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

Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena
by Tony Kelly 04 Feb '12

04 Feb '12

This will make me seem pretty dense, but I'm still trying to figure out how to reply to specific threads in the list-serve from my gmail, and I keep seeming to create new threads... for which I wholeheartedly apologize if it's becoming annoying. But I really do thank everyone for their help and patience thus far. What I've attempted since earlier today: 1. Completely reinstalling from older versions and newer versions of IFEFFIT onto the Mac. Didn't work. 2. I went to two other Macs, did a clean install of the newest iXAFS software and it worked fine... which can only mean something really crazy is going on with the Mac I am trying to use for my work. I'd like to mention again that I was able to import data just fine last night, and it was only this morning that things started breaking. 3. I've reinstalled X11 and XQuartz. 4. I've checked the data files on the other Mac machines (and Dr. Zając checked them) and the files were fine. 5. I attempted to run from the command line and found some errors that weren't there at one time. 6. I then checked my version of perl, and it is version 5 bash-3.2$ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 2 registered patches, see perl -V for more detail) 6. Something that MAY shed light on the situation... when I open iXAFS from the Application menu in the Dock (I'll try attaching an image), it seems that iXAFS is "broken" or not installing correctly. However, I can then open iXAFS up in the FINDER window, it looks "okay" and can be opened... it just doesn't function correctly. What I don't understand is why a clean install doesn't fit the problem... are there hidden files I should remove as well that aren't removed when I uninstall iXAFS from the application directory with (rm -rf ) ? 7. George mentions that his build is different than my own, so now I am looking at my structure (modified for more pleasant viewing), but the directory does seem to exist.: bash-3.2$ ls /Applications/iXAFS.app/ Contents ls /Applications/iXAFS.app/Contents/ Info.plist MacOS PkgInfo Resources ls /Applications/iXAFS.app/Contents/Resources/ Artemis.icns Athena.icns English.lproj Hephaestus.icns Horae iXAFS Shell.icns iXAFS Shell.sh iXAFS.icns ls /Applications/iXAFS.app/Contents/Resources/Horae/bin/ Aquaterm.app atoms crc32 feffit ifeffit libpng-config perlindex tkpod artemis autobk diffkk findatp ifeffit_shell.pl libpng12-config rdaj athena chartex feff6 hephaestus ixafs-env lsprj tkmore Tony Kelly, M.Sc. DTRA PhD Student Air Force Institute of Technology Nuclear Physics and Engineering On Thu, Feb 2, 2012 at 5:15 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Sudden Difficulty with Importing Data into Athena > (Dr. Dariusz A. Zaj?c) > 2. Sudden Difficulty with Importing Data into Athena (Tony Kelly) > 3. Re: Sudden Difficulty with Importing Data into Athena > (Bruce Ravel) > 4. Re: Sudden Difficulty with Importing Data into Athena (Tony Kelly) > 5. Re: Sudden Difficulty with Importing Data into Athena > (Dr. Dariusz A. Zaj?c) > 6. Re: Sudden Difficulty with Importing Data into Athena > (Dr. Dariusz A. Zaj?c) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 02 Feb 2012 19:07:32 +0100 > From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > Athena > Message-ID: <4F2AD0E4.3010107(a)ifj.edu.pl> > Content-Type: text/plain; charset=UTF-8; format=flowed > > check the data, if at the end of files are some zeros or strange > numbers or even empty line(maybe). That what you described can be > exactly caused by problem with the data in file, eg. injection during > measurements > > W dniu 12-02-02 18:22, Tony Kelly pisze: >> Hopefully this is not long winded, but I want to be as detailed with >> the problem as I can be. In the past, I have never had difficulty >> importing data into Athena, given it was formatted properly. It was >> working as recently as last night, but suddenly I have a problem >> today. >> >> 1. I open Athena >> 2. I go to File->Open Files >> 3. I click on the data file to bring me to the window where I choose >> Energy, Numerator, Denominator for the data and any reference spectra, >> etc >> 4. I choose the Energy, Numerator and Denominator >> >> This is when the first moment of "oddness" happens... I don't get a >> plot. Normally, I would get a plot of the spectra I am about to >> import to know if I selected the correct columns with the correct sign >> (and whether a Log is needed). >> >> 5. Confused, I continue anyway and import my choices. >> 6. I then get the following error from Athena: >> >> The following problems were found for group "Fe.060" >> 1 : The edge energy is unset >> 2 : The kmin for the forward transfer is negative (-2) >> You should fix these values before continuing analysis of these