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

copy and paste
by Li Dangdang 07 Sep '04

07 Sep '04

Hi, I've a question: Is there copy/ paster function in parameters input? I want to copy and paste when i define the math expressions for many parameters, but it seems to me that i can only reinput the expression for every new parameters. It's kind of unconfortable if my definition is complexed. DD _________________________________________________________________ 享用世界上最大的电子邮件系统― MSN Hotmail。 http://www.hotmail.com

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debian packages of horae and sixpack
by Carlo U. Segre 01 Sep '04

01 Sep '04

Hello All: I just finished making Debian packages of horae-041 and the newest sixpack (0.52) the new horae includes the development release, diana, but does not yet make a menu entry for it. So far it is only available for sid (unstable). I plan to get it to woody by the end of the weekend if possible. A sarge package should be available on Saturday at teh latest. sixpack is only available for sid and sarge. woody does not have Tix8.1 which is required, so I cannot really make a woody package. I have not had time to make sure that these programs work completely, please send me bug reports off the list. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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horae-041 ...
by Bruce Ravel 31 Aug '04

31 Aug '04

.... is on SF and my web site. http://sourceforge.net/project/shownotes.php?release_id=264607 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/

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RE: [Ifeffit] Artemis fit results question
by Kelly, Shelly D. 31 Aug '04

31 Aug '04

Hi Timm, You can use an expression that will return only positive values for you variables. sigma2 = abs(ss) guess ss This will force the model to use a positive values for sigma2. You can also use a penalty factor to keep the value inbetween a given range of values. I believe that there is an example of that in the Artemis or Ifeffit manual. -Most often negative values is a strong indication that something in the model is not quite right. Be sure to look at your data and fits showing the individual contribution from each path in the real or imaginary part of the FT. A negative sigma2 value or a really small sigma2 value usually indicates one of two different things. 1) You have included too much noise in the FT which is randomly adding signal all over in R-space hence your sigma2 values are unrealistically small to compensate. To check for this case, reduce the k-max value in the FT of the data by 1 1/angstrom and see what happens in the fit. 2) The path type is not right. sigma2 is small because you actually need more electron density for that scattering path. Hence try a path with larger Z. Negative values for the degeneracy would indicate that the path length and/or atom type is not correct. Set the degeneracy, sigma2, and delr to some reasonable values then look at the real/imaginary part of the FT for the data, fit and the contribution from the path of interest. Look to see if the signal from the path of interest has a positive contribution to the data before you try to optimize the parameters. Here is my rule of thumb for reasonable sigma2 (units= angstroms2) values sigma2 = 0.001 to 0.003 for double bonds that do not participate in binding to another atom. i.e. for the axial oxygen atoms of a uranyl moiety, UO2. sigma2 = 0.003 to 0.008 for "normal" well ordered shells. Like for Cu metal. This is the usual range. sigma2= 0.009 to 0.015 for disordered shells that are rather weekly bound. i.e. for the equatorial oxygen atom of the uranyl. There is usually 4 to 6 of them and they are not well ordered. Some times these shells can be split into two shells given enough data range in k-space. sigma2=0.015 to 0.025 for really soft bonds like solutions or squishy metals (AgCl) Sigma2 values also depend on the distance. The rules given above are for 1st and 2nd shells of atoms. HTH Shelly -----Original Message----- From: Strathmann, Timothy J. Sent: Monday, August 30, 2004 3:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis fit results question 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

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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/

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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

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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/

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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/

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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

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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

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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

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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

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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"

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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 > > >

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RE: [Ifeffit] MoS2 fit
by Kelly, Shelly D. 17 Aug '04

17 Aug '04

Hi Dan, Why are you using only one delr value and two dE values? I would suggest that you try it the other way around. two or more delr values with only one dE value. When you try the different models compare the reduced-chi-square values as you are doing but also look at the Backfourier transfrom of the data and the fit - or the chi(k) data if it is clean. Are they crossing zero at the same places. Do they miss more at low q or high q? Missing at low q/k would suggest separate dE values while missing at high q/k would suggest separate delr values. Would your model be better described by using an overall expansion/contraction term rather than one delr value? Using one delr means that all the paths move by -0.01 angstroms. Using one expansion term would allow all paths to contract by 0.1% which might be more reasonable. So that the long paths shrink in more than the short paths. To use a expansion term use the special "reff" variable which stands for the "effective r" i.e. the effective half path length. set delr1 = alpha*reff set delr2 = alpha*reff guess alpha= -0.01 -yes please drop the third cummulant. HTH Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Tuesday, August 17, 2004 1:24 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] MoS2 fit > > > Hi Mailing list, > > Well, the chief concern I have with my fit now is that > I have some > negative parameters (delr and e0_1): > > Guess parameters +/- uncertainties (initial guess): > > amp = 0.7709790 +/- 0.0631820 > e0 = 1.1165150 +/- 1.0100360 > delr = -0.0106440 +/- 0.0077110 > ss = 0.0032510 +/- 0.0005200 > e0_1 = -4.6848070 +/- 1.7781210 > third = 0.0000370 +/- 0.0001070 > > So, I guess I can drop the third cumulant. > > This is a fit using 6 paths (1,2,3,6 are single scatterers) > These are the results this time around: > > Reduced Chi-square = 410.285252396 > R-factor = 0.014599348 > > As you can see I am still using two e0's, it is still > dramatically improving > the fit. Without: Reduced Chi-square = 1133.485950636 > R-factor = 0.044551155 > > any advice welcomed, Dan > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Re: Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

<excerpt>Hi Dan, At 12:58 PM 8/16/2004 -0700, you wrote: >Scott-- > >Ok, I'll put it on the mailing list from now on, but I used a different model >from the ICSD and it worked muc better. I used the hexagonal model and this is >the results: > >Reduced Chi-square = 382.556284248 >R-factor = 0.015036203 >Do you use these to determine if the fit "doesn't work"? > The improvement in the stats is suggestive that the hexagonal model may be better than the trigonal model. As a rule of thumb, R-factors of below 0.02 are generally indicative of a <italic>statistically </italic>good fit (there may still be other reasons to doubt it!) and between 0.02 and 0.05 is indicative of some problems with the model (perhaps how the parameters are constrained or impurities), but is still on the right track (I've published at that level). The reduced chi-square is nearly worthless as an absolute measure, because of the necessity for having a good estimate of the measurement error. Reduced chi-square <italic>is</italic> useful in the way you're already using it, though...for comparing two fits of the same data. >About separation of the three paths they are here: > ># degen reff amp fs scattering path > 0001 6 2.414 100.00 : [+] S_1 [+] > 0002 6 3.150 59.25 : [+] Mo_1 [+] > 0003 6 3.968 21.22 : [+] S_3 [+] > >What is fitting a third cumulant? You'll see it as a path parameter in Artemis under "third." It is a measure of the asymmetry of the absorber scatterer distance: a positive third cumulant means it is more likely to find the absorber and scatterer a large distance above the mean than a large distance below the mean. It is sometimes helfpul to fit a third cumulant for nearest-neighbors because they are bonded; it is less appropriate for further shells, because the atoms move more independetly. >The two e0's really seems to improve the reduced chi-square. >The two ss's increased the reduced chi-square. > Hmmm...I don't know how you're grouping them between the three paths. I'd try one ss for the nearest-neighbor, and one for the next two paths. You might be doing one for Mo and one for S. > Thanks, Dan > --Scott Calvin Sarah Lawrence College > </excerpt><<<<<<<<

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Re: Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

Dan Carter wrote: >Ok, I'll put it on the mailing list from now on, but I used a different model >from the ICSD and it worked muc better. I used the hexagonal model and this is >the results: > >Reduced Chi-square = 382.556284248 >R-factor = 0.015036203 >Do you use these to determine if the fit "doesn't work"? > >About separation of the three paths they are here: > ># degen reff amp fs scattering path > 0001 6 2.414 100.00 : [+] S_1 [+] > 0002 6 3.150 59.25 : [+] Mo_1 [+] > 0003 6 3.968 21.22 : [+] S_3 [+] > >What is fitting a third cumulant? >The two e0's really seems to improve the reduced chi-square. >The two ss's increased the reduced chi-square. > > Thanks, Dan >

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Re: Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

> >Hi Dan, > >At 12:27 PM 8/16/2004 -0700, you wrote: >> Should I add more paths? > >I always feel more paths are better, until the fit stops working. They will >reduce correlations and uncertainties in general, and also reduce the >incidence of false minima. That does mean you'll have to include some >multiple scattering once you get far enough out, but IMHO poorly >constrained multiple scattering is better than none at all. > >>Is there other parameters that I should add? >>Was it Ok to make 2 separate e0's? > >This is an ongoing debate--it cropped up again on the Ifeffit list >recently. I am not enamored of separate E0's without a very good reason, >but others use them more freely. On the other hand, a separate ss for the >nearest-neighbors from paths further out (I can't tell from your >description if there's a significant separation between the three paths) is >often called for. You might also consider fitting a third cumulant; the >effect on a spectrum is not unlike fitting a separate E0. > >>I think this is a pretty good fit, but I >>feel like there has to be something to improve it. >> > >Seems not unreasonable, although it's hard to tell without uncertainties. >That r-factor is a bit high for a three-path, five parameter fit, though. > >--Scott Calvin >Sarah Lawrence College > >

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Artemis Fit Questions
by Scott Calvin 17 Aug '04

17 Aug '04

Hi all, I've been exchanging emails with Dan Carter, a recent newcomer to EXAFS analysis, and I thought some of the other novices out there might find pieces of it useful. Also, it's always interesting to watch the interplay of the advice from the more experienced users on these basic issues! Therefore, I'm forwarding (with Dan's permission) our exchanges so far to this list (don't worry, there's only a handful!). --Scott Calvin Sarah Lawrence College >Hi Scott, > > Here at Hunter we are trying to make some Li -- MoS2 batteries. >Therefore, I'm trying to do EXAFS on MoS2 and running Artemis on the same. >Basically, I'm trying to create the best fit possible and I was hoping that if >I gave you what I know so far you might be able to give me some suggestions to >improve the fit. > > MoS2 is trigonal or hexagonal depending on who you talk to. >I have 3 paths -- All single scattering below reff = 4 Angstroms. >I made two e0's one for the first path and one for the second, it improved the >fit. All parameters are guesses. > > This is the result I got: >Reduced Chi-square = 809.564600728 >R-factor = 0.039774809 > amp = 0.7511730 > e0 = -1.0221910 > delr = 0.0010090 > ss = 0.0031050 > e0_1 = 2.3828120 > > Should I add more paths? Is there other parameters that I should add? >Was it Ok to make 2 separate e0's? I think this is a pretty good fit, but I >feel like there has to be something to improve it. > > Please help, Dan Carter > >

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a message
by Bruce Ravel 16 Aug '04

16 Aug '04

Hi, A couple weeks ago I received an email from a student at one of the Sao Paolo University campuses named Luis Silva. Luis asked me a question about how to obtain the Ifeffit software. I tried a couple of times to respond to his email, the mail keeps bouncing back with an error message of "Host or domain name not found." I feel badly because he probably thinks I am ignoring him! Does anyone (perhaps one of the Brazilians) on the list know Luis Silva? If so, could you contact him and tell him where to download the Ifeffit package. Thanks! 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/

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Topical issue for XAFS 12
by Scott Calvin 11 Aug '04

11 Aug '04

Hi all, I contacted the Physica Scripta staff about when the XAFS 12 topical issue will be out...thought you might want to know it will be some time next year. --Scott Calvin Sarah Lawrence College > >Dear Dr Calvin, > >The proceedings will be published during the first half of 2005. > >Sincerely, > >Katarina Lundin >Production Editor, Physica Scripta >The Royal Swedish Academy of Sciences >Box 50005 >SE-10405 STOCKHOLM, Sweden >Email: kat(a)physica.kva.se >Voice: +46 8673 9528 >Facsimile: +46 8673 9590 >

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It works great now -- Re: Running Feff
by dmc＠pdx.edu 11 Aug '04

11 Aug '04

Hi, I just clicked on the default value under the "Feff Executable" branch under "Feff" under "Setting." The default is "Feff6I" with an "I" not a "1" and it works great now. Also, next time I forget about the output window, just say so. I was looking in the Artemis Palletes for an output since it pops up and did not see the window behind. Thanks again, Dan

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Running Feff in Artemis -- More info
by dmc＠pdx.edu 11 Aug '04

11 Aug '04

Hi guys, Thanks for the help, I'm sorry I wasnt completely clear. I thought there might be an easy answer and there still may. I will elaborate. I have tried to 'Run Feff' several times. Including several of the Cu database files one your suggestion. Every time, I 'run Atoms' without a hitch and then when I 'run Feff' I get the error message: There are no feffNNNN.dat files...etc. The output window says: 'feff6' is not recognized as an internal or external command, operable program or batch file. I am indeed operating in Windows. I do have the latest updated for Ifeffit. The Feff.INP file does get created in this directory: C:\Ifeffit\horae\stash\artemis.project.3\data0.feff0 It is 6 KB. Maybe this helps some, I will look at some more of your comments to see if I can figure it out. Thanks Again, Dan

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Running Feff -- In Artemis
by dmc＠pdx.edu 10 Aug '04

10 Aug '04

Hi Feff guys, I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out. Thanks, Dan Carter

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Re: Ifeffit Digest, Vol 18, Issue 2
by m.bondin＠pgrad.unimelb.edu.au 03 Aug '04

03 Aug '04

Hi Shelly - thankyou for your detailed response - it helps greatly and is most appreciated. Cheers, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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info sought regarding file locking
by Bruce Ravel 03 Aug '04

03 Aug '04

Hi! In the recent release of Athena and Artemis, I believe I fixed the problem that Windows users were observing that files would get locked when in use by one of my programs. This would be a problem if, say, you imported a file into Athena and then wanted to rename or move that file using the file manager. I am interested to know if anyone is still experiencing any problems of this sort. If so, please describe to me in as much detail as possible what lead to a file getting locked by my program. I will assume that if I do not hear from anyone regarding this, that means that this is working properly. Thanks, 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/

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RE: [Ifeffit] Re: EXAFS analysis of homonuclear metal clusters
by Kelly, Shelly D. 02 Aug '04

02 Aug '04

Dear mailing list - This is a general EXAFS question I decided to post in regards to your collective thoughts and/or experience with this EXAFS analysis approach. I am currently attempting to model a number of Fe-S clusters with nuclearities of 2, 3, 4, 5, and 6. In some cases (where all the Fe atoms are chemically equivalent i.e. same oxidation state and coordination geometry) it is easy to approach this by assuming a single Fe absorber model. When the Fe atoms become inequivalent (oxidation states which may be a mixture of I, II or III, and different coordination geometry) I can average the environments (by including all interactions and ajusting coordination numbers for the different iron atoms accordingly) again into a single Fe absorber model. The fits go well, giving realiable bond lengths (when compared to available crystallographic data), DW's, and statistics (I am also keeping in mind the number of refined parameters to ensure a well over-determined fit for each of the models). My only hesitation, and main reason I am posting this question, is that I am not completely sure this is a reasonable assumption as the Fe atoms are in different oxidation states and will have different E0's. What I do know is there is a shift of roughly 2 to 3 eV in E0 to higher energy for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)). Is there any way of determining if this small difference in energy, and hence E0, between the Fe atoms in the clusters can or cannot be neglected in modelling the EXAFS? Regards, Mark -- Hi Mark, I liked Bruce's response, but since you asked again. I will go out on a limb. I believe that your assumption is justified. The theoretical models built using Feff7 or less do not have different Ezero values based on the valence state of the absorbing atom. The difference is made by choosing a slightly different Ezero at the edge, rather than a difference in K=0 in the theoretical model. In addition, different Ezero's become important at low k-values. Using a kmin of 3.0 inverse angstrom or greater, I would not expect you to need different Ezero's. If you move kmin from something like 3.0 inverse angstroms to 1.5 inverse angstroms you might find that your model no longer works with one Ezero. Also, Ezero and Delr are correlated. So say you know delr then you might be able to "see" a few eV shift in Ezero, assuming that you are using a lot of low k in the data range. If you want to see the shift. Then I would get my hands on the metal oxides for each valence state. And then simultaneously fit each oxidation state together with the mixture...You might be able to pull the info out this way. -As Bruce suggested. It is unlikely that your data range and fit range will support more than one Ezero. To verify that only one Ezero is needed: Try several models with a each shell having it's own Ezero, or two Ezeros or one Ezero. Compare the reduced chi square values of the different models. If the reduced chi square value decreases by a factor of two or more then your data will supports more than one Ezero. Also check the uncertainty in the values for Ezero. If the values overlap considering the error then these Ezero-values are the same and should be only one variable instead of two. I am sure that you can find EXAFS papers of mixed Fe(II)/Fe(III) oxides such as magnetite, Fe2O3. I would guess that they are modeled with a single Ezero. HTH Shelly

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Re: EXAFS analysis of homonuclear metal clusters
by m.bondin＠pgrad.unimelb.edu.au 01 Aug '04

01 Aug '04

Thanks Bruce, I will of course be honest and self critical of my findings in order to support my approach to modelling the data. I also thought I would place this on the list to see if anyone else had encountered, or seen examples re EXAFS analysis of such systems. Apologies about the double post - my email told me the first was not sent and then lost the draft. Cheers, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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EXAFS analysis of homonuclear metal clusters
by m.bondin＠pgrad.unimelb.edu.au 30 Jul '04

30 Jul '04

Dear mailing list - This is a general EXAFS question I decided to post in regards to your collective thoughts and/or experience with this EXAFS analysis approach. I am currently attempting to model a number of Fe-S clusters with nuclearities of 2, 3, 4, 5, and 6. In some cases (where all the Fe atoms are chemically equivalent i.e. same oxidation state and coordination geometry) it is easy to approach this by assuming a single Fe absorber model. When the Fe atoms become inequivalent (oxidation states which may be a mixture of I, II or III, and different coordination geometry) I can average the environments (by including all interactions and ajusting coordination numbers for the different iron atoms accordingly) again into a single Fe absorber model. The fits go well, giving realiable bond lengths (when compared to available crystallographic data), DW's, and statistics (I am also keeping in mind the number of refined parameters to ensure a well over-determined fit for each of the models). My only hesitation, and main reason I am posting this question, is that I am not completely sure this is a reasonable assumption as the Fe atoms are in different oxidation states and will have different E0's. What I do know is there is a shift of roughly 2 to 3 eV in E0 to higher energy for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)). Is there any way of determining if this small difference in energy, and hence E0, between the Fe atoms in the clusters can or cannot be neglected in modelling the EXAFS? Regards, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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one more thing about atoms error
by Carlo U. Segre 29 Jul '04

29 Jul '04

Bruce: One more thing I noticed. If I try FEFF7 there is an error at the same spot, however, FEFF8 and FEFF8-exafs do work. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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EXAFS analysis of homonuclear metal clusters
by m.bondin＠pgrad.unimelb.edu.au 29 Jul '04

29 Jul '04

Dear mailing list, This question relates to an EXAFS analysis approach I am currently investigating in respect to a number of iron-sulfur clusters with nuclearities of 2, 3, 4, 5 and 6. The analysis is easy enough to perform when the Fe atoms in the clusters are chemically equivalent (i.e. same oxidation states and coordination environments) and can be simplified to a single Fe absorber model. The analysis gets a little tricky when the oxidation states of the Fe atoms, and also coordination environments are different hence the sites become chemically inequivalent. The approach that I use takes into account these different environments and resulting populations for each of the iron atoms, again collapsing into a single Fe absorber model and I am able to obtain nice fits of the data with bond distances in close agreement with compounds in which these distances have been obtained through crystallography. The DWs, visual fit and statistics are also well behaved and I have taken into consideration the number of refined parameters to ensure a well over-determined fit to the models (i.e. the data is not simply fitting to anything with lots of fitting variables). The main hesitation I have, and reason for me posting this question, is for the compounds in which the Fe atoms are in different oxidation states we would expect there to be differences in the E0 of these atoms. I know that for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)) there is a shift in E0 to higher energy by roughly 2 to 3 eV (as can be observed in the XANES from studies conducted on mononuclear Fe compounds). I am really not sure as to what extent this effect may alter the EXAFS signal for a cluster. From what I observe in the fitting I would say not much, but I would like to know if this has been encountered, or thought about before by anyone else (i.e. maybe in reference to EXAFS studies on other homonuclear metal cluster systems in catalysis). Regards, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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problems with atoms and tkatoms
by Carlo U. Segre 29 Jul '04

29 Jul '04

Bruce: I have been trying to generate a feff input file with atoms and tkatoms. Here is what happens when I work within artemis I import an atoms.inp that I wrote out previously (attached). This file written out previously when I used it with tkatoms to make a *.xyz file. I notice that it does not properly read the angles but I fill them in anyway. When I run atoms to get the FEFF input file I get the following error: Tk::Error: Illegal division by zero at /usr/share/perl5/Xray/ATP.pm line 634. Xray::ATP::ATP_corrections at /usr/share/perl5/Xray/ATP.pm line 634 Xray::ATP::parse_atp at /usr/share/perl5/Xray/ATP.pm line 387 main::run_atoms at /usr/bin/artemis line 5565 [\&main::run_atoms] Tk callback for .frame3.canvas2.frame.notebook.atoms.frame2.button1 Tk::__ANON__ at /usr/lib/perl5/Tk.pm line 225 Tk::Button::butUp at /usr/lib/perl5/Tk/Button.pm line 111 (command bound to event) main::__ANON__('Tk::Error: Illegal division by zero at /usr/share/perl5/Xray/...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 409 Tk::Error('MainWindow=HASH(0x96d864c)', 'Illegal division by zero at /usr/share/perl5/Xray/ATP.pm line...', 'Xray::ATP::ATP_corrections at /usr/share/perl5/Xray/ATP.pm li...', 'Xray::ATP::parse_atp at /usr/share/perl5/Xray/ATP.pm line 387', 'main::run_atoms at /usr/bin/artemis line 5565', '[\&main::run_atoms]', 'Tk callback for ..frame3.canvas2.frame.notebook.atoms.frame2.b...', 'Tk::__ANON__ at /usr/lib/perl5/Tk.pm line 225', 'Tk::Button::butUp at /usr/lib/perl5/Tk/Button.pm line 111', ...) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1792 If I run the same input file in tkatoms, I get a popup saying there is a divide by zero in ATP.pm line 634. If I try to generate an *.xyz file it works fine. I am using the latest version of horae. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Importing in Athena
by Dave Baker 29 Jul '04

29 Jul '04

I have recently been looking at some standards and I came across some Cu foil data in a two-column .dat format; "energy" and "xmu". (Incidentally, it is standard data taken in '92 by none other than Bruce R. and Matt. N.) Anyway, the data seems to load just fine using either the "xmu.dat" or the "Mu(E)" import profile, and I can remove backgrounds, do both forward and backward FT's and generally manipulate the data normally. Everything is fine until I try to save the chi(k) data. The program displays that it's saving the file, but does not report success. The file is indeed written, but with a file size of zero. Following this attempt, the graph may or may not be stuck in the last plot, and if it is stuck, no amount of frantic clicking on my part changes it. The Ifeffit buffer is empty, and there are no error trap files. -Dave Baker ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ --

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RE: [Ifeffit] artemis development in the near future
by SCHLEGEL Michel 177447 29 Jul '04

29 Jul '04

Bruce, > * Windows users who would like to be involved with the development > branch should consider installing ActiveState's perl distribution > on their computers as that would allow you to test the source code > as it becomes available. If anyone is interested in this, I can > help get you started. But I would encourage only the enthusiastic > to consider this. Most users will prefer to use the executables > that I will build for the stable version. Well, to paraphrase some recent declaration, sometimes you have Activestate, sometimes, you haven't, there's this little third category... Yes, I have installed ActiveState a long time ago, but that was just to run some script, and it is unclear to me if you plan to run the development versions of Athena and Artemis as script, or if you will ask each and every Windows user to compile his/her own little executable. In the later case, You'll have to explain me. Othervise, the new version runs fabulously great, apart from a minor point: I can't fit simultaneously several spectra (polarization data) in q-space. TApparently Artemis traps some kind of error message. but the software keeps on running. Otherwise, there's a little practical point which bothers me: when it comes to publishingand citing, we know how to shower praise on Matt, but we are still yearning for some sound reference for the Ravelware. Is there any chance that this 'bug' will get fixed in the near future? Best regards, Michel Schlegel

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RE: [Ifeffit] artemis development in the near future
by SCHLEGEL Michel 177447 29 Jul '04

29 Jul '04

Bruce, > On Wednesday 28 July 2004 12:47 pm, SCHLEGEL Michel 177447 wrote: > > versions of Athena and Artemis as script, or if you will ask each and > > every Windows user to compile his/her own little executable. In the > > later case, You'll have to explain me. > > Well, the point I was trying to make was that building and testing > windows executables adds considerably to my work. I would like to be > able to release the development version frequently -- the > early-and-often approach to software development. If I have to build > windows exes everytime, that will slow me down, wear me out, and make > it not worth my time to bother with the whole idea of a fork. Yes, I now, we Windows user recriminate a lot, demand even more, and offer little in return.. ;-) > > Othervise, the new version runs fabulously great, apart from a minor point: > > I can't fit simultaneously several spectra (polarization data) in q-space. > > TApparently Artemis traps some kind of error message. but the software > > keeps on running. > > OK, thanks for the report. I'll look into it. q-space fitting is not > one of the well-tested corners of the code since I never do > that myself. I am aware of Matt's recommandation - that fitting in R-space should be preferred. However, there are sometimes informations in the q-space on the nature of backscatterers from, e.g., the shape of the amplitude enveloppe of the Fourier-filtered contribution. Plus, it is always interesting to compare fitting results in both spaces. I ran a test fit in q-space with four spectra and Artemis 0.7.008. It seems that the fitting stage is performed well, and the fitting results in the q-space are even displayed in the Graphics windows. Trouble seems to arise when Artemis tries to write the log file. The 'Artemis palettes' windows doesn't appear on the screen. I then tried to fit into R-space (worked well), and again into q-space: the same error message appeared. I copied the message displayed on the console into the attached file. Best regards, Michel Schlegel

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RE: Ifeffit Digest, Vol 17, Issue 23
by yaelp 29 Jul '04

29 Jul '04

didnt get any instruction thanks yael >===== Original Message From ifeffit(a)millenia.cars.aps.anl.gov ===== >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: weights data processing (Bruce Ravel) > 2. Re: EXAFS question (Bruce Ravel) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 26 Jul 2004 09:06:13 -0400 >From: Bruce Ravel <ravel(a)phys.washington.edu> >Subject: Re: [Ifeffit] weights data processing >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <200407260906.13553.ravel(a)phys.washington.edu> >Content-Type: text/plain; charset="iso-8859-1" > > >I wanted to add a coupe more comments on Stafano's questions regarding >k-weighting in Athena and Artemis. > >Regarding k-weights in Athena: Athena's default for the k-weight using >background removal is 1. I chose that pretty much for the reason that >Scott gave. Ifeffit's default is 0, so this is a situation where >Athena and Ifeffit have different default behavior. As for the >insensitivity of your data to this value, I would say that it is >situational. Sometimes, the k-weight can have a dramatic influence on >the background removal. Stability of the background removal and its >impact on subsequent analysis has been a frequent topic of discussion >in this forum. k-weight, then, is yet another parameter that can >impact the stability of your spline. > >Rgearding k-weights in Artemis: Scott and Matt covered the "why" of >k-weights. How k-weights are actually used by Artemis when fitting >and plotting is a bit complicated. See section 5.8.4 of the >(incomplete) artemis document for a detailed explanation of how >k-weighting is used in Artemis. > http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf > >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/ > > > >------------------------------ > >Message: 2 >Date: Mon, 26 Jul 2004 09:37:31 -0400 >From: Bruce Ravel <ravel(a)phys.washington.edu> >Subject: [Ifeffit] Re: EXAFS question >To: "Norman White" <gn-white(a)tamu.edu> >Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <200407260937.31266.ravel(a)phys.washington.edu> >Content-Type: text/plain; charset="iso-8859-1" > >Norman, > >Your question is the sort of thing that is appropriate for the Ifeffit >mailing list, so I am CCing my answer there. You should consider >joining the mailing list. It is a great resource and gives you access >to a large number of experts who can answer your questions. > > >On Friday 23 July 2004 03:38 pm, Norman White wrote: >NW> In going through Matt Neville's xas_fun_slides.pdf file that was >NW> included with the Athena software, I noticed on slide 36: > > MN > The Fe-O distance in FeO is 2.14 � A, but the first peak is at 1.6 � A. > MN > This shift in the first peak is due to the phase-shift, > MN > delta(k): sin[2kR + delta(k)] . > MN > A shift of -0.5 � A is typical. > > >NW> I asked him in an e-mail about the shift and he said (edited): > > MN > For traditional XAFS analysis, we do a relatively simple Fourier > MN > transform. This simple FT would give a peak in chi(r) at 'R' if > MN > the oscillatory part was sin[2kR]. Since it's sin[2kR + delta(k)] > MN > instead, there's a shift. > MN > > MN > It turns out that, to first order, delta(k) is linear and has a > MN > negative slope of about 1: > MN > delta(k) ~= -k ~= -2k (0.5), > MN > > MN > so that the shift in phase is about 0.5A. > >NW> I asked if this was true for all elements and he said: > > MN > It's a typical value for most bonds, but shouldn't be taken as an > MN > accurate number (and it's easy enough to calculate). > >NW> >NW> How is an accurate shift calculated? Is this correction performed > >This calculation is computed quite accurately by Feff. Indeed, >getting that calculation (and the related calculation of the >scattering amplitude) correct is the raison d'etre of Feff. > >NW> automatically in Athena? If it is a constant, why is it not simply >NW> included in the step producing the radial distribution function from >NW> the k values? Can it be accurately calculated? The manual had >NW> statements that seemed to imply that it could be calculated with the >NW> Atoms program but did not explain how at a level I understood. >NW> >NW> Matt neville stated in an e-mail that: > MN > The phase shift correction can be made fairly easy with > MN > SixPack and with Artemis as well as Ifeffit. > >It's not a constant and treating it as such would be specious at best, >and it is not something that Athena intends to compute. However, >since it is something that Feff computes, one can imagine using the >results of Feff. How this is done is slightly different in Athena as >in Artemis. > >At the level of Athena, we know the absorbing atom but it is not >actually necessary to know what the material is to use Athena >effectively. In Artemis, on the other hand, we do have to know >something about what the materials is. This difference between the >two explains the rationale for how phase correction works i the two >programs. > >In Athena, only a central atom phase correction is supported. This is >enabled by clicking the button that says "phase correction" in the >forward trasform section of the mail window. With that button >clicked, the central atom phase shift is subtracted from the data >before the transform is made. When you plot chi(R), then, the >transform will be peaked a little bit to the right of where it was >peaked without that button clicked. > >Artemis does a somewhat better job of this. In Artemis, you can >select a path to use for pase correction. With a path selected, the >central *and* scattering atom phase shifts will be subtracted before >transforming. This is possible in Artemis because we have the fuill >information about the material and the full feff calculation at our >disposal. In Athena, in contrast, we only know about the absorber and >I have never implemented (and don't really intend to do so) a way of >reading in a feff path for the purpose of phase shifted transforms. > >NW> >NW> I could not find where it explained how to do this. > >Did you read any of the documentation? > >For Athena: >http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Athena/athena… isc.html > The document is also available within Athena via the Help menu. > >For Artemis: Section 5.8.5 of >http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf > > >NW> I am looking at As adsorption on Fe-Al oxides and other minerals >NW> I know what the central atom is As. >NW> I can also estimate the oxygen bondlengths and the As-cation distance from >NW> the "corrected" EXAFS pattern and the literature. Is it possible to >NW> simulate an EXAFs pattern? >NW> Is so, how? > >Yes. > >Have you read the Artemis manual? > >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/ > > > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 17, Issue 23 >***************************************

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athena 0.8.030, artemis 0.7.008, hephaestus 0.04
by Bruce Ravel 28 Jul '04

28 Jul '04

Hi folks, A new tarball of the source for Athena, Artemis, and Hephaestus is now available at SourceForge and at my website. Linux, unix, and Mac OSX users can grab it or use the horae_update script at their leisure. Windows users will have to wait just a bit longer. Matt and I have almost settled on the new Windows release. More details should follow later this week. There are only a few new features in the codes this time around. The bulk of the changes are various bug fixes which should address the majority of the problems reported in the last two months. In particular, Artemis should now be a lot more stable. As always, please report any new problems you find with the new versions or any old problems that I did not actually fix! Among the changes to the Artemis: 1. An autosave file is written at certain times so that you can recover work in the event of a crash. 2. Artemis now uses a native menubar. This means that the menus can be driven entirely from the keyboard using (on PC keyboards) the Alt key. 3. There are a couple of small changes in functionality on the GDS page. Now, if you click on a different variable while editing a variable, the first variable will be defined before the new one is displayed. 4. The General->workspace variable is no longer used. I apologize to those who used this feature, but it was the source of too many problems. 5. The writing of trap files has been disabled in this version, but the same information still gets written to the console and should be included by cut-n-paste in bug reports. In Hephaestus there is a new page which shows a chart of the electronic transitions associated with the various single-electron fluorescence lines. Athena just has a bunch of bug fixes. It does not yet use a native menu bar. (Next time for sure!) A final note about Artemis. There is no drag-n-drop functionality anywhere in the program. It is quite easy to trigger a bug when the GDS page is displayed if you click the mouse button and then drag the mouse to another part of the Artemis window. I do not know the cause of this bug, but it is easy to avoid. Regards, 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/

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artemis development in the near future
by Bruce Ravel 28 Jul '04

28 Jul '04

Hi folks, As some of you may know, I have been planning for a while to fork Artemis into two branches -- stable and development. It's going to work something like this: * The current version (0.7.008) will be the stable version. (Yes, I am fully aware of the irony of calling any version of Artemis "stable". ;-) For the next couple of months the feature set of stable Artemis will not change. I will only be fixing bugs as they become known. This will be the version recommended for most users. * The current version will be the base of the development version. I will add new features to this branch. Hopefully there will be enough users of the development branch that these new features will be sufficiently exercised as I get them written. * At some point I will decide to freeze the development branch and shift it down to the stable branch. That way, new features will eventually become available to the users of the stable branch, but only after they have been tested for a while. Hopefully, that will avoid some of the troubles we have had since version 0.7.000. * I will promise to make windows executables for every release of the stable branch. I won't promise to do so for every release of the development branch. * I haven't quite decided how to deal with numbering, but the stable branch will continue incrementing the minor number. The development branch will either start at 0.8.000 or at 0.7.500. In either case, the horae_update script will be modified to update either branch. * Windows users who would like to be involved with the development branch should consider installing ActiveState's perl distribution on their computers as that would allow you to test the source code as it becomes available. If anyone is interested in this, I can help get you started. But I would encourage only the enthusiastic to consider this. Most users will prefer to use the executables that I will build for the stable version. * I am not planning to fork any of my other programs. Specifically, I do not see a benefit to forking Athena. Finally, here is a partial list of features that are on the drawing board for the development branch: 1. Update the atoms page to use an interface modeled on the new GDS page. 2. Enhanced functionality of the feff interpretation page 3. Keep a history of all fits run. This will allow such things as over-plotting of different fits with the data, comparison of the log files from different fits, and so on. 4. Generation of math expressions for delta_R based on the crystal parameters used in atoms. 5. Import of CIF files. 6. Import of PDB files and conversion to feff.inp format. 7. A bunch of internal modifications that will not be user visible but will support some of the changes above and will need extensive testing. OK, that's all the news that's fit to print. I hope that people are downloading and trying out the new release. 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/

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horae 038 Debian packages
by Carlo U. Segre 28 Jul '04

28 Jul '04

The horae packages for Debian have been built and are at my apt repository. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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RE: [Ifeffit] artemis development in the near future
by Jensen, Mark P. 28 Jul '04

