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

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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