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

two issues with horae-040
by Bruce Ravel 31 Aug '04

31 Aug '04

Hi, For those trying to use yesterday's source tarball, I noticed a serious issue last night. There is a bug in the build script. Building will fail during the "make" step of "perl Makefile.PL; make; make install". There is a simple work-around (type "make" a second time) but this problem breaks the horae_update script. Consequently, I will be releasing a new tarball today. It should be on SourceForge and my web site before noon (North American Eastern Standard Time -- same as New York City). Sorry for the inconvenience, thanks for your patience. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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/

1 0

Artemis fit results question
by Timm Strathmann 30 Aug '04

30 Aug '04

This may be a question related to Artemis or to EXAFS fitting in general for a relative newcomer. Over the past months, when I've fit EXAFS data using Artemis and feff-derived single-scattering paths, I sometimes end up with best fit values for 2nd-shell coordination numbers or sigma squared values that are negative. Do these values have any meaning, or do they most likely signify that the chosen paths are not appropriate for fitting the spectral region in question? Also, is there a way to constrain the parameters to only consider positive values. Thanks. Timm Strathmann

1 0

the development branch of Artemis
by Bruce Ravel 30 Aug '04

30 Aug '04

Hi! As I mentioned in my last email, today's source code release includes the new development branch of Artemis. As I said about a month ago, I am now maintaining a stable branch, which will usually only get bug fixes, and a development branch, which is where I will be working on new features. I put a few notes and a screenshot on my Artemis page: http://leonardo.phys.washington.edu/~ravel/software/exafs/aboutartemis.html scroll down to the middle of the page. There is a box labeled "Development Branch". I want to clarify how this is going to work: 1. The source tarball has both branches and both get built and installed. The development version gets installed as "diana". This allows you to try out the development version but still have the stable version to fall back on. 2. I don't intend to build Windows executables of the development version until it is almost ready for normal release. This is in part to save myself some work and in part to keep the development branch out of wide use until it has been much better tested. 3. The development version involves some changes to the project file format. It will read projects from the stable version, but some information will get lost in the other direction. 4. If you use the development version, you should anticipate that there will be problems and be prepared to submit good, clear, helpful bug reports. If you expect stable behavior, use the stable version. That said, I have been using the development version for my own analysis. It ain't perfect, but I am getting work done. Here are a few notes to get you started with the new features. You might want to go take a look at the screenshot on the Artemis web page. 1. The window is much larger now. This takes up more screen real estate, but the paths list is much taller. The blank area in the lower right hand corner will get filled with new plotting controls in the future. 2. Fits get added to the Data and Paths List as seen in the screen shot. Old fits are plotted just like anything else -- just select it and click a plot button. 3. Background functions and residuals can still be plotted, but they are no longer displayed in the Data and Paths List. Now to get a bkg or res plot, click the check buttons in the plot controls panel. Whenever you plot a fit, the background and residual functions from that fit will be plotted along with best fit function. 4. When you click on a fit entry, the main panel will display a tool for viewing and exploring the log files from the fits you have done. This is essentially the same as the log viewer that Stefano was asking about last week. There is a list of fits on the left side of the panel -- double-click and right-click are both useful. The main use of this page is to write little reports about parameters so you can compare your various fits. Fits are included into reports by selecting them from the list on the left and not by selecting them from the Data and Path List. 5. In many situations (plotting, saving files, etc) selecting the head of the fit branch means to use the most recent fit. Selecting both the head of the fit branch and the most recent fit is redundant, but should not cause any problems. 6. The fit entries in the Data and Paths List may behave a little surprisingly in the case of a multiple data set fit. Some things, like plotting, depend upon which data set the selected list item is under. Other things, like discarding a fit, will effect every data set. 7. In the upper right corner is a little box which tells you when you have modified your project and, therefore, might want to consider saving it. Keep an eye on that box and let me know if there are situations where it gets set incorrectly. 8. I have written some documentation for viewing inside Artemis. There are lots of buttons scattered around the program for displaying context appropriate documentation (you can see a couple in the screenshot). Feel free to read through this and suggest ways to improve upon it or even write some of it yourself! Lots of the documentation is still unwritten. Things that don't work correctly yet that I know about: 1. Saving fits to multi-column files certainly doesn't work. Saving individual fits to column data files should work. 2. Hiding individual or selected fits (see the Fit menu) is flaky. Things to remember about using the development branch: 1. You can always go back to the stable branch, they are installed side-by-side. 2. It's a development branch -- it's going to have lots of bugs. 3. I want to hear about your problems and your suggestions for new & better features. Have fun! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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/

