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

Re: ifeffit list index
by Peter Southon 28 Jan '04

28 Jan '04

> Date: Mon, 26 Jan 2004 17:02:24 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > > Could this FAQ sufficiently fill the role you're thinking of? Not precisely what I had in mind, its better. Would it be possible to add links from the faq to threads in the archived mailing list? This way somone (anyone) can add important mailing list discussions to the faq without re-typing a whole bunch of stuff. Peter ------------------------------------------------- This mail sent through IMP: www-mail.usyd.edu.au

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ifeffit list index
by Peter Southon 26 Jan '04

26 Jan '04

> > And while I'm about it ... it occurred to me that these questions above > > could well have been asked before, but as a newcomer to this list it is > > quite difficult to trawl through the archives to find relevant answers. Is > > there any possibility and/or interest in some kind of index of these > > discussions? > > Yay! Excellent suggestion. In fact, in one of my recent rants about > all the ways that people could contribute to the ifeffit family > without actually writing code for ifeffit, athena, or artemis, I > mentioned precisely this. > > I have been with the ifeffit list from the beginning and I have many > times wished their were an index. > > So... any takers? Here's a place to start: http://www.htdig.org/ Matt, Bruce et al. A search-generated index (or search function for the archive pages such as htdig) would indeed be comprehensive, useful, and easy(ish) to impliment. However, what I originally had in mind was a human-collated index (more like a 'contents page'), which might make it easier for people to find related groups of contributions - although more time-consuming to put together. Perhaps it would be useful to have both types (the former would certainly help in compiling the latter). What do y'all think? -- Peter Southon Research Fellow School of Chemistry University of Sydney Australia ------------------------------------------------- This mail sent through IMP: www-mail.usyd.edu.au

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A few questions...
by Peter Southon 23 Jan '04

23 Jan '04

Hello all, Just a couple of questions for Bruce. Artemis: I've tried using the "Sum of paths" feature, which I assume is the equivalent of ifeffit's ff2chi command. For some reason it doesn't work if no data file has been opened, even though the operation does not refer to any data. Its easy to work around, but perhaps something to be fixed? Atoms: Has there been any thought of allowing Atoms to open up standard crystallographic data files, even CIF files? (I know CIF can be quite complicated) Some crystallographer colleagues are hand-typing quite a few structures from cif files into Atoms, and I suspect many others might do the same. Alternately, is there a friendly programmer out there who can write a script to extract the relevant details out of cif and write an atoms input file? And while I'm about it ... it occurred to me that these questions above could well have been asked before, but as a newcomer to this list it is quite difficult to trawl through the archives to find relevant answers. Is there any possibility and/or interest in some kind of index of these discussions? Peter

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Re: [Ifeffit] Spectra for ions?
by k-kupiecki＠northwestern.edu 22 Jan '04

22 Jan '04

Thanks, My understanding is that he has X-ray data where he went through both the MnL2 and MnL3 edges... (to me it looks kinda like XPS data as opposed to EXAFS spectra)... he wants to simulate what it should look like from Mn of different valences (Mn+2, Mn+3, Mn+4, etc.) so that he can try to determine a ratio within his sample.... if that makes sense. It is a very different use for FEFF than what I'm used to but I'm trying to help him out. When we pulled up his data in Athena it looked very weird since it looked like Athena was expecting it to be over a range of energies applicable for EXAFS. thanks for the input! -Kristine ==============Original message text=============== On Thu, 22 Jan 2004 3:48:54 pm CST Bruce Ravel wrote: On Thursday 22 January 2004 04:28 pm, k-kupiecki(a)northwestern.edu wrote: > We were also trying to figure out a way to remove the background from his > experimental absorption spectra -- can Athena do this (or does Athena > only work on EXAFS spectra)? If not, does anyone do this type of thing > and have suggestions? I'm a little confused. Could you be more explicit about what kind of data you are talking about? In general, though, if the problem of removing background from data can be expressed in the terms of the autobk algorithm, that is removing the low frequency Fouirer components and leaving the high frequency ones, then probably Athena will handle is ok. You could always just read the data in and see what happens. ;-) 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 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/ ===========End of original message text===========

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Spectra for ions?
by k-kupiecki＠northwestern.edu 22 Jan '04

22 Jan '04

Hi , I'm trying to help a collegue who would like to use FEFF to simulate X-ray absorption spectra for a single ion (i.e. Mn+2, Mn+3, Mn+4...) through the Mn L3/L2 edge. Since this is quite different from using FEFF for EXAFS like I'm used to... I could really use some help in figuring out how to accomplish this. We were also trying to figure out a way to remove the background from his experimental absorption spectra -- can Athena do this (or does Athena only work on EXAFS spectra)? If not, does anyone do this type of thing and have suggestions? Thanks!!! Sincerely, Kristine Witkowski Northwestern University

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Re: Artemis question
by Bruce Ravel 22 Jan '04

