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

new development version of Artemis
by Bruce Ravel 07 Sep '04

07 Sep '04

Hi, For those interested in the development version of Artemis, I released a new source tarball this morning. It can be found on SourceForge or on my website. There are no changes to the stable version of Artemis or to the other programs. Here is a quick summary of the changes to the development version: http://sourceforge.net/project/shownotes.php?release_id=266237 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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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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