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

new release of Athena
by Bruce Ravel 01 Oct '02

01 Oct '02

Hi folks, This morning I posted a new version of the source code package and a new windows executable for Athena on my web site. The changes in Athena include: 1. The ability to read a data file from a multi-element detector and have each channel be made into a separate group. This allows you to examine and discard individual channels before making a summation. 2. Added a simple log-ratio/phase-difference analysis. This can be accessed from the "Analysis" menu. It is currently undocumented, but if you already know how log-ratio works, it should be fairly clear what is going on. 3. Fixed (I think!) a bug in which reading in data and selecting the raw detector data type would crash the program on Windows. 4. Fixed a bug that made it impossible to save chi(q) data correctly. There are some outstanding problems with both the multi-element thing and the log-ratio thing. The most serious of these is one that effects a multi-element file with very many columns. It is quite possible for most of the columns not to be displayed in the column selection dialog. This will be fixed next time. I want to thank Dale Brewe and Oded Kleifeld for their useful bug reports. I also want to thank all of the participants and instructors of the recent EXAFS course at NSLS for putting Athena and Artemis through their paces. Several issues, mostly with Artemis, surfaced at the course and will get my serious attention this fall. *** For those of you receiving this who are not subscribed to the ifeffit mailing list, please consider subscribing. Go to http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/ and follow the instrctions. *** For those of you wanting to use the new Windows executable of Athena, grab it from the downloads page of my website (URL below in my .sig) and drop it on top of the old one in the C:\Program Files\Ifeffit folder. Please note that the installer has NOT been updated to include it. *** For those of you having strange problems on Windows 98, there are some links on my downloads page that may help you deal with certain inherent limitations of that charming operating system. 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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Re: Ifeffit digest, Vol 1 #60 - 1 msg
by Grant Bunker 30 Sep '02

30 Sep '02

Hi, Matt - you might also add that if the energy resolution is small enough (<3 eV say), differences in resolution don't affect the EXAFS, because the EXAFS oscillates much more slowly than the energy width, except perhaps right near the edge. Only in cases where the resolution (or core hole lifetime) is really large (>5 eV) will you see any noticeable effect, and the effect is smaller the farther above the edge that you go. The effect is always important for XANES though, and that can cause a slight change in the EXAFS analysis. If the resolution is large for one scan, and small for another, the detailed shape of the edge can be altered. If the edge position is judged by the first derivative maximum or some other metric of the edge shape, the nominal edge position could be shifted an eV or two. This isn't an issue as long as people don't overinterpret the edge positions, but it could confuse those who do. Similar things happen with thickness effects and particle size effects and self-absorption effects. It is of course straightforward to compensate for spectral the differences by convolution/deconvolution. thanks - grant On Mon, 30 Sep 2002 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-admin(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. experimental resolution (Matt Newville) > > --__--__-- > > Message: 1 > Date: Mon, 30 Sep 2002 10:09:06 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > To: Irina Pirog <pirog(a)ip.rsu.ru> > cc: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] experimental resolution > > Dear Irina, > > On Wed, 25 Sep 2002, Irina Pirog wrote: > > > > Dear Dr. M. Newville. I'm a researcher of X-Ray department at > > Physical Research institute of Rostov State university. In our > > laboratory we use UWXAFS code treating experimental data. I will be > > very gratitude to you, if you would answer me: how is experimental > > resolution is taken into account in UWXAFS. > > > > Sincerely yours > > > > Irina Pirog. > > This is an excellent question that I'm sure other people may have, so > I hope it's OK with you that I am responding to the Ifeffit mailing > list, which we've set up to share such questions about EXAFS and > Feff, Feffit, Ifeffit, etc. > > By itself, the UWXAFS programs (atoms, autobk, and feffit) don't know > what the experimental resolution is. In principle, the experimental > resolution is important only to the extent that it is different > between two measurements or between a measurement and a theoretical > calculation. For the UWXAFS programs, the only place this becomes > important is when comparing Feff calculations to data in feffit. > > Generally speaking, Feff includes terms that effect the resolution > and all other loss terms in the mean-free-path, lambda. Feff > includes contributions from the core-hole lifetime and some many-body > electron loss terms in lambda, but it does not explicitly put in an > experimental resolution. But Feff usually has a little too much loss > (ie, lambda is a little smaller than it should be), which turns out > to be fine for experiments , with a resolution of ~1eV or so. > > But sometimes you know what the experimental resolution is and > want to include it in the analysis. To account for that, > Feffit has an energy-broadening Path Parameter, ei, that gives > an additional broadening term in the EXAFS equation through > p^2 = (k_real + i/lambda)^2 + ei * 2m / hbar^2 > > where k_real and lambda are taken from the feff0001.dat file for > each path (though they are the same for any one Feff calculation), > and then, the k and lambda terms used in the EXAFS equation are: > k = Re[sqrt(p)] > lambda = 1/Im[sqrt(p)] > > To use this, you would have a feffit.inp with something like this: > > Path 1 feff0001.dat > id 1 path 1 > s02 1 amp_factor > ei 1 1.0 # add 1 eV broadening to Feff calc. > ... > > I mention the s02 parameter here because ei will be very highly > correlated with s02 (and sigma2). In fact, I'd guess that much of > the variation in the observed s02 parameter for different > measurements is actually due to differences in energy resolution. > > > Finally, you may be interested in using the greatly revised versions > of the UWXAFS programs, including graphical user interfaces for data > processing and fitting: > http://cars.uchicago.edu/ifeffit > > Ifeffit also uses a Path Parameter called ei with the same effect, > though the syntax would be slightly different: > > path(1, file=feff0001.dat, s02=amp_factor, ei= 1.) > > Anyway, I hope that answers the question, > > --Matt > > |= Matthew Newville mailto:newville@cars.uchicago.edu > |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 > |= Argonne Natl Lab fax: (630) 252-0436 > |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ > |= Argonne, IL 60439 USA > > > > > --__--__-- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest >

