[Ifeffit] This might be a silly question....

Bruce Ravel ravel at phys.washington.edu
Wed Oct 29 16:44:03 CST 2003

On Wednesday 29 October 2003 04:55 pm, k-kupiecki at northwestern.edu wrote:
> Hi,
> I'm also a novice with the Athena/Artemis Ifeffit software.
> I've read through the online documentation for both and I'm now trying to 
> go through the Cu example in Chapter 2 of the Artemis manual.
> Can someone please tell me where I input the following information into
> Artemis (I've tried in the fields on the Path parameter screen, but it
> gives me an error when I go to fit)?  (from page 19 of the manual):
>     We will then define extremely simple math exressions for the
> corresponding path parameters of the first shell.
>      s02     0:1     amp
>      e0      0:1      e0
>      delr    0:1      delr
>      sigma2 0:1    ss


Hmmm.... this is a little embarassing.  I have to apologize for the
state of the Artemis document.  It suffers rather alot right now from
bad stream-of-consciousness writing.

My goal in the chapter on the copper fit was to walk through the steps
of an increasingly complicated fit.  Start with single shell, then two
shells, then three.  Then do four shells + all the necessary multiple
scattering.  Then introduce the concept of multiple-data-set fitting.
As I was writing it a few months ago, I didn't want to interupt my
(ever-so-brilliant) train of thought to make a bunch of screenshots
demonstrating what I was talking about, so I tried to develop a
text-only shorthand to explain what I meant.

The "0:1" was my shorthand for indicating that this was path number 1
(i.e. the first one) from data set number 0 (also intended to be the
first one).  Obviously confusing.  Sigh.

In an attempt to clarify the situation, I made four screenshots from
the single shell project file that gets distributed with the program.

Point your browser at this directory:

You will find the four screenshots I just made:
   artemis_cu1.png      the view of the data
   artemis_cu2.png      the view of the guess and set parameters
   artemis_cu3.png      the view of the description of the feff calculation
   artemis_cu4.png      the view of the first path

I think this should make it clear what goes where.  Note that these
shots were taken of Artemis getting ready to fit just the fist shell
of the copper data.  Thus paths contained in feff0002.dat through
feff0005.dat are not included in the fit.  The ones not included in
the fit are written in brown text in the list on the right side of the
window.  In subsequent fits, when those included in the fit, you can
edit their parameters by clicking on them.  That will display
something that looks very much like the artemis_cu4.png image, but
with the information relevant to that path.

Taking language from those images on my web site, the bit in the
document that you are asking about would have been much better
written as:

   FEFF0: feff0001.dat
      s02      =    amp
      e0       =    e0
      delr     =    delr
      sigma2   =    ss

That would have, perhaps, been clearer.  Certainly more consistent
with the appearence of the program.  And still more concise than an
entire screenshot at that point in the doc.

Hope that helps, sorry for the confusion, and don't hesitate to keep
asking questions on the mailing list.  And, contrary to the sentiment
in your subject line, there are no silly questions, just silly



 Bruce Ravel  ----------------------------------- ravel at phys.washington.edu
 Code 6134, Building 3, Room 222
 Naval Research Laboratory                          phone: (1) 202 767 5947
 Washington DC 20375, USA                             fax: (1) 202 767 1697

 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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