Dear Nick, I am a graduate student in theoretical chemistry who recently started using Transiesta/TBtrans. My objective is to compute I vs V curve on 1,4-benzenediammine (BDA) between linear chains of Au atoms. I am using siesta-4.1-b3 on a Unix/64 machine with Ubuntu 14.04. I am facing the following problems : 1) TBTrans has been compiled using NetCDF4 support using the bash script you provide in /Docs folder. I have added the requisite libraries mentioned by executing your script to the arch.make file while compiling TBtrans. Transiesta and Siesta has been compiled without the Netcdf4 support using the usual gfortran arch make file. The compilation of TBTrans is successful and I make a soft link (ln -s) of the executable to whichever directory I work or add the absolute path to the pbs . The electrode calculation (with 5 Au atoms) seems to go fine and generates the .TSHS which then feeds into the transiesta calculation submitted using the fdf named as Aul_bda_Aur_NEW.fdf (attached). Thereafter I do the TBTrans run using the same fdf but changing TS.Voltage everytime. TS run goes fine so does TBT run . However in the attached TBT output file (named as Aul_bda_Aur_0.25_TBT.out where 0.25 V is the voltage) I dont see the current in the scattering region or the voltage displayed like in older versions. The TBTrans is compiled with Netcdf4 , so where is the current printed ? Am I missing a keyword for this in the .fdf file or is it a different issue? 2) Also the manual states that there will be TBT.nc , .DOS, .FDOS, .TRANS,. AVTRANS files etc also with NetCDF4 support. I dont see it generated . I believe I am missing something stupid in the process, just dont know what ? I have the .TBT.TRANS-Left-Right folder which gives the transmission as a function for E and for a single k in the grid this is average transmission but still the .AVTRANS file should have been generated anyway right ? What am I doing wrong? 3)Just to clarify the whole process so that I am not missing anything : (a) one does an electrode run at zero bias to get .TSHS ....(b) use that for the TS calculation with the full electrode -device set-up in and generate a scattering region .TSHS ........(c) the latter files are used for the TBT calculation to generate transport properties using the same fdf as (b) . For finite bias just change the TS.Voltage in (b) and (c) and repeat the two steps .....right ? thats all the steps ? <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< TS/TBtrans input file (Aul_bda_Aur_NEW.fdf) <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< SystemName Transport # Descriptive name of the system SystemLabel Aul_bda_Aur # Short name for naming files # SPECIES AND BASIS NumberOfAtoms 27 NumberOfSpecies 4 LatticeConstant 1.0000 Ang %block LatticeVectors 30.000 0.000 0.00000 0.000 30.000 0.00000 0.00000 0.00000 39.32218 %endblock LatticeVectors #--BASIS SET PAO.BasisType split PAO.SplitNorm 0.15 # PAO.BasisSize DZP #This flag sets the same basis set for all atoms %block PAO.BasisSizes Au DZ H DZP N DZP C DZP %endblock PAO.BasisSizes PAO.EnergyShift 0.01 eV # K-POINTS %block kgrid_Monkhorst_Pack 1 0 0 0.0 0 1 0 0.0 0 0 1 0.0 %endblock kgrid_Monkhorst_Pack BandLinesScale ReciprocalLatticeVectors # GENERAL VARIABLES #--Exchange-correlation functionals XC.functional GGA # LDA or GGA XC.authors PBE # CA = PZ, PW92, PBE MeshCutoff 200.0 Ry # SPIN OPTIONS #SpinPolarized F # T, F #FixSpin F #TotalSpin 0.0 #NonCollinearSpin F # T, F # SCF OPTIONS ElectronicTemperature 300 K MaxSCFIterations 30000 DM.MixingWeight 0.02 DM.NumberPulay 4 # Pulay convergency accelerator #DM.MixSCF1 T #DM.MixH T #DM.PulayOnFile F # Store in memory (F) or in files (T) DM.Tolerance 1.0D-5 DM.UseSaveDM T # SYSTEM %block ChemicalSpeciesLabel 1 79 Au 2 1 H 3 7 N 4 6 C %endblock ChemicalSpeciesLabel AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies ..........CO-ORDINATES OF LEFT ELEC-DEVICE-RIGHT ELEC (usual format) %endblock