If _everything_ is multiplied by 2, be aware of spin multiplicity. The transmission plot looks correct for a pristine system.
Secondly, how should the kpoints influence the result? There are no k-points in the device calculation. If you mean in the electrodes, then fine. 2015-10-31 19:53 GMT+01:00 Damien Tristant <[email protected]>: > Dear Nick > > Thanks to your advice, I got the transmission spectrum (for 3 unit cells > for right and left electrodes and 3 unit cells for device). Thank you very > much. I have attached it. But I get 4 conduction channels at the Fermi > level, instead of 2. I think that I have to play with parameters, the > electronic temperature and Kpoints. > Best regards. > > Damien > > > On 30/10/2015 12:42, Nick Papior wrote: > > Great. Note, it will not print whether your device region is too small. > > 2015-10-30 12:08 GMT+01:00 Damien Tristant <[email protected]>: > >> You are right Nick. When I use trunk version I get this message : >> >> WARNING: Connections across 2 unit cells or more in the transport >> direction. >> WARNING: This is inadvisable. >> WARNING: Please increase the electrode size in the transport direction. >> WARNING: Will proceed without further notice. >> >> >> >> On 30/10/2015 10:53, Nick Papior wrote: >> >> Well, all of those calculations have errors ;) >> >> 1) Too short electrode, too short device >> 2) Electrode (seems!) ok, too short device >> 3) too short electrode, device (seems!) ok. >> >> The device *must* also be so big that no direct interaction between >> left-right takes place. >> >> You can check how the interaction table is by looking at the BONDS file. >> There has been several questions about this previously so search the >> mailing list. >> >> Lastly, you may want to try the trunk version which prints out if your >> electrode is too small. >> >> 2015-10-30 10:31 GMT+01:00 Damien Tristant <[email protected]>: >> >>> Thank Nick Papior for your help, but unfortunately I got the same >>> problem. Enclosed, I put the Transmission spectra and a picture of 3 >>> different systems : >>> - 96 atoms (1 unit cell for left electrode ; 1 unit cell for the sample >>> ; 1 unit cell for the right electrode) >>> - 160 atoms (2 unit cells for left electrode ; 1 unit cell for the >>> sample ; 2 unit cells for the right electrode) >>> - 128 atoms (1 unit cell for left electrode ; 2 unit cells for the >>> sample ; 1 unit cell for the right electrode) >>> As you can see the problem remains the same. >>> May be the problem comes from the calcul of the complex contour? >>> Best regards. >>> >>> Damien >>> >>> >>> >>> On 30/10/2015 07:23, Nick Papior wrote: >>> >>> Your electrode length is almost certainly too small, you must ensure >>> principal cell connections, only. Try and double your electrode. >>> >>> -- >>> >>> Kind regards Nick Papior >>> On 30 Oct 2015 00:54, "Damien Tristant" <[email protected]> >>> wrote: >>> >>>> Dear Everybody >>>> >>>> I am trying to obtain the transmission spectrum of a metallic carbon >>>> nanotube (8,8), carried out with Transiesta code. Unfortunately I don’t get >>>> the right spectrum (normally at the