Mr. Calvin,

I've gotten as far as my brain can manage with the Bi edge of the SBT fits, so I'm switching over to the Ta edge now. I can tell you that

Um, Hello all then? I don't know why this was sent to the mailing list, so please disregard everyone aside from Mr. Calvin... Sorry for the confusion... - Sean ----- Original Message ----- From: To: "XAFS Analysis using Ifeffit" Sent: Wednesday, June 16, 2004 6:55 PM Subject: [Ifeffit] XRD Diffractographs preliminarily,

the Ta edge is fitting a lot easier than the Bi. I've not done too much yet, just the first 10 paths, and even now it looks good. So I'll continue with that. Otherwise, I'm missing the XRD data for the diffractographs. I have the graphs, but no way to manipulate the data and merge them into one graph. Do you happen to have those?

- Sean

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

I thought I would add some more confusion to the issue and mention that on my system (Mac 10.3.4 with perl 5.008001, Artemis 0.7.006, Tk804.027, and Ifeffit 1.2.5 -- as reported in the properties window of artemis) I am *not* having any problems opening the ZnO3.apj project under horae-036/Examples. The specific procedure I used was to start artemis, load the project ZnO3.apj. I then plotted the FT os some of the loaded paths and did a fit. I then loaded the additional paths 10 & 11 did a fit without error and finally loaded paths 25 and 28 and also did a fit without error (or a Trap file being generated). Note I loaded the additional files from the ..horae/stash/artemis.project.1/data0.feff0 folder which was the current directory when I selected add a feff path from the FEFF menu as the journal entry said. This would seem to imply that the problems that was being reported by Stefano and Carlo are not unavoidable but may stem from some detail of the library being used or some other fixable entity. Since it works on my machine without error, perhaps we can track things down by looking at the details... I have tacked on the echo buffer as well as the results buffer from the ZnO3.apj after I followed the tutorial's advice and added the additional single scattering paths. Note I added the feff paths from the .horae/stash folder. Is there any obvious difference that might help track down the problem -- e.g. the path names or somesuch? Paul Here is a copy of the echo buffer: Showing new GDS page Using Ifeffit 1.2.5 Copyright (c) 2004 Matt Newville, Univ of Chicago Artemis may be freely redistributed under the terms of its license. Artemis comes with absolutely NO WARRANTY. HINT: A def parameter's math expression is stored and updated throughout a fit. Opening project zipfile /Users/paulfons/Ports/horae-036/examples/artemis/ZnO/ZnO3.apj ... Opening project zipfile ZnO3.apj ... done! Importing atoms.inp file ... Importing atoms.inp file ... done! Doing intrp for FEFF0 ... Doing intrp for FEFF0 ... done! amp: Plotting in r space ... Plotting in r space ... done! Opened project file `/Users/paulfons/.horae/stash/artemis.project.1/descriptions/artemis'. Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 1.102200 +/- 0.222995 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 0.907452 +/- 0.110477 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0025.dat" had Macintosh EOL characters and was fixed. "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0028.dat" had Macintosh EOL characters and was fixed. Running fit (this could take a few minutes, please be patient) ... amp = 0.911856 +/- 0.106227 Writing log file ... Running fit ... done! For reference here are the results from the fitting as well: Project title : Fitting ZnO.chi Comment : Prepared by : Contact : Started : 14:30:05 on 1 November, 2003 This fit at : 11:51:37 on 11 June, 2004 Environment : Artemis 0.7.006 using darwin, perl 5.008001, Tk 804.027, and Ifeffit 1.2.5 ============================================================ Independent points = 10.044921875 Number of variables = 4.000000000 Chi-square = 8182.854180122 Reduced Chi-square = 1353.674100233 R-factor = 