1 0

news and new releases
by Bruce Ravel 30 Aug '04

30 Aug '04

Hi folks, I just uploaded a new source code tarball of Athena, Artemis, and Hephaestus to SourceForge. This release includes several bug fixes from the last couple of months and a few new features. An updater for the Windows users should follow soon. Here are the release notes on SF: http://sourceforge.net/project/shownotes.php?release_id=264418 The highlights: 1. The first tarball with a version of the development branch. I'll discuss this more in another message to the mailing list later this afternoon. 2. You can now use CIF files for your crystallography data. I added funtionality to one of the libraries associated with Atoms to handle CIF files. This means than any program built off of those libraries automatically reads CIF files. The one caveat is that atoms and tkatoms will only read the first record in a multi-record CIF file. Extracting a later record requires some additional code at the level of the application rather than the library. Artemis will pop up a dialog for selecting from a multi-record CIF file. TkAtoms will not. You should consider the CIF functionality experimental. There are some tricky parts and I am not sure that my implementation will work in all situation. Please contact me in person or via the list if you have any trouble with CIF files. 3. A new look, a new utility, and several bug fixes in Hephaestus. 4. The horae_update script was updated to loop through the SF servers until it finds one that responds with the tarball. Special thanks this time to Dave Barton, my CIF implementation borrowed heavily from his handy cif2inp tool. Dave also made a number of good sugestions regarding Athena and Hephaestus. Also thanks to Tony Lanzirotti and Sean Luo, both of whom reported significant bugs that got fixed. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 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/

1 0

trying to start...
by Mauricio 30 Aug '04

30 Aug '04

Dear Ifeffit users, Sorry if it's an idiot question, but I'm in troubles when trying to work with my L3-Pb absorption data with Athena. I'm a beginner with the Ifeffit stuffs... Also, sorry if this report is not correctly posted, but I will try to give you the maximum information I can... Let's go. The data were taken at the Brazilian syncrotron laboratory, and the "important" data are in columns 3 (energy), 4 (Io) and 6 (It). The file is of the following form: "Data" "Hora" "Ponto X" "CION1(CURTA)" "CION3(Longa)" "CION2(Média)" "Det. D" "Translonga" "Transmédia" "Det. G" "Det. H" "Det. I" 04/02/04 12:32:51 12899.99 1671379 865008 1244452 0 0.658666 -0.363712 0 0 0 04/02/04 12:32:54 12901.16 1668799 863916 1242264 0 0.658384 -0.363215 0 0 0 04/02/04 12:32:57 12904.32 1661863 860550 1237862 0 0.658123 -0.363569 0 0 0 04/02/04 12:33:00 12905.99 1660709 860007 1237669 0 0.658059 -0.364045 0 0 0 04/02/04 12:33:03 12907.65 1656852 858657 1236381 0 0.657305 -0.364574 0 0 0 04/02/04 12:33:05 12909.82 1655818 858151 1236604 0 0.657270 -0.365344 0 0 0 04/02/04 12:33:08 12912.15 1655627 857952 1236890 0 0.657387 -0.365807 0 0 0 04/02/04 12:33:11 12913.82 1655763 858599 1238443 0 0.656715 -0.366308 0 0 0 When I try to open it, with the latest version (ifeffit-1.2.6) installed in a Windows XP computes, Athena says that the file has fewer than 10 data points. And the following message was trapped by Athena: Athena0.8.030warnC:\Arquivos de programas\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x 3be700c) at athena line 1349 main::__ANON__('Use of uninitialized value in concatenation (.) or string at ath...') called at athena line 3658 main::read_raw('D:/meus documentos/LNLS/D04B-XAS 1832-03/data/B040006.DAT', '', undef, 'SCALAR(0x3a80b78)') called at athena line 3516 main::read_file(0) called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at athena line 1411 The files in the /examples/Athena folder open correctly. Do I need to "clean" the data, leaving only the desired columns, E, Io and It? Again, sorry if it's a dumb question and if the report is incomplete... Thank you in advance Mauricio ************************************** Maurício Antonio Pereira da Silva Departamento de Física Grupo de Dinâmica Molecular Universidade Federal de São Carlos - UFSCar Via Washington Luiz, km 235 Vila Monjolinho 13565-905 São Carlos - SP Brasil Tel: +55 (16) 33 51 82 22, ramal 262 Fax: +55 (16) 33 61 48 35 *************************************** --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com) Version: 6.0.742 / Virus Database: 495 - Release Date: 19/8/2004

