Table of Contents

Table of Contents 1
Transport calculations with QuantumATK 2
Introduction 3
Tutorial objectives 3
Geometry for transport calculations 3
Important notes 4
The screening region 5
Getting started 7
Convergence of electrode parameters 7
Split the device configuration 8
Mesh cut-off 8
Transverse k-points 9
Check the electrode geometry and size 10
Zero-bias analysis 12
Transmission spectrum analysis 13
Running the calculation 15
Transmission Analyzer 15
Transmission eigenstates 17
Convergence of k-points for transmission spectrum 20
Further analysis 21
Device density of states 22
Electrostatic difference potential 23
Finite-bias calculations 24
Set up the calculation 24
Analyzing the results 28
Voltage drop 29
I–V curve 31
Calculations 31
Visualization 33
Summary 35

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Docs » Tutorials » Getting started with QuantumATK » Transport calculations with QuantumATK

Transport calculations with QuantumATK

Version: 2015

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 zn-zno-zn.py
 zero-bias.py
 analysis.py
 finite-bias.py
 iv-curve.py
Basic QuantumATK Tutorial
ATK Reference Manual

This tutorial introduces you to one of the most important functionalities in QuantumATK, namely electron
transport calculations.

The system you will investigate is a Zn|ZnO|Zn junction, which is selected for demonstration purposes, in
order to make calculations relatively fast. However, this system does encapsulate many of the relevant
and interesting physical effects present in more realistic devices, and these will be discussed in the
tutorial.

Fig. 39 The Zn-ZnO-Zn system to be studied in this tutorial. Note that the configuration is repeated 5 times along the B axis to
improve the visual clarity.

 Note

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 In order to run the calculations in this tutorial, you must have a license for the ATK-SE tight-binding
engine. If you do not have one, you may obtain a time-limited demo license by contacting us via our
website: Contact QuantumWise.

 Attention

This tutorial was prepared using QuantumATK version 2016.3. Downloadable scripts and output files
may therefore not work with QuantumATK 2015 and earlier.

Introduction
In this tutorial, the electronic structure of the Zn-ZnO-Zn junction will be calculated using a tight-binding
(TB) model in combination with the non-equilibrium Green’s function (NEGF) technique for the actual
calculation of the electron transport through this junction. A detailed description of technical aspects of
the computational parameters and models can be found in the ATK Reference Manual.

To set up the calculations, you will use the graphical interface QuantumATK (QuantumATK). If you have
never worked with QuantumATK before, it is highly recommended to first go through the Basic
QuantumATK Tutorial to become familiar with the basics of how to operate the software.

You will here use a predefined device configuration, but we have many other tutorials that show you how
to set up other device geometries - see the Structure Building section in Getting started with QuantumATK.

Tutorial objectives
We will first introduce the central concepts involved in a device calculation, and then present a range of
tools that can be used to analyze the electronic transport properties of the device.

After reading this tutorial and performing the calculations, you will be able to:

Understand the general concept of a device configuration.

Test convergence of physical quantities with respect to computational parameters.
Check if a given bulk configuration is suitable as an electrode.
Calculate the transmission spectrum at zero and finite bias voltage.
Analyze the transmission spectrum using the Transmission Analyzer.
Calculate and plot transmission eigenstates.
Calculate and plot the projected device density of states.
Calculate the potential profile (voltage drop) across the device.
Calculate the I–V curve and analyze it.

Geometry for transport calculations

The type of atomic configuration needed for an electron transport calculation is fundamentally different
from the configurations used in atomic-scale simulations of periodic and finite structures. This is
because an electron transport calculation requires open boundary conditions in the transport direction.
Open boundary conditions make it possible for incident electrons coming from the source electrode to be
partially transmitted through the central part of the device and end up in the drain electrode, and partially
reflected back to the source.

One may see the device configuration as a combination of periodic and finite configurations, as shown in

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the figure below. The left and right bulk (periodic) electrodes (source and drain, in a transistor
perspective) are attached to the central region of the device, which is finite (non-periodic) along the
transport direction. The central region is often called the scattering region, because the charge carriers
traveling between the two electrodes are scattered by changes to the physical and chemical environment
in the central region, for example by interfaces and defects. The central region therefore determines the
functionality of the device, while the left and right electrodes are modeled as perfect leads that connect
the device to the external source and drain.

