Structure setup for TranSIESTA calculations
Nick Papior Andersen & Pablo Ordejón
Tel Aviv SIESTA/TranSIESTA workshop
10. September 2014
Technical University of Denmark 1/16
Outline
1 General considerations
2 Simple example – 1D chain
3 The Electrode
Self-energies
Constructing an electrode
4 Building ones first structure
Electrode
Molecule
Intermediate
Intermediate electrode layers
Finalising simulation
5 FDF flags for structural setup
Repetition (Bloch’s theorem)
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TranSIESTA setup vs. SIESTA setup
Periodicity
SIESTA
Fully periodic in 3 (all) cell directions
Periodicity handled by k-points
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TranSIESTA setup vs. SIESTA setup
Periodicity
SIESTA
Fully periodic in 3 (all) cell directions
Periodicity handled by k-points
TranSIESTA
Transport
Periodic in 2 cell directions
−∞ +∞
Periodicity handled by k-points
−∞ +∞ −∞ +∞
Semi-infinite in 1 cell direction
Semi-infinite directions handled by −∞ +∞
self-energies (Σ)
Technical University of Denmark 3/16
The perfect chain
Transport
−∞ +∞
Perfect systems can be handled equivalently, yet with different methods
However, SIESTA is the best method for fully periodic systems when not applying a
bias
SIESTA k → ∞ TranSIESTA k = 1
Σ Σ
Left Device / Right
Scattering region
Technical University of Denmark 4/16
The electrodes
Semi-infinite — bulk
Self-energies Σ, VERY IMPORTANT
We utilise the method by Sancho, Sancho, and Rubio, DOI: 10.1088/0305-4608/15/4/009
which is an iterative scheme for calculating the bulk/surface self energies.
It requires only principal cell interactions
H00 H01 0 ...
H10 H11 H12 0 . . .
. .
.
0 H21 H22 H23
..
.. .. . .
. 0 . . .
Sets a lower boundary on cell size in transport direction
No limitation on two other direction cell sizes
High k-point sampling in transport direction and same k-point sampling in transverse
directions
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Electrodes
Your first setup
1 An electrode is a pure SIESTA calculation with a high number of k-points in the
transport direction.
Why is that?
3 Solve it with SolutionMethod diagon using the transiesta executable (we only use
transiesta to get the TSHS-file)
4 Ensure only principal cell interactions! (see WARNING in output)
5 Same k-point sampling in the transverse directions are required
Technical University of Denmark 6/16
Electrodes
Your first setup
1 An electrode is a pure SIESTA calculation with a high number of k-points in the
transport direction.
2 The structure needs to be periodic in the transport direction
3 Solve it with SolutionMethod diagon using the transiesta executable (we only use
transiesta to get the TSHS-file)
4 Ensure only principal cell interactions! (see WARNING in output)
5 Same k-point sampling in the transverse directions are required
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Benzene dithiol (BDT)
Electrode
BDT attached to Gold electrodes
We utilise 100 surface (AB-stacking)
Decide k-point sampling in transverse direction (converge)
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Benzene dithiol (BDT)
BDT
Define the molecule
Relax structure using SIESTA (lecture tomorrow)
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Benzene dithiol (BDT)
Intermediate connect
Attach gold connection to the molecule
Consider stacking of pyramids
A-BDT-A
A-BDT-B
B-BDT-B
Relax structure again, constrain the pyramids
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Benzene dithiol (BDT)
Intermediate electrode layers
Attach a couple of electrode layers
Follow the stacking!
Relax structure again, constrain the electrode layers
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Benzene dithiol (BDT)
Attach electrode and more intermediate layers
Attach the electrodes on both sides (converge number of intermediate layers)
Follow the stacking!
Relax structure again, constrain the electrode layers
Determining the extra number of layers:
Consider the molecule as a “defect”
The defect has a screening length in the central region
(the extra electrode layers)
Ensure that the electrodes “behave as bulk” electrodes
(away from defect)
Technical University of Denmark 11/16
Benzene dithiol (BDT)
Attach electrode and more intermediate layers
Attach the electrodes on both sides (converge number of intermediate layers)
Follow the stacking!