Fermi level I should see two conduction >>>> channels appear, I have attached the file). I have changed the settings >>>> several times but the result is never correct. In the following there is my >>>> input files for the electrodes and the scattering zone. >>>> Could you please check if one of my parameters is wrong or if I forgot >>>> something? >>>> Thank you very much for your help. >>>> Best regards. >>>> >>>> Damien >>>> >>>> >>>> *Electrode :* >>>> >>>> >>>> # General system descriptors >>>> SystemName cnt >>>> SystemLabel cnt >>>> NumberOfAtoms 32 >>>> NumberOfSpecies 1 >>>> >>>> %block ChemicalSpeciesLabel >>>> 1 6 C.gga # Species index, atomic number, species label >>>> %endblock ChemicalSpeciesLabel >>>> >>>> #Unit cell for the calculation >>>> LatticeConstant 1 Ang >>>> %block LatticeVectors >>>> 30.0000000000000000 0.0000000000000000 0.0000000000000000 >>>> 0.0000000000000000 30.0000000000000000 0.0000000000000000 >>>> 0.0000000000000000 0.0000000000000000 2.4617000000000000 >>>> %endblock LatticeVectors >>>> >>>> # Lattice, coordinates, k-sampling >>>> >>>> AtomicCoordinatesFormat Fractional >>>> AtomicCoorFormatOut Fractional >>>> >>>> %block AtomicCoordinatesAndAtomicSpecies >>>> 0.684228479 0.500102328 -0.000000000 1 >>>> 0.677959183 0.547673034 0.000000000 1 >>>> 0.670191861 0.570611130 0.500000000 1 >>>> 0.646198057 0.612161657 0.500000000 1 >>>> 0.630219773 0.630352389 0.000000000 1 >>>> 0.592119446 0.659511823 -0.000000000 1 >>>> 0.570405934 0.670221335 0.500000000 1 >>>> 0.524063557 0.682647265 0.500000001 1 >>>> 0.499897672 0.684228479 -0.000000000 1 >>>> 0.452326966 0.677959184 -0.000000000 1 >>>> 0.429388870 0.670191860 0.500000000 1 >>>> 0.387838343 0.646198057 0.500000000 1 >>>> 0.369647610 0.630219773 0.000000000 1 >>>> 0.340488177 0.592119446 -0.000000000 1 >>>> 0.329778665 0.570405934 0.500000000 1 >>>> 0.317352735 0.524063557 0.500000000 1 >>>> 0.315771521 0.499897672 0.000000000 1 >>>> 0.322040816 0.452326966 -0.000000000 1 >>>> 0.329808140 0.429388870 0.500000000 1 >>>> 0.353801943 0.387838343 0.500000000 1 >>>> 0.369780227 0.369647611 -0.000000000 1 >>>> 0.407880554 0.340488177 0.000000000 1 >>>> 0.429594066 0.329778665 0.499999999 1 >>>> 0.475936443 0.317352735 0.500000001 1 >>>> 0.500102328 0.315771521 -0.000000000 1 >>>> 0.547673034 0.322040816 -0.000000000 1 >>>> 0.570611130 0.329808139 0.500000001 1 >>>> 0.612161657 0.353801943 0.500000000 1 >>>> 0.630352390 0.369780227 -0.000000000 1 >>>> 0.659511823 0.407880554 -0.000000000 1 >>>> 0.670221335 0.429594066 0.500000000 1 >>>> 0.682647265 0.475936443 0.500000000 1 >>>> %endblock AtomicCoordinatesAndAtomicSpecies >>>> >>>> # K-sampling (alternative specification using kgrid_cutoff) >>>> %block kgrid_Monkhorst_Pack >>>> 1 0 0 0.0 >>>> 0 1 0 0.0 >>>> 0 0 100 0.0 >>>> %endblock kgrid_Monkhorst_Pack >>>> >>>> # Basis set definition >>>> PAO.BasisSize DZP >>>> PAO.EnergyShift 50 meV >>>> PAO.SplitNorm 0.15 >>>> >>>> # Real space grid >>>> MeshCutoff 200.0 Ry >>>> >>>> #Convergence of SCF >>>> MaxSCFIterations 100 >>>> DM.MixingWeight 0.05 >>>> DM.NumberPulay 10 >>>> DM.Tolerance 0.0001 >>>> >>>> # Eigenvalue