[gpaw-users] Problems running GPAW

[Augustus Low]

Hi Jess,

Your input has certainly been really helpful for me. In other words, if I
want to create a bulk structure, I should use the parameters pbc = (1,1,1)?
Will this give me a better DFT reading for my structure as well?

Regards,
Augustus

On Thu, Apr 7, 2011 at 6:40 PM, Jess Wellendorff Pedersen <
jesswe at fysik.dtu.dk> wrote:

> 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
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>
> --
> Jess Wellendorff Pedersen
>
> ph.d student
> Center for Atomic-scale Materials Design (CAMD)
> Department of Physics
> Technical University of Denmark (DTU)
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20110407/7e705d87/attachment.html