22 Jan '04

On Wednesday 21 January 2004 12:22 pm, Daniel Carter wrote: > Dear Bruce -- > > I've read as much material as I can find and I can't figure out how > to use the restrain parameter in the Guess, Set, Def parameters window in > Artemis. > > Say I want to limit Amp between 0.7 to 1.0, how do I do it? > Do I use restrain or def and then what to I enter in the "Math Expressions > field." I really need to find more info on what can be entered in math > expr. field. > > Thanks, Dan Carter > Hunter College NY, NY Dan, I trust you won't mind if I answer your question on the Ifeffit mailing list. That way others can see the question and you might hear words of wisdom from some of the gurus who hang out on the list. As to what can be entered in the math expression field, well -- just that. Any valid math expression (which can be as simple as a number or a complex combination of functions and infix binary operators) goes in there. If you "def" a parameter to be a number (e.g. def foo=5), that is the same as setting it to a number (e.g. set foo=5).. If you def a parameter to be a set parameter, i.e. set a = 5 def b = a that will, in effect, be the same as setting both a and b to 5, although deffing parameters in this way can often be a pleasant convenience at the user interface level. Things get more interesting when you start using more extensive math expressions. Take this, for example: guess a = 0 def b = abs(a) a will then float in the fit and may be positive or may be negative. b will always be positive, but its value will depend on where a ends up as a floating variable. Another example. Consider a mixed first shell with 6 atoms. Further suppose that about half of them are of atom X and the rest are atom Y. You might float an s02 variable and then use a weighting parameter to adjust the relative amounts of atoms X and Y. guess amp = 0.9 # this is our s02 parameter guess frac = 0.5 def amp_x = amp * frac def amp_y = amp * (1-frac) You would then use amp_x and amp_y as the s02 path parameters when you go define paths. In the fit, both the s02 and the mixing fraction would be determined. Alright.... that gives you some sense of the kinds of math expressions you can use. Binary operators (+ - * / ^ for addition, subtraction, multiplication, division, and exponentiation) are all available. Many functions (such as abs(), exp(), cos(), and so on) are also available. See the Ifeffit manual on Matt's web site for the full list of functions. So, finally, I am going start answering your question about getting an s02 value to come out between 0.7 and 1.0. There are two ways, constraints and restraints. You can constrain (i.e. force) that parameter to be between those values. To do this you can use the standard min/max idiom. guess a = 0.9 def b = min( max(0.7, a), 1.0 ) Deconstruct that idiom by working from the inside out. The "max(0.7, a)" part forces b to be no smaller than 0.7. If a drifts below 0.7, b will then be pegged at 0.7. The "min()" part does the same thing on the other side. If a is above 0.7, then b will equal a. But if a drifts above 1.0, then b will equal 1.0. Using a constraint is fairly simple. A bit more complicated is the use of a restraint. I trust that Matt or Scott will help me out if I mis-state anything at this point. The logic of a restraint is a bit different than a constraint. With a restraint, you want to penalize the fit if the value of the parameter drifts too far away from some acceptable value. So we will set the restraint up in this way: guess amp_guess = 0.85 set amp_target = 0.85 set scale = 100 restrain amp = abs(amp_guess - amp_target) * scale So, what does this all mean? Well, amp_guess is the floating parameter which will, well, float during the fit. amp_target is the value that you think the amplitude should be. I chose the midpoint of your range for this example. Before I explain scale and the actual restraint, let's talk about how Matt implemented restraints in Ifeffit. Ifeffit decides on its set of best-fit values by minimizing a statistical metric called chi-square. This is essentially the sum of the difference of squares between the data and the theory evaluated only over the fitting range and normalized in a way that considers the approximate amount of information left unused in the fit. The best-fit values are those that minimize chi-square. When you use a restraint, you add one more term to the quantity that is minimized during the fit. That is, the *sum* of chi-square and all of your restraints are minimized. Thus the restraint offers an incentive to the fit to meet the criteria of the restraint (or, equivalently, a penalty for not meeting the criteria), without forcing it to do so. Probably, the sum of chi-square and the restraints will be minimized when the constraint is minimized, but it is allowed for the guess parameter upon which the restraint depends to drift away from the restraining condition so long as the *sum* of chi-square and the restraint is minimized. OK? So, in the math expressions above, I have made a restraint that gives a penalty when the value of amp_guess drifts away from amp_target in either direction. The scale parameter is chosen to adjust the importance of the restraint. Since scale is a multiplicative parameter, the restraint will be more important (in the context of minimizing the sum of chi-square and the restraint) if scale is larger and the restraint will be less important if scale is smaller. How big should scale be? Well that depends on how big chi-square is for your fits and how strong of a restraint you actually want. Basically the scale parameter lets you fine tune the importance of the restraint. A word of caution. Restraints can be dangerous. Here is a quiz: Why is this definition of the restraint a bad idea? set scale = -100 restrain amp = abs(amp_guess - amp_target) * scale Finally, I never actually told you how to set up a restraint that offers no penalty if the s02 is between 0.7 and 1.0 but to start applying a penalty if it drifts out of that range. I'm leaving that as an exercise for the reader. I am doing so largely because I can't think of the answer off the top of my head. ;-) Hope that helps and don't hesitate to ask more questions on the mailing list in the future. 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 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: Another Artemis question
by Bruce Ravel 21 Jan '04