AtomicCoordinatesAndAtomicSpecies # TRANSPORT VARIABLES SolutionMethod transiesta TS.Voltage 0.00000 eV %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 ./Au5.TSHS chem-pot Left semi-inf-dir -a3 elec-pos begin 1 used-atoms 4 %endblock TS.Elec.Left %block TS.Elec.Right HS ./Au5.TSHS chem-pot Right semi-inf-dir +a3 elec-pos end -1 used-atoms 5 %endblock TS.Elec.Right TS.Contours.Eq.Pole 2.50000 eV %block TS.Contour.c-Left part circle from -20.00000 Ry + V/2 to -10. kT + V/2 points 25 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 -20.00000 Ry - V/2 to -10. kT - V/2 points 25 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 0.0136058000 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.Elecs.Eta 0.0001000000 eV TBT.Voltage 0.00000 eV %block TBT.Contours neq %endblock TBT.Contours %block TBT.Contour.neq part line from -5.25000 eV to 5.25000 eV delta 0.00040 eV method mid-rule %endblock TBT.Contour.neq ************************************************END ********************************** <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< TBtrans output file display (Aul_bda_Aur_0.25_TBT.out) <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< INPUT DATA (AS ABOVE) DISPLAY ....... ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: Transport reinit: ----------------------------------------------------------------------- reinit: System Label: Aul_bda_Aur reinit: ----------------------------------------------------------------------- Kpoints in: 1 . Kpoints trimmed: 1 tbt: Number of transport k-points = 1 tbt: Method = Monkhorst-Pack grid. tbt: k-grid: Supercell and displacements tbt: 1 0 0 0.000 tbt: 0 1 0 0.000 tbt: 0 0 1 0.000 tbt: ************************************************************** tbt: Electronic temperature (reference) = 299.9978 K tbt: Voltage = 0.2500 Volts tbt: Calculate transmission only using diag(Gf) = F tbt: Saving bulk transmission for electrodes = F tbt: Saving DOS from bulk electrodes = F tbt: Saving DOS from Green function = F tbt: Saving DOS from spectral functions = F tbt: Saving bond currents (orb-orb) = F tbt: Calc. # transmission eigenvalues = 0 tbt: Calc. T between all electrodes = F tbt: Calc. total T out of electrodes = F tbt: Single spin Hamiltonian tbt: BTD creation algorithm = speed tbt: BTD spectral function algorithm = propagation tbt: Divide and conquer diagonalization = F tbt: Assume LAPACK = delta_ij = F tbt: Saving down-folded self-energies not enabled (NetCDF4) tbt: delta-Hamiltonian not enabled (NetCDF4) tbt: Data files stored in current folder tbt: >> Electrodes << tbt: >> Left tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3 tbt: In-core GF tbt: Electrode TSHS file = ./Au5.TSHS tbt: # atoms used in electrode = 4 tbt: Electrode Bloch expansion [E1 x E2 x E3] = 1 x 1 x 1 tbt: Position in geometry = 1 -- 4 tbt: Semi-infinite direction for electrode = negative wrt. E3 tbt: Chemical shift = 0.125000 eV tbt: Electronic temperature = 299.997806 K tbt: Bulk values in electrode = T tbt: Hamiltonian E-C Ef fractional shift = 0.0000 tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV tbt: Electrode self-energy accuracy = 0.1000E-13 eV tbt: Electrode inter-layer distance (semi-inf) = 2.8800 Ang tbt: >> Right tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3 tbt: In-core GF tbt: Electrode TSHS file = ./Au5.TSHS tbt: # atoms used in electrode = 5 tbt: Electrode Bloch expansion [E1 x E2 x E3] = 1 x 1 x 1 tbt: Position in geometry = 23 -- 27 tbt: Semi-infinite direction for electrode = positive wrt. E3 tbt: Chemical shift = -0.125000 eV tbt: Electronic temperature = 299.997806 K tbt: Bulk values in electrode = T tbt: Hamiltonian E-C Ef fractional shift = 0.0000 tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV tbt: Electrode self-energy accuracy = 0.1000E-13 eV tbt: Electrode inter-layer distance (semi-inf) = 2.8800 Ang ts: >> TBtrans contour << ts: Device Green function imaginary Eta = 0.000 eV ts: Contour name = TBT.Contour.neq ts: line contour E_min = -5.2500 eV ts: line contour E_max = 5.2500 eV ts: line contour points =26250 ts: line contour method = Mid-rule tbt: ************************************************************** tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< %block TBT.Contours neq %endblock TBT.Contours %block TBT.Contour.neq from -5.25000 eV to 5.25000 eV delta 0.00040 eV method mid-rule %endblock TBT.Contour.neq tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ************************ Begin: TBT CHECKS AND WARNINGS ************************ ** Use TBT.Atoms.Device for faster execution ************************ End: TBT CHECKS AND WARNINGS ************************** Device information (full): Electrode information: Left principal cell is perfect! Right principal cell is perfect! tbtrans: Analyzing electrode sparsity pattern to create optimal tri-diagonal blocks tbtrans: BTD pivoting scheme for electrode (Left): atom+Left tbtrans: BTD pivoting scheme for electrode (Right): atom+Right tbtrans: Analyzing device sparsity pattern to create optimal tri-diagonal blocks tbtrans: BTD pivoting scheme in device: atom+Left tbtrans: Done analyzing sparsity pattern tbtrans: Reducing matrix (H, S) sparsity patterns by: 720 tbtrans: # of device region orbitals: 168 Region (18): [A]-device [ 5 -- 22 ] tbtrans: # of Left scattering orbitals: 139 tbtrans: # of Left down-folding orbitals: 187 Region (4): [A]-Left folding region [ 1 -- 4 ] Region (16): [A]-Left folding in D [ 5 -- 19, 22 ] tbtrans: # of Right scattering orbitals: 139 tbtrans: # of Right down-folding orbitals: 199 Region (5): [A]-Right folding region [ 23 -- 27 ] Region (16): [A]-Right folding in D [ 5, 8 -- 22 ] tbtrans: Creating electrode tri-diagonal matrix blocks tbtrans: Creating device tri-diagonal matrix blocks Region (2): [TRI] device region [ 84, 84 ] tbtrans: Matrix elements in BTD: 28224 tbtrans: Electrodes tri-diagonal matrices Region (2): [TRI] Left [ 48, 139 ] Region (2): [TRI] Right [ 60, 139 ] tbtrans: Electrode memory: 0.693 MB tbtrans: Sparse Hamiltonian and overlap memory: 1.298 MB tbtrans: Sum of electrode and sparse memory: 1.991 MB tbtrans: LHS Green function size / memory: 46800 / 0.71 MB tbtrans: RHS Green function size / memory: 38642 / 0.59 MB tbt: Initial ETA in 3018.189 s tbt: Calculated 5.002 %, ETA in 3116.556 s tbt: Calculated 10.004 %, ETA in 3177.799 s tbt: Calculated 15.006 %, ETA in 3079.509 s tbt: Calculated 20.008 %, ETA in 2940.548 s tbt: Calculated 25.010 %, ETA in 2723.195 s tbt: Calculated 30.011 %, ETA in 2342.675 s tbt: Calculated 35.013 %, ETA in 2022.291 s tbt: Calculated 40.015 %, ETA in 1776.793 s tbt: Calculated 45.017 %, ETA in 1654.081 s tbt: Calculated 50.019 %, ETA in 1540.865 s tbt: Calculated 55.021 %, ETA in 1417.547 s tbt: Calculated 60.023 %, ETA in 1285.787 s tbt: Calculated 65.025 %, ETA in 1144.315 s tbt: Calculated 70.027 %, ETA in 995.702 s tbt: Calculated 75.029 %, ETA in 841.912 s tbt: Calculated 80.030 %, ETA in 685.330 s tbt: Calculated 85.032 %, ETA in 520.031 s tbt: Calculated 90.034 %, ETA in 347.838 s tbt: Calculated 95.036 %, ETA in 174.302 s tbt: Completed in 3521.622 s Section Calls Walltime % global_section 1 3535.201 100.00 tbtrans 1 3535.201 100.00 tri-init 1 0.007 0.00 tri-init-elec 1 0.003 0.00 TS-rgn2tri 2 0.000 0.00 TS-rgn2tri 1 0.000 0.00 TBT 1 3535.070 100.00 read-GS 26250 2503.273 70.81 SE-dwn 26250 209.024 5.91 ts_expand 52500 0.279 0.01 Gf-prep 26250 317.007 8.97 V_TM_Pinv 26250 285.601 8.08 DOS-Gf-A-T 26250 505.431 14.30 >> End of run: 4-APR-2018 7:25:57 ******************************************************END********************************************************* Any help will be greatly appreciated as I am struggling with these for a while now with no direction to move forward at all. Thanks a lot. Hoping to hear from you at the earliest. With Regards, Manas

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