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

Re: Amplitude and the EXAFS equation
by Scott Calvin 30 Oct '02

30 Oct '02

Hi all, I thought I'd add my two cents: I agree with everything Bruce said (!), but I think it is worth emphasizing one aspect of this issue. Basically, unless I'm using a mutiple-element fit with some clever constraints (not yet available in Artemis, but soon, I gather), any determination of coordination number is likely to be pretty uncertain. Not only does N correlate completely with S02 for a single shell fit, it is also likely to correlate strongly with sigma2 (or the Debye or Einstein temperature or whatever I'm using as the free parameter). Multiple-shell fits help when I can use them, but if I don't know the coordination number for the first shell, how likely is it that I know the structure of the material well enough to fit outer shells? Although you may see coordination numbers determined by EXAFS with an "uncertainty" of 1 in publications, this is usually something like the uncertainty reported in IFEFFIT--it probabIy doesn't include systematic errors like the effect of assumptions concerning the Debye-Waller factor or S02. In most cases if I'm looking for a first shell coordination number via EXAFS I'm not counting on better than a factor of two accuracy. That may still be useful in some cases, but doesn't help distinguish between, say, tetrahedral and octahedral coordination. So, if I'm only looking for a factor of 2, and if I'm pretty sure my sample is homogenous and of a consistent and appropriate thickness, I'm happy to just constrain S02 to 0.90 or 0.85 or whatever, knowing that the arbitrary choice of S02 is probably introducing an uncertainty of less than 20% in the coordination number. Since this is still considerably less than I generally believe is introduced by other issues (such as the scheme used for the Debye-Waller factors), it's good enough for me. --Scott Calvin Naval Research Lab --

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Amplitude and the EXAFS equation
by Bruce Ravel 29 Oct '02

