Path updating in Artemis
Dear List (and especially Bruce) I recently restarted using Artemis after a hiatus. I seem to be confused about a key procedure used to worked before (unless I'm deluded). I load in an Athena project (a single curve to be fitted), and then a feff file that contains an approximation to my atomic positions (8 atoms). Then I run feff via artemis, and I guess/set/def the variables for each path. The paths to sulfur use the variables ampS, delrS, ssS; those to carbon use ampC, delrC, etc. (Not all variables are floated independently, but I like to keep the names separate and express dependencies explicitly.) Now suppose I tweak my feff data (in the feff.inp tab of Artemis) and rerun feff. If I DON'T import any paths at the end, as recommended by the dialog, the Reff, amp, etc. associated with each path in the "Data & Paths" panel remain unchanged, while the data for the paths in "Interpretation" panel get updated. The two columns are now out of sync, and pressing the Fit button merely redoes the computation using the old paths. If I rerun feff and DO import paths at the end, I end up with duplicate paths; the new ones have the the right Reff etc., but they use the default variables rather than the ones that I laboriously associated with the earlier paths. How can I get paths that have the variable scheme I created, but new data for each feff run? The only way I seem to be able to do this is by closing the project and reopening it. But I could swear that earlier this was not the case. What am I missing? Silvio
On Saturday 29 December 2007 00:05:45 Silvio Levy wrote:
Now suppose I tweak my feff data (in the feff.inp tab of Artemis) and rerun feff. If I DON'T import any paths at the end, as recommended by the dialog, the Reff, amp, etc. associated with each path in the "Data & Paths" panel remain unchanged, while the data for the paths in "Interpretation" panel get updated. The two columns are now out of sync, and pressing the Fit button merely redoes the computation using the old paths.
If I rerun feff and DO import paths at the end, I end up with duplicate paths; the new ones have the the right Reff etc., but they use the default variables rather than the ones that I laboriously associated with the earlier paths.
How can I get paths that have the variable scheme I created, but new data for each feff run? The only way I seem to be able to do this is by closing the project and reopening it. But I could swear that earlier this was not the case.
What am I missing?
Hi Silvio, You're not missing a thing. You have discovered one of the serious shortcomings of Artemis. Changing the structure in the feff.inp file and rerunning feff is high likely to change the list of paths in some way that artemis is not currently clever enough to track. Quitting and restarting is one work-around. Another would be to re-read the feff.inp file, thus starting another Feff entry in the paths list. Modify the feff.inp file, run feff, import paths, parametrize them. Then, exclude *all* of the paths from the previous Feff calculation. I confess that this is also a clunky work-around. But it has an advantage over stopping and restarting in that it maintains a single fit history inside the project file. For what it's worth, the problem you are asking about is something that my Demeter project will be able to handle gracefully. In fact, I have spent much of the last week working on Demeter's Feff interface. It is coming along nicely, but I've still got a long path ahead. Rgeards, 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 (2)
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Bruce Ravel -
Silvio Levy