Dear NickThanks 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] <mailto:[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] <mailto:[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] <mailto:[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 twoconduction channels appear, I have attached the file). I have changed the settings several times but the resultis 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
cnt-M.pdf
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