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

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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