Example: Electronic transport with NEGF
***************************************

"Download conductance.run"

   #!/bin/sh

   # ==================================
   # First test: Aluminum chain (DFTB0)
   # ==================================

   # Lead:
   # =====

   AMS_JOBNAME=Al_lead $AMSBIN/ams <<EOF
       Task SinglePoint
       System
           Atoms
               Al 0.0  0.0 0.0
               Al 2.83 0.0 0.0
               Al 5.66 0.0 0.0
               Al 8.49 0.0 0.0
           End

           Charge 0

           Lattice
               11.32 0.0 0.0
           End
       End

       Engine DFTB
          ResourcesDir QUASINANO2013.1
          StoreMatrices yes
          Model DFTB0
          Occupation Strategy=Fermi Temperature=5
          KSpace
            Type Symmetric
            Symmetric KInteg=13
          End
       EndEngine
   EOF

   # Scattering region:
   # ==================

   AMS_JOBNAME=Al_scattering $AMSBIN/ams <<EOF
       Task SinglePoint
       System
           Atoms
               Al -14.15 0.0 0.0
               Al -11.32 0.0 0.0
               Al -8.49 0.0 0.0
               Al -5.66 0.0 0.0
               Al -2.83 0 0
               Al 0 0 0
               Al 2.83 0 0
               Al 5.66 0.0 0.0
               Al 8.49 0.0 0.0
               Al 11.32 0.0 0.0
               Al 14.15 0.0 0.0
           End

           Charge 0
       End

       Engine DFTB
          ResourcesDir QUASINANO2013.1
          StoreMatrices yes
          Model DFTB0
          Occupation Strategy=Fermi Temperature=5
       EndEngine
   EOF

   # Conductance:
   # ============

   $AMSBIN/conductance <<EOF
       EnergyGrid min=-5 max=5 num=500

       Files
          Leads      Al_lead.results/dftb.rkf
          Scattering Al_scattering.results/dftb.rkf
       End
   EOF

   mv ConductanceResults.kf Al_ConductanceResults.kf

   echo "Extract DOS from the kf file Al_ConductanceResults.kf:"
   $AMSBIN/amsreport Al_ConductanceResults.kf -r "results%dos#12.5f##1"

   echo "Extract transmission from the kf file Al_ConductanceResults.kf:"
   $AMSBIN/amsreport Al_ConductanceResults.kf -r "results%transmission#12.5f##1"


   # ==========================================
   #   Second test: CO on gold chain (SCC-DFTB)
   # ==========================================

   # Lead:
   # =====

   AMS_JOBNAME=Au_lead $AMSBIN/ams <<EOF
       Task SinglePoint
       System
           Atoms
               Au 0.0 0.0 0.0
               Au 2.884996 0.0 0.0
               Au 5.769992 0.0 0.0
           End

           Charge 0

           Lattice
               8.654988 0.0 0.0
           End
       End
       Engine DFTB
          Model SCC-DFTB
          ResourcesDir QUASINANO2013.1
          Occupation Strategy=Fermi Temperature=5
          StoreMatrices yes
          KSpace
            Type Symmetric
            Symmetric KInteg=13
          End
       EndEngine
   EOF

   # Scattering region:
   # ==================

   AMS_JOBNAME=Au_scattering $AMSBIN/ams <<EOF
       Task SinglePoint
       System
           Atoms
               Au -20.194972   0.0 0.0
               Au -17.309976   0.0 0.0
               Au -14.42498    0.0 0.0
               Au -11.539984   0.0 0.0
               Au -8.654988    0.0 0.0
               Au -5.769992    0.0 0.0
               Au -2.884996    0.0 0.0
               Au 0.0          0.0 0.20
               Au 2.884996     0.0 0.0
               Au 5.769992     0.0 0.0
               Au 8.654988     0.0 0.0
               Au 11.539984    0.0 0.0
               O 0.0           0.0 3.12
               C 0.0           0.0 1.96
               Au 14.42498     0.0 0.0
               Au 17.309976    0.0 0.0
               Au 20.194972    0.0 0.0
           End

           Charge 0

           Lattice
               43.27494 0.0 0.0
           End
       End

       Engine DFTB
          Model SCC-DFTB
          ResourcesDir QUASINANO2013.1
          Occupation Strategy=Fermi Temperature=5
          StoreMatrices yes
       EndEngine
   EOF

   # Conductance:
   # ============

   $AMSBIN/conductance <<EOF
       EnergyGrid min=-3.5 max=3 num=200

       Files
         Leads      Au_lead.results/dftb.rkf
         Scattering Au_scattering.results/dftb.rkf
       End
   EOF

   mv ConductanceResults.kf Au_ConductanceResults.kf

   echo "Extract DOS from the kf file Au_ConductanceResults.kf:"
   $AMSBIN/amsreport Au_ConductanceResults.kf -r "results%dos#12.5f##1"

   echo "Extract transmission from the kf file Au_ConductanceResults.kf:"
   $AMSBIN/amsreport Au_ConductanceResults.kf -r "results%transmission#12.5f##1"