data. >> >> Note 1: I was trying with some old data that I have analyzed in the >> past from Athena through Artemis and know to be okay for analysis. >> Note 2: I then tried studying some MnO spectra by importing that data >> taken during the 2011 XAFS Summer School in Chicago taken from APS. I >> know these text files to work, as we looked at them AT the summer >> school. >> Note 3: As a last resort, I tried downloading the Fe example from the >> Athena website (as you can see above from Fe.060), but it can't even >> read this in. >> Note 4: Athena CAN open old projects where the data was already >> imported without problems... it just seems I can't start a new project >> and import data into it successfully. I have tried searching all >> through the internet for anyone who had the error above or my >> difficulties to no avail. I have tried making sure the line breaks >> were correct by resaving data into new files through textwrangler and >> even going through vim in a terminal, to no avail. >> Note 5: As a last resort, I reinstalled iXAFS, but this hasn't fixed >> the problem. >> >> Anyone have any suggestions? Am I suddenly forgetting a step in the >> data import process? >> >> Thanks, >> >> Tony Kelly >> Air Force Institute of Technology >> Nuclear Physics and Engineering >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Feb 2012 13:18:14 -0500 > From: Tony Kelly <tkelly72(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Sudden Difficulty with Importing Data into Athena > Message-ID: > <CAOOxQkMUGzwk-0wxDuipd9_VFh3iodgY+WBF0xwLzddvJMNfZA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Bruce, > > Thank you for the quick reply. I tried uninstalling and reinstalling > twice, though I suppose I could try a different version. I have also > made sure that my x11/xquartz software was up to date, though I have > not changed or added software or updates between the last time it > worked and now. > > It literally worked last night, then it no longer worked this morning. > > I've never had antivirus software on my macs, but I could download one > and do a scan to see what that gives me. > > If I find a clear solution to what may have happened, I'll be sure to > reply again to share the answer. > > Tony Kelly > Air Force Institute of Technology > Nuclear Physics and Engineering > > > ------------------------------ > > Message: 3 > Date: Thu, 2 Feb 2012 13:27:37 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > Athena > Message-ID: <201202021327.38153.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Thursday, February 02, 2012 01:18:14 pm Tony Kelly wrote: >> Thank you for the quick reply. I tried uninstalling and reinstalling >> twice, though I suppose I could try a different version. I have also >> made sure that my x11/xquartz software was up to date, though I have >> not changed or added software or updates between the last time it >> worked and now. > > I have to ask the obvious questions ... :) > >> It literally worked last night, then it no longer worked this morning. >> >> I've never had antivirus software on my macs, but I could download one >> and do a scan to see what that gives me. > > I am not suggesting that. I was suspicious that AV software had > deleted something as a false positive. > > You might have mentioned in your original email that you were using > the Mac. In this case, I don't see yet how it matters, but it > certainly is awfully big omission. > >> If I find a clear solution to what may have happened, I'll be sure to >> reply again to share the answer. > > Try opening a terminal and running athena from the command line. The > advantage of this is that you will get to see whatever error messages > get issued when Athena runs into her problems. > > Also Darek's suggestion of checking to make sure the input data has not > been somehow corrupted is a good one. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > > ------------------------------ > > Message: 4 > Date: Thu, 2 Feb 2012 14:23:07 -0500 > From: Tony Kelly <tkelly72(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > Athena > Message-ID: > <CAOOxQkP72UoA-8Z_NkcPRDX1+tD4_CwsWdyiRBMtXb3DvYJoeg(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 1. I made sure to check the data files for strange behavior, > definitely a good idea. I know when I use other software such as > ROOT, file structure and pat names can become problems. This didn't > fix the problem, however :-/ > > 2. I then ran Athena from the command line as was suggested, and it > seems that there is a major problem there: > > bash-3.2$ athena > Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle' > for module Ifeffit: > dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle, > 1): Library not loaded: libifeffit.so > Referenced from: > /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle > Reason: image not found at > /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm > line 204. > at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67 > Compilation failed in require at > /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. > BEGIN failed--compilation aborted at > /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. > > > 3. Then I became more curious and attempted ifeffit itself: > > bash-3.2$ ifeffit > dyld: Library not loaded: libpgplot.dylib > Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit > Reason: image not found > Trace/BPT trap > > > I am using Max OSX 10.6.8. > Intel Core i5. > > Any other Mac users out there have ideas? > > Thanks much, > > Tony Kelly > Air Force Institute of Technology > Nuclear Physics and Engineering > > > ------------------------------ > > Message: 5 > Date: Thu, 02 Feb 2012 20:56:44 +0100 > From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > Athena > Message-ID: <4F2AEA7C.8070400(a)ifj.edu.pl> > Content-Type: text/plain; charset=UTF-8; format=flowed > > can you send me this file you can not open? > > W dniu 12-02-02 20:23, Tony Kelly pisze: >> 1. I made sure to check the data files for strange behavior, >> definitely a good idea. I know when I use other software such as >> ROOT, file structure and pat names can become problems. This didn't >> fix the problem, however :-/ >> >> 2. I then ran Athena from the command line as was suggested, and it >> seems that there is a major problem there: >> >> bash-3.2$ athena >> Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle' >> for module Ifeffit: >> dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle, >> 1): Library not loaded: libifeffit.so >> Referenced from: >> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle >> Reason: image not found at >> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm >> line 204. >> at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67 >> Compilation failed in require at >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. >> BEGIN failed--compilation aborted at >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. >> >> >> 3. Then I became more curious and attempted ifeffit itself: >> >> bash-3.2$ ifeffit >> dyld: Library not loaded: libpgplot.dylib >> Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit >> Reason: image not found >> Trace/BPT trap >> >> >> I am using Max OSX 10.6.8. >> Intel Core i5. >> >> Any other Mac users out there have ideas? >> >> Thanks much, >> >> Tony Kelly >> Air Force Institute of Technology >> Nuclear Physics and Engineering >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 6 > Date: Thu, 02 Feb 2012 23:15:48 +0100 > From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > Athena > Message-ID: <4F2B0B14.2070807(a)ifj.edu.pl> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hmm, > under Win XP I had no problems to open files, together with the > reference. For Tony's data as well as downloaded from internet's one. > I'm just thinking - this maybe is some problem with the settings in open > window, or with compilation of Athena. > About second case I have not to much to say, > About first - maybe some option for opening file and processing data? I > tried to see each counter separately and I had no problems, also with > negate function... > any ideas? > darek > > W dniu 12-02-02 20:23, Tony Kelly pisze: >> 1. I made sure to check the data files for strange behavior, >> definitely a good idea. I know when I use other software such as >> ROOT, file structure and pat names can become problems. This didn't >> fix the problem, however :-/ >> >> 2. I then ran Athena from the command line as was suggested, and it >> seems that there is a major problem there: >> >> bash-3.2$ athena >> Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle' >> for module Ifeffit: >> dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle, >> 1): Library not loaded: libifeffit.so >> Referenced from: >> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle >> Reason: image not found at >> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm >> line 204. >> at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67 >> Compilation failed in require at >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. >> BEGIN failed--compilation aborted at >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. >> >> >> 3. Then I became more curious and attempted ifeffit itself: >> >> bash-3.2$ ifeffit >> dyld: Library not loaded: libpgplot.dylib >> Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit >> Reason: image not found >> Trace/BPT trap >> >> >> I am using Max OSX 10.6.8. >> Intel Core i5. >> >> Any other Mac users out there have ideas? >> >> Thanks much, >> >> Tony Kelly >> Air Force Institute of Technology >> Nuclear Physics and Engineering >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 108, Issue 3 > ***************************************

