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 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
