January 2004 - Ifeffit - millenia.cars.aps.anl.gov

re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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ifeffit and Mac OSX
by Matt Newville 03 Jul '04

03 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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Spine Clamps and Some Fit Results
by dmc＠pdx.edu 29 Jan '04

29 Jan '04

Dear Panel of Feffit Experts, I have two questions for you, with several parts. I am looking at Lithium Cobalt Oxide annealed at 200 C. (1) In Athena what exactly do the varying levels of spine clamps mean? When do I need to use them? I've been ignoring them up to now, but I think that it might help my resulting fit, which brings me to my second part. (2) By looking at my results is there any advice you can give me? Do my reduced chi-squared, R-factor and correlated variables look good? I know that the R-Factor should be below 0.05, but what about red chi-squared (depends on the material)? Also, I am concerened that my amp (SO^2) should be closer to 1. I am using the einstien model and e01 refers to the farther 3 of my 4 paths. What else should I consider? Thanks, Dan Carter Hunter College Results: Independent points = 11.225585938 Number of variables = 5.000000000 Chi-square = 66.894398861 Reduced Chi-square = 10.745076774 R-factor = 0.040027549 Measurement uncertainty (k) = 0.002990761 Measurement uncertainty (R) = 0.069932022 Number of data sets = 1.000000000 Guess parameters +/- uncertainties: e0 = -3.9151859 +/- 2.3534572 delr = -0.0189516 +/- 0.0134287 ampg = 0.9492922 +/- 0.0001603 e01 = -9.3741702 +/- 2.5615506 theta = 415.2229263 +/- 89.8481275 Restraints: amp = 0.7077880 Set parameters: ampt = 0.9500000 scale = 1000.0000000 temp = 300.0000000 Correlations between variables: ampg and theta --> -0.9015 delr and e01 --> 0.8551 e0 and delr --> 0.7809 e0 and e01 --> 0.6858 All other correlations are below 0.25

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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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