28 Jul '04

Michel is right Bruce! We need a Ravelware reference to cite. That is a major bug! ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: SCHLEGEL Michel 177447 [mailto:schlegel@azurite.cea.fr] > Sent: Wednesday, July 28, 2004 10:48 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] artemis development in the near future > > Bruce, > > > * Windows users who would like to be involved with the development > > branch should consider installing ActiveState's perl distribution > > on their computers as that would allow you to test the > source code > > as it becomes available. If anyone is interested in this, I can > > help get you started. But I would encourage only the > enthusiastic > > to consider this. Most users will prefer to use the executables > > that I will build for the stable version. > > Well, to paraphrase some recent declaration, sometimes you > have Activestate, sometimes, you haven't, there's this little > third category... > > Yes, I have installed ActiveState a long time ago, but that > was just to run some script, and it is unclear to me if you > plan to run the development versions of Athena and Artemis as > script, or if you will ask each and every Windows user to > compile his/her own little executable. In the later case, > You'll have to explain me. > > Othervise, the new version runs fabulously great, apart from > a minor point: > I can't fit simultaneously several spectra (polarization > data) in q-space. > TApparently Artemis traps some kind of error message. but the > software keeps on running. > > Otherwise, there's a little practical point which bothers me: > when it comes to publishingand citing, we know how to shower > praise on Matt, but we are still yearning for some sound > reference for the Ravelware. > Is there any chance that this 'bug' will get fixed in the near future? > > Best regards, > > Michel Schlegel > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Ifeffit 1.2.6 for Windows
by Matt Newville 27 Jul '04

27 Jul '04

To follow up on Bruce's announcement: The full installer for Windows is now ready and available from http://cars9.uchicago.edu/ifeffit/download.html The Windows installer includes Ifeffit 1.2.6, and the latest versions of SixPack (0.50) and Horae (that is, Athena 0.8.030, Artemis 0.7.008, Hephaestus 0.04, and TkAtoms 3.0beta9), and can be downloaded either from the cars.uchicago.edu server or from the sourceforge.net server. An update for Windows (update #10) is also available, though this update is relatively large (~12Mb: almost half the size of the installer itself!). For those of you who are using the programs regularly, it may be worth the effort to download the full installer. --Matt

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RE: [Ifeffit] Re: Artemis Question
by Kelly, Shelly D. 27 Jul '04

27 Jul '04

Hi John, I have a couple of comments to add to Bruce's reply: Feff is truly amazing. You can take a crystal structure for a Metal-oxide and apply it to a hydrated metal atom in solution with great success. -You can also do other non-physical things to the feff list of atoms and apply it to a real problem. There are a couple of thing to keep in mind. 1) Feff needs to have a list of atoms that extends well beyond the paths that are actually used in the fit. Always pad the feff.inp file by at least an Angstrom. If you are using feff calculation for the first time. Pad the feff list by one angstrom and then by two angstroms and check that the paths that you are going to use are the same. You do not want to use paths from the edges of the cluster that you give to feff in the feff.inp file. -Hence you need to use a structure like a metal-oxide to model a hydrated metal. 2) If you think that you have some unique geometry, linear multiple scattering paths then you need to be more careful to get these paths correct in the feff.inp file since they will have unique scattering amplitudes. 3) If the actually distance for the path included in the fit is different from the starting distance as given by the feff list, then you need to re-run the feff calculation. If you are just playing around you can move the paths by 0.5 Angstroms to get an idea that the path will work. In the final published fit, I like to see the change in the path length much less than this. If you are looking at solutions a great place to start is with the metal and the metal-oxide. Shelly > -----Original Message----- > From: Bruce Ravel [mailto:ravel@phys.washington.edu] > Sent: Tuesday, July 20, 2004 5:40 PM > To: XAFS Analysis using Ifeffit > Cc: John Butler > Subject: [Ifeffit] Re: Artemis Question > > > On Sunday 18 July 2004 11:38 pm, John Butler wrote: > > Basically, the problem that I'm having is that the system > I'm working > > on is a solution (to start I'm trying to look at a solution of Zinc > > Sulfate and then look at data with other components we're > interested > > in). Unfortunately, the part of the manual dealing with solution > > analysis hasn't been written yet, and the people I know who > use EXAFS > > don't do anything with solutions. > > > > I was hoping that you could point me in the right direction > for how to > > proceed with the analysis (e.g. is there anywhere I'm > likely to find > > the FEFF files ... is there a 'standard' way to attack this kind of > > problem). Of course I assume you're a pretty busy guy and have > > neither the time nor inclination to give me a detailed step by step > > guide or anything ... I was just hoping you could point me in the > > right direction, give me a couple of tips, and/or show me where to > > look. > > John, > > As you can see, I have forwarded you question along with my > answer to the > Ifeffit mailing list. > > You are correct to assume that I'm a busy guy. This week > (like each of the > other weeks this month) I am at NSLS collecting some data and > helping our > users. Fortunately, the mailing list is a solution to the > "busy expert" > problem. Enough people read and respond to the mailing list > that someone > should be available to answer just about every question. > > I doubt, actually, that you problem is really so hard to get > started with.. > Lots of problems in XAFS do not fall into nice little pigeon > holes. One > knows how to deal with data on an iron foil because one knows > what the > structure of iron metal is. Most real research problems, > obviously enough, > are problems precisely because the structure is not perfectly > well known. > > In the case of a solvated complex, there is probably some > sort of analogue > which can be used as a starting place. Perhaps there is some similar > compound whose structure *is* known. Perhaps your solvated > complex has a > crystalline form that is similar, at least in the local > environment, to the > solvated form. In any case, find something that is similar > to your real > material. Run feff and compare to the data. Perhaps your > analogue structure > will be close to your data. In that case, you should be able > to parameterize > the feff calculation in such a way that you can begin to > understand the ways > in which your complex differs from your analogue. > > Perhaps the analogue structure is a very poor match for the > data. That in > itself is information, in that it tells you to go look for a > different > analogue. > > The common theme to what I have said here (and indeed to any > analysis problem) > is that you make some educated guesses as to what you real > sample looks like. > You test those guesses. If they seem to be leading you in the right > direction, super. If not, make new (and newly educated!) guesses. > > My other piece of advice would be to spend some time fitting > known spectra. > If you are new to XAFS, then you are learning two things at > the same time: > how to interpret XAFS data and how to use my and Matt's > screw-ball analysis > programs! I consider it a good idea to spend some time > fitting data for > which you know the answer so that you can learn how to use > the codes before > plunging into the harder but more interesting problem of your > own research. > > Good luck and join the mailing list, > B > > > -- > Bruce Ravel ----------------------------------- > ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 > 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/ > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Re: EXAFS question
by Bruce Ravel 26 Jul '04

26 Jul '04

Norman, Your question is the sort of thing that is appropriate for the Ifeffit mailing list, so I am CCing my answer there. You should consider joining the mailing list. It is a great resource and gives you access to a large number of experts who can answer your questions. On Friday 23 July 2004 03:38 pm, Norman White wrote: NW> In going through Matt Neville's xas_fun_slides.pdf file that was NW> included with the Athena software, I noticed on slide 36: MN > The Fe-O distance in FeO is 2.14 ° A, but the first peak is at 1.6 ° A. MN > This shift in the first peak is due to the phase-shift, MN > delta(k): sin[2kR + delta(k)] . MN > A shift of -0.5 ° A is typical. NW> I asked him in an e-mail about the shift and he said (edited): MN > For traditional XAFS analysis, we do a relatively simple Fourier MN > transform. This simple FT would give a peak in chi(r) at 'R' if MN > the oscillatory part was sin[2kR]. Since it's sin[2kR + delta(k)] MN > instead, there's a shift. MN > MN > It turns out that, to first order, delta(k) is linear and has a MN > negative slope of about 1: MN > delta(k) ~= -k ~= -2k (0.5), MN > MN > so that the shift in phase is about 0.5A. NW> I asked if this was true for all elements and he said: MN > It's a typical value for most bonds, but shouldn't be taken as an MN > accurate number (and it's easy enough to calculate). NW> NW> How is an accurate shift calculated? Is this correction performed This calculation is computed quite accurately by Feff. Indeed, getting that calculation (and the related calculation of the scattering amplitude) correct is the raison d'etre of Feff. NW> automatically in Athena? If it is a constant, why is it not simply NW> included in the step producing the radial distribution function from NW> the k values? Can it be accurately calculated? The manual had NW> statements that seemed to imply that it could be calculated with the NW> Atoms program but did not explain how at a level I understood. NW> NW> Matt neville stated in an e-mail that: MN > The phase shift correction can be made fairly easy with MN > SixPack and with Artemis as well as Ifeffit. It's not a constant and treating it as such would be specious at best, and it is not something that Athena intends to compute. However, since it is something that Feff computes, one can imagine using the results of Feff. How this is done is slightly different in Athena as in Artemis. At the level of Athena, we know the absorbing atom but it is not actually necessary to know what the material is to use Athena effectively. In Artemis, on the other hand, we do have to know something about what the materials is. This difference between the two explains the rationale for how phase correction works i the two programs. In Athena, only a central atom phase correction is supported. This is enabled by clicking the button that says "phase correction" in the forward trasform section of the mail window. With that button clicked, the central atom phase shift is subtracted from the data before the transform is made. When you plot chi(R), then, the transform will be peaked a little bit to the right of where it was peaked without that button clicked. Artemis does a somewhat better job of this. In Artemis, you can select a path to use for pase correction. With a path selected, the central *and* scattering atom phase shifts will be subtracted before transforming. This is possible in Artemis because we have the fuill information about the material and the full feff calculation at our disposal. In Athena, in contrast, we only know about the absorber and I have never implemented (and don't really intend to do so) a way of reading in a feff path for the purpose of phase shifted transforms. NW> NW> I could not find where it explained how to do this. Did you read any of the documentation? For Athena: http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Athena/athena… The document is also available within Athena via the Help menu. For Artemis: Section 5.8.5 of http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf NW> I am looking at As adsorption on Fe-Al oxides and other minerals NW> I know what the central atom is As. NW> I can also estimate the oxygen bondlengths and the As-cation distance from NW> the "corrected" EXAFS pattern and the literature. Is it possible to NW> simulate an EXAFs pattern? NW> Is so, how? Yes. Have you read the Artemis manual? 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/

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RE: [Ifeffit] Re: Artemis Question
by Kelly, Shelly D. 26 Jul '04

26 Jul '04

Hi Scott, Feff uses the placement of the atoms to determine the size of the muffin tin radius and the norman radius, which define where the atom is verse where the atom is not. If there are no neighboring atom then these radii become unphysically large and then the scattering amplitudes will not be accurate. -Copper is kinda special. Copper has 12 neighboring atoms, so the muffin tin radii are pretty well constrained even with one shell. If you run a feff calculation with all the Cu atoms in a cluster to 7 Angstroms the top of the feff0001.dat file shows the radii for the atoms and it looks something like this: For large cluster Rmax=7.0 Angstroms: #Copper, Kittel, ISSP Feff 7.02 # metal, fcc # Abs Z=29 Rmt= 1.305 Rnm= 1.454 K shell # Pot 1 Z=29 Rmt= 1.273 Rnm= 1.391 # Gam_ch=1.761E+00 H-L exch # Mu=-5.472E+00 kf=1.724E+00 Vint=-1.679E+01 Rs_int= 2.104 Now do it again for N=12 and Rmax=3.0 For small cluster Rmax=3.0 Angstroms, N=12 # Copper, Kittel, ISSP Feff 7.02 # metal, fcc # Abs Z=29 Rmt= 1.233 Rnm= 1.467 K shell # Pot 1 Z=29 Rmt= 1.282 Rnm= 1.570 # Gam_ch=1.761E+00 H-L exch # Mu=-4.594E+00 kf=1.474E+00 Vint=-1.287E+01 Rs_int= 2.461 And again for N=2 and Rmax =3.0 For small cluster Rmax=3.0 Angstroms, N=2 #Copper, Kittel, ISSP Feff 7.02 # metal, fcc # Abs Z=29 Rmt= 1.256 Rnm= 1.815 K shell # Pot 1 Z=29 Rmt= 1.296 Rnm= 1.872 # Gam_ch=1.761E+00 H-L exch # Mu=-3.892E+00 kf=1.204E+00 Vint=-9.411E+00 Rs_int= 3.013 You can see that the norman radius gets really big for the last case, 1.391 to 1.570 to 1.872 and as a result the scattering amplitude changes. I show a comparison of the chi(k)xk for each of these inputs with a N=1.0, DE=0, SS=0, S02=1.0, DR=0 in the attached clustersize.jpg file. Shelly > -----Original Message----- > From: Scott Calvin [mailto:SCalvin@slc.edu] > Sent: Wednesday, July 21, 2004 9:53 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Re: Artemis Question > > > Shelly said: > > > > >Feff is truly amazing. > > Amen! > > >1) Feff needs to have a list of atoms that extends well beyond the > >paths that are actually used in the fit. Always pad the feff.inp > >file by at least an Angstrom. If you are using feff calculation for > >the first time. Pad the feff list by one angstrom and then by two > >angstroms and check that the paths that you are going to use are the > >same. You do not want to use paths from the edges of the cluster > >that you give to feff in the feff.inp file. -Hence you need to use > >a structure like a metal-oxide to model a hydrated metal. > > Under what circumstances does FEFF actually need these extra atoms? > When I take the copper example included by Artemis, for example, I > can rerun the FEFF calculation with a cluster size of 3 angstroms, so > that FEFF only has the nearest-neighbors to deal with. The path > generated is identical to when a cluster size of 7 angstroms. > Certainly if someone is using FEFF8 with a self-consistent field > calculation it is necessary to have the cluster extend beyond the > furthers paths, but with FEFF6L is this true? > > (Incidentally, for the novices out there, I do NOT recommend being > satisfied with a single-shell fit when you have a reasonable guess as > to the structure beyond the first-shell. One reason can be seen > easily with Artemis: paths beyond the first-shell often have low-R > "tails" that contribute to the signal even at the first-shell peak. > Although the FEFF calculation for the first path may be the same > whether or not you also calculated paths further out, the Ifeffit fit > will be different depending on whether you include those "outer" > paths or not.) > > --Scott Calvin > Sarah Lawrence College > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] weights data processing
by Kelly, Shelly D. 23 Jul '04

23 Jul '04

> -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Friday, July 23, 2004 6:31 AM > To: ravel(a)phys.washington.edu; XAFS Analysis using Ifeffit > Subject: [Ifeffit] weights data processing > > > Hi folks, > > 1) when removing background using athena, there is an option of using > a k-weight different than 1 (I am NOT talking about k-weight for FT). > I noticed that changing this parameter the resulting chi(k) does not > change significantly. Actually, going from 1 to 4 as a value for > k-weight for Bkgd removal, the only effect I see is a significant > reduction of the peak below the first coordination shell in chi(R) > while the other features of the spectrum are essentially the same in > terms of absolute and relative intensity. A drastic change in both > chi(k) and chi(R) is seen if I use k-weight = 5 and above. What is > the exact meaning of it? I know what the meaning is in the FT > process, but I do not see the reason why I should use a weight > different than 1 (let's say 3 for my noisy data) for background > removal. How should I behave? Should I take the largest value of > k-weight so that the essential features of the chi(k) and chi(R) do > not change? Hi Stefano, I have found a procedure for removing the background that "almost" always works well. It goes something like this and uses different k-weightings in the background removal process. 1) Check out the curvature of the XANES region and how quickly the data goes from zero to 1, call this DExanes. There are in my small opinion two categories for each of these different parameters. Curvature of Xanes can be step like or it can have a large peak. DExanes can be small ~10eV for k-edges of Cu or wide ~30eV for L3-edge of U. 2) Choosing Ezero for the first time: If you have a wide DExanes, then choose Ezero up near the top of the edge. If you have a small DExanes, then choose Ezero around the middle of the edge. 3)Set kweight equal to one or zero (and no theory) and remove the background. This will emphasize the low k-region around the edge, but often get the background for the higher k-region not as well...especially for noisy data. 4)Check out the shape of the background function, the chi(k) data and the FT. Make sure that rbkg=1.0 is a reasonable thing to do. Make sure that you look at the chik data with all three k-weights. Often people say that there is no change in the chik data by changing the kwieght but they are looking at the chik*k3. The change will be greatest at low k, which you don't really see with chik*k3. 5) If you have a large peak in the XANES region, Athena may need help getting the bkg to go through that peak. You have two options. A) increase rbkg so that the spline has more freedom to curve in this region. or B) increase kmin of the spline range, essentially removing the large peak from the data. 6) Fit the first shell of your data, use a well padded chik data range...don't include at least one full oscillation at the beginning. i.e. use kmin=3 or greater. Monitor the value for ezero. If it is greater than 10eV you need to start over. (I have some more details on how to create a theory to be used for bkg removal on my web site http://www.mesg.anl.gov/Skelly.html from the 2004 NSLS EXAFS workshop presentation) 7) Read the theory back into Athena. Now Athena knows what the low k-range should look like, and you can increase the k-weight of the background, use kw=2 or 3, to get the high k-range part of the data correct as well. 8) Fit the data again and use as much of the k-range as possible. > > 2) In artemis, is it a bug or a wanted feature to have the > possibility to activate more than one button for k-weight for the fit > and FT? I suppose it is a wanted feature, but then I wonder what is > the meaning of using more than one weight for the fit and FT. I am > sure some of you can unveil this enigma. > Another couple of reasons to use more than 1 k-weight in the FT of the data: I have found that the uncertainties in the fitted values are about half as big by using all three k-weights, as opposed to using just one k=weight. I have also found that using all three k-weights will force you to model the data much more correctly. When you look at the fits, you need to look at the FT and the chi(k) data using all three k-weights. HTH Shelly

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Re: [Ifeffit] Solution flow cells
by Scott Calvin 23 Jul '04

23 Jul '04

Thanks to all for the references, advice, etc.! This list really works wonders sometimes... --Scott Calvin Sarah Lawrence College

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using atoms and feff
by Barton, David (DG) 23 Jul '04

23 Jul '04

I agree with Scott, the ICSD database of crystallographic structures has also been invaluable to my work on inorganic solids. However, the ICSD is truly an inorganic database in that it does not contain any compounds that contain carbon. For small molecule crystalline compounds that contain carbon the Cambridge Structural Database (http://www.ccdc.cam.ac.uk/ <http://www.ccdc.cam.ac.uk/> ) is quite useful. It contains ~300,000 crystal structures of organic and organometallic compounds. However, this database comes with a significant price tag, but if you can get access it is an amazing tool. Both of these crystallographic databases will write out the records in the CIF (Crystallographic Information File) format. I have written a command line Perl program which converts these CIF records to Atoms.inp files which can be used directly with Artemis. Shelly Kelly was kind enough to host the files: http://146.137.194.45/exafs.html <http://146.137.194.45/exafs.html> . Eventually, we may see a CIF import feature based on this code included in Artemis. Another Crystallographic File converter that I have found useful is CRYSCON (ShapeSoftware: http://www.shapesoftware.com/ <http://www.shapesoftware.com/> ). This shareware program will interconvert nearly all crystallographic file formats and, at my request, the author recently added support to export files with Ravel's ATOMS file format. Dave Barton The Dow Chemical Company, DND-CAT member at APS

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RE: Ifeffit Digest, Vol 17, Issue 18: RE: Solution flow cells
by Wojciech Gawelda 23 Jul '04

23 Jul '04

Dear Scott, We have done some time-resolved XAFS measurements on aqueous solution of Ru(II)(bpy)3 complex using free-flowing jet. It forms a liquid sheet of approx. 100 microns thickness and thus you can avoid windows etc. However you might run into some trouble when using in vacuum. In principle you can find many manufacturers who provide these kinds of jets equipped with sapphire nozzles for dye lasers. I know that some of these jets are also used for cutting and polishing jewelry...if you need any more details you could look up our paper about the setup: M. Saes et al., Rev. Sci. Instrum., 75(2004), 24-30. I hope it helps, Wojciech Gawelda ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: wojciech.gawelda(a)epfl.ch WWW: http://lsu.epfl.ch ********************************************************************* -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: vendredi, 23. juillet 2004 08:47 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 17, Issue 18 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. Solution flow cells (Scott Calvin) 2. RE: Solution flow cells (Kelly, Shelly D.) 3. Re: Solution flow cells (Tsu-Chien Weng) 4. RE: Solution flow cells (Matt Newville) 5. RE: Solution flow cells (Jensen, Mark P.) 6. RE: Solution flow cells (SCHLEGEL Michel 177447) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Jul 2004 15:34:00 -0400 From: Scott Calvin <scalvin(a)slc.edu> Subject: [Ifeffit] Solution flow cells To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <3.0.1.32.20040722153400.00b14170(a)mail.slc.edu> Content-Type: text/plain; charset="us-ascii" Hi all, I've been doing a literature search for an article I'm writing up, and I can't seem to find any examples of an XAS flow cell desgined for liquids. Sealed cells for liquids, yes; flow cells for passing gases over solids, yes; but no solution-chemistry flow cell. I feel like someone must have published work in that area before, but I can't seem to find it. So, does anyone know of any work done using a liquid-phase XAS flow cell? --Scott Calvin Sarah Lawrence College ------------------------------ Message: 2 Date: Thu, 22 Jul 2004 14:55:29 -0500 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: RE: [Ifeffit] Solution flow cells To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A267F(a)ANLMAIL.anl.gov> Content-Type: text/plain; charset="us-ascii" Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly ------------------------------ Message: 3 Date: Thu, 22 Jul 2004 16:44:40 -0400 From: Tsu-Chien Weng <tsuchien(a)umich.edu> Subject: Re: [Ifeffit] Solution flow cells To: Scott Calvin <scalvin(a)slc.edu>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <F452155A-DC1F-11D8-8255-000A959EB970(a)umich.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Scott, > I've been doing a literature search for an article I'm writing up, and > I > can't seem to find any examples of an XAS flow cell desgined for > liquids. > Sealed cells for liquids, yes; flow cells for passing gases over > solids, > yes; but no solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase XAS flow > cell? We (Penner-Hahn group) have done solution EXAFS measurement and time-resolved XAS at Bio-CAT at the APS. A Kapton tube is used for x-ray window and connected to PE tubes using epoxy glue. Tsu-Chien <Chien>001000</Chien> ------------------------------ Message: 4 Date: Thu, 22 Jul 2004 15:55:07 -0500 (CDT) From: Matt Newville <newville(a)cars.uchicago.edu> Subject: RE: [Ifeffit] Solution flow cells To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <Pine.LNX.4.44.0407221538340.2941-100000(a)millenia.cars.aps.anl.gov> Content-Type: TEXT/PLAIN; charset=US-ASCII Just to follow up on and add to Shelly's and Tsu-Chien's responses: There's a paper by M. Hoffmann, et al (J. Fulton, and others from PNNL) on a flow-cell, especially for high pressure fluids. I believe it's in J Phys Chem (1999), but don't have the exact citation. This might be the one Shelly saw at PNC CAT. Mark Antonio has a nice electrochemical cell in which he can change both potential, but can't remember if he can flow in a changed solution... is that "flow"? I believe the catalyst people who run at ESRF (esp. the DXAFS line) have some nice flow cells too, but don't know if or where it's published. --Matt ------------------------------ Message: 5 Date: Thu, 22 Jul 2004 16:06:41 -0500 From: "Jensen, Mark P." <mjensen(a)anl.gov> Subject: RE: [Ifeffit] Solution flow cells To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <0D4E53E4DC6CA449B9F71E5282984F8C2F0DE3(a)anchim2.chm.anl.gov> Content-Type: text/plain; charset="us-ascii" And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 6 Date: Fri, 23 Jul 2004 08:45:10 +0200 From: SCHLEGEL Michel 177447 <schlegel(a)azurite.cea.fr> Subject: RE: [Ifeffit] Solution flow cells To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <3808A7D2DCEAD6118B63009027287265078A27(a)azurite.saclay.cea.fr> Content-Type: text/plain; charset="iso-8859-1" Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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Re: Ifeffit Digest, Vol 17, Issue 18
by m.bondin＠pgrad.unimelb.edu.au 23 Jul '04

23 Jul '04

Hi Scott, I have read a paper in a recent issue from Journal of Synchrotron Radiation which may be of interest: J. Synchrotron Rad. (2004). 11, 204-208 [ DOI 10.1107/S0909049503028474 ] A versatile rapid-mixing and flow device for X-ray absorption spectroscopy K. Zhang, R. Liu, T. Irving and D. S. Auld Synopsis: A low-temperature rapid-mixing and flow system has been designed and implemented to monitor catalysis involving metal ions by X-ray absorption spectroscopy at the ID-18 beamline of the Advanced Photon Source. The results of the initial testing of the system are presented. The reseach in our group (Stephen Best) in Australia involves EXAFS of short-lived electrochemically generated solution species prepared via an "ex situ" continuous flow electrosynthesis cell (Australian Journal of Chemistry, Volume 54, page 705, 2001) - from what I understand though you are more interested in an "in situ" method as mentioned above. Cheers, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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RE: [Ifeffit] Solution flow cells
by Irit Sagi 23 Jul '04

23 Jul '04

Dear Scott Enclosed is our NSB paper on rapid XAS of metalloenzyme + the news and views article written by J. Penner-Hahn on this article. Irit Prof. IRIT SAGI Department of Structural Biology The Weizmann Institute of Science ISRAEL Tel : 972-8-9342130 http://www.weizmann.ac.il/sb/faculty_pages/Sagi/home.html e-mail: irit.sagi(a)weizmann.ac.il >>> schlegel(a)azurite.cea.fr 23/07/04 09:45:10 >>> Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by SCHLEGEL Michel 177447 23 Jul '04

23 Jul '04

Scott, > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an > XAS flow cell desgined for liquids. > Sealed cells for liquids, yes; flow cells for passing gases > over solids, yes; but no solution-chemistry flow cell. I > feel like someone must have published work in that area before, > but I can't seem to find it. Maybe not exactly a flow cell, but a rapid biblio research on "Web of Science" using the"stopped-flow" and "EXAFS or XAS or XANES" keywords has unearthed some 23 references over the last ten years, many of them probably utterly irrelevant. Nevertheless, I copied them in the attached text file. Best regards, Michel Schlegel

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RE: [Ifeffit] Solution flow cells
by Jensen, Mark P. 22 Jul '04

22 Jul '04

And just to add to Matt, Shelly, and Tsu-Chien's responses. Matt mentioned Mark Antonio's electrochemical cell. It is not a flow cell, though we did design a closely related, but unpublished, cell design for in the beam titrations. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Newville, Matthew G. > Sent: Thursday, July 22, 2004 2:55 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Solution flow cells > > Just to follow up on and add to Shelly's and Tsu-Chien's > responses: > > There's a paper by M. Hoffmann, et al (J. Fulton, and others > from PNNL) on a flow-cell, especially for high pressure fluids. > I believe it's in J Phys Chem (1999), but don't have the > exact citation. This might be the one Shelly saw at PNC CAT. > > Mark Antonio has a nice electrochemical cell in which he can > change both potential, but can't remember if he can flow in a > changed solution... is that "flow"? > > I believe the catalyst people who run at ESRF (esp. the DXAFS > line) have some nice flow cells too, but don't know if or > where it's published. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Solution flow cells
by Kelly, Shelly D. 22 Jul '04

22 Jul '04

Hi Scott, See below: > Hi all, > > I've been doing a literature search for an article I'm > writing up, and I can't seem to find any examples of an XAS > flow cell desgined for liquids. Sealed cells for liquids, > yes; flow cells for passing gases over solids, yes; but no > solution-chemistry flow cell. I feel like someone must have > published work in that area before, but I can't seem to find it. > > So, does anyone know of any work done using a liquid-phase > XAS flow cell? Simon Bare uses a flow cell for passing liquids/gasses over a sample. This one is a glass container with kapton windows with ports for input and output. Also I have seen something like that at PNC cat. I think that Ed Stern et. al. was using it. The one at PNC cat circulated the liquid through a boron carbide section that is x-ray transparent. Shelly

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using atoms and feff
by Bruce Ravel 21 Jul '04

21 Jul '04

Hi folks, I suppose I should preface this message by saying that I will not say anything new and profound. Indeed, this email is something of a rant -- so some of you may want to click ahead to the next email right now and avoid the whole darn thing! Today I was asked a Frequently Asked Question about using atoms and feff and getting started with some fits. This particular question is pretty common, but it's one that kind of bugs me. It's been rattling around in my brain for the remainder of the evening. To get it out of my brain, I figured I would write a message to the mailing list. A colleague showed me some data and explained a bit about the sample. This person had the lattice constants and space group for the oxide form of the absorbing element but expressed a confusion about how to proceed. I asked to see the rest of the crystallographic data -- specifically the atomic positions. I was shown a printout of some stuff from webelements.com or some similar web compilation of information about the elements. Sure enough, the lattice constants were given for the oxide form, but neither complete crystallographic data nor a crystallographic reference were listed. As everyone here should know, feff requires a list of atomic coordinates as its input data. To get a feff calculation, you must tell feff where the atoms are. Ifeffit and Artemis rely upon feff to provide theoretical fitting standards, thus to start fitting you need somehow to run feff. It is a syllogism, then, that you need some kind of list of atomic coordinates before you can begin fitting with Ifeffit and Artemis. With but a passing understanding of crystallography, it should be clear that you cannot generate a list of atomic coordinates given *only* the space group and lattice constants of a crystal. The space group and lattice constants tell you the shape and size of the unit cell, but, by themselves, do not tell you what is inside the unit cell. You see, a unit cell is just like a birthday present. The box might be big and pretty, but it's not a very good present until you open it up and find out what's inside. So........ if you intend to start your analysis by using Atoms, you have to find the COMPLETE crystallographic data. Often, this is one of the more difficult parts of the analysis problem. Sometimes crystallography data is hard to find. Matt keeps a big pile of atoms.inp files on one of his web sites and that helps a lot. Many libraries have copies of Wyckoff -- that also helps a lot. Google can be awfully handy -- indeed I ended up finding the missing crystallographic data earlier today with the help of Google. Often times you will be reduced to an exhausting search through the crystallography journals looking for the data you need. Other times you will never find what you are looking for and will just have to use something similar (but not the same) as your starting point. I presume it was already abundantly clear to everyone reading this message that the space group and lattice constants by themselves are not enough to use Atoms. But I needed to vent and so availed myself of this public forum. B P.S. The question of what to do when your sample is different from its crystalline form or when your sample is not a crystal at all has been discussed several times recently. If, after reading this little rant, that's your concern, you should read and respond to one of those threads rather than to this one. P.P.S. The next time you dig through the literature to find some obscure crystal structure, save someone else the effort. Be a hero, donate the atoms.inp file to Matt's database. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 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/

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Artemis on Mac OSX
by POGER David 202545 21 Jul '04

21 Jul '04

Hi all I am quite new in the 'EXAFS community' and I have a problem with Artemis (v 0.7.007) on my Mac (OS X, v 10.3). When I try to load a FEFF path file (feffxxxx.dat), the program simply crashes and there's nothing I can do then, but killing the program. It creates the file 'ARTEMIS.TRAP' that I have attached. Could anyone help me? I would really appreciate your help. Thanks. David __________________________________________ POGER David Département de Réponse et Dynamique Cellulaires Laboratoire de Biophysique Moléculaire et Cellulaire Bat. K - P 215A - CEA Grenoble 17 rue des Martyrs 38054 GRENOBLE Cedex 9 FRANCE Tel: +33 (0)4 38 78 48 48 Fax: +33 (0)4 38 78 54 87 Email : david. <mailto:david.poger@cea.fr> poger(a)cea.fr

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New Comer
by jawad shah 21 Jul '04

21 Jul '04

Hi friends! I am the new commer in this field.I hope that all of you will guide and wellcome me.I am a person having no PC, With a brilliant academic record. DEar friends i hope that all of you will help me in this field. Best Regards to all friends Jawad __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/

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Re: Artemis Question
by Bruce Ravel 20 Jul '04

20 Jul '04

On Sunday 18 July 2004 11:38 pm, John Butler wrote: > Basically, the problem that I'm having is that the system I'm working > on is a solution (to start I'm trying to look at a solution of Zinc > Sulfate and then look at data with other components we're interested > in). Unfortunately, the part of the manual dealing with solution > analysis hasn't been written yet, and the people I know who use EXAFS > don't do anything with solutions. > > I was hoping that you could point me in the right direction for how to > proceed with the analysis (e.g. is there anywhere I'm likely to find > the FEFF files ... is there a 'standard' way to attack this kind of > problem). Of course I assume you're a pretty busy guy and have > neither the time nor inclination to give me a detailed step by step > guide or anything ... I was just hoping you could point me in the > right direction, give me a couple of tips, and/or show me where to > look. John, As you can see, I have forwarded you question along with my answer to the Ifeffit mailing list. You are correct to assume that I'm a busy guy. This week (like each of the other weeks this month) I am at NSLS collecting some data and helping our users. Fortunately, the mailing list is a solution to the "busy expert" problem. Enough people read and respond to the mailing list that someone should be available to answer just about every question. I doubt, actually, that you problem is really so hard to get started with. Lots of problems in XAFS do not fall into nice little pigeon holes. One knows how to deal with data on an iron foil because one knows what the structure of iron metal is. Most real research problems, obviously enough, are problems precisely because the structure is not perfectly well known. In the case of a solvated complex, there is probably some sort of analogue which can be used as a starting place. Perhaps there is some similar compound whose structure *is* known. Perhaps your solvated complex has a crystalline form that is similar, at least in the local environment, to the solvated form. In any case, find something that is similar to your real material. Run feff and compare to the data. Perhaps your analogue structure will be close to your data. In that case, you should be able to parameterize the feff calculation in such a way that you can begin to understand the ways in which your complex differs from your analogue. Perhaps the analogue structure is a very poor match for the data. That in itself is information, in that it tells you to go look for a different analogue. The common theme to what I have said here (and indeed to any analysis problem) is that you make some educated guesses as to what you real sample looks like. You test those guesses. If they seem to be leading you in the right direction, super. If not, make new (and newly educated!) guesses. My other piece of advice would be to spend some time fitting known spectra. If you are new to XAFS, then you are learning two things at the same time: how to interpret XAFS data and how to use my and Matt's screw-ball analysis programs! I consider it a good idea to spend some time fitting data for which you know the answer so that you can learn how to use the codes before plunging into the harder but more interesting problem of your own research. Good luck and join the mailing list, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 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/

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Re: Athena & artemis download
by Scott Calvin 17 Jul '04

17 Jul '04

Hi Sabyasachi, It is best to address questions like this to the Ifeffit mailing list, since others may also be interested. If you are not yet a subscriber to that list, you can join at http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I have forwarded your question to this list. I recall seeing the problem you describe before, and I think it had something to do with the updater. Try going in to your ifeffit directory and finding updater.exe. If you run that directly, you may find the updater kicks in and after grabbing about half a dozen updates, has your Artemis up to speed. --Scott Calvin Sarah Lawrence College >Scott, >I was one of the participants of this year's EXAFS short course at >BNL last month. It was a great course and I have learnt a lot about >the latest of what's happening in the field. > > I am having trouble downloading the correct version of Artemis from >the website. I have downloaded Ifeffit 1.2.5a.exe from the website >(I have Windows 2000) and when I am trying to open Artemis it opens >the 0.6 version instead of the latest 0.7 version. Could you please >let me know what's the best way to download the suite of EXAFS >software ? > >Many thanks in advance. > >Sabyasachi

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ParseCIF added to web page
by Kelly, Shelly D. 16 Jul '04

16 Jul '04

Hi Dave, I added your program to my little web page. Take a look see. http://146.137.194.45/exafs.html Thanks for contributing! Shelly ****************************************************************** Shelly Kelly EMAIL: skelly(a)anl.gov Argonne National Laboratory PHONE: 630-252-7376 9700 South Cass Ave. FAX: 630-252-9793 Argonne, IL 60439

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CIF to Atoms.inp-v2
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, Sorry about the resend of my previous message, but the file wasn't attached correctly so I am trying alternate mail settings to attach the file..... There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. <<ParseCIF.zip>> cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/ <http://pdb.sdsc.edu/S! TAR/> ) but they are given away fr ee for any non-commercial use. Matt or Shelly--feel free to post the files on your websites if you see the value in sharing them. Regards, Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-9350 Email: dgbarton(a)dow.com

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CIF to ATOMS.inp
by Barton, David (DG) 16 Jul '04

