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

contributing to the Ifeffit family
by Bruce Ravel 28 Oct '03

28 Oct '03

Hi folks, On occassion, the topic comes up of contributions to the ifeffit universe from other people besides Matt, Sam, and myself. Indeed, there have been some excellent examples centered around this mailing list. For example, a few months ago, we had a really useful discussion, including code examples, about rebinning data. As a somewhat smaller example, two fine souls responded to my request for some example data from NSLS X10C. Last week, Scott asked this: Oh, and I've been thinking. [Matt and Bruce] spend enormous amounts of time on this software, and it's a big contribution to the field. As I explained above, I'm not willing to help on the coding end, but I'd like to support the project in some way. I know Bruce has mentioned the need for more/better Athena and Artemis documentation...I was hesitant to suggest I help with that until I got more familiar with the software, but I think I'm now getting to that point. So Bruce--what is the most pressing need in that area? I'll see if I can start devoting some time to it... I thought I would answer Scott's question in public. Who knows, maybe I'll start something ;-) I will divide this up into a few categories. If you dig into any of these, we should probably communicate so that you produce something in a format that will be useful to us developers. Pure documentation ================== 1. Edit and expand upon the documentation that exists for Athena. The Athena doc is actually in pretty good shape. Most parts of the code are at least mentioned in the doc. If you are not familiar with the POD markup that is used in Athena's docs, don't worry. If you do some significant editing, I'll be happy to touch up the mark-up. 2. The Artemis document needs serious work. Pick a topic that interests you (or one of the unwritten topics in the current document) and start writing. You don't have to write in Latex. If you write in Word or some other format, all I'd ask is that you not format what you write too heavily and that you provide me with external copies of all images in appropriate formats. 3. Write a FAQ (frequently asked/answered/anticipated questions). Documentation by example ======================== One of the neat (IMHO, anyway) ways that I have documented Athena is the collection of demo projects, which are just normal Athena projects with extensive commentary in the Journal area. 1. Make more Athena projects. Improve upon the ones that are already there. 2. Make some nice Artemis projects. Even better, make a sequence of Artemis projects which demonstrate the steps one might take in building a sophisticated fitting model. Programming and related chores ============================== If you are inclined to deal with code, but don't necessarily want to dive into Athena or Artemis, here are some smaller projects. 1. Write an object-oriented module in Perl for accessing Spec data files. I could then use this in Athena. 2. Volunteer to maintain and build the Windows distribution and updates. 3. Collect examples of data from every dedicated XAFS beamline in the world. (Really, I mean it, every one.) Figure out which ones can be read by Ifeffit and which cannot. Figure out how to preprocess the ones that aren't read properly by Ifeffit and explain to us how to recognize them and how to preprocess them. 4. Think up a battery of tests. Subject Athena and Artemis to those tests soon after (or even prior to) every release. Let me know about any problems. Web-based projects ================== 1. Set up a web site for a FAQ which allows searching the FAQ for keywords. 2. Set up a web page which indexes the Ifeffit mailing list archives and allows searching by keywords. 3. Set up and administer a Wiki so everyone can participate in the process of documenting Ifeffit, SixPack, Athena, and Artemis. 4. Set up and administer a community discussion board. My inclination would be to use Slash (http://slashcode.com) which has a comination of features that I think could provide a valuable service to the XAFS community. 5. Collect and organize new material for the databases that Matt maintains which contain atoms input files and standards spectra. Well, that ought to be enough suggestions to get anyone started. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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questions
by J. M. An 28 Oct '03