Fig. 40 A two-probe device configuration consists of two electrodes and a central region. Both ends of the central region, called the
electrode extensions, must be exact replicas of the corresponding electrode structures.

For reasons of numerical stability during QuantumATK device calculations, there is a region in both ends
of the central region where the element types and ionic positions are fixed to match the electrodes –
these are the electrode extensions. Both must always be an exact replica of the corresponding electrode,
and are therefore not allowed to change during geometry optimization of the device.

 Hint

In both figures above, the device configuration is periodically repeated 5 times along the B axis (which
points “up” in both figures) to improve visual clarity. However, just like in standard atomistic
simulations one should always use device configuration with the smallest lateral unit cell area, taking
advantage of any structural periodicity of the device in the A and B directions (orthogonal to the
transport direction, C).

Important notes

The C-direction in the device configuration is the transport direction, meaning that the electrodes are
always connected to the central region in this direction.
The electrodes are by default assumed to be periodic in the A and B directions, i.e., perpendicular to
the transport direction. When simulating transport through 1D or 2D confined systems, such as wires,
tubes, ribbons, and sheets, a sufficiently large vacuum padding should be added along the confined
direction(s). This allows the electron density and electrostatic potential to decay correctly in the
vacuum region, and this also avoids spurious interactions with repeated images of the system.
The central region can take many different forms. For example, it can be a metal–semiconductor–
metal “sandwich”, as in this tutorial, a molecule between the two electrodes, or a piece of a nanotube
or a graphene flake with a defect.
In the Zn|ZnO|Zn device treated here, the two electrodes are identical, but this is not a general
requirement. For example, QuantumATK can easily simulate the electron transport through an
interface between two different materials.
In addition to source and drain electrodes, QuantumATK supports inclusion of electrostatic gates for

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 transistor simulations. This will not be covered here, but is addressed in several other tutorials.

The screening region

The central region should normally involve some structural inhomogeneity (interfaces, surfaces,
molecules, defects, etc.) that leads to rearrangements in the electron density and hence in the self-
consistent potential felt by the electrons. This electronic rearrangement may be further enhanced by
structural relaxation effects inside the central region (excluding the electrode extensions, which are not
allowed to relax). This deviation of the central region potential from the bulk electrode potential causes
the electrons to be scattered, which will cause a voltage drop across the central region at finite bias.

 Note

Simulating the transport properties of a perfectly periodic structure is only possible at zero bias (since
there is no place for the voltage to naturally drop in a perfectly periodic structure, as there is no
scattering), and can moreover be done in a simpler way, using just a periodic bulk configuration

The NEGF formalism assumes that the potential in the central region converges smoothly towards the
electrode potentials, such that there is no scattering at the two electrode–central region interfaces. In the
sketch of the Zn|ZnO|Zn device shown below, the Zn metal regions in both ends of the central region are
on a gray background, just like in the electrodes, in order to indicate the so-called screening regions, in
which the potential and charge rearrangements at the Zn–ZnO interfaces are screened and smoothly
approach the electrode potentials. If the screening regions are shorter than the actual (physical) screening
length of the system, spurious scattering may take place at the electrode–central region interfaces. This
may give rise to poor convergence of the self-consistent calculation and inaccurate results in finite-bias
calculations.

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Fig. 41 Top: Electrostatic potential along the transport direction. Bottom: Device geometry. The screening regions in the left and
right parts of the central region, indicated by gray background, must be longer than the screening length of the system to ensure a
smooth transition between the potential of the central region and electrodes.

The figure above shows the potential profile due to an applied bias voltage of U = -0.5 Volt in the
Zn|ZnO|Zn device considered here, meaning that the voltage on the left electrode is 0.5 V lower than that
on the right electrode. Most of the “voltage drop” occurs in the ZnO region while the potential in the
metallic screening regions is virtually flat, so no scattering takes place in these screening regions. In the
section Finite-bias calculations you will reproduce this potential profile.

