December 2007 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Mac OS 10.4.11 upgrade and no more Ifeffit
by Andrew Feitz 13 Dec '07

13 Dec '07

Hi Jeff, Thanks for the tip. I installed iXAFS, ran the program, and got a prompt telling me X11 couldn't be located. So looks like my X11 is somehow corrupted. I'll reinstall the developer tools and hopefully that will solve the problem. Cheers, Andrew > ------------------------------ > > Message: 4 > Date: Tue, 11 Dec 2007 10:06:53 -0600 > From: Jeff Terry <terryj(a)iit.edu> > Subject: Re: [Ifeffit] Mac OS 10.4.11 upgrade and no more Ifeffit > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <C8F3AC38-C356-4A80-BA26-7BDD24E6C7A0(a)iit.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Andrew, > > I don't really have any idea what is causing the problem that you are > having. But if you don't need a specially installation, you might try > the iXAFS version at http://mrcat.iit.edu > > We don't have any reports of trouble with 10.4.11. > > Jeff > > On Dec 11, 2007, at 9:32 AM, Andrew Feitz wrote: > > > Hi, > > > > I had a working version of Ifeffit 1.2.9 on my mac powerbook G4 but > > after upgrading to 10.4.11, Athena, Artemis and Hephaestus briefly > > launch, give a display option and then promptly die. Feff6 works > > fine and I have X11 installed. Any good ideas? I've tried deleting > > files from Applications/Ifeffit, /Library/Perl and /Library/Receipts/ > > Ifeffit-.* and reinstalling. I guess it has something to so with Tk > > but I'm unsure which version to install and whether that is really > > the problem. Suggestions very welcome! > > > > Cheers, > > > > Andrew > > > >

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problems with ATHENA
by chiara 12 Dec '07

12 Dec '07

Dear all, it seems I have a great problem with athena. As I write "athena" on the terminal to launch the program, it says: :~$ athena bad geometry specifier "15x-204+652+393" at /usr/lib/perl5/Tk/Submethods.pm line 37. :~$ On my desktop, I can see only the pgplot screen (I'm sending a screenshot of what I see), but the athena screen with all commands does not appear. Can someone help-me? I have reinstalled all ifeffit packages, and horae as well, but with no result. Artemis, on the other hand, works well! Thank you. Chiara p.s. I'm using Ubuntu 7.10 gutsy gibbon

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Mac OS 10.4.11 upgrade and no more Ifeffit
by Andrew Feitz 11 Dec '07

11 Dec '07

Hi, I had a working version of Ifeffit 1.2.9 on my mac powerbook G4 but after upgrading to 10.4.11, Athena, Artemis and Hephaestus briefly launch, give a display option and then promptly die. Feff6 works fine and I have X11 installed. Any good ideas? I've tried deleting files from Applications/Ifeffit, /Library/Perl and /Library/Receipts/Ifeffit-.* and reinstalling. I guess it has something to so with Tk but I'm unsure which version to install and whether that is really the problem. Suggestions very welcome! Cheers, Andrew

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problems with opennig of data files with Athena
by Iztok Arčon 11 Dec '07

11 Dec '07

Dear Bruce, today I found a serious problem with Athena on my computer: I cannot open any data files. If I use standard open command, nothing happens, only the following message appears: Tk::Error: can't call method "writeConfig" on an undefined value at athena line 21584 Any ideas what to do? I already reinstalled iffefit ifeffit-1.2.10.exe <http://prdownloads.sourceforge.net/ifeffit/ifeffit-1.2.10.exe?download> on my windows XP system Athena can still open old projects, but no individual data files thanks for help in advance best regards Iztok -- Iztok Arcon University of Nova Gorica Vipavska 13, POB 301 5001 Nova Gorica, Slovenia tel: +386 5 331 5227 fax: +386 5 331 5240 e-mail: iztok.arcon(a)p-ng.si http://www.p-ng.si/~arcon http://www.p-ng.si/~arcon/xas

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Re: [Ifeffit] iXAFS 2 beta 1 released
by Hind Al-Abadleh 07 Dec '07