28 Oct '03

On Monday 27 October 2003 03:10 pm, J. M. An wrote: >/ Dear IFEFFIT helper, />/ />/ I am a novice of IFEFFIT and would like to ask some questions about />/ fitting variables used in the program. />/ I've been trying to fit my FEFF 8 calculation result to an experimental />/ data for a bulk compound CdSe. />/ Essentially, the fitting variables, S02 and DW factor (the correlated />/ Debye model) for the first-shell, />/ are used for the fit. I can manage to fit quite nicely with those />/ variables, but the problem is that I want to use the values />/ of the resulting fitting variables as input for CdSe quantum dot />/ calculations. />/ />/ Normally, S02 and Debye keywords in FEFF are global paramaters, not />/ restricted to a single shell, so there seems to be />/ no way that I can put the fitting values obtained from the fit into new />/ FEFF calculations. />/ I was wondering if someone has experience to use bulk fitting values as />/ input in a new FEFF calculation. / I don't think I quite understand what you want to do, but here are a couple pieces of advice: 1. It is my strong preference never to introduce S02 or sigma^2 into the feff calculation when I am doing exafs analysis. It is much easier and much less confusing to use S02=1.0 and all sigma^2=0 in the feff calculation. That way, any values that you get for those parameters from a fit using ifeffit are absolute numbers and do not require that you remember what you did in feff in order to interpret the ifeffit result. 2. I do think that redoing the feff calculation might be useful at some time during the fit, but only if I have reason to believe that the *structural* parameters used in the feff calculation were in error relative to the real material. If the distance between atoms in the real material are quite different from what you used in the feff calculation, then you might worry that the phase shifts and scattering amplitudes are not as good as they might be. Given all that, I am not sure what you hope to accomplish by your new feff calculation. Hope that helps, B *********************************************************************** Thank you for the advice. The idea behind my research is (1) to extract information S02 and Sigma2 by fitting my feff result to experiment in crystal CdSe. (2) then to use this information to perform feff calculations for quantum dots CdSe of a certain shape. In other words, the info in (1) will be used as input to quantum dot calculations in (2). The reason is that no one knows how the surface terminates in the dot. To this end, I need to know reasonable fitting values of S02 and Sigma2 to be used in a feff input file. Suppose that I have obtained S02 and Sigma2 by doing (1) only for the first shell, leaving all other shells intact. (This is because in crystal CdSe, our calculated FEFF chi(k) using correlated Debye model differs from experiment for large k.) However, my problem is how we put these fitting values in (2), since SO2 and Sigma2 are global to all paths in Feff. Another complication may be that in (2) I am performing a set of calculations for different Se absorbing atomic sites. At the end, add all contribution from different Se sites to total chi(k), which is exactly what experimentalists measure. That is why I need to put resonable S02 and Sigma2 before I essentially perform quantum dot calculations. I will appreciate any further advice of yours on this, and let me know if this is not sufficient for you to understand what I intend to do. Joon Lawrence Berkeley National Lab

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questions
by J. M. An 27 Oct '03

27 Oct '03

Dear IFEFFIT helper, I am a novice of IFEFFIT and would like to ask some questions about fitting variables used in the program. I've been trying to fit my FEFF 8 calculation result to an experimental data for a bulk compound CdSe. Essentially, the fitting variables, S02 and DW factor (the correlated Debye model) for the first-shell, are used for the fit. I can manage to fit quite nicely with those variables, but the problem is that I want to use the values of the resulting fitting variables as input for CdSe quantum dot calculations. Normally, S02 and Debye keywords in FEFF are global paramaters, not restricted to a single shell, so there seems to be no way that I can put the fitting values obtained from the fit into new FEFF calculations. I was wondering if someone has experience to use bulk fitting values as input in a new FEFF calculation. Joon Lawrence Berkeley National Lab

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NSLS X10c
by Bruce Ravel 24 Oct '03

24 Oct '03

Hi folks, Last week when I was at NSLS, I had a conversation with someone about his difficulty reading data measured at beamline X10c into Athena. Unfortunately, I cannot remember with whom I had that conversation. The bottom line was that ifeffit was getting confused figuring out where the header ended and the data began in X10c's data file format. I am willing to make X10c's format a special case in Athena, but I will need some examples if I am to do so. If someone can send me a few example data files measured at X10c, that would be helpful. Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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data files for Athena
by k-kupiecki＠northwestern.edu 22 Oct '03