Relax structure again, constrain the electrode layers
Determining the extra number of layers:
Consider the molecule as a “defect”
The defect has a screening length in the central region
(the extra electrode layers)
Ensure that the electrodes “behave as bulk” electrodes
(away from defect)
What does a metallic electrode require:
1 Bad screening → many electrode layers
2 Good screening → few electrode layers
What does a semi-conducting electrode require:
1 Bad screening → many electrode layers
T 2 Good screening → few electrode layers
Technical University of Denmark 11/16
Benzene dithiol (BDT)
Attach electrode and more intermediate layers
Attach the electrodes on both sides (converge number of intermediate layers)
Follow the stacking!
Relax structure again, constrain the electrode layers
Determining the extra number of layers:
Consider the molecule as a “defect”
The defect has a screening length in the central region
(the extra electrode layers)
Ensure that the electrodes “behave as bulk” electrodes
(away from defect)
What does a metallic electrode require:
1 Bad screening → many electrode layers
2 Good screening → few electrode layers
What does a semi-conducting electrode require:
1 Bad screening → many electrode layers
T 2 Good screening → few electrode layers
Technical University of Denmark 11/16
Structure setup
System, always consecutive
%block AtomicCoordinatesAndAtomicSpecies
0. 0. 0.00 1 # 1
0. 0. 1.42 1 # 2 Left electrode
0. 0. 2.84 1 # 3
0. 0. 4.26 1 # 4
0. 0. 5.68 1 # 5
0. 0. 7.10 1 # 6
0. 0. 8.52 1 # 7
Electrodes (yes you can use the same 0. 0. 9.94 1 # 8 Device
electrodes on both sides) 0. 0. 11.36 1 # 9
0. 0. 12.78 1 # 10
%block AtomicCoordinatesAndAtomicSpecies 0. 0. 14.20 1 # 11
0. 0. 0.00 1 # 1 0. 0. 15.62 1 # 12
0. 0. 1.42 1 # 2 0. 0. 17.04 1 # 13
0. 0. 2.84 1 # 3 0. 0. 18.46 1 # 14 Right electrode
0. 0. 19.88 1 # 15
0. 0. 4.26 1 # 4 0. 0. 21.30 1 # 16
%endblock AtomicCoordinatesAndAtomicSpecies %endblock AtomicCoordinatesAndAtomicSpecies
# Define the left electrode
TS.HSFileLeft elec/siesta.TSHS
# Define the right electrode
TS.HSFileRight elec/siesta.TSHS
# any relative paths are usable
Technical University of Denmark 12/16
Structure setup
System, always consecutive
%block AtomicCoordinatesAndAtomicSpecies
0. 0. 0.00 1 # 1
0. 0. 1.42 1 # 2 Left electrode
0. 0. 2.84 1 # 3
0. 0. 4.26 1 # 4
0. 0. 5.68 1 # 5
0. 0. 7.10 1 # 6
0. 0. 8.52 1 # 7
Electrodes (yes you can use the same 0. 0. 9.94 1 # 8 Device
electrodes on both sides) 0. 0. 11.36 1 # 9
0. 0. 12.78 1 # 10
%block AtomicCoordinatesAndAtomicSpecies 0. 0. 14.20 1 # 11
0. 0. 0.00 1 # 1 0. 0. 15.62 1 # 12
0. 0. 1.42 1 # 2 0. 0. 17.04 1 # 13
0. 0. 2.84 1 # 3 0. 0. 18.46 1 # 14 Right electrode
0. 0. 19.88 1 # 15
0. 0. 4.26 1 # 4 0. 0. 21.30 1 # 16
%endblock AtomicCoordinatesAndAtomicSpecies %endblock AtomicCoordinatesAndAtomicSpecies
# Define the left electrode
TS.HSFileLeft elec/siesta.TSHS
# Define the right electrode
TS.HSFileRight elec/siesta.TSHS
# any relative paths are usable
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Electrodes using Bloch’s theorem
In case the electrode has simple periodicity in the transverse direction it is
encouraged to utilise Bloch’s theorem to reduce electrode size
Requires number of repeated times larger Monkhorst-Pack grid in each direction
Faster calculation time of electrodes
Heavily reduces computation time of self-energies
# first unit-cell vector
TS.ReplicateLeftA1 3
# second unit-cell vector
TS.ReplicateLeftA2 3
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Reducing self-energy region
For short orbital range, and atomic plane stacking creates long electrode we can reduce
self-energy region (a stacking of ABAB with short orbital cutoff is a good candidate!)