29 Oct '02

Hi folks, Today I received one of the top-ten most asked questions. I am going to take a stab at answering it here in an archived forum. I am sort of hoping to get a discussion going and get several people's viewpoints. An Artemis user observed in her email that, in the EXAFS literature, people often publish values for coordination number. She asked how one obtains that using Artemis/Ifeffit. If only there were an easy answer to this question! It turns out that, in the EXAFS equation, there are two terms that directly affect the amplitude. One is N, the coordination number (or one might say "the path degeneracy"), and the other is S02, the so-called passive electron reduction factor. S02 is, according to popular wisdom, chemically transferable. This means that if you somehow have determined S02 for a given central atom in one compound, you can use this value for some other compound. While this may be true, particularly if a standard and a sample are measured back-to-back under identical experimental conditions, it is not a safe course of action. The problem is that lots of empirical effects can also change the measured amplitude. These may include things like detector response, sample inhomogeneity, and those annoying gremlins that sneak into the hutch when you're not looking. Assuming, though,that you know S02 and you are confident that empirical problems are a small factor, then the "S02" path parameter can often be interpreted simply as the coordination. If, however, you are not confident of S02 or of the smallness of the empirical effects, the situation is somewhat more complicated. A common assumption is that you should be able to determine S02 *and* coordination simultaneously from data. This is, at best, extremely difficult to do with statistical significance and, at worst, flatly impossible. If you are fitting only one shell of data, then it is certainly impossible. Why do I say that? Well, consider how coordination (N) and S02 enter the EXAFS equation: N * S02 * F(k) chi(k) = ------------------ sin( 2kR + delta(k) ) exp(-2ksigma^2) 2kR This is the generic formula. In Feff, Ifeffit, and Artemis, this is the the expression for chi(k) for a particular path. The data chi(k) is fit by evaluating this equation for one or more paths then summing them up. In that equation, note that N and S02 are both multiplicative factors. If your fit considers only one path, then N and S02 have *exactly the same effect* on the equation. They cannot be measured independently. In the absence of knowledge about either N or S02, the only thing you can do is measure the product (N*S02). How does one then report on coordination in a journal article? You have to somehow interpret the product (N*S02) and determine how much of that is N and how much is S02. There is no generic answer to how that is done -- it depends on the details of the sample and the experiment. To return to last week's silly posts about training monkeys -- it is yet another reason why data analysis requires a thinking human being. If you are fitting many shells or many data sets (the latter is something that Artemis does not yet allow you to do -- it's coming soon!), then you may have enough information in your data to uncouple the correlation between N and S02 and somehow fit them independently. Again, there is no generic way of doing so -- each situation is different. It is common to do as I suggested above and determine S02 from a well known standard that was measured at the same time as your sample. If there are no significant empirical effects in the sample that do not exist in the standard, then the value of S02 is probably useful for your unknown sample. Armed with that, it is much easier to then determine coordination. The discussion up to now has been conceptual. How are the amplitude terms handled in Artemis. Well, start by taking a look at a screenshot of the path page from a recent version of Artemis: http://feff.phys.washington.edu/~ravel/software/exafs/images/artemis/artemi… Note that there is an entry box labeled "N" and another labeled "S02". The one labeled "N is filled with the path degeneracy when the feffNNNN.dat file is imported. The one labeled S02 is intended to be filled with a math expression used to describe all remaining terms that may effect the amplitude. In the example shown, I have left N equal to the value from the feffNNNN.dat file and set S02 to a very simple math expression. The variable "amp" is being floated in this fit to copper foil data and used to evaluate the S02 term in the EXAFS equation for each path. In this case I am using knowledge of the system to uncouple N and S02. This is a copper foil, thus I am confident that the coordination is as expected from crystallography. I am also confident that the empirical effects are negligible. Whatever value amp ends up being, I will interpret that as S02. Now suppose I want to measure a nano-particulate copper oxide. In such a system, I may expect coordination to be reduced relative to the bulk oxide. For that, I may do the following: 1. Run feff using the crystal structure of bulk copper oxide. This will give me a copper/oxygen path to use to fit the first shell of my nanoparticle. 2. Read that feff path into Artemis along with my data 3. Set amp to the value determine from the copper foil (this is done by selecting "set" rather than "guess" from the appropriate optionmenu on the "Guess, Def and Set" page in Artemis. 4. For the first shell path, set N to 1 (rather than what ever value it was in the feffNNNN.dat file) 5. Set S02 for the first path to this math expression: n_first * amp 6. On the "Guess, Def and Set" page, define n_first as a guess parameter and choose a sensible starting value. The N and S02 part of the screenshot above will then look something like this: ___ ___________________________________ N |_1_| * S02 |_ n_first * amp ___________________| Here I have fixed amp to represent the known value of S02, I have set the N term in the EXAFS equation to be 1, and I have made a math expression, "n_first * amp", that will be evaluated and used for the S02 term in the EXAFS equation. n_first will be adjusted in the course of the fit and can be directly interpreted as a coordination number. Is this the only way of dealing with coordination? Certainly not. Is this the "official" way of measuring coordination? No. There isn't one. Every situation is different. Should you apply this example to every one of your analysis problems? No way! Did this example help you understand how N and S02 are used in Artemis and Ifeffit? I hope so. May this example be applicable to some analysis problem you run into at some point in your career? Quite possibly. Do you need to think hard about every analysis problem and figure out the best way to deal with the problem of N and S02 being coupled parameters? Absolutely! Hope that helps, 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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detaching plot buttons in Athena on Windows
by Bruce Ravel 25 Oct '02

25 Oct '02

Hmmm.... the situation with the detaching plot buttons is actually worse than I thought when I wrote my last (and somewhat sarcastic) message. It turns out that the mechanism I used to handle the detaching and reattaching of the plot buttons will not work on Windows. It seems to be one of the very few things in perl/Tk that does not port from Unix to Windows. Unless I can find a better way, in the next release I will remove this option from the Plot menu on Windows. For now, just don't use it. Thanks for the report, Raul. It's appreciated, as always. 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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detaching plot buttons in Athena on Windows
by Bruce Ravel 25 Oct '02