 Attention

In systems with semiconductor electrodes, the screening length can be quite long, and a very long
central region may be required before the potential approaches the bulk value. However, in most real
situations, the semiconductor electrodes are doped, which brings the screening length down to
manageable simulation sizes, provided the doping level is high enough.

 Note

The entire treatment of electron transport is in this context coherent and elastic, i.e. there is no
scattering by phonons.
The NEGF formalism assumes that the electrodes are in thermal equilibrium, which formally
requires that the electrical current through the device is low. This always holds true at low voltage,
and may also be a valid assumption at higher voltage, provided that the transmission probability
through the central region is sufficiently low.

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Getting started
Start up QuantumATK and create a new project. You would normally use the Builder to create the
device configuration, but here we will use the Zn|ZnO|Zn device already defined in the QuantumATK
Python script  zn-zno-zn.py.

Download the script and save it in the project folder. It will then show up on in the Project Files list.

Drag the script onto the Builder to access a large palette of tools for creating new configurations and
modifying existing ones.

Convergence of electrode parameters

An QuantumATK device calculation is performed in multiple steps. First, the electrode(s) and the central
region are treated as (periodic) bulk systems, and the self-consistent electron density is calculated for
each of them. The device calculation is then started, using the central region bulk electron density as an
initial guess, and matching the electronic structure at the two electrode/central region boundaries to that
of the electrodes. Finally, the self-consistent electronic structure of the central region is determined, and
thereby of the full device.

It is important to the procedure outlined above that the electrode bulk calculations are well converged,
both in electrode lengths and numerical accuracy. The purpose of this section is to demonstrate the
convergence of two very important numerical accuracy parameters; the mesh cut-off and the number of k-
points in the transverse directions (A and B).

The convergence test will here be performed only on the left electrode, since the two electrodes are
(physically) identical. In case the electrodes are not identical, the required mesh cut-off and k-point

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sampling should be determined separately for both of them. However, since these numerical parameters
must be the same in the two electrodes in the device calculation, in the end they need to be chosen large
enough that both electrodes are accurately described.

Split the device configuration

Use the Splitter tool in the top toolbar to split the device into electrodes and central region. This will
add 3 new configurations to the Stash, corresponding to the left and right electrodes and the central
region.

You can now highlight the left electrode configuration and use the botton to send it to the Script
Generator and set up a range of bulk calculations for the electrode using different density mesh cut-offs
and k-point samplings to study the numerical convergence.

For convenience, scripts have already been prepared for the calculations needed in the two convergence
studies. In the following, you should simply download and run them.

Mesh cut-off

The first numerical parameter to converge is the density grid cut-off. This controls the density of the real-
space grids in QuantumATK, which represent e.g. the electrostatic potential and real-space electron
density. The density cut-off is specified as an energy
E; the corresponding distance between the grid points is given by

πℏ
Δx = ,
√2mE
where
m is the electron mass.

The script  mesh_loop.py performs calculations of the ground state of the electrode for different mesh
cut-offs ranging from 2.5 Ha to 80 Ha. All other numerical accuracy parameters are kept constant. The
convergence observable is the Fermi level (chemical potential) of the electrode.

The script simply loops over the mesh cut-offs, performs the calculation for each value, and finally plots
the results. Download the script, and then run it using the Job Manager. If you are not familiar with the
QuantumATK Job Manager, please refer to the tutorial Job Manager for local execution of QuantumATK
scripts. You can of course also run the script from command line:

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 $ atkpython mesh_loop.py > mesh_loop.log

The plot will automatically appear once the calculations are done (in less than a minute). The plot is
shown below. It is clear that the default 10 Ha mesh-cut-off for tight-binding calculations is a perfectly
sufficient default, since the Fermi level changes by less than 10 meV when using larger values (which are
computationally more expensive), and we will keep it for further calculations.

 Attention

This weak dependence of computed quantities on the mesh cut-off is typical of tight-binding models.
The same would generally not be true for DFT calculations, where the default mesh cut-off with the
cheapest pseudopotentials is 75 Ha.

