Hi, 1. Original poster. Could you please try read the manual. Your problem are multiple, the electronic structure parameters are insufficient and you are not using the electrodes as they should. I.e. they are not bulk like.
Your simulation requires the use of real-space self-energies, see https://journals.aps.org/prb/abstract/10.1103/PhysRevB.100.195417 . However, if you are a first in doing transiesta/tbtrans calculations you should not start with something this complicated... :( 2. @El-abed Haidar <ehai2...@uni.sydney.edu.au>, a comment on the input suggested. from -999.99893 eV - V/2 to -10. kT - V/2 Don't do this! You should probably never go below -100 eV, the default -40 eV should be sufficient for most systems, but -1000 eV is definitely too much. Also, "used-atoms 63" should only be supplied in case you have a subset electrode calculation. Otherwise remove this line. / Nick Den man. 15. jun. 2020 kl. 22.02 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Hi Rayan > > Quick question what is the transport direction? > > I feel there are some essential blocks missing. Those are generally > required for a TranSIESTA and TbTrans calculation. Good luck! > > > > %block TS.ChemPots > > Left > > Right > > %endblock TS.ChemPots > > %block TS.ChemPot.Left > > mu V/2 > > contour.eq > > begin > > c-Left > > t-Left > > end > > %endblock TS.ChemPot.Left > > %block TS.ChemPot.Right > > mu -V/2 > > contour.eq > > begin > > c-Right > > t-Right > > end > > %endblock TS.ChemPot.Right > > TS.Elecs.Bulk true > > TS.Elecs.DM.Update cross-terms > > TS.Elecs.GF.ReUse true > > %block TS.Elecs > > Left > > Right > > %endblock TS.Elecs > > %block TS.Elec.Left > > HS ./left.TSHS > > chem-pot Left > > semi-inf-dir -a2 > > elec-pos begin 1 > > used-atoms 63 > > %endblock TS.Elec.Left > > %block TS.Elec.Right > > HS ./right.TSHS > > chem-pot Right > > semi-inf-dir +a2 > > elec-pos end -1 > > used-atoms 63 > > %endblock TS.Elec.Right > > TS.Contours.Eq.Pole 2.50000 eV > > %block TS.Contour.c-Left > > part circle > > from -999.99893 eV + V/2 to -10. kT + V/2 > > points 50 > > method g-legendre > > %endblock TS.Contour.c-Left > > %block TS.Contour.t-Left > > part tail > > from prev to inf > > points 10 > > method g-fermi > > %endblock TS.Contour.t-Left > > %block TS.Contour.c-Right > > part circle > > from -999.99893 eV - V/2 to -10. kT - V/2 > > points 50 > > method g-legendre > > %endblock TS.Contour.c-Right > > %block TS.Contour.t-Right > > part tail > > from prev to inf > > points 10 > > method g-fermi > > %endblock TS.Contour.t-Right > > TS.Elecs.Eta 0.0001000000 eV > > %block TS.Contours.nEq > > neq > > %endblock TS.Contours.nEq > > %block TS.Contour.nEq.neq > > part line > > from -|V|/2 - 5 kT to |V|/2 + 5 kT > > delta 0.01 eV > > method mid-rule > > %endblock TS.Contour.nEq.neq > > # TBtrans options > > TBT.T.Eig 5 > > TBT.Elecs.Eta 0.0000136058 eV > > %block TBT.Contours > > neq > > %endblock TBT.Contours > > %block TBT.Contour.neq > > part line > > from -2.00000 eV to 2.00000 eV > > delta 0.00800 eV > > method mid-rule > > %endblock TBT.Contour.neq > > > > TBT.DOS.A.All true > > TBT.CDF.MPI true > > TS.Voltage 0.0 eV > > > > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > *From: *rayan moukhadder <rayanroro321...