21 Jan '04

On Wednesday 21 January 2004 01:22 pm, Daniel Carter wrote: > How do I constrain the ss (sigma^2) parameter to the Debye Model? The > Einstein Model? Dan, Let me be a little more explicit this time. Please go to the web site for the ifeffit mailing list http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/ and register yourself. Then ask these questions on the mailing list rather than of me privately. There are many good reasons to do so. One is that you get to hear from other voices besides mine (although, if you find my prose irresistable for some strange reason, I do respond regularly to questions on the list). Another is that if you ask on a day when I am on travel (which is often) I may not respond for quite some time. Finally, your question will probably be of interest to someone else, as well. OK, so now that I have vented my spleen, on to your question. The Debye and Einstein models work very similarly in Ifeffit. guess theta = 350 set temperature = 150 # or whatever temperature in Kelvins you # measured at then, later on, in the path definitions, do sigma2 debye(temperature, theta) or sigma2 eins(temperature, theta) Artemis will tell ifeffit which feffNNNN.dat file corresponds to this path, so that the geometric components of the Debye and Einstein models are properly determined from the feffNNNN.dat file. If you do this for two or more paths, then theta is the variable and sigma^2 is computed for multiple paths from that single variable. These two models are neither interchangable nor always appropriate. You should read what the Feff and Ifeffit manuals have to say about them. Some other good references are Ania Poirakova's thesis and PRB, 20:12 (1979) pp. 4908--4911. 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 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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fitting with lots of variables
by k-kupiecki＠northwestern.edu 21 Jan '04

21 Jan '04

Hi, Just a quick question... Currently I'm fitting experimental spectra to feff results from two different atomic configurations to try and figure out which scenerio is a better fit and what the ultimate atom positions are.... In doing this I'm already fitting for different sigma^2 for each path (since I'm not dealing with a monoatomic system).... Now I think I would like to fit for each path's individual DelR (....previously I'd been fitting with eta*reff for each but I'm expecting the displacement about the core atom to be quite different than further away from it).... My problem is... I don't have enough independent points to accomodate all the variables given the paths included when fitting over a specific R range. Currently I figure I have at least 2 options: 1)(Assuming I'm already using the largest suitable k-range) -- Increase the r-range for the fit (i.e. if fitting the single scattering paths to 4 Ang requires 18 variables but I only have 15 independent points with r-range 1-4... perhaps increase the r-range 1-4.5 (18 ind. points in this case) or 1-5 (20 ind. points in this case) while still including the paths less than 4Ang in the fit. 2) Lump some of the paths' DelRs into expressions (i.e. having DelRs = eta1*reff, or eta2*reff, or eta3*reff etc for groupings of paths dependent upon distance from core atom). Any suggestions about these ideas, or any other ideas-- I greatly appreciate the input! Thanks a ton! -Kristine

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Debye-Waller factors for MS paths
by Peter Southon 14 Jan '04

14 Jan '04

Dear everyone, One of the features of constructing models with Ifeffit is that we are forced to think long and hard about the parameters to use for each path. In particular I have had a great deal of difficulty in deciding how to approach the Debye-Waller factors for with multiple scattering (MS) paths. The ideal approach is to define the D-W factors for the MS paths in terms of the factors for the single scattering paths. That way you add no further variables to the model. But if you think about it you will realise that you cannot simply add all the relevant SS factors up to get a sum for your MS path - it all depends on the geometry, the direction of vibration, correlation of vibrations, etc. Its all a bit tricky for those of us dealing with intense MS paths. So what I am asking is, does anyone know of a general method or approach to define the Debye-Waller factors for MS paths (in terms of SS paths or otherwise)? How do all you Ifeffiters deal with the problem? I've found a few papers that discuss it (listed below) but they generally assume that all vibrations are uncorrelated, which is seldom a realistic situation in continuous solids. Munoz-Paez, A. (2000). Inorganic Chemistry 39(17): 3784-3790. Sakane, H. (1998). Journal of the American Chemical Society 120(40): 10397-10401. Haskel, D. (1998). PhD thesis, University of Washington. (appendix) http://www.aps.anl.gov/xfd/people/haskel/PS/thesis.ps Is there anything out there that I've missed? I'd be particularly interested in anything relating to continuous solids or correlated vibrations. Comments/questions/pearls of wisdom very welcome. Peter Peter Southon Research Fellow - School of Chemistry University of Sydney, NSW 2006, Australia +61 2 9351 4425

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Re: Ifeffit Digest, Vol 11, Issue 5
by Grant Bunker 14 Jan '04

