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

[Jouko Nieminen]

Hi,

Our group has also been struggling with this very same cut-off problem 
in STM-simulations:

> RuntimeError: Atom at 0.506 0.503 0.496 too close to boundary (beg. of box [1 1  1], end of box [36 35 35])

and useful ideas to deal with this are very welcome.

We have in principle just run the scripts of the following tutorial
https://wiki.fysik.dtu.dk/gpaw/tutorials/negfstm/negfstm.html
but changed from Aluminium to Copper or Palladium, and the geometry from 
fcc(100) to fcc(111) and changing the thickness of the slab.


Jussi suggests that centering the atoms in the cell would help. 
Referring to the tutorial above, where exactly the centerings should be 
done? After setting up the surface or surface principal layers? Or the 
tip or the principal layers?

This cut-off issue seems to be a persistent problem, and browsing the 
discussions some years backwards, it was somewhere suggested there is a 
bug in the stm code
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-July/000236.html

Is there anyone developing STM codes at the moment? Since this seems to 
be a recurrent problem, it would be nice to get this fixed.

with kind regards,

                          Jouko Nieminen

PS.  Here is the error message in total:

> Traceback (most recent call last):
>   File "STMsimu.py", line 54, in <module>
>     stm.initialize()
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/transport/jstm.py
> ", line 352, in initialize
>     self.tip_cell.initialize(tip_indices, tip_atom_index)
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/transport/jstm.py
> ", line 1265, in initialize
>     f = AtomCenteredFunctions(self.gd, [phit], spos_c, i)
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/transport/jstm.py
> ", line 160, in __init__
>     smallgd.N_c)
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/lfc.py", line 260
> , in set_positions
>     movement |= sphere.set_position(spos_c, self.gd, self.cut)
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/lfc.py", line 89,
>  in set_position
>     for beg_c, end_c, sdisp_c in gd.get_boxes(spos_c, rcut, cut):
>   File "/v/linux26_x86_64/appl/nano/gpaw/0.7.2/lib/python/gpaw/grid_descriptor.p
> y", line 262, in get_boxes
>     (tuple(spos_c) + (beg_c, end_c)))
> RuntimeError: Atom at 0.506 0.503 0.496 too close to boundary (beg. of box [1 1
> 1], end of box [36 35 35])
> srun: error: c235: task0: Exited with exit code 1


-- 
Jouko Nieminen,
Associate professor,
Dept. of Physics, TUT

GSM +358 40 849 0264 (work)
     +358 45 672 6962 (private)
Skype address: dr-jouko
http://butler.cc.tut.fi/~jniemine/
http://www.tut.fi/compphys