22 Oct '03

Hi, I'd like to start using Athena and Artemis to do some feff- fitting to my data but I'm having some problems loading in my two column data files (E (keV) & Intensity (Flourscence signal/reflectivity detector) ) of the spectra into Athena. I get the following message when I try to load the data file: ************ This file: c:/My Documents/25min_trying.txt contins data that are not monotonically increasing in energy. (check data points 101) Athena cannot import data in this state. You may sort these by energy, discading repeated points, or you may simply discard these data. ************ *If I select sort, Athena "finishes" and has the comment Error: Runtime exception I don't think there are any duplicate energies in my spectra... to give you an idea here are the first couple lines of my text file: 11.8946 0.135782452 11.8951 0.137828398 11.8956 0.137274903 11.8961 0.137603924 11.8966 0.136993206 11.8971 0.135301602 11.8976 0.139005468 Is there are particular format I need to have this file in? Thanks, Kristine Witkowski Northwestern University

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Dragon NaturallySpeaking and Athena/Artemis
by Adam Webb 19 Oct '03

19 Oct '03

Dear Ifeffit users, I have begun using Dragon NaturallySpeaking with programs such as Ifeffit and specifically Athena and Artemis. Due to strain/decay of the tendons of my wrists I have been trying to type less. I have had mixed success with Dragon NaturallySpeaking. I am using Dragon NaturallySpeaking Professional which has a large vocabulary and allows for scripting. There are times when the dictation works very well, and times when it does not work at all. I assume that as I train at it it will get better. One of the key things is that you have to know what you want to type before you type. And it works much better if you can simply talk and say a complete sentence without any pauses. My problem is that I don't always know what I'm saying even as I am saying it :-) Using the program is as much self training how to talk to a machine as it is training the machine how to understand you. Dragon NaturallySpeaking has two basic modes. Dictation mode, which I'm using to dictate this letter, simply writes whatever you say directly into the application. In this mode the program is replacing the keyboard. Command mode on the other hand, sends particular keystrokes with a verbal command. For example if I say the command "file", the file menu will be activated. I can then select the desired option. In this case Dragon NaturallySpeaking is simply sending the keys "alt+f" to the application. By writing scripts I can create commands to send whatever key combination I wish. These can be quite simple as above or complex. Athena and Artemis are quite mouse intensive. But I have begun making scripts for some of the most common commands that I use. For example, open and close project. I have also created scripts to click on the graphing keys. I don't think there are shortcut keys for these functions (?) so I had to be more creative. By using a mouse capture function to get mouse position, I could create a script to move the mouse over a button and click it. For example the command "current E" moves the mouse over the button E under the 'plot current group in' section and clicks it. So far scripting this way seems to work quite well. The difficulty arises with correction. As you dictate mistakes are made. This may be because Dragon NaturallySpeaking misunderstands you, or you have spoken word that is not in its vocabulary. It is important to correct Dragon NaturallySpeaking in order for it to learn how you speak and learn new words. This is typically done by using the "correct that" command. This brings up a dialog window which you can then use to enter the word that you meant. Once you select the word that you want then the program corrects the word in the application. However, this does not work very well with many applications including Athena and Artemis. This appears to be a failing of Dragon NaturallySpeaking. Its correction feature works very well with the included DragonPad application and mostly well with Microsoft Word but other applications are hit or miss. One of the difficulties is non-standard shortcut keys. For example, if in the application control-c does something other than copy. In this case it is necessary to write a script specifically for that application which overrides what the "copy that" function does. If anyone has any interest in using Dragon with Athena and Artemis or any other application, I would be happy to help them as I can. Or just to talk about program. I'm just learning the program myself and there is very little official support for scripting. Cheers, Adam ------------------------------------------------------ M Adam Webb Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

