Hi Carlo,
could this be the same bug we discussed on the list in may (incorrect
setting of the angles when reading hexagonal structures, see below)?
Have you tried the "workaround" of manually reentering the correct
angles each time?
Best, Peter
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Date: Wed, 21 May 2003 14:22:33 -0500 (CDT)
From: "Carlo U. Segre"
Subject: [Ifeffit] TkAtoms weirdness
Bruce:
I have recently encountered a weird problem with TkAtoms. Let me detail
it setp by step.
1. Start TkAtoms and build a model from scratch.
2. Press the "Run Atoms" button. The output of this is correct and can
be saved to disk.
3. Save the "atoms.inp" file associated with the model that has been
successfully run and exit TkAtoms.
4. Start TkAtoms again and load the previous "atoms.inp" file.
5. Press the "Run Atoms" button again. This time the output (the FEFF
input file) is completely different than in step 2. It is also
completely incorrect. Many of the x,y,z coordinates are set to zero.
In fact the x coordinate is always zero.
If I clear the data boxes and re-enter the original numbers, the results
are correct once again.
This is extremely confusing to me. I have only tried it with a single
structure but it shows this behavior consistently. I have attached the
offending atoms.inp file.
Carlo
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Date: Thu, 22 May 2003 11:27:08 +0200
From: Peter Pfalzer
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] TkAtoms weirdness
Hi all,
I encountered a problem similar to the one Carlo describes in his mail.
I believe there is a bug in how TkAtoms reads 90 deg. angles from input
files and (maybe) treats trigonal systems in hexagonal notation.
Carlo: After reading in the input file, complete the lattice parametes
by hand, i.e. enter the angles (90 deg) into the blank fields for alpha
and beta. Then the calculation should work.
If you don't enter the angles manually TkAtoms will obscure your
structure. Watch the lattice parameters *after* running atoms! The value
for the c axis will have changed so that a=b=c and you will get
alpha=beta=gamma=120 deg.
The other day I complained to Bruce about the calculation of the unit
edge length (in the absorption card), printing out way to large sample
thicknesses for an edge step of 1.
In the meantime I noticed that the values for absorption length and unit
edge length depend on whether I use the trigonal or the rhomohedral
representation for my unit cell.
Bruce: The values for the trigonal unit cell seem okay, maybe the
problem is the treatment of the rhombohedral structure (not the specific
wheight as I originally speculated). I have attached the two input files.
Hope I could help!
Best,
Peter
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--
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Peter Pfalzer
Universitaet Augsburg Tel: +49-821-598-3215
Lehrstuhl fuer Experimentalphysik II Fax: +49-821-598-3411
Universitaetsstr. 1
D-86135 Augsburg
Germany Peter.Pfalzer@physik.uni-augsburg.de
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