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

[Alex Eftimiades]

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, 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
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