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

[Kristian Sommer Thygesen]

Dear all

Unfortunately the STM code is not being developed or maintained at the moment. The student who wrote most of the code left one year ago and since then nobody has really touched it. This is of course unfortunate. Have you tried a standard Tersoff-Haman calculation (essentially the LDOS at the Fermi level). According to our experience that gives qualitatively the same result as the more realistic approach where the tip is included (I assume this is the type of calculation you are trying now)

Best regards
Kristian
________________________________________
From: gpaw-users-bounces at listserv.fysik.dtu.dk [gpaw-users-bounces at listserv.fysik.dtu.dk] On Behalf Of Jouko Nieminen [jouko.nieminen at tut.fi]
Sent: Monday, February 20, 2012 12:40 PM
To: gpaw-users at listserv.fysik.dtu.dk
Subject: Re: [gpaw-users] Transport calculation--atom "too close to boundary"

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
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