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

[jingzhe Chen]

Hi,

       One possibility is that your system's pbc is not (1,1,1), change to
(1,1,1)
and retry.

       Best.
       Jingzhe



2011/10/18 Alex Eftimiades <alexeftimiades at gmail.com>

> 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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