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Tk804.025_beta
by Bruce Ravel 15 Oct '03

15 Oct '03

Hi everyone, Guoqiang Pan has reported problems getting perl/Tk compiled and installed on his Red Hat system. Matt and Shelly both suggested that the problem was an unset environment variable and they suggested a solution. Guoqiang has told me privately that the suggestion helped and that he was then able to compile perl/Tk. Yay! He followed Matt's suggestion of using perl's CPAN interface for installing perl Tk (i.e. do "perl -MPCAN -e shell" at the command line, then "install Tk" at the cpan> prompt). This is a fine way of installing things, but Tk is a little bit different from most perl modules in that it's purpose is to draw things on the screen using X windows. X windows has some quirks and Guoqiang ran into a common stumbling block. The installation using the CPAN interface was proceeding properly until it got to the "make test" stage of the installation, which is when a bunch of tests are run to verify that the modules were built correctly. Most of the tests involve drawing things on the screen -- unsurprising since Tk is a GUI widget set. If you are logged in as a normal user, then you, the normal user, own the X windows process and only you or those to whom you have specifically granted permission can draw on the screen. Even root cannot do so unless you allow it. So, if you became root to run the CPAN interface by typing the "su" comand or the "sudo" command, you may not be able to successfully run the "make test" stage. To allow the "make test" thing to work, you need to execute the following command BEFORE becoming root and running CPAN: xhost + localhost This allows any user logged into your computer to write to the screen under X windows when you own the X windows process. Thus, it should also allow the "make test" stage to work. Alternately, you can log out as a normal user and log back in as root. Then root will own the X windows process and the "make test" stage of the CPAN installation or Tk should proceed without a problem. The good news is that once you get Tk installed, you almost certainly will not need to update it the next time that you update Athena and Artemis. The other good news (but not for Red Hat users apparently) is that installing from an RPM sidesteps this whole issue. I use SuSE (which I have long prefered to Red Hat -- two thumbs up for German engineering!) and its perl/Tk rpm works just fine. Hope that helps, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Tk804.025_beta
by Kelly, Shelly D. 14 Oct '03

14 Oct '03

> So what did you do for perl/Tk? Did you install from a supplied RPM? > No, I didn't install perl/Tk from an RPM. I looked for one for RedHat and didn't find it. So I just grabbed a Tar ball from CPAN. It looks like I'm using version 800.025. Shelly

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RE: [Ifeffit] Tk804.025_beta
by Kelly, Shelly D. 14 Oct '03

14 Oct '03

> On Tuesday 14 October 2003 04:02 am, Guoqiang Pan wrote: > > Dear ifeffit colleagues, I would like to install the Linux version > > for Artemis in my RedHat8.0 system, as suggested in download page it > > should install first pgplot, ifeffit, and the latest version of > > perl/Tk. The first two are OK, but for perl/Tk I had some problem. I > > downloaded Tk804.025_beta.tar.gz, and unzipped the file. Using perl > > Makefile.PL to produce the Makefile file. But after type make, I had > > the problem: [root@localhost Tk804.025_beta2]# make Makefile:95: *** > > missing separator. Stop. > > > > I had tried other versions for perl/Tk, but the problem is the > > same. Please help me to solve it. Thank you very much. I attached > > the Makefile and Makefile.PL.log , the file produced after perl > > Makefile.PL > Makefile.PL.log > On this same subject, RedHat 9.0 has a broken perl installation. The environmental language variable is set incorrectly. The result is a similar error message. Using tcsh type "echo $LANG" the result should be "lang_us". You can set this variable by typing "setenv LANG lang_us". www.linuxforum.com/forums/index.php?showtopic=1481&view=new Gives some more details. I just recently installed all of these same packages on a new RedHat 9.0 system. -This was the only bump that I ran into. Shelly