problem: order-N or diagonalization >>>> SolutionMethod diagon >>>> ElectronicTemperature 5.0 K >>>> >>>> >>>> # Density functional (Notice that Xc.authors and XC.functional) >>>> XC.functional VDW >>>> XC.authors KBM >>>> >>>> # Molecular Dynamics and relaxations >>>> MD.TypeOfRun CG >>>> MD.NumCGsteps 0 >>>> MD.VariableCell .false. >>>> MD.ConstantVolume .true. >>>> >>>> # Output options >>>> WriteCoorInitial .false. >>>> WriteCoorStep .true. >>>> WriteForces .false. >>>> WriteKpoints .false. >>>> WriteEigenvalues .false. >>>> WriteDM .true. >>>> WriteKbands .false. >>>> WriteBands .false. >>>> WriteWaveFunctions .true. >>>> WriteMullikenPop 0 >>>> WriteCoorXmol .true. >>>> WriteCoorCerius .true. >>>> WriteMDXmol .true. >>>> WriteMDhistory .true. >>>> >>>> *Scattering zone :* >>>> >>>> # General system descriptors >>>> SystemName cnt-system >>>> SystemLabel cnt-system >>>> NumberOfAtoms 96 >>>> NumberOfSpecies 1 >>>> >>>> %block ChemicalSpeciesLabel >>>> 1 6 C.gga # Species index, atomic number, species label >>>> %endblock ChemicalSpeciesLabel >>>> >>>> #Unit cell for the calculation >>>> LatticeConstant 1 Ang >>>> %block LatticeVectors >>>> 30.0000000000000000 0.0000000000000000 0.0000000000000000 >>>> 0.0000000000000000 30.0000000000000000 0.0000000000000000 >>>> 0.0000000000000000 0.0000000000000000 7.3851000000000000 >>>> %endblock LatticeVectors >>>> >>>> # Lattice, coordinates, k-sampling >>>> >>>> AtomicCoordinatesFormat Fractional >>>> AtomicCoorFormatOut Fractional >>>> >>>> %block AtomicCoordinatesAndAtomicSpecies >>>> 0.6842284789999999 0.5001023280000000 0.0000000000000000 1 >>>> 0.6779591830000000 0.5476730340000000 0.0000000000000000 1 >>>> 0.6701918610000001 0.5706111300000000 0.1666666666666667 1 >>>> 0.6461980570000000 0.6121616570000000 0.1666666666666667 1 >>>> 0.6302197730000000 0.6303523890000000 0.0000000000000000 1 >>>> 0.5921194460000000 0.6595118230000000 0.0000000000000000 1 >>>> 0.5704059339999999 0.6702213350000000 0.1666666666666667 1 >>>> 0.5240635570000000 0.6826472649999999 0.1666666670000000 1 >>>> 0.4998976720000000 0.6842284789999999 0.0000000000000000 1 >>>> 0.4523269660000000 0.6779591840000000 0.0000000000000000 1 >>>> 0.4293888700000000 0.6701918600000000 0.1666666666666667 1 >>>> 0.3878383430000000 0.6461980570000000 0.1666666666666667 1 >>>> 0.3696476100000000 0.6302197730000000 0.0000000000000000 1 >>>> 0.3404881770000000 0.5921194460000000 0.0000000000000000 1 >>>> 0.3297786650000000 0.5704059339999999 0.1666666666666667 1 >>>> 0.3173527350000000 0.5240635570000000 0.1666666666666667 1 >>>> 0.3157715210000000 0.4998976720000000 0.0000000000000000 1 >>>> 0.3220408160000000 0.4523269660000000 0.0000000000000000 1 >>>> 0.3298081400000000 0.4293888700000000 0.1666666666666667 1 >>>> 0.3538019430000000 0.3878383430000000 0.1666666666666667 1 >>>> 0.3697802270000000 0.3696476110000000 0.0000000000000000 1 >>>> 0.4078805540000000 0.3404881770000000 0.0000000000000000 1 >>>> 0.4295940660000000 0.3297786650000000 0.1666666663333333 1 >>>> 0.4759364430000000 0.3173527350000000 0.1666666670000000 1 >>>> 0.5001023280000000 0.3157715210000000 