0.025528340 Measurement uncertainty (k) = 0.000496786 Measurement uncertainty (R) = 0.000798106 Number of data sets = 1.000000000 Guess parameters +/- uncertainties: amp = 0.9118560 +/- 0.1062270 (1.0000) e0 = 5.4996840 +/- 0.7722610 (0.0000) ss = 0.0073380 +/- 0.0017720 (0.0030) delscale = 0.0031830 +/- 0.0037480 (0.0000) Def parameters: delr = 0.0145400 Correlations between variables: amp and ss --> 0.8234 e0 and delscale --> 0.8012 All other correlations are below 0.25 ===== Data set >>ZnO.chi<< ======================================== file: /Users/paulfons/.horae/stash/artemis.project.1/chi_data/ZnO.chi title lines: Merge in n space of: ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.032 (_013_032) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.033 (_013_033) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.034 (_013_034) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.035 (_013_035) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.036 (_013_036) ** C:/Documents and Settings/Scott/My Documents/Projects/ZnO/Data/011113.037 (_013_037) k-range = 3.000 - 10.000 dk = 2.000 k-window = kaiser-bessel k-weight = 1 R-range = 1.000 - 3.300 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.02553 ===== Paths used to fit ZnO.chi FEFF0: feff0001.dat (ifeffit group = feff0_1) .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0001.dat id = reff= 1.9593, degen= 3.0, path: Zn->O->Zn r = 1.965537 reff = 1.959300 degen = 3.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.006237 ss2 = 0.007338 FEFF0: feff0002.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0002.dat id = reff= 2.0396, degen= 1.0, path: Zn->O->Zn r = 2.046093 reff = 2.039600 degen = 1.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.006493 ss2 = 0.007338 FEFF0: feff0003.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0003.dat id = reff= 3.1675, degen= 1.0, path: Zn->O->Zn r = 3.177583 reff = 3.167500 degen = 1.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010083 ss2 = 0.007338 FEFF0: feff0004.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0004.dat id = reff= 3.2093, degen= 6.0, path: Zn->Zn->Zn r = 3.219516 reff = 3.209300 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010216 ss2 = 0.007338 FEFF0: feff0005.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0005.dat id = reff= 3.2501, degen= 6.0, path: Zn->Zn->Zn r = 3.260446 reff = 3.250100 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.010346 ss2 = 0.007338 FEFF0: feff0011.dat (ifeffit group = feff0_6) .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0011.dat id = reff= 3.7950, degen= 3.0, path: Zn->O->Zn r = 3.807081 reff = 3.795000 degen = 3.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.012081 ss2 = 0.007338 FEFF0: feff0012.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0012.dat id = reff= 3.8371, degen= 6.0, path: Zn->O->Zn r = 3.849315 reff = 3.837100 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.012215 ss2 = 0.007338 FEFF0: feff0025.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0025.dat id = reff= 4.5383, degen= 6.0, path: Zn->O->Zn r = 4.552747 reff = 4.538300 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.014447 ss2 = 0.007338 FEFF0: feff0028.dat .. feff = /Users/paulfons/.horae/stash/artemis.project.1/data0.feff0/feff0028.dat id = reff= 4.5675, degen= 6.0, path: Zn->Zn->Zn r = 4.582040 reff = 4.567500 degen = 6.000000 s02 = 0.911856 e0 = 5.499684 dr = 0.014540 ss2 = 0.007338 On 2004/06/11, at 5:11, Stefano Ciurli wrote:

Carlo,

I have been having consistent problems running the tutorials on my MacOSX G4 portable PC. I have posted several times the tect of the trap files I am getting. .Apparently, there is no definitve answer (yet). I am sure Bruce will try to clean up things whenever he has time. But, if for some reason, some of you out there knows a way out, I'll be one of the many to be happy to read it.

Stefano.

...

One of my students is just trying Scott's ZnO tutorial and we are finding a consistent problem when trying to work with the third project file.

