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

SCF convergence
by Christopher Patridge 13 Feb '12

13 Feb '12

Dear All, I recently starting using FEFF9 for XANES and I am trying to calculate LiCoO2 structure with deintercalation. The SCF iteration fails to converge at the 3rd iteration and I do not understand what setting I have used which is causing this hang up. I tried several different SCF radii in the attached feff input file and read in the manual that a cluster of about 30 atoms should be enough for a solid to reach convergence. Thank you in advance for any help, buena salud, Chris -- Christopher J. Patridge PhD. Contact: (315)-529-0501

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CLnorm Background - Possible Bug?
by Ashley Norris 10 Feb '12

10 Feb '12

Dear All, I was going to post this directly to Bruce, but the website asks for feedback to be directed to the list, so here it is. I'm a novice Athena user, but so far have found it to work very well for my needs. What I am writing about is that I have a problem with the CLnorm background routine: when there is a pre-edge peak present the edge is assigned to this peak position, instead of to the true edge position. I have attached a sample spectrum that shows exactly what I mean. Is there any way to work around this? Is it a limitation of the software or a bug? Is it even a problem? ...see, novice! :) It is particularly surprising to me because the marker (orange circle) shows the E0 position correctly, but the CLnorm routine is ignoring this...which is why I'm suspicious that it could be a bug. If CLnorm used this E0 position for its edge then everything would be well. I'm not jumping up and down in despair here as AutoBK will serve my immediate needs for now, but for what I want to do I am suspecting that CLnorm will be better*. Thanks again for a great program and all of the development work that has gone into it, Ash *open to suggestions as to why I am wrong about this. -- --- Ashley Norris Experimental Petrology Department of Earth Sciences Oxford University, UK --- ashley.norris(a)earth.ox.ac.uk --- +44 1865 272 051 ---

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Re Iffeffit LCF
by fred.mosselmans＠diamond.ac.uk 09 Feb '12

09 Feb '12

Dear Niken, I have had a look and i am afraid there are some problems, so what follows is not very positive. I am not sure your normalisation of the dilute samples is very good i ended up treating each spectrum slightly individually using a post-edge range of about 40-90 and adjusting the pre-edge range depending on the curviness of the pre-edge background. This is not ideal for linear combination fitting but i got spectra that looked like they had an edge step of 1. So That's fixable. But as you noticed the thiophene-10 and thiophene spectra are quite different. (you call it disulfide in your email but there are two thiophene and 1 disulfide spectra in the project. Ignoring self absorption which might give some relative peak intensity changes, i think this means they aren't the same thing Preparing your dilute samples some surface oxidation may have occurred in thiophene-10 there's a lump at 2481 or so that is bigger and displaced from the pure thiophene sample, this lump is quite reminiscent of some sulfate being present - this may be trace surface amounts, but the experiment will be sampling only about 10 microns worth of real sample so can be very important. This unfortunately is i think pretty unrecoverable. If the samples weren't well enough mixed and i mentioned earlier you are looking at only about 10 microns worth of powder in the post edge, then of course the sample you looked at is actually an unknown and not a standard, so a good fit in LCF might be the correct answer. Regards Fred BTW please use Dear Fred, dear professor fred just seems ridiculous to me. Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- 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 Iffeffit LCF
by fred.mosselmans＠diamond.ac.uk 08 Feb '12

08 Feb '12

Dear Niken, To my untutored eye your normalisation and fitting look OK so thus it comes down to the data or whether the treatment is valid: Did you collect the data in fluorescence mode? Two possible problems occur to me. As thiophene is a liquid at RT unless you did the experiment cryogenically I think 2 is unlikely. 1) Most probably there is an inherent self-absorption problem with S XANES LCF which was written about by G. Almkvist, K. Boye and I. Persson J. Synchrotron Rad. (2010). 17, 683-688 [ doi:10.1107/S0909049510022946 ] K-edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration. The self-absorption seen can affect the results of simple LCF data quite alot. 2) the samples were not well enough mixed, hence the data collected does not reflect the real mixture but a fraction that is more like the values you obtain by the LCF. S K-edge measurements don't sample much sample (sorry for that) so mixing solid standards is not necessarily trivial but for liquids/solutions this should not apply. Cheers Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- 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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LCF
by Niken Wijaya 07 Feb '12

07 Feb '12

Dear Everyone, I did S K-edge XANES spectra for a variety of standard mixtures (disulphide and thiophene) with known different concentrations. I also attached the ATHENA project file here. My problem is: some of the fitting results I acquired using LCF do really not represent the actual weight percentage. The condition of my standards mixtures is as follow: For sample S3: ~59% disulphide and 41% thiophene. The reported value from LCF is 81.6% disulphide and 18.4% thiophene. For sample S4: ~79% disulphide and 21% thiophene. The reported value from LCF is 95% disulphide and 5% thiophene. I am not really sure what I did wrong, but I really hope the experts here can help me with this issue. Regards, Niken

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Quantitative estimation according to LCF
by David Morse 07 Feb '12

07 Feb '12

I guess it is a simple question, but would be happy to get a statistical advise over here: I have the total concentration of metals in my samples and their standard deviation. I did a linear combination fit according to their EXAFS and got the best fit for a certain composition. I am aware of the limitations of this interpretation; still want to get some quantitative estimation of each component in my sample. I am multiplying its fraction (according to LCF) in the total concentration... that's easy.. but how should I treat the standard deviation of each fraction in this case?

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XAFS for electride
by Ping, Yuan 06 Feb '12

06 Feb '12

Dear XAFSers, Recently there has been a growing interest in the electride phase of sp-bonded materials at extremely high pressures >Mbar (see attached paper for example). This phase is characterized by a matrix of positive ions and interstitial electron blobs. I am wondering how XAFS signal would change when these electron blobs are present. The x-ray diffraction probably won't detect them directly. But XAFS might be able to show their existence if they behave like additional scattering centers. Any thought or information would be appreciated. Yuan

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Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena
by Tony Kelly 03 Feb '12

03 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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