSLS. My biggest challenge with the current Athena code. 0.8.041 in fitting many XANES spectra was not having a single report where all fitting results could be exported to. I would imagine if you automated the fitting routine you would produce some report that lists all fitting results including fitting statistics in a single file. In addition, in the current fitting utility there was a few wasted clicks and edits because the fitting range kept reverting back to -15 to 45 eV... My fitting range was different than the default and every time I choose another data set to fit the fitting range reverted back to the default which meant I had to choose each box and make the appropriate changes for each new data set. Regardless of these issues, the LCF module is fantastic. I truly appreciate the ease of use, the ability to view the fit along with components of the fit, and the ability to plot the residual. Thanks for another useful tool to make my life easier. Regards, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 6:02 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Friday 02 September 2005 16:12, Barton, David (DG) wrote: > > >It makes me kind of sad to think that some of these neat-o > features > > >are not widely used. > > > > If it makes you feel any better, I just used your linear > combination > > module in Athena to fit 165 XANES spectra. > > Spectacularly so! Thanks for the big smiley at the end of the week. > > So would it be useful to have some more automation in the LCF > utility. What occured to me as I read this was to have a way > to fit a fixed set of standards to all the marked groups and > right a big report at the end. That is, play around with > spectrum #1 until you have decided which standards to use and > how to do the fit. Then mark spectra 2-165, press the > button, and go get a cup of coffee. That seems like a good > idea to me. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > 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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

new source code release
by Bruce Ravel 04 Sep '05

04 Sep '05

Hi folks, I have released the latest source code tarball for my codes. Tarball 054 is now available on my web site and at Source Forge. I am continuing Matt's experiment providing an Ifeffit Wiki by posting the change log on my wiki page: http://cars9.uchicago.edu/iffwiki/BruceRavel Scroll to bottom of the page (after smiling at the photo of me and my adorable niece) to find the page documenting the new features and bug fixes in this release. Matt and I are getting close to having a completely new Windows installer prepared. The new package has a more sensible file structure, a much improved launching tool for the programs, and new executables of my codes made with PerlApp. This version of my codes will be in the first release of the new Windows installer. Hopefully that will be ready soon. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu 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/

1 0

Ifeffit Wiki
by Matt Newville 02 Sep '05

02 Sep '05

Hi Folks, I've created and started a wiki for Ifeffit and related topics. Currently, this is at http://cars9.uchicago.edu/iffwiki At this point, this should be considered experimental. I'm still ambivalent about the whole thing, but we definitely need *something* to allow outside people to add content. Please feel free to play with this wiki, and let me know what you think. If this is something we decide we want to keep, I'll have this become part of the main set of Ifeffit and XAFS pages. I'd like to give it a trial run first, and hear some feedback. For those who aren't familar with wikis, these are set of web pages that are editable and expandable by users. There are all sorts of features for adding content -- too many to explain here. The basic idea is that you log onto the system, and edit the web pages using a web browser in a simplified structured text -- NOT directly editing HTML. Anyway, it's pretty easy to use, and there's plenty of documentation on how to use it. --Matt

2 1

compilation problem under MacOSX 10.4 - again
by Hugh Harris 02 Sep '05

02 Sep '05

Hi all, I'm new to the list and ifeffit. I've tried to get ifeffit 1.2.7 installed (for the first time) under tiger (on a system upgraded from panther) according to the instructions posted in the FAQ and the following modification on the list; > 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 I have Xcode installed, g77 via fink, and ran the ifeffit binary installer. Perl/Tk seemingly builds and installs ok but when I try to build horae 0.5.3 I get the following error; [harris:~/Desktop/horae-053] hugh% perl Makefile.PL === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is Mac OSX. Checking dependencies ... Dependencies ok. Cool! Reading configuration file: Ifeffit/lib/athena/athena.config Wrote Ifeffit/lib/athena/athenarc Ifeffit/lib/athena/athenarcw Ifeffit/lib/athena/athena.ini athena_parts/rc.pl Reading configuration file: Ifeffit/lib/artemis/artemis.config Wrote Ifeffit/lib/artemis/artemisrc Ifeffit/lib/artemis/artemisrcw Ifeffit/lib/artemis/artemis.ini diana_parts/rc.pl Assembled athena.pl from its parts (athena_parts/). Assembled artemis.pl from its parts (diana_parts/). Assembled hephaestus.pl from its parts (hephaestus_parts/). Fixing execution path in the Athena, Artemis, and Hephaestus executables... Changing athena.pl to /usr/bin/perl Changing artemis.pl to /usr/bin/perl Can't process diana.pl: No such file or directory Changing hephaestus.pl to /usr/bin/perl Changing ifeffit_shell.pl to /usr/bin/perl Changing horae_update to /usr/bin/perl Changing rdaj.pl to /usr/bin/perl Changing atoms.pl to /usr/bin/perl Ifeffit's installations directory is (found by capturing `ifeffit -i`) Could not open /config/Config.mak file for reading [harris:~/Desktop/horae-053] hugh% Trying to run athena from the xterm gives; Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/ perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level / System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread- multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/ 5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/ Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread- multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. Any ideas? Am I missing something obvious? Cheers, Hugh -- ------------------------------------------------------------------ Hugh Harris ASRP Postdoctoral Fellow School of Chemistry, Building F11 University of Sydney, NSW, 2006, Australia Office: +612-9351-2745 -------------------------------------------------------------------

2 2

Re: Fitting an Extended R-range
by Michel Jaouen 31 Aug '05

31 Aug '05

>Shelly wrote: > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. Hi Shelly, You can add to Scott's list the following entry: Mutiple-scattering EXAFS and EXELFS of titanium alloys T. Sikora, G. Hug, M. Jaouen, and J.J. Rehr, PRB 32, n°3, 1723 (2000) Best regards, M. Jaouen -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

1 0

RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hi Scott, Thank you for the help. Have a good one. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Monday, August 29, 2005 10:10 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Sorry, the first one should have been: > >"Estimating crystallite size in polydispersed samples using EXAFS," S. >Calvin, C. J. Riedel, E. E. Carpenter, S. A. Morrison, R. M. Stroud, & V. >G. Harris, Physica Scripta, T115, 744 (2005). >> --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hello Friends, I was hoping that you could help me put together a list of EXAFS papers that fit the R-space data out to at least 5 Angstroms. Thank you Shelly

4 4

RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hi Michel, Since I'm not getting a huge list of papers from anyone, I will take all that you think might be appropriate. SK -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Michel Schlegel Sent: Monday, August 29, 2005 2:24 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hello Shelly, >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. > >Thank you >Shelly Does comparison of fourier transforms count as well ? (or are you just interested in the accuracy/uncertainty on the fitting parameters?) Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0