16 Jul '04

Users, There have been several instances of Artemis users asking Bruce for the ability to input CIF crystallographic files directly into Artemis. In my attempt to learn Perl and produce something of value to more than one person, I wrote a program that converts CIF crystallographic files into Atoms.inp files. Bruce may implement this sometime directly into Artemis, but in the meantime I will offer the standalone, command-line conversion program to anyone who can use it. Attached is a zip file with my first version of the Perl CIF->atoms.inp file converter. The main program was snarfed from Bruce's amc2inp.pl program which converts mineral files to atoms input files. cif2inp.pl ---main Perl program. Converts .CIF files to atoms.inp file usage: perl cif2inp.pl aucl.cif parser.pm ---parser module written by Wolfgang Bluhm of PDB at UCSD, parses CIF file into an array of hash arrays. This should be put into the STAR:: subdirectory in the perl library directory. datablock.pm ---reads the hash dictionary.pm ---dictionary of CIF terms (not used) AuCl.cif ---example CIF file from ICSD database with two records in it. The converter currently imports a single CIF file (which may have multiple CIF records) located in the \CIF directory and outputs a *.inp file for each CIF record into the \inp directory. This program has been tested with hundreds of CIF files from the ICSD and CSD databases. I cannot claim if they will work with CIFs from other sources, but I attempted to trap as many errors as I could. This program could easily be expanded to work on multiple CIF files (similar to amc2inp.pl) or...preferably....included directly in Artemis and/or ATOMS as a direct CIF file importer into these programs. I am sure there are many people that would benefit from the ability to directly open CIF files in ATOMS/Artemis and not have to worry about running a standalone application to convert their CIF files to atoms.inp files. Feel free to use any of the code that I have attached. The parser.pm and datablock.pm modules are copyrighted by UCSD (http://pdb.sdsc.edu/STAR/) but they are given aw! ay free for any non-commercial use

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Atoms restraints
by Massimiliano Stola 15 Jul '04

15 Jul '04

Thank you for all the explanations about constraints for the histidine ring within Artemis. Well, I think that it will be easier, but boring, building several reasonable structures and test them one by one... I think I'll finally follow this way. I'll be interested as well in the possibility to simulate exafs data for several structures at once, like Stefano asked. It would be a nice feature for the next releases of the program! Regards Max

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Chi^2 and R-factor reporting requirements
by Stanislav Stoupin 12 Jul '04

12 Jul '04

Hello all, I would like to hear your opinion about reporting Chi^2 and R-factor values in EXAFS studies. I found that Chi^2 and R-factor values are not provided by many EXAFS papers. However, according to standards of The International XAFS Society (http://ixs.iit.edu/) both these values should be reported. My understanding is that the reduced Chi^2 should be close to 1 in ideal case. In practice however, the value is always greater than 1 because of systematic errors. For example, my reduced Chi^2 values are around 300. However, the R-factor values are about 3% which doesn't look as "ugly" as Chi^2 reduced. On the other hand, ifeffit overestimates uncertainties using reduced Chi^2 value. Thus, all errors are taken into account. The final question: Is it appropriate to report just R-factor calculated by ifeffit and the obtained uncertainties (which look reasonable) without reporting the "ugly" Chi^2/reduced Chi^2 values? Stanislav Stanislav Stoupin ----------------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

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RE: [Ifeffit] multiple fits
by Kelly, Shelly D. 12 Jul '04

12 Jul '04

Hi Stefano, > > I have the following question: let's say I have a data set for which > I would like to try a long series of possible models and monitor the > result of the fits. The models are geometric variations of a > starting structure.I have all related feff.inp files for each model > ready. Is there a way to process the data so that I can get out the > related fits? I do not think I can do this using artemis, but maybe > there is a set of commands to be given from the command line? > > Thanks > Stefano The short answer is no. The long answer is sure. But the script that you need to write is long and complicated. You have to teach the computer how to model the structure for all the variations so that it will make the appropriate variables to determine in the fit, and also how to handle the output. These tools are not incorporated into ifeffit. I am responding to your request, because I did this as a graduate student. Back in the old days, I was using atoms, feff, and feffit. The program that I wrote moves the atoms in a unit cell, writes out a atoms.inp file, runs atoms, runs feff, makes a feffit.inp file and runs a fit, and then makes a spread sheet to compare the answers. If you are interested, I wrote is a small EXAFS paper about this script, and would be happy to share. S.D. Kelly, R. Ingalls, and E. A. Stern, "Determining crystalline atomic positions using XAFS, a new addition to the UWXAFS analysis package," Journal of Synchrotron Radiation. 8 311-313, 2001. In the end, I think that you will agree that you have a lot of work ahead of you. HTH Shelly

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multiple fits
by Stefano Ciurli 12 Jul '04

12 Jul '04

Hello, I have the following question: let's say I have a data set for which I would like to try a long series of possible models and monitor the result of the fits. The models are geometric variations of a starting structure.I have all related feff.inp files for each model ready. Is there a way to process the data so that I can get out the related fits? I do not think I can do this using artemis, but maybe there is a set of commands to be given from the command line? Thanks 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"

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Ifeffit 1.2.6
by Matt Newville 09 Jul '04

09 Jul '04

Hi Everyone, I've posted Ifeffit 1.2.6 source code and Mac disk-image-installer today. This fixes two important bugs: 1. path lists in feffit() and ff2chi() could get polluted so that doing a second feffit() or ff2chi() using _fewer_ paths would some paths left over from the previous sum of paths. The path list is now initialized correctly. 2. reading of feff.inp with feff6 no longer fails because of line endings that don't match the standard for that platform. In addition, plot markers and arrows now support color, plot_arrow(...,color=red) plot_marker(...,color=blue) and the location of the legend in the plot window is now more customizable using either plot(...., key='data', key_x=0.9, key_y0=0.9,key_dy=0.1) or setting the variables &plot_key_x = 0.9 &plot_key_y0 = 0.9 &plot_key_dy = 0.1 where 'key_x' is the x-location of the legend, 'key_y0' is the y-location of the first key, and 'key_dy' is the vertical offset between keys. The Mac OS installer includes a pre-release of horae-037. I believe Bruce will be releasing new versions of his codes soon. When he does, we'll make a new installer for Windows as well as the usual automated update -- probably next week. Please let me know if there are any troubles with these versions, --Matt

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RE: [Ifeffit] Atoms restraints
by Jensen, Mark P. 06 Jul '04

06 Jul '04

Here are my 2 cents worth on how to constraint the histidine ring within Artemis. Don't lose heart, Max. Both Scott and Bruce are right. There is no simple command to hold two scattering atoms in a particular relationship in Ifeffit, but the problem is easily solvable for this system partly because multiple scattering paths won't be too important and partly because the ring is quite rigid. (Actaully based on my experience with other organic ligands, the non-coordinated atoms in the histidine ring is probably not too important for EXAFS, but if you want to use the whole ring, this is how I would approach the problem using information external to the EXAFS data.) The histidine ring is a 5-membered (planar) aromatic ring, with 2 nitrogens and 3 carbons. That makes visualizing things a lot easier. Off-hand, I don't know what the bond lengths and bond angles within the ring are, but you could find that information from x-ray crystal structures of histidine complexes and it would be contained in the feff.inp file (which you could make using the procedure Shelly Kelly distributed to the list morning). But, somehow you have to build a feff.inp file and do the feff calculations so you have some paths to fit. Assuming that the absorbing atom , "M", is at coordinates (0,0,0) makes things simpler. Fortunatley that should be the case for a feff.inp file. You will have to define at least 17 new "set" variables in Artemis, one x, y, and z coordinate for each of the 5 atoms in the ring, as well as the angles theta and phi. The x,y,z coorinates have to be manually input from the feff.inp file. You will also need some other variables to hold intermediate coordinates, for example del_x, del_y, and del_z. As Scott pointed out, EXAFS is mostly sensative to the radial distance, and our case that's exactly what Artemist/Ifeffit is varying by adding del_r to the scattering path length. What you want to do is move the other 4 atoms of the histidine ring in conjunction with the del_r changes in the M-N bond length. First, convert the x,y,z coordinates of the coordinated nitrogen atom (I'll call these (xN, yN, zN) ) to spherical coordinates (r_eff, theta, phi). You need to put the values of theta and phi into the Guess,Set,Def parameters as set parameters because you will need them later to convert from spherical coordinates back to regular 3D-rectangular (x,y,z) coordinates. In the fitting, the changes in the M-N single scattering path length (i.e., the M-N bond distance) will not effect the two angles theta and phi for the coordinated N. However, changing the M-N distance will change theta and phi (relative to the absorbing atom) for the other 4, so there is some algebra to do. Now this is where the whole approach might fail. I don't know if it is possible to to incorporate the delr or the delr+reff value from a specific feff path into an algebraic expressions in the Guess,Set,Def panel. Bruce or Matt or someone else will have to comment on this and explain how to do it. However, assuming that there is a straigforward way to do it, then... for each iteration of the fit in Ifeffit/Artemis there is a particular M-N distance for the scattering path of the coordinated histidine nitrogen, Artemis calls this "r" (for each path) and it is equal to reff+delr for each path (also using the Artemis nomenclature). Using theta and phi (which haven't changed for the coordinated N) and "r", a new set of coordinates in regular space (x_new,y_new,z_new) for the coordinated nitrogen can be calculated within Artemis using the standard equations for spherical coordinates. (Like I said, if we can't access "r" from the alegbraic expressions in Guess,Set,Def this won't work, though). Then, taking the difference of the current position and the original position of the coordinated nitrogen in x,y,z coordinates, we get (del_x,del_y,del_z). In other words del_x = (x_new - xN) can be defined as a DEF parameter in the Guess,Set,Def panel. This single set (del_x,del_y,del_z) vector is going to be added to the (x,y,z) coordinates of each of the 4 other atoms in the histidine ring to get their current coordinates in the next and final step. Finally, to get the change in the radial distance of each of the 4 other ring atoms, put the expression [(x_orig+del_x)^2+(y_orig+del_y)^2+(z_orig+del_z)^2]^0.5 - [x_orig^2+y_orig^2+z_orig^2]^0.5 in the "delr" blank (where [x_orig^2+y_orig^2+zorig^2]^0.5 is actually reff for the path) for each of the 4 feff paths of the 4 non-coordinated ring atoms. In this equation, "x_orig" is the original x-coordinate of the non-coordinated ring atoms and "del_x" was calculated from the new position of the coordinated nitrogen atom above. Things can get trickier if you want to incorporate multiple scattering paths, but I think that woiuld probably not be a fruitful line of inquiry anyway. If you stick to singlescattering paths, that's all there is to it! ;) Good Luck, Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: scalvin(a)slc.edu [mailto:scalvin@slc.edu] > Sent: Friday, July 02, 2004 9:19 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Atoms restraints > > If I understand your question correctly, the answer is no. > You cannot tell Ifeffit or Artemis to constrain the distance > between two atoms with a simple command. The reason is > simple--EXAFS doesn't directly contain that information; it > only contains it implicitly (maybe). For direct-scattering > paths, EXAFS only provides radial information. > Multiple-scattering does provide some information along other > axes, but this causes a greater effect in some cases than others. > > What Ifeffit and Artemis do allow is for you to constrain the > parameters related to individual scattering paths in pretty > much any way you desire. > So, for example, you can constrain the distance to the direct > scattering path to atom A, the direct scattering path to atom > B, and the multiple-scattering path that hits A and B in such > a way that the distance between A and B remains constant. But > this takes careful geometrical thinking on your part. > > Incidentally, restraints are different from constraints. > "Constraints" are forces and cannot vary. "Restraints" > penalize the fit if it drifts too far, but allows some variation. > > Hope that helps. > > --Scott Calvin > Sarah Lawrence College > > > So I understand that I can just tell Ifeffit/Artemis: > distance between > > Atom#1 > > and Atom#2 is equal to "x" Angstroms, and that will be > forced for all > > the next calculations. Did I understand well?? > > If this is true I believe that this way is easier than > build a lot of > > structures to test (If you have more than one histidine the > number of > > structures increases...). > > > > Anyway, I had a look at many .inp the examples but I did not > > understand well how to give this command to the program. > Can you write > > me an example? > > It would be much easier for me to start from that example > and add many > > atom-atom distance restraints to keep a rigid structure. > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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athena: larger data visualisation window size
by biquard xavier 06 Jul '04

06 Jul '04

Hi ! I have been using athena under LinuX with great satisfaction for a long time now. Recently, I changed my old portable computer for a brand new one: my Xwindow screen size went from 1024x768 to 1920x1250, but all windows opened by athena for data visualisation have the same old size of around 870x670: I cannot take advantage of my new screen size! As I compiled athena from scratch (horae-021), I wonder if I should not modify athena files set_properties.pl and draw_properties.pl that seems to me to be defining window size. If anyone knows for sure how to do it, please let me know! cheers, Xavier -- ------------------------------------------------------------------- Biquard Xavier Tél CEA : 0438785413 CEA-Grenoble Fax : 0438785138 DSM/DRFMC/SP2M/NRS mailto:xbiquard@cea.fr 17, av des Martyrs 38054 Grenoble Cedex 9 ------------------------------------------------------------------- 2nd chance : Tél ESRF1 : 0476882546 Tél ESRF2 : 0476882598 -------------------------------------------------------------------

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updating the faq with OSX-specific information
by Bruce Ravel 05 Jul '04

05 Jul '04

Hi folks, The last email got me thinking about the documentation for the various installers and updaters and such. I would like to ask one of the OSX users on the list to create a new FAQ entry in section 2 explaining how to update Athena and Artemis from source code once Ifeffit has been installed from the OSX disk image. (That is, I'd like an expert OSX user to walk the novice OSX user through the process of building from source and using sudo to install the newly built code.) Similarly, section 2 needs an entry explaining how the unix updater works. I plan to write that in the coming days. A section 2 entry from Carlo or one of the other debian users would probably be a good idea as well. Thanks, 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/

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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

4 4

protein data base to feff.inp file
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hello All, I just updated my little web page to share the protein data base file converter that I wrote. You can find the perl program and some instructions at: http://www.mesg.anl.gov/exafs.html If you use the program, let me know how it goes. Shelly > -----Original Message----- > From: Kelly, Shelly D. > Sent: Friday, July 02, 2004 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Atoms restraints > > > Hi Max, > > > > > Anyway, I had a look at many .inp the examples but I did not > > understand well > > how to give this command to the program. Can you write me an > > example? It would be much easier for me to start from that > > example and add many > > atom-atom distance restraints to keep a rigid structure. > > I do not understand this question. What kind of .inp file are you > looking at? Is this the input to feff? The feff.inp file needs to > have a list of atoms with their corrdinates in x, y, and z. > For a hystatine you will want to make a feff.inp file from > the crystal structure. From this list feff makes a theory > that has the contriution to the EXAFS data for each path of > the photo-electron in a different feffxxxx.dat file. Then > Ifeffit/Athena can be used to fit these paths to the data. > During the fitting process you can change the distance > between the atoms by a little bit (<0.5 Angstroms). To > change the distance during the fitting process you need to > define delr for each path included in the fit. > > I am attaching a catalase protien feff.inp file that I made > from a 7CAT.pdb file. > Hum...I see that I wrote a perl program to help do this. I > must appologize that I forgot that I had this program. > Others have asked for it in the past. > > The proceedure that I used to create this file goes like this. > 1) Get your hands on a crystal structure with the same core > hole atom. (i.e. Fe-oxide for my case) > 2) Run atoms inside of Artemis to generate a feff.inp file. > 2b) save the feff.inp file to disk. > 2c) open feff.inp file in a text editor and remove the ipot > and x,y,z coordinates. > 3) Get the pdb file for the protein, or use mine for an > example 7CAT.pdb. > 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. > 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" > 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a > 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z > coordinates for the atoms in the pdb file. > 4d) To use the program on your own system, open pdf2fi.pl and > edit a few of the lines at the top. Don't worry it is easy > to do and you will not mess it up. You have to tell the > program what atoms are in the pdb file and which one is the core. > 5) paste the file from 4c into the feff.inp file from 2. > 6) Save the feff.inp file to disk and open it in Artemis and run feff. > > > HTH > Shelly >

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Re: [Ifeffit] Atoms restraints
by scalvin＠slc.edu 02 Jul '04

02 Jul '04

If I understand your question correctly, the answer is no. You cannot tell Ifeffit or Artemis to constrain the distance between two atoms with a simple command. The reason is simple--EXAFS doesn't directly contain that information; it only contains it implicitly (maybe). For direct-scattering paths, EXAFS only provides radial information. Multiple-scattering does provide some information along other axes, but this causes a greater effect in some cases than others. What Ifeffit and Artemis do allow is for you to constrain the parameters related to individual scattering paths in pretty much any way you desire. So, for example, you can constrain the distance to the direct scattering path to atom A, the direct scattering path to atom B, and the multiple-scattering path that hits A and B in such a way that the distance between A and B remains constant. But this takes careful geometrical thinking on your part. Incidentally, restraints are different from constraints. "Constraints" are forces and cannot vary. "Restraints" penalize the fit if it drifts too far, but allows some variation. Hope that helps. --Scott Calvin Sarah Lawrence College > So I understand that I can just tell Ifeffit/Artemis: distance between > Atom#1 > and Atom#2 is equal to "x" Angstroms, and that will be forced for all the > next calculations. Did I understand well?? > If this is true I believe that this way is easier than build a lot of > structures to test (If you have more than one histidine the number of > structures increases...). > > Anyway, I had a look at many .inp the examples but I did not understand > well > how to give this command to the program. Can you write me an example? > It would be much easier for me to start from that example and add many > atom-atom distance restraints to keep a rigid structure. > >

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, I forgot to include the perl program. Here it is. Shelly > -----Original Message----- > From: Kelly, Shelly D. > Sent: Friday, July 02, 2004 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Atoms restraints > > > Hi Max, > > > > > Anyway, I had a look at many .inp the examples but I did not > > understand well > > how to give this command to the program. Can you write me an > > example? It would be much easier for me to start from that > > example and add many > > atom-atom distance restraints to keep a rigid structure. > > I do not understand this question. What kind of .inp file are you > looking at? Is this the input to feff? The feff.inp file needs to > have a list of atoms with their corrdinates in x, y, and z. > For a hystatine you will want to make a feff.inp file from > the crystal structure. From this list feff makes a theory > that has the contriution to the EXAFS data for each path of > the photo-electron in a different feffxxxx.dat file. Then > Ifeffit/Athena can be used to fit these paths to the data. > During the fitting process you can change the distance > between the atoms by a little bit (<0.5 Angstroms). To > change the distance during the fitting process you need to > define delr for each path included in the fit. > > I am attaching a catalase protien feff.inp file that I made > from a 7CAT.pdb file. > Hum...I see that I wrote a perl program to help do this. I > must appologize that I forgot that I had this program. > Others have asked for it in the past. > > The proceedure that I used to create this file goes like this. > 1) Get your hands on a crystal structure with the same core > hole atom. (i.e. Fe-oxide for my case) > 2) Run atoms inside of Artemis to generate a feff.inp file. > 2b) save the feff.inp file to disk. > 2c) open feff.inp file in a text editor and remove the ipot > and x,y,z coordinates. > 3) Get the pdb file for the protein, or use mine for an > example 7CAT.pdb. > 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. > 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" > 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a > 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z > coordinates for the atoms in the pdb file. > 4d) To use the program on your own system, open pdf2fi.pl and > edit a few of the lines at the top. Don't worry it is easy > to do and you will not mess it up. You have to tell the > program what atoms are in the pdb file and which one is the core. > 5) paste the file from 4c into the feff.inp file from 2. > 6) Save the feff.inp file to disk and open it in Artemis and run feff. > > > HTH > Shelly >

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 02 Jul '04

02 Jul '04

Hi Max, > > Anyway, I had a look at many .inp the examples but I did not > understand well > how to give this command to the program. Can you write me an > example? It would be much easier for me to start from that > example and add many > atom-atom distance restraints to keep a rigid structure. I do not understand this question. What kind of .inp file are you looking at? Is this the input to feff? The feff.inp file needs to have a list of atoms with their corrdinates in x, y, and z. For a hystatine you will want to make a feff.inp file from the crystal structure. From this list feff makes a theory that has the contriution to the EXAFS data for each path of the photo-electron in a different feffxxxx.dat file. Then Ifeffit/Athena can be used to fit these paths to the data. During the fitting process you can change the distance between the atoms by a little bit (<0.5 Angstroms). To change the distance during the fitting process you need to define delr for each path included in the fit. I am attaching a catalase protien feff.inp file that I made from a 7CAT.pdb file. Hum...I see that I wrote a perl program to help do this. I must appologize that I forgot that I had this program. Others have asked for it in the past. The proceedure that I used to create this file goes like this. 1) Get your hands on a crystal structure with the same core hole atom. (i.e. Fe-oxide for my case) 2) Run atoms inside of Artemis to generate a feff.inp file. 2b) save the feff.inp file to disk. 2c) open feff.inp file in a text editor and remove the ipot and x,y,z coordinates. 3) Get the pdb file for the protein, or use mine for an example 7CAT.pdb. 4) Save the pdf2fi.pl file to disk and the 7CAT.pdb file to disk. 4b) make the pdf2fi.pl executable by typing "chmod 777 pdf2fi.pl" 4c) type "pdf2fi.pl 7CAT.pdb" This will generate a 7CAT.pdb-feff.inp file. This file has the ipot and the x,y,z coordinates for the atoms in the pdb file. 4d) To use the program on your own system, open pdf2fi.pl and edit a few of the lines at the top. Don't worry it is easy to do and you will not mess it up. You have to tell the program what atoms are in the pdb file and which one is the core. 5) paste the file from 4c into the feff.inp file from 2. 6) Save the feff.inp file to disk and open it in Artemis and run feff. HTH Shelly

1 0

Atoms restraints
by Massimiliano Stola 02 Jul '04

02 Jul '04

Thank you guys for your answers, Bruce, you said: "The central point here is that Ifeffit (and by extension, Artemis) allows you to write such things as the distance between atoms in the form of an almost arbitrary algebraic expression." So I understand that I can just tell Ifeffit/Artemis: distance between Atom#1 and Atom#2 is equal to "x" Angstroms, and that will be forced for all the next calculations. Did I understand well?? If this is true I believe that this way is easier than build a lot of structures to test (If you have more than one histidine the number of structures increases...). Anyway, I had a look at many .inp the examples but I did not understand well how to give this command to the program. Can you write me an example? It would be much easier for me to start from that example and add many atom-atom distance restraints to keep a rigid structure. Thank you very much Max

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Re: Artemis download
by Bruce Ravel 30 Jun '04

30 Jun '04

On Wednesday 30 June 2004 01:39 pm, Sen, Sabyasachi wrote: > Bruce, I was one of the participants of this year's EXAFS short > course at BNL last week. It was a great course and I have learnt a > lot about the latest of what's happening in the field. I am having > trouble downloading the correct version of Artemis from the website. > I have downloaded Ifeffit 1.2.5a.exe from the website (I have > Windows 2000) and when I am trying to open Artemis it opens the 0.6 > version instead of the latest 0.7 version. Could you please point > out what I might be doing wrong and what's the best way to download > the suite of EXAFS softwares? Many thanks in advance. Sabyasachi, First off, let me repeat one thing that was said during the course: These questions are best directed to the mailing list. Helping new users solve installation problems is among the many purposes of the list. By asking a question of the list rather than of me directly, you get to tap into a much larger pool of knowledge. As you can see, I have forwarded this email to the list. The mailing list isn't the only splendid source of information available to the Ifeffit newbie. We also have a Frequently Asked Questions page at http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz The FAQ is great -- it contains tons of useful information and it's a wiki. That means that anyone in the Ifeffit community can share knowledge by authoring or editing a FAQ entry. Pretty cool! There are FAQ entries that discusses the Windows installer and updater at great length: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#2.4 http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#2.8 If that does not help you solve your problem, post a question to the list and I am sure that one of the Windows experts who reads the list will be happy to help you out. 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/

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Re: [Ifeffit] Atoms restraints
by Matt Newville 28 Jun '04

28 Jun '04

Dear Max, > I'm a new user of the Feffit package and I have a question about > atom restraints for the fitting. > > I'm dealing with metal binding protein, and somehow I need to > keep some atoms in a fixed structure (mainly histidine rings) > while leaving a certain degree of freedom to the remaining atoms > of the environment. > > I'd like to know if there is a library containing histidine > structure restraints or if exists any input file of a similar > matter. I don't know of any such library, though such constraints and restraints could be done -- at least in principle. (I)Feffit is very strongly tied to the Sum-Of-Paths approach to EXAFS, which is not particularly good at dealing with groups of atoms as aingle entities. I believe this would be a significant amount of work. Since (I)Feffit uses a sum-of-paths and since paths (in the form of Feff's feffnnnn.dat files) do not necessarily come from a single cluster of atoms (this is by design and is a _benefit_ in many cases, though not here!), it will not necessarily be easy to identify the x,y,z coordinates of the individual atoms in a ring, let alone know that certain atoms belong together. The path to each atom would have to be identified by hand. Then, the mathematical constraints keeping the distances and angles between atoms within the ring fixed while allowing the group to move relative to the central atom would have to be worked out in terms of the allowed motions. To be honest, I haven't really thought about how to do this in any detail. --Matt

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RE: [Ifeffit] Atoms restraints
by Kelly, Shelly D. 27 Jun '04

27 Jun '04

Hi Matt, My program for rotating a phosphate group can be easily modified to rotate any group of atoms. The problem being that you need to know a little bit of perl to do it. The top part of the perl script has a lot of comments showing you where you would want to make these changes. Basically you have to tell the program where all the atoms are and how you want to rotate them. I could easily modify the script to run from an input file, but it seems like I should write a gui interface to the program so that it would be more user friendly...hum..? I wonder if PGplot could be used to display a ball and stick model and then be used to transfer information back and forth from perl? Would anyone be interested in helping me figure that part out? Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Sunday, June 27, 2004 12:41 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Atoms restraints > > > Dear Matt, > > I also had asked a similar question some time ago, and Bruce said > that it should be easy to build such restraints using his programs. I > asked the question because I have several colleagues working with > EXCURVE, a program that implements the histidine ring as a group and > modifies distance and orientation with respect to the scattering atom > to which it is bound. I do not want to use EXCURVE for several > reasons, and I like FEFF much better. There must be people out there > in the mailing list that deal with biological samples, most often > containing a histidine ring bound to a metal ion, and use ifeffit. I > think the question that Max asked should be dealt with in detail. I > think that many more people would use these programs if a routine for > histidine ring would be implemented. Some time ago Shelly Kelly > proposed one of her programs to rotate a phosphate group bound to a > metal ion, and the program was made available. This is the kind of > things, that, when implemented by experienced people like many in > this list, would help many non-experienced people in this list. > > Another possibility is of course to build several models of M(His)n, > with varying the number of histidines and their distances and angles. > So far, this is the best I could think of. > > Stefano > > >I don't know of any such library, though such constraints and > >restraints could be done -- at least in principle. (I)Feffit is very > >strongly tied to the Sum-Of-Paths approach to EXAFS, which is not > >particularly good at dealing with groups of atoms as aingle entities. > > > >I believe this would be a significant amount of work. Since > (I)Feffit > >uses a sum-of-paths and since paths (in the form of Feff's > feffnnnn.dat > >files) do not necessarily come from a single cluster of > atoms (this is > >by design and is a _benefit_ in many cases, though not > here!), it will > >not necessarily be easy to identify the x,y,z coordinates of the > >individual atoms in a ring, let alone know that certain atoms belong > >together. The path to each atom would have to be identified > by hand. > >Then, the mathematical constraints keeping the distances and angles > >between atoms within the ring fixed while allowing the group to move > >relative to the central atom would have to be worked out in terms > >of the allowed motions. To be honest, I haven't really thought > >about how to do this in any detail. > > > >--Matt > > > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > ____________________________________________ > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Atoms restraints
by Massimiliano Stola 25 Jun '04

25 Jun '04

Hi, I'm a new user of the Feffit package and I have a question about atom restraints for the fitting. I'm dealing with metal binding protein, and somehow I need to keep some atoms in a fixed structure (mainly histidine rings) while leaving a certain degree of freedom to the remaining atoms of the environment. I'd like to know if there is a library containing histidine structure restraints or if exists any input file of a similar matter. Looking forward to hearing from you Max

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Re: [Ifeffit] Re: A very quick question
by Scott Calvin 19 Jun '04

19 Jun '04

Dave wrote: >And....one other feature request for Bruce for Athena version 2.3. It would be nice if we could put constraints on each of the fitting variables. This would help prevent fits where the variables quickly spin off into meaningless territory. Of course, implemenation of this feature could get complex given the number of variables to be fit. An easier implemenation of constraints would be a checkbox and a % deviation field that would let the variables chosen float within that %deviation. >> Ifeffit (and thus Artemis) already has "max" and "min" features that allow you to approximate this. For example, to require S02 to be between 0.60 and 1.00, you can do the following: guess S02p = 0.80 def S02p = max(0.60,min(1.00,S02p)) Admittedly that is a bit awkward, and Bruce could implement it as you suggest in Artemis. My experience is, however, that this does not work very well. A fit which likes to "spin off" tends to pin itself to one of the edges of the allowed range anyway, and then the ifeffit routines for working out uncertainties and correlations lose their ability to figure out what is going on (the fitted parameter can become in some sense meaningless to the fit). So I think if Bruce implements it that it would just be a source of frustration. You could use "restraints" instead, although that raises its own issues of defensibility and how to choose the weighting function. My preference is to find other ways to make the fit conform to the real world, e.g. I include more paths, or more k-weights, or other constraints, or values from a standard... --Scott Calvin Sarah Lawrence College

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two comments
by Bruce Ravel 19 Jun '04

19 Jun '04

Hi! Just now I was reading through some of the mail I missed while away at a conference and I have a few general comments. 1. Doug Pease had some problems with Artemis being bigger than the size of his screen. This is a problem I am aware of, but haven't got around to fixing. All my GUI codes are written assuming that your screen is at least 1024x768. They just don't display properly at lower resolution. Similarly, there is an option under Windows XP for using fonts larger than normal for the specified resolution. That is, you can set resoution at 1024x768 but have windows use scaled up fonts such that, say, a 10pt font would display as if the resolution were 800x600. This feature is nice those with untrustworthy eyes, but my GUI codes play poorly with this. Bottom line: to use my codes you need to set your resolution to 1024x768 or higher and not use the scaled up fonts. My apologies to anyone stuck with weak eyes or a old monitor. 2. Lots of people have complained trap files being written to a place that includes this string: __ENV__IFEFFIT_DIR. Although people reported several different situations, everytime you see that string, it is the same bug. I am aware of this bug and I think I have fixed it. I am going to try to get a new version out sometime during the week of June 27th. 3. Peter Southon made a very clever suggestion one day which I would like to modify just slightly. Make a desktop shortcut to C:/Program Files/Ifeffit/horae/stash/ This will allow you to quickly find trap files written by Athena and Artemis and also to very quickly find Artemis' workspace. Ta ta, 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/

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a few words...
by Bruce Ravel 18 Jun '04

18 Jun '04

Hi folks, This is just a quick note to let everyone know that I have read all of the traffic on the mailing list from the last two weeks. Clearly there are some serious issues with the current release of artemis that need my attention. I am still in the middle of a very busy period and won't have much time to devote to the codes for a couple more weeks, but I wanted everyone to know that I have read about the problems and will work on solutions just as soon as I get a chance. Thanks to those who commented for your input. As I have said many times before, the codes are only usable because of the contributions of their users. It seems that most of the non-bug report traffic was answered to some extent. I probably will not respond to any of the mail from the last two weeks, so if anyone posted a question for me that didn't get answered to your satisfaction, I would recommend posting it again. I also wanted to comment on a couple of things that made me laugh out loud. One was was Paul's comment to Chris Derr asking him to inform the list of the answer once he gets EXAFS all figured out. (Is it 42?) The other was when Doug Pease (sorry for picking on you Doug, but this *was* funny) refered to Shelly Kelly as Mary Shelly. Mary Shelley, of course, was the author of Frankenstein. I would say that it is unfair to burden Shelly with the responsibility of creating a Frankenstein monster. That would be me or Matt, I think, depending on whether the interior part or the exterior part seems more monstrous to you ;-) 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/

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Fwd: Alignment!
by Bruce Ravel 18 Jun '04

18 Jun '04

Hi folks, I received this (rather vague) question this morning and thought I would forward it along to the list for discussion. A couple of FAQ entries seem relevant: http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#5.6 and http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#5.7 Perhaps someone could write a FAQ entry on the topic of data alignment... B ---------- Forwarded Message ---------- Subject: Alignment! Date: Friday 18 June 2004 10:20 am From: Nasser Afify <n_afify(a)science.unitn.it> To: ravel(a)phys.washington.edu Dear Prof., I need to align my fluorescence spectra to the one of the reference before the extraction of the signals, but it is too difficult to align, what is the best way for alignment and what is the best choice of E0 in the case of noisy data. thank you for your time best regards, Yours Nasser ------------------------------------------------------- -- 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/

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Re: A very quick question
by Barton, David (DG) 18 Jun '04

18 Jun '04

On Thursday 17 June 2004 03:17 pm, Ahmed M Shahin wrote: AM> Hello, I would like to ask a very quick question and I would AM> appreciate if someone can help me. While running XANES fitting AM> for mixed valence state metals such as cerium (3/4), should I use AM> two arctangent functions with selected group of Lorentzian AM> functions or I have to use only one arctangent function with a AM> group of Gaussian functions? I would appreciate if someone give AM> some advice. Yours, Ahmed I have used the XANES peak fitting option some in Athena and would concur with Bruce's suggestions that peak fitting needs to be handled in a *consistent* manner to be useful. With that said, I appreciated Bruce adding the feature to be able to fit multiple arctangents because it can help tease out the relative ratios of mixed valence state metals. However, one must be careful to not overinterpret these fits because of the sensitivity of the XANES edges to coordination changes as well as oxidation state. With the appropriate set of standards this fitting can be a useful tool especially when the data quality does not permit a full blown EXAFS analysis. In regards to the other peak shapes (Lorentzian or Gaussians)....use what fits best. This fitting is just a tool to help describe your datasets and is not a fundamental approach to XANES interpretation. One other suggestion, be patient with the fitting and play around. Try multiple initial guesses, don't let all variable float in the initial fit, consider fitting the energy first and then fix it and fit the other variables. Once you get a good fit, use this solution as the initial guesses for all your other datasets. And....one other feature request for Bruce for Athena version 2.3. It would be nice if we could put constraints on each of the fitting variables. This would help prevent fits where the variables quickly spin off into meaningless territory. Of course, implemenation of this feature could get complex given the number of variables to be fit. An easier implemenation of constraints would be a checkbox and a % deviation field that would let the variables chosen float within that %deviation. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Email: dgbarton(a)dow.com

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Regarding XANES spectra of Manganese oxides
by Grant Bunker 17 Jun '04

17 Jun '04

This is in response to Prof. Gang Ho Lee's question. There is indeed a spinel form of Mn2O3 which is isostructural with Mn3O4, except (as I recall from twenty years ago) that the +2 and +3 ion populations are reversed (2/3 of the ions are in octahedral sites, and 1/3 in tetrahedral). So even though the average charge state is changed, the structure isn't. The XANES and XRD are virtually the same because the structures are virtually the same. grant bunker On Thu, 17 Jun 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. Re: a few words... (scalvin(a)slc.edu) > 2. A very quick question (Ahmed M Shahin) > 3. Re: A very quick question (Bruce Ravel) > 4. Reagrding Xanes spectra of manganese oxides (Gang Ho Lee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Jun 2004 14:01:28 -0400 (EDT) > From: scalvin(a)slc.edu > Subject: Re: [Ifeffit] a few words... > To: ravel(a)phys.washington.edu, "XAFS Analysis using Ifeffit" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <2823.138.110.111.207.1087495288.squirrel(a)mail.slc.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Bruce said: > > > I also wanted to comment on a couple of things that made me laugh out > > loud. One was was Paul's comment to Chris Derr asking him to inform > > the list of the answer once he gets EXAFS all figured out. (Is it > > 42?) > > > > Bruce! I'm shocked at you! Everyone knows that legitimate EXAFS results > must always be reported with the uncertainty; the answer is actually 42 > +/- pi. > > --Scott Calvin > Sarah Lawrence College > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jun 2004 14:17:38 -0500 > From: "Ahmed M Shahin" <shahin(a)umr.edu> > Subject: [Ifeffit] A very quick question > To: <Ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <001a01c4549f$c0ece3a0$fc689783(a)chem.umr.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > I would like to ask a very quick question and I would appreciate if someone can help me. > While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? > I would appreciate if someone give some advice. > Yours, > Ahmed > >

