[Ifeffit] Generating single scattering paths in Artemis
ravel at phys.washington.edu
Thu Jan 6 14:47:05 CST 2005
Several approaches to the problem of a simple, one-shell fit were
proposed with different ideas about incorporating them into Artemis:
1. Scott suggested a solution involving a low symmetry group, but ran
into a problem that required some knowledge of Feff to solve -- a
situation he suggested that Artemis is supposed to protect the
2. Anatoly suggested using Feff's overlap and ss keywords. Those
features of Feff were certainly designed for simple fitting
problems, but, I agreed with Carlo when he pointed out that the
documentation is a bit cryptic.
3. Mark suggested using the Feff templates in Artemis. That's a good
idea and certainly why I included the templates, but it fails to
protect the user in the manner Scott recommends.
4. Sam explained how SixPack uses simple coordination geometries and
a periodic table interface to address this problem.
5. Finally, I suggested one way of solving the problem using Artemis
as it is today.
Scott made this comment: "So I vote for changing the way Artemis works
in such circumstances so that less editing is needed". OK! I agree!
We now agree on what we don't want (lots of editing). Now we need to
discuss what we *do* want.
None of the solutions above are perfect:
1. The low symmetry solution suffers from requiring the user to
understand enough crystallography and enough about Feff to get that
solution to run to completion.
2. Like Carlo, I have never quite understood the whole overlap thing
in Feff. In any case, I think that the user should eventually be
forced to think about paths. Today you might analyse the first
shell, but tomorrow you will want to roll up your sleeves and
start doing a much better analysis. There is no smooth transition
from an overlap first shell analysis to a more sophisticated
path-based analysis. It is better, IMHO, to start with paths and
stick with paths.
3. The problem with the templates is having to know what to write in
the templates. The templates are super-helpful if you can, say,
cut and paste atomic coordinates from a Protein Data Bank file,
but not so convenient otherwise.
The solution I see is a combination of Sam's periodic table thing and
the solution I suggested two emails ago. It could work something like
a. Choose "Single scattering fit" from one of the menus
b. Pop up a dialog in which the user tells Artemis:
i. the species of the absorber
ii. the species of the scatterer
iii. the approximate distance to the first shell
iv. the geometry
c. Artemis constructs a suitable feff.inp file, runs Feff without
asking for confirmation, and imports only the first path
d. Variables for amplitude, sigma^2, delr, and e0 are generated
automatically, just like they are now
e. Artemis pops up a dialog asking the user if she wants to run the
fit immediately or later. The immediate choice is just like the
big green button, the later choice lets the user examine things
before pressing the big green button.
A few comments:
Regarding step b.i. and b.ii.: This could be a periodic table, like
Sam uses or a couple of entry boxes, which would be more compact
Regarding step b.iv.: I think I would include some real diatomic
crystal structures, such as rock salt, cesium chloride, zinc
sulfide, along with the things in Sam's list (square planar,
octahedral, tetrahedral, according to the screenshot on his web
This approach is simpler than how Artemis currently works only in that
it automatically jumps through several steps without stopping. Once
the fit is done, the user is still looking at Artemis and Artemis is
just as complicated as it ever was.
However, the advantage of this approach over, say the overlap thingie,
is that one is in a position to begin using some of Artemis' tools to
look beyond a simple first shell fit.
In short, the bad news is that it is still Artemis, but the good news
is that it is still Artemis.
Like Scott, we all vote that Artemis work better. But Artemis is the
product of a benevolent dictatorship rather than of a democracy.
While you all are welcome to cast a vote for the goodness of Artemis,
I'm really looking for concrete design suggestions.
Bruce Ravel ----------------------------------- ravel at phys.washington.edu
Code 6134, Building 3, Room 405
Naval Research Laboratory phone: (1) 202 767 2268
Washington DC 20375, USA fax: (1) 202 767 4642
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
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