Transverse k-points

In the same fashion as above, you will now study the electrode Fermi level as a function of the number of
k-points in the transverse directions (A and B), which are orthogonal to the transport direction (C).

The number of k-points in the transport direction should be quite large in a device calculation, so keep it at
nC = 51. All other numerical accuracy parameters should be kept at their default values, including the grid
mesh cut-off (10 Ha).

Use the script  kpts_loop.py for this convergence study. It is identical to the one used above for the
mesh cut-off, but loops over odd transverse k-points in the range 1 to 11.

Download and run the script, which will produce the plot shown below. It is quite clear that the calculation
with only 1 k-point along the A and B directions fails completely in describing the periodic Zn electrode
bulk, while the calculations with 5 or more transverse k-points are much better.

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Check the electrode geometry and size

After having performed the electrode calculator convergence tests, the final preparatory step consists of
checking the electrode geometry, using the Electrode Validator plugin. This tool checks if the electrode
configuration has the appropriate geometry (viz. if the C axis is parallel to the Z coordinate axis, and if the
AB plane is perpendicular to C) and if the electrode is long enough along C.

You first need to do a ground state calculation for the electrode. Follow these steps to set up the
calculation:

Open the Builder and select the left electrode. Then use the botton to send the electrode to the
Script Generator. Change the default output file name to electrode.hdf5 .

Add a New Calculator block and double-click it to open it. Select the Slater-Koster tight-binding

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 calculator engine, make sure “No SCF iteration” is not checked, and set up a 7x7x7 k-point grid.

Finally, in the Slater-Koster basis set calculator settings, choose the self-consistent DFTB CP2K basis
set.

Save the script as electrode.py and run the calculation. The script can also be obtained here:
 electrode.py. The results should soon appear on the LabFloor. Select the bulk configuration saved in
the output file ( electrode.hdf5 ), open the Electrode Validator plugin in the right-hand plugins toolbar, and
click Check.

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You should see a message saying The configuration is a valid electrode, indicating that the electrode
geometry and length are fine. In case the electrode for some reason fails the check, a warning and an
explanation will be presented.

 Note

Whether an electrode is long enough in the C direction depends to some extend on the basis set used.
The Electrode Validator uses the criterion that any discarded matrix elements of the Hamiltonian
should not exceed 10-10 eV.

The reason for this is that only the nearest-neighbor interactions of the electrode along C are kept in
the device calculation. Specifically, this is the interaction between the electrode and the electrode
extension. This is necessary in order to describe the electrodes as semi-infinite rather than fully
periodic along C).

If the electrode is deemed too short, you can still proceed with the device calculation, but, depending
on how large the discarded matrix elements are, you risk that the calculation will not converge or that
the results are inaccurate.

 Tip

The screenshots for this tutorial have been made after unticking the option Show unavailable plugins
in the File ‣ Preferences menu in the QuantumATK main window. This causes QuantumATK to
dynamically change the list of available plugins in the right-hand plugins bar, such that plugins that are
not compatible with the selected LabFloor item are not shown.

Zero-bias analysis
Having confirmed that the geometry of the electrodes is indeed suitable for QuantumATK device
calculations, you are now ready to continue with the actual transport calculations. In the Builder, Select
the Zn|ZnO|Zn device configuration, named zn-zno-zn.py , and send it to the Script Generator.

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Transmission spectrum analysis
In the Script Generator, follow these steps to set up a script that calculates the electronic transmission
spectrum of the Zn|ZnO|Zn device:

Change the default output file name to zero-bias.hdf5 .

Add a New Calculator block to the script.
Add also the Analysis ‣ TransmissionSpectrum block.

Then edit the calculator settings by double-clicking in the script:

Choose the ATK-SE: Slater-Koster (Device) tight-binding calculator engine.

Set the transverse k-point samplings (along A and B) to 5.
Uncheck the box No SCF iteration to run a self-consistent calculation.
Verify that the Slater-Koster basis set is set to DFTB CP2K .

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Next, edit the settings in the TransmissionSpectrum block:

Increase the energy window such that it ranges from -4 eV to +4 eV.