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Reagrding Xanes spectra of manganese oxides
by Gang Ho Lee 17 Jun '04

17 Jun '04

Dear Sirs I am writing to you because we are not familiar with xanes. We took xanes spectra of both sample (synthesized by us and we think it as gamma-Mn2O3 ) and Mn3O4 (reference) to make sure that we synthesized gamma-Mn2O3 nanoparticles. The particle diameters ranged from 10 to 15 nm. By using XRD pattern, the structure of sample was determined to be tetragonal with lattice constants of a=5.79 A and c=9.4 A, similar to Mn3O4. From the XRD patterns, we can not distinguish between gamma-Mn2O3 and Mn3O4 because both show nearly identical XRD patterns (JACS 72, 856 (1950)). We attached a data file. Could you please tell us whether the sample is gamma-Mn2O3 nanoparticles or not. Sincerely, Prof. Gang Ho Lee Department of Chemistry College of Natural Sciences Kyungpook National University Taegu 702-701, South Korea tel: 001-82-53-950-5340 fax: 001-82-53-950-6330 e-mail: ghlee(a)bh.knu.ac.kr

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A very quick question
by Ahmed M Shahin 17 Jun '04

17 Jun '04

Hello, I would like to ask a very quick question and I would appreciate if someone can help me. While running XANES fitting for mixed valence state metals such as cerium (3/4), should I use two arctangent functions with selected group of Lorentzian functions or I have to use only one arctangent function with a group of Gaussian functions? I would appreciate if someone give some advice. Yours, Ahmed

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Artemis: Error in laoding additional FEFF paths?
by Carlo U. Segre 17 Jun '04

17 Jun '04

Hello All: One of my students is just trying Scott's ZnO tutorial and we are finding a consistent problem when trying to work with the third project file. When we get to the point of adding an additional path, (feff0011.dat), artemis crashes with the following message: --------------------------------- The following message was trapped by Artemis: Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0x9652e54)/home/segre/.horae/stash/artemis.project.2/ at /usr/bin/artemis line 1562 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 7313 main::read_feff('^^') called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1707 -------------------------------- This is happening on all of my Linux machines. They are using my Debian packages and so I have not tried with the tarball installation. Has anyone else had this problem? I hesitate to report it as a bug until it is confirmed. In a previous version of horae, it worked fine. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, I said earlier: "Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm" No, the problem is really with the ZnO tutorial .apj files. I get aquaterm starting when I open a Cu.chi file, but I do not get it to open when I try to read the ZnO1.apj file. I think this is due to some bug in horae, which makes the programs not really good at managing project files. I think Bruce said something like that some time ago. 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

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Re: [Ifeffit] Iffeffit1.5.2a compilation troubles
by Stefano Ciurli 16 Jun '04

16 Jun '04

Hello folks, following the "lost" message from yesterday, and in order to solve the apparent bug that aquaterm does not start automatically etc etc, I reinstalled 1.2.5a using the binary installer AND, this time, restarted the computer (the same old trick). This time aquaterm opens again.... Then, after running the horae_update --force command, aquaterm does not open automatically. BUT, if I restart again the PC, the aquaterm opens. Apparently, I need to restart the PC any time that somethig goes wrong with aquaterm. 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Matt, as to the following question: QUESTION: I do not seem to have, in tcsh, the command "configure" I think I solved this one by entering the /Users/stefano/Tk-804.027/ifeffit-1.2.5 directory I am proceeding with the resto of the indicated protocol, so far not caring about the downloading directory (I am using my home directory right now). Please let me know whether I can change the Tk-804.027 directory from my home directory to where it is more right to move it (which I do not know). Thanks, 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Paul, this is my .cshrc file: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source /Library/Scripts/iterminal_custom.tcsh source /sw/bin/init.csh source /Users/stefano/Programs/XtalView/XtalView.env setenv PATH `echo $PATH`:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Users/stefano/Programs/modeller6v2:/Users/stefano/Programs/o/bin/:/Users/stefano/Programs/autodock/dist305/bin:/Users/stefano/Programs/autodock/dist305/share/:/Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin/bin:/Users/stefano/Programs/XtalView/bin/powerpcDarwin5/ defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv RCSBROOT /Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT source /Library/Scripts/settitle.csh source /Users/stefano/Programs/NMRPipe/com/nmrInit.mac.com alias ono osx_ono ### begin MODELLER6v2 ###################################################### setenv MODINSTALL6v2 /Users/stefano/Programs/modeller6v2 setenv EXECUTABLE_TYPE6v2 mac10v2-absoft setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib setenv KEY_MODELLER6v2 MODELIRANJE alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) limit stacksize unlimited ### end MODELLER6v2 ######################################################## # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ so I think I do have the instruction for aquaterm. It is not a very nasty bug. I just have to remember to start aquaterm first... and the only bugging idea is that it worked once... Ciao, Stefano > In my case, aquaterm opens automatically. I did set in my .cshrc >(shell script initialization file), the variable >PGPLOT_DEV=/AQT >I do know that aquaterm started even automatically even when I was >building horae using the pgplot in fink as well. > > Paul -- ____________________________________________ 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello Matt, after having installed 1.2.5a, the aquaterm is now opening ok: am currently trying artemis ZnO tutorials... 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

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello again, after running horae_update, and having now horae-036, I still do not get aquaterm to open.... SHould I reinstall ifeffit1.2.5a??? Trying to do so... 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

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Re: PCA
by Webb, Samuel M. 12 Jun '04

12 Jun '04

Hi Ethan, Glad to hear you've been checking out the PCA routines in SixPACK. I'm away from the office until after the July 4th holiday, so email access will be a little impeded. Your're right, the "save component" menu feature doesn't work, much to my surprise. I'll have this fixed in my next release. However, until that time (I won't be able to make an improved version until post July 5th), here is a quick work-around. You can plot the components, then use the "copy plot data to clipboard" option in the plot menu. This will place all current plots on the clipboard, which can then be pasted into any other application you'd like for further examination. If you want to save the components for further use in Sixpack or Athena/Artemis, any 2 column ascii format will work. As for the target transform, I can put that information of that fit into the next relase as well. As a temporary fix again, you can take the saved components (saving each of the plots above into its own text file) and then do a linear combo fit to get that data, using the PCA components as the components and the target transform file as the sample. This should give you the same fit as the target transform does in the PCA routine. Thanks for the feedback. Its always good to get comments from other users -- particularly on things that I didn't think of on the first time around. I'll try to have those improvements in the PCA released when I get back to my office. Sam ******************************************** Sam Webb SSRL/SLAC Bldg. 137, MS 69 2575 Sand Hill Rd. Menlo Park, CA 94025 Phone: (650)-926-3734 FAX: (650)-926-4100 E-mail: samwebb(a)slac.stanford.edu *******************************************

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trying to run artemis again
by doug pease 11 Jun '04

11 Jun '04

Hi Scott, This may duplicate the essentials of another e mail I sent to an address I found at the Sarah Lawrence home page, which looks a little different from this address. I would be delighted if you could look at my problem with ARTEMIS, and thank you for the generous offer!. My computer is presently at my home on 140 Sawka Drive, East Hartford, Connecticut, 06118. My phone is 860 - 568 - 5055. Once the bugs are out of these programs enough so that I can do a basic analysis, and I know I won't need to download anything I will move this computer to U. Conn. (My U. Conn. computer will only support 98, whereas my home computer supports XP. The home computer is closer to working with these programs than the one at U. Conn.) My home is about 35 minutes further from Holyoke and 35 minute closer to New Haven than U. Conn. Anytime is great for me except during the work day on Friday next week the 18th, when I have TEM time. We will cook for you if you wish, and thank you so much! Let me know the best time for you. Sincerely, Doug

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Bruce is away. I'm sure that he fix this bug when he gets back. Shelly > -----Original Message----- > From: Segre, Carlo U. > Sent: Friday, June 11, 2004 9:15 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > > > Shelly: > > Reading them in all at once is not a problem. It is just > when you read 10 in at once and then try to add another one > that we get problems. Specifically, Scott's ZnO tutorial does > this and has given light to the bug. > > I think that if one does as you propose, there is no problem > and artemis is functional. > > Carlo > > On Fri, 11 Jun 2004, Kelly, Shelly D. wrote: > > >Hi Carlo, > > > >Here is something to try. Put all the feffxxxx.dat files > into a single > >directory. Rename them so that you do not have repeating numbers. > >Then try to read them in all at one time. > > > >Shelly > > > >> -----Original Message----- > >> From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > >> Sent: Thursday, June 10, 2004 3:12 PM > >> To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > >> Subject: Re: [Ifeffit] Artemis: Error in laoding additional FEFF > >> paths? > >> > >> > >> Carlo, > >> > >> I have been having consistent problems running the tutorials on my > >> MacOSX G4 portable PC. I have posted several times the tect of the > >> trap files I am getting. .Apparently, there is no definitve answer > >> (yet). I am sure Bruce will try to clean up things whenever he has > >> time. But, if for some reason, some of you out there knows > a way out, > >> I'll be one of the many to be happy to read it. > >> > >> Stefano. > >> > >> >One of my students is just trying Scott's ZnO tutorial and we are > >> >finding a consistent problem when trying to work with the > >> third project > >> >file. > >> > > >> >When we get to the point of adding an additional path, > >> (feff0011.dat), > >> >artemis crashes with the following message: > >> > > >> >--------------------------------- > >> > > >> >The following message was trapped by Artemis: > >> > > >> >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > >> x9652e54)/ > >> >home/segre/.horae/stash/artemis.project.2/ > >> >at /usr/bin/artemis line 1562 > >> > main::__ANON__('Use of uninitialized value in > string eq at > >> >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > >> > main::read_feff('^^') called at > >> /usr/lib/perl5/Tk.pm line 225 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > >> > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', > 'active') called > >> >at /usr/lib/perl5/Tk/Menu.pm line 531 > >> > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) > called at > >> >/usr/lib/perl5/Tk.pm line 347 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > >> > Tk::MainLoop() called at /usr/bin/artemis line 1707 > >> > > >> >-------------------------------- > >> > > >> >This is happening on all of my Linux machines. They are using my > >> >Debian packages and so I have not tried with the tarball > >> installation. > >> > > >> >Has anyone else had this problem? I hesitate to report > it as a bug > >> >until it is confirmed. In a previous version of horae, it > >> worked fine. > >> > > >> >Carlo > >> > > >> > > >> >-- > >> >Carlo U. Segre -- Professor of Physics > >> >Associate Dean for Special Projects, Graduate College Illinois > >> >Institute of Technology > >> >Voice: 312.567.3498 Fax: 312.567.3494 > >> >Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > >> >_______________________________________________ > >> >Ifeffit mailing list > >> >Ifeffit(a)millenia.cars.aps.anl.gov > >> >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > >> -- > >> ____________________________________________ > >> > >> 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 > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit > >> > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Special Projects, Graduate College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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MacOS X 10.3 - Athena Starts...then Stops
by Christopher Derr 11 Jun '04

11 Jun '04

I'm attempting to install Ifeffit 1.25 on a new Powerbook G4 with MacOS X 10.3. I've downloaded the installer (actually I've tried the stable and test versions) and installed into Applications. Clicking on Athena, however, starts Athena (you see the menu at the top change) and then it just goes away. Same with Artemis. Feffit asks for a file to load, but then goes the same route as Athena and Artemis...just goes away. I'll supply more information as needed. It's a brand new laptop with nothing really untoward installed. Thanks for any thoughts whatsoever. Chris

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Here is something to try. Put all the feffxxxx.dat files into a single directory. Rename them so that you do not have repeating numbers. Then try to read them in all at one time. Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Thursday, June 10, 2004 3:12 PM > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > Carlo, > > I have been having consistent problems running the tutorials on my > MacOSX G4 portable PC. I have posted several times the tect of the > trap files I am getting. .Apparently, there is no definitve answer > (yet). I am sure Bruce will try to clean up things whenever he has > time. But, if for some reason, some of you out there knows a way out, > I'll be one of the many to be happy to read it. > > Stefano. > > >One of my students is just trying Scott's ZnO tutorial and we are > >finding a consistent problem when trying to work with the > third project > >file. > > > >When we get to the point of adding an additional path, > (feff0011.dat), > >artemis crashes with the following message: > > > >--------------------------------- > > > >The following message was trapped by Artemis: > > > >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > x9652e54)/ > >home/segre/.horae/stash/artemis.project.2/ > >at /usr/bin/artemis line 1562 > > main::__ANON__('Use of uninitialized value in string eq at > >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > > main::read_feff('^^') called at > /usr/lib/perl5/Tk.pm line 225 > > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at > >/usr/lib/perl5/Tk/Menu.pm line 531 > > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at > >/usr/lib/perl5/Tk.pm line 347 > > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > > Tk::MainLoop() called at /usr/bin/artemis line 1707 > > > >-------------------------------- > > > >This is happening on all of my Linux machines. They are using my > >Debian packages and so I have not tried with the tarball > installation. > > > >Has anyone else had this problem? I hesitate to report it as a bug > >until it is confirmed. In a previous version of horae, it > worked fine. > > > >Carlo > > > > > >-- > >Carlo U. Segre -- Professor of Physics > >Associate Dean for Special Projects, Graduate College > >Illinois Institute of Technology > >Voice: 312.567.3498 Fax: 312.567.3494 > >Carlo.Segre(a)iit.edu http://www.iit.edu/~segre > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > ____________________________________________ > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Running FEFF
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Poorani, I believe that Athena and Artemis do not work properly when installed in the C:/program files/ifeffit directory. The installation proceedures say to specify C:/ifeffit instead. To fix if, but all of C:/program files/ifeffit into the trash and then re-install. Shelly -----Original Message----- From: Ssk0016(a)aol.com [mailto:Ssk0016@aol.com] Sent: Thursday, June 10, 2004 9:55 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Running FEFF Hello All, I"m a graduate student and trying to use Athena and Artemis for EXAFS analysis.I just follow the steps ,as mentioned in the manual,to do Cu example.this is what I did. * First I opened the Chi file * Then I imported the Atoms input file,and typed all the informations and pressed "run atoms". * It gave me Feffinput.Then I pressed "run Feff".Then the bar at the bottom of the screen blinked and in very short time it asked "how many paths I want",and I clicked the button. ....It supossed to give the message screen with all the details and then all the paths should be displayed at "data & Paths". But it didn't,insted the message screen was displayed with no messages.Also there was a warning at the bottom says "Message dumped to C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP". So i went to file menu and clicked "import feff calculations" and import ARTEMIS.TRAP.then in the interpretation page ,there was a message screen saying "couldnot find feff.inp,files.dat,paths.dat". I don't know how to solve this problem.Can anyone help me to overcome this? NOTE: I'm using windows XP. thanks Poorani ' i opened th

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Running FEFF
by Ssk0016＠aol.com 10 Jun '04

10 Jun '04

Hello All, I"m a graduate student and trying to use Athena and Artemis for EXAFS analysis.I just follow the steps ,as mentioned in the manual,to do Cu example.this is what I did. * First I opened the Chi file * Then I imported the Atoms input file,and typed all the informations and pressed "run atoms". * It gave me Feffinput.Then I pressed "run Feff".Then the bar at the bottom of the screen blinked and in very short time it asked "how many paths I want",and I clicked the button. ..It supossed to give the message screen with all the details and then all the paths should be displayed at "data & Paths". But it didn't,insted the message screen was displayed with no messages.Also there was a warning at the bottom says "Message dumped to C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP". So i went to file menu and clicked "import feff calculations" and import ARTEMIS.TRAP.then in the interpretation page ,there was a message screen saying "couldnot find feff.inp,files.dat,paths.dat". I don't know how to solve this problem.Can anyone help me to overcome this? NOTE: I'm using windows XP. thanks Poorani ' i opened th

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PCA
by ebrown＠slc.edu 10 Jun '04

10 Jun '04

I've just started doing EXAFS analysis and I have a few questions. I imported EXAFS data (prepared by Athena) into SixPack and ran a principle component analysis on the date. I then ran some target transforms of the dominant components targeting different compounds we thought could be part of the data. This has yielded some extremely useful indicators of which compounds are most likely in the sample. However, there's a limited amount of information available from the SixPack PCA. Is there any way to find out information about the makeup of components? The "Save Components" option doesn't work. Also, for the target transform feature: is there any way to find out how much of each component is used to make the transform? Presumably, this information would need to be calculated in order to make the transform in the first place, but I can't find any way to access that information. I've found SixPack very helpful, but if there's other PCA's that provide these features, that would also be useful. Thanks, Ethan Brown

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trying to run artemis again
by doug pease 10 Jun '04

10 Jun '04

Thank you Carlo and Shelly, I think the warning message is that "rmax is greater than the distance to the most distant atom" . My cluster size I put into ATOMS the last time I ran this is 5.5. The message then says rmax,ratx 5.5000 5.09117. (My experimental data goes to R = 6.) No matter what cluster size I choose I get the same warning with ratx less than rmax by a small amount. I have tried several cluster sizes and always get the same warning. Sincerely, Doug

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Re: [Ifeffit] more fun with FFTs
by Scott Calvin 10 Jun '04

10 Jun '04

Thanks to both Matt and Grant for clarifying several issues. You've given me a lot to chew on and inspired me to go back and take another close look at all of this. Hopefully I'll have more to add to this discussion once I do! --Scott Calvin Sarah Lawrence College >

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more fun with FFTs
by Grant Bunker 09 Jun '04

09 Jun '04

....to clarify my earlier remarks... The experimental chi is the amplitude times the sine of the phase, and is of course a real number. However, if you determine the amplitude and phase, you do it by separating the real chi into two complex functions Amplitude*Sin(phase) = (Amplitude*(Exp(I phase) - Exp(- I phase))/(2 I) which have most of their spectral power at distinct locations in the r-space transform. This is done by k->r transform, zeroing one of terms, multiplying by 2I, and backtransforming r->k. The amplitude and phase are easily determined from the real and imaginary parts of the complex result. When using Fourier methods it is most useful to look at chi as the imaginary part of this "complex chi"= Amplitude Exp(I phase), and that was what I meant. It's just like saying the "scattering amplitude" F(k) and phase are two components of the complex scattering ampltude: scattering amplitude = |scattering amplitude| * Exp(I scattering phase). This mathematics is implicit in all of scattering theory and XAFS in particular. Regarding window effects, I think the most useful way to think about them is to realize the Fourier transform of windowed weighted chi is the convolution of the fourier transforms of the k-window and the unwindowed weighted chi (convolution theorem). What the window does is give an r-space transform that is the convolution of a scraggly function (~ sin(x)/x for a sharp k-space cutoff) with the nice peak you (probably) would have had if you had an infinite range of chi. The width of the r-space peaks and the structure of the side lobes is principally due to the fourier transform of the k-space window. If the k-window doesn't have sharp corners (like a box does) its fourier transform will be smoother and there will be less truncation ripple in r-space. That's why tapered windows are helpful. One is free to use arrays of other lengths, or to eschew zero padding altogether, but I don't think the transforms would be very useful at a quarter angstrom sampling, certainly not in the sense they normally are. thanks - grant On Wed, 9 Jun 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. Re: E0 correction in EXAFS fitting (Matt Newville) > 2. more fun with FFT's (Grant Bunker) > 3. Re: more fun with FFT's (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Jun 2004 13:19:22 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] E0 correction in EXAFS fitting > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0406082306500.28025-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Dear Wojciech, > > It seems like this question has been asked many times, possibly in > slightly different form. > > Feff's choice of E0 can be off by several eV. Also, Feff is not > good at distinguishing formal oxidation state. So believing > Feff's E0 may not be the best idea. In my experience, Feff tends > to pick an E0 that is relatively far up the main absorption edge, > generally several eV above the maximum of the first derivative. > That's consistent with the traditional lore that says the max of > the first derivative is the Fermi level, not E0 (lowest unoccupied > orbital). > > If athena/autobk pick E0 to be on a sharp pre-edge peak, you > probably want to move it. But the best placement for E0 is not > easy to make when there is a large pre-edge peak. > > One camp says that since there is absorption, then it's at E_0, > and the pre-edge peak is really the absorption edge, followed by a > large negative EXAFS 'black line' oscillation that nearly sends > mu(E) to zero. The other camp invokes localized states (either > excitons or empty molecular orbitals) to say the pre-edge peaks > are really quasi-bound transitions, but below the real continuum. > I'll try to avoid that debate. > > I couldn't tell whether there was a large pre-edge peak followed > by the main absorption edge or a very large white line. If I > understand, it sounds like Feff is trying to put E0 at the > pre-edge peak... is that correct? > > I'm sure that leaves unanswered questions, but I hope it helps > show the general level of confusion about E0. > > --Matt > > On Tue, 8 Jun 2004, it was written: > > > Dear Bruce and other mailing list users, > > > > I have a very basic question concerning the choice of E0 in EXAFS data > > analysis. Recently I have been working on Ru solvated complex. I don?t > > go into too many details but I can say it?s a pretty large molecule in > > aqueous solution with 3 ligands containing 6 N atoms and 30 C atoms in > > D3 symmetry. Now, we have measured the L3 edge XANES and EXAFS of this > > molecule and I have recently tried to analyze it. Now, what bothers me a > > lot is the following observation: once I start processing the data > > (meaning background removal, pre-edge subtraction etc.) AUTOBK in both > > Ifeffit and Athena ?proposes? to place the edge energy E0 at the > > inflection point of the spectrum which lies at about 2838-2839 eV (which > > corresponds to atomic Ru L3 edge absorption energy). You might say it?s > > ok but I cannot accept this value. The inflection point lies on a huge > > pre-edge peak which is the 4d bound-to-bound transition (white line) > > which in principle I don?t want to include in my chi(k) because it?s > > still below the ionization energy as I understand it. I guess the > > continuum states should start higher in energy and actually from other > > spectroscopies one would suspect the E0 to be around 2847 eV (so about > > 7-8 eV higher in energy space). Now I set my E0 to this value and I > > started fitting the spectrum with FEFF calculation performed on > > crystalline structure of the same complex. What I end up with is always > > E0 correction for the first shell of neighbors (meaning N atoms) between > > -6 to -7.5 eV. I check in chi.dat and xmu.dat files that in my FEFF > > calculation the k=0 value was assigned to approx. 2839 eV so it?s the > > same atomic value again. However I know it shouldn?t be like that (apart > > from a simple fact that Ru in my compound is in its 2+ oxidation state > > which surely moves the E0 toward higher energies, doesn?t it?). So, I > > tried to fool FEFF and make some tricks like shift my data in energy > > space or fit the white line and subtract it form the data but it always > > consistently converges to place the E0 value at the first inflection > > point meaning between 2839-2842 eV. I thought that when fitting the > > experimental data with FEFF scattering paths one can choose E0 and then > > refine its value by shifting the FEFF-calculated E0 by the amount which > > comes out of the fit. So if I have some value of E0 coming out of my fit > > then I just shift the initial k=0 value as estimated by FEFF using k? -> > > sqrt( k-E0(2m/h_bar^2) ) (in other words the negative E0 correction > > would always shift the origin in k-space towards larger k values which > > means lower values in energy space). Ok, so now my question is the > > following: is there an explicit way to set E0 value before letting FEFF > > to do its job or it will always use the tabulated atomic value? So, if I > > don?t know my E0 a priori how can I refine it for a complex or molecule > > which has different oxidation state than 0? I mean it?s a serious > > question in my opinion and I wish I could get some feedback from people > > who have been doing it for so many years. > > I hope I made my point clear enough to you. Let me know if you need any > > more feedback in order to answer my question. I?ll be glad to give more > > details. > > Best regards, > > > > Wojciech > > > > ********************************************************************* > > Wojciech Gawelda > > > > Laboratoire de Spectroscopie Ultrarapide (LSU) > > Institut des Sciences et Ing?nierie Chimiques (ISIC), > > Facult? des Sciences de Base (SB-BSP) > > Ecole Polytechnique F?d?rale de Lausanne (EPFL) > > > > CH-1015 Lausanne-Dorigny, Switzerland > > Tel.: +41 (21) 693 0452 > > Fax.: +41 (21) 693 0422 > > E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch > > WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch > > ********************************************************************* > > > >

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need more help with artemis
by doug pease 09 Jun '04

09 Jun '04

Hi, I tried Mary Shelly's suggestion to increase the resolution for my Windows XP monitor and this worked. Now I can run ATOMS from Artemis. Now the following happens: Running simple copper metal I generate an input file for FEFF that looks o.k. to me. I run FEFF and it generates paths that make sense....12 near neighbors of the right distance and so on. The Cu CHI function data is imported o.k. and a FT is displayed that looks fine. But the expected path input dialog box never comes up. According to the manual, once I start FEFF this dialog box is supposed to pop up asking how many paths I want to import and THEN FEFF is supposed to compute. The dialog box step is skipped. It says "message dumped to ENV-IFEFFIT-DIR-\HORAE\STASH\ARTEMIS.TRAP" I don't know where to look for this message , or why the dialog box never shows up. Any suggestions? Sincerely, Doug Pease

2 1

Re: [Ifeffit] more fun with FFT's
by Scott Calvin 09 Jun '04

09 Jun '04

Thanks to Matt and Grant for the comments. After reading Grant's comments, it appears I have some significant gaps in my understanding of some basic EXAFS concepts: Chi(k) is complex? That's a completely new concept to me. I thought chi(R) was complex because a complex Fourier transform was used, and that chi(k) was real. After all, the peaks of chi(k) correspond to peaks in the energy spectrum...if that is the real part of chi(k), what does the imaginary part correspond to? I still disagree with the assertion that you always have truncation effects when using a finite k-range. As I understand the properties of Fourier transforms, using a finite range is identical to using an infinite range with a periodic function that repeats the pattern seen in the finite range over and over. So if it happens that the function at the end of the range connects smoothly with the function at the beginning of the range, there should be no truncation effects. This can also be looked at another way. In terms of the sinc function due to the finite range, the zeroes of the sinc function correspond exactly with the points in r-space at which the Fourier transform is evaluated, and thus the Foruier transform is only non-zero at one point. I have simulations that show this, but if I missed that chi(k) was complex, that could mean there is an error in this logic. As I understand Grant's comments, you can show that the sinc function is "really" still there by padding with zeroes, thus improving the resolution in r-space, and revealing the side-band structure. I agree that this is what will be observed, but if I consider this from the point of view of a FT of a finite range being the same as the FT of an infinite function which repeats the finite section periodically, then the zero-padding is introducing discontinuities which were not previously there. It is, I think, a matter of semantics whether one considers the side-bands to be "really" there when the FT is not evaluated at values of r where it is non-zero. But in either way of looking at it, padding with zeroes introduces non-zero values to the discrete FT outside of a region where there were only zero values before. None of this is meant in any way as a criticism of the algorithm used by Ifeffit as Matt described it. Windowing and then padding with zeroes makes the truncation effects relatively consistent...if there is a downside to forcing chi(k) to go to zero at the endpoints, so be it, but this strategy means the downside is always present. Alternative strategies which encourage picking whole periods of chi(k) for the data range, for example, risk being self-fulfilling, so that the period chosen for the data range might be emphasized in the Fourier transform at the expense of other spectral frequencies. To sum up, I am now very curious as to whether there is some sense in which chi(k) is complex. If that's true, I'll have to rethink a lot of my understanding as to how this all fits together. --Scott Calvin Sarah Lawrence College At 02:26 PM 6/9/2004 -0500, Grant wrote: >This is in response to Scott's remarks about zero padding and windows. >The basic point is that you *always* have fourier truncation effects if >you are using a finite k range. If you Fourier transform a pure sine wave >over a finite range you will get side lobes that go like |sin(x)/x|. This >is true whether you zero pad or not. You won't be able to resolve the side >lobe structure if you don't zero-pad however. All you will see is a single >point. A useful way to think about it is to view the discrete FFT as a sampled >version of the continuous transform (side lobes and all) where the r-space >sampling is controlled by size N of the zero padded array (and dk). >Hhe zero padding doesn't change the window distortions, it just allows you >to see them better. > >You can of course mitigate the side lobes by applying a k-window to taper >the amplitude down to zero at the cutoff, but at the expense of broadening the >central part of the peaks. > >There also is a common myth that if you choose the cutoff to be where >chi is zero anyway, that you don't get fourier truncation effects. This is >not true. Even if chi (Amplitude*sin(phase)) is zero at a particular k >value the amplitude may not be. Imagine a thought experiment in which >you shift the phase of chi by a Pi/2, so a node becomes an antinode. >Mathematically this is the same as multiplying the complex chi >A exp(i phi) by exp(i Pi/2). Since the fourier transform is linear, the >filtered (transformed, r-windowed, and inverse transformed) data are just >shifted in phase by Pi/2. The fourier filtering distortions are precisely >the same when you cut at a node or an antinode. > >I'll try to dig up some simulations I did many moons ago and post >them. >>>

2 1

more fun with FFT's
by Grant Bunker 09 Jun '04

09 Jun '04

This is in response to Scott's remarks about zero padding and windows. The basic point is that you *always* have fourier truncation effects if you are using a finite k range. If you Fourier transform a pure sine wave over a finite range you will get side lobes that go like |sin(x)/x|. This is true whether you zero pad or not. You won't be able to resolve the side lobe structure if you don't zero-pad however. All you will see is a single point. A useful way to think about it is to view the discrete FFT as a sampled version of the continuous transform (side lobes and all) where the r-space sampling is controlled by size N of the zero padded array (and dk). Hhe zero padding doesn't change the window distortions, it just allows you to see them better. You can of course mitigate the side lobes by applying a k-window to taper the amplitude down to zero at the cutoff, but at the expense of broadening the central part of the peaks. There also is a common myth that if you choose the cutoff to be where chi is zero anyway, that you don't get fourier truncation effects. This is not true. Even if chi (Amplitude*sin(phase)) is zero at a particular k value the amplitude may not be. Imagine a thought experiment in which you shift the phase of chi by a Pi/2, so a node becomes an antinode. Mathematically this is the same as multiplying the complex chi A exp(i phi) by exp(i Pi/2). Since the fourier transform is linear, the filtered (transformed, r-windowed, and inverse transformed) data are just shifted in phase by Pi/2. The fourier filtering distortions are precisely the same when you cut at a node or an antinode. I'll try to dig up some simulations I did many moons ago and post them. grant On Tue, 8 Jun 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. more fun with FFTs (Grant Bunker) > 2. E0 correction in EXAFS fitting (Wojciech Gawelda) > 3. Re: more fun with FFTs (Scott Calvin) > 4. beginning with ARTEMIS (doug pease) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jun 2004 12:34:58 -0500 (CDT) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] more fun with FFTs > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0406081222050.25188-100000(a)biocat1.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Just to amplify Matt's remarks - the purpose of padding with zeros is to > deliver a finer grid in r-space. There is a relationship between the > r-space grid dr, the k-space grid dk, and the number of points in the > array (N): N dk dR = Pi. So, for a k-space grid of .05/A and 2048 > points, you get an r-grid spacing of .0307 A. This gives pretty good > sampling of the fourier transform. If you only use say 256 points in your > array (i.e. you don't pad with zeroes) the r-space sampling is .245 A, > which is too coarse to be useful. > > You might ask whether zero padding botches up the data. It can be shown > (I worked it out once) that zero padding is exactly equivalent to > an interpolation of the unpadded data witha specific interpolation kernel > (a sinc function or something as I recall). What happens is that as you > pad with more zeros into a longer array, the sampling in r-space increases, > and ultimately the curve looks just like what you would get with a continuous > fourier transform (with cutoff effects from the finite k-space window). > > grant > > On Tue, 8 Jun 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. Re: FFT in Ifeffit (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 7 Jun 2004 22:55:28 -0500 (CDT) > > From: Matt Newville <newville(a)cars.uchicago.edu> > > Subject: Re: [Ifeffit] FFT in Ifeffit > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: <Pine.LNX.4.44.0406072214290.13810-100000@corvette> > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > Hi Scott, > > > > All Fourier transforms in Ifeffit use arrays of length 2048, > > padding with zeros as needed. > > > > In earlier versions of Feffit, doing repeated FTs in the fitting > > loop was noticeably slow. This is probably one of the reasons > > fitting in R-space was uncommon. Anyway, using arrays of length > > N_fft = 1024, 512, or 256 definitely helped speed things up. > > > > In principle, one could use N_fft ~= N_idp, but it turns out that > > if you use too few FT points, you can easily get into a real > > 'false, local, minima'. So Feffit used 1024,512,or 256 for fits, > > and then go back to 2048 to write out the data. Strictly speaking, > > the FFT doesn't need to use an array size that is a power of 2, > > but it turns out to make a very noticeable difference with the FFT > > routines used. > > > > With Ifeffit, several "anti-optimizations" were made that make > > the fits slightly slower but be more straightforward and simple > > (relatively speaking, anyway!). The use of double precision and > > N_fft=2048 being the main examples. Part of the reason for > > sticking with 2048 is that you want to be able to view the data at > > any point in the process so 'pretty output' is always needed. > > Also, I doubt many people will be trying to run artemis on a 386 > > or a microVAX. > > > > --Matt > > > > > As I was working on my talk for the EXAFS workshop, I came across a > > > rather technical question: how does Ifeffit choose the number of > > > points for the Fourier transforms? As I recall, FEFFIT used an > > > algorithm which required an integer power of 2, so its default > > > behavior was to use the smallest integer power of 2 greater than the > > > number of points in the chi(k) data, and then pad the rest with 0's. > > > This default behavior could also be over-ridden if desired. > > > > > > It doesn't look to me like Ifeffit is handling that in the same > > > way--is it always using a very large number of points and padding > > > with 0's, or is it using an algorithm that doesn't require the > > > integer power of 2, or is it interpolating the chi(k) on to a grid of > > > the appropriate size first, or...? > > > > > > I appreciate any info you can give me on this. > > > > > > --Scott Calvin > > > Sarah Lawrence College > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 16, Issue 7 > > ************************************** > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Jun 2004 20:04:25 +0200 > From: "Wojciech Gawelda" <wojciech.gawelda(a)epfl.ch> > Subject: [Ifeffit] E0 correction in EXAFS fitting > To: <ravel(a)phys.washington.edu> > Cc: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <!~!UENERkVCMDkAAQACAAAAAAAAAAAAAAAAABgAAAAAAAAA+oqSCNd0OEmvPV/OsrrrucKAAAAQAAAAqvlml9Ymw0KfPXsmOeouUQEAAAAA(a)epfl.ch> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Bruce and other mailing list users, > > I have a very basic question concerning the choice of E0 in EXAFS data > analysis. Recently I have been working on Ru solvated complex. I dont > go into too many details but I can say its a pretty large molecule in > aqueous solution with 3 ligands containing 6 N atoms and 30 C atoms in > D3 symmetry. Now, we have measured the L3 edge XANES and EXAFS of this > molecule and I have recently tried to analyze it. Now, what bothers me a > lot is the following observation: once I start processing the data > (meaning background removal, pre-edge subtraction etc.) AUTOBK in both > Ifeffit and Athena proposes to place the edge energy E0 at the > inflection point of the spectrum which lies at about 2838-2839 eV (which > corresponds to atomic Ru L3 edge absorption energy). You might say its > ok but I cannot accept this value. The inflection point lies on a huge > pre-edge peak which is the 4d bound-to-bound transition (white line) > which in principle I dont want to include in my chi(k) because its > still below the ionization energy as I understand it. I guess the > continuum states should start higher in energy and actually from other > spectroscopies one would suspect the E0 to be around 2847 eV (so about > 7-8 eV higher in energy space). Now I set my E0 to this value and I > started fitting the spectrum with FEFF calculation performed on > crystalline structure of the same complex. What I end up with is always > E0 correction for the first shell of neighbors (meaning N atoms) between > -6 to -7.5 eV. I check in chi.dat and xmu.dat files that in my FEFF > calculation the k=0 value was assigned to approx. 2839 eV so its the > same atomic value again. However I know it shouldnt be like that (apart > from a simple fact that Ru in my compound is in its 2+ oxidation state > which surely moves the E0 toward higher energies, doesnt it?). So, I > tried to fool FEFF and make some tricks like shift my data in energy > space or fit the white line and subtract it form the data but it always > consistently converges to place the E0 value at the first inflection > point meaning between 2839-2842 eV. I thought that when fitting the > experimental data with FEFF scattering paths one can choose E0 and then > refine its value by shifting the FEFF-calculated E0 by the amount which > comes out of the fit. So if I have some value of E0 coming out of my fit > then I just shift the initial k=0 value as estimated by FEFF using k -> > sqrt( k-E0(2m/h_bar^2) ) (in other words the negative E0 correction > would always shift the origin in k-space towards larger k values which > means lower values in energy space). Ok, so now my question is the > following: is there an explicit way to set E0 value before letting FEFF > to do its job or it will always use the tabulated atomic value? So, if I > dont know my E0 a priori how can I refine it for a complex or molecule > which has different oxidation state than 0? I mean its a serious > question in my opinion and I wish I could get some feedback from people > who have been doing it for so many years. > I hope I made my point clear enough to you. Let me know if you need any > more feedback in order to answer my question. Ill be glad to give more > details. > Best regards, > > Wojciech > > ********************************************************************* > Wojciech Gawelda > > Laboratoire de Spectroscopie Ultrarapide (LSU) > Institut des Sciences et Ingénierie Chimiques (ISIC), > Faculté des Sciences de Base (SB-BSP) > Ecole Polytechnique Fédérale de Lausanne (EPFL) > > CH-1015 Lausanne-Dorigny, Switzerland > Tel.: +41 (21) 693 0452 > Fax.: +41 (21) 693 0422 > E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch > WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch > ********************************************************************* > >