0.0000000000000000 1 >>>> 0.5476730340000000 0.3220408160000000 0.0000000000000000 1 >>>> 0.5706111300000000 0.3298081390000000 0.1666666670000000 1 >>>> 0.6121616570000000 0.3538019430000000 0.1666666666666667 1 >>>> 0.6303523900000000 0.3697802270000000 0.0000000000000000 1 >>>> 0.6595118230000000 0.4078805540000000 0.0000000000000000 1 >>>> 0.6702213350000000 0.4295940660000000 0.1666666666666667 1 >>>> 0.6826472649999999 0.4759364430000000 0.1666666666666667 1 >>>> 0.6842284789999999 0.5001023280000000 0.3333333333333333 1 >>>> 0.6779591830000000 0.5476730340000000 0.3333333333333333 1 >>>> 0.6701918610000001 0.5706111300000000 0.5000000000000000 1 >>>> 0.6461980570000000 0.6121616570000000 0.5000000000000000 1 >>>> 0.6302197730000000 0.6303523890000000 0.3333333333333333 1 >>>> 0.5921194460000000 0.6595118230000000 0.3333333333333333 1 >>>> 0.5704059339999999 0.6702213350000000 0.5000000000000000 1 >>>> 0.5240635570000000 0.6826472649999999 0.5000000003333334 1 >>>> 0.4998976720000000 0.6842284789999999 0.3333333333333333 1 >>>> 0.4523269660000000 0.6779591840000000 0.3333333333333333 1 >>>> 0.4293888700000000 0.6701918600000000 0.5000000000000000 1 >>>> 0.3878383430000000 0.6461980570000000 0.5000000000000000 1 >>>> 0.3696476100000000 0.6302197730000000 0.3333333333333333 1 >>>> 0.3404881770000000 0.5921194460000000 0.3333333333333333 1 >>>> 0.3297786650000000 0.5704059339999999 0.5000000000000000 1 >>>> 0.3173527350000000 0.5240635570000000 0.5000000000000000 1 >>>> 0.3157715210000000 0.4998976720000000 0.3333333333333333 1 >>>> 0.3220408160000000 0.4523269660000000 0.3333333333333333 1 >>>> 0.3298081400000000 0.4293888700000000 0.5000000000000000 1 >>>> 0.3538019430000000 0.3878383430000000 0.5000000000000000 1 >>>> 0.3697802270000000 0.3696476110000000 0.3333333333333333 1 >>>> 0.4078805540000000 0.3404881770000000 0.3333333333333333 1 >>>> 0.4295940660000000 0.3297786650000000 0.4999999996666666 1 >>>> 0.4759364430000000 0.3173527350000000 0.5000000003333334 1 >>>> 0.5001023280000000 0.3157715210000000 0.3333333333333333 1 >>>> 0.5476730340000000 0.3220408160000000 0.3333333333333333 1 >>>> 0.5706111300000000 0.3298081390000000 0.5000000003333334 1 >>>> 0.6121616570000000 0.3538019430000000 0.5000000000000000 1 >>>> 0.6303523900000000 0.3697802270000000 0.3333333333333333 1 >>>> 0.6595118230000000 0.4078805540000000 0.3333333333333333 1 >>>> 0.6702213350000000 0.4295940660000000 0.5000000000000000 1 >>>> 0.6826472649999999 0.4759364430000000 0.5000000000000000 1 >>>> 0.6842284789999999 0.5001023280000000 0.6666666666666666 1 >>>> 0.6779591830000000 0.5476730340000000 0.6666666666666666 1 >>>> 0.6701918610000001 0.5706111300000000 0.8333333333333334 1 >>>> 0.6461980570000000 0.6121616570000000 0.8333333333333334 1 >>>> 0.6302197730000000 0.6303523890000000 0.6666666666666666 1 >>>> 0.5921194460000000 0.6595118230000000 0.6666666666666666 1 >>>> 0.5704059339999999 0.6702213350000000 0.8333333333333334 1 >>>> 0.5240635570000000 0.6826472649999999 0.8333333336666667 1 >>>> 0.4998976720000000 0.6842284789999999 0.6666666666666666 1 >>>> 0.4523269660000000 0.6779591840000000 