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

Athena 0.8.014
by Bruce Ravel 06 Mar '03

06 Mar '03

Hi folks, I am pleased to announce a new version of Athena today. The source code tarball and windows executable are on my web site. Today's version offers three significant new features: 1. A fairly major user-interface change 2. The ability to fetch data files from web sites 3. An improved merging algorithm Please note that I am making use of a very recent feature of Ifeffit (the "nofx" array function) in the new merging algorithm. Windows users need to update to the version of the big Ifeffit installer from January 22, 2003. Linux, Unix and OSX users should be using Ifeffit version 1.0076 or later. The Windows installer and the ifeffit source code can be found at Matt's web site http://cars9.uchicago.edu/ifeffit/download.html If you are not running Ifeffit 1.0076 or later, then merging WILL NOT WORK in Athena 0.8.014. So, please, upgrade. I'll describe each of those features in detail below. I'd like to specifically thank Matt (who suggested the web thing) and Adam Web (who pointed out a problem with the merging algorithm). I'd also like to mention to all the people who have been asking for PCA in Athena that it's moving closer to the front of my TODO list. The change to the user interface is needed to be able to put PCA into Athena in a sensible manner. Regards B The details about each new feature: 1. Although the user interface change is pretty significant, I think it will be easy for current users to adapt to. Indeed, I think most people will appreciate the added functionality that the change allows. In earlier versions of Athena, data processing and analysis chores such as alignment, calibration, and log-ratio were done by interacting with a special dialog that popped up in a separate window. This separate window performed a grab, which means that you could not interact with the main window until you were done with the dialog and had dismissed it. Now, each of the various chores that previously used a pop-up dialog works by replacing the main part of the main window with the dialog specific to that analysis chore. Thus, when you, say, go to align data, the part of the main window where you specify background removal and Fourier transform parameters gets replaced by various menus and entry boxes relevant to that chore. If that's not clear, check out the new screenshots at http://leonardo.phys.washington.edu/~ravel/software/exafs/screenshots.html#… There are screenshots showing each of the eight alternate views in Athena. Not only does this reduce the number of windows that Athena throws up on the screen, it also allows you to use the groups list and the plotting buttons while one of the alternate views is displayed. For example, you can now view one or more data groups in R-space *while* aligning. Chores like alignment and difference spectra which require specifying a second data data group now work by selecting the second data group from the group list. 2. You can now read data files from web sites using an extremely primitive interface. In the File menu, there is an item which says "Open URL". When you select this, the Echo area at the bottom of the screen gets replaced by a bright orange text entry box. If you type in the fully resolved URL of a data file somewhere on the web, Athena will fetch and import that file. This is not extremely convenient because you have to type in the exact URL (or use cut and paste, of course). I have not (yet) implemented a mouse-driven browser of any sort. I may in the future if this feature proves popular. One helpful feature I did implement is that Athena keeps a history of files downloaded during the current Athena session. If you hit the up or down arrows while the URL text entry box has the focus, you will scroll up and down in the history of fetched data files. If you want to try it, I put some iron foil data on my web site. Enter this URL in the orange box: http://leonardo.phys.washington.edu/~ravel/misc/fe.060 This feature will work for Windows users. It will work for other platforms only if you have the LWP perl modules installed. Because that is a very large and frequently changing package, I am not comfortable distributing it with the horae package. If you are a linux, unix, or OSX user and the "Open URL" thing is greyed out, then you will need to install LWP. You can grab the latest version of the Bundle::LWP package from http://search.cpan.org/author/GAAS/libwww-perl-5.69/ Alternately, you can use perl's CPAN interface. At the command line, type perl -MCPAN -e shell then at the CPAN prompt type install Bundle::LWP 3. The merging algorithm has changed. Before, the marked data groups were merged after interpolating them onto the abscissa grid of the first marked group in the groups list. Now, Athena determines what is the longest abscissa range common to all marked groups. The reason for this change is that the prior algorithm would extrapolate if a marked group had a shorter abscissa range than the first group. Often this isn't a problem, but it can lead to very strange and undesirable results in the merged data. I am modestly confident that I have merging working correctly again in all cases. I encourage anyone using the merging algorithm to send me a project file if they suspect that bugs remain. -- 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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[Ifeffit] ldd /usr/local/bin/ifeffit ldd: /lib/ld-linux.so.2 exited with unknown exit code (139)
by Jacques Roux 04 Mar '03

