[gpaw-users] Error in gpaw transport

[jingzhe Chen]

Hi Georg,

         If you do it in parallel, the K points in Z direction are
distributed with such
setting. As said in the description of pl_kpts in the wiki, we want to keep
the numbers
of k points in X and Y direction same in scattering region and leads,  and
the only K
points in these two directions are distributed, and the safe way is to use
a prime
number in the Z direction of pl_kpts. In your case, choosing
pl_kpts=[1,1,13] or [1,1,17]
should be ok.

        Best.
        Jingzhe
 ,




On Wed, Oct 2, 2013 at 6:36 AM, Georg Kastlunger <georg.kast at hotmail.com>wrote:

> Dear mailing list,
>
> recently I have tried to apply the transport routine implemented in gpaw.
> Unfortunately I experience an error which I don't really understand.
> The error is the following:
>
> Traceback (most recent call last):
>   File "gpaw_transport.py", line 36, in <module>
>     t.calculate_iv()
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**calculator.py", line 2402, in calculate_iv
>     self.negf_prepare()
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**calculator.py", line 1239, in negf_prepare
>     self.initialize_transport()
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**calculator.py", line 402, in
> initialize_transport
>     self.calculate_leads()
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**calculator.py", line 342, in
> calculate_leads
>     self.collect_leads_matrices(**atoms.calc, i)
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**calculator.py", line 1098, in
> collect_leads_matrices
>     direction=lead_direction)
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**tools.py", line 344, in get_pk_hsd
>     hl_spkmm = substract_pk(d, npk, ntk, kpts, hl_skmm, hors='h',
> magnet=magnet)
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**tools.py", line 215, in substract_pk
>     tkpts = pick_out_tkpts(d, npk, ntk, kpts)
>   File "/home/lv70174/georg/gpaw_**inst_10428/lib64/python2.6/**
> site-packages/gpaw/transport/**tools.py", line 232, in pick_out_tkpts
>     tkpts[i, d] = kpts[i, d]
> IndexError: index (8) out of range (0<=index<8) in dimension 0
>
> As far as I understand from the code the index d defines the axis and i is
> the number of kpoints in this specific direction. Am I wrong with that?
>
> The calculator I am defining uses 1 kpoint in the scattering region and
> 1,1,15 in the leads as identical as in the tutorial:
>
> t = Transport(h=0.18,
>               xc='PBE',
>               kpts=(1,1,1),
>               occupations=FermiDirac(0.1),
>               mode='lcao',
>               basis='dzp',
>               poissonsolver=PoissonSolver(**nn=2, relax='GS'),
>               txt='transport.txt',
>               mixer=Mixer(0.05, 5, weight=100.0),
>               pl_atoms=[pl_atoms1, pl_atoms2],
>               pl_cells=[pl_cell1, pl_cell2],
>               pl_kpts=(1,1,16),
>               non_sc=True)
>
> Has anyone experienced this problem and knows how to solve it? I would be
> very grateful if someone could help me with that.
>
> Best regards,
> Georg
>
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