TS.NumUsedAtomsLeft 3
TS.NumUsedAtomsRight 3
%block AtomicCoordinatesAndAtomicSpecies
0. 0. 0.00 1 # 1
0. 0. 1.42 1 # 2 Left electrode
Electrodes (yes you can use the same 0. 0. 2.84 1 # 3
electrode on both sides) 0. 0. 4.26 1 # 4
0. 0. 5.68 1 # 5
%block AtomicCoordinatesAndAtomicSpecies 0. 0. 7.10 1 # 6
0. 0. 0.00 1 # 1 0. 0. 8.52 1 # 7
0. 0. 1.42 1 # 2 0. 0. 9.94 1 # 8 Device
0. 0. 11.36 1 # 9
0. 0. 2.84 1 # 3 0. 0. 12.78 1 # 10
0. 0. 4.26 1 # 4 0. 0. 14.20 1 # 11
%endblock AtomicCoordinatesAndAtomicSpecies 0. 0. 15.62 1 # 12
0. 0. 17.04 1 # 13
0. 0. 18.46 1 # 14
0. 0. 19.88 1 # 15 Right electrode
0. 0. 21.30 1 # 16
%endblock AtomicCoordinatesAndAtomicSpecies
Technical University of Denmark 14/16
Reducing self-energy region
For short orbital range, and atomic plane stacking creates long electrode we can reduce
self-energy region (a stacking of ABAB with short orbital cutoff is a good candidate!)
TS.NumUsedAtomsLeft 3
TS.NumUsedAtomsRight 3
%block AtomicCoordinatesAndAtomicSpecies
0. 0. 0.00 1 # 1
0. 0. 1.42 1 # 2 Left electrode
Electrodes (yes you can use the same 0. 0. 2.84 1 # 3
electrode on both sides) 0. 0. 4.26 1 # 4
0. 0. 5.68 1 # 5
%block AtomicCoordinatesAndAtomicSpecies 0. 0. 7.10 1 # 6
0. 0. 0.00 1 # 1 0. 0. 8.52 1 # 7
0. 0. 1.42 1 # 2 0. 0. 9.94 1 # 8 Device
0. 0. 11.36 1 # 9
0. 0. 2.84 1 # 3 0. 0. 12.78 1 # 10
0. 0. 4.26 1 # 4 0. 0. 14.20 1 # 11
%endblock AtomicCoordinatesAndAtomicSpecies 0. 0. 15.62 1 # 12
0. 0. 17.04 1 # 13
The order is determined by the attached 0. 0. 18.46 1 # 14
Right electrode
0. 0. 19.88 1 # 15
orientation 0. 0. 21.30 1 # 16
%endblock AtomicCoordinatesAndAtomicSpecies
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Electrode – All together
A short orbital cutoff, long stacking order, Bloch’s theorem applicable
# Contains the silver atoms: # Contains the silver atoms:
TS.HSFileLeft ../ELEC/siesta.TSHS TS.HSFileRight ../ELEC/siesta.TSHS
TS.ReplicateLeftA1 3 TS.ReplicateRightA1 3
TS.ReplicateLeftA2 3 TS.ReplicateRightA2 3
# Do not use the green atoms: # Do not use the green atoms:
TS.NumUsedAtomsLeft 3 TS.NumUsedAtomsRight 3
Technical University of Denmark 15/16
Electrode – All together
A short orbital cutoff, long stacking order, Bloch’s theorem applicable
# Contains the silver atoms: # Contains the silver atoms:
TS.HSFileLeft ../ELEC/siesta.TSHS TS.HSFileRight ../ELEC/siesta.TSHS
TS.ReplicateLeftA1 3 TS.ReplicateRightA1 3
TS.ReplicateLeftA2 3 TS.ReplicateRightA2 3
# Do not use the green atoms: # Do not use the green atoms:
TS.NumUsedAtomsLeft 3 TS.NumUsedAtomsRight 3
Technical University of Denmark 15/16
FDF flags
SolutionMethod diagon/transiesta
%block AtomicCoordinatesAndAtomicSpecies
TS.HSFileLeft
TS.ReplicateLeftA1/TS.ReplicateLeftA2
TS.NumUsedAtomsLeft
TS.HSFileRight
TS.ReplicateRightA1/TS.ReplicateRightA2
TS.NumUsedAtomsRight
Doing TranSIESTA calculations:
1 calculate electrodes (transiesta < elec.fdf | tee elec.out)
2 solve using (transiesta < chain.fdf | tee chain.out)
3 calculate transmission (tbtrans < chain.fdf | tee chain.tbt-out)
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