04 Mar '03

This is a short report of various successful installations of ifeffit (and companion programs athena, artemis etc...) on linux boxes running Mandrake 8.1 8.2 and 9.0. However I would like to report one nagging failure which is summarized in the subject line of the message. On my office DELL under Linux Mandrake 9.0 ifeffit core dump and ldd issues the rather terse error message "unknown exit code (139)". The very same code runs fine and (ldd gives a meaningfull answer!) on other machines running the very same version of linux (including gcc, ld, glib etc...). I checked on google and found other people running into very similar problem (OK on one machine, wrong on the other). I tried to recompile ifeffit.f using --static but I could not get the static version of libX11 so for the time being I gave up. BTW it is not too bad as I can use the software on the same computer booting an older version (mdk 8.1) and at home on a 9.0 ! I hope this information may be useful to someone sometime ? -- J. Roux, CNRS-Institut des Sciences de la Terre 1a rue de la Férollerie, 45071 ORLEANS cedex 2, France

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:)
by Du Yonghua 04 Mar '03

04 Mar '03

Dear adaministrator: I have met some unknow problems that I cannot download the iffefit setup file. So I wonder whether you will be so kind to send me a copy of iffefit. The system of my computer is windows and the limination of my mail box is 100MB. Thank you very much! Du Yonghua Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P.O.Box 918 2-7 Tel: (86)01088235980 19(B) Road Yuquan Beijing China

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XANES
by Ahmed M Shahin 03 Mar '03

03 Mar '03

I have some question. I have mixed oxidation states and I would like to fit XANES, to determine the ratio of the mixed oxidation states I have. I looked at the documentations in the Ifeffit website but I could not find it. I have a license of feff. Would you please help me in how to fit XANES. I appreciate your help Ahmed ***************************************************** Ahmed Shahin Chemistry Department University of Missouri-Rolla 142 Schrenk Hall, Rolla, MO 65409-0010 E-mail: shahin(a)umr.edu Phone (573) 341-4083 "Make yourself a better person and know who you are before you try and know someone else and expect them to know you." *********************************************************

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feff8
by shahin 26 Feb '03

26 Feb '03

Bruce, I have recieved the liscence to install and use FEFF8. Would you please tell me how to upgrade the FEFF6 tiral version, so that, I can use ifeffit with FEFF8 instead of FEFF6. I appreciate your help. Ahmed

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Fresh installations of linux and ifeffit
by Bruce Ravel 14 Feb '03

14 Feb '03

Hi folks, This message is partly in response to Norbert's post from last week and partly because I noticed some things today that may trip up others in my situation. I wanted to post something here so that the solution to a similar problem might be found in the mailing list's archive. Yesterday and today I have been entertaining myself by updating my desktop computer to SuSE's Office Desktop edition of SuSE 8.1 It's pretty nifty and the installation was a breeze. Installing Ifeffit and my programs was not a breeze, however, because of some issues related to a linux distribution with a name like "Office Desktop". Because this distribution is targeted at people who use office applications, it was pretty weak in terms of software development. I had to go to SuSE's online distribution to get rpms for such obviously necessary things as C and Fortran compilers and make! Once I installed all the obvious development stuff, I made a stab at compiling Ifeffit. I immediately saw the problem that Norbert reported, which was the configure script complaining about not being able to find the "tputs" function in any of the terminal libraries. I solved this problem by downloading and installing the ncurses development package. SuSE and Red Hat give names like "ncurses-devel" to these packages, which contain header files and the like. After that, no problem. Ifeffit compiled up just fine. As did Athena and Artemis. However, trying to start Athena it became obvious that I had forgotten to install PGPLOT. Matt's PGPLOT_install script did it's magic exactly as expected. However, to get the compilation of PGPLOT to finish, I had to install the development packages for the PNG, zlib, and X windows libraries. Again, my "Office Desktop" system was lacking the header files needed to compile software. Once those were installed, PGPLOT compiled fine. I recompiled Ifeffit and my codes and I was happy. To summarize: 1. Don't forget to install PGPLOT. 2. If you have a choice about which linux distribution to choose, go for one of the "professional" distributions and make sure to install development packages up front. 3. If your CDs did not have the development packages on them, go to your vendors website and download them. If you ever want to compiler other stuff from the web, you will want these anyway. 4. To compile Ifeffit and PGPLOT, you need the header files for -- ncurses (or whichever terminal library you have on your system) -- the PNG library -- the zlib library -- the X windows headers Hope that's helpful to someone sometime. 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 digest, Vol 1 #109 - 2 msgs
by Zhan Zhang 12 Feb '03

