Example: Main NEGF flavors
Download NEGF_Cr_wire.run
#! /bin/sh
# This example shows how to use the NEGF functionality.
# Note: Setting up a NEGF calculation is quite hard without the GUI.
# It starts of with Method 1: the non-self consistent approach. Here, BAND
# merely serves to provide matrix elements, being unaware of the electrodes.
# Then follows Method 2: here the NEGF density is really used to calculate the
# matrix elements.
# Method 3 is a variation on Method 2, and includes an extra alignment run.
# ==============================================================================
# Method #1: non-self consistent NEGF (uses the conductance program, like DFTB)
# ==============================================================================
# ========================= Method #1. Run #1 ==============================
AMS_JOBNAME=lead_1 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1 0.0 0.0 0.0
Cr.2 2.5 0.0 0.0
END
Lattice
5.0 0.0 0.0
End
End
Engine Band
Title method_1_run_1
KSpace
Quality Good
End
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
StoreHamiltonian2
EndEngine
eor
# ======================== Method #1. Run #2 ===============================
AMS_JOBNAME=scattering_1 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1L -10.0 0.0 0.0
Cr.2L -7.5 0.0 0.0
Cr.C -5.0 0.0 0.0
Cr.C -2.5 0.0 0.0
Cr.C 0.0 0.0 0.0
Cr.C 2.5 0.0 0.0
Cr.C 5.0 0.0 0.0
Cr.1R 7.5 0.0 0.0
Cr.2R 10.0 0.0 0.0
END
Lattice
22.5 0.0 0.0
End
End
Engine Band
Title method_1_run_2
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
StoreHamiltonian2
StoreHamAsMol
EndEngine
eor
# ========================== Method #1. Run #3 =============================
$ADFBIN/conductance <<EOF
EnergyGrid min=-5 max=5 num=200
Files
Leads lead_1.results/band.rkf
Scattering scattering_1.results/band.rkf
End
EOF
# Compy the content of the "reseults" section from ConductanceResults.kf to band.rkf and rename the section to NEGF
$ADFBIN/cpkf "ConductanceResults.kf" "scattering_1.results/band.rkf" "results --rename NEGF"
echo "Extract transmisstion from rkf file (Method 1)"
$ADFBIN/adfreport scattering_1.results/band.rkf -r "NEGF%transmission#12.5f##1"
# ==============================================================================
# Method #2: self consistent NEGF without alignment
# ==============================================================================
# ========================= Method #2. Run #1 ==============================
AMS_JOBNAME=lead_2 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1 0.0 0.0 0.0
Cr.2 2.5 0.0 0.0
END
Lattice
5.0 0.0 0.0
End
End
Engine Band
Title method_2_run_1
KSpace
Quality Good
End
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
StoreHamiltonian2
EndEngine
eor
# ============================= Method #2. Run #2 ==========================
$ADFBIN/sgf <<eor
TITLE Test for NEGF inputs
SAVE SIGMA
SURFACEGF
RKFFileName lead_2.results/band.rkf
SCMCode
KT 0.001
ContourQuality normal
END
eor
mv SigmaSCM Sigma.kf
# ============================= Method #2. Run #3 ==========================
AMS_JOBNAME=scattering_2 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1L -10.0 0.0 0.0
Cr.2L -7.5 0.0 0.0
Cr.C -5.0 0.0 0.0
Cr.C -2.5 0.0 0.0
Cr.C 0.0 0.0 0.0
Cr.C 2.5 0.0 0.0
Cr.C 5.0 0.0 0.0
Cr.1R 7.5 0.0 0.0
Cr.2R 10.0 0.0 0.0
END
End
Engine Band
Title method_2_run_3
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
NEGF
LeadFile lead_2.results/band.rkf
SGFFile Sigma.kf
ApplyShift2 False
ContourQuality normal
EMin -5
EMax 5
NE 200
End
EndEngine
eor
echo "Extract transmisstion from rkf file (Method 2)"
$ADFBIN/adfreport scattering_2.results/band.rkf -r "NEGF%transmission#12.5f##1"
# ==============================================================================
# Method #3: self consistent NEGF wit alignment run
# ==============================================================================
# ======================= Method #3. Run #1 ================================
AMS_JOBNAME=lead_3 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1 0.0 0.0 0.0
Cr.2 2.5 0.0 0.0
END
Lattice
5.0 0.0 0.0
End
End
Engine Band
Title method_3_run_1
KSpace
Quality Good
End
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
StoreHamiltonian2
EndEngine
eor
# ============================ Method #3. Run #2 ===========================
$ADFBIN/sgf <<eor
TITLE Test for NEGF inputs
SAVE SIGMA
SURFACEGF
RKFFileName lead_3.results/band.rkf
SCMCode
KT 0.001
ContourQuality normal
END
eor
mv SigmaSCM Sigma.kf
# ============================ Method #3. Run #3 ===========================
AMS_JOBNAME=align $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1L 0.0 0.0 0.0
Cr.2L 2.5 0.0 0.0
Cr.C 5.0 0.0 0.0
Cr.C 7.5 0.0 0.0
Cr.C 10.0 0.0 0.0
Cr.C 12.5 0.0 0.0
Cr.1R 15.0 0.0 0.0
Cr.2R 17.5 0.0 0.0
END
End
Engine Band
Title method_3_run_3
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
NEGF
DoAlignment True
LeadFile lead_3.results/band.rkf
SGFFile Sigma.kf
ContourQuality normal
EMin -5.0
EMax 5.0
NE 200
AlignChargeTol 0.0001
End
EndEngine
eor
# ============================= Method #3. Run #4 ===========================
AMS_JOBNAME=scattering_3 $ADFBIN/ams <<eor
Task SinglePoint
System
ATOMS
Cr.1L -10.0 0.0 0.0
Cr.2L -7.5 0.0 0.0
Cr.C -5.0 0.0 0.0
Cr.C -2.5 0.0 0.0
Cr.C 0.0 0.0 0.0
Cr.C 2.5 0.0 0.0
Cr.C 5.0 0.0 0.0
Cr.1R 7.5 0.0 0.0
Cr.2R 10.0 0.0 0.0
END
End
engine Band
Title method_3_run_4
NumericalQuality Basic
Basis
Type DZ
Core Large
End
Unrestricted
NEGF
LeadFile lead_3.results/band.rkf
SGFFile Sigma.kf
AlignmentFile align.results/band.rkf
ContourQuality normal
EMin -5.0
EMax 5.0
NE 200
End
EndEngine
eor
echo "Extract transmisstion from rkf file (Method 2)"
$ADFBIN/adfreport scattering_3.results/band.rkf -r "NEGF%transmission#12.5f##1"
