Example: NEGF using the non-self consistent method¶

#! /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"