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Re: [Ifeffit] demeter on xp access for all users (Bruce Ravel) (Bruce Ravel)(ted)
by fred.mosselmans＠diamond.ac.uk 03 Feb '12

03 Feb '12

Hi Bruce, I have now with your help solved this . For info the is %APPDATA% is the standard xp C:\documents and settings\userid\application data\ (there are some upper case letters due but that would be complex typing for me.) The problem seems to be although the user has write permission to this folder, Demeter doesn't try to create Its own folder (does this happen during a standard install for the installer?) so it seems when in startup it finds there is no %APPDATA%/Demeter folder to put the log in it gives up. Hence by first creating a Demeter folder in %APPDATA% folder, the program runs happily. Thanks for the help in figuring it out. Cheers Fred ted is short for sorted BTW. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Re: [Ifeffit] demeter on xp access for all users (Bruce Ravel)
by fred.mosselmans＠diamond.ac.uk 03 Feb '12

03 Feb '12

Hi Bruce, Thanks for the help I attach two text files of what I got back from perl –V for a user and for myself. they to my eye are identical I can change the default pdf viewer on the system if I want , not sure if a user could. In terms of logs the user never gets that far. i.e. no %appdata%\demeter directory is created or log file residing there started. This does get written for me. I tried turning echo on to see if I’d see anything but the command window doesn’t stay open for long enough. I assume thus the log file is failing to be written causing the program not to run. the path on the user account looks ok i think PATH=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Program Files\NuGraf;C:\Program Files\QuickTime\QTSystem\;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin; Thanks Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Artemis: How to treat Neglected? DS path
by Takahide Yamaguchi 03 Feb '12

03 Feb '12

Dear all, I have been analyzing some EXAFS data based on crystal structure by Artemis. The model construction and analysis within the First shell had come along OK. And I would like to refine the analysis of higher shell including multiple scattering. But the problem about "How to treat the MS path(especially DS)" is existing in the way to goal. Generally, Considering triangle arrangement (A-B-C; A is Absorber, B is nearest neighbor, C is the next neighbor) offers the possibility of two double scattering paths. Stated another way, the following two type can be readily considerable. "Type I: A-->B-->C-->A and Type II; A-->C-->B-->A" By calculation of FEFF on Artemis, a number of DS is computed and listed, of course on my computer. However, I could find JUST ONLY type II double scatter, no type I. In this case, should I simply multiply the amplitude by two? Or, are there reasonable answer to neglected type I path? I will be glad with your help. Best regards, Takahide

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Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

1. I made sure to check the data files for strange behavior, definitely a good idea. I know when I use other software such as ROOT, file structure and pat names can become problems. This didn't fix the problem, however :-/ 2. I then ran Athena from the command line as was suggested, and it seems that there is a major problem there: bash-3.2$ athena Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle' for module Ifeffit: dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle, 1): Library not loaded: libifeffit.so Referenced from: /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle Reason: image not found at /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm line 204. at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67 Compilation failed in require at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67. 3. Then I became more curious and attempted ifeffit itself: bash-3.2$ ifeffit dyld: Library not loaded: libpgplot.dylib Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit Reason: image not found Trace/BPT trap I am using Max OSX 10.6.8. Intel Core i5. Any other Mac users out there have ideas? Thanks much, Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

Hi Bruce, Thank you for the quick reply. I tried uninstalling and reinstalling twice, though I suppose I could try a different version. I have also made sure that my x11/xquartz software was up to date, though I have not changed or added software or updates between the last time it worked and now. It literally worked last night, then it no longer worked this morning. I've never had antivirus software on my macs, but I could download one and do a scan to see what that gives me. If I find a clear solution to what may have happened, I'll be sure to reply again to share the answer. Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Sudden Difficulty with Importing Data into Athena
by Tony Kelly 02 Feb '12

02 Feb '12

Hopefully this is not long winded, but I want to be as detailed with the problem as I can be. In the past, I have never had difficulty importing data into Athena, given it was formatted properly. It was working as recently as last night, but suddenly I have a problem today. 1. I open Athena 2. I go to File->Open Files 3. I click on the data file to bring me to the window where I choose Energy, Numerator, Denominator for the data and any reference spectra, etc 4. I choose the Energy, Numerator and Denominator This is when the first moment of "oddness" happens... I don't get a plot. Normally, I would get a plot of the spectra I am about to import to know if I selected the correct columns with the correct sign (and whether a Log is needed). 5. Confused, I continue anyway and import my choices. 6. I then get the following error from Athena: The following problems were found for group "Fe.060" 1 : The edge energy is unset 2 : The kmin for the forward transfer is negative (-2) You should fix these values before continuing analysis of these data. Note 1: I was trying with some old data that I have analyzed in the past from Athena through Artemis and know to be okay for analysis. Note 2: I then tried studying some MnO spectra by importing that data taken during the 2011 XAFS Summer School in Chicago taken from APS. I know these text files to work, as we looked at them AT the summer school. Note 3: As a last resort, I tried downloading the Fe example from the Athena website (as you can see above from Fe.060), but it can't even read this in. Note 4: Athena CAN open old projects where the data was already imported without problems... it just seems I can't start a new project and import data into it successfully. I have tried searching all through the internet for anyone who had the error above or my difficulties to no avail. I have tried making sure the line breaks were correct by resaving data into new files through textwrangler and even going through vim in a terminal, to no avail. Note 5: As a last resort, I reinstalled iXAFS, but this hasn't fixed the problem. Anyone have any suggestions? Am I suddenly forgetting a step in the data import process? Thanks, Tony Kelly Air Force Institute of Technology Nuclear Physics and Engineering