14 Jan '04

Hello, folks - In regard to Peter's question regarding multiple scattering DWFs: Matt was correct that there have been two approaches (to my knowledge) that attempt to directly address the problem: Poiarkova and Rehr's approach, and our approach. There are pros and cons to each. We (Nick Dimakis and I) have focussed on coordination complexes of metals with amino acid and similar ligands to directly address metalloproteins. The approach probably would work on other systems as well. Our method works like this: we calculate using DFT the normal modes (vibrational eigenvectors and eigenvaluesof model complexes as a function of interatomic distance and bond angles (as needed). We started this about ten years ago, and initially tried force constant models and various approximate quantum mechanical methods but found them inadequate. DFT level give sufficient accuracy and speed. Fortunately computers are fast and cheap nowadays. We have written a programs that take the eigenvalues and eigenvectors and the feff output and generates MS DWFs for each path. We have found that a "group fitting" approach works well, i.e. neglecting the inter-group multiple scattering to a first approximation. It has worked well in the cases we've tried. Since it isn't really practical to expect people to do these DFT calculations themselves (it's difficult to get convergence in many cases, it's easy to get trapped in a local minimum, and the minimization algorithms in the commercial codes are fairly antiquated), we have tried and succeeded in parameterizing the DWF for each MS path as a function of distance (and temperature). In almost all cases they are easily parameterized with polynomials as a function of both distance and temperature. So far we have done this with Zn coordinated to cysteine, histidine, and carboxylate ligands (e.g. glu), and also Cu(I) and Cu(II). We are working on Fe, Mn and other metal-ligand complexes as well, depending on funding. Hope that helps. Grant On Wed, 14 Jan 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Spline clamps (SCalvin100(a)aol.com) > 2. Re: Spline clamps (Bruce Ravel) > 3. Re: Spline clamps (Matt Newville) > 4. Debye-Waller factors for MS paths (Peter Southon) > 5. RE: Debye-Waller factors for MS paths (Kelly, Shelly D.) > 6. Re: Debye-Waller factors for MS paths (Bruce Ravel) > 7. Re: Debye-Waller factors for MS paths (Matt Newville) > 8. linux: wouldn't it be cool... (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 13 Jan 2004 15:41:47 EST > From: SCalvin100(a)aol.com > Subject: [Ifeffit] Spline clamps > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <1cf.17c88a73.2d35b20b(a)aol.com> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > > Happy New Year to all! I've been busy pushing the new versions of Artemis and > Ifeffit pretty hard (3-edge fits, over 100 paths, also over 100 guess,def,set > parameters) and they seem to be behaving pretty nicely. There are certainly > some advantages and some disadvantages to this compared to the old FEFFIT > package; one major advantage is this will certainly reduced the learning curve for > new undergraduates in my group. > > I am posting now because I am not sure I understand the behavior of the > spline clamps in Ifeffit. When I set a top end to the spline range that is below > the top of the data range, the high spline clamp has very little, if any, > effect. (As a simple example, if I take the "clamp.prj" project that comes with > Athena and set all of the spline ranges to top out at 400 eV, all four backgrounds > look the same.) Is this what should be happening, or is this a bug? > > In case this is a bug, here's the version information: > > Athena 0.8.024 and ifeffit 1.2.4 running on Windows XP. > > I'll also be glad to send a project file to Bruce or Matt if they wish, > although it would just be the clamp.prj file with the top of the spline range > changed... > > --Scott >

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linux: wouldn't it be cool...
by Bruce Ravel 14 Jan '04

14 Jan '04

Hi, I was just thinking that it would be nice to be able to install ifeffit and friends into either the KDE or GNOME menus. For example, one could imagine installing athena and artemis by doing perl Makefile.PL make make install make install-kde or make install-gnome where the last step makes the menu entries for the codes. Do any of the linux hacks out there know how this is done (at the level of a script -- I know how to do it by hand)? 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 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] Debye-Waller factors for MS paths
by Kelly, Shelly D. 14 Jan '04

14 Jan '04

Hi Peter, Please see below: > > Dear everyone, > > One of the features of constructing models with Ifeffit is > that we are > forced to think long and hard about the parameters to use for > each path. In > particular I have had a great deal of difficulty in deciding how to > approach the Debye-Waller factors for with multiple > scattering (MS) paths. > > The ideal approach is to define the D-W factors for the MS > paths in terms > of the factors for the single scattering paths. That way you > add no further > variables to the model. But if you think about it you will > realise that you > cannot simply add all the relevant SS factors up to get a sum > for your MS > path - it all depends on the geometry, the direction of vibration, > correlation of vibrations, etc. Its all a bit tricky for those of us > dealing with intense MS paths. > > So what I am asking is, does anyone know of a general method > or approach to > define the Debye-Waller factors for MS paths (in terms of SS paths or > otherwise)? How do all you Ifeffiters deal with the problem? > I've found a > few papers that discuss it (listed below) but they generally > assume that > all vibrations are uncorrelated, which is seldom a realistic > situation in > continuous solids. > > Munoz-Paez, A. (2000). Inorganic Chemistry 39(17): 3784-3790. > Sakane, H. (1998). Journal of the American Chemical Society 120(40): > 10397-10401. > Haskel, D. (1998). PhD thesis, University of Washington. (appendix) > http://www.aps.anl.gov/xfd/people/haskel/PS/thesis.ps > > Is there anything out there that I've missed? I'd be particularly > interested in anything relating to continuous solids or correlated > vibrations. Comments/questions/pearls of wisdom very welcome. > > Peter > > > Peter Southon > Research Fellow - School of Chemistry > University of Sydney, NSW 2006, Australia > +61 2 9351 4425 > There are a couple of ideas that I have found that work pretty well for determining sigma2 values for a lot of scattering paths. Idea 1: Try to use a correlated debye model or the eins model. You can have more than one debye/eins temperature depending on the atom types and path lengths. Idea 2: Group paths that are similar in distance and atom types and set their sigma2 values to the same value, including the M.S. paths. -use the abs function in defining a value for sigma2 to force it to be positive. sigma2 path1 abs(sig) guess sig 0.010 Idea 3: Usually, the triangle paths that have a really large degeneracy end up with their own sigma2 value. Most models can be close to working without these paths, and then added them at the end to clean up the fit. Idea 4: Linear paths can be quantified in terms of the sigma2 values of the single scatting paths that contain the end atoms. Another paper that talks about this is: E A Hudson, J J Rehr and J J Bucher. "Multiple-scattering calculations of the uranium L3-edge X-ray-absorption near-edge structure." Phys. Rev. B 52(19): pp 13815-3826, 1995. -For a forward linear path A-B-C, sigma2(A-B-C-A)=sigma2(A-B-C-B-A)=sigma2(A-C-A) -For a backward scattering linear path B1-A-B2, and if A is a lot heavier than B then Sigma2(A-B1-A-B2-A)~sigma2(A-B1-B2-A)~2xsigma2(A-B), and sigma2(A-B1-A-B1-A)=4xsigma2(A-B) (John Rehr and I had a previous discussion about this with the subject "relation between DW factors in uranyls") Golden Rule: You have to try A LOT of different models, always try to start with the simplest model and make it more complex as the data requires. For example: Start with a eins model and use only one eins temp. See where the model works and were it fails. In the regions that it fails add another eins temp...and so on. Shelly Kelly