25 Oct '02

Raul said: RB> I just downloaded your last exe files of Athena and Artemis. I RB> tried the detach plot buttons feature and I found that the Data RB> group card is gone. I've done this before and after loading some RB> data and it happened in both cases. Then I selected the replace RB> option and nothing happened except the message "this may take a RB> few seconds". So, there is no way to select any data after RB> select this option. Hmmm.... that's a problem.... I guess I forgot to test that little feature on Windows before releasing. Drat! Fortunately, the work-around is really obvious ;-) 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 #70 - 1 msg
by Raul Barrea 25 Oct '02

25 Oct '02

Hi Bruce, I just downloaded your last exe files of Athena and Artemis. I tried the detach plot buttons feature and I found that the Data group card is gone. I've done this before and after loading some data and it happened in both cases. Then I selected the replace option and nothing happened except the message "this may take a few seconds". So, there is no way to select any data after select this option. Thanks Raul Barrea ----- Original Message ----- From: <ifeffit-request(a)millenia.cars.aps.anl.gov> To: <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Friday, October 25, 2002 12:00 PM Subject: Ifeffit digest, Vol 1 #70 - 1 msg > 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. Athena 0.8.004 and Artemis 0.5.001 (Bruce Ravel) > > --__--__-- > > Message: 1 > Date: Thu, 24 Oct 2002 15:48:34 -0400 > To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> > Reply-To: ravel(a)phys.washington.edu > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: [Ifeffit] Athena 0.8.004 and Artemis 0.5.001 > > > Hi everyone, > > I posted a new source tarball (horae-005.tar.gz) and new windows > executables on my webpage today. Both Athena and Artemis have > significant new features and bug fixes. > > Athena: > The biggest new feature is the many new keyboard shortcuts. Here's > a summary: > Ctrl-t toggle marking of current group > Ctrl-p e plot current in energy > Ctrl-p k plot current in k-space > Ctrl-p r plot current in R-space > Ctrl-p q plot current in q-space > Meta-p e plot marked in energy > Meta-p k plot marked in k-space > Meta-p r plot marked in R-space > Meta-p q plot marked in q-space > Ctrl-k select group above > Ctrl-j select group below > It is now possible to do much more work with Athena without taking > your hands of the keyboard. > > You can now save derivative of mu(E) spectra to files. The > auto-alignment algorithm changed slightly. Let me know if it is > better or worse than before. You can detach the plot buttons from > the main window. That's rather wacky, but people may like it. See > the "Plot" menu. > > Artemis: > I fixed a half dozen really serious bugs that were discovered during > and after the recent analysis course at NSLS. I will certainly not > claim that artemis is bug-free -- you just have to go find new ways > to break it ;-) > > The most significant new feature is on the paths page. There is now > a little box for the degeneracy. It is filled automagically with > the degeneracy from the feffNNNN.dat file. It must be a number and > must not be a variable. I hope this will help clarify the inherent > confusion between N, S02, and other terms which affect the > amplitude. There are menu items for setting all degeneracies to 1 > or resetting them to their feffNNNN.dat values. > > Also I changed the background color of Artemis so that, if you have > both Athena and Artemis open at the same time, they are easier to > tell apart. > > The complete lists of changes and bug fixes are available on the web > site. > > Extra special thanks this time to Mark Jensen (YeS, i fiXeD YouR bUg), > Jia Liu (who was *very* patient in helping me track down some serious > Artemis bugs, thanks!), Shelly Kelly (whose mouse avoidance regimen is > proceeding nicely), and Scott Calvin (for color consultation). > > Have fun! > 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

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Athena 0.8.004 and Artemis 0.5.001
by Bruce Ravel 24 Oct '02

