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

Re: [Ifeffit] Re: Questions about IFEFFIT and Windows 98
by krk511＠casbah.it.northwestern.edu 07 Feb '03

07 Feb '03

Bruce and Matt, Thank you for your help. Things appear to be working now. I made the change to the config.sys file (which changed the message from 'Out of environment space' to 'Too many parameters'). I then went to look at the xxxx.bat files and saw that they weren't there. After hitting the make bats application to generate them and then clicking on the executable (from the C:/Program Files/Ifeffit/ folder) things seem to be OK. (I didn't need to make changes to the bat files I guess)... though I'm still perplexed that I still get the "Too many parameters" message if I click on the icon on the desktop, while if I actually click on the executable in the folder I have no problem. I'm very glad that it appears to be working now. Thanks, Kristine Bruce Ravel <ravel(a)phys.washington.edu> writes on Fri, 7 Feb 2003 09:53:25 -0500: > > > > On Thu, 6 Feb 2003, Matt Newville <newville(a)cars.uchicago.edu> said: > > MN> I thought the 'Too many parameters - Files\Ifeffit Bad command or > MN> file name' message was somehow related to that, but maybe not. > MN> If not, it may be due to a mistake in the files C:\Program > MN> Files\Ifeffit\xxxx.bat (xxx = athena, artemis, ifeffit, > MN> sixpack,....) which all have this line: > MN> @echo off SET IFEFFIT_DIR=C:\Program Files\Ifeffit > > MN> Could the space in the file name be a problem for Windows98 but > MN> not Win2000??? If so, maybe adding quotes will do it: > MN> SET IFEFFIT_DIR='C:\Program Files\Ifeffit' > > I just wanted to say that if the solution to your problem is, indeed, > adding quotes to the .bat files, please let us know so we can do so in > the next version of the installer package. Of course, if the solution > is something else entirely, let us know that also ;-) > > 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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Re: Questions about IFEFFIT and Windows 98
by Matt Newville 07 Feb '03

07 Feb '03

Hi Kristine, On Thu, 6 Feb 2003 krk511(a)casbah.it.northwestern.edu wrote: > Matt, > > I'm trying to get IFEFFIT to work on a Windows 98 machine and I'm trying to > figure out what my options are. (Currently the three machines I use at > Northwestern, home, and Argonne are all Win 98.) > > I've installed IFEFFIT, and did some original changes to correct the "Out of > environment space" problem, now I have a: "Too many parameters Too many > parameters - Files\Ifeffit Bad command or file name " problem. > > I'm looking for suggestions. Just to be sure, I believe the 'Out of environent space problem' on Windows98 can be solved by putting SHELL=C:\COMMAND.COM /E:4096 /P in the config.sys file. Is that right? I thought the 'Too many parameters - Files\Ifeffit Bad command or file name' message was somehow related to that, but maybe not. If not, it may be due to a mistake in the files C:\Program Files\Ifeffit\xxxx.bat (xxx = athena, artemis, ifeffit, sixpack,....) which all have this line: @echo off SET IFEFFIT_DIR=C:\Program Files\Ifeffit Could the space in the file name be a problem for Windows98 but not Win2000??? If so, maybe adding quotes will do it: SET IFEFFIT_DIR='C:\Program Files\Ifeffit' To be honest, I'm not sure, but it's probably something simple like that. Anyone else know how to do this or have ifeffit/athena working on Windows 98? Thanks, --Matt

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A question ...
by Bruce Ravel 06 Feb '03

06 Feb '03

Hi folks, Matt and I are wondering what everyone's opinion is of the Windows installer package. We are concerned that it's huge size is an impediment to you, the users. The installer file is currently over 23 Mb and the full installation is using up over 56 Mb of your disk-space. A significant amount of that is for things like documentation and example files that could be (and in many cases are) found on the web. We are worried about people who are not in North America (as are Matt and I) or about people who do not have high bandwidth internet connections. So, we want to solicit some opinions from the windows users about the installer package. Should we: 1. Release the full, huge installer once per year or less and release smaller patches to the base installation as needed? 2. Release the huge installer, but allow more control over which components get installed? 3. Continue doing what we have been doing? 4. Try to find volunteers to set up mirrors on other continents? Feel free to offer any suggestions you might have about these distribution issues to this list or to Matt or I privately. 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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new version of Athena and new Windows installer package
by Bruce Ravel 06 Feb '03

06 Feb '03

Hi Folks, There is a new version of Athena (0.8.013) ready for use. Along with several small bug fixes are significant improvements to Athena's (but, sadly, not Artemis's) documentation. Because the new documentation involves lots of external files, there is a new version of the big Windows installer on Matt's web site. Unix and OSX people should grab the latest source code tarball from my web site. Windows people should grab the latest installer package from Matt's web site. Along with some work on the on-line document, I have written a selection of demos for Athena. The demos are project files with data that demonstrates some feature of Athena and Ifeffit and uses the journal space to provide an explanation and suggestions for things to try to better understand the demonstrated feature. You can browse the demo projects by selecting the appropriate item from the Help menu. When you read in a project that way, the journal will automatically open up so you can start reading about the feature being demonstrated. For many of you on this list, the demos probably explain things with which you are already familiar. But check them out -- you may learn about a feature you didn't know about. And, as you introduce new users to Athena, point them in the direction of the demo projects. 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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RE: [Ifeffit] athena 0.9.012 + an updater utility
by Kelly, Shelly D. 30 Jan '03

