Example: NEGF using the non-self consistent method
**************************************************

"Download NEGF_Conductance.run"

   #! /bin/sh

   # In this example we demonstrate how to run a Band-NEGF calculation using the non
   # self consistent approach (using the conductance program). In the first example
   # we study the conductivity of a mono-atomic gold chain with a CO molecule
   # adsorbed on top. Such calculation consists of three separate runs. See the
   # documentation for more details.

   # ==============================================================================
   #                             CO on gold chain
   # ==============================================================================

   # =======
   # Au lead
   # =======

   AMS_JOBNAME=Au_lead $AMSBIN/ams <<eor

   Task SinglePoint 

   System
       ATOMS
           Au 0.0       0.0  0.0 region=1
           Au 2.884996  0.0  0.0 region=2
           Au 5.769992  0.0  0.0 region=3
       END

       Lattice
           8.654988  0.0  0.0
       End
   End

   Engine Band 
       TITLE Au_lead

       KSpace
           Quality VeryGood
       End

       SoftConfinement
           Quality Basic
       End

       Basis
           Type DZ
           Core Large
       End

       StoreHamiltonian2
   EndEngine 
   eor

   # =============
   # Au scattering 
   # =============

   AMS_JOBNAME=Au_scattering $AMSBIN/ams <<eor

   Task SinglePoint

   System
       ATOMS
           Au    -20.194972  0.0  0.0   region=1L
           Au    -17.309976  0.0  0.0   region=2L
           Au    -14.42498   0.0  0.0   region=3L
           Au    -11.539984  0.0  0.0   region=C
           Au    -8.654988   0.0  0.0   region=C
           Au    -5.769992   0.0  0.0   region=C
           Au    -2.884996   0.0  0.0   region=C
           Au     0.0        0.0  0.20  region=C
           Au     2.884996   0.0  0.0   region=C
           Au     5.769992   0.0  0.0   region=C
           Au     8.654988   0.0  0.0   region=C
           Au     11.539984  0.0  0.0   region=C
           O      0.0        0.0  3.12  region=C
           C      0.0        0.0  1.96  region=C
           Au     14.42498   0.0  0.0   region=1R
           Au     17.309976  0.0  0.0   region=2R
           Au     20.194972  0.0  0.0   region=3R
       END

       Lattice
           43.27494  0.0  0.0
       End
   End

   Engine Band 
       TITLE Au_scattering

       SoftConfinement
           Quality Basic
       End

       Basis
           Type DZ
           Core Large
       End

       StoreHamiltonian2
       StoreHamAsMol
   EndEngine

   eor

   # ==============
   # Au Conductance
   # ==============

   $AMSBIN/conductance <<EOF
   EnergyGrid min=-3.5 max=3 num=200
   Files
     Leads         Au_lead.results/band.rkf
     Scattering    Au_scattering.results/band.rkf
   End
   EOF

   mv ConductanceResults.kf Au_ConductanceResults.kf 


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

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


   # ==============================================================================
   #                          Spin-unrestricted Cr chain
   # ==============================================================================

   # =======
   # Cr Lead
   # =======

   AMS_JOBNAME=Cr_lead $AMSBIN/ams <<eor

   Task SinglePoint 

   System
       ATOMS
           Cr 1.18995235  0.0  0.0 region=1
           Cr 4.00745359  0.0  0.0 region=2
           Cr 6.82495483  0.0  0.0 region=3
       END

       Lattice
           8.45250372  0.0  0.0
       End
   End

   Engine Band 
       TITLE Cr_lead

       KSpace
           Quality VeryGood
       End

       SoftConfinement
           Quality Basic
       End

       Basis
           Type DZ
           Core Large
       End

       UNRESTRICTED

       StoreHamiltonian2
   EndEngine

   eor

   # =============
   # Cr Scattering
   # =============

   AMS_JOBNAME=Cr_scattering $AMSBIN/ams <<eor

   Task SinglePoint 

   System
       ATOMS
           Cr  -10.08005261  0.0  0.0  region=1L
           Cr   -7.26255137  0.0  0.0  region=2L
           Cr   -4.44505013  0.0  0.0  region=3L
           Cr   -1.62754889  0.0  0.0  region=C
           Cr    1.18995235  0.0  0.0  region=C
           Cr    4.00745359  0.0  0.0  region=C
           Cr    6.82495483  0.0  0.0  region=1R
           Cr    9.64245607  0.0  0.0  region=2R
           Cr   12.45995731  0.0  0.0  region=3R
       END

       Lattice
           25.35751116  0.0  0.0
       End
   End

   Engine Band 
       TITLE Cr_scattering

       KSpace
           Quality Good
       End

       SoftConfinement
           Quality Basic
       End

       Basis
           Type DZ
           Core Large
       End

       UNRESTRICTED
       StoreHamiltonian2
       StoreHamAsMol
   EndEngine

   eor

   # ==============
   # Cr Conductance
   # ==============

   $AMSBIN/conductance <<EOF
   EnergyGrid min=-4 max=4 num=200
   Files
     Leads      Cr_lead.results/band.rkf
     Scattering Cr_scattering.results/band.rkf
   End

   EOF

   mv ConductanceResults.kf Cr_ConductanceResults.kf 

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

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