24 Oct '02

Hi everyone, I posted a new source tarball (horae-005.tar.gz) and new windows executables on my webpage today. Both Athena and Artemis have significant new features and bug fixes. Athena: The biggest new feature is the many new keyboard shortcuts. Here's a summary: Ctrl-t toggle marking of current group Ctrl-p e plot current in energy Ctrl-p k plot current in k-space Ctrl-p r plot current in R-space Ctrl-p q plot current in q-space Meta-p e plot marked in energy Meta-p k plot marked in k-space Meta-p r plot marked in R-space Meta-p q plot marked in q-space Ctrl-k select group above Ctrl-j select group below It is now possible to do much more work with Athena without taking your hands of the keyboard. You can now save derivative of mu(E) spectra to files. The auto-alignment algorithm changed slightly. Let me know if it is better or worse than before. You can detach the plot buttons from the main window. That's rather wacky, but people may like it. See the "Plot" menu. Artemis: I fixed a half dozen really serious bugs that were discovered during and after the recent analysis course at NSLS. I will certainly not claim that artemis is bug-free -- you just have to go find new ways to break it ;-) The most significant new feature is on the paths page. There is now a little box for the degeneracy. It is filled automagically with the degeneracy from the feffNNNN.dat file. It must be a number and must not be a variable. I hope this will help clarify the inherent confusion between N, S02, and other terms which affect the amplitude. There are menu items for setting all degeneracies to 1 or resetting them to their feffNNNN.dat values. Also I changed the background color of Artemis so that, if you have both Athena and Artemis open at the same time, they are easier to tell apart. The complete lists of changes and bug fixes are available on the web site. Extra special thanks this time to Mark Jensen (YeS, i fiXeD YouR bUg), Jia Liu (who was *very* patient in helping me track down some serious Artemis bugs, thanks!), Shelly Kelly (whose mouse avoidance regimen is proceeding nicely), and Scott Calvin (for color consultation). Have fun! 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: problems at the Bi L3 edge
by Carlo U. Segre 23 Oct '02

23 Oct '02

Bruce: I have encountered some strange behavior at the Bi L3 edge. I have a file which runs out about 1200eV above the edge (13419eV). While Athena does find the high energy when setting the default normalization and spline ranges, it does not plot any of the data beyond 14220 (about 800eV above the edge). In fact, there seems to be a hard limit of about 800eV above the edge for all data and this translates into the k-space plot as well. I am now unsure of what effect this might have on the back transform if the defaults are not touched but certainly the graphical setting of limits for normalization, spline fit, fourier transform and back transform wil not work since the plot does not show the complete data range. Another problem I have found is that the Auto Align feature is somewhat unreliable and does not always yield a visually correct shift. I haven't characterized when exactly this happens but it has seemed to work once on a file and then not work later on the same two files. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Artemis and templates
by Bruce Ravel 22 Oct '02

22 Oct '02

Hi folks, I received this question today: > The third question is about the fitting templates provided in your > software, such as firstshell, mixedshell, three shell, etc. How > can I predict which one is good for the fitting? What are the > differences among them? A bit of recent history. The templates are a feature of Artemis that I started working on just prior to last month's EXAFS course at NSLS. The concept seemed to be working pretty well for copper metal ($ironic_mode=1), so I decided to put the templates in the official release. The thing that the templates have been most useful for so far is to point out that Artemis remains almost completely undocumented. The templates are but one confusing part of the program. Once a user gets confused, there is no place (other than, of course, this mailing list) for the user to turn for information. Sigh. Let me start by explaining what the templates are not: They are not intended to be a complete description of any fit to any data set. That is, you cannot expect to choose an item from the Templates menu, click the big green fit button, and be ready to publish. The templates are intended to help you start a new fitting project by filling in many of the little entry boxes scattered throughout the program with reasonable first guesses for interesting parameters. Another way to say this is that the templates will hopefully help save you from having to do a certain amount of really tedious typing. As an example, the template called "firstshell" makes a non-stupid guess about what kinds of parameters you might want for a fit to the first shell of your data. You will almost certainly have to edit the guess/set/def parameters as well as the path parameters to get a fit to your data that is statistically valid and physically reasonable. Some of the templates ("threeshell" for example) do nothing at all at this time. So, to answer the questions directly: > How can I predict which one is good for the fitting? In a sense, none of them are. However, if you want to do a fit to the first shell, the "firstshell" template may be helpful. If you want to do a fit for which the correlated Debye model is valid, the "debye" template may be helpful. > What are the differences among them? Their names tend to explain the kind of situation in which they might be helpful. Let me end by saying my main point one more time in different language: Templates are the *starting points* for fits. Use them in that sense. They are NOT complete fitting models. Do not use them as such. Hope that helps, 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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SUIs
by Bruce Ravel 22 Oct '02