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Spline clamps
by SCalvin100＠aol.com 13 Jan '04

13 Jan '04

Hi all, Happy New Year to all! I've been busy pushing the new versions of Artemis and Ifeffit pretty hard (3-edge fits, over 100 paths, also over 100 guess,def,set parameters) and they seem to be behaving pretty nicely. There are certainly some advantages and some disadvantages to this compared to the old FEFFIT package; one major advantage is this will certainly reduced the learning curve for new undergraduates in my group. I am posting now because I am not sure I understand the behavior of the spline clamps in Ifeffit. When I set a top end to the spline range that is below the top of the data range, the high spline clamp has very little, if any, effect. (As a simple example, if I take the "clamp.prj" project that comes with Athena and set all of the spline ranges to top out at 400 eV, all four backgrounds look the same.) Is this what should be happening, or is this a bug? In case this is a bug, here's the version information: Athena 0.8.024 and ifeffit 1.2.4 running on Windows XP. I'll also be glad to send a project file to Bruce or Matt if they wish, although it would just be the clamp.prj file with the top of the spline range changed... --Scott

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Feff Compatability
by Vivek S. Murthi 12 Jan '04

12 Jan '04

Hi Matt/bruce I would like to know if it is possible to run the Feff program on a Unix system. Right now I am running it on a PC which takes a long time to run. If it is possible, is there anything else I would need for Feff to run other than the executable and maybe the DOS compiler. Thanks vivek Vivek S. Murthi Graduate Research Assistant 419 Egan Research Center Northeastern Univeristy Boston, MA 02115 Phone: 617-373-8949

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fitting questions
by k-kupiecki＠northwestern.edu 07 Jan '04

07 Jan '04

Hi, Just wondering if anyone out there can help answer a few questions I have.... I've been using Ifeffit/Artemis to try and fit to some experimental spectra.... and in trying to determine the best fitting parameters (k-range, r-range etc.)... I've come across a few things I'm not quite clear on..... (1) I was wondering (this might be a silly question) whether it was considered inappropriate to fit over a range larger than your spectra? (i.e. k-range of fit set to 2-15 when in actuality the spectra data only goes to ~12.5?) (2) I don't quite understand the following the significance of the following statement: These are not yet computed quite right in all situations... Chi-square for this data set = 9.01156 R-factor for this data set = 0.01651 When previously in the results the Chi-square and R-factor were given as: Independent points = 11.272460938 Number of variables = 11.000000000 Chi-square = 4.505779601 Reduced Chi-square = 16.537341618 R-factor = 0.016508545 Measurement uncertainty (k) = 0.007252615 Measurement uncertainty (R) = 0.091026879 Number of data sets = 1.000000000 I'm confused by the different Chi-square values, and what values of Chi square and R-factor for the data set would Artemis be satisfied with? (3) Also is there anyway to have Artemis deternine the best k-range (or perhaps a way to have it step through different values of kmin and kmax) ? Just wishful thinking on my part probably... Please let me know if you can help me understand these issues a bit better. Thanks!!!!!! Kristine Witkowski Northwestern University

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RE: Ifeffit Digest, Vol 11, Issue 1
by Vivek S. Murthi 07 Jan '04

