# Archivos de Entrada

### Cálculo SPE de la región de scattering con SIESTA

SystemLabel scattering_hb1_cl

%include scattering_hb1_cl.fdf

%block kgrid.MonkhorstPack
 100  0    0    0.0
  0   1    0    0.0
  0   0    1    0.0
%endblock kgrid.MonkhorstPack

SolutionMethod          diagon
Diag.ParallelOverK      true

#       Calculation Parameters
#PAO.BasisSize          DZP
#PAO.EnergyShift        0.006 Ry
XC.functional          GGA
XC.authors             PBE
MeshCutoff             250.0 Ry

#       System Variables
ElectronicTemperature  300 K
OccupationFunction     FD
NetCharge               0
SpinPolarized           false

#       Density Matrix
DM.Tolerance            1e-5
DM.NumberPulay          5
DM.UseSaveDM           true

#       SCF Mixing parameters:
MaxSCFIterations       100
MinSCFIterations       3
SCF.Mixer.Weight       0.30
SCF.Mixer.History      6
SCF.Mix.First          true

#       Geometry Optimization
#MD.TypeOfRun           CG
#MD.NumCGSteps          500
#MD.MaxForceTol         0.01 eV/Ang
#MD.MaxCGDispl          0.05 Bohr
#MD.VariableCell                true
#MD.UseSaveXV           true
#MD.UseSaveCG           true
#       Aditionals
WriteCoorXmol           true

#WriteDenchar            true
#WriteWaveFunctions      true
#%block WaveFuncKPoints
# 0.0 0.0 0.0
#%endblock WaveFuncKPoints

######   DZP Basis for Au Cubic  with EnergyShift=0.032 Ry  ##########
PAO.BasisType split

%block PAO.Basis                 # Define Basis set
Au                    2                    # Species label, number of l-shells
 n=6   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.787      5.644
   1.000      1.000
 n=5   2   2                         # n, l, Nzeta
   3.977      2.733
   1.000      1.000
%endblock PAO.Basis

##################################################################################
######           DZP Basis for viologen model with EnergyShift=0.006 Ry  ##########
PAO.BasisType split
%block PAO.Basis                 # Define Basis set
C                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   4.750      3.432
   1.000      1.000
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.949      3.699
   1.000      1.000
N                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   4.175      2.905
   1.000      1.000
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.228      3.092
   1.000      1.000
S                     2                    # Species label, number of l-shells
 n=3   0   2                         # n, l, Nzeta
   4.723      3.543
   1.000      1.000
 n=3   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.914      3.964
   1.000      1.000
H                     1                    # Species label, number of l-shells
 n=1   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.610      4.002
   1.000      1.000
%endblock PAO.Basis
##################################################################################

### Cálculo del electrdo con SIESTA

SystemLabel ELEC

%include STRUCT_ELEC.fdf

%block kgrid.MonkhorstPack
 100  0    0 	0.0
  0   1    0 	0.0
  0   0    1  	0.0
%endblock kgrid.MonkhorstPack

#PAO.BasisSize          SZP
#PAO.EnergyShift        0.016 Ry
XC.functional          GGA
XC.authors             PBE
MeshCutoff             250.000000 Ry
FilterCutoff           150.000000 Ry

ElectronicTemperature  300 K
OccupationFunction     FD

MinSCFIterations       3
MaxSCFIterations       100
SCF.DM.Tolerance       0.00001
# Mixing parameters:
SCF.Mixer.Weight       0.30
SCF.Mixer.History      6
SCF.Mix.First          true
DM.UseSaveDM           true

MD.NumCGSteps          0

SaveHS                 	true
TS.HS.Save		true
TS.DE.Save		true

######   DZP Basis for Au Cubic  with EnergyShift=0.032 Ry  ##########
PAO.BasisType split

%block PAO.Basis                 # Define Basis set
Au                    2                    # Species label, number of l-shells
 n=6   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.787      5.644
   1.000      1.000
 n=5   2   2                         # n, l, Nzeta
   3.977      2.733
   1.000      1.000
%endblock PAO.Basis