22 Oct '02

Matt said: MN> Bruce also points out (again, correctly) that we have very little MN> experience training monkeys. OK. You caught me in a little, white lie. Perhaps it is possible to train a monkey to do data analysis. In fact, all my experience is in writing GUIs for Ifeffit. I actually have no experience writing SUIs (simian user interfaces). Perhaps one of our eager users would be interested in doing the pioneering work in this field. ;-) 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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measurement uncertainty
by Bruce Ravel 22 Oct '02

22 Oct '02

Gustavo de Medeiros Azevedo said: GdMA> I''ve recently started using IFEFFIT, and I'm a bit confused on GdMA> the way it estimates the error bars. In the IFEFFIT Reference GdMA> guide, (page 38) you mention the variables epsilon_k and GdMA> epsilon_r, where the measurement uncertainty is stored. In GdMA> that same page, you remark that changing the values of GdMA> epsilon_k and epsilon_r will change chi_squared, Chi-reduced GdMA> but won't affect R_factor and the error bars. As far as I GdMA> understand, the error bars should given by the diagonal GdMA> elements of the co-variance matrix, multiplied by the square GdMA> root of Chi_reduced. In this way, I would expect that varying GdMA> epsilon_k or epsilon_r should affect the estimated GdMA> uncertainties. GdMA> Could you, please, clarify this point? Gustavo, Well, I live one time zone to the east of Matt, so I guess I'm seeing this before he does ;-) I'll take a stab at your question. epsilon_r is measured from the data by performing the Fourier transform of chi(k) and then computing the root mean square value of the magnitude of chi(R) between 15 and 25 Angstroms. The assumption is that, because of disorder and mean-free-path effects, any finite spectral content in that R range can only be due to white noise in the data. The relationship between epsilon_k and epsilon_r is established by the normalization of the Fourier transform. Because epsilon_R enters into the fitting metric, chi-square, when the fit is done in R-space (or epsilon_k for a fit in k space), you are correct that the value of chi-square and reduced chi-square are affected by the value of epsilon_r. The R_factor is just a percentage misfit and so is independent of epsilon. The error bars are independent of epsilon as reported by ifeffit, but the reason for this requires some explanation. The first question to ask at this point is whether it is valid to presume that the dominant error in the exafs measurement is the shot noise measured from the high-R portion of the Foruier spectrum. In most situations it is not -- that is, in most situations the shot noise is much smaller that detector non-linearity, sample inhomogeneity, errors in the theoretical fitting standards, errors in the empirical fitting standards, or a whole host of other problems you might have in a real experiment. Particularly at 3rd generation light sources, photon flux and the shot noise associated with it is the least of your problems. By a long stretch. Thus, the way ifeffit uses to estimate epsilon is manifestly wrong. It is way too small, thus chi-square is very large. Even for a fit that is clearly a good fit, such as the common example of a copper foil that comes with the Artemis, the reduced chi-sqare is much larger than 1. By the formalism of Gaussian statistics, we expect that a good fit has a reduced chi-square of about 1. So what's going on? Well, the problem is that ifeffit makes no attempt (since it operates within a Gaussian framework and not a Baysian framework) to estimate all the other sources of error besides shot noise. Thus it is almost always doomed to have reduced chi-square much larger than 1 (except in the odd case when the shot noise is quite large). So what about the error bars? The diagonal elements of the covarience matrix (i.e. the error bars) are much too small for the same reason that the reduce chi-square is too large, i.e. because epsilon has been vastly underestimated. Ifeffit then makes the assumption that the fit it just finished was, in fact, a good fit. It assumes that the reason that reduced chi-square is not near one is NOT because it is a bad fit, but rather because epsilon has been significantly underestimated. Multiplying the error bars by the square root of reduced chi-square is mathematically equivalent to re-evaluating the covarience matrix with epsilon set to the value it must be for reduced chi-square to equal 1. Thus, it is the mathematical equivalent of assuming that the fit is, in fact, a good fit. So finally, you asked how setting epsilon to some other value will effect the fit. The answer is "Not much." It will have some small effect in how the fit is evaluated numerically because chi-square may be of a different order of magnitude. However, because Ifeffit rescales the error bars under the assumption that the fit was good, manually changing epsilon will have little effect on the results. One more thing needs to be said. Because Ifeffit *always* assums that the fit is a good fit and reports statistics accordingly, it is the RESPONSIBILITY OF THE USER to actually evaluate the quality of the fit. Are the best fit values physically reasonable? Are the parameters highly correlated? Are the rescaled error bars of a reasonable size? Ifeffit cannot answer those questions. You must. And that, finally, is why a human needs to do data analysis. Sadly we cannot train a computer or a monkey to decide if the fit is, in fact, the one you want to publish. Hope that helps, 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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Re: Ifeffit digest, Vol 1 #67 - 1 msg
by Gustavo de Medeiros Azevedo 22 Oct '02