12 Feb '03

Matt, I tried on my Win98. Installing it into C:\Ifeffit solved this icon not run problem for me. In my case, I believe this make_bats.exe works fine all the time. It generates the right .bat files. I would believe that the two easy steps you listed below works well for me. Hope it is fine for all other Win98 users. Anyway, I am working primarily on Win2K or WinXP now. Thanks for the hard work maintaining this! Zhan >My guess is that make_bats.exe that is supposed to make >the *.bat files at the 'Finish installation' step may >also be choking on the space in 'C:\Program Files'. > >Could one or both of you try installing into 'C:\Ifeffit' >instead of 'C:\Program Files\Ifeffit'. That might get the >start menu and desktop icons to work better -- and >everything else is supposed to work fine. If that doesn't >work, we might have to figure out something better. > >In the end, it would be really nice to have a small list >of steps for getting Ifeffit installed on Win98. If it >was as easy as: > 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys > 2. run the installer, but install to C:\Ifeffit. > -------------------------- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Dept. Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Drive 9700 Cass Ave. Evanston, IL 60208 Argonne, IL 60439 U.S.A U.S.A. Email address: zhanzhang(a)northwestern.edu Office: (630) 252-8629 Fax: (630) 252-5498 --------------------------

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Procedure for Win 98 installation
by krk511＠casbah.it.northwestern.edu 11 Feb '03

11 Feb '03

Matt and Group, It appears that the following two steps should be all that is needed to install on Win 98 and make the desktop icons usuable. (THANKS!) I've tried this today on another computer in our lab, and it even managed to install the xxx.bat files without having to go to the Make bats application. (My guess is that when I originally tried this a couple of days ago I may have done the shell command with a number much smaller than 4096, and that was the difference between then and now.) The procedure below appears to work great, if someone has problems they should immediately look to see if the xxxx.bat files were generated, and if not use the Make bats application. -- Kristine MN> In the end, it would be really nice to have a small list MN> of steps for getting Ifeffit installed on Win98. If it MN> was as easy as: MN> 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys MN> 2. run the installer, but install to C:\Ifeffit. MN> MN> That would be good enough for now. MN> Thanks, MN> MN> --Matt

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Problems compiling ifeffit
by Norbert Weiher 11 Feb '03

11 Feb '03

Hi folks, I just got a new computer and put SuSE Linux 8.1 on it. Now I started compiling ifeffit (which worked fine with the 7.3 version on my old one) and it produced the following error: ./configure worked. When I tried to do "make", it gave me loads of "undefined references" to some commands (mainly: tputs and so on). I examined the output of ./configure and found the following lines: checking for tputs in -lncurses... (cached) no checking for tputs in -lcurses... (cached) no checking for tputs in -ltermcap... (cached) no checking for tputs in -lterminfo... (cached) no checking for tputs in -ltermlib... (cached) no Anyone who can help me with this? Thanks in advance :) Regards, Norbert Weiher