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Tk804.025_beta
by Guoqiang Pan 14 Oct '03

14 Oct '03

Dear ifeffit colleagues, I would like to install the Linux version for Artemis in my RedHat8.0 system, as suggested in download page it should install first pgplot, ifeffit, and the latest version of perl/Tk. The first two are OK, but for perl/Tk I had some problem. I downloaded Tk804.025_beta.tar.gz, and unzipped the file. Using perl Makefile.PL to produce the Makefile file. But after type make, I had the problem: [root@localhost Tk804.025_beta2]# make Makefile:95: *** missing separator. Stop. I had tried other versions for perl/Tk, but the problem is the same. Please help me to solve it. Thank you very much. I attached the Makefile and Makefile.PL.log , the file produced after perl Makefile.PL > Makefile.PL.log Besr Regards, Guoqiang Pan

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odd Athena behavior on file import
by Bruce Ravel 14 Oct '03

14 Oct '03

Hi folks, An odd situation was pointed out to me this weekend that I wanted to mention here on the list. I see the problem I'll describe below on both Windows and linux and I presume it is a problem on all platforms. The "Open many files" dialog in Athena is very handy for importing large numbers of data files. However, there is a strange interaction between this dialog and folders with apostrophes in the folder name. As an example, suppose I put my data file in a folder called "Bruce's Folder". If I try to read that data file using the many-files dialog, I get a strange pop-up error message stating that the data file is a directory and refusing to import the file. Some additional and inscrutable error messages are written to standard output. Interestingly, the single data file dialog has no such problem. Thus, if you put your data in a directory that has an apostrophe (such as "Bruce's Folder") you will not be able to use the many-file import dialog. The two options are to avoid apostrophes in directory names or to read in the data one-by-one. This seems to be a bug in something from the standard perl/Tk library and not in my own code. I'll contact the appropriate person, but I cannot guarantee a fix any time soon. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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problems with deglitching in Athena
by Carlo U. Segre 09 Oct '03

09 Oct '03

Hi Bruce: I have been using the single point deglitching in Athena and I find some strange behavior. It seems that the only thing that counts is the horizontal cross hair. This needs to be right at the vertical position of the point to be selected. The vertical cross hair does not seem to matter. This is sort of counterintuitive and it took me a while to figure out that the program was not just selecting random points on me. Perhaps, if this is a feature of PGPLOT, it should be docmented. I am using the latest version of IFEFFIT and horae on Linux. 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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30 element detector data in athena
by Vivek S. Murthi 07 Oct '03

07 Oct '03

Hi Matt, Bruce.. Athena could not open files from NSLS beamline X10C vax machine which has data in the form of .XFS. So, I converted it to *.dat and made it look like a dat file from NSLS beamline X 11a. Athena doesnot give me any prompt for incompatability but it simply crashes and closes. The data I have is from a 13 element detector, so there are about 38 columns of data. I am not sure if this would make Athena crash. If So, do you have any suggestions to overcome this. thnks vivek Vivek S. Murthi Graduate Research Assistant 419 Egan Center Northeastern University Boston, MA-02115 Phone: 617-373-8949 >

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Slight Problem with the new ARTEMIS
by Norbert Weiher 07 Oct '03

07 Oct '03

Dear Friends, I found a slight problem with the new ARTEMIS - I use the latest package for ifeffit (1.2.3) and HORAE (0.24). When you do a fit and look at the fit results for the current fit it seems that the program does not update all fit statistics the first time you do a fit. For example, when I switch from a single-shell fit to a dual-shell mode (from 4 to 8 variables), I get still 4 variables in the first run. When I re-calculate, it updates everything correctly. It's just for the number of variables - the rest seems to be updated in the first run. By the way: The chi-square maps are doing well. I am at the state of applying them to my systems. The GUI is horrible still, but the algorithm works. Thanks again to Matt for coding the library which does this work for me :) Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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Feff6l on Windows
by Matt Newville 29 Sep '03

