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

Novice seeks advice
by Dave Baker 29 Oct '03

29 Oct '03

I am a novice student in the EXAFS world, and I am starting to work my way through Athena and Artemis. Currently, I'm working with amorphous GeTe and the Atoms/FEFF runs are based on the crystalline data. I have performed a fit in Artemis of the Ge K edge, and my e0 for three contributing paths is exceedingly large, (-70 ~ -80 volts). Two questions: 1.) What symptom is this an indicator of, and 2.) What are some possible solutions? -Dave Baker

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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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