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Win 98 cont....
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group: Sorry about the incomplete message. In regards to getting IFEFFIT to work on Win 98: I changed config.sys per Matt's suggestion: -- that changed the MSDOS error message from "Out of environment space" to "too many parameters" when I hit the desktop icon (this is what I still see when I hit the desktop icons) On Matt's suggestion I then looked at the xxxx.bat files in c:\Program Files\Ifeffit: -- I noticed that they weren't automatically installed, so I ran the "Make bats" application, after which I was able to run all the software if I selected it directly from the c:\Program Files\Ifeffit folder. After reading the last message I added Zhan's command to my autoexec file -- but it hasn't seemed to have made a difference in being able to use the desktop icons on my computer. It does still appear that I can get at the software directly by clicking on it from it's actual folder. I hope this helps. I'm just excited to see that it appears to work! Thanks! Kristine Witkowski Northwestern University

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Re: Ifeffit on Win98 (version 1.0076)
by Zhan Zhang 10 Feb '03

10 Feb '03

Bruce, I tried with the version 1.0076 found on the download site. The results are basically same as for 1.0074 If I had SET IFEFFIT_DIR='C:\Program Files\Ifeffit' --no help. SET IFEFFIT_DIR="C:\Program Files\Ifeffit" --sovle the path problem, but introduce some other 'complaining' message shown below. Athena runs. print() on closed filehandle I at athena line 175. print() on closed filehandle I at athena line 196. Unable to write temp config file "C:\Program Files\Ifeffit"\athena.ini-new: No s uch file or directory at athena line 221 print() on closed filehandle M at athena line 240. SET IFEFFIT_DIR=C:\Progra~1\Ifeffit --Runs ok. Zhan -- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Department Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Dr 9700 Cass Ave Evanston, IL 60208 Argonne, IL 60439 Tel: (630) 252-8629 Fax: (630) 252-5498 zhanzhang(a)northwestern.edu

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Win 98 installation
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group, Currently it appears that I can get the various software running (SixPack, GIFEFFIT, etc.) just not from the desktop icons. I have done/tried the following: I made the changes suggested to the config.sys file -- this changed the error message (when hitting the desktop icon) from "Out of environment space" to "too many parameters" the later message I still see when I currently hit the desktop icons. After the previous step I checked the xxxx.bat files in c:\Program files\Ifeffit

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Win 98 installation
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group, Currently it appears that I can get the various software running (SixPack, GIFEFFIT, etc.) just not from the desktop icons. I have done/tried the following: I made the changes suggested to the config.sys file -- this changed the error message (when hitting the desktop icon) from "Out of environment space" to "too many parameters" the later message I still see when I currently hit the desktop icons. After the previous step I checked the xxxx.bat files in c:\Program files\Ifeffit

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Re: Ifeffit digest, Vol 1 #106 - 2 msgs
by Zhan Zhang 09 Feb '03

09 Feb '03

Bruce, My Win98 computer had a hard disk failure last year and I upgraded it to Win2K. However, I have another 98 running at home. But I don't have the lastest Ifeffit there. So I just tried this with 1.0074. I will try a latest version later. I don't recall anything about the 'out of memory' problem when installing on my office 98. But this time I do. After changing config.sys. It was gone. And from my experience here, the answer to the first question below is YES. I click the icon on desktop, a DOS shell window (minimized) showed up and the 'too many parameters' information given. Then, well, nothing happened then. I tired put quote on 'C:\Program Files\Ifeffit' in the .bat file. It did not help. And I tried put double quotes on "C:\Program Files\Ifeffit". It helps sovle the 'too many parameter' problem. But it seems introduced another problem. An error message 'bad side "": must be top, bottom, left, or right at Tk/Widget.pm line 1053' showed and quit. The last thing I did was changing it to C:\Progra~1\Ifeffit. And it worked. Putting single or double (' or ") around it would not work again. And the answer to the second question is YES, if the icons here mean the '.exe' file. NO for '.bat' file. It was also a NO if I tried to run them from 'Start-->Programs-->Ifeffit-->Athena(or anyother)'. I believe this means the icons on the desktop point to the correct files (.bat file). And the only problem is the bat file could not set up the path. This won't be a problem if the path is sort of a normal DOS path, say shorter than 8 characters and contains no space. Zhan > Zhan: I have the exact opposite question. Was changing the path to > have the tilde rather than the space required to get the desktop icons > to work? And do the programs run without editing if you click on the > icons in the C:\Program Files\Ifeffit folder? > > Perhaps someone who is python-savvy and has access to a Win98 machine > can help out by doing some tests and figuring out what the > make_bats.py needs to be in order to work correctly on Win9x *as well > as* the later Windows systems. There are some hints in the README.TXT > file in the build_setup folder for how make_bats and the installer > builder all work. > -- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Department Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Dr 9700 Cass Ave Evanston, IL 60208 Argonne, IL 60439 Tel: (630) 252-8629 Fax: (630) 252-5498 zhanzhang(a)northwestern.edu

