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

Artemis and atoms.inp/feff.inp files
by Bruce Ravel 14 Sep '04

14 Sep '04

Hi folks, This morning, a user pointed out an interesting problem in any version of Artemis up to and including 0.7.010. I thought I should mention it on the list because I would be surprised if no one else runs into this particular issue. Artemis currently does no error checking to determine if an atoms.inp file is actually an atoms.inp file. Similarly Artemis does no error checking to confirm the feff-ness of a feff.inp file. This is a problem because there are separate menu entries in the File menu for importing atoms.inp and feff.inp file. Different things happen when you select these two items. If you choose the wrong kind of file, Artemis will get confused trying to read one file type as the other file type. This will lead to lots of error messages and may result in project files that cannot be saved and re-read by Artemis. Currently there is no better solution than to be sure that, when you intend to import a feff.inp file. you select a feff.inp file and, when you intend to import an atoms.inp file, you select an atoms.inp file. If you make this mistake, the best solution may be to quit Artemis and try again. Clearly this is an untenable situation. Building enough intelligence into Artemis to distinguish between atoms.inp and feff.inp files is now high on my to-do list. 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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iPot Exceeded
by Barton, David (DG) 09 Sep '04

09 Sep '04

Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with most of my bug reports and suggestions for change. The implementation of reading CIF files directly into Artemis and Atoms makes going from crystal structures in a database to simulated EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question. Artemis 0.7.010, with FEFF6L on WinXP machine: What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique elements? Attached is a CIF file containing a Au cluster that has nine different elements, which is easily imported in to Artemis using Bruce's new import feature. When imported this compound has ~150 distinct atomic positions in the unit cell. Running FEFF within Artemis with this Atoms.inp file results in the error message: "Feff 6L.02 Unique potential 8 not allowed. Must be between 0 and 7 8 15 P Fatal Error: at RDINP" It appears that FEFF can only handle 8 unique elements at a time. No problem, I would like to ignore the H atoms anyway. Any suggestions on how to handle this within Artemis/FEFF? Otherwise, there is the obvious workaround, I can manually edit the CIF or Atoms.inp and eliminate the H atoms from one of those files and then run FEFF. It would be helpful if the Atoms input page would allow the user to sort the atomic positions by element and then select a range of these atomic positions and delete them all. Thanks Dave ipot Z element 0 79 Au 1 7 N 2 6 C 3 5 B 4 9 F 5 8 O 6 1 H 7 79 Au 8 15 P <<Au5N.cif>> David Barton The Dow Chemical Company Email: dgbarton(a)dow.com

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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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