When we get to the point of adding an additional path, (feff0011.dat), artemis crashes with the following message:

---------------------------------

The following message was trapped by Artemis:

Artemis0.7.006warn/home/segre/.horae/stash/ ARTEMIS.TRAPCODE(0x9652e54)/home/segre/.horae/stash/ artemis.project.2/ at /usr/bin/artemis line 1562 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 7313 main::read_feff('^^') called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1707

--------------------------------

This is happening on all of my Linux machines. They are using my Debian packages and so I have not tried with the tarball installation.

Has anyone else had this problem? I hesitate to report it as a bug until it is confirmed. In a previous version of horae, it worked fine.

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 Carlo.Segre@iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- ____________________________________________

Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203

"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官

Let me add one more thing, if I start from scratch with and load the ZnO.chi, then the first 10 FEFF paths and then try to add an additional path, in v034, there is no trapped warning (unlike when I loades Scott's project file) but v036 still freezes. Carlo On Thu, 10 Jun 2004, Carlo U. Segre wrote:

Paul:

Thanks for the details.

I tried reverting back to previous versions until the ZnO tutorial "worked". I found that version 035 freezes like version 036 but version 034 seems to work OK.

However, when I looked at the echo buffer, I noticed that despite apparently loading the new paths without any problem, there was a trapped error. It is a bit different than the one I get from v035 and v036 and it is a warning that does not crash the program, however, it does indicate that something is not quite right. Not that in the echo buffer, the loading of a path eventually reports an "Adding FEFF0 ... done!". This did not seem to be in Paul's file.

Finally, just to remove doubt about my Debian packages, I did a local install of v036 and the crash that I reported earlier still occurs albeit with a slightly different message than the original one I reported. In this case the error happened in the "main::add_a_path" routine, just like the non-fatal error in v034 reported below whereas in my Debian package version, the error is in "main::read_feff".

Clearly there is some inconsistency here.

Carlo

--------------- Echo Buffer -------------------- Running fit (this could take a few minutes, please be patient) ... amp = 0.906536 +/- 0.109976 Writing log file ... Running fit ... done! Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Adding FEFF0 ... "/home/segre/.horae/stash/artemis.project.0/data0.feff0/feff0025.dat" had Macintosh EOL characters and was fixed. Adding FEFF0 ... done! Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Artemis trapped a warning! Message dumped to /home/segre/.horae/stash/ARTEMIS.TRAP Adding FEFF0 ... "/home/segre/.horae/stash/artemis.project.0/data0.feff0/feff0028.dat" had Macintosh EOL characters and was fixed. Adding FEFF0 ... done!

and

------------------ ARTEMIS.TRAP ----------------- # Artemis 0.7.004 # This file created at 23:11:44 on 10 June, 2004 # using linux, perl 5.008004, Tk 800.025, and Ifeffit 1.2.5 # Workspace: /home/segre/.horae/stash/artemis.project.0/

The following message was trapped by Artemis on a SIGWARN:

Artemis0.7.004warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0x963f3dc)/home/segre/.horae/stash/artemis.project.0/ at /usr/bin/artemis line 1551 main::__ANON__('Use of uninitialized value in string eq at /usr/bin/artemis l...') called at /usr/bin/artemis line 5895

main::add_a_path('/home/segre/.horae/stash/artemis.project.0/data0.feff0/feff00...', 1, 0) called at /usr/bin/artemis line 3917 main::__ANON__() called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x9b2acac)', 'active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x9b2acac)', 1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1695 ------------------------------------------------------------------

On Fri, 11 Jun 2004, Paul Fons wrote:

...