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Re: [Ifeffit] Ifeffit Digest, Vol 107, Issue 16
by Carmelo Prestipino 02 Feb '12

02 Feb '12

Hi I have also some problems to start demeter ..... My computer is equipped with Vista Demeter is installed on C:\strawberry If I digit "C:\strawberry\perl\site\bin\datoms.bat" on the dos windows no output come out. Here bellow the text in file DATOMS.log Can't locate Demeter.pm in @INC (@INC contains: /usr/lib/perl5/5.8/msys /usr/lib/perl5/5.8 /usr/lib/perl5/site_perl/5.8/msys /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/msys /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at ./datoms.bat line 31. BEGIN failed--compilation aborted at ./datoms.bat line 31. DARTHEMIS.log Can't locate Demeter/Here.pm in @INC (@INC contains: /usr/lib/perl5/5.8/msys /usr/lib/perl5/5.8 /usr/lib/perl5/site_perl/5.8/msys /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/msys /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at ./C:\strawberry\perl\site\bin\dartemis.bat line 16. BEGIN failed--compilation aborted at ./C:\strawberry\perl\site\bin\dartemis.bat line 16. Thanks Again Carmelo -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, Bât 10B, bureau 122 F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959 >

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demeter on xp access for all users
by fred.mosselmans＠diamond.ac.uk 02 Feb '12

02 Feb '12

Hi I am sure this has probably been posted before but I couldn't find it on a rudimentary search of the mailing list archive- I think Bruce fixed it in a previous release after the course he gave at Diamond. I'd recommend it when the video comes out soon But having installed the latest Demeter release on my xp windows pc's on the beamline, I can use it fine but my users who log in to these pc's as themselves with few rights in the windows world cant. If they try to start the program the old dos window shows for milliseconds and that's it. I am sure it is a permissions issue for a log file or something so I have made the strawberry pearl directory full control for anyone but obviously I need to do something else as well. Ta Fred Prof JFW Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell campus Chilton Didcot OX11 0DE E fred.mosselmans(a)diamond.ac.uk<mailto:fred.mosselmans@diamond.ac.uk> P 00 44 1235778568 M 00 44 7785510211 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Au-foil (fcc) splitted peak
by grant bunker 29 Jan '12

29 Jan '12

Julian - the scattering amplitudes of all elements have structure in them that are connected to electron scattering (Ramsauer-Townsend) resonances within the backscattering atom. For light elements (e.g. O, S, Fe) they occur at energies that are lower than the typical transform range, so they usually are ignored. For heavier scatterers like Au there are strong minima and maxima in the Au scattering amplitude over the transform range. From a signal processing point of view, these amplitude modulations look like beats, which normally are due to different distances interfering. In the case of Au back scatterers, even if there is only one physical distance, you will get multiple peaks (perhaps overlapping). Mathematically the fourier transform is the distance distribution convoluted with the fourier transform of the amplitude. So, how do you deal with it? First, if you know what's going on that may be enough. Alternatively, if all the scatterers are the same, it's not difficult to divide out the scattering amplitude and subtract out the scattering phase before the transform to obtain an "optical transform", which eliminates the effect you're seeing. I don't know if that is supported by ifeffit but it's not hard to do. This approach is less useful if you have multiple types of scatterers (e.g. Au, S) because if you do the compensation for one type of scatterer it screws it up for the others. Techniques like regularization are probably better in that case. hope that helps grant bunker

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