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E0 correction in EXAFS fitting
by Wojciech Gawelda 09 Jun '04

09 Jun '04

Dear Bruce and other mailing list users, I have a very basic question concerning the choice of E0 in EXAFS data analysis. Recently I have been working on Ru solvated complex. I dont go into too many details but I can say its a pretty large molecule in aqueous solution with 3 ligands containing 6 N atoms and 30 C atoms in D3 symmetry. Now, we have measured the L3 edge XANES and EXAFS of this molecule and I have recently tried to analyze it. Now, what bothers me a lot is the following observation: once I start processing the data (meaning background removal, pre-edge subtraction etc.) AUTOBK in both Ifeffit and Athena proposes to place the edge energy E0 at the inflection point of the spectrum which lies at about 2838-2839 eV (which corresponds to atomic Ru L3 edge absorption energy). You might say its ok but I cannot accept this value. The inflection point lies on a huge pre-edge peak which is the 4d bound-to-bound transition (white line) which in principle I dont want to include in my chi(k) because its still below the ionization energy as I understand it. I guess the continuum states should start higher in energy and actually from other spectroscopies one would suspect the E0 to be around 2847 eV (so about 7-8 eV higher in energy space). Now I set my E0 to this value and I started fitting the spectrum with FEFF calculation performed on crystalline structure of the same complex. What I end up with is always E0 correction for the first shell of neighbors (meaning N atoms) between -6 to -7.5 eV. I check in chi.dat and xmu.dat files that in my FEFF calculation the k=0 value was assigned to approx. 2839 eV so its the same atomic value again. However I know it shouldnt be like that (apart from a simple fact that Ru in my compound is in its 2+ oxidation state which surely moves the E0 toward higher energies, doesnt it?). So, I tried to fool FEFF and make some tricks like shift my data in energy space or fit the white line and subtract it form the data but it always consistently converges to place the E0 value at the first inflection point meaning between 2839-2842 eV. I thought that when fitting the experimental data with FEFF scattering paths one can choose E0 and then refine its value by shifting the FEFF-calculated E0 by the amount which comes out of the fit. So if I have some value of E0 coming out of my fit then I just shift the initial k=0 value as estimated by FEFF using k -> sqrt( k-E0(2m/h_bar^2) ) (in other words the negative E0 correction would always shift the origin in k-space towards larger k values which means lower values in energy space). Ok, so now my question is the following: is there an explicit way to set E0 value before letting FEFF to do its job or it will always use the tabulated atomic value? So, if I dont know my E0 a priori how can I refine it for a complex or molecule which has different oxidation state than 0? I mean its a serious question in my opinion and I wish I could get some feedback from people who have been doing it for so many years. I hope I made my point clear enough to you. Let me know if you need any more feedback in order to answer my question. Ill be glad to give more details. Best regards, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

2 1

starting artemis
by doug pease 09 Jun '04

09 Jun '04

Hello All, My oversight not specifying the platform. When the ATOMS in ARTEMIS fills up the whole screen and the run button is off screen I am in Windows XP. I also have a - perhaps non standard - ViewSonic flat screen monitor, for what that is worth. Carlo, thank you for your interest. Do you or anyone else have a suggestion? Overnight I thought of perhaps trying to change my monitor settings to shrink my monitor display?? Sincerely, Doug Pease

2 1

RE: [Ifeffit] starting artemis
by Kelly, Shelly D. 09 Jun '04

09 Jun '04

-----Original Message----- From: doug pease [mailto:dougpease@comcast.net] Sent: Wednesday, June 09, 2004 6:57 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] starting artemis Hello All, My oversight not specifying the platform. When the ATOMS in ARTEMIS fills up the whole screen and the run button is off screen I am in Windows XP. I also have a - perhaps non standard - ViewSonic flat screen monitor, for what that is worth. Carlo, thank you for your interest. Do you or anyone else have a suggestion? Overnight I thought of perhaps trying to change my monitor settings to shrink my monitor display?? Sincerely, Doug Pease Hi Doug, If you can, you should increase the resolution of the display. On a win2k machine you go to the control panel and choose the Display icon. >From there you can increase the resolution by going to the setting tab and increase the screen area to be 1280 by 1024 pixels. (-I think that winXP should be similar.:) Shelly

1 0

beginning with ARTEMIS
by doug pease 08 Jun '04

08 Jun '04

Hello All, Just starting ARTEMIS for first time. Seems o.k. until I come to the place where I am to run ATOMS in ARTEMIS. The ATOMS view in ARTEMIS takes up the whole monitor screen and the button for running ATOMS is out of site. I cannot drag the view high enough to reveal the ATOMS run button. Any suggestions? Sincerely, Doug Pease

2 1

Re: [Ifeffit] more fun with FFTs
by Scott Calvin 08 Jun '04

08 Jun '04

First of all, thanks to Matt for the info--this seems to me to be a very sensible way for Ifeffit to handle the issue. In terms of Grant's comments, the interesting part to me (and I admit I am getting esoteric here) is that zero-padding has the potential to change the cutoff effects in some circumstances. If you're using a window that goes to zero anyway, then I think it has exactly the effect that Grant describes. But not all windows do this. As a particularly simple example, consider a perfect cosine function over an integer number of periods, with no window. Even though the transform is applied to a finite interval, the result is a spike to within the resolution discussed in Grant's post. (As I recall, the finite sampling also causes the transform to be periodic, but the period is large enough to be disregarded in EXAFS analysis.) But now consider the identical function over the identical interval with zero-padding. This introduces a sharp discontinuity, and causes lots of sidebands on the Fourier transform. Of course, I chose a very special case. Windows reduce this effect considerably, so I would certainly agree that zero-padding does not "botch up" the data. But I wonder if some reduction in sidebands could be achieved by, for example, using a window that goes to the average of the values of the function at the two ends of the interval rather than to 0 (and adjusting the windowing function accordingly). It's on my list of things to try when I get the chance...I don't expect it will make a dramatic difference, but it might make an incremental one. --Scott Calvin Sarah Lawrence College At 12:34 PM 6/8/2004 -0500, Grant wrote: >You might ask whether zero padding botches up the data. It can be shown >(I worked it out once) that zero padding is exactly equivalent to >an interpolation of the unpadded data witha specific interpolation kernel >(a sinc function or something as I recall). What happens is that as you >pad with more zeros into a longer array, the sampling in r-space increases, >and ultimately the curve looks just like what you would get with a continuous >fourier transform (with cutoff effects from the finite k-space window). >

1 0

more fun with FFTs
by Grant Bunker 08 Jun '04

08 Jun '04

Just to amplify Matt's remarks - the purpose of padding with zeros is to deliver a finer grid in r-space. There is a relationship between the r-space grid dr, the k-space grid dk, and the number of points in the array (N): N dk dR = Pi. So, for a k-space grid of .05/A and 2048 points, you get an r-grid spacing of .0307 A. This gives pretty good sampling of the fourier transform. If you only use say 256 points in your array (i.e. you don't pad with zeroes) the r-space sampling is .245 A, which is too coarse to be useful. You might ask whether zero padding botches up the data. It can be shown (I worked it out once) that zero padding is exactly equivalent to an interpolation of the unpadded data witha specific interpolation kernel (a sinc function or something as I recall). What happens is that as you pad with more zeros into a longer array, the sampling in r-space increases, and ultimately the curve looks just like what you would get with a continuous fourier transform (with cutoff effects from the finite k-space window). grant On Tue, 8 Jun 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. Re: FFT in Ifeffit (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Jun 2004 22:55:28 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] FFT in Ifeffit > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.44.0406072214290.13810-100000@corvette> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > All Fourier transforms in Ifeffit use arrays of length 2048, > padding with zeros as needed. > > In earlier versions of Feffit, doing repeated FTs in the fitting > loop was noticeably slow. This is probably one of the reasons > fitting in R-space was uncommon. Anyway, using arrays of length > N_fft = 1024, 512, or 256 definitely helped speed things up. > > In principle, one could use N_fft ~= N_idp, but it turns out that > if you use too few FT points, you can easily get into a real > 'false, local, minima'. So Feffit used 1024,512,or 256 for fits, > and then go back to 2048 to write out the data. Strictly speaking, > the FFT doesn't need to use an array size that is a power of 2, > but it turns out to make a very noticeable difference with the FFT > routines used. > > With Ifeffit, several "anti-optimizations" were made that make > the fits slightly slower but be more straightforward and simple > (relatively speaking, anyway!). The use of double precision and > N_fft=2048 being the main examples. Part of the reason for > sticking with 2048 is that you want to be able to view the data at > any point in the process so 'pretty output' is always needed. > Also, I doubt many people will be trying to run artemis on a 386 > or a microVAX. > > --Matt > > > As I was working on my talk for the EXAFS workshop, I came across a > > rather technical question: how does Ifeffit choose the number of > > points for the Fourier transforms? As I recall, FEFFIT used an > > algorithm which required an integer power of 2, so its default > > behavior was to use the smallest integer power of 2 greater than the > > number of points in the chi(k) data, and then pad the rest with 0's. > > This default behavior could also be over-ridden if desired. > > > > It doesn't look to me like Ifeffit is handling that in the same > > way--is it always using a very large number of points and padding > > with 0's, or is it using an algorithm that doesn't require the > > integer power of 2, or is it interpolating the chi(k) on to a grid of > > the appropriate size first, or...? > > > > I appreciate any info you can give me on this. > > > > --Scott Calvin > > Sarah Lawrence College > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 16, Issue 7 > ************************************** >

1 0

Re: [Ifeffit] Using more than one E0
by Scott Calvin 07 Jun '04

07 Jun '04

Hi Wojciech, I have another suggestion. It is my secret, completely untested belief (which I am now revealing to everyone on this mailing list!), that some of the cases of "successful" fits using multiple E0's are masking problems caused by not considering a third cumulant. For those who may not know the role of this parameter, it in essence measures asymmetry in the distribution associated with a path. For example, if a pair of atoms are more likely to separated by a distance considerably larger than the mean separation than by a distance considerably smaller than the mean separation, then the third cumulant is positive. (The mathematical definition is that the third cumulant is the mean cube of the difference from the mean, in the same sense that sigma2 is the mean square of the difference from the mean.) In most cases, the third cumulant is small. Nevertheless, if it were 0 in all cases, then materials would not show any expansion with temperature! Through symmetry arguments, it is pretty clear that the third cumulant is most likely to be significantly nonzero for nearest-neighbor paths. What does this have to do with fitting different E0's? E0 and the third cumulant both affect the phase of the EXAFS signal, although they are weighted in different ways by k. Nevertheless, if a nonzero nearest-neighbor third cumulant is called for, allowing a different E0 for the nearest-neighbor instead would probably also improve the fit statistically. In this case, however, while the use of a third cumulant can be justified on physical grounds relatively easily, the use of a separate E0 is an arbitrary non-physical attempt to improve the statistics. So as far as I am concerned, I am more inclined, if my fit is not quite working out, to try allowing the third cumulant for paths in the first coordination shell to vary than I am to introduce multiple E0's. In fact, I usually do this at some point during the fitting process even if my fit is behaving fairly well to reassure myself that the third cumulant is 0 to within the uncertainty of the fit, and that constraining it to 0 is not distorting the values of the parameters I am interested it. Take all of this with a grain of salt; I wrote my dissertation on the third cumulant, and, to paraphrase Bruce, since I've spent a lot of time making a nice hammer, everything tends to look like a nail... --Scott Calvin Sarah Lawrence College > >I would like to address a couple of questions which are partially >related to my recent struggles in fitting some EXAFS data. I'm >trying to fit my data using several shells of different neighbors >including a few single scattering paths and also so multiple >scattering contributions (mainly collinear multiple scattering >paths) all calculated with the help of FEFF 8.20. Now, I found once >in the FEFFIT manual the following suggestion: one might consider >using several different E0's for different paths in order to improve >the fit. Ok, the explanation was based on some approximations coming >from FEFF code which include incomplete core-hole shielding, lack of >angular variations of the valence charge distribution and charge >transfer between atoms in polar materials. >My question is the following: does anyone of you have some >experience with such procedure? And if yes, shall than distinguish >between the first shell of nearest neighbors and the rest of the >atoms in terms of their E0 corrections (using 2 parameters)? Or >perhaps one can use separate E0's for each path?

3 6

trouble with Atoms on Mac OSX
by Michel Jaouen 04 Jun '04

04 Jun '04

Hi folks, I'm using a PM (2X1.8 MHz processors) under OSX v 10.3.4 (Panther latest version). I have installed ifeffit-1.2.5a two weeks ago and used Atoms many times since. It works well till yesterday when I loose the ability to use the space group browser with an error reported on the herre attached file. It looks that I have a problem with Tk, but I don't understand why. I have tried to make a new install from scratch after putting in the trash the ifeffit and perl (the one I assume to be put by the iffit installer in the home/lib folder): it didn't fix the problem. I found rather puzzling to find several perl folders (one coming from ifeffit and one from Fink). Looking my environnement, I found the following: PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin. I therefore modify my profile making a setenv to force to use the perl from ifeffit without any change. So it seems some hidden file is responsible of this behavior. I must say that if I enter the space group by hand, Atoms runs (e.g. it creates the feff.inp file). If anybody has a solution, I will appreciate. Additional point: I have compliled feff7 using the GNU g77 from Fink, but it stops the run with a segmentation fault. Any hint? Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

3 2

Debian packages
by Carlo U. Segre 04 Jun '04

04 Jun '04

Hello All: I have now packaged the latest horae (036) for Debian stable and unstable. There was a problem in previous versions for stable which I just now figured out how to fix and it involved making a back port of a newer perl module for the archiving/zipping of the project files. Sorry if this caused anyone problems. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

2 1

trouble with Tk on Mac OSX
by Michel Jaouen 03 Jun '04

03 Jun '04

Hi folks, I think somethings is broken with Tk. As reported in my previous e-mail I found a problem (I have not before 1st june!) with the space group browser of Atoms. In fact I have the same error with Artemis when pressing the fit button! The following message was trapped by Artemis: Artemiswarn/Users/mjaouen/.horae/stash/ARTEMIS.TRAPCODE(0x1e18a84) at /Applications/Ifeffit/bin/artemis line 1491 main::__ANON__('Tk::Error: unknown option "background" at /Library/Perl/ 5.8.1...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) l ine 488 Tk::Error('MainWindow=HASH(0x61e5d8)','unknown option "background" at /Library/Perl/5.8.1/darwin-thr...','Tk callback for .sgb.frame','Tk callback for . sgb.frame.ysbslice','Tk callback for .sgb.frame.ysbslice.corner','Tk callback for ..sgb','Tk callback for .sgb.button1','Tk callback for .frame.menubutton5.menu', 'Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2leve...',...) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1627 What makes me crazy is that all was running smoothly before tuesday :-) Cheers Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

2 1

news
by Bruce Ravel 02 Jun '04

02 Jun '04

Hi everybody, Today I made another new release of the source code tarball and built a new Artemis executable for windows. Users of each of the three major platforms should read the notes below for information about this release. This will be the last release for a while. June and July will be very busy for me and I will have scant time to work on the codes until August at the earliest. I will be reading bug reports and suggestions and will address them when I get back to work on the codes -- so please continue to send them in. Hopefully whatever bugs are lurking in there will not prove too difficult to work around. This release attempts to fix a problem managing the project folder in Artemis, as reported by Stefano Ciurli. The new version works correctly for me, your milage may vary. If any of you will be at the ISSRNS conference in Zakopane Poland next week, please introduce yourself! I hope everyone has a great summer! (Or a great winter for those of you in the southern hemisphere!) B -------------------- O -------------------- Notes for each of the platforms follow: Linux (and other non-Mac OSX unixes): The source code tarball is on SourceForge and on my web site. If the horae_update script fails, try using the --mirror argument as described in the help text (horae_update -h). Mac OSX: There was no time to make a new installer package. For the time being, you can use the most recent installer package, then update to the latest source code tarball from the command line. This requires downloading the source tarball from SourceForge and unpacking it. Then, from the command line, type "perl Makefile.PL" then "make" then "sudo make install". The last step will prompt for the administrator password. If you run into trouble, ask on the mailing list and one of the Mac users should be able to help you. Windows: There was no time to prepare a new updater package for windows. Virtually all of the changes in my codes since the last updater package have been bug fixes to Artemis. So I have made a new Artemis executable and placed it here: http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/artemis_… If you are up to date with the most recent updater package, just download this executable and overwrite the "artemis.exe" file in the instalation directory: "C:\Program Files\Ifeffit" (or where ever you have ifeffit installed on your computer). -- 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/

2 1

trap file
by Stefano Ciurli 01 Jun '04

01 Jun '04

Hi Bruce, I installed the new horae (035) and played around with the ZnO tutorial using the new version of Artemis. I called the program in the directory where the ZnO dat file reside from the command line. The project apj1 (run with all the indications in the journal) worked smoothly. As soon as I try to read in the apj2, the following trap message pops up: # Artemis 0.7.005 # This file created at 00:19:09 on 31 May, 2004 # using darwin, perl 5.008001, Tk 804.027, and Ifeffit 1.2.5 # Workspace: /Users/stefano/.horae/stash/artemis.project.3/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.005warn/Users/stefano/.horae/stash/ARTEMIS.TRAPCODE(0x1e3dff8)/Users/stefano/.horae/stash/artemis.project.3/ at /Applications/Ifeffit/bin/artemis line 1562 main::__ANON__('Tk::Error: could not open /Users/stefano/.horae/stash/artemis...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 488 Tk::Error('MainWindow=HASH(0x8f44c)','could not open /Users/stefano/.horae/stash/artemis.project.3/...','main::nnnn_header at /Applications/Ifeffit/bin/artemis line 4386','main::read_path at /Applications/Ifeffit/bin/artemis line 10872','main::open_project at /Applications/Ifeffit/bin/artemis line ...','main::read_data at /Applications/Ifeffit/bin/artemis line 6901','main::dispatch_read_data at /Applications/Ifeffit/bin/artemis...','main::__ANON__ at /Applications/Ifeffit/bin/artemis line 586','Tk callback for ..frame.menubutton.menu.project_data',...) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1707 End of trap file. Exactly the SAME error message pops out when I try to save a fit as chi(k). Obviously I am stuck... Any help here? Again, there must be some problem with the perl libraries... HELP!!! 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 -- ____________________________________________ 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

3 7

source tarball for horae-035
by Bruce Ravel 01 Jun '04

01 Jun '04

Hi folks, I just released the source code tarball for the latest version of my software. Those of you who use the source can run the horae_update script now. Or, you can grab the new version of the horae_update script from here and try it: http://leonardo.phys.washington.edu/~ravel/software/exafs/utilities/horae_u… The new version allows connection to a local proxy and grabs the tarball from SourceForge. Type "horae_update -h" for help on using the new features. This new version of horae_update is included in the tarball. This release is purely a bug fix release, mostly for Artemis. It addresses all the outstanding issues brought to my attention over the last week, including the problems related to the Mac OSX package. A windows executable will be made next week. Thanks to all the folks who provided bug reports for this release, including Shelly Kelly, Stefano Ciurli, Gleb Pokrovsky, and Peter Southon. 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/

4 7

Athena normalization and deglitching bugs
by Scott Calvin 01 Jun '04

01 Jun '04

Hi Bruce, I figured I'd post this to the Ifeffit list so that others could be alerted to similar problems, but I'll send you an Athena project file exhibiting this problem separately, so that everyone's in-boxes don't get cluttered with attachments. I'm using Athena 0.8.028 on Windows XP. First of all, on any file, including the copper data that comes with Athena, there is a bug. To see it, go to the deglitch screen, and change Emax by picking a point off the plot. Then replot. From now on, the green "tolerance" lines extend from Emax up to the end of the plot, rather than from Emin to Emax. This seems to affect only the screen display (i.e. it still deglitches the intended range), but it does make it harder to see what will get deglitched. The second behavior is best revealed with the project I am sending you separately. I am not positive it is a bug, but it doesn't match what I would expect. In the project I am giving you, the data is very glitchy (lots of Bragg peaks). Go down to the group labeled SBT/B Bi LIII Merge and plot in E-space with the post-edge line. Does it look right to you? It looks like the normalization line is considerably higher than it should be given the normalization range chosen, with only a few glitches above it. Is that something I don't understand about the way the post-edge line is chosen, or is it displaying the line wrong, or is it calculating it wrong? Thanks--the new features in Artemis are great, by the way. --Scott Calvin Sarah Lawrence College

2 1

Updating problems.
by Dave Baker 28 May '04

28 May '04

Hello all. This message is directed mainly toward Bruce, but if anyone else has any suggestions, please feel free to contribute. For a while now, I have been using Athena and Artemis on my work computer with a broadband internet connection, and all the updates have auto-detected and installed without a hitch. The problem is that now, I want to use the programs on my home computer, for which I am simply too cheap to buy anything better than dialup service. The updater, unfortunately, has choked several times when trying to download and install the 9 updates it says I need. (In fact, one time the echo screen stated that all the updates were installed, but when I restarted and opened Athena and Artemis, I was confronted with the old versions of the programs.) I haven't seen any "new and fully updated windows installers" on either Matt's or Bruce's pages, and it isn't clear to me how to get at the update files without the assistance of the updater itself. (I seem to recall reading that one can simply unzip the ifup_00x.zip file in the Ifeffit directory, run make_bats.exe, and all will be well.) Is there a way I can use the broadband connection at school to grab the updates and install them myself on the home computer without the use of the updater? Or, is there a place that the updater stores the .zip files after it's done updating the program, so I can just grab them off the work computer? Thanks for your help! -Dave ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ --

2 1

an update on the Mac OSX problem
by Bruce Ravel 28 May '04

28 May '04

Hi, I just wanted to let the mac users know that I have finally flushed out the problem that Stefano and Matt reported. There is most certainly a crippling problem with 0.7.004 on the Mac. In fact, the problm does not have to do with the Mac per se, but with the version of perl/Tk used to build the codes in the Mac installer. As some of you may be aware, the perl/Tk world is in the middle of a transition between two major versions of the toolkit. One of the challanges for me has been to write code that works seamlessly despite certain internal differences. It turns out that I finally traced the problem to a rather obscure difference between the older and new perl/Tk code bases. Fortunately there is an easy solution (although it will take me a while to find all the places where I need to apply it) and I think that I'll be able to post a new source code tar ball by the end of the day. Also fortunately, Windows users will not see this problem using the current builds of the windows executables. Note that the Mac installer currently has 0.7.003, so those who have installed the installer but not updated to 0.7.004 are unaffected. Finally, linux and other unix users who are using a perl/Tk 800 release will be unaffected. The bug is specific to perl/Tk 804. The amusing thing is that Stefano originally reported this as a problem loading an atoms.inp file. That turned out to be quite a red herring. The problem has nothing to do with the part of the code that handles atoms or feff files! Regards, 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/

2 1

Using more than one E0
by Wojciech Gawelda 28 May '04

28 May '04

Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. Im trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0s for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0s for each path? Thats one thing The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess Im still somewhat confusedhow one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering pathseven if the background parameters dont correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, Ill greatly appreciate any comments and feedback from all you guys. I hope Ill be able to share some of my own soon :-) Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

4 7

Question about the R_factor in artemis/ifeffit
by Wayne Lukens 28 May '04

28 May '04

Dear Matt and/or Bruce, First, thank you for the great software! I am a former EXAFSPAK user and have been really impressed by Artemis/ifeffit. It's easier to use, more flexible, and gives more reasonable errors for the fit parameters. My question is about the value of the R_factor for R-space fitting. This seems to be the R_factor for the real component of the Fourier transform only although the fitting is performed on both the real and imaginary components. Is there a reason that the contribution of the imaginary component to the R_factor is not included? Sincerely, Wayne --- Wayne Lukens Scientist Lawrence Berkeley National Laboratory email: wwlukens(a)lbl.gov phone: (510) 486-4305 FAX: (510) 486-5596

4 14

RE: Using more than one E0 correction
by Wojciech Gawelda 27 May '04

27 May '04

Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. Im trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0s for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0s for each path? Thats one thing The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess Im still somewhat confusedhow one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering pathseven if the background parameters dont correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, Ill greatly appreciate any comments and feedback from all you guys. I hope Ill be able to share some of my own soon J Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: wojciech.gawelda(a)epfl.ch WWW: http://lsu.epfl.ch ********************************************************************* -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: jeudi, 27. mai 2004 18:46 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 15, Issue 23 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: Autobk parameters (Kelly, Shelly D.) 2. Re: Autobk parameters (Bruce Ravel) 3. Re: Autobk parameters (Stefano Ciurli) 4. Re: Autobk parameters (Stefano Ciurli) 5. A saving problem in newest Artemis version (Aria) ---------------------------------------------------------------------- Message: 1 Date: Wed, 26 May 2004 12:18:01 -0500 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: RE: [Ifeffit] Autobk parameters To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <1C1577844A0BDF448E14E8CCB2F7442401006AF1(a)ANLMAIL.anl.gov> Content-Type: text/plain; charset="us-ascii" Hi Stefano, > 1) I understand that energy calibration should be performed, and I > did so by using the atomic edge energy. I also understand that this > parameter could be fluctuating in the subsequent fitting. Any comment > on this procedure? I agree that all the energy shift stuff can be confusing. The important end result for Extended X-ray Absorption Fine Structure Analysis is to get the energy-grid of the data to match the energy-grid of the theory with the zero energy of the photo-electron somewhere on the absorption edge. In the process of doing this you may have more than one data set from the same sample with different energy-grids... Furthermore you may have more than one sample which may have different energy-grid from the other samples and the theory. Then to make things all the more complicated X-rays can change the oxidation state of metals in organic materials. So that the energy grid is supposed to be different and the data is useless. After all that, here are some answers. 1) Always measure a foil reference at the same time that you measure any EXAFS data. It is easy to do. Here is a reference for how to do it when your sample is too thick and you can not simply put the foil behind the It ion chamber. J L Cross and A I Frenkel. "Use of scattered radiation for absolute energy calibration." Rev. Sci. Instrum. 70: pp 38-40, 1998 2) Align each data scan: 2a) Without an energy reference. Align the data to one of the data sets (remember which one you used) so that the edges are all right on top of each other. Each sample has it's own energy-grid. 2b) By using the energy reference of the foil measured simultaneously with each scan. Align all the reference spectra to one of the reference spectra. Then shift each of the data sets that belong to the reference spectra by the same amount. Now each scan is independently aligned and you have an absolute energy reference for each scan. This is useful for XANES comparisons or if you suspect changes in the data while the measurement was taking place. The difference in energy from the reference to the data or from one data set to another is a real change and can be used to "say" stuff about the sample. 3) Check the alignment: Plot all the normalized xmu(E) data from the same sample in Athena, zoom in on the edge region -20 to 20 eV and take a good look. Hopefully they all line up. If there is a systematic change in the edge features? If so how much...less than 10 % (which is about the accuracy of the measurement). This means that you can most likely still use the data but that you have changes happening to your sample while the measurement was taking place and you should fix that next time. 4) Now the problem of alignment is somewhat smaller. All the data sets have the same energy grid if you used 2b...or all the data sets have there own energy grid if you used 2a. Now we need to align the data and the theory. To do this there are two steps. Choosing a zero energy of the photo-electron to define the k-grid in converting the data to chi(k), and then aligning the chi(k) data with the theory chi(k). 5) Choosing a Ezero in Athena: Pick any point that you like on the edge for Ezero in Athena. Plot the xmu data with the background and pre-edge and post-edge range. A circle on the plot shows the position of Ezero. Then right click The Ezero to set this energy to be the same value for all the data sets from this sample. Then plot the chi(k) data and see that the curves all look the same at low k-values. If not adjust Ezero a bit for the data sets that are different to get the chi(k) data to look the same. Then average the chi(k) data and write it out so that you can align it with the theory in Artemis. 6) Aligning data to theory: Read the data into Artemis. Read in what you think should work for a first shell feffxxxxx.dat file. Fit the data to the first shell. Plot the data and the theory in chi(k), take a look at the deltaE value from the fit. This value for deltaE is telling you how much the theory had to move to match-up with your choice of Ezero that you picked in step 5. If you think that the theory is correct and deltaE is larger than a few eV then you need to adjust your chi(k) data. But first write out what the theory should look like if you choose Ezero just right. 6b) Making a standard: In Artemis, set all the parameters to their best-fit values, except for deltaE. Set deltaE to zero and run the fit again. This is not really a fit. There are no parameters to optimize. Now the theory is showing you what the data should look like if you choose the perfect value for Ezero and the perfect background function in step 5. 7) Redo the background and energy choice: In Athena open up the chi(k).fit that was produced by step 6b. This is the "standard" that you can use to help get Ezero and the background correct. Then select individual scans taken from the sample and then open the standard menu and choose the theory chi(k) data. Right click on the standard to use the same standard for all data sets. Redo the background removal. Plot the chi(k) data and the standard. If they are different at low k you need to adjust Ezero so that they start at the same place. When you are done adjusting your choice for Ezero, plot the xmu(E) data and make sure that the circle that is your value for Ezero is on the edge. If it isn't, then the theory that you used to align the data doesn't work..and you need to start over in step 6. If the value is on the edge some where, right click on the Ezero choice and set its value for Ezero of all the scans. Then merge all the data in chi(k) and write it out for use in Artemis...as you did the first time making sure that all the scans have a similar bkg. 8) Redo the fit: Now the data and the theory are aligned and you can redo the fit varying all the parameters...deltaE in Artemis should be small..and the background should give a nice match at low-r values. Often this entire procedure is used at the end of your analysis to make a nice figure for publication. 9) Bonus of using an energy reference: If you used an energy reference measured simultaneously with the data sets then in the end you can simultaneously fit the different samples with only one deltaE in the fit for all of the samples. If you aligned each one independently then each data set should have it's own deltaE value..unless you have more information and can prove that they should be the same. HTH Shelly ------------------------------ Message: 2 Date: Wed, 26 May 2004 16:56:37 -0400 From: Bruce Ravel <ravel(a)phys.washington.edu> Subject: Re: [Ifeffit] Autobk parameters To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200405261656.37396.ravel(a)phys.washington.edu> Content-Type: text/plain; charset="iso-8859-1" Okee dokee, a few more thoughts after Matt's and Shelly's posts... SC> 2) The next parameter is Rbkg. I have read the literature about this SC> parameter, especially the 1993 paper by Matt. I sort of understood SC> the rationale and method, but I also gathered that the default SC> parameter of 1.0 can be changed. What are the criteria for changing SC> this? I tend to keep it to the default value, but I feel a bit uneasy SC> about not being able to control this parameter intelligently. Unfortunately there is not a really good rule of thumb. One might say "half the distance to the first peak", but that's not really a very good rule. The issue is that choice of Rbkg can have a profound impact on the low frequency Fourier components. (Try setting Rbkg to an absurdly large value, say 2 or 3, and see what damage that does to your data!) I would say the real answer is that the choice of Rbkg shouldn't be too strongly correlated with the things you are trying to measure -- N, delta_R, sigma^2. Once you have set up your fitting model in Artemis, a little experiment to try is to save chi(k) using several different values of Rbkg and see how the answers change when you do the fits. To completely make up an example, suppose that you save chi(k) for Rbkg=0.75 and 0.95, then do the fits. If the best fit values of N, delta_R and so on are the same within their error bars, then it doesn't matter which Rbkg you use in Athena. In that case you would probably use the larger one because it probably makes the "prettier" picture in terms of removing very low frequency Fourier components. SC> 3) I understood from the paper by Matt (and from the "Using Athena" SC> manual by Bruce) that one could use a "standard" to estimate the SC> level of leakage into the small chi(R) region (apodization effects SC> due to Fourier window filtering). The manual states that one can read SC> in a chi.dat file produced with feff. However, I do not understand SC> how to build the feff.inp for feff and produce a useful chi.dat to SC> use as a "standard". Please help? In your follow-up to my original answer to this question, you made it clear that the role of the standard is still not clear to you. As Matt said, the standard need not be perfect. Let me explain why. The autobk algorith works by "optimizing" the low frequency Fourier components in order to select the correct spline function. In the absence of a standard, "optimize" means "minimize". That is, without a standard, autobk finds the spline that makes the chi(R) spectrum as small as possible between 0 and Rbkg. Again as Matt said, low Z ligands often benefit by using a standard. The reason is that low Z ligands tend to have quite short distances resulting in a peak in chi(R) that has a significant tail into the region below Rbkg. In that case, *minimizing* the components between 0 and Rbkg is a poor idea because they are *supposed* to be non-zero. A standard then is used to tell the autobk algorithm what the components between 0 and Rbkg are supposed to look like and the spline is chosen to make the data look that way between 0 and Rbkg. In that context, the standard need not be perfect -- close should be good enough. Oh yeah. The feff run should produce a file called "chi.dat". That's a good one to use as a standard. Matt's ifeffit recipe for converting a feffNNNN.dat file into a chi(k) works, too. SC> 4) Then there is the k-weight parameter to be changed for the SC> background removal. The default value for this is 1, but higher SC> values are allowed. I noticed that increasing the k-weight for SC> background removal produces a curve in the chi(E) which more and more SC> appear to disregard the edge peak, resembling more and more a SC> smoothly monotonically increasing curve. Consequently, the chi(k) SC> changes depending on this parameter, and I again start to be worried SC> about the following fit of it. What are the criteria to choose this SC> k-weight for the background? With noisy spectra, the high energy portion of the data might be dominated by fluctuations that have nothing to do with the exafs. In that case a large k-weight for the background removal might be unduly influenced by stuff that is not the data you want to analyze but instead are detector problems, sample inhomogeneity problems, gremlins, crap, whatever ;-) SC> 6) Spline range: this is another important issue, I think. In the SC> paper by Matt it is stated that "standard practice ... has been to SC> ignore everything below an energy typically 30 eV above the E0" and SC> that Autobk is an advantage because it can read in data very close to SC> the E0. My question is: the default value for k in the spline range SC> is set to 0.5 eV (0.952 eV). What are the criteria to change this SC> default value? Also, is there any relationship between this range and Matt said: MN> I typically use kmin=0, kmax=last_data_point, dk=0 for the spline MN> (which are the defaults). Bruce seems to prefer kmin=0.5 or so: MN> it shouldn't make a difference. The reason I chose to make 0.5 the default is so that Athena will stand a better chance of dealing well with data that have a large white line. For data like that spline_kmin=0.0 often leads to a poor background removal because the spline just doesn't have the freedom to deal with such a quickly changing part of the spectrum. For many materials 0.0 is probably a better choice, but in Athena I want the default behavior to always be non-stupid. ("Smart" is a bit too difficult for me ;-) SC> the range subsequently used for FT? My guess is that the k-min for FT SC> should be always higher that the k-min for the spline range, but SC> please comment on this. Also, what are the criteria to set the Well, the FT range must be equal to or smaller than the spline range, but you probably already figured that out! Other than that there is not relationship. It is certainly useful in practice for them not to be the same. Getting back to the problem of deling with a white line, I often find it useful to make spline_kmin 1 or even larger to avoid the white line altogether. That means that the FT range will also be smaller resulting in less data for fitting, but it seems worth it. Since it is so hard to distinguish data from background under the white line, it is often better to just avoid the problem altogether. SC> 7) for the FT parameters: Shelly's protocol to define the k-range to SC> best calculate the chi(R) was clear and useful to me. However, I SC> would like to know more about choosing the dk parameter and the SC> window-type. I need some general criteria to choose between the SC> various possibilities. I noticed that the kaiser-bessel window is SC> the default, but in the literature I almost invariably find the SC> Hanning window. Please comment. Matt summed this up. (I liked the historical context!) Here is a talk that Shelly gave last year at the NSLS exafs course: http://cars9.uchicago.edu/xafs/NSLS_EDCA/July2003/Kelly.pdf Check out page 21. It demonstrates really clearly how little the choice of window shape matters. As for dk, I don't have a good rule of thumb. I generally choose a smallish number. I wanted also to say a few words about your question regarding peak fitting. In a numerical sense, peak fitting is harder than fitting exafs spectra. An exafs spectra is basically one or more damped sine waves. If you try to fit that with any ol' damped sine wave that's not too far out of phase, you won't go too far wrong. The same is not true of fitting peak shapes to xanes data. That kind of non-linear fit is notoriously unstable. In my experience, it can be very difficult to fit the centroid of a peak shape to a feature in a xanes spectrum. That is why Athena has the centroid not flagged as a variable by default. I am not completely clear on what's going on with your data, but it seems as though you want to fit a very tiny feature at the very beginning of the data. The problem there is that, if the pre-edge is not completely flat, the lineshape used for the edge step might through the peak or well below the peak. If so, the peak shape you are trying to use to fit that feature might be poorly defined numerically. I would recommend trying to adjust the parameters by hand until you geta fairly decent representation of the data, then let some of the parameters float in a fit to start understanding where the parameters will want to float off to. If you try to fit the whole xanes spectrum in one quick swoop, though, you are indeed likely to get a poor fit. SC> I feel like a naive cook who is afraid of making mistakes, and SC> therefore reads a receipe very carefully, not to mix the wrong SC> ingredients in the wrong amounts. So, again, please bear with me. Well, I have enjoyed cooking my entire life and I like to think I am not so bad at it. In my experience, the one way to truly learn how to make a really good dish is to make some bad ones and think about what went wrong. You'll know when you're getting there because the dish will start to taste good. The same applies to using the codes. Poke at the buttons and don't fret if weird stuff happens. Think about what it means and why the weird results are inconsistent with what you know about your sample. Eventually the results from the analysis will start to make sense in the context of what you know about your samples. Mmmmmm.... that's good analysis! 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/ ------------------------------ Message: 3 Date: Thu, 27 May 2004 15:21:49 +0200 From: Stefano Ciurli <stefano.ciurli(a)unibo.it> Subject: Re: [Ifeffit] Autobk parameters To: ravel(a)phys.washington.edu, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <a06100508bcdb9b73cde8(a)[137.204.93.158]> Content-Type: text/plain; charset="us-ascii" ; format="flowed" Bruce, >SC> 4) Then there is the k-weight parameter to be changed for the >SC> background removal....What are the criteria to choose this >SC> k-weight for the background? > >With noisy spectra, the high energy portion of the data might be >dominated by fluctuations that have nothing to do with the exafs. In >that case a large k-weight for the background removal might be unduly >influenced by stuff that is not the data you want to analyze but >instead are detector problems, sample inhomogeneity problems, >gremlins, crap, whatever ;-) so I conclude that I should use a LOW k-weight in my case, right? 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 ------------------------------ Message: 4 Date: Thu, 27 May 2004 15:18:21 +0200 From: Stefano Ciurli <stefano.ciurli(a)unibo.it> Subject: Re: [Ifeffit] Autobk parameters To: ravel(a)phys.washington.edu, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <a06100507bcdb99ed729e(a)[137.204.93.158]> Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi Bruce, >Oh yeah. The feff run should produce a file called "chi.dat". That's >a good one to use as a standard. Matt's ifeffit recipe for converting >a feffNNNN.dat file into a chi(k) works, too. when I run feff, I do not get any chi.dat file. Why? I tried to use artemis to do that, but right now the new version I installed crashes when I try to read in a feff calculation (which btw I performed on something that should be similar to my metal site and was about to use it for standard...) The trap message states: # Artemis 0.7.004 # This file created at 12:59:30 on 27 May, 2004 # using darwin, perl 5.008001, Tk 804.027, and Ifeffit 1.2.5 # Workspace: /Users/stefano/.horae/stash/artemis.project.0/ The following message was trapped by Artemis on a SIGDIE: Artemis0.7.004die/Users/stefano/.horae/stash/ARTEMIS.TRAPCODE(0x1e38760) /Users/stefano/.horae/stash/artemis.project.0/ at /Applications/Ifeffit/bin/artemis line 1550 main::__ANON__('Callback called exit.\x{a}') called at /Applications/Ifeffit/bin/artemis line 0 Stefano PS: I am using the OSX 10.3 version -- ____________________________________________ 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 ------------------------------ Message: 5 Date: Thu, 27 May 2004 12:46:39 -0400 From: "Aria" <fyang(a)ECE.NEU.EDU> Subject: [Ifeffit] A saving problem in newest Artemis version To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <000001c4440a$2e89efd0$443d0a81@harrispc> Content-Type: text/plain; charset="us-ascii" Hi folks, First, thank Bruce and Matt so much for their non-stopping work in updating those beautiful pieces of software. Somehow, another problem occurred to me after the auto-updating days ago. I am not sure if this only happened to me. Artemis so far has no problems in dealing with those project files which were created by the old versions. But when I tried to create a new project importing more than one FEFF calculations, after I saved and tried to reload it, Artemis simply failed to do so. The only FEFF path showed in the 'Data & Paths' panel is the first path in the first FEFF calculation. This is the message I copied from echo: Opening project zipfile C:/.../artemis60mT_C_100 ... Opening project zipfile artemis60mT_C_100 ... done! Doing intrp for CuOct ... Doing intrp for CuOct ... done! Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAP The artemis.trap files is shown as below: # Artemis 0.7.004 # This file created at 12:28:24 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Tk::Error: could not open C:\Program Files\Ifeffit\horae\stash\a...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al) line 402 Tk::Error('MainWindow=HASH(0x387c174)', 'could not open C:\Program Files\Ifeffit\horae\stash\artemis.proj...', '[\&main::dispatch_read_data]', '(menu invoke)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 When I click on the only path, another warning is trapped: # Artemis 0.7.004 # This file created at 12:39:51 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Use of uninitialized value in split at artemis line 5800, <PROJ>...') called at artemis line 5800 main::populate_path('data0.feff0.0') called at artemis line 2475 main::display_properties('Tk::Ev=SCALAR(0x3327260)', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/Widget.pm line 988 eval {...} called at /PerlApp/Tk/Widget.pm line 988 Tk::Widget::Callback('Tk::Tree=HASH(0x32d2c3c)', '-browsecmd', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/HList.pm line 181 Tk::HList::Button1('Tk::Tree=HASH(0x32d2c3c)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 I am not sure the information is enough. Hope it helps. Best regards, Aria