07 Jan '04

Hi Matt Earlier, I have also faced the problem faced by Tamas about the feff6 not running even though feff.inp is in the same folderas the executable. I was able to figure it out in my case. The problem was that the feff.inp file that we get from Tkatoms had to be for the right version of the Feff. There are different versions for the output availabe. If you trying running a feff.inp for feff8 format, it wouldnt run in feff6. I am not sure if tamas is also facing the same issue. thanks vivek Vivek S. Murthi Graduate Research Assistant 419 Egan Center Northeastern University Boston, MA-02115 Phone: 617-373-8949 On Tuesday, January 06, 2004 1:00 PM, ifeffit-request(a)millenia.cars.aps.anl.gov [SMTP:ifeffit-request@millenia.cars.aps.anl.gov] wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: maximum argument length? (Matt Newville) > 2. Re: running feff - a problem (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 5 Jan 2004 17:45:25 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] maximum argument length? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0401051739360.18361-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Peter, > > Sorry for the delay... Christmas/New Year's holidays. I'll be back > for real later this week. > > On Tue, 23 Dec 2003, Peter Southon wrote: > > > Is there a limit on the total length of arguments that follow an Ifeffit > > command? If so, is there a way of expanding the limit? > > Yes, there is a limit. Actually, there are several limits that can > affect how long the command line can be. The length limit on the > strings in the code are 2048 characters, but the strings get passed > back and forth enough times that I wouldn't claim that a single > command with 2047 characters will always work. More importantly, > there are various limits on different parts of the command length, > which is what I think you're seeing. > > > I've constructed a rather complicated model which uses 37 paths (mostly > > multiple scattering). Furthermore, quite a few of these paths are sensitive > > to scattering angle, so I have calculated FEFF files for three versions > > each of most paths (each for a different scattering angle), as suggested in > > the course "EXAFS Analysis with FEFF and FEFFIT" and the old Feffit manual. > > Thus the final Ifeffit command calls on a lot of FEFF paths, each > > specifically numbered according to path and angle. > > Unfortunately, after adding a few extra paths I get error messages when > > running the feffit command: "feffit:unknown key" followed by a list of > > paths about halfway through my list, and also "feffit: no chi(k) data > > array?". I assume that this is because ifeffit will only swallow half the > > command, which is: > > > > feffit(1-4,500,510,520,600,610,620,700,710,720,800,810,820, > > 9-13,15-16,1700,1710,1720,1800,1810,1820,1900,1910,1920,2000,20 10,2020, > > 37, 3800,3810,3820,3900,3910,3920,4000,4010,4020,4100,4110,4120, > > 4200,4210,4220,4300,4310,4320,4400,4410,4420,4500,4510,4520, > > 4600,4610,4620,4700,4710,4720,4800,4810,4820,4900,4910,4920, > > 5000,5010,5020,5100,5110,5120,5200,5210,5220,5300,5310,5320, > > 5400,5410,5420,5500,5510,5520, > > chi = data15.chi, macro = plot_fit) > > > > Short of actually renumbering all my paths so that they run sequentially, > > is there any solution...? > > Eek. This is my mistake, and I'll have to send repaired code for > this to work, which could be as soon as the end of this week. You're > hitting an accidentally low limit on the length of the 'path list'. > The string '1-4,500,...,5520' needs to be converted to a list of > integers: the limit on this string is currently only 256 characters, > which is definitely a mistake and will be increased to 1024 shortly. > > Another possible approach for this problem is to use the > unadvertised, "slightly magic" behavior that an undefined path is > silently ignored in the sum-over-paths. That is, if you define > paths 500, 510, 520, but not any of the path numbers in between, > using '500-520' would be the same as '500,510,520'. Though this > will give the same sum of paths, it _currently_ won't help you, as > it will quickly use up too many of the paths in the number of > internally stored paths used in the code. This will be fixed and > documented for the next version too (which should be within a couple > weeks), and the path indices will be checked to be between 1 and > 9999, so that saying '1-9999' will mean "use all defined paths". > > In principle, that could make the sort of problem you're dealing > with easier, but it might be real work for you at this point too. > > Sorry for all the trouble, and hopefully we can get it to work soon. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Mon, 5 Jan 2004 17:47:16 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] running feff - a problem > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0401051745310.18361-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Tamas, > > > I'm trying to run feff to do the feff paths calculation the same way I've > > done before (feff file from TkAtoms and the executable feff6l are in the > > same folder), and now it just doesn't want to work. > > Hitting feff6l causes the opening of the DOS window, but it closes > > immediately and doesn't do the calculation. Does anyone know what's the > > cause of this? > > (I have the updates version of Ifeffit and the updater, too.) > > With 1.2.4(+ the updates), it should be that clicking on the feff6l batch > file brings up a dialog to browse for feff.inp, and then runs feff6l on > that file, in that directory. I think this batch file could be copied > from C:\Program Files\Ifeffit (or whereever Ifeffit is installed) and > still run OK. But I believe a shortcut to the executable (feff6l.exe) in > another directory will not work, as this executable needs to find DLLs to > run properly. That's why there are the batch files. > > If the proper environmental variables are set and the Ifeffit directory > is in your path, the executable should run from a DOS command window. > You could add this to autoexec.bat (or look at feff6l.bat): > SET IFEFFIT_DIR=C:\Program Files\Ifeffit > SET PATH=%PATH%;%IFEFFIT_DIR% > SET PGPLOT_DIR=%IFEFFIT_DIR% > SET PGPLOT_DEV=/GW > > or set these environmental variables from the Control Panel (Generally > Control Panel -> Settings -> Advanced -> Environmental Variables, though > it does vary with versions of Windows). Actually, for Feff6, only the > path needs to be set to include the Ifeffit directory. > > Please let me know if these suggestions don't help enough to get > fef6l working for you... > > --Matt > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 11, Issue 1 > **************************************

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RE: [Ifeffit] fitting questions
by Kelly, Shelly D. 07 Jan '04

07 Jan '04

Hi Kristine, I feel like I can add something to question number 3. Please see below > (3) Also is there anyway to have Artemis determine the best > k-range (or perhaps a way to have it step through different > values of kmin and kmax) ? Just wishful thinking on my part > probably... No, Artemis does not do this automatically. Here is a recipe that I use to determine the k-range. 1. back-up to the Athena stage. Look closely at the edge of the xmu(e) data and the background. Count the number of oscillations until you get to the flat region of the sepctra (about 30 eV away from the edge or so). Then plot the chi(k) data and count the oscillations to figure out where this node is in the chi data and set that to kmin. Usually the value for kmin is a node around 2 to 3 1/Angstroms. 2. Make about 6 copies of the chi(k) data. In each of the copies make sure that all the parameters are the same. Set kmin to the value from step 1. Then choose a node for kmax that looks really clean around 8 1/Angstroms. Then for the following copies choose the next and next nodes for kmax. Then compare the Fourier transform of all the copies. As you include more data the peaks should become more well defined but smooth. If you see a bunch of oscillations with a high frequency all over then you have gone too far for kmax. 3. Model the data with these conservative choices for the data range. Once you have a model that you like, try including another oscillation or two on both sides and see if the theory agrees. At this point you can also include a theory in the bkg subtraction step to get down to lower k. Shelly