29 Sep '03

Hi Everyone, The Feff6l executable included with the Ifeffit 1.2.3 windows installer is broken. The source is OK (and I expect the version of feff6l in Carlo's new debian packages too), but it looks like an older, broken version of the binary got included with the 1.2.2 windows distribution in late August. Anyway, I have a fixed version of feff6l.exe that runs correctly. But since running feff on Windows has always been a pain -- requiring you to use the DOS command shell -- so I also added a program (runfeff6l.exe) that pops up a file browser pops up so that you can select a feff.inp file (doesn't need to be called feff.inp, either) and will run feff6l for you. This is not a complete Feff GUI, but it is easier to use than the older executable. The feff6l.bat file and the 'feff' shortcut now point to this program. Since there were questions about (and problems with) the automatic updater, I have not yet made this an 'update'. I'd like to hear some feedback (either here or by private email) on how to deal with such small changes. Forcing people to downlod an install another 28Mb setup.exe seems sort of silly. Some of the options I see are: 1. assume the updater is working for most people, and just make this an automatic update. 2. scrap the automatic updater altogether, and just make this a new Ifeffit version. 3. make a separate installer for Feff6L. Any other suggestions are welcome. If you have Ifeffit 1.2.3 installed and want to try the new Feff6l, follow these instructions: 1. download http://cars9.uchicago.edu/ifeffit/updates/ifup_002.zip 2. unzip this into your main Ifeffit directory (probably C:\Program Files\Ifeffit or C:\Ifeffit ) 3. IMPORTANT: after unzipping this file, double-click on make_bats.exe This will re-make the batch files and shortcuts that run the programs. 4. If you're interested, more details can be found in IFEFFIT_DIR\updates\readme_002.txt For now, I'll leave this version of Feff6 in this zip file, so that you can test it out if you want but aren't forced to do so. If the consensus is to make this a regular update, I can do that easily. If having feff6l is important to you, please let me know whether these binaries work for you. Any feedback will be greatly appreciated. Thanks, --Matt

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new ifeffit and horae packages
by Carlo U. Segre 28 Sep '03

28 Sep '03

Hello All: After some time being unable to work on this (I skipped a few releases), I have Debian/Linux binary and source packages for ifeffit 1.2.3 and horae 024 for both the stable and testing releases of Debian. I can also make rpms of the two even though I have not tested these. The Debian packages can be accessed with the following lines in the /etc/apt/sources.list file. # X-Ray Software Archive deb http://fermi.phys.iit.edu/debian/woody binary/ #deb http://fermi.phys.iit.edu/debian/sarge binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ #deb-src http://fermi.phys.iit.edu/debian/sarge source/ Note, the testing archive has been commented out. Just uncomment it and comment the stable (woody) lines. Cheers, -- 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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IFEFFIT error messages
by SCalvin100＠aol.com 26 Sep '03

26 Sep '03

Hi Matt, Bruce, et al., Does Artemis somewhere provide any clue as to where the error was found when it says "Fit aborted due to errors in parameters and math expressions"? FEFFIT used to highlight the last line successfully read, which was helpful for finding unbalanced parentheses and the like. But I don't see an equivalent message here. --Scott

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ifeffit 1.2.3
by Matt Newville 19 Sep '03

19 Sep '03

Hi Everyone, I've just posted Ifeffit version 1.2.3. As with earlier versions in the 1.2.x series, this is a bug-fix release. The changes are: 1) setting 'path_index' now causes the given path to be the 'current path', so that 'reff', 'degen', and any parameters that might depend on them are automatically updated. 2) spline() now passes all of the arguments to pre_edge() correctly. There is now an updater program for Windows is now available. If you already have 1.2.2 installed, you do not need to download the 30Mb full installation, just the 2Mb program ifeffit_update-1.0.exe from either http://cars9.uchicago.edu/ifeffit/download.html or https://sourceforge.net/project/showfiles.php?group_id=80919 Once installed, the updater program will automatically run just before all Ifeffit applications, checking whether updates are available and installing them if desired. This should make it a lot easier to keep up-to-date with the latest versions of Ifeffit, athena, artemis, sixpack, etc... If you have any questions or trouble, let me know, --Matt

