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 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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