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experimental resolution
by Matt Newville 30 Sep '02

30 Sep '02

Dear Irina, On Wed, 25 Sep 2002, Irina Pirog wrote: > > Dear Dr. M. Newville. I'm a researcher of X-Ray department at > Physical Research institute of Rostov State university. In our > laboratory we use UWXAFS code treating experimental data. I will be > very gratitude to you, if you would answer me: how is experimental > resolution is taken into account in UWXAFS. > > Sincerely yours > > Irina Pirog. This is an excellent question that I'm sure other people may have, so I hope it's OK with you that I am responding to the Ifeffit mailing list, which we've set up to share such questions about EXAFS and Feff, Feffit, Ifeffit, etc. By itself, the UWXAFS programs (atoms, autobk, and feffit) don't know what the experimental resolution is. In principle, the experimental resolution is important only to the extent that it is different between two measurements or between a measurement and a theoretical calculation. For the UWXAFS programs, the only place this becomes important is when comparing Feff calculations to data in feffit. Generally speaking, Feff includes terms that effect the resolution and all other loss terms in the mean-free-path, lambda. Feff includes contributions from the core-hole lifetime and some many-body electron loss terms in lambda, but it does not explicitly put in an experimental resolution. But Feff usually has a little too much loss (ie, lambda is a little smaller than it should be), which turns out to be fine for experiments , with a resolution of ~1eV or so. But sometimes you know what the experimental resolution is and want to include it in the analysis. To account for that, Feffit has an energy-broadening Path Parameter, ei, that gives an additional broadening term in the EXAFS equation through p^2 = (k_real + i/lambda)^2 + ei * 2m / hbar^2 where k_real and lambda are taken from the feff0001.dat file for each path (though they are the same for any one Feff calculation), and then, the k and lambda terms used in the EXAFS equation are: k = Re[sqrt(p)] lambda = 1/Im[sqrt(p)] To use this, you would have a feffit.inp with something like this: Path 1 feff0001.dat id 1 path 1 s02 1 amp_factor ei 1 1.0 # add 1 eV broadening to Feff calc. ... I mention the s02 parameter here because ei will be very highly correlated with s02 (and sigma2). In fact, I'd guess that much of the variation in the observed s02 parameter for different measurements is actually due to differences in energy resolution. Finally, you may be interested in using the greatly revised versions of the UWXAFS programs, including graphical user interfaces for data processing and fitting: http://cars.uchicago.edu/ifeffit Ifeffit also uses a Path Parameter called ei with the same effect, though the syntax would be slightly different: path(1, file=feff0001.dat, s02=amp_factor, ei= 1.) Anyway, I hope that answers the question, --Matt |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0436 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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Fixed a major bug in Athena
by Bruce Ravel 20 Sep '02

