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

an input data question of Athena
by hsnuboy 05 Feb '04

05 Feb '04

Dear IFEFFIT folks, Hello, I've been on the mailing list for a long time. It's really helpful for the advice from every expert. I have a problem about data input into Athena. When I want to input my experimental data, Athena replied the cord said that: ############################################################ Use of uninitialized value in subtraction (-) at athena line 2828, <F> line 1. Tk::Error: wrong # args: should be ".frame3.frame.canvas bbox tagOrId ?tagOrId .. ...?" at Tk.pm line 228, <F> line 1. Tk callback for .frame3.frame.canvas [\&main::read_file,0] (menu invoke) ############################################################ and I caanot input my data in to Athena. Is there anyone happens to know this problem? Thank you! Good day Yu-Chuan Lin

2 1

W-O ss
by Tamas Varga 05 Feb '04

05 Feb '04

1 0

Ifeffit 1.2.5
by Matt Newville 05 Feb '04

05 Feb '04

Hi Everyone, I've just posted Ifeffit 1.2.5 on the Ifeffit web pages and to Sourceforge.net. Source code, full windows installer, and Mac OS 10.3 installer are available. The automatic update for windows should be posted in the next couple of days. There are several bug fixes / improvements in the base Ifeffit library. Very briefly, the changes are: - improved feff path lists - fixed problems with spline() clamps - fixed problems with restraints in feffit(), - chi_noise() now estimates 'kmax_suggest', approximately the k-value above which the data is dominated by noise. - added random() command to generate arrays of random numbers. - screen messages for autobk/feffit/feff6 are now sent to a *.run file, and any errors cause a *.err file to be written. On Windows and Mac, the 'choose an input file' wrapper for these programs warn if an error happened, and offer to show you the *.run file. A more complete list of changes is below. The Windows installer contains (what I believe are) the latest versions of Athena, Artemis, and SixPack. The Mac version includes the latest versions of Athena and Artemis. Let me know if you have any questions or problems, --Matt * Version 1.2.5: bug fixes, improved feff path lists, fixed problems with spline() clamps, restraints in feffit(), altered screen messages for autobk/feffit/feff6, and added random() command to generate arrays of random numbers. - path lists for feffit(), ff2chi(), erase(), and show() can now range over undefined paths, so that feffit(1-100,...) will use all *currently defined* paths between 1 and 100 (inclusive), even if only paths 2, 8, and 55 are defined. Here are some related changes: o path indices are strictly checked to be in the range 1..9999. o since the maximum path index is 9999, the list '1-9999' means 'all defined paths'. This can be abbreviated as 'all', as in: ff2chi(all,group=ff) which will sum all curently defined paths. o erase(@paths) and erase(@path=all) are now equivalent, both erasing all defined paths. o when erasing a path, the feff data associated with a path will be freed (if it's not in use by another path) so that new feff paths can be used. - added random() command, to generate an array of random numbers, using uniform, gaussian, or normal distributions. syntax is: random(output=my.random, npts=200, dist=normal, sigma=2.) where sigma will be (approximately) the standard deviation of the normal and gaussian distributions, or the scale of the uniform distribution. Sigma is 1 unless explicitly set. You can optionally reset the seed of the random number generator with the seed keyword. The gaussian and normal distribution appear very similar, and can both be used to simulate noise in data. - chi_noise() now generates 'kmax_suggest', an estimate of the maximum usable k-value for the data, based on the estimated noise in the data. In early tests, this appears to be a reasonable estimate for 'noisy data', and a bit pessimistic for clean data. Please use view this value as a guide. - clamps in spline() now try to bring chi() to zero at kmax/emax and kmin/emin instead af last and first data point. - an error in feffit() for how multiple restraints were applied has been fixed. multiple restraints can now be applied and mixed freely with multiple k-weights and multiple data sets. - improved screen messages printed by autobk/feffit/feff6: o replaced all print* statements with 'call echo()' o messages 'echo'ed to the screen are now 'tee'd to the run files autobk/feffit/feff6.run o replace all 'stop' statements with a 'call echo()' and the creation of an error file autobk/feffit/feff6.err. If this file exists after a run of autobk/feffit/feff6, then an error did occur; after successful runs, the error file will not exist.

1 0

combining marked groups
by dmc＠pdx.edu 04 Feb '04

04 Feb '04

Ifeffit Dudes, I've tried to plot several groups together in Athena and then saved them together under "Save Marked Groups---chi(k)." It seems to work fine, but then when I try to open it up in Artemis I can't do anything. If I try to graph something, it closes. I can't do a fit b/c there are no parameters. My question is this: how can I average and then fit several data files? Thanks, Dan

2 1

the exact edge position
by gabriel rosenblum 02 Feb '04

02 Feb '04

Hi I would like to know what is the exact way to find the edge position of a sample, and I wonder If anyone can help. Currently, I analyze few samples with minor changes, and I suspect those changes might affect edge shifts. The different samples are absolutely aligned, and the next step is to find the edge position of each, and compare the shifts with respect to the reference. When using ATHENA, a circle appears approximately where the edge should be, whereas a different result for the edge position appears when analyzing with UWEXAFS package � by viewing the maximum point of the first derivative of mu(E). I would also like to know, what is the correct definition of the edge position. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/

2 1

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

2 1

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

4 3

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