[gpaw-users] An error occurs when performing STM simulation using GPAW

[Christian Glinsvad]

kgd wrote:
> Dear Glinsvad,
> Thank you for your detaied reply. A important question to me is to
> inquire the dimension of V_12(V_21,a1,a2). And a few problems still
> confuse me.
> 
> you wrote,
>> There's your problem. I examined your POSCAR file and found that the Cu
>> atom closest to the z=0 plane is just 4 Å from the boundary but 8.9 Bohr
>> is 4.7 Å so you'll need at least 5 Å of vacuum if you want that DZP
>> basis.
>
> we have set vacuum 6 Å ( don't use the patch) and run it, the same
> error occurs. That is "RuntimeError: Atom at 0.500 0.500 0.504 too
> close to boundary (beg. of box [-2 1 1], end of box [23 24 25])" To
> my understanding, the negative value in [-2 1 1 ] means periodic X
> direction too close to bondary but non-periodic Z. The strange thing
> is that when we enlarge the cell from 1x1x1 to 3x1x1 the error
> dissappear.
>  

It's a bug for sure. The patch I made should be a decent work-around.
Like I mentioned in my latest mail, the STM code creates a smaller grid
around each atom to do some augmentation sphere integrals and this is
done with zero-BC along all three axes. It seems like it's hit-and-miss
whether the code chooses a small grid large enough to contain all of the
augmentation sphere or just 99% of it, hence the error for (1,1,1) but
not for (3,1,1) etc.


Regards
Christian Glinsvad