@gmail.com> > *Sent: *Monday, 15 June 2020 6:04 AM > *To: *siesta-l@uam.es > *Subject: *[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank > > > > Dear all, > > > > I am a phd student and I am new to siesta , I am doing a Transiesta > calculation for a system that consist of two graphene sheets sandwiching > three cobalt atoms, as the electrode calculation is successfully done, the > SCF iterations in SR calculation are not converging where my input file is > > > > SystemName SR.Co > SystemLabel SR.Co > > NumberOfAtoms 131 > NumberOfSpecies 2 > > %block ChemicalSpeciesLabel > 1 6 C > 2 27 Co > %endblock ChemicalSpeciesLabel > > PAO.BasisSize SZP > PAO.EnergyShift 0.05 Ry > PAO.SplitNorm 0.2 > > ================================================== > ================================================== > # K-points > > %block kgrid_Monkhorst_Pack > 1 0 0 0.0 > 0 1 0 0.0 > 0 0 1 0.5 > %endblock Kgrid_Monkhorst_Pack > ================================================== > ================================================== > # UNIT CELL AND ATOMIC POSITIONS > > # UNIT CELL > LatticeConstant 1.00 Ang > > %block LatticeVectors > 17.016 0.000 0.000 > 0.000 9.824 0.000 > 0.000 0.0000 14.000 > %endblock LatticeVectors > AtomicCoordinatesFormat Ang > > %block AtomicCoordinatesAndAtomicSpecies > > 0.000 0.000 0.000 1 > 1.418 0.000 0.000 1 > 2.127 1.228 0.000 1 > 3.545 1.228 0.000 1 > 4.254 0.000 0.000 1 > 5.672 0.000 0.000 1 > 6.381 1.228 0.000 1 > 7.799 1.228 0.000 1 > 8.508 0.000 0.000 1 > 9.926 0.000 0.000 1 > 10.635 1.228 0.000 1 > 12.053 1.228 0.000 1 > 12.762 0.000 0.000 1 > 14.180 0.000 0.000 1 > 14.889 1.228 0.000 1 > 16.304 1.228 0.000 1 > 0.000 2.456 0.000 1 > 1.418 2.456 0.000 1 > 2.127 3.684 0.000 1 > 3.545 3.684 0.000 1 > 4.254 2.456 0.000 1 > 5.672 2.456 0.000 1 > 6.381 3.684 0.000 1 > 7.799 3.684 0.000 1 > 8.508 2.456 0.000 1 > 9.926 2.456 0.000 1 > 10.635 3.684 0.000 1 > 12.053 3.684 0.000 1 > 12.762 2.456 0.000 1 > 14.180 2.456 0.000 1 > 14.889 3.684 0.000 1 > 16.307 3.684 0.000 1 > 0.000 4.912 0.000 1 > 1.418 4.912 0.000 1 > 2.127 6.140 0.000 1 > 3.545 6.140 0.000 1 > 4.254 4.912 0.000 1 > 5.672 4.912 0.000 1 > 6.381 6.140 0.000 1 > 7.799 6.140 0.000 1 > 8.508 4.912 0.000 1 > 9.926 4.912 0.000 1 > 10.635 6.140 0.000 1 > 12.053 6.140 0.000 1 > 12.762 4.912 0.000 1 > 14.180 4.912 0.000 1 > 14.889 6.140 0.000 1 > 16.307 6.140 0.000 1 > 0.000 7.368 0.000 1 > 1.418 7.368 0.000 1 > 2.127 8.596 0.000 1 > 3.545 8.596 0.000 1 > 4.254 7.368 0.000 1 > 5.672 7.368 0.000 1 > 6.381 8.596 0.000 1 > 7.799 8.596 0.000 1 > 8.508 7.368 0.000 1 > 9.926 7.368 0.000 1 > 10.635 8.596 0.000 1 > 12.053 8.596 0.000 1 > 12.762 7.368 0.000 1 > 14.180 7.368 0.000 1 > 14.889 8.596 0.000 1 > 16.307 8.596 0.000 1 > 7.0900 4.912 1.400 2 > 7.0900 4.912 3.900 2 > 7.0900 4.912 6.400 2 > 0.000 0.000 7.800 1 > 1.418 0.000 7.800 1 > 2.127 1.228 7.800 1 > 3.545 1.228 7.800 1 > 4.254 0.000 7.800 1 > 5.672 0.000 7.800 1 > 6.381 1.228 7.800 1 > 7.799 1.228 7.800 1 > 8.508 0.000 7.800 1 > 9.926 0.000 7.800 1 > 10.635 1.228 7.800 1 > 12.053 1.228 7.800 1 > 12.762 0.000 7.800 1 > 14.180 0.000 7.800 1 > 14.889 1.228 7.800 1 > 16.304 1.228 7.800 1 > 0.000 2.456 7.800 1 > 1.418 2.456 7.800 1 > 2.127 3.684 7.800 1 > 3.545 3.684 7.800 1 > 4.254 2.456 7.800 1 > 5.672 2.456 7.800 1 > 6.381 