2 1

A saving problem in newest Artemis version
by Aria 27 May '04

27 May '04

Hi folks, First, thank Bruce and Matt so much for their non-stopping work in updating those beautiful pieces of software. Somehow, another problem occurred to me after the auto-updating days ago. I am not sure if this only happened to me. Artemis so far has no problems in dealing with those project files which were created by the old versions. But when I tried to create a new project importing more than one FEFF calculations, after I saved and tried to reload it, Artemis simply failed to do so. The only FEFF path showed in the 'Data & Paths' panel is the first path in the first FEFF calculation. This is the message I copied from echo: Opening project zipfile C:/.../artemis60mT_C_100 ... Opening project zipfile artemis60mT_C_100 ... done! Doing intrp for CuOct ... Doing intrp for CuOct ... done! Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAP The artemis.trap files is shown as below: # Artemis 0.7.004 # This file created at 12:28:24 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Tk::Error: could not open C:\Program Files\Ifeffit\horae\stash\a...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al) line 402 Tk::Error('MainWindow=HASH(0x387c174)', 'could not open C:\Program Files\Ifeffit\horae\stash\artemis.proj...', '[\&main::dispatch_read_data]', '(menu invoke)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 When I click on the only path, another warning is trapped: # Artemis 0.7.004 # This file created at 12:39:51 on 27 May, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.004warnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3372680)C:\Program Files\Ifeffit\horae\stash\artemis.project.1\/ at artemis line 1551 main::__ANON__('Use of uninitialized value in split at artemis line 5800, <PROJ>...') called at artemis line 5800 main::populate_path('data0.feff0.0') called at artemis line 2475 main::display_properties('Tk::Ev=SCALAR(0x3327260)', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/Widget.pm line 988 eval {...} called at /PerlApp/Tk/Widget.pm line 988 Tk::Widget::Callback('Tk::Tree=HASH(0x32d2c3c)', '-browsecmd', 'data0.feff0.0', 0, 'imagetext', 'body') called at /PerlApp/Tk/HList.pm line 181 Tk::HList::Button1('Tk::Tree=HASH(0x32d2c3c)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1695 I am not sure the information is enough. Hope it helps. Best regards, Aria

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RE: [Ifeffit] Autobk parameters
by Kelly, Shelly D. 26 May '04

26 May '04

Hi Stefano, > 1) I understand that energy calibration should be performed, and I > did so by using the atomic edge energy. I also understand that this > parameter could be fluctuating in the subsequent fitting. Any comment > on this procedure? I agree that all the energy shift stuff can be confusing. The important end result for Extended X-ray Absorption Fine Structure Analysis is to get the energy-grid of the data to match the energy-grid of the theory with the zero energy of the photo-electron somewhere on the absorption edge. In the process of doing this you may have more than one data set from the same sample with different energy-grids... Furthermore you may have more than one sample which may have different energy-grid from the other samples and the theory. Then to make things all the more complicated X-rays can change the oxidation state of metals in organic materials. So that the energy grid is supposed to be different and the data is useless. After all that, here are some answers. 1) Always measure a foil reference at the same time that you measure any EXAFS data. It is easy to do. Here is a reference for how to do it when your sample is too thick and you can not simply put the foil behind the It ion chamber. J L Cross and A I Frenkel. "Use of scattered radiation for absolute energy calibration." Rev. Sci. Instrum. 70: pp 38-40, 1998 2) Align each data scan: 2a) Without an energy reference. Align the data to one of the data sets (remember which one you used) so that the edges are all right on top of each other. Each sample has it's own energy-grid. 2b) By using the energy reference of the foil measured simultaneously with each scan. Align all the reference spectra to one of the reference spectra. Then shift each of the data sets that belong to the reference spectra by the same amount. Now each scan is independently aligned and you have an absolute energy reference for each scan. This is useful for XANES comparisons or if you suspect changes in the data while the measurement was taking place. The difference in energy from the reference to the data or from one data set to another is a real change and can be used to "say" stuff about the sample. 3) Check the alignment: Plot all the normalized xmu(E) data from the same sample in Athena, zoom in on the edge region -20 to 20 eV and take a good look. Hopefully they all line up. If there is a systematic change in the edge features? If so how much...less than 10 % (which is about the accuracy of the measurement). This means that you can most likely still use the data but that you have changes happening to your sample while the measurement was taking place and you should fix that next time. 4) Now the problem of alignment is somewhat smaller. All the data sets have the same energy grid if you used 2b...or all the data sets have there own energy grid if you used 2a. Now we need to align the data and the theory. To do this there are two steps. Choosing a zero energy of the photo-electron to define the k-grid in converting the data to chi(k), and then aligning the chi(k) data with the theory chi(k). 5) Choosing a Ezero in Athena: Pick any point that you like on the edge for Ezero in Athena. Plot the xmu data with the background and pre-edge and post-edge range. A circle on the plot shows the position of Ezero. Then right click The Ezero to set this energy to be the same value for all the data sets from this sample. Then plot the chi(k) data and see that the curves all look the same at low k-values. If not adjust Ezero a bit for the data sets that are different to get the chi(k) data to look the same. Then average the chi(k) data and write it out so that you can align it with the theory in Artemis. 6) Aligning data to theory: Read the data into Artemis. Read in what you think should work for a first shell feffxxxxx.dat file. Fit the data to the first shell. Plot the data and the theory in chi(k), take a look at the deltaE value from the fit. This value for deltaE is telling you how much the theory had to move to match-up with your choice of Ezero that you picked in step 5. If you think that the theory is correct and deltaE is larger than a few eV then you need to adjust your chi(k) data. But first write out what the theory should look like if you choose Ezero just right. 6b) Making a standard: In Artemis, set all the parameters to their best-fit values, except for deltaE. Set deltaE to zero and run the fit again. This is not really a fit. There are no parameters to optimize. Now the theory is showing you what the data should look like if you choose the perfect value for Ezero and the perfect background function in step 5. 7) Redo the background and energy choice: In Athena open up the chi(k).fit that was produced by step 6b. This is the "standard" that you can use to help get Ezero and the background correct. Then select individual scans taken from the sample and then open the standard menu and choose the theory chi(k) data. Right click on the standard to use the same standard for all data sets. Redo the background removal. Plot the chi(k) data and the standard. If they are different at low k you need to adjust Ezero so that they start at the same place. When you are done adjusting your choice for Ezero, plot the xmu(E) data and make sure that the circle that is your value for Ezero is on the edge. If it isn't, then the theory that you used to align the data doesn't work..and you need to start over in step 6. If the value is on the edge some where, right click on the Ezero choice and set its value for Ezero of all the scans. Then merge all the data in chi(k) and write it out for use in Artemis...as you did the first time making sure that all the scans have a similar bkg. 8) Redo the fit: Now the data and the theory are aligned and you can redo the fit varying all the parameters...deltaE in Artemis should be small..and the background should give a nice match at low-r values. Often this entire procedure is used at the end of your analysis to make a nice figure for publication. 9) Bonus of using an energy reference: If you used an energy reference measured simultaneously with the data sets then in the end you can simultaneously fit the different samples with only one deltaE in the fit for all of the samples. If you aligned each one independently then each data set should have it's own deltaE value..unless you have more information and can prove that they should be the same. HTH Shelly

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Autobk parameters
by Stefano Ciurli 26 May '04

26 May '04

Hi folks, guess what, another question... I would like to estimate the area of a small pre-edge peak in a Nickel spectrum. It is known that the area of this peak, compared to the XANES, is correlated to the degree of symmetry for the Ni(II) ion. I tried to use the peak fitting procedure implemented in Athena, but unsuccessfully. If I limit the fitting region to close to the pre-edge peak, and use either gaussian or lorentzian lineshape, the fitting is bad, really bad (shift of the fitted maximum, wrong linewidth). Maybe the peak is just too small. If I try to fit the entire XANES in addition to this small peak, I get very good fit for the XANES features, but negative intensities for the pre-edge peak. Any clues? 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

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[help] ifeffit -i = segmentation fault
by mauro＠rulp.org 26 May '04

26 May '04

Hi to all, I'm having big troubles with iFEFFIT. I have updated the systems (Linux GNU Debian/ Testing) and I realized that version 800.025 of perl-tk was automatically installed. After that, obviously, everything crashed with Artemis and friends. So I have downgraded perl-tk to 800.024 using a non standard debian package (because the standard one requires perl-base 5.6.1 and I'm working with perl-base 5.8.3) from here: http://snapshot.debian.net/cgi-bin/packages.cgi (I have used perl-tk_800.024-1.2_i386.deb) After that I decided to recompile everything... bad idea! ifeffit-1.2.5 recompiled fine (no errors appeared in the configure/make/make install process). *BUT* when I try to recompile horae-034 it crash on determining ifeffit version. In fact, if I run "ifeffit -i" it gives me: Segmentation fault (Killed, on another machine) I hope someone could help me because at the moment I can do nothing! :( Thanks, Mauro -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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athena 0.8.028, artemis 0.7.004, and hephaestus 0.02
by Bruce Ravel 25 May '04

25 May '04

Hi folks, I have just posted a new source code package for my codes on my web page and on SourceForge. You can now run the horae_update script. I have also assembled the contents of the Windows updater, which should be available in the next few days. When it is ready, the windows updater will notice and update you automatically. Along with many bug fixes and feature enhancements in Athena and Hephaestus, there are a large number of improvements in Artemis. As you all no doubt remember, there were quite a large number of serious bugs reported after the last release of Artemis. With the generous and patient help of several users I was able to understand and correct about two dozen problems leading to all sorts of misbehavior ranging from simple trap file generation to program crashes. I am guardedly optimistic that you will find the new release to be a significant improvement over the last in terms of stability and usability. Among the big new features of Artemis are: 1. An revamped Guess, Def, Set page with lots of new features. I'll be sending out an email later this afternoon explaining the new GDS page. 2. The ability to clone feff calculations. This will be very helpful for those of you doing multiple data set fits. This, too, will get its own email later today. 3. New ways of viewing the log file. 4. Expanded information about each path displayed on the paths page. and lots of minor enhancements. See the change log on my web site for the complete list. One caveat -- I once again made some changes to the format of the artemis project file. I will not be able to guarantee stability of the project file format for a long time to come. I'll make sure Artemis can read in project files from previous versions, but it is likely that any new version will write a project file that cannot be completely imported by older versions. That's just one more reason to stay up-to-date! Several people get an acknowledgement for their contributions to this release: David Barton, Gerrit Schmithals, Aria Yang, Scott Calvin, Peter Southon, and Dogan Paktunc all deserve a tip of the cap for excellent suggestions and useful bug reports. Shelly Kelly was amazingly generous with her time in the last few weeks helping me to debug the current version. She also helped me design the new GDS page and pushed me to add several of the other new features in the code. All of you should buy Shelly a beer the next time you see her -- I certainly will! As always, let me know what suggestions you have or problems you run into. Bruce -- 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/

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that didn't take long...
by Bruce Ravel 24 May '04

24 May '04

Hi, Once again a serious bug has cropped up in artemis within 24 hours of a new release. Sigh... I'm pretty good at the first 95% of making a new release, but I seem to suck at the last 5%! ;-( The problem this time is in trying to do the background corefinement. If you click on the "Fit background" button, the fit will run to completion but the log file will not be written. Fortunately, the fix is extremely simple. I will post a new source code tarball by the end of the day. I will also try to get a new executable built so that the windows updater can be updated. Until then, you should consider background corefinement to be broken. Thanks go to Gleb Pokrovski for pointing this out (as well as racing out to try the new version!). 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/

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New horae library setup
by Paul Fons 24 May '04

24 May '04

I was going to roll my own version of the latest incarnation of horae, but I noticed the library structure and install location has changed (at least on os x). Can you elaborate on this (Matt or Bruce)? Better yet, is there a tar image of the source available for the mac os x version. Earlier I upgraded perl to 5.8.3 and then the older Tk broke so I was off on my own, so I was compiling everything myself, but now that the install is becoming more and more os x aware (thanks to Matt) it would seem to make sense to downgrade to Apple's older perl (which has prebinding enabled). Of course, now it only makes sense to get in sync with the official sources. Would it be possible to put up the sources on your web site Matt? Paul (an Italian (Elettra) for a ten days)

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graphics and fit
by Stefano Ciurli 22 May '04

22 May '04

Hello, just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite? 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

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a cautionary tale
by Peter Southon 21 May '04

21 May '04

Hello fellow Ifeffiters This a story about making feff.inp input files for FEFF. The more experienced readers of this list will probably be well aware of the issues involved, but I thought that relative newcomers such as myself might not know (which is why I'm posting this on the Ifefft list rather than the Feff list). In a nutshell, it is wise to create a large cluster of atoms to put into Feff (ie use a large Rmax in Atoms), but limit the number of paths with a reduced Rmax in Feff. I used Artemis/Atoms to make up a Feff input file (feff.inp) from crystallographic parameters, setting Rmax in Atoms to a relatively large value of 7.5 Å to create quite a large cluster of atoms. I then used FEFF to calculate scattering paths within the cluster, but first reduced the Rmax in feff.inp to 5.5 Å to limit the number of paths. So far so good. I then (for reasons too involved to discuss here) edited the feff.inp file to delete all atoms more than 5.5 Å from the centre, and ran Feff again. The results (judging from the relative amplitude values) were different, and in the case of some paths very different. Some intense paths changed in amplitude by a factor of 2 or greater, although I haven't looked at the finer details of the Feff results. The paths that changed the most were high-order multiple scattering paths, and surprisingly those paths did not involve atoms at the edges of the 5.5 Å radius. Now I'm sure that someone else can explain the reasons for this much better than I can, but I assume that the potentials for the atoms outside the 5.5 Å radius (which were neglected in the second calculations) significantly affect those inside the radius. I know that its always been my practice to perform the Feff calculation using only those atoms that I think are contributing to my spectrum, and I'm sure that others do the same. My advice is to use a larger cluster of atoms in Feff if you can - but as to how large I might leave that to someone else to comment. Regards, Peter PS - and four cheers to Bruce for improvements to Artemis, I can't wait for the Windows update. Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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horae 034 Debian packages
by Carlo U. Segre 20 May '04

20 May '04

Packages of the new horae are available for the unstable and stable distributions of Debian at # stable deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ # unstable deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Please contact me if you have any problems installing them. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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cloning feff calculations
by Bruce Ravel 20 May '04

20 May '04

Hi! Artemis now allows you to easily reuse entire feff calculations within a project. This is something you might want to do in a variety of situations. Here is one example: You have data at several temperatures. After spending some time working on your fitting model for a single data set and at one temperature, you decide to convert your project to a multiple data set, multiple temperature model. You would like to use the same feff calculation and all the same paths to fit each data set, changing only those parameters related to the changing temperature. This is now easy. In the Data menu is an option for "Clone a FEFF calculation". Here is how it works: 1. Select the data set for which you wish to use an already-defined feff calcultion. In my example, you would select the most recetly imported data set. 2. Choose the Clone option from the Data menu. This will pop up a dialog box listing all feff calculations used throughout the project. (If there is only one, it will be a short list!) 3. Choose a feff calculation and click OK. That calculation, all its paths, and all path parameters associated with the paths will be copied to the new data set. You may need to play around with it to see how it works. Once you see, it's quite simple: you select a data set and apply an existing feff calculation to the selected data set. There are two options for cloning a feff calculation. They are called "linking" and "copying". The difference between them is how the files from the feff calculation are handled. A linked clone points at the same set of files, a copied clone makes its own copies of all the files from the feff calculation. You should link when you want to be 100% sure that the exact same feffNNNN.dat files will be used each time the calculation is used. Also, the project file will be significantly smaller when you link compared to when you copy. You should copy if you think you might need to alter the feff calculation in one case separately from the other. Since this is a brand new feature, I suspect that people will find ways to break it. Let me know when that happens. Bruce -- 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/

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the new GDS page
by Bruce Ravel 20 May '04

20 May '04

Hi! The biggest new feature of Artemis in today's release is the new page for setting the Guess, Def, and Set parameters. Here is a screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… The document has been updated to describe the new format of the GDS page. http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf See section 5.7.9. As you can see, the parameters are now displayed in a list structure rather than as a stack of entry boxes. This allows many more parameters to be displayed at one time in the same space. The new layout also allocates more horizontal space to the display of the math expressions. The different kinds of parameters are displayed according to their type. The color of the text and the content of the second column indicate the parameter type. Guess parameters are in purple text and have the "g:" tag in the second column. Set parameters are in black text and have the "s:" tag. Defs are green and have "d:". Skip parameters are grey and have no tag. Not shown in the screenshot are restrains, which are pink and have the "r:" tag in the second column. To edit a parameter, click on its entry in the list. This highlights that parameter in grey, as shown for the "fee0" parameter in the screenshot. The name, type, and math expression for that parameter are entered in the space at the bottom of the page and are ready to be edited. Click the "New" button to create a brand new parameter. The neatest new feaure is what I call parameter annotation. An annotation is a short text string which says something useful about the parameter. An example of this is seen in the screen shot. The selected parameter was annotated after the fit with its best fit value and error bar. Whenever you click on a parameter, its annotation is shown in the echo area. If you double-click on a parameter, you will be prompted to supply an annotation for that parameter. This provides a nice way of documenting the role each parameter plays in the fit. There are lots of other neat features of the new GDS page. For instance, Artemis does not allow you to define a parameter more than once. And there is a very useful context menu that gets posted when you right-click on a parameter. It may take a bit of getting used to, but I suspect that you will enjoy the new GDS page. I find it to be both more powerful and easier to use than the previous format. Enjoy, B P.S. Thanks go to Scott, who I hope does not mind that I used his project file for the screenshot. -- 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/

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Starting out with Artemis 0.7.003
by m.bondin＠pgrad.unimelb.edu.au 18 May '04

18 May '04

Hi all - I am starting out with the latest release of Artemis on Win XP (thought I would give the new and improved version a go since I like the idea of incorporating atoms in the fitting interface). I read in my data file and atoms file, got my feff.inp then attempted to generate my feff paths - Artemis asked me to pick an option (first ten, all etc) and gave me a new window with no paths listed and the message "Artemis trapped a warning! Message dumped to C:\Program Files\Ifeffit\horae\ARTEMIS.TRAP" Is Atoms now able to claculate feff paths and display them within Artemis or does it not yet have this capability? Many thanks, -- Mark Bondin PhD student School of Chemistry, University of Melbourne

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[HOWTO] converting experimental mu(E) in cm^-1
by mauro＠rulp.org 14 May '04

14 May '04

Hi, I would like your opinion on the procedure to convert the experimental mu_exp(E) in arbitrary units (counts) to mu(E) in cm^-1. This is my "student" procedure: 1. take mu_exp(E) - with EXAFS - spectrum in counts 2. take mu_th(E) - without EXAFS - spectrum in cm^-1 (from MacMaster or XOP software) 3. plot 1+2 4. while mu_exp(E) != mu_th(E) do (by hand!) 4a. mu(E) = A * mu_exp(E) + B When the two spectra coincide (more or less) I assume that the mu(E) is converted in cm^-1 units. Is this right? Does it already exist a software that makes this work automatically? Could be interesting to implement it in Athena? Thanks, M. -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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RE: RE: [Ifeffit] graphics and fit
by Kelly, Shelly D. 13 May '04

13 May '04

Hi Mark and Jeff, Here is a copy of the program. I tried to document the script well. If you have trouble, let me know. You can e-mail me off of the list. skelly(a)anl.gov. Shelly > -----Original Message----- > From: Jensen, Mark P. > Sent: Thursday, May 13, 2004 1:33 PM > To: Kelly, Shelly D. > Subject: RE: [Ifeffit] graphics and fit > > > Shelly, > > I can see several metal-ligand complexes that I have looked > at recently where your program for manipulating groups of > atoms would probably have been very useful. If you really are > willing to share, I would sure appreciate having a chance to > try it out. > > Mark Jensen > > > ------------------------------ > Mark P. Jensen > Chemistry Division > Argonne National Laboratory > 9700 South Cass Avenue > Argonne, Illinois 60439-4831 > USA > 630-252-3670 > 630-252-7501 FAX > mjensen(a)anl.gov >

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RE: [Ifeffit] graphics and fit
by Kelly, Shelly D. 13 May '04

13 May '04

Hi Stefano, Another free program that can read the output from atoms is ghemical. http://www.uku.fi/~thassine/ghemical/ I have written a rather specialized code that allows you to rotate a group of atoms until one of those atoms is at a determined distance from the original atom. Here let me explain for the specific example that I used it for. Say you have a Uranium atom and attached to it through an oxygen atom you have a PO4 group. One of the oxygen atoms of the PO4 group is shared with the uranium atom. Now from your exafs data you know that the U-P distance should be some number call it Rp. This program will leave the shared oxygen atom at the same spot, but move the PO3 atoms until the distance for U-P matches Rp. There are lots of ways that you can move the PO3 atom. The program is written to try to bend the PO3 group first and then translate the PO3 group to make the distance match. Then the program writes out the coordinates for all the atoms. This code is written in perl and doesn't have a gui interface, but I would be happy to share. Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Thursday, May 13, 2004 5:31 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] graphics and fit > > > Hello, > > just a thought: wouldn't it be nice to be able to read the feff.inp > file directly into a simple molecular graphics program in order to > see if the used coordinates contain any error? Maybe it is possible > already and I am not aware of it. I understand that the program is > mainly used by material scientists, but for us working with > biological samples of metalloproteins it would be nice. > Another suggestion: I know that Excurve is able to treat the > histidine rings as a unity, and when performing the fit that program > is able to maintain the ring rigid while fitting the distance between > the metal and the imidazole ring of the histidine. How can I do that > simply using your suite? > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Re: [Ifeffit] newcomer's simple trouble
by Stefano Ciurli 13 May '04

13 May '04

Problem solved! Textedit (the program I used this morning and that I thought was like vi, instead...) messes up the file format. Now I have a working feff.inp file and can start to work. Sorry for bothering. 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

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newcomer's simple trouble
by Stefano Ciurli 12 May '04

12 May '04

Hello, this is a more intelligent input file which still gives the same error: Stefano TITLE Ni(H2O)6 HOLE 1 1.0 * Ni K edge (8333.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 6.0 POTENTIALS * ipot Z element 0 28 Ni 1 8 O ATOMS * this list contains 7 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ni1 0.00000 1.91860 0.00000 0.00000 1 O1_1 1.91860 0.00000 1.91860 0.00000 1 O1_1 1.91860 0.00000 0.00000 1.91860 1 O1_1 1.91860 -1.91860 0.00000 0.00000 1 O1_1 1.91860 0.00000 -1.91860 0.00000 1 O1_1 1.91860 0.00000 0.00000 -1.91860 1 O1_1 1.91860 END

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status of self-absorption corrections
by mauro＠rulp.org 11 May '04

11 May '04

Hi to all, I would like to ask you which is the status of the discussion on the self-absorption corrections to fluorescence EXAFS. I'm working on Mo/Si multilayers, studied by standing-wave-assisted EXAFS. My data are collected at grazing incidence (phi + theta = 90 deg) with a Ge (13 elements) detector. I have done data analysis without self-absorption corrections and I have found good results, except for the amplitude (S_0^2) that is very low (~0.50). I think this low value is due to self-absorption, so I would like to demonstrate it. My dilemma is: Troger's approach or Booth's one? I personally think that Booth's (simple) approach, could be used in this particular case (Ge detector, phi+theta=90deg), but my tutor told me that I can't assume a neglectable solid angle for a Ge detector so I have to use the Troeger's (quite difficult) approach. >From the mailing-list archive, I have read your discussion about this topic but I haven't found something like a "conclusion". Is there anyone who use Booth's approach with good results? Have you already done "tests" of this method? Is it possible to improve it? Finally, what about the software status? Matt, have you done something on Booth's Fortran code? Thanks, Mauro -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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[Ifeffit]
by Webb, Samuel M. 10 May '04

10 May '04

Aaron -- That worked perfectly. Thanks! (it is the system32 directory) The default windows one (although "newer") was 10k short of the one that is distributed with IFEFFIT. Sam >Sam, > I ran into this about a week before the APS Users Meeting. Right after I >upgraded to the newest version of Athena/Artemis/et al. I did find the >solution. Check in your system32 subdirectory (I think, it may be system) of >the windows directory. There could be a DFORRT.dll located there. The >DFORRT.dll file in that location was rather date, possibly from '99. This old >file was set in the windows path, and it was accessing it even though newer >versions were available. I found that replacing the old DFORRT.dll file with >the newer version fixed the problem. You might have to do a google search if >you don't have a newer version on your computer. If you can't find a newer >version of DFORRT.dll that works, I'll post the one that I am using up online. > > >Sorry guys, I guess I should have sent something to the list about this >immediately.. > >Aaron Stuckey

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[Ifeffit]
by Webb, Samuel M. 10 May '04

10 May '04

Quick question for everyone about the behavior of the latest updates on WinXP with Athena and Artemis et al. I manually unzipped all the updates and ran into the following error (which is likely due to my own problems). When I click on the hephaestus.bat file (WinXP), I get "The procedure entry point _FIIfexp_ could not be located in the dynamic link library DFORRT.dll." in a dialog box, then everything closes. This is also the case for Artemis.bat and Athena.bat. My version of IFEFFIT that was not updated does not have this problem. Copying the former version of DFORRT.dll from my working installation does not appear to help either. Going thru the updates from the start, I found that this error arises in update 007 and 008, but not 006. The same behavior happens for me if I use the autoupdater, rather than manually installing the updates. Sixpack seems to be unaffected. Anyone have any idea or seen this before? Sam ******************************************** Sam Webb SSRL/SLAC Bldg. 137, MS 69 2575 Sand Hill Rd. Menlo Park, CA 94025 Phone: (650)-926-3734 FAX: (650)-926-4100 E-mail: samwebb(a)slac.stanford.edu *******************************************

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Upgrade issues
by Webb, Samuel M. 10 May '04

10 May '04

>I've never heard of this, and don't know what FIIfexp might mean. >There wasn't much change between 006 and 007 -- certainly not to >DFORRT.dll or ifeffit_10.dll, so it seems pretty strange. It does >appear that the DFORRT.dll in ifeffit/sixpack/ is older than the one >in ifeffit/. I'd be surprised if that had an affect, but it's easy >enough to try both versions of the dll. There's also a MSVCRT.dll >that you could try moving away, so that the system one gets used. > >Does this problem happen with ifeffit.bat? One thing that did >change between 006 and 007 was that the perl-generated executables >got smaller by a factor of 2. This might suggest that the perl >codes depend more heavily on other dlls for code, but I don't know >any of the details... > >--Matt Well, after some more investigation, I can get the upgrades to work on just about every other computer on site except for mine. The .bats all look fine, as near as I can tell. As you suggested Matt, it only appears that the perl codes -- the ones that depend on IFEFFIT are problematic. The rest (such as ifeffit.bat and sixpack) seem fine. Even uninstalling everything and reinstalling doesn't seem to help at all. I guess I'll manage with the old versions for now. Thanks all! Sam

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RE: [Ifeffit]
by Jensen, Mark P. 10 May '04

10 May '04

Regarding Sam's question. > Quick question for everyone about the behavior of the latest > updates on WinXP with Athena and Artemis et al. I manually > unzipped all the updates and ran into the following error > (which is likely due to my own problems). When I click on > the hephaestus.bat file (WinXP), I get "The procedure entry > point _FIIfexp_ could not be located in the dynamic link > library DFORRT.dll." in a dialog box, then everything closes. I haven't had any problems running Hephaestus on 2 Windows XP machines under update 008. One of the machines was updated automatically, and one was updated by unzipping the downloaded files. Both approaches worked equally well for me. Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov > -----Original Message----- > From: Webb, Samuel M. [mailto:samwebb@slac.stanford.edu] > Sent: Monday, May 10, 2004 1:45 PM > To: 'ifeffit(a)millenia.cars.aps.anl.gov' > Subject: [Ifeffit] > > > > Quick question for everyone about the behavior of the latest > updates on WinXP with Athena and Artemis et al. I manually > unzipped all the updates and ran into the following error > (which is likely due to my own problems). When I click on > the hephaestus.bat file (WinXP), I get "The procedure entry > point _FIIfexp_ could not be located in the dynamic link > library DFORRT.dll." in a dialog box, then everything closes. > This is also the case for Artemis.bat and Athena.bat. My > version of IFEFFIT that was not updated does not have this > problem. Copying the former version of DFORRT.dll from my > working installation does not appear to help either. Going > thru the updates from the start, I found that this error > arises in update 007 and 008, but not 006. The same behavior > happens for me if I use the autoupdater, rather than manually > installing the updates. Sixpack seems to be unaffected. > Anyone have any idea or seen this before? > > Sam > > ******************************************** > Sam Webb > SSRL/SLAC Bldg. 137, MS 69 > 2575 Sand Hill Rd. > Menlo Park, CA 94025 > > Phone: (650)-926-3734 > FAX: (650)-926-4100 > E-mail: samwebb(a)slac.stanford.edu > ******************************************* > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: Help
by Bruce Ravel 07 May '04

