These are my input files for the device and electrodes. On Mon, Feb 3, 2020 at 9:32 AM Ziba Torkashvand <[email protected]> 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 <[email protected]> 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 < >> [email protected]>: >> >>> 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 <[email protected]> >>> 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 < >>>> [email protected]>: >>>> >>>>> 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/) >> >
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-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
