Fit with Artemis in Demeter
On Thursday, September 29, 2011 11:26:08 am Kleper Rocha wrote:
I am trying to use the Artemis in Demeter to fit a spectra of Pt foil (data treated in Athena follow in attachement).
Hi Kleper, That's not Pt foil data. You got that data from the examples/recipes/Histogram/ folder in the source distribution. The data are from a nanoparticle, so the results you get will be quite different from a Pt foil. The purpose of the things in that folder are to demonstrate a still-experimental, largely undocumented interface in Artemis to the results of a molecular dynamics simulation.
I am utilizing the first shell coordination and, exactly as demonstrated in Bruce's videos, I put the parameters amp, enot, delr and ss. If I make all parameter as "guess" the fit is not good and the value of amp is low as expected from old Artemis. In this way, I make amp equal 1, delr equal 0, ss equal 0.003 and set these values. The enot was equal 5, maked as "guess" and the fit was made. The value found for enot was "grab" and then maked as "set". Then, the ss parameter was make as "guess" and when I press the Fit button, all windows of Artemis are closed. Please, what's the matter?
So, here's the thing about Demeter -- it's brand new software and still being beta tested. If it crashes, it's because you found a bug. It's not that you did something wrong -- you have found a problem that I need to correct. If you are running this on Windows, please send me the file %APPDATA%\demeter\dartemis.log, which contains the error messages associated with the crash you observed. On Windows XP, %APPDATA% = C:\Documents and Settings\<user name>\Application Data\ On Windows 7, %APPDATA = C:\Users\<user name>\AppData\Roaming If you are running this on linux, start artemis from the command line by typing "dartemis", then cut and paste the error messages from the crash into your email. When the new software crashes, a useful bug report contains those error messages. If you do not send me those error messages, I will not be able to help you. 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/ifeffit/Demeter
On Thursday, September 29, 2011 11:26:08 am Kleper Rocha wrote:
Hi for all, I am trying to use the Artemis in Demeter to fit a spectra of Pt foil (data treated in Athena follow in attachement). I am utilizing the first shell coordination and, exactly as demonstrated in Bruce's videos, I put the parameters amp, enot, delr and ss. If I make all parameter as "guess" the fit is not good and the value of amp is low as expected from old Artemis. In this way, I make amp equal 1, delr equal 0, ss equal 0.003 and set these values. The enot was equal 5, maked as "guess" and the fit was made. The value found for enot was "grab" and then maked as "set". Then, the ss parameter was make as "guess" and when I press the Fit button, all windows of Artemis are closed. Please, what's the matter? Thanks
Kleper, I was able to reproduce this problem on my computer. It turns out the problem was a typo. You can fix this on your computer relatively easily. Download this file from the git repository: https://raw.github.com/bruceravel/demeter/master/lib/Demeter/templates/repor... It is a one-line file. Now find where Demeter is installed on your computer. On Windows, it is probably C:\strawberry\perl\site\lib. On linux you can figure it out by typing the following at the command line perl -e 'use Demeter;use File::Basename;print dirname($INC{"Demeter.pm"})' Move the file you just downloaded to Demeter/templates/report/standard/setme.tmpl under that location. The correct folder has a bunch of files with the .tmpl extension. The first in the list shoudl be "after.tmpl". Once you put that one-line file in the correct place and with the correct name, the crash you experienced will not happen again. This will, of course, be corrected in the next release. And this fix has already been pushed to github. Thanks for finding this problem, 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/ifeffit/Demeter
On Thursday, September 29, 2011 01:16:23 pm Kleper Rocha wrote:
I did what you requested and now I'm able to make the adjustment in the way I had reported. However, there has appearing a message in a window, I am sending in attachment.
Sorry. I don't know how I missed that. I just pushed the correction to github. Download the same file from the same place and put it in the same place on your computer. This time for sure!
From what I understand from your first email, you were thinking that the data that I was using is from example, but, in fact is a data that I obtained experimentally.
You chose really similar names for the data groups. And I am easily confused :) 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/ifeffit/Demeter
Is ATOMS available as an executable program anymore? I can't seem to find a download for it on the IFEFFIT site. Is the idea to only use the web version? mam
On Thursday, September 29, 2011 05:25:49 pm Matthew Marcus wrote:
Is ATOMS available as an executable program anymore? I can't seem to find a download for it on the IFEFFIT site. Is the idea to only use the web version?
I stopped supporting a stand-alone version of atoms for a while, although a command line version comes with the windows installer and it lives in Artemis, of course. There is a stand-alone Atoms in the new, Demeter-based version of my codes. I'm still beta testing (i.e. squishing numerous bugs), however. 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/ifeffit/Demeter
participants (3)
-
Bruce Ravel -
Kleper Rocha -
Matthew Marcus