[gpaw-users] Error in gpaw transport

[jingzhe Chen]

Hi Georg,

          That should be ok. Can you send me your structure and running
script?
how many cpus do you use?

            Best.
            Jingzhe


On Thu, Oct 3, 2013 at 6:09 AM, Georg Kastlunger <georg.kast at hotmail.com>wrote:

>  Hi Jingzhe,
>
> I have now tried to do the calculation using pl_kpts=(1,1,13), which
> unfortunately this didnt work either.
>
> I habe noticed that you are defining the pl kpoints in a list (i.e.
> pl_kpts=[1,1,13] ), while I am defining them in a tuple as shown above.
> Could this be the reason of my problem?
>
> Best wishes,
> Georg
>
>
>
> On 10/02/2013 02:03 PM, jingzhe Chen wrote:
>
> 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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>> gpaw-users at listserv.fysik.dtu.dk
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>>
>
>
>
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