I thought I would add some more confusion to the issue and mention that on my system (Mac 10.3.4 with perl 5.008001, Artemis 0.7.006, Tk804.027, and Ifeffit 1.2.5 -- as reported in the properties window of artemis) I am *not* having any problems opening the ZnO3.apj project under horae-036/Examples. The specific procedure I used was to start artemis, load the project ZnO3.apj. I then plotted the FT os some of the loaded paths and did a fit. I then loaded the additional paths 10 & 11 did a fit without error and finally loaded paths 25 and 28 and also did a fit without error (or a Trap file being generated). Note I loaded the additional files from the ...horae/stash/artemis.project.1/data0.feff0 folder which was the current directory when I selected add a feff path from the FEFF menu as the journal entry said. This would seem to imply that the problems that was being reported by Stefano and Carlo are not unavoidable but may stem from some detail of the library being used or some other fixable entity. Since it works on my machine without error, perhaps we can track things down by looking at the details... I have tacked on the echo buffer as well as the results buffer from the ZnO3.apj after I followed the tutorial's advice and added the additional single scattering paths. Note I added the feff paths from the .horae/stash folder. Is there any obvious difference that might help track down the problem -- e.g. the path names or somesuch?

Paul

Here is a copy of the echo buffer:

Showing new GDS page Using Ifeffit 1.2.5 Copyright (c) 2004 Matt Newville, Univ of Chicago Artemis may be freely redistributed under the terms of its license. Artemis comes with absolutely NO WARRANTY. HINT: A def parameter's math expression is stored and updated throughout a fit. Opening project zipfile /Users/paulfons/Ports/horae-036/examples/artemis/ZnO/ZnO3.apj ... Opening project zipfile ZnO3.apj ... done! Importing atoms.inp file ... Importing atoms.inp file ... done! Doing intrp for FEFF0 ... Doing intrp for FEFF0 ... done! amp: Plotting in r space ... Plotting in r space ... done! Opened project file `/Users/paulfons/.horae/stash/artemis.project.1/descriptions/artemis'. Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 1.102200 +/- 0.222995 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! Running fit (this could take a few minutes, please be patient) ... amp = 0.907452 +/- 0.110477 Writing log file ... Running fit ... done! Plotting in r space ... Plotting in r space ... done! "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0025.dat" had Macintosh EOL characters and was fixed. "/Users/paulfons/.horae/stash/artemis.project.1/data0.feff1/ feff0028.dat" had Macintosh EOL characters and was fixed. Running fit (this could take a few minutes, please be patient) ... amp = 0.911856 +/- 0.106227 Writing log file ... Running fit ... done!

-- 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@agni.phys.iit.edu http://www.iit.edu/~segre

Hi Paul, as I have been seeing strange things happening (also reported in this mailing list) I decided to remove all the programs and re-install everything from scratch. I am right now downloading: ifeffit-1.2.5a_Mac10.3.dmg horae-036.tar.gz Tk-800.024.tar.gz (I have read on Bruce's site that the newest version 025 is not good, but I wonder...) I have removed the /Applications/Ifeffit directory I have removed the /Library/Perl directory I have the latest version of fink, updated, in the /sw directory could you guide me into the exact installation procedure step by step??? Thanks Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

Hi Matt and thanks for your message. I have a couple of addiitonal questions:

0. install fink and fink's g77 and wget.

done, using fink install wget; OK

1. install the Ifeffit binary from ifeffit-1.2.5a_Mac10.3.dmg. This step is to install PGPLOT correctly: the problem in question is not with PGPLOT.

done. OK.

2. install Perl/Tk from source: 2.1 download Tk-804.027.tar.gz from a CPAN site ~> wget http://www.cpan.org/modules/by-authors/id/NI-S/Tk-804.027.tar.gz

QUESTION: is there a directory where I should download the file and then follow up with the subsequent instructions?

2.2 unpack Tk-804.027 ~> tar xvzf Tk-804.027.tar.gz 2.3 change line 2809 of pTk/mTk/tixGeneric/tixHList.c from '#if 0' to '#if 1' 2.4 build Perl/Tk: ~>perl Makefile.PL ; make 2.5 install Perl/Tk ~>sudo make install

3. install ifeffit from source: 3.1 download: ~>wget http://cars9.uchicago.edu/ifeffit/src/ifeffit-1.2.5.tar.gz

QUESTION: : is there a directory where I should download the file and then follow up with the subsequent instructions?

