#! /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.1 0.0       0.0  0.0
        Au.2 2.884996  0.0  0.0
        Au.3 5.769992  0.0  0.0
    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.1L -20.194972  0.0  0.0
        Au.2L -17.309976  0.0  0.0
        Au.3L -14.42498   0.0  0.0
        Au.C  -11.539984  0.0  0.0
        Au.C  -8.654988   0.0  0.0
        Au.C  -5.769992   0.0  0.0
        Au.C  -2.884996   0.0  0.0
        Au.C   0.0        0.0  0.20
        Au.C   2.884996   0.0  0.0
        Au.C   5.769992   0.0  0.0
        Au.C   8.654988   0.0  0.0
        Au.C   11.539984  0.0  0.0
        O.C    0.0        0.0  3.12
        C.C    0.0        0.0  1.96
        Au.1R  14.42498   0.0  0.0
        Au.2R  17.309976  0.0  0.0
        Au.3R  20.194972  0.0  0.0
    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 1.18995235  0.0  0.0
        Cr.2 4.00745359  0.0  0.0
        Cr.3 6.82495483  0.0  0.0
    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.1L -10.08005261  0.0  0.0
        Cr.2L  -7.26255137  0.0  0.0
        Cr.3L  -4.44505013  0.0  0.0
        Cr.C   -1.62754889  0.0  0.0
        Cr.C    1.18995235  0.0  0.0
        Cr.C    4.00745359  0.0  0.0
        Cr.1R   6.82495483  0.0  0.0
        Cr.2R   9.64245607  0.0  0.0
        Cr.3R  12.45995731  0.0  0.0
    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"