[Ifeffit] Something has gone wrong (was: Running Feff -- In Artemis)

Bruce Ravel ravel at phys.washington.edu
Tue Aug 10 08:59:13 CDT 2004


Hi,

I apologize for being so peevish yesterday.  Matt is correct that Dan
asked a legitimate question and I offered a very snarky response.
Someone just starting out with XAFS doesn't deserve that kind of
attitude and should not be discouraged from posting to the mailing
list.

Dan, I apologize for the 'tude.  Please don't let one day in which I
was in a bad mood keep you from participating in the community on the
mailing list.


That said, this line:

   I entered all the information into Atoms correctly and Atoms ran
   fine, but when I run Feff I get this message.

was the part that triggered my peevish response.  Instead of being
peevish, though, I should have explained how to better ask the
question.  Now, I still don't know what the problem was, so I'll use
as an example another problem that exists in the current version of
Artemis and about which there has been some discussion recently here
on the list.

There are situations where the potentials list contains atoms that are
not in the atoms list and so Feff does not run to completion.  One
such material that readily triggers this problem is YBa2Cu3O7, the
superconductor.  Suppose a posting to the mailing list said "I entered
the data for YBa2Cu3O7 correctly and atoms ran but then Feff did not
run."  It is very hard for me to know how to address that because I
have run Atoms and Feff within Artemis hundreds of times without any
problem.  Without more information, I cannot offer good advice.

Now consider a posting that says this:

  I entered the following data for YBa2Cu3O7 into the atoms page in
  Artemis 0.7.008 on my linux machine:

   title = YBCO: Y Ba2 Cu3 O7 
   space = P M M M 
   a = 3.8230   b = 3.8860      c = 11.6810
   core = cu1    rmax = 5.20
   atoms
   ! elem   x          y          z       tag    
     Y     0.50000    0.50000    0.50000       
     Ba    0.50000    0.50000    0.18400       
     Cu    0.00000    0.00000    0.00000  cu1  
     Cu    0.00000    0.00000    0.35600  cu2  
     O     0.00000    0.50000    0.00000  o1   
     O     0.00000    0.00000    0.15800  o2   
     O     0.00000    0.50000    0.37900  o3   
     O     0.50000    0.00000    0.37700  o4   

  Atoms ran to completion, and the feff.inp file looked ok, but when I
  ran Feff, I saw this written in the window where feff's runtime
  messages are written:

    Feff 6L.02
    No atoms or overlap cards for unique pot     1
    Cannot calculate potentials, etc.
    Fatal Error: at RDINP

  What is the meaning of this error and how can I fix it?


Do you see how that is a much better explanation of the problem?
Rather than asserting that the atoms data was correct, the atoms data
used was cut and pasted into the email.  That way, I can enter the
exact same data into my running copy of Artemis and observe the
problem myself.  Then, the messages from Feff were transcribed into
the email.  While I admit that what Feff says is cryptic, I actually
understand that message and would have recognized the problem for what
it was.  Also note that the improved explanation started by stating
the version number of Artemis and the computer platform used.

(The answer to the example problem: there is a bug in Atoms.  The
work-around is to increase Rmax in Atoms, then rerun Atoms and Feff.)

There are some other places to look for useful clues as to the
problem.  You will notice that the window that displays the feff
runtime messages also contains several other spaces arranged as note
tabs.  The one marked "Echo" shows every message that has been written
to the echo area at the bottom of the main window.  Sometimes a useful
message gets written to the echo area but then something else comes
along.  Looking at the history of echo messages sometimes helps.

The other space that is very useful is the one labeled "Ifeffit".
That space records the most recent 2000 lines of communication between
Artemis and Ifeffit.  If Ifeffit has ever become confused by something
Artemis asks it to do, it's response will be printed in blue text.  By
examining this text, you can actually uncover lots of clues about the
inner workings of Artemis.

Another useful bit of information, and one that speaks directly to
Dan's original question, can be found in the "Theory" menu.  Selecting
"Identify this feff calculation" will write something like
 
  This Feff: data0.feff0    This 
project: /home/bruce/.horae/stash/artemis.project.2/

in the echo area.  This identifies the space on your hard drive where
artemis stores all the data and information from feff that it is using
in the current project.  It also identifies the current feff
calculation with an identifier that is used both internally in the
program and as the name of the folder in the project space containing
the results of the atoms and feff runs.  Thus the feff.inp file
generated by atoms in this example would be found at:

  /home/bruce/.horae/stash/artemis.project.2/data0.feff0/feff.inp



I could write up a thorough explanation of the project file format and
the contents of its files if anyone is interested.

HTH,
B



-- 
 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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