### Cálculos con Transiesta

SolutionMethod transiesta

SystemLabel scattering_hb1_cl 
%include scattering_hb1_cl.fdf

%block kgrid.MonkhorstPack
   100 0  0  0.
    0  1  0  0.
    0  0  1  0.
%endblock kgrid.MonkhorstPack


# This below input options for transiesta
# are automatically generated using the
# tselecs.sh script which enables easy
# creation of input options for N-electrodes
# (up to 9).

TS.Voltage 0 eV

# To perform bias calculations one is FORCED to define the *different* chemical potentials. 
# Note that there will NEVER be more chemical potentials than electrodes. In this example we call the chemical potentials by the names of the electrodes. However, you may call them as you wish.
%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots

%block TS.ChemPot.Left
  # The left chemical potential is lifted half the applied bias.
  mu V/2
  # this block defines the contours used for integrating the equilibrium part of the density.
  contour.eq
    begin
      C-Left
      T-Left
    end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  # The right chemical potential is downshifted half the applied bias.
  mu -V/2
  contour.eq
    begin
      C-Right
      T-Right
    end
%endblock TS.ChemPot.Right

# From this cutoff-energy the number of poles will be calculated from the energy and the temperature.
TS.Contours.Eq.Pole 3.5 eV

# The following two blocks are the LEFT equilibrium contour
%block TS.Contour.C-Left
  part circle
   from -40. eV + 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

# The following two blocks are the RIGHT equilibrium contour
%block TS.Contour.C-Right
  part circle
   from -40. eV -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

# In addition to defining the equilibrium contours one also has to define the non-equilibrium contours to denote the integration in the bias-window.
# NOTE that one may define as many integration partitions as one wishes, but generally only one is needed. If you are used to the older transiesta version you will be happily surprised that the new transiesta need not change options for different applied bias'
%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


# Here comes the electrode definitions
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  HS ELEC.TSHS
  chemical-potential Left
  semi-inf-direction -a1
  electrode-position 1
%endblock
%block TS.Elec.Right
  HS ELEC.TSHS
  chemical-potential Right
  semi-inf-direction +a1
  electrode-position end -1
%endblock

# This is the remaining default SIESTA options

#PAO.BasisSize         SZP
XC.functional     GGA
XC.authors        PBE
MeshCutoff        250.000000 Ry
FilterCutoff      150.000000 Ry

ElectronicTemperature   300 K

MinSCFIterations       3
SCF.DM.Tolerance       0.00001
# Mixing parameters:
SCF.Mixer.Weight       0.10
SCF.Mixer.History      12
SCF.Mix.First          true
DM.UseSaveDM           true

MD.NumCGSteps 0

SaveElectrostaticPotential 	true	
SaveHS                          true

######   DZP Basis for Au Cubic  with EnergyShift=0.032 Ry  ##########
PAO.BasisType split

%block PAO.Basis                 # Define Basis set
Au                    2                    # Species label, number of l-shells
 n=6   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.787      5.644
   1.000      1.000
 n=5   2   2                         # n, l, Nzeta
   3.977      2.733
   1.000      1.000
%endblock PAO.Basis

######		 DZP Basis for viologen model with EnergyShift=0.006 Ry  ##########

%block PAO.Basis                 # Define Basis set
C                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   4.750      3.432
   1.000      1.000
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.949      3.699
   1.000      1.000
N                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   4.175      2.905
   1.000      1.000
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.228      3.092
   1.000      1.000
S                     2                    # Species label, number of l-shells
 n=3   0   2                         # n, l, Nzeta
   4.723      3.543
   1.000      1.000
 n=3   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.914      3.964
   1.000      1.000
H                     1                    # Species label, number of l-shells
 n=1   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   5.610      4.002
   1.000      1.000
%endblock PAO.Basis