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/)
