Like I mentioned, your lattice vectors are not parallel, see device
lattice vectors and electrode lattice vectors. They need to be parallel in
case you want to use k-points.

Den man. 3. feb. 2020 kl. 22.10 skrev Ziba Torkashvand <
zi.torkashv...@gmail.com>:

> These are my input files for the device and electrodes.
>
> On Mon, Feb 3, 2020 at 9:32 AM Ziba Torkashvand <zi.torkashv...@gmail.com>
> wrote:
>
>> Thanks for your response Nick,
>> Previously, I have used the following lattice vectors for the device
>> %block LatticeVectors
>>   24.8355890   0.0312245  -0.2325957
>>    0.0300392  22.4960510  -0.2979615
>>   -0.2501458  -0.3417446  26.7881732
>> %endblock LatticeVectors
>> and
>> %block LatticeVectors
>> 15.5329     0           0
>> 0           5.98023     0
>> 0           0           6.24937
>> %endblock LatticeVectors
>> for the left electrode and
>> %block LatticeVectors
>> 15.5329  0           0
>> 0        5.98023     0
>> 0        0           6.26654
>> %endblock LatticeVectors
>> for the right electrode after fully relaxation.
>> But as I see in the example ts_term4
>> %block LatticeVectors
>>     31.75        0.0000      0.0000
>>      0.0000     12.0000      0.0000
>>      0.0000      0.0000     31.75
>> %endblock LatticeVectors
>> was used for the device and
>> %block LatticeVectors
>>     5.08      0.0000      0.0000
>>     0.0000   12.0000      0.0000
>>     0.0000    0.0000     12.0000
>> %endblock LatticeVectors
>> and
>> %block LatticeVectors
>>     0.0000    0.0000      5.08
>>     0.0000   12.0000      0.0000
>>    12.0000    0.0000      0.0000
>> %endblock LatticeVectors
>> for the elec-x and elec-z, respectively.
>> So, based on this example should I change the order of lattice vectors
>> for the electrodes (y-direction) which are perpendicular to the device
>> region (z-direction)?
>> Or, what is your suggestion for my case?
>>
>> Thanks in advance,
>> Ziba Torkashvand
>>
>>
>> On Fri, Jan 24, 2020 at 6:08 AM Nick Papior <nickpap...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Sorry, I don't understand your response. I referred to the lattice
>>> vectors in the two calculations not being parallel.
>>> It is not due to your k-point samplings.
>>>
>>>
>>> Den ons. 22. jan. 2020 kl. 22.01 skrev Ziba Torkashvand <
>>> zi.torkashv...@gmail.com>:
>>>
>>>> Actually, I just have two electrodes (in the y-direction) and both of
>>>> them are perpendicular to the device region (in the z-direction). As I see
>>>> in the example of Au 111 it has the largest kpoint along the semi-infinite
>>>> direction of electrodes for the electrode run (2 2 10) which in my work is
>>>> in the y-direction and (2 2 2) for the device region. Also, I have tried (2
>>>> 20 2) for the electrode run and (2 2 2) for the scattering region but again
>>>> I have received an error.
>>>>
>>>> Thanks
>>>>
>>>> [image: Mailtrack]
>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
>>>>  Sender
>>>> notified by
>>>> Mailtrack
>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
>>>>  01/22/20,
>>>> 11:15:34 AM
>>>>
>>>> On Wed, Jan 22, 2020 at 6:01 AM Nick Papior <nickpap...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Your 3rd electrode and device lattice vector are not parallel. Please
>>>>> make sure they are parallel. :)
>>>>>
>>>>> Den man. 20. jan. 2020 kl. 22.04 skrev Ziba Torkashvand <
>>>>> zi.torkashv...@gmail.com>:
>>>>>
>>>>>> Hello everybody
>>>>>> I want to do a transiesta calculation with Siesta 4.1-b4.
>>>>>> In my device, two bulk electrodes are on the top of a monolayer
>>>>>> hexagonal system. The transport direction is in z direction so the
>>>>>> electrode direction is y.
>>>>>> I have used kpoint sampling
>>>>>> 1 0 0
>>>>>> 0 20 0
>>>>>> 0 0 40
>>>>>> for the electrodes and
>>>>>> 1 0 0
>>>>>> 0 1 0
>>>>>> 0 0 40
>>>>>> for the scattering region
>>>>>> but I receive the error
>>>>>>
>>>>>>
>>>>>> transiesta: k-grid: Number of Green function k-points =    20
>>>>>> transiesta: k-grid: Supercell and displacements
>>>>>> transiesta: k-grid:    1   0   0      0.000
>>>>>> transiesta: k-grid:    0   1   0      0.000
>>>>>> transiesta: k-grid:    0   0  40      0.500
>>>>>> Erroneous electrode setup, check out-put
>>>>>> Stopping Program from Node:    0
>>>>>> ERROR: Electrode: elecl
>>>>>> Electrode direction = 3
>>>>>> Projected direction = 3
>>>>>> |elec_cell(:, 3) . cell(:,3)| - 1 = -.1249E-03
>>>>>> Erroneous electrode setup, check out-put
>>>>>> Stopping Program from Node:    0
>>>>>> application called MPI_Abort(comm=0x84000000, 1) - process 0
>>>>>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
>>>>>> :
>>>>>> system msg for write_line failure : Bad file descriptor
>>>>>>
>>>>>> and here is some part of my input
>>>>>>
>>>>>> block TS.Elec.elecl
>>>>>> TSHS ./elecl.TSHS
>>>>>> chem-pot Left
>>>>>> semi-inf-dir +a2
>>>>>> elec-pos begin 1
>>>>>> used-atoms 54
>>>>>> %endblock TS.Elec.elecl
>>>>>>
>>>>>> %block TS.Elec.elecr
>>>>>> TSHS ./elecr.TSHS
>>>>>> chem-pot Right
>>>>>> semi-inf-dir +a2
>>>>>> elec-pos end -1
>>>>>> used-atoms 54
>>>>>> %endblock TS.Elec.elecr
>>>>>>
>>>>>> any suggestions for my problem would be kindly appreciated.
>>>>>>
>>>>>> Thanks in advance
>>>>>> Ziba Torkashvand
>>>>>>
>>>>>>
>>>>>> [image: Mailtrack]
>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
>>>>>>  Sender
>>>>>> notified by
>>>>>> Mailtrack
>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
>>>>>>  01/20/20,
>>>>>> 12:52:58 PM
>>>>>>
>>>>>> --
>>>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Kind regards Nick
>>>>>
>>>>> --
>>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>>>
>>>>
>>>> --
>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>> --
>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>
>>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 
Kind regards Nick
-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

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