20 Sep '02

Well, it took a mere two days for someone to find a serious bug in my "great" new release of Athena. Sigh.... ;-) In 0.8.000, there is a serious bug associated with deleting data groups ("Delete group" or "Delete marked groups" in the "Group" menu). The bug makes it impossible to select one or more of the remaining groups. The unselectable groups are below the group that was deleted, unless you have rearranged the list with Alt-u and Alt-d, in which case the unselectable groups will be hard to predict. I posted a source tarball (horae-002.tar.gz) and a new athena.exe for you Windows users. I strongly encourage upgrading if you installed the release from earlier this week. For those of you Windows users who are new to the ifeffit world, when I update my codes I usually post updated windows executables on my web site. Usually I do NOT rebuild the entire Windows installer. The way to use the updated executable is to download the .exe file from the Windows section of http://feff.phys.washington.edu/~ravel/software/exafs/download.html and replace the .exe file in C:\Program Files\Ifeffit (or where ever you actually installed Ifeffit on your computer) with the new one. Many thanks to Adam Webb for pointing out the problem and for *not* waiting until next week to tell me about it! 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 1.0074, new windows installer
by Matt Newville 18 Sep '02

18 Sep '02

Hi Everyone, As Bruce promised, there's a new windows installer for Ifeffit available that includes his latest versions of athena and artemis. There are also some fixes to ifeffit for phase-corrected FTs, and to both ifeffit and Feffit for semi-related bugs in which values from the debye() and eins() functions not always being updated, especially in 'no fit' mode. Ifeffit is now at version 1.0074. The standalone source code for the Feffit program has also been fixed, and is now at version 2.98. Hopefully, we'll get some Mac updates of these fairly soon. Let me know if there are any questions or problems, --Matt

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new releases of Athena and Artemis
by Bruce Ravel 18 Sep '02

18 Sep '02

Hi folks, Today I posted new source tarballs of Athena and Artemis on my web site. A new Windows installer will be available later today from Matt's web site. This time there are some big changes. 1. I am now distributing Athena and Artemis in a single source tarball called `horae-001.tar.gz'. http://homepage.mac.com/cparada/GML/HORAE.html 2. Windows users should download and install the new installer package because there are several new library and example files. I will continue the practice of posting replacement executables when I _next_ update Athena and Artemis. 3. I have started numbering Athena and Artemis differently. Both programs are getting within striking distance of becoming the magical 1.0. Because of that and other reasons, I want to start using actual version numbers rather than dates to identify the versions. Athena is starting at 0.8 and Artemis at 0.5. The version number on the source tarball will simply be an incremented counter unrelated to the version numbers of the programs. 4. I have made a very large number of changes to Artemis. I'll refer you to the change logs for all the details. In addition to many, many squished bugs, the most important change is that reading in feffNNNN.dat files now works in a much more sensible manner. You can read in individual feffNNNN.dat files or read in all at once by selecting the feff.inp file. In either case, the feffNNNN.dat files should be grouped in a sensible manner in the list in the skinny part of the window. 5. The other big new feature in Artemis is templates. This is a scheme I am working on to help automate the creation of fitting models. The idea is that after reading in data and a feff calculation, you can select, for example, "FirstShell" from the Templates menu. Artemis reads an external file which described a prototypical first shell fit and generates guess, set, and path parameters that hopefully are close to an appropriate fitting model. For copper data, you can hit the big green fit button right after reading in the template file and get a reasonable fit. Some tweaking is usually necessary, but the templates are a decent start. 6. The most interesting change to Athena is that you can now save your data as a "chi(k) record". This is a special file that has the same structure as a normal Athena project file, but which contains only a single entry. That entry is saved as chi(k) rather than as mu(E). The purpose of this kind of file is for reading into Artemis. The advantage of a chi(k) record over chi(k) column data is that the values for things like the Fourier transform parameters that you chose in Athena will be set in Artemis. As always, let me know about problems and feature requests, Enjoy, Bruce -- 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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athena and artemis on Mac OS X 10.2
by Dr. Paul Fons 06 Sep '02

