# Example: Benzenedithiol junction¶

Download green_BDT.run

In this example of green, the DOS and transmission of a benzenedithiol molecule between gold electrodes is calculated. The calculation uses the self-energies obtained in the example for the gold electrodes. Note that this is a relatively expensive calculation.

First a fragment of the isolated molecule is constructed. Next the molecule is sandwiched between the electrodes in the configuration of Fig. 2. For this the fragment of the principal layer obtained in the example for the gold electrodes is needed.

Figure 2: Geometry of the extended molecule used in the calculation of a benzenedithiol junction. The molecule is shown in green, while the left and right contact regions are shown in red and blue, respectively. Note that the red region corresponds to the blue surface layer in Figure 1 of the example for the gold electrodes and vice versa.

The final results are shown in the following figure:

The Fermi energy of the electrodes is -0.2 Hartree (see the example for the gold electrodes). This is just above the HOMO of the molecular junction. Consistent with literature, the HOMO and lower orbitals are combined into a broad peak just below the Fermi energy, while the LUMO is much sharper and situated about 2 eV above the Fermi energy.

The current can be calculated by integrating the transmission around the Fermi energy. At low temperatures this means that the differential conductance is equal to the transmission times the quantum of conductance.

#!/bin/sh

# In this example of green, the DOS and transmission of a benzenedithiol molecule
# between gold electrodes is calculated.
# The calculation uses the self-energies obtained in the example for the gold electrodes,
# green_Au.run.
# Note that this is a relatively expensive calculation.

cp $AMSHOME/examples/adf/green_Al/Au.5p . cp$AMSHOME/examples/adf/green_Al/Au.5p.dirac .

$AMSBIN/dirac < Au.5p.dirac mv TAPE12 t12.rel AMS_JOBNAME=Au$AMSBIN/ams <<eor
System
Atoms
Au 0.0 0.0 0.0
End
end
corepotentials t12.rel
end
create Au   file=Au.5p
relativity
level scalar
formalism ZORA
end
xc
lda SCF VWN
end
EndEngine
eor

AMS_JOBNAME=layer $AMSBIN/ams <<eor System atoms Au -2.355588 -6.662612 0.000000 Au -2.355589 -4.164133 -1.442498 Au -2.355589 -4.164133 1.442498 Au -2.355589 -1.665653 -2.884996 Au -2.355589 -1.665653 0.000000 Au -2.355589 -1.665653 2.884996 Au -2.355589 0.832826 -1.442498 Au -2.355589 0.832826 1.442498 Au -2.355589 3.331306 0.000000 Au 0.000000 -4.996959 0.000000 Au 0.000000 -2.498480 -1.442498 Au 0.000000 -2.498480 1.442498 Au 0.000000 0.000000 -2.884996 Au 0.000000 0.000000 0.000000 Au 0.000000 0.000000 2.884996 Au 0.000000 2.498480 -1.442498 Au 0.000000 2.498480 1.442498 Au 0.000000 4.996959 0.000000 Au 2.355589 -3.331306 0.000000 Au 2.355589 -0.832826 -1.442498 Au 2.355589 -0.832826 1.442498 Au 2.355589 1.665653 -2.884996 Au 2.355589 1.665653 0.000000 Au 2.355589 1.665653 2.884996 Au 2.355589 4.164133 -1.442498 Au 2.355589 4.164133 1.442498 Au 2.355588 6.662612 0.000000 end end Task SinglePoint Engine ADF fragments Au Au.results/adf.rkf end relativity level scalar formalism ZORA end symmetry NOSYM title Principal layer xc lda SCF VWN end EndEngine eor AMS_JOBNAME=bulk$AMSBIN/ams <<eor
System
atoms
end
end

fragments
end
relativity
level scalar
formalism ZORA
end
symmetry NOSYM
title Bulk gold
xc
lda SCF VWN
end
EndEngine
eor

$AMSBIN/green << eor SURFACE bulk.results/adf.rkf FRAGMENTS center right END EPS -0.5 0 1000 ETA 1e-6 eor mv SURFACE left.kf$AMSBIN/green << eor
FRAGMENTS center left
END
EPS -0.5 0 1000
ETA 1e-6
eor
mv SURFACE right.kf

# A fragment of the isolated molecule is constructed:

AMS_JOBNAME=molecule $AMSBIN/ams <<eor System atoms C -1.400000 0.000000 0.000000 C -0.700000 0.000000 -1.200000 C -0.700000 0.000000 1.200000 C 0.700000 0.000000 -1.200000 C 0.700000 0.000000 1.200000 C 1.400000 0.000000 0.000000 H -1.200000 0.000000 -2.200000 H -1.200000 0.000000 2.200000 H 1.200000 0.000000 -2.200000 H 1.200000 0.000000 2.200000 S -3.200000 0.000000 0.000000 S 3.200000 0.000000 0.000000 end end Task SinglePoint Engine ADF basis type DZP core Large createOutput None end relativity level scalar formalism ZORA end symmetry NOSYM title Benzenedithiol xc lda SCF VWN end EndEngine eor # Next the molecule is sandwiched between the electrodes: AMS_JOBNAME=fock$AMSBIN/ams <<eor
System
atoms
end
end

fragments
end
relativity
level scalar
formalism ZORA
end
symmetry NOSYM
title Benzenedithiol
xc
lda SCF VWN
end
EndEngine
eor

# The DOS and transmission can now be calculated:

\$AMSBIN/green << eor
EPS -0.5 0 1000
ETA 1e-6
LEFT left.kf
FRAGMENT left
END
RIGHT right.kf
FRAGMENT right
END
NOSAVE DOS_B, TRANS_B
eor

echo ""
echo "Contents of DOS_A:"
cat DOS_A
echo "END"
echo ""
echo "Contents of TRANS_A:"
cat TRANS_A
echo "END"