07 Dec '07

Thanks Jeff and Matt for your timely reply. The software runs just fine now. Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ---------------------------- >>>terryj(a)iit.edu 12/07/07 9:11 am >>> Hind, X11 would be in /Applications/Utilities/ You should install X11 off of your 10.4 DVD and then apply the update. Jeff On Dec 7, 2007, at 5:42 AM, Hind Al-Abadleh wrote: >Hi Jeff, > >This is great news. I downloaded the beta version, and got the error >message Apple's X11 for Mac OSX is not installed.... So, I >downloaded >the latest update for X11 from Apple's website from this page: >http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113… > >And when I tried to install it, an alert message came this system >doesn't need this update. So, now I'm baffled, and truly don't know >where to go from here. How would I check my system (OSX 10.4.11) for >the X11 already installed? > >Any advice will be very much appreciated. >Thanks, >Hind > > > > > >---------------------------- >Hind A. Al-Abadleh, Ph.D. >Assistant Professor >Chemistry Department, Wilfrid Laurier University >Science Building 3020F >75 University Ave. W. >Waterloo, Ontario N2L 3C5 Canada >Ph.: (519) 884-0710 ext. 2873 >Fax: (519) 746-0677 >URL: http://www.wlu.ca/science/chemistry/halabadleh/ >---------------------------- > >>>>terryj(a)iit.edu 12/07/07 12:15 AM >>> >Hi All, > >iXAFS version 2 for Mac OS X 10.4 and above has been released as a >beta version. We have tested this version on ppc and intel macs >running OS X 10.4 and 10.5. > >You must have Apple's version of X11 installed in order to use iXAFS. > >Ken McIvor put in yeoman's work to build the full ifeffit, horea suite >as a universal binary. He packaged it as a single drag and drop >installation within iXAFS. > >Ken wanted to post this message but had an illness in the family. >Hopefully, we can all thank Ken for his work to get this built in a >manner that should work on all modern Macs. > >A link to download this version of iXAFS can be found at the MRCAT >website: > >http://mrcat.iit.edu > >We forgot to put in the documentation that the iXAFS shell allows you >to run any of the programs from the command line ifeffit, feff6, etc. > >Jeff > > >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 Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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iXAFS 2 beta 1 released
by Jeff Terry 07 Dec '07

07 Dec '07

Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff

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Re: [Ifeffit] Graphics Problems in ATHENA
by Ravel, Bruce 05 Dec '07

05 Dec '07

Hi Sola, This is the sort of question that should go to the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. > I recently encountered a problem with a .prj file in ATHENA. The first > issue was the notification that ATHENA may be out of memory and when I > checked the memory usage under the help menu, I found out that I was not > even using up to 1% of the memory. So, after closing the saved .prj > files, one with some groups removed and another one without removing > some groups, I tried to reopen the .prj but the graphics refused to > display. I have since rebooted the system and updated IFEFFIT, but still > no luck! This is not really enough information for me to figure out the nature of the problem you are seeing and I have never seen the behavior you describe, but I can give you a few hints. 1. Athena's way of guessing memory usage is extremely unreliable. In general it is a poor idea to import more than about 60 scans into Athena (that is, 60 scans of the typical step-scan variety with 10 volts steps in pre-edge, 1/2 volt steps through the edge, and 0.05 A^-1 steps in the EXAFS) or fewer if you are importing MED files with lots of columns or quick scans with lots of data points. This is not a shortcoming of Athena, rather it is a result of Ifeffit being written in Fortran. If you are running into memory issues, you should group your data in smaller chunks for import into Athena. 2. Perhaps there is something abnormal about the prj file, but I cannot know unless you attach an example that produces the poblem reliably. 3. Are there any messages in the console window that starts when you start Athena? That's the window that stays on the task bar after Athena starts. The messages i that window may be gobbledigoop to you, but they may provide me with information about the nature o fthe problem. If Athena is exiting before you can look at the console, try opening up a command window, changing directory to C:\Program Files\Ifeffit\bin (or wherever Ifeffit is installed) and running athena from the command line. That way, any error messages will be preserved. B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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problems running athena on macOSX
by Hind Al-Abadleh 05 Dec '07

05 Dec '07

I have downloaded and successfully installed Ifeffit-1.2.10-Mac10.4_PPC_horae66. But every time I click on athena, the X11 and aquaterm message appears, and regardless of my choice, Athena won't launch and will automatically quit! I downloaded X11 from Mac website and while installing, a message came up telling me that I have a later version already installed on my mac. But still, can't get Athena to work. I also downloaded and installed iXAFS.app. After clicking on the iXAFS icon, a window appears to specify the path to data and three icons to Athena, Artimis, etc, but clicking on the icons won't take me any where! Any insight would be greatly appreciated. Thanks, Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ----------------------------

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Re: [Ifeffit] Log-Ratio
by Frenkel, Anatoly 05 Dec '07

05 Dec '07

It adds (or subtracts) 2pi to the phase difference between the unkown and the standard as some times it does not eztrapolate to zero as 2k*delta r term should. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Wed Dec 05 06:22:28 2007 Subject: [Ifeffit] Log-Ratio Dear all, i have a question to the Log-Ratio/Phase-Differnce Analysis in Athena. What means the parameter 2pi jump? I did not find any help file for the ratio method. Best regards Jörg Haug _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Log-Ratio
by Jörg Haug 05 Dec '07

05 Dec '07

Dear all, i have a question to the Log-Ratio/Phase-Differnce Analysis in Athena. What means the parameter 2pi jump? I did not find any help file for the ratio method. Best regards Jörg Haug

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