06 Sep '02

I have successfully installed the latest tarballs for athena and artemis on Mac OS 10.2 (Jaguar) and thought I would share with the list the necessary steps to do the installation. 0. Install 10.2 and the latest development tools (included with 10.2) 1. install the latest patch for xterm from the sourceforge site: ceforge.net/projects/xonx/ and install Xfree86 4.2.0.1 2. rebuild the readline libraries within fink after updating from cvs (I use the fink unstable branch) 3. recompile Tk after making the following modification: in Tk/MMutil.pm replace the subroutine const_config with the following code: sub const_config { my $self = shift; my $name; foreach $name (grep /(%|\.(old|bak|q4|orig|rej))$/,keys %{$self->{PM}}) { delete $self->{PM}->{$name}; } my $flags = $self->{'CCCDLFLAGS'}; $flags =~ s/(-[fK]?\s*)pic\b/${1}PIC/; $self->{'CCCDLFLAGS'} = $flags; if ($^O eq 'MSWin32' && $Config{'ccflags'} =~ /-DPERL_OBJECT/) { $self->{'LDFLAGS'} =~ s/-(debug|pdb:\w+)\s+//g; $self->{'LDDLFLAGS'} =~ s/-(debug|pdb:\w+)\s+//g; } elsif ($^O eq 'darwin' ) { $self->{'LDDLFLAGS'} =~ s/-flat_namespace\s+//; $self->{'LDDLFLAGS'} =~ s/-undefined\s+suppress\s+//; if ( -e "$Config{'archlib'}/CORE/$Config{'libperl'}" ) { $self->{'LDDLFLAGS'} .= " -L\${PERL_ARCHLIB}/CORE -lperl "; } elsif ( -e "/System/Library/Perl/darwin/CORE/libperl.dylib" ) { $self->{'LDDLFLAGS'} .= " -L/System/Library/Perl/darwin/CORE -lperl "; } else { warn "Can't find libperl.dylib"; } $self->{'LDFLAGS'} =~ s/-flat_namespace\s+//; $self->{'LDFLAGS'} =~ s/-undefined\s+suppress\s+//; } elsif ($^O =~ /(openbsd)/i) { # -Bforcearchive is bad news for Tk - we don't want all of libpTk.a in all .s o-s. $self->{'LDDLFLAGS'} =~ s/-Bforcearchive\s*//g; } return $self->MM::const_config; } The only thing that is different is a new conditional block in a if block, but I thought it would be easier just to copy and paste. This hack was taken from Bug's Macintosh Page at http://www.lehigh.edu/~sol0/Macintosh/X/ptk/. It turns out it is no longer necessary to hack the dynamic library loader dylib. After changing the subroutine const_config in MMutil.pm, mumble the usual incantations: perl Makefile.PL make make test sudo make install 4. rebuild the ifeffit source cd ifeffit/src/macosx make clean make sudo make install cd ../../wrappers/perl perl Makefiile.PL make sudo make install cd ../python sudo python setup.py install 5. Rebuild athena and artemis cd athena perl Makefile.PL make sudo make install cd artemis perl Makefile.PL make sudo make install You are done! Caveats: I (being perverse) have not done the installation exactly this way. I have compiled xfree86 4.2.99.1 from the online cvs sources and have in addition installed perl 5.8.0. This is a little more complicated (but not much). I also found that ifeffit was looking for a library libg2c.a and made a symbolic link from /usr/lib/gcc/darwin/2.95.2/libg2c.a to /usr/local/lib so that the ifeffit compilation could proceed normally. I am not sure if this step is necessary for all. I don't think perl 5.8.0 and the newest build of Xfree86 are necessary (but on the other hand that is all I have and can't check the alternatives). The version of perl installed by 10.2 is still 5.6. Any questions? Send me email if you have problems and I will help if I can. Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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athena and artemis updates
by Bruce Ravel 26 Aug '02

