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

[Alex Eftimiades]

That makes more sense, but even so, the system as a whole is not
periodic--even along the transport direction. Consider this example:
(forgive the bad ACII drawing)

[Pt]--[Pt]--[Pt]--[H]  [H]--[Na]--[Na]--[Na]

Clearly the left lead is period along the transport direction, and the right
lead is periodic along the transport direction, but the system as a whole is
not. That is my only concern in setting the pbc of the system periodic along
any direction.

Unless the code never applies this condition to the system as a whole and
only applies the setting to each lead--so if I set system pbc to (0,0,1) I
am really only setting the left and right lead unit cells' pbc to (0,0,1).
That would be fine, although it would raise the question of dealing with a
situation in which one of the leads had a pbc of say (1,0,1) and you wanted
the other lead to have a pbc of (0,0,1).

Thanks for the quick responses.
Alex Eftimiades

On Tue, Oct 18, 2011 at 1:14 PM, jingzhe Chen <jingzhe.chen at gmail.com>wrote:

> At least you should set 1 for the transport direction,  if you have enough
> vacuum space in the other two directions.
> It is not periodic, you are right, setting it True is just to bypass the
> the raising error you reported. In the code,
> it is solved in fixed boundary condition.
>
>
> Best.
> Jingzhe
>
> 2011/10/18 Alex Eftimiades <alexeftimiades at gmail.com>
>
>> 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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