Hi all, I am performing EXAFS measurements on amorphous Indium Zinc Oxide (In and Zn edges) thin films and have a question about methods to break correlations. We have the films grown at several compositions ranging from 50/50 to 90/10 (In/Zn wt.%). We expect these films to display first NN shells very similar to their pure oxide cases, but the are interested in changes to the next-NN shells. I was wondering if folks on the mailing had some good references on multiple data set fits using doping fractions to break correlations. Would it be worth doing temperature dependent (or perhaps just cold) measurements to try and break correlations that way? Another couple unrelated questions... I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install? Does anyone have an Athena plugin for the SSRL data Collector v2.0? The SSRL plugins available make the program crash when I try and use them. (moderators, let me know if these questions should have been in a separate posting) Regards, Brandon
On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote:
Does anyone have an Athena plugin for the SSRL data Collector v2.0? The SSRL plugins available make the program crash when I try and use them. (moderators, let me know if these questions should have been in a separate posting)
Here is the SSRL binary plugin from the svn repository http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athen... And here is the one for data files that have been converted to ascii http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athen... They should be placed in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ I am willing to take a look at the problem you are seeing, but "it crashes" doesn't give me much to work with. Obviously the plugins worked for me otherwise I would not have considered them ready for release. You need to provide some clue as to what the problem is. Either supply a data file that triggers the problem or by cut and paste what gets written after starting Athena in a terminal window or (preferably) both. B -- Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/
On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote:
I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install?
That is actually a question I need to know the answer to as well. In fact, our group's post-doc has the same question, so I plan to look into it this week. (Since I did not make the iXAFS package, I am not 100% clear on how it works -- which is actually true of most things on a Mac!) I believe the answer is yes, but I'll let you know what I know more. B -- Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/
iXAFS originally started out as a wrapper to launch the individual programs. At that time, it was a simple matter to replace any of the individual programs. Ken McIvor has improved iXAFS so that it now builds universal projects but has perl code embedded. This makes it more difficult to update.
That said there is a directory structure within iXAFS and I would guess that replacing the individual programs would work. I make no guarantees though as I am not sure of all the changes that Ken has made since I initially wrote the cocoa wrapper.
Jeff
Sent from my iPhone
On Aug 30, 2010, at 9:11 AM, Bruce Ravel
On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote:
I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install?
That is actually a question I need to know the answer to as well. In fact, our group's post-doc has the same question, so I plan to look into it this week. (Since I did not make the iXAFS package, I am not 100% clear on how it works -- which is actually true of most things on a Mac!)
I believe the answer is yes, but I'll let you know what I know more.
B
--
Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/
On Monday 30 August 2010 10:11:06 am Bruce Ravel wrote:
On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote:
I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install?
That is actually a question I need to know the answer to as well. In fact, our group's post-doc has the same question, so I plan to look into it this week. (Since I did not make the iXAFS package, I am not 100% clear on how it works -- which is actually true of most things on a Mac!)
I believe the answer is yes, but I'll let you know what I know more.
B
Hi Brandon, I just managed to update Athena and Artemis in situ on a colleague's Mac laptop. It is possible, but it is not pretty. I will give the steps below, but BY FAR the better solution would be to say really nice things to Ken and Jeff so that they will update the iXAFS package to include the latest versions. It is certainly true that I have only figured out *a way* of doing this. I have certainly not found *the best way* of doing so. I should also say that I was sitting next to one of my linux computers while working on this. That + a memory stick made step 1 very easy. I have never used svn on a Mac and cannot advise you about how to install it or how to get it to work on that platform. 1. To begin, you need to download a copy of the horae package from its svn repository. svn export http://cars9.uchicago.edu/svn/horae/trunk horae In a terminal window, go into the newly made horae folder and run the scripts "mkartemis.PL", "mkathena.PL" and "mkhephaestus.PL". This will generate the athena, artmeis, and hephaestus programs and place them in the bin folder. Those are perl scripts and will only work if perl works on your computer. 2. Open the copy of the athena program that is in this folder in a text editor: /Applications/iXAFS/Contents/Resources/bin Copy (in the sense of copy in Edit menu) the lines that appear between #!/usr/bin/perl and the first line containing only hash marks (#). 3. Copy the three programs from the bin folder into /Applications/iXAFS/Contents/Resources/bin This will overwrite the old version. 4. Edit each of the three files that you just copied. Place the lines from step 2 after #!/usr/bin/perl in each of the three files. Those cryptic lines are absolutely essential to making the programs work. Crazy, but true. 5. Copy all the .pm files from lib/Ifeffit/ folder into this folder: /Applications/iXAFS/Contents/Resources/lib/perl5/site_perl/5.8.8/darwin- thread-multi-2level/Ifeffit/ 6. Copy this file: http://cars9.uchicago.edu/svn/libperlxray/Absorption/lib/Xray/FluorescenceEX... into /Applications/iXAFS/Contents/Resources/lib/perl5/site_perl/5.8.8/darwin- thread-multi-2level/Xray/ 7. Edit the file FluorecenceEXAFS.pm that you just installed in a text editor (*not* a word processor). Remove the line that says use Readonly; and edit the line that says Readonly my $ETOK => 0.2624682917; to instead read my $ETOK = 0.2624682917; Having done all those things, my colleague's computer was up to date and all the programs seemed to work normally. Obviously, all of that is not for the casual user of my software. Please remember that I am not your computer administrator and it is not my responsibility to walk you through all these steps. Typing up this email is already more than I actually feel responsible for. Really ... make nice to Ken and Jeff. That's a much better solution. Or, volunteer to help maintain the iXAFS package. That's the best solution of them all! B -- Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/
participants (3)
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Brandon Reese -
Bruce Ravel -
Jeff Terry