22 Oct '02

Dear Bruce and Matthew, I''ve recently started using IFEFFIT, and I'm a bit confused on the way it estimates the error bars. In the IFEFFIT Reference guide, (page 38) you mention the variables epsilon_k and epsilon_r, where the measurement uncertainty is stored. In that same page, you remark that changing the values of epsilon_k and epsilon_r will change chi_squared, Chi-reduced but won't affect R_factor and the error bars. As far as I understand, the error bars should given by the diagonal elements of the co-variance matrix, multiplied by the square root of Chi_reduced. In this way, I would expect that varying epsilon_k or epsilon_r should affect the estimated uncertainties. Could you, please, clarify this point? Best Regards, Gustavo Azevedo At 12:00 PM 17/10/2002 -0500, you 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. Re: using Artemis (Bruce Ravel) > >--__--__-- > >Message: 1 >Date: Thu, 17 Oct 2002 09:33:37 -0400 >To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] using Artemis >Reply-To: ravel(a)phys.washington.edu >From: Bruce Ravel <ravel(a)phys.washington.edu> > > >John, > >I think you replied to me rather than to the list, so I am answering >to list. > >You said: > > jjr> It's great to have the hints on artemis usage. My friendly > jjr> suggestion would be to complement this with sample input/output > jjr> so one can follow along a worked example. The "examples" in the > jjr> artemis source are somewhat useful in this respect, but hacking > jjr> one's way wasn't completely straightford for me. > >I have been thinking about how to provide useful, interactive examples >and documents for the programs. It's difficult. > >The example projects for Artemis are certainly incomplete works-in- >progress. > >There is a README file in the examples directory for Athena that is >helpful, but should, I guess, be an html file. The project files in >both programs' examples directories do have journal entries that help >explain what's going on and give suggestions for other things to do. > >The journals are accessible from the Edit menu in either program and >are a space for writing notes about the project. The journal is saved >in the project file along with all the data. The idea is that you have >a space to record note so that, in 6 months, you can recall why you >did all the wacky things in the project. Not using the journals? You >should be ;-) > > > >So, I agree that the examples are not all they could be. It is >actually hard for me to make good examples since I already know how >the programs work. Good examples are something the people on this >list could put together and contribute. That would be extremely >welcome and an excellent, non-programmer's way of giving something >back to Matt and I. > > > >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/ > > >--__--__-- > >_______________________________________________ >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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Re: [Ifeffit] using Artemis
by Bruce Ravel 17 Oct '02