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Re: Ifeffit Digest, Vol 7, Issue 4
by Charles Bouldin 17 Sep '03

17 Sep '03

Just and FYI for the Mac OS X crowd: IBM has released their splendid optimizing C and Fortran compilers for OSX. See http://www-3.ibm.com/software/awdtools/fortran/ These are -great- compilers, and best of all, you can trivially modify standard makefiles and compile fortran programs. Definitely worth investigating. I can send a makefile for Feff to anyone interested. Haven't tried feffit or ifeffit yet, but thought others would be interested to know this, if you don't know it already.

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integrating difference spectra
by Bruce Ravel 16 Sep '03

16 Sep '03

Hi folks, In response to a request from an Athena user, I am incorporating a feature that will allow the user to integrate difference spectra. I suspect that this will prove most useful for XANES studies and for XMCD studies. I was wondering if someone on the mailing list would be so kind as to send me some sample XMCD data, either in the form of raw data or as an Athena project file, so I can test this. The most useful example at this stage would be a model system -- i.e. something that demonstrates a large dichroic effect. It would also be useful if your data set has a well known value for the integral of the difference spectrum. That way I'll have a bit of confidence that my algorithm is working. Thanks in advance! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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path-sensitive math expressions
by Bruce Ravel 05 Sep '03

05 Sep '03

Hi Matt, I have some questions about a subtle detail in ifeffit. It is possible to make a def parameter which is path sensitive in the sense that it will evaluate differently for different paths. Any def parameter which includes reff, eins(), or debye() in its math expression will be that way. Here is a simple, if slightly silly, example: def rrr = reff/10 path(1, feff=feff0001.dat, dr=rrr) path(2, feff=feff0002.dat, dr=rrr) Then show rrr will report 1/10 the R_eff of the *second* path. So here are my questions: 1. Are all def parameters reevaluated every time a new path is evaluated? Or only if the path uses the def parameter in one of its math expressions? (I think the answer is the former.) 2. Is it possible to ask ifeffit which def parameters are path sensitive? Of course, I can scan the def parameters at the level of perl to see if any of them obviously are, but ifeffit might already know that. 3. If you do show ss the value is the value of the last path evaluated. Doing show @path N show ss will indeed display the value of the def parameter appropriate to the Nth path. Is there another way of forcing ss to be evaluated appropriate to a desired path? Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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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how Atoms builds clusters
by Bruce Ravel 04 Sep '03

