[ase-users] jacapo cell optimization broken

[John Kitchin]

hmm... I see the problem, a StrainFilter is not an atoms object, and so has
no arrays. It looks like at some point I added code to jacapo for
determining if an atoms had changed. the reason for that is related to some
issues with 32-bit and 64-bit representations of floats being just different
enough to make atoms that were unchanged not equal the atoms read from a
file that should have been the same.

I am not sure how to fix this without putting the (filtered) arrays onto the
StrainFilter. any ideas?

John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu




On Wed, Aug 24, 2011 at 12:27 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>wrote:

> Hi,
>
> running "2.3.2.3. Complicated unit cell optimization" from
> http://gilgamesh.cheme.cmu.**edu/jacapo/jacapo/2-bulk/2.2-**
> unitcell-optimization/2.2.0-**unit-cell-optimization.html<http://gilgamesh.cheme.cmu.edu/jacapo/jacapo/2-bulk/2.2-unitcell-optimization/2.2.0-unit-cell-optimization.html>
> results with the latest ase 2260 with:
> Traceback (most recent call last):
> ...
>  File "/home/camp/dulak/tmp/alex/**ase/ase/optimize/optimize.py", line
> 119, in run
>   self.step(f)
>  File "/home/camp/dulak/tmp/alex/**ase/ase/optimize/**bfgslinesearch.py",
> line 91, in step
>   e = self.func(r)
>  File "/home/camp/dulak/tmp/alex/**ase/ase/optimize/**bfgslinesearch.py",
> line 151, in func
>   return calc.get_potential_energy(**self.atoms,force_consistent=**True) /
> self.alpha
>  File "/home/camp/dulak/tmp/alex/**ase/ase/calculators/jacapo/**jacapo.py",
> line 2305, in get_potential_energy
>   if self.calculation_required(**atoms):
>  File "/home/camp/dulak/tmp/alex/**ase/ase/calculators/jacapo/**jacapo.py",
> line 2638, in calculation_required
>   if not self.atoms_are_equal(atoms):
>  File "/home/camp/dulak/tmp/alex/**ase/ase/calculators/jacapo/**jacapo.py",
> line 963, in atoms_are_equal
>   b = atoms.arrays
> AttributeError: StrainFilter instance has no attribute 'arrays'
>
> Marcin
>
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