#!/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"