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an artemis question
by Bruce Ravel 06 Jan '04

06 Jan '04

Hi folks, Artemis has a feature which will generate an ifeffit script appropriate to your fitting model without actually running the fit. This feature is found as the second item in the Edit menu. This script can be examined or saved to a file. My question is this: does anyone out there make regular use of this feature? If so, could you please let me know by private email. If anyone does use this feature, I would like to know what the context is in which it is used. Thanks, 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 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 FEFF calc to create "data"?
by sej9＠cornell.edu 06 Jan '04

06 Jan '04

Dear all, Is there any way to create "data" using just a FEFF calculation? I mean, can I use Artemis to create a theoretical EXAFS spectrum from a FEFF calculation without fitting it to any actual data? After seeing my data (from messy environmental soil samples), I came up with another idea for a compound that might be in it (a compound that I hadn't thought of before and so do not have real data from having run it as a model compound), and am trying to figure out the best way to incorporate that new compound into my fit. Thanks, Sarah Johnson

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running feff - a problem
by Tamas Varga 05 Jan '04

05 Jan '04

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maximum argument length?
by Peter Southon 05 Jan '04

05 Jan '04

Hello all, Is there a limit on the total length of arguments that follow an Ifeffit command? If so, is there a way of expanding the limit? I've constructed a rather complicated model which uses 37 paths (mostly multiple scattering). Furthermore, quite a few of these paths are sensitive to scattering angle, so I have calculated FEFF files for three versions each of most paths (each for a different scattering angle), as suggested in the course "EXAFS Analysis with FEFF and FEFFIT" and the old Feffit manual. Thus the final Ifeffit command calls on a lot of FEFF paths, each specifically numbered according to path and angle. Unfortunately, after adding a few extra paths I get error messages when running the feffit command: "feffit:unknown key" followed by a list of paths about halfway through my list, and also "feffit: no chi(k) data array?". I assume that this is because ifeffit will only swallow half the command, which is: feffit(1-4,500,510,520,600,610,620,700,710,720,800,810,820, 9-13,15-16,1700,1710,1720,1800,1810,1820,1900,1910,1920,2000,2010,2020, 37, 3800,3810,3820,3900,3910,3920,4000,4010,4020,4100,4110,4120, 4200,4210,4220,4300,4310,4320,4400,4410,4420,4500,4510,4520, 4600,4610,4620,4700,4710,4720,4800,4810,4820,4900,4910,4920, 5000,5010,5020,5100,5110,5120,5200,5210,5220,5300,5310,5320, 5400,5410,5420,5500,5510,5520, chi = data15.chi, macro = plot_fit) Short of actually renumbering all my paths so that they run sequentially, is there any solution...? Have a merry Christmas, Peter Peter Southon Research Fellow - School of Chemistry University of Sydney, NSW 2006, Australia +61 2 9351 4425

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Installer for Mac OS 10.3
by Matt Newville 19 Dec '03

19 Dec '03

Hi Everyone, I think I have a reasonably well-tested installer for Mac OS 10.3 (ifeffit-1.2.4_Mac10.3.dmg) at the usual download sites (see http://cars.uchicago.edu/ifeffit/download.html) Please try it out, and let me know how it works. This disk image contains a normal Mac Installation package, which will install clickable Applications for Athena, Artemis, TkAtoms, PeriodicTable, Feffit, Autobk, and Feff6, putting them in /Applications/Ifeffit. The "Ravelware" programs all launch the GUIs directly (and X11 is automatically started if it is not running). Clicking on the applications for Feffit, Autobk, or Feff6 will open a file chooser for you to choose the appropriate input file, which will then run the corresponding program in that folder. For those interested in using the Unix command-line all of these programs, plus the ifeffit command-line program and diffkk can be run from a regular Terminal or xterm. This installer does not require any Fink-based software, but it does require OS 10.3 and X11 to be installed. (X11 can be installed from the OS 10.3 disks or from Apple's web pages). The installer here WILL NOT WORK with OS 10.2. If you're planning on using 10.2 for awhile and really need to get Ifeffit running, please contact me. I think this is possible, but a little more work than can easily put into a single installer. SixPack is not included in this distribution. This may be possible, but I have not gotten SixPack (more accurately, some of the python GUI tools that SixPack depends on) to run on 10.3. If you've been following along with the conversations with Paul Fons on getting Perl/Tk, Athena, etc running on 10.3 from sources, please be aware that this installation will _OVERWRITE_ many perl modules (Tk, Xray, Ifeffit, etc) in /Library/Perl. My experience is that it is perfectly safe to overwrite, rename, and move this folder, but you should be aware that this installer will write to /Library/Perl as well as /Applications/Ifeffit. The installer here assumes Perl 5.8.1 (that's the system-supplied one), and uses Tk-804_025_beta6. If you have Fink installed, there should be no conflict with that software. This Ifeffit distribution is _not_ using Fink's PGPLOT, but it shouldn't cause problems unless you are using that PGPLOT for another purpose. If you know _anything_ about AppleScript or Apple Programming or are just interested, please don't hesitate to play with the scripts in the Ifeffit/applescript folder and make suggestions. If you have any trouble or questions, please let me know. --Matt