30 Jan '03

Hi Bruce, I believe that the set edge step button is broken in Athena when the Clnorm background is used. To reproduce this error: 1 read in a xmu data set 2 set the background to clnorm and plot the normalized bkg. 3 push the set step height button and change the value. 4 replot the background and watch the set height value go back to the original value. If you need a project file let me know. Shelly > -----Original Message----- > From: Bruce Ravel [mailto:ravel@phys.washington.edu] > Sent: Thursday, January 30, 2003 10:21 AM > To: ifeffit mailing list > Subject: [Ifeffit] athena 0.9.012 + an updater utility > > > > Hi folks, > > I just release a new version of Athena, a new Windows executable for > Athena, and a new source code tarball. You can find them in the > normal places. There are only two new things, but they are both > pretty important. > > 1. Fixed a serious bug in how Athena handles filenames with long, > similar names. There was a problem in how Athena was translating > long filenames into ifeffit group names that could lead to very > broken behavior. > > 2. For unix and Mac users, I wrote a perl script called > "horae_update" which gets installed upon installation into > /usr/local/bin (or wherever athena and artemis go). The purpose > of this script is to automate updating athena and artemis to the > very latest versions. It fetches the latest source code tarball > from the web, unpacks it, builds it, and (if you run it as root) > installs it. Very handy. > > The updater is only loosely tested, so I am eager for feedback > from people, and particularly from the OSX crowd. It seems to > work ok for me and makes updating the codes a snap. > > I plan to write a similar program for Windows users soon. My plan > is to have a button in the Ifeffit menu on the Start Menu that > says something like "Update Athena and Artemis". Clicking it will > fetch and install the latest Windows executables. I'll make an > announcment here when it is ready. > > 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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athena 0.9.012 + an updater utility
by Bruce Ravel 30 Jan '03

30 Jan '03

Hi folks, I just release a new version of Athena, a new Windows executable for Athena, and a new source code tarball. You can find them in the normal places. There are only two new things, but they are both pretty important. 1. Fixed a serious bug in how Athena handles filenames with long, similar names. There was a problem in how Athena was translating long filenames into ifeffit group names that could lead to very broken behavior. 2. For unix and Mac users, I wrote a perl script called "horae_update" which gets installed upon installation into /usr/local/bin (or wherever athena and artemis go). The purpose of this script is to automate updating athena and artemis to the very latest versions. It fetches the latest source code tarball from the web, unpacks it, builds it, and (if you run it as root) installs it. Very handy. The updater is only loosely tested, so I am eager for feedback from people, and particularly from the OSX crowd. It seems to work ok for me and makes updating the codes a snap. I plan to write a similar program for Windows users soon. My plan is to have a button in the Ifeffit menu on the Start Menu that says something like "Update Athena and Artemis". Clicking it will fetch and install the latest Windows executables. I'll make an announcment here when it is ready. 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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minimize function
by Kelly, Shelly D. 28 Jan '03

28 Jan '03

Hi, I would like to use the minimize function to fit a line to some data points. I could not find documentation on the r-square factor that is referred to as the confidence level for the fit. Thanks Shelly

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Ifeffit 1.0076
by Matt Newville 27 Jan '03

27 Jan '03

Happy New Year Everyone, I've just posted a new release of Ifeffit: 1.0076. This has many small fixes and added features, including: - fixed plotting bug in which all legends were not always shown - added 'unguess' command - added 'window' command (generate an FT window without actually doing the FT) - fixed a bug in reading 1-row data files - allow (consistently) '&', ':', and '?' in variable and group names - added the math functions nofx(), join(), and slice() for array manipulations - further tweaks to configuration procedure. There are a few more details are in the ChangeLog. I hope to get changes to the Reference Manual posted within a week. The Windows installer now includes the current versions of Athena, Artemis, Atoms, SixPack, and GIFEFFIT. I have not tried this version on Mac OS X. The installation using Fink and PGPLOT (not to mention Perl/Tk for Athena and Artemis) on Mac OS 10.2 seems especially fragile. For future work, the changes at the top of my list include: - adding an automated way to have feffit() apply more than 1 k-weight at a time, to help overcome the k-dependent biases due to the high correlations of XAFS parameters. - trying to improve the pre-edge subtraction and normalization algorithms. - getting the docs up-to-date. - working on changing the interface of Feff6 so that it can be included in Ifeffit. The still seem to be unresolved issues with QEXAFS data, and probably other things that should be done. Suggestions for improvements or added features are welcome. In fact, I'd like to ask everyone to think about what features you'd like to see added or changed. Thanks, --Matt Newville

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athena 0.8.010
by Bruce Ravel 15 Jan '03

15 Jan '03

Hi folks, The release I made of my software last week was riddled with problems. While I think the Windows executable was ok, the source code tarball for use on linux and Mac OSX was horribly broken. Thanks to helpful interactions with Paul Fons, Jeff Terry, and Shelly Kelly I think I have ironed out all the problems. This release, therefore, is mostly a bug-fix release. The only new bit of functionality this time involves some changes to how derivative spectra are plotted. There are no changes to artemis in this release. The source code and the new Windows executable for athena 0.8.010 are in their normal locations. If you use the source code, you should be running at least version 1.0072 (which dates all the way back to June 2002) of ifeffit. If you ifeffit is older than that, you should upgrade to the latest from Matt's website before installing athena and artemis. 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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trouble, trouble, trouble
by Bruce Ravel 10 Jan '03

10 Jan '03

Hi folks, The release I made yesterday seems to be the buggiest one I have released in quite some time. I have been getting lots of reports of problems with the latest source code tarball. Sigh. I am working on a new release -- hopefully things will be looking better on Monday. If anyone needs a copy of the previous release, you can grab it at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/horae-00… The entire archive of old versions is at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/ Sorry for the confusion and thanks especially to Jeff Terry, Paul Fons, and Shelly Kelly who have been very generous with their time and their useful bug reports. 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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