[gpaw-users] Transport calculation--atom "too close to boundary"
jingzhe Chen
jingzhe.chen at gmail.com
Tue Oct 25 16:52:44 CEST 2011
Hi,
Could u send me your script and structure file?
Best.
Jingzhe
2011/10/24 Alex Eftimiades <alexeftimiades at gmail.com>
> Hello all,
>
> It would seem making setting the system pbc to (0,0,1) did not make a
> difference, however I found that the reason it was not working was because
> the lead atoms were not centered within *pl_cell*
> I have no idea how to fix this problem. Where is pl_cell usually centered
> about anyway?
>
> Alex
>
> On Oct 20, 2011, at 11:49 AM, jingzhe Chen wrote:
>
> Hi Alex,
>
> You are right, leads are periodic while scattering region not. When
> u set pbc as (0,0,1), lead calculation follow it,
> and the scattering region use (0, 0). (It does not make sense you have
> left lead is (0, 0, 1) and right lead is (1, 0 ,1), the
> pbc in x, y directions should be consistent for leads and scattering
> region). As for scattering region,the pbc in z
> direction has no physical meaning, because 0 means zero boundary, 1 for
> periodical, you only have these two options, and each of them is not fit,
> but 1 can bypass that error. Anyway, it may be better to fix it as 1 in the
> code.
>
> Best.
> Jingzhe
>
>
>
> 2011/10/18 Alex Eftimiades <alexeftimiades at gmail.com>
>
>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> gpaw-users mailing list
>>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> gpaw-users mailing list
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>>>>
>>>
>>>
>>
>
>
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