[gpaw-users] Transport calculation--atom "too close to boundary"

[Jussi Enkovaara]

Hi Alex,
are you atoms in the center of the cell (concerning the non-periodic directions)?
Otherwise, the augmentation spheres will cross the cell boundaries whatever cell 
size you have, e.g.

atoms = Atoms('H')
atoms.set_cell((10, 10, 10))
...

will give you the error whatever cell size one specifies. You can center the atoms 
along all directions with

atoms.center()

or along specified directions

atoms.center(axis=0)   # x-direction
atoms.center(axis=1)   # y direction

Best regards,
Jussi



On 2011-10-18 17:01, Alex Eftimiades wrote:
> While doing a transport calculation with gpaw, I keep getting the following error message:
> Traceback (most recent call last):
>    File "<stdin>", line 1, in<module>
>    File "/media/8051-29A1/nanotube_transport2.py", line 75, in<module>
>      t.calculate_iv()
>    File "/usr/lib/python2.7/dist-packages/gpaw/transport/calculator.py", line 2292, in calculate_iv
>      self.negf_prepare()
>    File "/usr/lib/python2.7/dist-packages/gpaw/transport/calculator.py", line 986, in negf_prepare
>      self.initialize_transport()
>    File "/usr/lib/python2.7/dist-packages/gpaw/transport/calculator.py", line 306, in initialize_transport
>      calc.set_positions(atoms)
>    File "/usr/lib/python2.7/dist-packages/gpaw/paw.py", line 301, in set_positions
>      spos_ac = self.initialize_positions(atoms)
>    File "/usr/lib/python2.7/dist-packages/gpaw/paw.py", line 294, in initialize_positions
>      self.density.set_positions(spos_ac, self.wfs.rank_a)
>    File "/usr/lib/python2.7/dist-packages/gpaw/density.py", line 104, in set_positions
>      self.ghat.set_positions(spos_ac)
>    File "/usr/lib/python2.7/dist-packages/gpaw/lfc.py", line 260, in set_positions
>      movement |= sphere.set_position(spos_c, self.gd<http://self.gd>, self.cut)
>    File "/usr/lib/python2.7/dist-packages/gpaw/lfc.py", line 89, in set_position
>      for beg_c, end_c, sdisp_c in gd.get_boxes(spos_c, rcut, cut):
>    File "/usr/lib/python2.7/dist-packages/gpaw/grid_descriptor.py", line 263, in get_boxes
>      (tuple(spos_c) + (beg_c, end_c)))
> RuntimeError: Atom at 0.736 0.949 0.750 too close to boundary (beg. of box [ 88 117   6], end of box [113 142  31])
>
> I know this has to do with the augmentation sphere being out of bounds--not the atom itself
> mentioned here https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-July/000227.html
>
> I am only working with carbon nanotubes (carbon and hydrogen atoms) so I am not using any heavy metals. I can of course avoid the error by imposing periodic boundary conditions, but it is troubling that no matter how big the box is (note the size mentioned in the error message) this error still comes up.
>
> Does this suggest my basis set is not right (I just used dzp since that seems to be the standard for most atoms)? What do I have to do to fix this?
>
> Thank you,
> Alex Eftimiades
> ________________________________
>