0.6666666666666666 1 >>>> 0.4293888700000000 0.6701918600000000 0.8333333333333334 1 >>>> 0.3878383430000000 0.6461980570000000 0.8333333333333334 1 >>>> 0.3696476100000000 0.6302197730000000 0.6666666666666666 1 >>>> 0.3404881770000000 0.5921194460000000 0.6666666666666666 1 >>>> 0.3297786650000000 0.5704059339999999 0.8333333333333334 1 >>>> 0.3173527350000000 0.5240635570000000 0.8333333333333334 1 >>>> 0.3157715210000000 0.4998976720000000 0.6666666666666666 1 >>>> 0.3220408160000000 0.4523269660000000 0.6666666666666666 1 >>>> 0.3298081400000000 0.4293888700000000 0.8333333333333334 1 >>>> 0.3538019430000000 0.3878383430000000 0.8333333333333334 1 >>>> 0.3697802270000000 0.3696476110000000 0.6666666666666666 1 >>>> 0.4078805540000000 0.3404881770000000 0.6666666666666666 1 >>>> 0.4295940660000000 0.3297786650000000 0.8333333330000000 1 >>>> 0.4759364430000000 0.3173527350000000 0.8333333336666667 1 >>>> 0.5001023280000000 0.3157715210000000 0.6666666666666666 1 >>>> 0.5476730340000000 0.3220408160000000 0.6666666666666666 1 >>>> 0.5706111300000000 0.3298081390000000 0.8333333336666667 1 >>>> 0.6121616570000000 0.3538019430000000 0.8333333333333334 1 >>>> 0.6303523900000000 0.3697802270000000 0.6666666666666666 1 >>>> 0.6595118230000000 0.4078805540000000 0.6666666666666666 1 >>>> 0.6702213350000000 0.4295940660000000 0.8333333333333334 1 >>>> 0.6826472649999999 0.4759364430000000 0.8333333333333334 1 >>>> %endblock AtomicCoordinatesAndAtomicSpecies >>>> >>>> # K-sampling (alternative specification using kgrid_cutoff) >>>> %block kgrid_Monkhorst_Pack >>>> 1 0 0 0.0 >>>> 0 1 0 0.0 >>>> 0 0 70 0.0 >>>> %endblock kgrid_Monkhorst_Pack >>>> >>>> # Basis set definition >>>> PAO.BasisSize DZP >>>> PAO.EnergyShift 50 meV >>>> PAO.SplitNorm 0.15 >>>> >>>> # Real space grid >>>> MeshCutoff 200.0 Ry >>>> >>>> #Convergence of SCF >>>> MaxSCFIterations 100 >>>> DM.MixingWeight 0.05 >>>> DM.NumberPulay 10 >>>> DM.Tolerance 0.0001 >>>> DM.UseSaveDM .true. >>>> >>>> # Eigenvalue problem: order-N or diagonalization >>>> SolutionMethod transiesta >>>> ElectronicTemperature 5.0 K >>>> >>>> TS.WriteHS .true. >>>> TS.NumUsedAtomsLeft 32 >>>> TS.NumUsedAtomsRight 32 >>>> TS.HSFileLeft 'cnt.TSHS' >>>> TS.HSFileRight 'cnt.TSHS' >>>> TS.TBT.HSFile 'cnt-system.TSHS' >>>> TS.TBT.Emin -4.0 eV >>>> TS.TBT.Emax 4.0 eV >>>> TS.TBT.NPoints 200 >>>> >>>> # Density functional (Notice that Xc.authors and XC.functional) >>>> XC.functional VDW >>>> XC.authors KBM >>>> >>>> # Molecular Dynamics and relaxations >>>> MD.TypeOfRun CG >>>> MD.NumCGsteps 0 >>>> MD.VariableCell .false. >>>> MD.ConstantVolume .true. >>>> >>>> # Output options >>>> WriteCoorInitial .false. >>>> WriteCoorStep .true. >>>> WriteForces .false. >>>> WriteKpoints .false. >>>> WriteEigenvalues .false. >>>> WriteDM .true. >>>> WriteKbands .false. >>>> WriteBands .false. >>>> WriteWaveFunctions .true. >>>> WriteMullikenPop 0 >>>> WriteCoorXmol .true. >>>> WriteCoorCerius .true. >>>> WriteMDXmol .true. >>>> WriteMDhistory .true. >>>> >>>> >>> >> >> >> -- >> Kind regards Nick >> >> >> > > > -- > Kind regards Nick > > > -- Kind regards Nick