3.2 unpack: ~>tar xvzf ifeffit-1.2.5.tar.gz 3.3 configure ~>./configure --prefix=/Applications/Ifeffit

QUESTION: I do not seem to have, in tcsh, the command "configure"

3.4 build ~> make 3.5 install ~> sudo make install

4. install horae 4.1 set up to use ifeffit: ~>. /Applications/Ifeffit/bin/iff_init.sh if you're using bash and ~>source /Applications/Ifeffit/bin/iff_init.csh if you're using csh or tcsh (if you don't know which shell you're using, try both and whichever complains is the wrong one!) 4.2 install horae ~>horae_update --force

QUESTION: Is there a directory where I should download the file and then follow up with the subsequent instructions? The directories location may be crucial, as well as the solution to the configure command. another QUESTION: are there any files I should delete and from which directory before doing the whole thing from scratch? Also: Is the question related to which Tk/perl version I should have installed still valid? It is not clear, from your web page, whether the comments for the Linux installation are also related to the OSX. Looking forward to hearing from you. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

Hi Matt,

But for what it's worth here's what I recommend as a 'source install' on Mac OS X, assuming you have a machine with a fast internet connection:

at the end of all this, I have: ifeffit 1.2.5 athena 0.8.027 artemis 0.7.003 when, at this point, I run athena or artemis, I do not get aquaterm to open... I realize I have horae-033 I am trying to run the horae_update command, just in case... I'all let you know what will happen... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

In my case, aquaterm opens automatically. I did set in my .cshrc (shell script initialization file), the variable PGPLOT_DEV=/AQT I do know that aquaterm started even automatically even when I was building horae using the pgplot in fink as well. Paul On Jun 14, 2004, at 10:18 AM, Jeff Terry wrote:

Stefano,

It has been a while since I have used aquaterm but I believe that I had to open aquaterm before launching ifeffit. Although, it is certainly possible that my memory is faulty.

Jeff

On Jun 13, 2004, at 6:57 PM, Stefano Ciurli wrote:

...

Hi Matt,

...

But for what it's worth here's what I recommend as a 'source install' on Mac OS X, assuming you have a machine with a fast internet connection:

at the end of all this, I have: ifeffit 1.2.5 athena 0.8.027 artemis 0.7.003

when, at this point, I run athena or artemis, I do not get aquaterm to open... I realize I have horae-033

I am trying to run the horae_update command, just in case... I'all let you know what will happen... Stefano -- ____________________________________________

Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203

"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官

Paul, this is my .cshrc file: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source /Library/Scripts/iterminal_custom.tcsh source /sw/bin/init.csh source /Users/stefano/Programs/XtalView/XtalView.env setenv PATH `echo $PATH`:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Users/stefano/Programs/modeller6v2:/Users/stefano/Programs/o/bin/:/Users/stefano/Programs/autodock/dist305/bin:/Users/stefano/Programs/autodock/dist305/share/:/Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin/bin:/Users/stefano/Programs/XtalView/bin/powerpcDarwin5/ defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv RCSBROOT /Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT source /Library/Scripts/settitle.csh source /Users/stefano/Programs/NMRPipe/com/nmrInit.mac.com alias ono osx_ono ### begin MODELLER6v2 ###################################################### setenv MODINSTALL6v2 /Users/stefano/Programs/modeller6v2 setenv EXECUTABLE_TYPE6v2 mac10v2-absoft setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib setenv KEY_MODELLER6v2 MODELIRANJE alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) limit stacksize unlimited ### end MODELLER6v2 ######################################################## # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ so I think I do have the instruction for aquaterm. It is not a very nasty bug. I just have to remember to start aquaterm first... and the only bugging idea is that it worked once... Ciao, Stefano

In my case, aquaterm opens automatically. I did set in my .cshrc (shell script initialization file), the variable PGPLOT_DEV=/AQT I do know that aquaterm started even automatically even when I was building horae using the pgplot in fink as well.

Paul

-- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI