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

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

2 1

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

3 3

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===========

2 1

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

4 3

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/

2 3

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/

2 2

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

3 2

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

4 3

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 >

1 0

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/

2 1