Increase the number of sampled energy points to 201.
Set the transverse k-point sampling to 7x7.
Change the self-energy calculator to Krylov.

 Note

The density of energy points will determine the accuracy of the computed current at finite bias.
For the energy window, it is recommended to choose a wide interval at zero bias to get a picture of

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 where the transmission peaks are located, but for finite bias, a proper convergence study should be
performed, since a too wide energy spacing (too low density of energy points) may mean that
narrow peaks in the transmission spectrum are not captured.
The k-point sampling used in the transmission analysis (and in most post-SCF analysis
calculations) does not need to be the same as used in the calculator. Typically, you need more k-
points in the transmission analysis than in the SCF calculation.
The Krylov self-energy calculator is chosen here because it is the fastest method available, but in
some cases it can give negative transmission values due to some approximations made.

The script is now ready, so save it as zero-bias.py . If needed, you can also download the final script here:
 zero-bias.py.

Running the calculation

Execute the script using either the Job Manager or from command line. The calculation should finish
in a few minutes.

You should have a look through the job log file to follow the progress of the device calculation. You will
see that the following sequence of calculations are carried out:

1. Left electrode SCF (bulk).

2. Right electrode SCF (bulk).
3. Device SCF (NEGF).
4. Transmission spectrum analysis.

Congratulations! You have now performed a complete transport calculation with QuantumATK. The basic
work flow is similar for all transport calculations. Please proceed to the next section to visualize and
analyze the results.

Transmission Analyzer

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The calculation output should now have appeared on the LabFloor. Locate and select the file
zero-bias.hdf5 . It contains two objects:

DeviceConfiguration contains the two-probe device configuration and the self-consistent state of
the attached calculator.

TransmissionSpectrum contains all information about the computed transmission spectrum,

including settings and results.

Select the TransmissionSpectrum object, and click the Transmission Analyzer in the right-hand panel bar.

The Transmission Analyzer plugin opens. On the left, named Spectrum, is shown the k-point averaged
transmission spectrum as function of energy. The average Fermi energy of the two electrodes is set to
zero and indicated with a dashed line. It is evident that there is a broad energy range from -2.5 eV to +2.5
eV with very low transmission values. This corresponds to the band gap in the semiconducting ZnO.

The transmission and energy values in the point marked by the red dot are shown below the plot. You can
use the mouse to move the dot along the

( )
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T (E) curve and read off the values. The Curves drop-down menu lets you select the spin components to
be plotted. Note that the transmission for spin types X, Y, and Z are only non-zero for calculations with
noncollinear spin.

At any particular energy (defined by the red dot), the total transmission is computed as an average over
the transmission coefficients in the sampled k-points. The right-hand plot, named Coefficients, shows an
interpolated contour plot of the transmission coefficients vs. reciprocal vectors
kA and
kB.

In the figure above, it is clear that the main contributions to electronic transmission through the Zn|ZnO|Zn
device at the average Fermi level come from k-points around the
Γ-point, where
kA = kB = 0 . The situation is very different at other energies, such as e.g.
E = -3.16 eV, as shown in the figure below.

 Tip

By increasing the number of k-points sampled in the transmission spectrum calculation, the resolution
of the contour plot can be improved – and thereby also the accuracy of the total transmission
spectrum. In many devices, a large number of k-points may be required to obtain a converged
spectrum.

Transmission eigenstates

By clicking on the contour plot you can also move the red dot to a desired k-point. The chosen k-point is
shown in the Selection box. At a particular energy and spin (chosen in the Spectrum plot) and a particular
k-point (chosen on the Coefficients contour plot) you can obtain the transmission eigenvalues and
eigenstates:

Select a k-point with high transmission value; (

kA ,

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 kB) = (0.15, 0.05) at energy -3.16 eV.
Click Eigenvalues in the lower left part of the window.

The transmission eigenvalues for the selected energy, k-point and spin are calculated, and after a couple
of seconds the eigenvalues are listed.

 Hint

If several transmission channels contribute to the transmission, more than one eigenvalue will be
shown. Each eigenvalue is restricted to the range [0, 1], but the sum of the eigenvalues, which equals
the k-point resolved transmission
T (E, k), may be larger than 1, just like the total transmission
T (E) can be.