07 May '04

On Thursday 06 May 2004 06:05 pm, chachi rojas wrote: > I am a graduate student in physics at San Marcos University, Lima,Peru > and I'm interested in studying the intermetalic alloys Fe2Zr and Fe3Zr by > EXAFS (K-Fe-edge), this samples was prepared by mechanical milling. > I am a beginner in this technique (EXAFS), I try search some information > about these system, analysed by EXAFS. I use IFEFFIT (feff6) and Artemis > programs on Linux Slackware. > Bien, in my fit i find e0= -45.34 +/- 2.15, that is a error??.. a fit the > first shell in Fe2Zr system. > please help me, if is posible, send me some information, about these > systems analysed by EXAFS or some references on it, specially Fe2Zr. > I really appreciated it if you could help me. > Thanks > Chachi Chachi, This is a very good question. In fact, I think it is important enough that I am taking the liberty of CCing my response to the ifeffit mailing list (pues, escribiendo en ingles y no en espanol). This is most definately a problem. A huge E0 like that is probably coincident with an unphysical value for one or more bond lengths. I could explain, but fortunately Alain Michalowicz gave an excellent talk on this very topic a while back at NSLS. Here is the PDF of his talk, which provides an excellent overview of the "large-E0" issue: http://cars9.uchicago.edu/xafs/Advanced_Methods/BNLworkshop2001/michalowicz… So that helps explain what went wrong, but not how to make it right. Here are some suggestions and I imagine that some folks on the mailing list might have more: 1. Make sure that your E0 was set sensibly and calibrated to a sensible value way back in Athena. Metallic zirconium tends to have the annoying feature of a double peak in the first derivative spectrum and typically the second peak is larger than the first. (That is true both in pure Zr and in Zr-alloyed Sm2Co17.) Consequently, the algorithm used by Ifeffit (and so by Athena) to automatically determine E0 will choose the second peak, since it is bigger. This places E0 10s of volts above the real E0, thus introducing an enormous E0 shift into the data. Your fit might be conpensating for that or your fit might simply be resolving to a non-physical minimum of chi-square. (I know you said you are measuring the Fe edge, but a similar thing could happen elsewhere.) 2. There is documentation under Athena's Help menu about how to use the calibration tool in Athena. There is also a demo project (also under the Help menu) explaining how the calibration tool works. Make sure you know how this is done. 3. If your data are very noisy for any reason, the algorithm used by ifeffit to find E0 could be confused by the noise. It is even possible that it will choose an E0 value well in the pre-edge if the pre-edge is noisy enough. So watch out for that. 4. Last month, there was an interesting discussion on the mailing list about background removal and noisy spectra. It covered a lot of ground, but Shelly's response: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-April/000860.html includes an excellent point about the relationship of E0 in Athena and the later fit in Artemis. 5. Finally, it is possible that you need to take a more cautious approach to using Artemis. Have you read this web page: http://leonardo.phys.washington.edu/~ravel/software/exafs/startfitting.html It outlines my philosophy for how to start doing a fit using feff, ifeffit, and Artemis. By adopting this stategy and slowly building upi the parts of your fiting model, it is much easier to avoid some of the most common pitfalls. Hope that helps, 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/

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Another R-factor question
by Wayne Lukens 06 May '04

06 May '04

Hi Matt, Thanks again for clearing up my confusion over the origin of the R factor for fits in R-space. I now have a different and unrelated question about the R factor. From looking through the ifeffit code, it appears that the R factor is defined as sum(data-fit)/sum(data). Is this correct? The reason that I am asking is that I would like to use Hamilton's test (Acta Cryst 1965, V18, p.502) to determine whether adding additional shells to a fit actually results in a better fit. Hamilton's test uses the "crystallographic R factor", which is sqrt(sum(data-fit)/sum(data)), so I would like to know whether or not to take the square root of the R-factor ratios in Hamilton's test. Thanks again for the help! Sincerely, Wayne --- Wayne Lukens Scientist Lawrence Berkeley National Laboratory email: wwlukens(a)lbl.gov phone: (510) 486-4305 FAX: (510) 486-5596

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reporting bugs
by Bruce Ravel 04 May '04

04 May '04

Hi folks, Of late, I have received a large number of well-intentioned but incomplete bug reports. While I am always pleased when people let me know about the in my programs that need improvement, it seems prudent for me to spend a little bit of time educating all of you in the art of reporting bugs. The most important thing for you to remember is this: +------------------------------------------------------+ | If I cannot replicate the problem you are seeing, I | | will not be not be able to fix it. | +------------------------------------------------------+ I do not knowingly release software with show-stopping bugs (i.e. bugs that cause crashes or generate trap files). Thus, if you do see such an event, it is likely that I am not aware of it. You need not only to tell me *that* it happened, but to show me *how* to make it happen. Often showing me involves sending the data or project file that triggers the problem. Other times it involves sending me an explicit "recipe" of steps to take which demonstrate the problem. Sometimes both. When I receive a bug report with insufficient information, I cannot do anything until we have exchanged email a few more times. By sending me what I need to replicate the problem, you may reduce the amount of communication required and speed up the response. I have a somewhat long list of suggestions for reporting bugs at this web page: http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html If you have not read that page recently, please take a few minutes to do so again. Regards, 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/

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New binary installer for testing on Mac OS X
by Matt Newville 03 May '04

03 May '04

Hi Folks, There's a new version of a Mac Binary Disk image for testing at http://cars9.uchicago.edu/ifeffit/downloads Currently labeled ifeffit-1.2.5a-Mac10.3.dmg. This include horae-033, and uses the Aquaterm Plotting terminal by default, but supports the X-window plotting as well. This version is also ready for horae-update to work if Fink and Fink's g77 are installed on your system. This has been tested on exactly one machine and will require small changes to horae by Bruce, so we won't know how it really works until horae-034 is ready. Please try this out and let me know how it works. I have not yet put this version on Sourceforge.net, and will wait to do so until I hear a few positive responses that it works ok. --Matt

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Re: A question about the new Artemis version
by Peter Southon 02 May '04

02 May '04

As Bruce and Matt already know, I also have been trying to get Artemis to use the same FEFF calculation set for multiple data sets (in my case fewer data sets than Scott but with more paths). I've been taking the 'bite the bullet' approach and re-entering all the path parameters for each sample, but the ability to clone the calculations would help me a lot as well. I came up against two limits. First there is Ifeffit's limit of 256 paths, so I think Scott's student will hit this in the project he described (11 x 25). Matt has kindly sent me a modified version of Ifeffit which should have an increased limit, but I haven't had the chance to test it yet (partly for reasons described below). The second limit is when Artemis checks that there are not more than 256 paths before running a fit. When I tried running one fit I found that Artemis counts all the files that are opened, not just those selected to be included in the fit, but Bruce is fixing this. However, I suspect that Artemis too will have to be modified before it will let you run a fit with more than 256 paths using a modified Ifeffit. This is where Bruce's suggestion of writing a Ifeffit script and then editing with cut & paste (and find & replace) becomes particularly useful. This is quite similar to what I did with Feffit and Ifeffit before I started using Artemis, and works well but is rather time consuming. I understand that an item on Bruce's (very long) 'to do' list is to allow Artemis to open a Ifeffit script into a project - so that once manually modified you could transfer the project back into Artemis. There is another thing to look out for when constructing very large or complex Artemis projects. I have found that very occasionally Artemis will save a project into Bruces' new zip file format, but neglect to actually add in some (or any) of the data and feff files. The first symptom is that the size of the saved project is much smaller than it should be. Thus when re-opened, the project looks fine, but Artemis cannot open any of the required files when a fit is attempted. The data can be replaced, but I can't find a way of replacing any feff calculations without re-entering all of the parameters. Anyway, the purpose of all that is that if you are putting a lot of work into your Artemis project, it may be worthwhile to back it up occasionally, or save under a new name. >P.S. Thanks to Matt and Bruce again for even making such a thing >conceivable. Hear hear Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Substrate material question
by Kropf, Arthur Jeremy 29 Apr '04

29 Apr '04

Paul, Silicon is quite strong. However, it is also brittle. For detectors I have been able to bend 200 micron silicon to less than a 200mm radius. That should be plenty of strain. Virginia Semiconductor is great. Look at their double-side polished stock and you can typically find one or two batches with less than 200 micron thickness. Wafers thinner than 100 microns begin to get quite fragile. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Fons Sent: Tuesday, April 27, 2004 7:59 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Substrate material question I have still not decided on the final substrate material, but I have a couple of samples coming from Dupont of polyimide (same composition as Kapton) material called vespel. It is essentially inert as one would expect (like Kapton), but due to differences in manufacture I understand it is hydroscopic. From this I assume that the reaction for making Kapton is diffusion limited and Vespel is essentially a "polycrystalline" -- in the sense there are grains between which water can absorb -- form of Kapton. The energy in question is 11.6 keV (the Ge edge). Si is an interesting idea but the loss for a 200 micron thick substrate is essentially 1/e. It is certainly worth considering for higher energies though! The 1/e value for polyimide is about 3500 microns in contrast, while the 1/e value for MgO is about 300. As in my experiment I want to create biaxial stress in a thin film on the substrate, I worry that the stress/strain curves for MgO are too stiff. On the other hand, thin S! i is a real possibility (darn, Si technology is everywhere!). I like the Si idea and might try that in parallel. Has anyone tried using thinned Si wafers (Virginia Technology ? sells mechanically thinned wafers I think -- I saw them at a MRS booth a long time ago). How fragile are the wafers? On 2004/04/28, at 0:32, Jeff Terry wrote: Hi Matt, Both items are good to know. I didn't realize that the laminated kapton structures still had good heat resistance. Jeff On Apr 27, 2004, at 10:22 AM, Matt Newville wrote: Hi Paul, I think you can get polyimide thicker than 175 microns. It may not go as Kapton, but maybe as Cirlex or Torlon or something else. I think goodfellow.com carries these in millimeter thick sheets and rods, and that they're still radiation and heat resistant. Goodfellow tends to be pricey, but has excellent information on thermal and mechanical properties. Using MgO, sapphire, or even diamond might be reasonable too. --Matt PS: I have a working build of PGPLOT with all of Aquaterm, X11, Postscript, and Png devices on Mac OS X. I'm still tweaking the makefile so that it links directly to the png objects to avoid possible conflicts with dynamic png and zlib libraries, but I should have a working ifeffit binary using this in a matter of days, and then be ready to tweak horae's Makefile.PL so that horae_update works. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 29 Apr '04

29 Apr '04

Along the topic of not being able to run Artemis and Athena simultaneously under Windows. 1. Lack of complaints doesn't mean that he problem is rare. I have consistently seen this behavior (run either Artemis or Athena) on 3 different Windows NT/Win 2000 (incidently 128 Mb RAM) machines. I recall pointing it out to Bruce many moons ago, and just accepting it as the way things were. Matt and Bruce obviously spend a lot of time working on their programs to our benefit, and I didn't think it was worth Bruce's time to chase a small, possibly not fixable, problem like that down. Thus, I did not bug him about it after the first mention of it. I would just extract the EXFAS signal in Athena, save the file, close Athena, open Artemis, and fit. It seemed like a small price to pay for being able to use a great set of programs. 2. However, the recent exchanges on this matter got me to look closer. Now I see that I can run both programs simultaneously on my brand-spanking-new 1 Gb RAM Windows XP computer. I'll have to try it under WinXP and 512 Mb RAM at home this evening. Maybe this is indeed a memory size problem. 3. It seems like more and more of the posts to the Ifeffit list are about general EXAFS things like (for a recent example), what k-range to use. Bruce and Matt and others have been very helpful to the needy, and I can tell it has been much appreciated. (I think I already know the answer to my following question). Has it been considered to "split" the Iffefit list into 2 topics, 1 for general XAFS and 1 for Ifeffit and related programs. (Suspected answer.... "Great idea Mark, we've talked about this before, why don't you volunteer?") Mark J. ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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Re: Artemis Crashed too often
by Aria 29 Apr '04

29 Apr '04

After reading these days' discussion in 'minor bugs report' thread, it reminds me of keeping a track of memory usage in my case. Here is a detailed list. Artemis starts: 56,100 K Loads project file: 59,180 K Save: 65,256 K After 1st fit: 88,252 K 2nd fit: 88,824 K 3rd fit: 89,320 K Save: 98,160 K 4th fit: 97,840 K Save: 98,164 K 5th fit: 298,152 K Crash I have also noticed the CPU usage is normally 25% during the fit process. But in the 5th fit, it went up to 25% for first several seconds, then drops to 0% suddenly. The memory usage jumps to 298,152K at the same time, and stayed for a few seconds before it finally crashed. Meanwhile, another process called 'dwwin.exe' with memory usage of 248,016K appeared. After the error message showed up, and closed all the Artemis windows, both of those big memory consuming processes disappeared. This practice is reproducible. I hope it helps a little bit. Best regards, Aria

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 29 Apr '04

29 Apr '04

I agree with Gerrit on this. This morning I took a look at the two "nearly identical" computers and found that 1. Athena and Artemis each consume about 230 MB of memory to run on my Windows 2000 or XP computers. 2. That the computer that could run both Athena and Artemis with 128 MB RAM had a considerably larger maximum virtual memory setting (600 MB) than the computer that would not (300 MB). Increasing the size of the virtual memory on the latter computer allows both to run. Bruce, as long as that is the amount of memory the programs should use, I guess that means this is not a minor bug in your software. In my case, it's a user that was being miserly with hard drive space. Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov -----Original Message----- From: Schmithals [mailto:schmithals@hmi.de] Sent: Thursday, April 29, 2004 3:06 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Minor bugs in the new versions Matt Newville schrieb: > 2 I can definitely run artemis and athena at the same on a Windows > machine, so I doubt there's a lock on Perl's Ifeffit.dll. I'd > assume that if other people could only run one of these at a > time there would be many complaints. > > 3 On my WinXP box, athena and artemis each use about 55Mb at > startup -- without reading in any data. That seems to be about > 50% Ifeffit / 50% Perl/Tk (the ifeffit shell takes ~24Mb). > I don't know enough about what changed to guess why the memory > usage would've changed between versions of artemis and athena, > but I think they should both be able to run in 256Mb. Anyway, > I'd suggest watching the memory usage in TaskManager as you > start athena and artemis to see if it really is a memory issue. I now think its a memory problem, too. My computer is running Win2000, 256 MB of RAM, virtual memory is fixed to 400 MB. I started the Windows Task manager to watch memory usage: - without any programs running (except virus scanner, ..) its 119 MB - After starting Artemis it goes up to 412 MB - Athena won't run Then I set the virtual memory to fixed 600 MB. - After starting Artemis it again takes ~400 MB - Athena now starts! Memory usage is ~700 MB. But shutting down one program before starting the other has been OK for me, too. Regards, Gerrit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Minor bugs in the new versions
by Schmithals 29 Apr '04

29 Apr '04

Dear Bruce, I installed the new versions of the programs. Many thanks for your ongoing work and especially for the new feature of exporting parameter values in Athena. While working with the new versions I listed the problems that I still ran over (all just minor problems that are not critical or for which I figured out a workaround). Some of the bugs have already been mentioned, but I was not sure if they should already be fixed with this release - if not please just ignore these points. Hope it helps to improve the software. My System is Win2000. Artemis 0.7.003 - After the update the path to the stash-folder is set to the default path: "c:\Program Files\Ifeffit\horae\stash" although my Ifeffit is installed at "c:\Programme\Ifeffit" and previously the stash folder was "c:\Programme\Ifeffit\horae\stash". Is it possible to set the stash folder automatically to the subfolder in the installation directory? Obviously, this should be corrected via: Options | General | Workspace. But Artemis will not let me do that. I included the messages that Artemis gives when I change the path and press "Save changes to future sessions" and "return to main window". In the latter case Artemis will ask if I want to keep changes for future sessions (obviously it recognizes that changes have not been saved) but will not return to the main program (and not change the path). However, it does affect working with Artemis in any other way (as far as I can tell). - Atoms potential cards (in feff.inp) is sometimes wrong. (work-around: enlarge r_max in atoms.inp) - Artemis will stumple if I try to import 30 paths (my default) but feff generated less than that (no paths will be loaded and and error message generated, see ARTEMIS Import.TRAP). - If I run feff, import 30 paths and then do that a second time, Artemis does not delete the old entries in the "data&paths"-window but just append the new entries with names "feff0001.dat:2" etc., is that the intended behaviour? The problem is that if I decrease r_max in feff.inp before doing the second run (to a value so that feff produces less than 30 path-files) Artemis will generate error messages when trying to plot the first path entries (obviously because they dont exist anymore). - Function "discard this dataset" does not delete the main folder "data0.feff.0". Therefore, after deleting a few FEFF-datasets I end up with a lot of folders "data0.feff.x", because the empty ones are not reused. The function also does not delete the corresponding parameter values (which is probably better than deleting them). - Set-up of Atoms/Feff-page before loading a datafile will lead to errors (already discussed) Athena 0.8.027 - Athena does not start when Artemis is running. Two new Windows will show up for a moment in the taskbar and disappear again, no error logs are written to the stash-folder. No problems occur if Artemis is not running. Also Artemis will not start when Athena is running. - When using the export function via "File | Save marked groups as data" Athena will state that I may not export more than 15 datafiles. But it also produces errors with less files: it seems that the maximum line width is limited to 259 characters. The line with the names of the datagroups is usually longer and therefore gets truncated. - Access to last opened files is not released: it is not possible to rename/delete project files that just have been closed or data files that just have been read in. This is possible after a new project file is opened or a new data file imported. - Sometimes the selection of groups gets faulty: when clicking on one of the groups it will not be highlighted. Instead the previously selected group will be redisplayed (and remains highlighted). Sometimes a completly different group will be highlighted and displayed. Closing and reopening will not solve the problem, but restarting of Athena does. I could not figure out how to reproduce this error and nothing is written to the stash-folder. - Athena sometimes resizes the width of the right panel (Data groups) by itself. E.g. when exporting data via "File | Save chi(R)" the window becomes wider and gets small again when clicking on a datagroup afterwards (but not always ?!). Atoms ? - I am not sure about the version number because "Help"|"About Atoms" displays "left" (?!) instead of version number. - The "Browse Space Groups" will still invoke the browser only once. Hephaestus 0.01 - Multiple choosing of Settings | Energies will TOGGLE between display in energies/wavelengths (instead of just keeping displaying in terms of energy). Moreover, the checkmark in the Settings-Dialog will stay at "Energies", even when displaying in wavelengts. Despite of this I would propose to display the unit on the main page anyway. - On my machine the checkmarks are hard to recognize as they only shown up as two tiny red dots. But they will show up as checkmarks when I hover over them with the mouse. (This behaviour is common to all the programs, also in previous versions). I also have some general question: - Is it possible to do an offline installation on a computer not connected to the internet? (e.g. by manually loading the updates-files and changing "update_site" in updater.ini) - Is there a way in Athena to display the raw data of a group as a text file? Athena will not allow to edit this data via "Edit | Edit data as text". I only had the idea of saving the group and looking at the resulting text file. - This raised another point: if I compare the file I read into Athena with the file I exported then I notice that they have a different scaling (abszissae values) - does Athena automatically change the scaling when importing data files? I also noticed that when exporting multiple groups then all groups are scaled to the same abszissae values which is not the case when I export them separately. Regards, Gerrit

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RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 28 Apr '04

28 Apr '04

Ifeffit friends, I have done several test with Athena and Artemis this afternoon, and the problem of running Athena and Artemis at the same time does not seem to be solely memory related. On two similar Win2000 machines, my old one with 128 Mb behaved as usual, only Artemis or Athena would run at one time. The first "program box" for Aretmis representing the text window would appear in the task bar, the updater program box would appear and then both would disappear instantly. I do not observe the Aretmis splash screen and she never really starts. It happens so fast that I can't read anything in the text window. This was it's "usual" behavior on the 3 computers I mentioned in the previous e-mail. This happens right from the get-go. Nothing else, other than the manditory windows services and the lab mandated anti-virus software was running. On the other machine, with 256 Mb, I could run both simultaneously. Aha! I'm on to something! When I took 128 Mb out of this 2nd computer, though, I could still start Athena and Artemis simultaneously! Rats, foiled again! Unfortunatley, I couldn't bump up that 1st computer to 256 Mb to see if that would enable both to run simultaneously on that computer. In the past, on the first computer, I have had to shut down other programs to get enough memory to run either Athena or Artemis. Maybe, people with this problem will just have to adopt my old approach and put up with this glitch. Mark ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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RE: [Ifeffit] Minor bugs in the new versions
by Scott Calvin 28 Apr '04

28 Apr '04

At 02:57 PM 4/28/2004 -0500, you wrote: >1. Lack of complaints doesn't mean that he problem is rare. > Mark brings up an interesting issue. I'd kind of like to get the sense of the community on this. Given that, unlike Ifeffit itself, Artemis and Athena are beta versions (a "0" starts the version number), all of us who use that software are beta testers. Thus part of our responsibilities, in exchange for getting to use really nifty and cutting-edge software, is to report bugs to Bruce. Unfortunately, reporting bugs in a responsible way is somewhat time-consuming (not nearly as time-consuming as writing the software in the first place, of course!). For example, a really minor bug which has already been discussed is the one that occasionally makes the right panel of Athena get wide. It's not something that bothers me, but it's clearly a bug. I don't feel like I'm being helpful, though, if I report to Bruce that something like this "occasionally" happens without being able to make it happen reproducibly. So I never reported it. If, on the other hand, some bug is either making it harder for me to do what I want to do, or it seems likely to cause some other unsuspecting user grief, or I can see exactly under what circumstances it occurs, I generally investigate and make a bug report. So my question is what perspective everyone (and especially Bruce) has on the trade-off between tracking down every bug so as to give Bruce full reports and spending the time actually using this great software for analysis. --Scott Calvin Sarah Lawrence College

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RE: [Ifeffit] k range
by Kelly, Shelly D. 28 Apr '04

28 Apr '04

Hi Steven, > On Tue, 27 Apr 2004, Steven Sangyun Lim wrote: > > > My question is how low can I set the k range? Is there any minimum > > range for reliable result? Please let me get out of this dilemma... > Scott and Matt both answered this question differently than I would. I guess I am very practical. If I was asking this question I would want a set of rules that would help me figure it out the k-range. So here one way to do that. 1) Look at the data in Athena to determine a good k-range to use. Here is how. 1a) As Matt suggested find a node in the chi(k) data that is around 3 inverse angstroms and set that to the kmin value. 1b) make about 6 copies of the chi(k) data set, all with the same kmin value. All the other FT values should be as you used in Artemis. (k-weight, window, dk) 1c) highlight each data set choosing a larger and larger node for kmax. Start really safe value around 8 inverse angstroms. Then pick the next node for the next copy and so forth using up all the data. For example, the first copy of the data set has a k-range [3.2 to 8.2] the next copy has k-range [3.2 to 9.3] and so forth....until the last has a k-range of [3.2 to 14] 1d) Plot the FT of the first three data sets all together (using the purple buttons to select them and the purple R button). Look at the data with the magnitude and the real or imaginary part. With a small k-range the FT signal will be very smooth curve in the magnitude, real and imaginary parts. You will tend to see two types of changes as you increase the k-range. 1) peaks will become more resolved, larger amplitude and thinner. --this is a good kind of change 2) eventually you will see noise in the FT of the data. The noise will look like high frequency pulses in the real and imaginary part of the spectra all over in R. From one data set to the next random signals will appear and disappear as you include noise in the data. --this is the bad kind of change. Keep comparing three data sets, drop the first one then add another with slightly larger k-range. You should be able to find the cross over from the good kind of a change to the bad kind of a change. 1e) By using this comparison you should be able to choose a k-range that is large but not too large. It should result in a conservative k-range to use as a starting point for your modeling. Be careful about the k-weight that you use when you make this comparison. It needs to be the same that you are using in Artemis to model the data. Larger k-weights will have smaller "good" k-ranges for the data. 2) Pull your data into Artemis. Use the good k-range that you determined from step one. 2b) Determine a model that works and look at the results including the uncertainties. 2c) Increase the k-range and compare the results. Try to decrease kmin and increase kmax. Do one thing at a time and see how the results vary. You will need to make a lot of comparisons, see how your results and uncertainties change as you adjust these values. 2d) Decide on a k-range that gives you the "best" results. 3) You may want to go back into Athena and use a standard to adjust the low k region of the chi(k) data, depending on how your FT looks at low R. This can help you stretch the kmin value. HTH Shelly

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RE: [Ifeffit] k range
by Kelly, Shelly D. 28 Apr '04

28 Apr '04

Hi Steven, In general you can use as small of a k-range as you want but you loose the number of variable that you can determine and your uncertainty in those variable gets really big too. If those trade offs are acceptable then there is no problem. I assume that you want to determine a few variables so Scotts equation is all you need to determine the minimum k-range. Artemis also lists the number of independent points in the log file. That number has to be greater than the number of variables you can determine in the fit. In practice, you need about twice as many independent points as variables to get reasonable uncertainties. But if what you say about your data is true then the metal peak is not real. In the chi(k) data the signal for each peak starts at k=0 and goes until the sigma2 term damps it out, usually around 8 to 10 inverse angstroms for oxygen, but usually much larger values for atoms with more electrons. It is physically impossible for the signal of the metal peak to only exist between 6 and 8 inverse angstroms. I would compare the data set that you are having troubles with to the other data sets that you indicated gave a consistent peak in the FT. I would bet that the troubled data set has some artifact in it that is distorting the FT. Shelly -----Original Message----- From: Steven Sangyun Lim [mailto:steven.lim@yale.edu] Sent: Tuesday, April 27, 2004 6:31 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] k range Thank you all very much for the immediate help. One more question, may I??? What can the minimum kmax be? I think it can be about 8 according to Scott. If I use kmin=2, can it be 7 or 6? The reason why I ask this is that when I plot R space with my sample, which has been reduced and needs to be confirmed if there is any metal cluster, the metal peak shows at kmax=8, but it disappears at kmax=6 or 7. At kmax=10, it is hard to tell because the spectrum is very noisy (it shows split peak). When there are extremely small metal clusters (even at CN=0.6), I can see a distinct metal peak that does not change no matter what k range and weight I use. I wonder any further advice can be suggested. Thank you for your help in advance. Steven

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Substrate material question
by Paul Fons 27 Apr '04

27 Apr '04

OK, I admit this isn't an athena question (but it is about how to take the raw data for it!). I want to do biaxial strain measurements. The idea is to deposit a thin film of the material to be investigated on a substrate and then deform the plate with a form of cylindrical symmetry. One can then solve for the stress of a plate using elasticity theory. The twist is that I need a plate that is stiff and (surprise) x-ray transparent ... and heat resistant to about 250 C. Kapton would be a wonderful choice, but is only made in thicknesses up to 175 microns (hardly stiff enough). There must be someone out there in the collective iffeffit world who knows of an appropriate material. Doing some web surfing, I came across another product by DuPont called Vespar that *may* be available in thicker forms. The specs I am looking for are: a thin (semiconducting) film has to stick to the surface, heat resistant to <=250 C, thick enough to be elastically stiff, and x-ray transparent. Any suggestions? Thanks for any help that may come my way in advance! Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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k range
by Steven Sangyun Lim 27 Apr '04

27 Apr '04

Thank you all very much for the immediate help. One more question, may I??? What can the minimum kmax be? I think it can be about 8 according to Scott. If I use kmin=2, can it be 7 or 6? The reason why I ask this is that when I plot R space with my sample, which has been reduced and needs to be confirmed if there is any metal cluster, the metal peak shows at kmax=8, but it disappears at kmax=6 or 7. At kmax=10, it is hard to tell because the spectrum is very noisy (it shows split peak). When there are extremely small metal clusters (even at CN=0.6), I can see a distinct metal peak that does not change no matter what k range and weight I use. I wonder any further advice can be suggested. Thank you for your help in advance. Steven

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k range
by Steven Sangyun Lim 27 Apr '04

27 Apr '04

Dear all, I always appreciate the big useful help from everyone. I have a basic question. I think a similar question has been arose long time ago. (But I lost the mail..) My sample has very small amount (under 1 wt%) and cluster size (< 1nm). The spectrum is always noisy at high k range, so I use usually k=2 to 10 or 12. It depends on the noise of the spectrum. Of course, if I go further down, it is better. My question is how low can I set the k range? Is there any minimum range for reliable result? Please let me get out of this dilemma... Thank you always. Steven

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RE: Ifeffit Digest, Vol 14, Issue 23
by Aria 27 Apr '04

27 Apr '04

Hi, Bruce For the first question, after I answered 'yes'. Artemis will run well without problems. But after running fits for four (sometimes even three) times, it will crash again. And the next cycle begins. As for reproducible, only after I finished the updates, it will crash every four or three fits, no matter what fits I am running. The fits paths included might be around 100. By the way, I did not notice if Artemis posts a message or not before. But this time, it do pop up a message at the first time I run the fit (not at the time it crashes). This is the message I got: # This file created at 11:01:54 on 27 April, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 The following message was trapped by Artemis on a SIGWARN: ArtemiswarnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3525f58) at artemis line 1491 main::__ANON__('Tk::Error: Can\'t locate utf8.pm in @INC (@INC contains: C:\DOCU...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al) line 402 Tk::Error('MainWindow=HASH(0x394d430)', 'Can\'t locate utf8.pm in @INC (@INC contains: C:\DOCUME~1\VINCEH...', '[\&main::__ANON__]', '(menu invoke)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1627 Here attached is the file. Thanks a lot, Aria ------------------------------ Message: 2 Date: Mon, 26 Apr 2004 17:04:59 -0400 From: Bruce Ravel <ravel(a)phys.washington.edu> Subject: Re: [Ifeffit] Artemis Crashed too often To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200404261704.59318.ravel(a)phys.washington.edu> Content-Type: text/plain; charset="iso-8859-1" On Monday 26 April 2004 04:27 pm, Aria wrote: > I began to use the old version of Artemis in last September, and did not > update till days ago. But after the installation, Artemis crashed very > often. After running four fits, it will crash without any reasons (I did > not close the graphics window). And when I restart the Artemis, sometimes > it will give out information like: 'There seems to be a large number of > abandoned project folders. This might be due to past program crashes or > other past problems. I can clean these up at this time.' I am not sure if > it happens to others. I work in Windows XP platform. You seem to be reporting two different problems here, but have not given me enough information to do anything useful about either one. 1. What happens when you answer yes to the question about cleaning up abandoned project folders? Does Artemis crash again right after that? How about the next time you start Artemis? 2. It is really not adequate just to say "Artemis crashed very often." If you do not give me enough information to reproduce the problem myself, then I cannot fix whatever is causing the crash. Indeed, I cannot even begin to search for the problem because you haven't told me anything about it. Please read this page carefully: http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html and the consider trying your bug report again. If Artemis beeps and posts a message to the echo area about a TRAP file, please send me the specified file along with a description of how you got to the situation. 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/

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Artemis Crashed too often
by Aria 26 Apr '04

26 Apr '04

Hello, I began to use the old version of Artemis in last September, and did not update till days ago. But after the installation, Artemis crashed very often. After running four fits, it will crash without any reasons (I did not close the graphics window). And when I restart the Artemis, sometimes it will give out information like: 'There seems to be a large number of abandoned project folders. This might be due to past program crashes or other past problems. I can clean these up at this time.' I am not sure if it happens to others. I work in Windows XP platform. Regards, Aria

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Re: [Ifeffit] Re: A question about the new Artemis version
by Scott Calvin 22 Apr '04

22 Apr '04

Hi Matt, FYI, the path limit in the current version appears to be set to 256 paths. --Scott Calvin Sarah Lawrence College At 02:53 PM 4/1/2004 -0600, you wrote: >The latest version of the ifeffit_10.dll windows binary should >support 1024 paths, and 16 data sets. You can see what these >limits are for your system by typing > show &max_paths, &max_data_sets > >at the command line prompt. The limits are set to their current >values so that Ifeffit+Athena takes well under 64Mb RAM. But these >limits are set in one place in the source code (src/lib/consts.h) so >that you can easily change them and recompile if you need these >limits to be higher. max_paths can be increased easily up to 9999, >but going above that would take more work. >>

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new versions of my programs
by Bruce Ravel 22 Apr '04

22 Apr '04

Hi folks, I have just finished the new release of my data analysis programs: Athena 0.8.027 and Artemis 0.7.003. This release contains mostly bug fixes and feature enhancements. As you may recall, last month's release of Artemis generated a very large amount of traffic on this list due to several problems surrounding the new project file format and other file management issues. I have addressed almost all of the problems that were reported and am cautiously optimistic that this release of Artemis will be much more solid than the last. There is one significant new feature in this release -- the program Hephaestus, which will be a permanent part of future releases. Hephaestus replaces the Atoms Periodic Table and expands greatly upon its functionality. I will describe Hephaestus in more detail in a message later this morning. Source code tarballs are already available on my web site and at SourceForge. The Windows updater package will be available soon. Change logs with all the details of the new features of Athena and Artemis are on my web site. Lots of people helped out this time with excellent suggestions and bug reports. Special thanks to Mauro Ravezzi, David Barton, Peter Pfalzer, Gerrit Schmithals, Stanislav Stoupin, and Shelly Kelly. Regards, 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/

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Re: Truncate, Post-edge Athena Issues
by Bruce Ravel 21 Apr '04

21 Apr '04

On Tuesday 20 April 2004 11:56 pm, Barton, David (DG) wrote: > One final question. I often see a strong discontinuity near the edge > energy in the background subtraction. The attached Athena project clearly > shows this discontinuity, any thoughts about this? Dave, I am CCing the answer to this one to the mailing list. The background spline is evaluated between the energies (or k values) specified. Outside that range the spline is not evaluated at all. To make the arrays conatining the data and background spectra easier to handle when interacting directly with Ifeffit, Matt wisely chose to make the background array the same length as the data array. At energies within the spline range, the background array contains the background spline. Outside the spline range, that background array contains the original data. Not only does this make the arays the same length, but it makes computation of chi(E) completely trivial -- you can just subtract the background array from the data array point by point. If the first or last few points of the spline are not near in value to the data (which can happen since a spline can be poorly constrained at the ends), then the plot of the data and background arrays will be as you described. The background array will have a discontinuity, but that is not a bug. Regardless of the constraint of the spline near its ends, the criterion for choosing the spline is met. That is, the spline is always chosen to minimize the low-R Fourier components (possibly with respect to a standard spectrum). Sometimes this minimization results in a spline that deviates from the data at the ends. Constraining that deviation is the purpose of the spline clamps. > I typically have ignored this since it is outside the EXAFS fitting > region and the XANES background subtraction routines are not > affected by it. That is completely correct. HTH, 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/

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Athena Minor Error
by Norbert Weiher 21 Apr '04

21 Apr '04

Hey Bruce, I found a minor error in athena: When want to select the spline range for my spectrum and accidentially press the "k" button (but have the spectrum plotted in E), athena crashes as soon as I click on the graph to select some value. Its not bothering much (actually I should be aware of pressing the right button - I know :)), just wanted to tell you. 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

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noisy spectrum and AUTOBK
by gabriel rosenblum 20 Apr '04

20 Apr '04

Hi all. Sorry for not being specific. I am trying to do background removal with AUTOBK. The parameter emax is present at autobk.inp file under the UWEXAFS package. Emax � means the region after the edge in the xmu file to be taken by AUTOBK to perform the spline. For example, if emax is set to 400 eV, it means the spline and the subtraction will be carried 400 eV over the edge. After the subtraction I FT the data and observe chi(R ). I guess the noise problem is more pronounced 350 to 550 eV over the edge, and not near the edge. However I will sure try the recipe offered by Shelly. Still waiting for an answer. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25� http://photos.yahoo.com/ph/print_splash

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RE: [Ifeffit] Noisy spectrum and AUTOBK
by Kelly, Shelly D. 20 Apr '04