5 7

Re: High-R data
by Peter Southon 27 Aug '04

27 Aug '04

Bruce, Matt, Thanks for your help, I obviously haven't properly found my way around the Ifeffit manual yet! The rmax_out parameter was just what I needed. My apologies Bruce - I must have been sloppy in checking the k-plots of data. Athena indeed plots all the data beyond 20 Å-1. Thanks also for the advice on epsilon_k. It seems that I won't have to change the rwgt1 and 2 after all, there isn't anything above 15 Å. (In fact has anyone seen exafs at 15 Å?) Regards, Peter

2 1

High-R data
by Peter Southon 26 Aug '04

26 Aug '04

Hello all, Athena and Artemis do not plot chi beyond 20 Å-1 or the Fourier transform beyond 10 Å. Is this a limitation of Athena/Artemis or of Ifeffit? Can it be changed? We have exafs data that may be usable almost to 21 Å-1, and with quite a strong FT peak (from a Pt atom) at 10.5 Å. The latter we would not even have noticed had we been using only Athena to process our data. The 10.5 Å peak raises another issue. I understand that Ifeffit by default assumes that the high-R region is pure noise in order to make its estimates of uncertainty. (I know the actual R-range that is used was mentioned recently but I can't find it in the list archives or any of my manuals.) Can this range be changed? Does anyone have any advice on how to deal with this issue? Thanks, Peter Peter Southon Postdoctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 7482

3 3

Export "flattened" normalized spectra
by Norbert Weiher 25 Aug '04

25 Aug '04

Dear Bruce, I was just wondering if you could implement saving the "flattened" Norm(E) spectra from ATHENA. I really like the plotting option for the XANES, but do my final plots always with grace... so I need to put the data in there. Would be great to have a quick option to have these data at hand... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

2 3

statistics
by Stefano Ciurli 24 Aug '04

24 Aug '04

Hello folks, I am sure this is an easy question answered many times, but I need some refresh: When it comes down to compare fits using different models, which is the relevant parameter? Chi square (and reduced) or R-factor? I have fits with smaller chi square and larger Rfactor and viceversa... Is it possible that a rationale would be that when the models to compare have the same number of atoms these parameters go in parallel? And that when the number of atoms is different one must rely more on chi square rather than R-factor (or viceversa)? Oh well. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

2 2

Last few questions
by Scott Calvin 24 Aug '04

24 Aug '04

Dan Carter wrote: > Thats great about the R-factor, I was very impressed to see it so low. > Reduced Chi-square = 382.556284248 > R-factor = 0.015036203 > (fit I started with--two e0's: one for 1st path/1 for others) > > I'm wasn't positive about how to use the third cumulant. So, I made a >variable third to guess in that position for the first path (the nearest >neighbor, right). Here are the results: > Reduced Chi-square = 415.039996182 > R-factor = 0.014768538 > third = 0.000045 > (Can you tell if this is a better fit from the Reduced Chi-square) > > If I separate ss's for the first path and the others (leaving the third >parameter) I get this: > Reduced Chi-square = 462.878645915 > R-factor = 0.014748364 > (not much improvement) > > One more thing, for the mailing list: How can I find out if it is ok to >separate the e0's of the nearest neighbor from the others? > > Thanks, Dan > > >

4 7