17 Oct '02

John, I think you replied to me rather than to the list, so I am answering to list. You said: jjr> It's great to have the hints on artemis usage. My friendly jjr> suggestion would be to complement this with sample input/output jjr> so one can follow along a worked example. The "examples" in the jjr> artemis source are somewhat useful in this respect, but hacking jjr> one's way wasn't completely straightford for me. I have been thinking about how to provide useful, interactive examples and documents for the programs. It's difficult. The example projects for Artemis are certainly incomplete works-in- progress. There is a README file in the examples directory for Athena that is helpful, but should, I guess, be an html file. The project files in both programs' examples directories do have journal entries that help explain what's going on and give suggestions for other things to do. The journals are accessible from the Edit menu in either program and are a space for writing notes about the project. The journal is saved in the project file along with all the data. The idea is that you have a space to record note so that, in 6 months, you can recall why you did all the wacky things in the project. Not using the journals? You should be ;-) So, I agree that the examples are not all they could be. It is actually hard for me to make good examples since I already know how the programs work. Good examples are something the people on this list could put together and contribute. That would be extremely welcome and an excellent, non-programmer's way of giving something back to Matt and I. 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 disappears instantly if a new graph is being presented.
by Bruce Ravel 15 Oct '02

15 Oct '02

Kotoro, This is a question of broad interest. I hope you don't mind that I forward it to the ifeffit mailing list. > On Tue, 15 Oct 2002, "Kotaro Sasaki" <ksasaki(a)bnl.gov> said: KS> Dear Bruce, I was an attender at EXAFS workshop at NSLS last KS> month; I have just updated the syetem of my computer from WINDOW KS> 98 to XP. Now ATHENA seems to run on this system. Yay! Sorry for the hassle. There are just too many operating systems and too few of us working on the software! The situation with 9x/ME is fragile. KS> However I encountered the following problem. When I try to replot KS> a new graph after closing a previous graph, the program is KS> suddenly shot down. This is a known problem with PGPLOT on windows. At this time neither Matt nor I know any better solution than "don't close the plot window." Just get in the habit of NEVER closing the plot window unless you are done with Athena (Same holds true for Artemis) and things should work OK. 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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using Artemis
by Bruce Ravel 14 Oct '02

14 Oct '02

Hi folks, Based on feedback from last months EXAFS course at NSLS and on some email I received last week, I decided there was a need to start working on a beginner's guide to using Artemis and Ifeffit for fitting data. Here is the URL for this new document: http://leonardo.phys.washington.edu/~ravel/software/exafs/startfitting.html Please feel free to send me comments. Feel free to edit it heavily or add material. I would like this to develop into a collaborative, community document. This is not meant to be a comprehensive guide to fitting. Nor is it intended to replace my book of analysis tricks at http://leonardo.phys.washington.edu/~ravel/course/notes/ It is intended to get people over the initial potential barrier of using Artemis and Ifeffit and start them down the road of using them cleverly and intelligently. 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 0.8.003 released
by Bruce Ravel 14 Oct '02

14 Oct '02

Hi! I just updated the source code tarball and the windows executable for Athena. I added several features last week while I was at the synchrotron and wanted to get them out there. New features include: 1. Energy calibration using the mouse. See the end of the Group menu. 2. Data smoothing. The Fourier filter smoothing is flaky and smoothing is a suspicious thing to do in any case. Take this feature with a grain of salt. 3. Save many marked groups as columns in a single data file. See the File menu. This is handy for exporting much data from Athena to a plotting program 4. Fixed a bug whereby the pre-edge line energy range was not being respected. 5. Athena will now tell you how many spline knots it intends to use. See the Data menu. Thanks to Shelly Kelly for the pre-edge bug and thanks to Dean Hesterberg, Suzanne whose-last-name-I-can't-remember, Kumi Pandya, and Mali Balasubramanian for several good suggestions. There are some new notes on the download page for Windows 9x/ME users and a new page about how to write a good bug report. Check 'em out! 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 and Mac OS X
by Jeff Terry 11 Oct '02

11 Oct '02

Hi all, fink is not that hard to use. I believe that the firewall problem is due to the APS blocking the cvs port. I forget which one it is. Jeff

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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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