04 Sep '03

Hi everyone, I have twice recently been asked about how Atoms converts from its input data, which is the minimal set of positions necessary to describe the crystal, to the cluster that gets reported in the feff.inp file. Since there seems to be some interest in this question, I thought I would send a message to the mailing list with the answer. That way it'll be archived and anyone can go back and look at the answer. If you've ever wondered about this, read on. If the thought never crossed your mind, this is a good moment to go on to your next email message ;-) Here is the broad outline: 1. Atoms fills out the unit cell in the first octant. By "first octant" I mean that all fractional coordinates of all positions are non-negative and less than 1. 2. Enough unit cells are stacked up like blocks to make a rhomboid large enough to entirely encompass a sphere of the radius specified by the Rmax parameter. (If you poke hard enough at Atoms, you will find a situation where it fails to create a large enough rhomboid. It's an odd situation, though, and you won't run into it if your space group is orthogonal.) 3. The fractional coordinates are converted to their Cartesian equivalents. 4. All the atoms within the rhomboid but outside the sphere are tossed. 5. The atoms are translated such that the absorber is at the origin and the list is sorted by distance from the absorber. The non-obvious part of this algorithm is the first step. To fill out the unit cell, these steps are taken: a. For each atomic position given to Atoms, apply the symmetry operations associated with the point group. These are the operations reported in the symmetry.dat output file. They are also given in the International Tables of Crystallography for each space group. b. For each position found from the point group, apply the Bravais translations, if any. c. Some of the coordinates found from applying the point and Bravais operations will fall outside the first octant, that is, there may be coordinates smaller than 0 or larger than or equal to 1. Translate those positions back to the first octant by adding the appropriate integer to the offending coordinate. d. Weed through the list of positions and throw away any repeats. For high symmetry groups, the vast majority of generated positions will be repeats. For FCC copper, for example, you will find that the point and Bravais operations generate the same point 96 times. At the end of step 1, you have the contents of the P1 output file. That is, you have a description in fractional coordinates of the entire contents of the unit cell. For step 2 above, it is much easier to use the fractional coordinates to stack up unit cells to make the rhomboid. The unit cell in the +x direction is made by adding 1 to all the x coordinates. The unit cell in the -y direction is made by subtracting 1 from all the y coordinates. And so on. The conversion to Cartesian coordinates is where the lattice constants and angles come into play. This is a tensor transform where the non-zero elements of the metric tensor are functions of a, b, c, alpha, beta, and gamma. This tensor is discussed in Volume A of the International Tables and in many crystallography textbooks. The geometrically inclined could probably derive it on the back of an envelope. Or see the subroutines Xray::Xtal::Cell::make and Xray::Xtal::Cell::metric in the file Xtal.pm from the Atoms distribution. The last interesting detail is how the absorber atom is chosen. In a space group of high symmetry, there may well be several examples of the absorber in the unit cell. Atoms chooses the one that is closest to the center of the unit cell, i.e. the one closest to (1/2, 1/2, 1/2). This choice minimizes the size of the rhomboid needed to encompass the sphere of radius Rmax. Now, wasn't that fascinating? B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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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Phase and Amplitude Correction
by Ian Drake 28 Aug '03

28 Aug '03

Hi Matt, I wanted to follow up on a suggestion by Grant Bunker (Aug.4th). He proposed that I look into doing both a phase and amplitude correction of the data as opposed to doing only a total phase correction. How might I achieve this using IFEFFIT commands? Thank you for your help, Ian Drake ***************************** UC Berkeley Dept. of Chem. Eng. Graduate Student Advised by Dr. Alex Bell Heterogeneous Catalysts ******************************

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and new features in sixpack
by Webb, Samuel M. 26 Aug '03

26 Aug '03

Hi all... As a follow up to the follow up to Matt and Bruce's announcements.... There have also been a lot of new features written into sixpack now as well, also as a response to a lot of useful input from everyone at XAFS12. The latest incarnation of these changes is included in the latest IFEFFIT installer. The continuing saga of updates can be always be found on the sixpack webpage (http://www-ssrl.slac.stanford.edu/~swebb/sixpack.htm) including source code. Thanks to everyone the last few months that have made suggestions for improvements and catching errors. I hope to make some more major renovations to some of the fitting interfaces in the coming months so those of you who are interested can keep an eye out for them. Thanks! Sam

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and new versions of Athena and Artemis as well
by Bruce Ravel 25 Aug '03

25 Aug '03

Hi folks, As a follow-up to Matt's email, the new release of ifeffit for Windows contains the latest versions of Athena and Artemis. The source code tarball for unix and Mac OSX users can be found on my web site or downloaded using the horae_update script after you have compiled and installed the new version of ifeffit. These new releases contain many improvements which are summarized here: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Included are lots of features responding to useful input that I received both at the XAFS conference in Malmo and at this summer's EXAFS workshop at the NSLS. Thanks to everyone who contributed useful feedback, comments, and suggestions. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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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