26 Aug '02

Hi Folks, I have just posted new source tarballs and windows executables for both athena and artemis. Both packages have significant new features and bug fixes. Please read the two special notes at the end of this announcement regarding a couple of bugs that I know about. I will be on vacation the rest of this week -- so I don't want anyone finding new bugs until next week! Athena: 1. fixed a problem that prevented one from plotting a chi(k) record (such as from feff's chi.dat file) 2. fixed a problem in which unmatched parentheses in the header of a data file would seemingly cause Athena to hang. Please note, that this was fixed by having Athena append the necessary close parens to title lines with unmatched open parens (i.e. by having Athena alter some title lines!) 3. Several usability improvements, including ability to specify a data or project file from the command line, remembering preprocessing parameters between files, and remembering the name of an input project file and using it as the default for saving a project file. 4. When records are saved as mu(E) or norm(E) column data, the e0 shift is applied before saving 5. project files now identify the operating system, perl version, and ifeffit version used to create the file. This makes project files more useful to me when submitting them with bug reports. (This was done without affecting compatibility in either direction.) (This is also a new feature in Artemis.) 6. several minor bug fixes Artemis: 1. The big box on the feff page is now filled with a schematic interpretation of the feff calculation. SS and colinear MS paths are highlighted and right-mouse clicking over a path description pops up a useful menu http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… 2. Began work on a templating system. This means that you can read in some data and a feff calculation, then select, say, the "FirstShell" template and Artemis will fill in guess, set, and path parameters with a model that should run to completion and may even be a decent stab at the fit you want to do. Note that the "Templates" menu does nothing on Windows at this time. Although this is undocumented, you can poke at it to see how it works. 3. Changed the color of the "fit" and "ff2chi" buttons. (See the screenshot mentioned above) 4. Several bug fixes and minor usability improvements. For complete details see the change logs in the tarballs or at http://leonardo.phys.washington.edu/~ravel/software/exafs/notes/ OSX users: It is the intended behavior of Athena and Artemis to remember the path whenever you use a file dialog and to use that path as the default the next time you use a file dialog. I am told that Athena does not behave this way on OSX. I am aware of the problem, but have not yet worked to fix it. All users: On your computer, there are probably a few seconds between the outline of Athena or Artemis window appearing on your screen and having all the features of the window be completely rendered. In that time, it is tempting to "jump the gun" and hit control-f so that the file dialog will appear just as soon as perl/Tk finishes rendering all the widgets. Doing this cause a minor race condition that will impede Athena's ability to monitor how much memory you are using and cause many scary-looking messages to be written to standard output. I haven't figured out how to prevent one from doing this, so my advice for the moment is to be patient and let the program finish rendering before using keyboard shortcuts. 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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athena and artemis under Mac OS X 10.2
by Dr. Paul Fons 26 Aug '02

26 Aug '02

I have successfully installed 10.2 on my Mac and found that, after a recompile readline is just fine. The only problem I am having is with Tk which is broken due to trouble with the new dynamic linker library. The author of the last hacked dyld loader Stephen.O.Lidie(a)lehigh.edu is working on a new version of dyld as we speak (write). It should be done tomorrow (hopefully) he says. What I wanted to add here is to warn people *not* to use to old hacked version of dyld on the new 10.2 as it will almost certainly break the system (e.g. every command as well as the OS uses the dynamic library loader). I will let the list know when things are working. For the moment I have my pismo laptop running 10.1.5 until I get this sorted out on my dual 500 MHz G4 desktop. Mac OS X 10.2 does seem nice and fast! Paul

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Warning: ifeffit users on Mac OS X
by Jeff Terry 24 Aug '02

24 Aug '02

Hello, If you are dependent upon ifeffit under OS X, DO NOT install the 10.2 upgrade. This upgrade breaks the readline library which is needed by ifeffit. A quick web search showed this to be a known problem with no current solution. Readline does not currently compile under 10.2. I tried a cursory effort compilation which resulted in many missing symbols. Jeff

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