20 Apr '04

Hi Gabi, I need some more information to address your concerns. See below: > I have a question regarding noisy EXAFS, since I > analyze biological zinc samples. I have seen Bruce's > data and it is quiet as a sleeping snail all the way > till chi(k)=16, however I have a completely different > situation since I encounter noise at high chi(k) and I > need an advice from whoever can supply it. > As I use AUTOBK with emax set to maximum I observe > chi(k) which is quiet at 0-9, and at 9-12 I obsrerve > clearly the oscillations but with the addition of > small spikes resulting from noise. At chi (R ) I see > the first shell peak at 1.5A with amplitude of 1. > Adjacent to this peak I observe a small peak at 1A > with 0.5 amplitude. What is emax? Do you mean that you set Ezero to the maximum of the first derivative of the xmu data? What does the background function look like? Does it have a large spike right at the beginning? If so adjusting Ezero can help reduce that. Usually kmin should be small like zero. The exception being if you have a large white line (peak at the top of the absorption step). Then you want to increase kmin to help the bkg go over the white line >As I change Rbkg and Knin I cannot > get rid of the small peak; the left region of the > small peak is situated between 0.5 to 1A at chi(R ), If you increase Rbkg to 2.5 you must be able to get rid of the low r peak. Although I don't recommend that you do that, for real. Try it, just for fun and see. Often the low r peaks really don't matter. To get rid of them, the most robust method is to fit the first shell peak with a theory then pull the fit back into Athena and remove the background with the fit as a "standard". --see below for a recipe. > and my attempts to keep this region "clean" failed. > However, if I lower emax to 400, corresponding to > approx. 10 at chi(K), and Fourier-transform the region > between 2 to 9 (the quiet region), the small peak > disappears and the region at Chi (R ) between 0 to 1A > is "clean", but since I utilize less information the > peaks at chi (R ) have lower resolution. > My questions are: > 1. What is the source of the small peak ? > 2. Is it a real contribution from scattering ligands ? > 3. How should I treat the small peak. > 4. Should I get rid of it by all means ? if so, how ? I don't understand the emax variable. But, Since the low r peak disappears as you move the k-range up a bit then I believe the low r peak is an incorrect bkg removal that can be fixed by including a standard in Athena. Here is a recipe to get a nice background function. I'm sure Bruce and Matt have this written down somewhere too. 1) Fit the first shell in Artemis. Using a limited k-range where you are really confident that the oscillations are not distorted by the bkg. k=[2:9] determine a value for deltaE, deltaR and N or SO2. DetlaR, N or SO2, should be reasonable. The value for DeltaE depends on your choice in Athena. 2) You have to decide if you original choice of Ezero (in Athena) was close enough. If deltaE (from the Artemis fit) is more than +/- 10eV you need to go back into Athena move Ezero and redo step 1. The rule is: deltaE + Ezero should be somewhere on the edge of the xmu data. 2b) If you can not get a reasonable deltaE then rethink your theory. Maybe R in the theory is way wrong? Maybe two shells are needed instead of one? Or maybe Ezero in Athena is way off? Maybe your k-range needs to be even smaller. 2c) Still having trouble with step 1? --you can also change the k-weight for the background removal. For this first step it is often useful to crank it up, so that the higher k-region has a nice bkg and then just don't use the low k-region in the fit to get the theory to "line up" with the data. For example: use k=[4:12] in Artemis, with k-weight=3 in Athena for the background. 3) Now you have a theory for the first shell peak with an Ezero somewhere on the edge, we want to match-up the data and theory before the first shell peak. Go back into Athena, read in the fit in k-space. Then highlight your data, pull down the standard menu and select the theory data file. Redo the bkg by plotting both the theory and the data in k-space. They should look similar at low k. Then plot the FT (using the same parameters as you did in Artemis) and they should look similar below the edge. 3b) If not: --If they do not cross zero in k-space (at low k-values) at the same places you need to adjust Ezero. --If they do not have the same amplitude you may need to adjust Rbkg slightly. Remember Rbkg can not be greater than Kmin in for the data region used in Artemis, but they can be equal and often are equal. 4) Redo the fit and add some more shells as needed, increase the data range in k-space. See how much data you can use and still get reasonable fit and uncertainties. 5) At the very end you might want to repeat this procedure to make a pretty picture for your pub. HTH Shelly

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Noisy spectrum and AUTOBK
by gabriel rosenblum 20 Apr '04

20 Apr '04

Hi all I have a question regarding noisy EXAFS, since I analyze biological zinc samples. I have seen Bruce�s data and it is quiet as a sleeping snail all the way till chi(k)=16, however I have a completely different situation since I encounter noise at high chi(k) and I need an advice from whoever can supply it. As I use AUTOBK with emax set to maximum I observe chi(k) which is quiet at 0-9, and at 9-12 I obsrerve clearly the oscillations but with the addition of small spikes resulting from noise. At chi (R ) I see the first shell peak at 1.5A with amplitude of 1. Adjacent to this peak I observe a small peak at 1A with 0.5 amplitude. As I change Rbkg and Knin I cannot get rid of the small peak; the left region of the small peak is situated between 0.5 to 1A at chi(R ), and my attempts to keep this region �clean� failed. However, if I lower emax to 400, corresponding to approx. 10 at chi(K), and fourier-transform the region between 2 to 9 (the quiet region), the small peak disappears and the region at Chi (R ) between 0 to 1A is �clean�, but since I utilize less information the peaks at chi (R ) have lower resolution. My questions are: 1. What is the source of the small peak ? 2. Is it a real contribution from scattering ligands ? 3. How should I treat the small peak. 4. Should I get rid of it by all means ? if so, how ? My confusion arises from the fact that AUTOBK should get rid of atomic exafs at chi(k), consequently, the contributions at chi (R ) between 0 to 1A should get lower. In my case it seems that this contribution is lower, but it still exist with half the amplitude of the first shell peak. Any help would be appreciated. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25� http://photos.yahoo.com/ph/print_splash

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[proposal] Artemis plotting option
by mauro＠rulp.org 20 Apr '04

20 Apr '04

Hi, I would like to know if it is possible to include in Artemis the "stack" plotting option, like the Athena's one. In fact, setting a y-offset value for the selected chi/paths/residual could be very useful. Thanks, M -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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S02-Interpretation
by Norbert Weiher 20 Apr '04

20 Apr '04

Dear Friends, I would like to ask a question on the interpretation of S02 in a fit. Although there has been some discussion on this parameter, I did not find exactly what I was looking for. Here it goes: To my knowledge, S02 accounts for intrinsic as well as extrinsic losses in the sample. Now, if I have two samples and determined the S02 value according to the way which Bruce has in his supplement to the FEFFIT course, I find two differing values for electrochemically prepared oxide (0.74) and crystalline gold oxide (0.92). This difference is independent of beamlines I measured and I can exclude quite safely that it is just a measurement error - it comes up with any spectrum I recorded on these systems. When discussing this with my colleagues, we interpreted the S02 difference as an indication of more disorder in case of the electrochemical system (which would well fit to my picture of the whole thing). BUT: Is there any physical reason to assign a difference in S02 (for "chemically equivalent" systems, where just the preparation is different) to a structural disorder? Regards, 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

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Windows Update
by Matt Newville 19 Apr '04

19 Apr '04

Hi Folks, I've posted a windows update that includes Bruce's latest Athena, and Hephaestus, that he described a week ago. It also has a couple other fixes: - a problem with runprog.exe got fixed so that running autobk,feffit, and feff6 now works correctly for directories that contain a space in their name. - the updater now includes two additional parameters that may help those people who were having problems with the updater timing out before downloading files. These are both in updates\updater.ini: timeout_connect is the time in seconds to connect to to http://cars9.uchicago.edu to read what the update level is and verify that a connection can be made. timout_download is the time in seconds to download a zip file. If you have problems with the updater, try increasing these numbers from their default values of 60seconds and 2400seconds. Sorry for taking so long on this. --Matt

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introducing Hephaestus ...
by Bruce Ravel 19 Apr '04

19 Apr '04

Hi folks, In his workshop he has handmaidens he has forged out of gold who can move and who help him in his work. ... With Athena, he [is] important in the life of the city. The two [are] the patrons of handicrafts, the arts which along with agriculture are the support of civilization. "Mythology", Edith Hamilton The big new feature in the latest release is a new program called Hephaestus -- in keeping with the Greek mythology theme. Hephaestus combines the functions of the old Atoms Periodic Table with a bunch of other small utilities based on the priodic table and on tabels of x-ray absorption coefficients. Hephaestus supercedes both the Atoms Periodic Table and the TkFormula programs, both of which are being retired. You should find that Hephaestus is a very handy tool both at home and at the beamline. Along with displaying edge and line energies, and computing absorption lengths of elements and compounds, Hephaestus offers tools for computing the absorption of ion chambers, displaying the anomalous scattering factors of the elements, and displaying chemical data about the elements. Here is a web page with descriptions and a few screenshots: http://leonardo.phys.washington.edu/~ravel/software/exafs/abouthephaestus.h… The Windows updater does not install shortcuts to the desktop or to the Start menu, so Windows users might want to do so by hand. The updater will put the hephaestus.exe and .bat files in the normal Ifeffit place and you will find the hephaestus.ico icon file there as well. It should be a simple matter to modify the desktop and Start menu shortcuts for the Atoms Periodic Table to launch hephaestus instead. If you do not know how this is done, post a question to the mailing list and hopefully someone will explain. For the unix users, there is an icon file for use on the desktop in the Ifeffit/lib/hephaestus directory when you unpack the source code tarball. The file vulcan.gif is the intended icon file. I hope that you will find Hephaestus useful and I look forward to hearing people's suggestions for improving it. 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/

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RE: [Ifeffit] S02-Interpretation
by Kelly, Shelly D. 16 Apr '04

16 Apr '04

Hi Matt > > Now, if I have two samples and determined the S02 value according to > > the way which Bruce has in his supplement to the FEFFIT course, > > How do you mean this? Is this the 'plot three curves of sigma2 v. > S02 curves for three different k-weights' again? I find this > approach puzzling and dangerous. I do not understand why the slope > (correlation) of sigma2 v. S02 should depend on k-weight in > any systematic way -- does anyone else know why it should?? > What you want is the S02 and sigma2 that gives the lowest > chi-square, not where these lines cross. I have found that usually there is a "larger than one would like" correlation between the amplitude and phase terms in the EXAFS equation. But the different terms have different k-dependencies. Low k-weights will give more weight to an accurate E0, whereas higher k-weights will give a more accurate deltar. Although the errors will be large. If you plot the dependence of these variables on the k-weight, or better yet use all three k-weights in the fit, you will find that the best-fit value is consistent with the one k-weight value but that the uncertainty is lower because you are distinguishing between the two coorelated variables by including the k-dependence in the fit. Shelly

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[HELP!] Athena and Artemis doesn't start
by mauro＠rulp.org 16 Apr '04

16 Apr '04

Hi to all, This morning the "story" started with some .TRAP files during an Artemis fit. From one of this I have understood the problem was again with conflicts between the compiled-by-hand horae version and Carlo's .deb (automatically installed) package. Here the ARTEMIS.TRAP file: # This file created at 10:32:53 on 16 April, 2004 # using linux, perl 5.008003, Tk 800.025, and Ifeffit 1.2.5 The following message was trapped by Artemis on a SIGWARN: Artemiswarn/home/mauro/.horae/stash/ARTEMIS.TRAPCODE(0x95e0a4c) at /usr/bin/artemis line 1491 main::__ANON__('Use of uninitialized value in concatenation (.) or string at ...') called at /usr/bin/artemis line 5809 main::set_degeneracy(1) called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x96c8228)','active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x96c8228)',1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1627 After this, I decided to reinstall everything. I have completely removed the previous software from "/usr/local" and I have used apt-get to reinstall horeae and ifeffit (also). The result is: Artemis and Athena doesn't start! These the errors: mauro@mac6npd2:~$ artemis Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: undefined symbol: PL_sv_undef at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/artemis line 49 Compilation failed in require at /usr/bin/artemis line 49. BEGIN failed--compilation aborted at /usr/bin/artemis line 53. mauro@mac6npd2:~$ athena Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: undefined symbol: PL_sv_undef at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/athena line 55 Compilation failed in require at /usr/bin/athena line 55. BEGIN failed--compilation aborted at /usr/bin/athena line 59. I really don't know what to do. I've tried different times reinstalling the ..deb package o recompiling the source. Please, help me! -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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Re[2]: a question about background refinement
by Stanislav Stoupin 15 Apr '04

15 Apr '04

To Matt: >Normally, you'd want to keep >Rbkg/Rmin below the 'first shell peak', which is sometimes difficult >to define for the asymmetric peak common with short metal-oxygen >distances, but if the peak is around 1.3Ang, the Rbkg/Rmin of 1.5Ang >seems like it might be too high. Can you get decent results with >a lower Rbkg/Rmin? No, I can not. 1.5A is around the minimum value in Chi(R) magnitude where the first peak can be separated from the others. However, the peak is a result of superposition of background, oxygen path and also the alloy structure. As for the correlation between Ru-O variables and the background parameters, they are somewhat correlated I think If I do not play with the rmin value and keep it equal to 1.0A these correlations are: delr_ru_o and bkg01_05 --> 0.5440 delr_ru_o and bkg01_04 --> -0.3878 dwf_pt_pt and bkg02_11 --> 0.3551 x_o and bkg01_01 --> -0.2856 delr_ru_o and bkg01_03 --> 0.2760 delr_ru_ru and bkg01_05 --> 0.2709 dwf_ru_o and bkg01_01 --> -0.2614 x_o and bkg01_02 --> 0.2600 dwf_ru_o and bkg01_02 --> 0.2595 delr_ru_pt and bkg02_11 --> 0.2562 x_o means the amplitude of Ru-O path e0 for Ru-O path is constrained to be the same as for all paths with Ru central atom To Jeremy: >You mention that the amplitude remains consistent at about 0.3. >However, what is happening to R and E0? Are these values also >reasonable? I have found that, on occasion, a negative DWF is telling >me that oxygen may not be the correct nearest neighbor. In these cases, >R and E0 are always anomalous for the metal-oxygen path. I have two e0 parameters in the model that correspond to ru and pt data sets (they are e0_ru and e0_pt) the same e0_ru I use for Ru-O path Typical values that they take are about: e0_pt = 7.2318013 +/- 1.0171952 (0.0000) e0_ru = -9.1526876 +/- 0.7730603 (0.0000) and this is consistent through all data that I have and also their values almost do not depend on whether I use rmin=1.0A or 1.5A the same I can say about Ru-O distance. Typical value is: delr_ru_o = -0.0899771 +/- 0.0406058 (0.0000) To Bruce: >I have a question for you. Are you trying to determine the oxide >content? That is, do you want to know what fraction of the Ru atoms >are in an oxide environment? Or are you trying to account for the >oxide so that you better measure the metallic component? My advisor (Carlo Segre) has already answered this question I just want to add that the observed amplitude of Ru-O path (0.3)is approximately in agreement with the number of atoms on the nanoparticle surface. This may indicate that all Ru atoms are on the surface and all they have oxygen bonds. Stanislav

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RE: [Ifeffit] crucial information
by SCHLEGEL Michel 177447 15 Apr '04

15 Apr '04

> the correct greek prononciation were > "hephaistos" which is the god of "smiths" > But this is from "old Europe", Yep, and he was the unfortunate husband of Venus. So Bruce, if you are planing some versatile companion software for "Hephaistus"... Best regards, Michel Schlegel

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RE: [Ifeffit] crucial information -oops
by SCHLEGEL Michel 177447 15 Apr '04

15 Apr '04

oops.. sorry, it's the Greek goddess Aphrodite > -----Message d'origine----- > De : SCHLEGEL Michel 177447 > Envoyé : jeudi 15 avril 2004 15:04 > À : 'XAFS Analysis using Ifeffit' > Objet : RE: [Ifeffit] crucial information > > > > > the correct greek prononciation were > > "hephaistos" which is the god of "smiths" > > But this is from "old Europe", > > Yep, and he was the unfortunate husband of Venus. > So Bruce, if you are planing some versatile > companion software for "Hephaistus"... > > Best regards, > > Michel Schlegel > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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crucial information
by Bruce Ravel 15 Apr '04

15 Apr '04

Hey, I've now been asked several times how to pronounce the word "Hephaestus". Although I am fairly confident that each of the people who asked owns a dictionary, here's some linkage to Merriam-Webster. The page includes a .wav file of someone saying it (click on the little red speaker icon). http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=hephaestus&x=0&y=0 ;-) 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/

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"FEFFs order" bug corrected in Artemis 0.7.003
by Stanislav Stoupin 14 Apr '04

14 Apr '04

From: Bruce Ravel <ravel(a)phys.washington.edu> >BTW, Does the new release of Artemis seem to address the many problems >you reported with your multiple data set, multiple feff calculation >fits? It does! I have just performed a couple of tests where I opened old-style project that had "incorrect" FEFF order: data_set1 FEFF0 FEFF1 FEFF4 data_set2 FEFF2 FEFF3 test #1 1. fit the data and saved as another project 2. opened the saved project no missing FEFFs were found nothing changed test#2 1. change data in the project 2. fit and saved as another project 3. opened the saved project again no missing FEFFs were found and no other suspicious behaviour was observed These things did't work before Stanislav

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RE: [Ifeffit] S02-Interpretation
by Kelly, Shelly D. 14 Apr '04

14 Apr '04

> To my knowledge, S02 accounts for intrinsic as well as > extrinsic losses in the > sample. Now, if I have two samples and determined the S02 > value according to > the way which Bruce has in his supplement to the FEFFIT > course, I find two > differing values for electrochemically prepared oxide (0.74) > and crystalline > gold oxide (0.92). This difference is independent of > beamlines I measured and > I can exclude quite safely that it is just a measurement > error - it comes up > with any spectrum I recorded on these systems. > > When discussing this with my colleagues, we interpreted the > S02 difference as > an indication of more disorder in case of the electrochemical > system (which > would well fit to my picture of the whole thing). > > BUT: Is there any physical reason to assign a difference in S02 (for > "chemically equivalent" systems, where just the preparation > is different) to > a structural disorder? > > Regards, > > Norbert Hi Norbert, I believe that the value for S02 should be the same in these two samples. But S02 is not the only amplitude term in the EXAFS equation. The degeneracy of the path, sigma2, and the step height normalization are also amplitude terms. One needs to be careful in processing the data so that the change in the amplitude between the two signals really belongs to the correct parameter. Here is a recipe for how I would try to solve the problem: 1st: Double check the step height normalization in Athena. 1) Make sure that Ezero is the same for both data set and that the data sets are aligned in energy. 2) Plot the xmu data along with the pre-edge and post-edge lines and check the step height that Athena reports...make sure it seems reasonable. 3) plot both chi(k) data sets with kweight of 1, and then 2 and then 3. You are looking to see if the change in amplitude between the data sets is the same for all k-range or if the ampliude changes more at high or low k. 4) you could also Fourier filter the data and do this again. If the change in amplitude is the same for all k, then the difference is because of SO2 or degeneracy or step height normalization. If the change in amplitude is more at high k than at low k the change is because of sigma2 term. If the change is more at low k than at high k then I would say different bkg curves or self absorption effects. 2nd: Say you think that the difference is due to a sigma2 term. I would fit both data sets with the same parameters for SO2 and different parameters for sigma2 for what ever paths you decide to include in your fit. If you want to prove that the change is a sigma2 and not a SO2 parameter then you do the fit using kweight of 1, and 2 and 3 all at the same time for both data sets, trying two different models, 1) where SO2 is different for both data sets but sigma2 is the same, and 2) another where sigma2 is different but SO2 is the same. You should see a difference in the goodness-of-fit parameters that is greater than one standard deviation. Using all three k-weights helps Artemis "see" the changes that you saw in Athena, by comparing the two data sets with the different k-weights. I just read Bruce's comment, If you think that the change should be in the coordination number then you should repeat the above models with the coordination numbers allowed to vary. To decouple SO2 and N you need to have more than one shell in the fit, otherwise they are exactly the same variable. H.T.H Shelly

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new Debian packages of horae-033
by Carlo U. Segre 14 Apr '04

14 Apr '04

Hello All: There are now new Debian packages of the latest horae available. Bruce, I noticed that you removed tkformula and apt in favor of the new combined application called Hephaestus. Hopefully I didn't miss any other big changes in the programs. The sources and binaries can be obtained at For the stable (woody) distribution deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ For the unstable (sid) distribution deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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a question about background refinement
by Stanislav Stoupin 13 Apr '04

13 Apr '04

Hello all, Recently, I was able to improve fitting results in one of my projects using background refinement/subtraction in some "strange" way. I have got reasonable results but I was not totally sure if that was a valid approach. So, any feedback is appreciated. Here is the story: The system I am working on is Ru-Pt fcc alloy in a form of nanoparticles which may be oxidized. There is a reason to suspect presence of Ru-O bonds in the system. For the moment I am doing only the first shell analysis and the model I am using includes a part that models alloy first shell structure and also Ru-O path. If I don't use the Ru-O path in my model all the alloy parameters that I get from the fit are reasonable but the fit works bad in low R region. In that region there is a broad peak around 1.3A. The rmin parameter which is responsible for background refinement is set to 1A ( the same value was used when I did initial background subtraction in Athena). What I found a long time ago is that the fit could be significantly improved if I add the Ru-O path in my model (all alloy parameters were even better in that case). However, the DWF of Ru-O bond always went negative (about -0.005). At the same time I got reasonable value for the Ru-O amplitude which was about 0.3. I attempted to get rid of the negative DWF value many times. For example, if I fixed or restrained the DWF to a reasonable value (0.01 is what I expect) it didn't help. Finally, I decided to play with background refinement and what I have done can be described as follows: 1. Set rmin to about 1.5 A 2. Fit with my model which included Ru-O path with fixed delr = 0 and DWF = 0.01 ( the Ru-O amplitude was allowed to vary). Backgound fitting was turned on. 3. Subtracted the background from the data 4. Moved rmin back to 1A and allowed Ru-O delr to vary (the DWF remained fixed to 0.01) 5. Fit again with no background fitting A very decent looking fit came out as a result. (Chi-square was improved) The Ru-O amplitude was about 0.3 (as expected) and I had the DWF set to 0.01. Thanks for you patience if you read it all the way through. My own impression of what I have done is that it looks very artificial and the fact that I use AUTOBK two times bothers me a lot. The second time it is supposed to remove all structural information below 1.5A (rmin value). However, with this approach I hope to get rid of the background that dominates the fine structure in the low R region (Ru-O scattering) using some preliminary knowledge about the compound. I will be happy to hear any point of view. Thank you in advance. If you are interested and want more details please let me know. Stanislav -------------------------------- Stanislav Stoupin Research Assistant/PhD student BCPS Department Illinois Institute Of Technology E-mail:stousta@iit.edu

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RE: [Ifeffit] a question about background refinement
by Kropf, Arthur Jeremy 13 Apr '04

13 Apr '04

Stanislav, You mention that the amplitude remains consistent at about 0.3. However, what is happening to R and E0? Are these values also reasonable? I have found that, on occasion, a negative DWF is telling me that oxygen may not be the correct nearest neighbor. In these cases, R and E0 are always anomalous for the metal-oxygen path. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Stoupin, Stanislav A. Sent: Tuesday, April 13, 2004 5:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] a question about background refinement Hello all, Recently, I was able to improve fitting results in one of my projects using background refinement/subtraction in some "strange" way. I have got reasonable results but I was not totally sure if that was a valid approach. So, any feedback is appreciated. Here is the story: The system I am working on is Ru-Pt fcc alloy in a form of nanoparticles which may be oxidized. There is a reason to suspect presence of Ru-O bonds in the system. For the moment I am doing only the first shell analysis and the model I am using includes a part that models alloy first shell structure and also Ru-O path. If I don't use the Ru-O path in my model all the alloy parameters that I get from the fit are reasonable but the fit works bad in low R region. In that region there is a broad peak around 1.3A. The rmin parameter which is responsible for background refinement is set to 1A ( the same value was used when I did initial background subtraction in Athena). What I found a long time ago is that the fit could be significantly improved if I add the Ru-O path in my model (all alloy parameters were even better in that case). However, the DWF of Ru-O bond always went negative (about -0.005). At the same time I got reasonable value for the Ru-O amplitude which was about 0.3. I attempted to get rid of the negative DWF value many times. For example, if I fixed or restrained the DWF to a reasonable value (0.01 is what I expect) it didn't help. Finally, I decided to play with background refinement and what I have done can be described as follows: 1. Set rmin to about 1.5 A 2. Fit with my model which included Ru-O path with fixed delr = 0 and DWF = 0.01 ( the Ru-O amplitude was allowed to vary). Backgound fitting was turned on. 3. Subtracted the background from the data 4. Moved rmin back to 1A and allowed Ru-O delr to vary (the DWF remained fixed to 0.01) 5. Fit again with no background fitting A very decent looking fit came out as a result. (Chi-square was improved) The Ru-O amplitude was about 0.3 (as expected) and I had the DWF set to 0.01. Thanks for you patience if you read it all the way through. My own impression of what I have done is that it looks very artificial and the fact that I use AUTOBK two times bothers me a lot. The second time it is supposed to remove all structural information below 1.5A (rmin value). However, with this approach I hope to get rid of the background that dominates the fine structure in the low R region (Ru-O scattering) using some preliminary knowledge about the compound. I will be happy to hear any point of view. Thank you in advance. If you are interested and want more details please let me know. Stanislav -------------------------------- Stanislav Stoupin Research Assistant/PhD student BCPS Department Illinois Institute Of Technology E-mail:stousta@iit.edu _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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[Ifeffit] Re: from I.Demchenko (PhD student at the Institute of Physics PAS)
by Bruce Ravel 07 Apr '04

07 Apr '04

Hi Iraida, I hope you don't mind that I CC my reply to the ifeffit mailing list. I have some suggestions for you, but I thought it might be helpful to you to see if anyone else has anything to contribute. (The attachments to Iraida's email included a couple of screenshots showing the plotting window with a very good-loooking fit. She also sent the artemis log file showing many of the numbers she quotes below.) On Tuesday 06 April 2004 12:12 pm, Iraida Demchenko wrote: > I have a problem with fitting of my data for 0.5 microns of Ge on > Si(001) substrate (grown by MBE). The spectrum for K-edge of Ge was > collected by TY mode. This sample is a standard for my next > fitting. >From this fitting (for 1 shell) I want to draw > So^2... But, if I apply a "trick" with k-weight determination as 1 > and So^2 value changing from 0.7 to 1.1 and repetition of this > operation for k^1, k^2, k^3, I get three parallel lines for > sigma^2(Ge-Ge) as function of So^2 :(. They aren't crossed in this > area. This is kind of surprising to me. I have used the three-lines trick many times and have never seen the situation of three parallel lines. I am a little confused how that is even possible. One might expect this trick to do strange things in the case of a first shell that is not well separated from higher shells, but my memory of Ge is that the first shell is well separated. Another situation that might lead to trouble is if strain induced by the substrate splits the first shell into two well-separated peaks. However, that does not seem to be the case for you either. 1/2 micron is (I think) thick enough so that the film should be bulk-like. Sadly, I am stumped. Has anyone else ever seen this? > On the other hand, I tried to fit my data (3 shells, k-w=2; dk=2; > Hanning; k(3.5-12.3)) and I've obtained: reduced chi-square=10.33; > R-factor=0.011; So^2=1.22 +/- 0.34; dr_1=0.0107+/-0.006; > sigma^2_1shell=0.0037+/-0.0019; sigma^2_2=0.0068+/-0.0033; > sigma^2_5=0.0096+/-0.0041(3 shell) (of course, that errors were > recalculated(following FEFFIT, p.44). I doubt about the obtained > value for So^2=1.22 +/-0.34. Within the error, of course, I can say, > that this value is in the range from 0.6 to1. But, the correlations > between variables are: amp (So^2) and sigma2_1: 0.916 :(; amp and > sigma^2_2: 0.498; amp and sigma^2_5: 0.49; sigma^2_1 and sigma^2_2: > 0.47; sigma^2_1 and sigma^2_5: 0.45.....all other correlations are > below 0.25. In the attachment there is a log file for this fitting, > as you can see sigma^2_3 is -0.0055+/-0.016 :(. > > Are there any other ways to determine our So^2? Or these actual results > (So^2=1.22) we can consider as good? What do You think about this fit? First, as you say, your value for S02 is not unreasonable in that the error bar covers a value that one might expect. Still, you are right that 1.22 is an oddly large best fit value and suggests that something else might be happening in the data. Second, I wouldn't be so concerned about the high correlation between S02 and sigma^2. It's normal. Here is a nice short piece by Matt about correlations: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000713.html The rest of thread might be of interest to you, as well. At another point in that thread, there is some discussion of how the normalization is done. Have you examined that carefully? If the post-edge line intersects E0 at an oddly low value, then the edge-step used in the normalization might be rather too small. This is certainly a possibility in fluorescence data where the region after the edge sometimes sweeps upward. In that case, the normalization range is such that the regressed post-edge line can be below the data near E0. I explained this in some more detail at http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000711.html That could be the cause of a best-fit S02 that is larger than 1, That's my best guess, given that I have not seen the mu(E) data, for what is happening. I was bit confused by thing about sigma^2_3. I saw in the log file that it was, as you said, negative. But none of the sigma^2 values for the paths were negative. It wasn't clear how that sigma^2 value was being used. Hope that helps, B P.S. I could tell from the log file that you sent me that you are using a *very* old version of Artemis and presumably of ifeffit as well. You may want to download the latest ifeffit installation package from http://cars9.uchicago.edu/ifeffit/download.html and then let the automatic updater bring your computer completely up to date. -- 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/

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simultaneous fitting of multiple data sets in ifeffit
by Stanislav Stoupin 05 Apr '04

05 Apr '04

Hello! First of all I would like to thank Bruce for answering my questions. As a beginner I very much appreciate your help. Now I am trying to compare my results using two possible ways of doing EXAFS analysis : 1. Artemis 2. ifeffit command line (loading input files) Here is my question: When I use ifeffit commands it is not clear to me how to assing different kmin/kmax (rmin/rmax) values to different data sets in a multiple data set fit. My current understanding of the problem is as follows: As ifeffit documentation says all variables are global. At the same time ifeffit tries to evaluate all parameters of feffit() command first and does the fit only after determination of kmin kmax rmin rmax. What happens is that the last given values are assigned to these variables. Could somebody show me an example of a script that allows to assing different values of kmin kmax rmin and rmax for different data sets? Stanislav

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A question about the new Artemis version
by Stanislav Stoupin 31 Mar '04

31 Mar '04

Hello all I just upgraded to the newest horae-031 package It looks to me that the new Artemis version (0.7.001) doesn't have that nice button "use previous background" anymore. If I am not mistaken the button allowed to subtract background fitted previously. Am I? Is it somehow hidden in the new version? Thank you in advance Stanislav

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parameters in Athena's output files
by Bruce Ravel 23 Mar '04

23 Mar '04

Hi folks, Recently two separate people requested that Athena write a summary of the various parameters into the header of the column output files for mu(E), chi(k), and so on. That's a great idea and the next version of Athena will do this. In the interim, I wanted to point out a feature of Athena that some of you may not be familiar with. At the bottom of the Edit menu is a submenu called "Write a report." A report is a summary either of all groups or of the marked groups. There are three different output formats, but I suspect that most people will prefer the Excel spreadsheet format. Rather than explain it further, I'll leave you to give it go. The .xls file that gets written should be readable by any version of Excel as well as OpenOffice, Gnumeric, and Kspread. HTH B P.S. The final option in the "Edit->Write a report" menu is a peculiar output file that is of interest to folks who use Athena to process their data but who prefer XFit to Artemis for the analysis. -- 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/

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uncertainties
by mauro＠rulp.org 23 Mar '04

23 Mar '04

Maybe this is a "newbie" question, but I have noticed that in artemis's new version after the uncertainties there are values in round parentesis. What they mean? Thanks, Mauro.

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Confirmation
by jawad shah 23 Mar '04

23 Mar '04

Dear Sir, Is i am registered on your web side. With best regards Jawad __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com

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Re: Athena Suggestions
by Bruce Ravel 22 Mar '04

22 Mar '04

Dave, I hope you do not mind that I am answering via the mailing list. The answer I have planned will be something that I think others will find useful. On Saturday 20 March 2004 03:30 pm, Barton, David (DG) wrote: > LOCATION OF Eo > -Attached is two Ga XAFS spectra in an Athena file project. Look > closely at the chosen Eo positions, I think you would agree that the > choice is not near the maximum of the first derivative. These data > sets both have a fairly reasonable signal/noise so that shouldn't be > the source of the error. > > Athena Report of Eo: > --Ga_035 (10372.6 eV) and Ga_32-8 (10374.1 eV) > ==Eo difference = 1.5 eV > Using another plotting program: > --Ga_035 (10373.3 eV) and Ga_32-8 (10373.5 eV) > ==Eo difference = 0.2 eV > > I understand that using the maximum in the first derivative is just > an approximation of the Fermi Energy so the absolute value may not > be so meaningful. However, we often use relative changes in the > position of Eo as an indication of structural changes in our > catalytic materials, so it would be helpful if Ifeffit was slightly > more robust and precise in choosing the Eo value. Maybe you could > consider incorporating a "smoothing" parameter which would help > reduce the noise in the first derivative or some other algorithm > which makes a better choice in the presence of some noise in the > data. For the sake of everyone else, I'll mention that the data Dave sent me had a slightly ambiguous e0 because the peaks in the first derivative were split into two peaks about the same height and about 1/2 volt apart. In one case, Ifeffit's algorithm for identifying the peak came up with a point a bit to the left of the two peaks and the other time a bit to the right. In neither case did Ifeffit (and hence Athena) pick one of the points at the peak. These choices to the left and right of the peaks result in the unphysically large energy separation that Dave is asking about. My initial response to questions like this is that it is rarely wise to blindly trust a program -- ours or anyone else's -- to do the right thing all the time. Just because we get one spectrum right or someone else gets another spectrum right is not sufficient reason to always trust any program. If you need it to be right, check and make sure it is right. That was fine advice -- possibly even tautological. But it wasn't very practical. The software really should work hard to get it right as often as possible. You suggest smoothing. That would probably work pretty well in this case. Indeed, it woul probably result in choosing a value between the two peaks. That's closer to correct and would probably at least be more reproducible between spectra than what happened with your data. But it would not be a panacea. Look at Zr 0+ some time. The maximum in the first derivative is more than 10 volts above the Fermi energy. Smoothing would not fix the "maximum in the first derivative" algorithm in that situation. So even with a more robust algorithm, you would be well served to be sceptical. I think the solution to your problem is to be a bit more hands-on and to make use of more of Athena's features. I typically use Athena's preprocessing features to handle ensembles of related data. The details of what you might do vary from situation to situation, but here is the outline: 1. Import one scan. This is going to be your "standard" against which the rest will be compared, so it should be a trustworthy one. Calibrate it by hand using the Calibration option in the Data menu. Play around with the background removal and FT parameters until you are reasonably happy with the data processing. 2. Use the "Open many files" option in the Files menu to import several more of the data files in that ensemble of related data files. 3. When the column selection dialog comes up, make sure that the columns are properly selected. Before hitting the OK button, hit the button that says "Set preprocessing parameters". This will expand the column selection dialog, showing a new menu and bunch of checkbuttons. 4. From the menu labeled "Standard" select the first data file that you read in. This will activate all the checkbuttons below. Now select the buttons for "Align to the standard" and "Set parameters to the standard". 5. Now click the OK button. As each data file is imported, it will be aligned and the parameters, including e0, the background parameters, and the FT parameters, will all be set to the values you settled on for the first data set. Magic!! If all went well, then each data set will be calibrated the same way as the first one and the background and FT parameters will be well set. The caveat is that the automated alignment does not always work well. A quick plot will let you know if it failed and you need to go back and align by hand. But with data that is low noise and similar, it tends to work ok. Depending on your data set and what you are aiming to do, you may need to do some variation of what I described above. Of course, a change in Ifeffit's algorithm might still be in order. But, in any case, I encourage you to resolve your e0 problems by explicitly examining one data file and using preprocessing to make the rest consistent with the first. HTH, 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/

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Re: [Ifeffit] beeps?
by SCalvin100＠aol.com 18 Mar '04

18 Mar '04

It beeps for me on Windows XP, although it's pretty subtle (more a burp than a beep). --Scott Calvin Sarah Lawrence College

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beeps?
by Peter Southon 18 Mar '04

18 Mar '04

>When this happens, is anything written to the screen? Does Artemis beep and >tell you to look at the ARTEMIS.TRAP file? If either is the case, I will >need to see what they say. Bruce, did you say Artemis beeps on errors? It doesn't seem to do that on my WinXP machine. I know its a simple thing (I have a simple mind), but it would be a great prompt to look at artemis.trap. Is there a sound problem with porting to Windows? Cheers, Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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