3.684 7.800 1 > 7.799 3.684 7.800 1 > 8.508 2.456 7.800 1 > 9.926 2.456 7.800 1 > 10.635 3.684 7.800 1 > 12.053 3.684 7.800 1 > 12.762 2.456 7.800 1 > 14.180 2.456 7.800 1 > 14.889 3.684 7.800 1 > 16.307 3.684 7.800 1 > 0.000 4.912 7.800 1 > 1.418 4.912 7.800 1 > 2.127 6.140 7.800 1 > 3.545 6.140 7.800 1 > 4.254 4.912 7.800 1 > 5.672 4.912 7.800 1 > 6.381 6.140 7.800 1 > 7.799 6.140 7.800 1 > 8.508 4.912 7.800 1 > 9.926 4.912 7.800 1 > 10.635 6.140 7.800 1 > 12.053 6.140 7.800 1 > 12.762 4.912 7.800 1 > 14.180 4.912 7.800 1 > 14.889 6.140 7.800 1 > 16.307 6.140 7.800 1 > 0.000 7.368 7.800 1 > 1.418 7.368 7.800 1 > 2.127 8.596 7.800 1 > 3.545 8.596 7.800 1 > 4.254 7.368 7.800 1 > 5.672 7.368 7.800 1 > 6.381 8.596 7.800 1 > 7.799 8.596 7.800 1 > 8.508 7.368 7.800 1 > 9.926 7.368 7.800 1 > 10.635 8.596 7.800 1 > 12.053 8.596 7.800 1 > 12.762 7.368 7.800 1 > 14.180 7.368 7.800 1 > 14.889 8.596 7.800 1 > 16.307 8.596 7.800 1 > > %endblock AtomicCoordinatesAndAtomicSpecies > > # General variables > > ElectronicTemperature 100 K > MeshCutoff 350. Ry > xc.functional GGA # Exchange-correlation functional > xc.authors PBE > SpinPolarized .false. > SolutionMethod Transiesta > > ================================================== > ================================================== > # SCF variables > > DM.MixSCF1 T > MaxSCFIterations 4000 # Maximum number of SCF iter > DM.MixingWeight 0.2 # New DM amount for next SCF cycle > DM.Tolerance 0.0009 # Tolerance in maximum difference > DM.UseSaveDM true # to use continuation files > DM.NumberPulay 5 > Diag.DivideAndConquer no > Diag.ParallelOverK yes > > ================================================== > ================================================== > # MD variables > > MD.FinalTimeStep 1 > MD.TypeOfRun CG > MD.NumCGsteps 000 > MD.UseSaveXV .true. > > ================================================== > ================================================== > # Output variables > > WriteMullikenPop 1 > WriteBands .true. > SaveRho .true. > SaveDeltaRho .true. > SaveHS .true. > SaveElectrostaticPotential True > SaveTotalPotential no > WriteCoorXmol .true. > WriteMDXmol .true. > WriteMDhistory .false. > WriteEigenvalues yes > > ================================================== > ================================================== > > # Transiesta information > > # GF OPTIONS > TS.ComplexContour.Emin -30.0 eV > TS.ComplexContour.NPoles 03 > TS.ComplexContour.NCircle 30 > TS.ComplexContour.NLine 10 > TS.RealContour.Emin -30.0 eV > TS.RealContour.Emax 20.0 eV > > # BIAS OPTIONS > TS.biasContour.NumPoints 10 > # TS OPTIONS > TS.Voltage 0.000000 eV > > # TBT OPTIONS > TS.TBT.Emin -5.0 eV > TS.TBT.Emax +5.0 eV > TS.TBT.NPoints 100 > TS.TBT.NEigen 3 > TS.TBT.Eta 0.000001 Ry > > # Write hamiltonian > TS.SaveHS .true. > > # LEFT ELECTRODE > TS.HSFileLeft ./elec.arm.TSHS > TS.NumUsedAtomsLeft 64 > TS.BufferAtomsLeft 0 > > # RIGHT ELECTRODE > TS.HSFileRight ./elec.arm.TSHS > TS.NumUsedAtomsRight 64 > TS.BufferAtomsRight 0 > UseSaveData true > > can please anyone help me to know how can i reach convergence knowing > that he SCF iterations reached about 300 iteration without showing any sign > of convergence. > > Thanks in advance > > > > > > -- > 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/)