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S02
by Dr. Paul Fons 09 Feb '03

09 Feb '03

I was curious to tap the collective wisdom of those on the list regarding the "true meaning" of S02, the passive electron reduction factor, at least with regards to fitting experimental data to feff calculated paths. I understand that S02 is an aggregate "energy losses related to core hole creation parameter", but am curious about experimental data fitting. In particular, I have have started probing both high and low energy ranges for exafs and find that my usual experience from the 10-15 keV range don't seem to apply. In particular, I have been measuring energies around the O edge (540 eV) as well as some rather high energies edges Te (31 keV), Cd (26.7 keV) etc.. I have heard (indirectly via my coworker) from Andrei Rogalev that he considers S02 to be just another parameter. As the correlation between S02 and N is unity, this leads to a fair amount of ambiguity in the determination of coordination to say the least. While we are on the subject, are there any general observations about the transferablility of S02 from standards. How about the expected temperature dependence of S02? I do recall reading from John Rehr's article in RMP that S02 (which feff does calculate by the way) is an path dependent, complex sum that must be phasor summed. What are some realistic approximations/trends regarding to S02 and temperature, energy, and/or structure dependence? Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Optoelectronics Division Umezono 1-1-4 Tsukuba, Ibaraki JAPAN 305-8568

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(no subject)
by Bruce Ravel 07 Feb '03

07 Feb '03

Hi Matt, I'm a little confused by the "resolution" of this Win98 issue. It seems as though the two Northwesterners had slightly different experiences. Kristine said: K> I made the change to the config.sys file (which changed the K> message from 'Out of environment space' to 'Too many parameters'). K> I then went to look at the xxxx.bat files and saw that they K> weren't there. After hitting the make bats application to K> generate them and then clicking on the executable (from the K> C:/Program Files/Ifeffit/ folder) things seem to be OK. So it seems as though re-running the make_bats thing was sufficient, although the "too many parameters" thing seems to indicate that there is still a problem with the space in the folder name. It seems that Zhan, on the other hand, needed to fix the space in the folder name to get things to work. ZZ> What I did was just give the path and file name exactly as shown ZZ> in the DOS shell. Something like: ZZ> SET IFEFFIT_DIR=C:\Progra~1\Ifeffit ZZ> After changing all the .bat files, they worked ok for me. Why would one Win98 user need to do that but another not need to? That doesn't seem outside the realm of possibility with the wonderful Win98, but it does seem odd. So I guess I have a couple of questions. Kristine: Do the desktop icons work? Or can you only run the programs if you click on the .bat icons in the C:\Program Files\Ifeffit folder? Zhan: I have the exact opposite question. Was changing the path to have the tilde rather than the space required to get the desktop icons to work? And do the programs run without editing if you click on the icons in the C:\Program Files\Ifeffit folder? Perhaps someone who is python-savvy and has access to a Win98 machine can help out by doing some tests and figuring out what the make_bats.py needs to be in order to work correctly on Win9x *as well as* the later Windows systems. There are some hints in the README.TXT file in the build_setup folder for how make_bats and the installer builder all work. Regards, B P.S. It would be nice if everyone, and particularly digest users, when quoting a previous post, would edit the quote to show just the bit that is relevant to the conversation. It is much easier to understand the flow of the conversation without dozens or hundreds of lines of extraneous stuff. -- 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] 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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