#! /bin/sh

# This example shows how to use the NEGF key when including a bias potential
# between the electrodes. It starts of with the usual tight-binding run,
# followed by an SGF one. The alignment run is omitted. Finally, there is a loop
# over bias potentials. Here the scale feature of the FuzzyPotential is used.
# The current is appended to a text file, which one could plot eg. with gnuplot.

# Note: Setting up a NEGF calculation is quite hard without the GUI.

AMS_JOBNAME=tight-binding $ADFBIN/ams <<eor

Task SinglePoint 

System
  Atoms
      Li.1 0.0 0.0 0.0
      Li.2 2.876 0.0 0.0
      Li.3 5.752 0.0 0.0
  End
  Lattice
   8.628 0.0 0.0
  End
End

Engine Band 
  TITLE tight-binding

  KSpace
    Quality VeryGood
  End

  SoftConfinement
    Quality Basic
  End

  Basis
    Type DZ
    Core Large
  End

  StoreHamiltonian2
EndEngine
eor


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

mv SigmaSCM Sigma.kf

REPORT=Li-CuAg.report
touch $REPORT

for bias in -0.01 0.01
do


AMS_JOBNAME=negf $ADFBIN/ams <<eor

Task SinglePoint

System
  ATOMS
      Li.1L -15.818 0.0 0.0
      Li.2L -12.942 0.0 0.0
      Li.3L -10.066 0.0 0.0
      Li.1C -7.19 0.0 0.0
      Li.2C -4.314 0.0 0.0
      Cu.C -0.7 -1.0 0
      Ag.C 0.7 1.0 0
      Li.3C 4.314 0.0 0.0
      Li.4C 7.19 0.0 0.0
      Li.1R 10.066 0.0 0.0
      Li.2R 12.942 0.0 0.0
      Li.3R 15.818 0.0 0.0
  END
End

Engine Band 
  TITLE bias=$bias

  SoftConfinement
    Quality Basic
  End

  Basis
    Type DZ
    Core Large
  End

  NEGF
    LeadFile tight-binding.results/band.rkf
    SGFFile Sigma.kf
    EMin -5.0
    EMax 5.0
    NE 200
    ApplyShift2 False
    BiasPotential $bias
  End

  FuzzyPotential
  scale $bias
  1   0.5
  2   0.5
  3   0.5
  4   0.5
  5   0.5
  6   0.2
  7   -0.2
  8   -0.5
  9   -0.5
  10  -0.5
  11  -0.5
  12  -0.5
  end
EndEngine

eor

current=`$ADFBIN/adfreport negf.results/band.rkf 'NEGF%current'`
echo "NEGFREPORT: Bias=$bias, Current=$current" >> $REPORT

fname=`ls Transmission_*.plt`

echo "start of transmission (bias=$bias)"
cat $fname
echo "end of transmission"

rm Transmission_*.plt

rm -r negf.results

done

echo "Start of report"
cat $REPORT
echo "End of report"