[gpaw-users] Problems running GPAW

[Jess Wellendorff Pedersen]

Hi augustus,

I'm not really certain what you are aiming at with this script, but 
there are at least a few issues with it:

Augustus Low wrote:
> Hi Jess,
>
> This is my script:
>
> from ase import Atoms
> from ase.visualize import view
> from ase.calculators.emt import EMT
> from ase.constraints import FixAtoms
> from ase.optimize import QuasiNewton
> from ase.lattice.cubic import BodyCenteredCubic
>
> a = 3.61
> bcc = BodyCenteredCubic(size=(1,1,1), symbol='Cu', pbc=(1,1,0), 
> latticeconstant=3.61)
this creates a bcc unit cell for you with two atoms in it and periodic 
boundary conditions in the x and y directions but not in the z 
direction. Doesn't really apply for an infinitely extended solid, for 
which pbc should be (1,1,1). pbc = (1,1,0) is mostly applicable to 
surface slab models and the likes.
>
> bcc.append(29)
> bcc.positions[2]=(a,a,a)
> bcc.append(29)
> bcc.positions[3]=(a,0,0)
> bcc.append(29)
> bcc.positions[4]=(0,0,a)
> bcc.append(29)
> bcc.positions[5]=(a,0,a)
> bcc.append(29)
> bcc.positions[6]=(0,a,0)
> bcc.append(29)
> bcc.positions[7]=(0,a,a)
> bcc.append(29)
> bcc.positions[8]=(a,a,0)
this is where it gets really problematic. All the above appends are bad, 
because the periodic boundary conditions "translate" the unit cell for 
you in the pbc=1 directions. Therefore, with a manual translation in say 
the x direction, you now put two atoms exactly on top of each other in 
the pbc=True directions.
>
> constraint = FixAtoms(mask=[a.symbol !='Cu' for a in bcc])
> bcc.set_constraint(constraint)
>
> view(bcc)
>
> bcc.set_calculator(EMT())
> dyn = QuasiNewton(bcc)
> dyn.run(fmax=0.05)
>
> print bcc.get_potential_energy()
>
> from gpaw import GPAW
> calc = GPAW(nbands= -10)
> bcc.set_calculator(calc)
> bcc.get_potential_energy()
I hope you realize that this would be an extremely crude DFT 
calculation, with default real-space density grid spacing, LDA 
exchange-correlation, and only a single k-point (the gamma point) in 
reciprocal space, meaning that even though you a using periodic boundary 
conditions such as to model an extended lattice you are not taking this 
periodicity into account in the electronic structure calculation.

/Jess

Augustus Low wrote:
> Hi all,
>
> I'm new to programming on GPAW and I need some help on this. I'm 
> trying to calculate the potential energy of this simple bcc structure 
> using both EMT and GPAW. Here is my script:
>
> from ase import Atoms
> from ase.visualize import view
> from ase.calculators.emt import EMT
> from ase.constraints import FixAtoms
> from ase.optimize import QuasiNewton
> from ase.lattice.cubic import BodyCenteredCubic
>
> a = 3.61
> bcc = BodyCenteredCubic(size=(1,1,1), symbol='Cu', pbc=(1,1,0), 
> latticeconstant=3.61)
>
> bcc.append(29)
> bcc.positions[2]=(a,a,a)
> bcc.append(29)
> bcc.positions[3]=(a,0,0)
> bcc.append(29)
> bcc.positions[4]=(0,0,a)
> bcc.append(29)
> bcc.positions[5]=(a,0,a)
> - Hide quoted text -
> bcc.append(29)
> bcc.positions[6]=(0,a,0)
> bcc.append(29)
> bcc.positions[7]=(0,a,a)
> bcc.append(29)
> bcc.positions[8]=(a,a,0)
>
> constraint = FixAtoms(mask=[a.symbol !='Cu' for a in bcc])
> bcc.set_constraint(constraint)
>
> view(bcc)
>
> bcc.set_calculator(EMT())
> dyn = QuasiNewton(bcc)
> dyn.run(fmax=0.05)
>
> print bcc.get_potential_energy()
> - Hide quoted text -
>
> from gpaw import GPAW
> calc = GPAW(nbands=-10)
> bcc.set_calculator(calc)
> print bcc.get_potential_energy()
>
> However, this was returned to me:
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/home/lowt0008/ase/ase/atoms.py", line 494, in 
> get_potential_energy
>     return self.calc.get_potential_energy(self)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/aseinterface.py", 
> line 32, in get_potential_energy
>     self.calculate(atoms, converge=True)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py", 
> line 226, in calculate
>     self.set_positions(atoms)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py", 
> line 301, in set_positions
>     spos_ac = self.initialize_positions(atoms)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/paw.py", 
> line 293, in initialize_positions
>     self.wfs.set_positions(spos_ac)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/fd.py", 
> line 45, in set_positions
>     FDPWWaveFunctions.set_positions(self, spos_ac)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py", 
> line 41, in set_positions
>     WaveFunctions.set_positions(self, spos_ac)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/wavefunctions/base.py", 
> line 226, in set_positions
>     rank_a = self.gd.get_ranks_from_positions(spos_ac)
>   File 
> "/home/lowt0008/python-2.7/lib/python2.7/site-packages/gpaw/domain.py", 
> line 102, in get_ranks_from_positions
>     assert (rnk_ac >= 0).all() and (rnk_ac < self.parsize_c).all()
> AssertionError
>
> Anyone had any idea where the problem could lie? Your help is greatly 
> appreciated.
>
> Regards,
> Augustus
> ------------------------------------------------------------------------
>
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-- 
Jess Wellendorff Pedersen

ph.d student
Center for Atomic-scale Materials Design (CAMD)
Department of Physics
Technical University of Denmark (DTU)