#! /bin/sh

# This example shows how to use the NEGF functionality.
# Note: Setting up a NEGF calculation is quite hard without the GUI.

# It starts of with Method 1: the non-self consistent approach. Here, BAND
# merely serves to provide matrix elements, being unaware of the electrodes.

# Then follows Method 2: here the NEGF density is really used to calculate the
# matrix elements.

# Method 3 is a variation on Method 2, and includes an extra alignment run.

# ==============================================================================
#  Method #1: non-self consistent NEGF (uses the conductance program, like DFTB)
# ==============================================================================


# =========================   Method #1. Run #1   ==============================

AMS_JOBNAME=lead_1 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
     Cr.1 0.0 0.0 0.0
     Cr.2 2.5 0.0 0.0
  END

  Lattice
     5.0 0.0 0.0
  End
End

Engine Band 
  Title method_1_run_1

  KSpace
      Quality Good
  End

  NumericalQuality Basic

  Basis
     Type DZ
     Core Large
  End

  Unrestricted

  StoreHamiltonian2
EndEngine
eor

# ========================   Method #1. Run #2   ===============================

AMS_JOBNAME=scattering_1 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1L -10.0 0.0 0.0
      Cr.2L  -7.5 0.0 0.0
      Cr.C   -5.0 0.0 0.0
      Cr.C   -2.5 0.0 0.0
      Cr.C    0.0 0.0 0.0
      Cr.C    2.5 0.0 0.0
      Cr.C    5.0 0.0 0.0
      Cr.1R   7.5 0.0 0.0
      Cr.2R  10.0 0.0 0.0
  END

  Lattice
     22.5 0.0 0.0
  End
End

Engine Band 
  Title method_1_run_2

  NumericalQuality Basic

  Basis
     Type DZ
     Core Large
  End

  Unrestricted

  StoreHamiltonian2
  StoreHamAsMol
EndEngine

eor

# ==========================   Method #1. Run #3   =============================

$ADFBIN/conductance <<EOF
EnergyGrid min=-5 max=5 num=200
Files
   Leads      lead_1.results/band.rkf
   Scattering scattering_1.results/band.rkf
End

EOF

# Compy the content of the "reseults" section from ConductanceResults.kf to band.rkf and rename the section to NEGF
$ADFBIN/cpkf "ConductanceResults.kf" "scattering_1.results/band.rkf" "results --rename NEGF"


echo "Extract transmisstion from rkf file (Method 1)"
$ADFBIN/adfreport scattering_1.results/band.rkf -r "NEGF%transmission#12.5f##1"

# ==============================================================================
#               Method #2: self consistent NEGF without alignment
# ==============================================================================


# =========================   Method #2. Run #1   ==============================

AMS_JOBNAME=lead_2 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1 0.0 0.0 0.0
      Cr.2 2.5 0.0 0.0
  END

  Lattice
   5.0 0.0 0.0
  End
End

Engine Band 
  Title method_2_run_1

  KSpace
      Quality Good
  End

  NumericalQuality Basic

  Basis
    Type DZ
    Core Large
  End

  Unrestricted
  StoreHamiltonian2
EndEngine 

eor

# =============================   Method #2. Run #2   ==========================


$ADFBIN/sgf   <<eor
TITLE Test for NEGF inputs
SAVE SIGMA
SURFACEGF
   RKFFileName lead_2.results/band.rkf
   SCMCode
   KT 0.001
   ContourQuality normal
END
eor

mv SigmaSCM Sigma.kf

# =============================   Method #2. Run #3   ==========================

AMS_JOBNAME=scattering_2 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1L -10.0 0.0 0.0
      Cr.2L -7.5 0.0 0.0
      Cr.C -5.0 0.0 0.0
      Cr.C -2.5 0.0 0.0
      Cr.C 0.0 0.0 0.0
      Cr.C 2.5 0.0 0.0
      Cr.C 5.0 0.0 0.0
      Cr.1R 7.5 0.0 0.0
      Cr.2R 10.0 0.0 0.0
  END
End

Engine Band 
  Title method_2_run_3

  NumericalQuality Basic

  Basis
    Type DZ
    Core Large
  End

  Unrestricted
  NEGF
    LeadFile        lead_2.results/band.rkf
    SGFFile         Sigma.kf
    ApplyShift2     False
    ContourQuality  normal
    EMin           -5
    EMax            5
    NE 200
  End
EndEngine
eor

echo "Extract transmisstion from rkf file (Method 2)"
$ADFBIN/adfreport scattering_2.results/band.rkf -r "NEGF%transmission#12.5f##1"

# ==============================================================================
#                Method #3: self consistent NEGF wit alignment run
# ==============================================================================

# =======================   Method #3. Run #1   ================================


AMS_JOBNAME=lead_3 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1 0.0 0.0 0.0
      Cr.2 2.5 0.0 0.0
  END
  Lattice
   5.0 0.0 0.0
  End
End

Engine Band 
  Title method_3_run_1

  KSpace
      Quality Good
  End

  NumericalQuality Basic

  Basis
    Type DZ
    Core Large
  End

  Unrestricted
  StoreHamiltonian2
EndEngine
eor

# ============================   Method #3. Run #2   ===========================


$ADFBIN/sgf   <<eor
TITLE Test for NEGF inputs
SAVE SIGMA
SURFACEGF
   RKFFileName lead_3.results/band.rkf
   SCMCode
   KT 0.001
   ContourQuality normal
END
eor

mv SigmaSCM Sigma.kf

# ============================   Method #3. Run #3   ===========================

AMS_JOBNAME=align $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1L 0.0 0.0 0.0
      Cr.2L 2.5 0.0 0.0
      Cr.C 5.0 0.0 0.0
      Cr.C 7.5 0.0 0.0
      Cr.C 10.0 0.0 0.0
      Cr.C 12.5 0.0 0.0
      Cr.1R 15.0 0.0 0.0
      Cr.2R 17.5 0.0 0.0
  END
End

Engine Band 
  Title method_3_run_3

  NumericalQuality Basic

  Basis
    Type DZ
    Core Large
  End

  Unrestricted
  NEGF
    DoAlignment True
    LeadFile lead_3.results/band.rkf
    SGFFile Sigma.kf
    ContourQuality normal
    EMin -5.0
    EMax 5.0
    NE 200
    AlignChargeTol 0.0001
  End
EndEngine 
eor

# =============================   Method #3. Run #4  ===========================

AMS_JOBNAME=scattering_3 $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Cr.1L -10.0 0.0 0.0
      Cr.2L -7.5 0.0 0.0
      Cr.C -5.0 0.0 0.0
      Cr.C -2.5 0.0 0.0
      Cr.C 0.0 0.0 0.0
      Cr.C 2.5 0.0 0.0
      Cr.C 5.0 0.0 0.0
      Cr.1R 7.5 0.0 0.0
      Cr.2R 10.0 0.0 0.0
  END
End

engine Band 
  Title method_3_run_4

  NumericalQuality Basic

  Basis
    Type DZ
    Core Large
  End

  Unrestricted

  NEGF
     LeadFile lead_3.results/band.rkf
     SGFFile Sigma.kf
     AlignmentFile align.results/band.rkf
     ContourQuality normal
     EMin -5.0
     EMax 5.0
     NE 200
  End
EndEngine
eor

echo "Extract transmisstion from rkf file (Method 2)"
$ADFBIN/adfreport scattering_3.results/band.rkf -r "NEGF%transmission#12.5f##1"