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Noise Generation in FEFFIT
by Norbert Weiher 17 Dec '03

17 Dec '03

Dear Friends, I am still going with the chi^2-scan business and need a fast way to modulate white noise on a spectrum for some proof of principle. Has anyone a good idea how to do this (or would it be even possible in ifeffit)? Thanx for helping Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)tech.chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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Re: upgrading iffefit and stuff on linux
by Bruce Ravel 11 Dec '03

11 Dec '03

On Thursday 11 December 2003 08:57 am, Gleb Pokrovski wrote: > Dear Bruce, > > I'm using your nice programs Athena & Artemis (+iffefit+tkatoms) on > linux Mandrake 9.1 (2.4.21-0.13mdk), and I currently have 1.2.1, > 0.8.020 and 0.6.005 versions of iffefit, athena and artemis, > respectively. I would like to update to more recent versions. Not > being an expert in linux (but rather a very beginner!), I'm asking > myself how the upgrading will happen. On the ifeffit websites I > did'nt find any instructions how to upgrade on unix, but probably my > questions are quite trivial and silly... > > When I installed the above versions I followed the instructions provided > with the package (unzip, configure, make, make install...) > and these versions and corresponding executables and libraries were built > in the default directories /usr/local/.../bin, lib, include etc... > > If now I redo these operations with the new packages, do they automatically > replace the old files and executables? > Or I have to do some preparations before upgrading? > > (I already have PGPLOT and perl-Tk (800.024) installed and running) Hi Gleb, I am always happy to see another linux convert! Your questions are most certainly not silly and trivial. I would be surprised if others would not benefit by my answer. So I am taking the liberty of CCing my response to the mailing list. To answer your principle question -- doing an update is just that. The new version will be written on top of the old version. [1] No further preparation is required. If you are a user of Debian linux, the problem of keeping up-to-date is very simple because Carlo Segre makes installation packages for Debian of ifeffit, atoms, and athena&artemis. No one is currently maintaining packages for other linux distributions, however. Assuming you have PGPLOT and perl/Tk [2] already installed, the updating is explained below. If you need to update both, do ifeffit first, then A&A. If you only need to update A&A, it is not necessary to reinstall ifeffit -- just build and install the new version of A&A on top of the existing version of ifeffit. To update ifeffit: download the latest source code tarball from Matt's website. Unpack it. [3] Next, in a terminal window, go to the directory that got unpacked and type the following three commands: ./configure make make install The last command will require either having root or having sudo permission to install software. To update A&A (on a computer connected to the net): this is very simple. For almost the last year, a program called "horae_update" has been installed alongside A&A. Simply type "horae_update". It will fetch the latest version from my web site, unpack it, build it, and install it. Again, you will need root to actually install it. [4] To update A&A (on a computer not connected to the net): download the latest horae tarball from my web site. Unpack it. [2] In a terminal window, go to the directory that got unpacked and type the following three commands: perl Makefile.PL make make install The last command will require either having root or having sudo permission to install software. I strongly encourage you to learn how to use the horae_update script. It really does make updating A&A much easier. It is a pretty smart script in that it does nothing if the version on my web site is not newer than the version on your computer. This means that you can make horae_update a cron [5] process and have A&A updated automatically. Hope that helps, B Notes: [1] A long time ago (more than a year ago) I was struggling with a bug in perl's build system which resulted in the end user (you!) having to worry about deleting old versions of the ifeffit library before building the new one. This problem was avoided (not solved, just sidestepped) by forcing you to install ifeffit first, then install my programs second. [2] The easiest way to install PGPLOT is to run the "PGPLOT_install" script that comes with the ifeffit package. To install perl/Tk for the first time, grab the tarball for version 800.024 from my web page and do "perl Makefile.PL; make; make install". Some linux distributions (SUSE does, but Red Hat does not) have a package for perl/Tk that you can install from your installation media. [3] At the command line, you can unpack it via the command "tar xvfz". Under KDE, you can use the program Ark, which is what Konqueror suggests for opening the file when you click on it. Under GNOME, File Roller does the same thing. Ark and File Roller both behave somewhat like the popular Windows program "WinZip". [4] Also, the first time you run horae_update, it may need to fetch some additional perl modules from the web. This is automated, but it does require root access. [5] A cron process is one that is scheduled to run periodically. For instance, you could have cron run horae_update every morning at 3 a.m. In that way, the freshest versions of A&A will always be waiting for you along with your morning coffee. Cron may prove a bit daunting for a linux newbie, though. Here's a decent explanation of what it is and how it works: http://www.gdn.net/help/howto/crontab_howto.html There is a KDE program called "kroneko" that serves as a GUI to making cron jobs. A GNOME program of the sort is called "gcrontab". Neither is a default part of the desktop but a google search should turn them up. -- 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 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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errors = 0?
by k-kupiecki＠northwestern.edu 09 Dec '03

09 Dec '03

Hi, I'm hoping someone out there has seen this before and can tell me what to do to remedy it... I've been using artemis at home all weekend on my Win 98 computer without incident.... now I'm working at home today with the same feff and data files working on fitting... and while Chi sq etc. is the same the +/- values on all my variables are now reading as 0, even though the values for the variables are what I would expect them to be. Any ideas about how I can fix this? Thanks, Kristine Witkowski Northwestern University

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