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

[Alex Eftimiades]

My system's pbc was not (1,1,1). I did not know that was necessary. Why does
the entire system need to have a pbc of (1,1,1)? The leads should be the
only component with periodicity--and that should only have to be applied
along the direction of transport (namely, the z axis.)

Thanks,
Alex

On Tue, Oct 18, 2011 at 10:39 AM, jingzhe Chen <jingzhe.chen at gmail.com>wrote:

> 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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>> gpaw-users at listserv.fysik.dtu.dk
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>>
>
>
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