You can now calculate and visualize the transmission eigenstate for each eigenvalue:

Select an eigenvalue and click Eigenstates. The 3D viewer opens after a few seconds.
Select the Cut plane plotting type and click OK.

The Viewer now displays the Zn|ZnO|Zn device configuration and a cut-plane representation of the
transmission eigenstate throughout the device central region.

Next, edit the visual properties of the cut-plane to focus the color palette on the finer features of the
eigenstate:

Open the Properties editor in the right side of the Viewer.

In the CutPlanes tab, change the colormap to “Hot”, then click Fit, and enter 0.3 for the maximum
eigenstate value to be visualized.

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The cut-plane visualization should now look as illustrated below. The eigenstate corresponds to a
scattering state coming from the left electrode and traveling towards the right. The eigenstates will
therefore always have a large amplitude in the left-hand part of the central region. Eigenstates with a
relatively high transmission eigenvalue will also have a relatively large amplitude in the right-hand part of
the scattering region. This simply reflects the relatively high transmission probability of an incoming state
(at a specific energy, spin, and k-point) that attempts to travel through the central region and into the right
electrode.

The transmission eigenstates in the left part of the scattering region are composed of an incoming (right-
moving) and a reflected (left-moving) state. This leads to interference effects, which can be observed in
the figure above: The eigenstate amplitude around the first Zn atom is relatively small due to destructive
interference between the incoming and reflected states. To the right of the ZnO, the eigenstate consists
only of the transmitted (right-moving) states, and no such interference effects are observed.

Try yourself to plot the transmission eigenstate at the Fermi level (energy E = 0 eV) and
kA = kB = 0 . By adjusting the plot properties you can get a plot similar to the one shown below. Now the
eigenstate has a vanishing amplitude in the middle and right parts of the scattering region, due to the low
transmission eigenvalue, i.e. only a tiny part of the scattering eigenstate is transmitted, and most of it is
reflected at the Zn–ZnO interface.

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  Tip

If you instead plot the transmission eigenstate as an isosurface, the isovalue corresponds to the
magnitude of the wave function, and the phase is used to color the isosurface.

Convergence of k-points for transmission spectrum

As already mentioned, more k-points are typically needed to obtain a well-converged transmission
spectrum than for the SCF calculation. As an example, consider the figure below, which shows the total
transmission (averaged over all k-points) evaluated at three different energies and plotted as function of
the number of k-points in the transverse A and B directions. The figure was generated using the script
 transmission_kpts.py.

Fig. 42 Total electronic transmission vs. the number of k-points in the transverse directions for the Zn|ZnO|Zn device evaluated at
three different energies: -3 eV (top), 0 eV (middle), and 3 eV (bottom).

The transmission converges very differently at different energies. While the transmission at the Fermi
energy is converged with just 5 or 7 k-points in the A and B directions, at -3 eV and +3 eV it looks like at
least 13 k-points are needed.

You may recall from above that the transmission spectrum has many sharp peaks in the region around -3

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eV. It is typically such, that many k-points are needed when sharp features are present. However, there
may also be isolated peaks that are “hidden” by too low k-point density, so one really needs to study the k-
resolved transmission plot to get an idea of the needed k-point sampling.

Additionally, in a region with many (sharp) transmission peaks as function of energy, a large number of
energy points are required to converge the integral over energy needed to compute the current.

Further analysis
This section will introduce some further ways to analyze the zero-bias calculation. An important feature in
QuantumATK is that you do not have to define all analysis quantities from the outset; you can always
calculate additional quantities without having to redo the self-consistent calculation from scratch.

You will now compute the device density of states (DDOS) of the Zn|ZnO|Zn configuration, and the
electrostatic difference potential:

Open a new Script Generator window.

Change the output file name to analysis.hdf5 , and add three blocks to the script:
Analysis from File
DeviceDensityOfStates
ElectrostaticDifferencePotential

Open the Analysis from File block. This is the part of the QuantumATK script that is responsible for
reading the converged state of the zero-bias calculation. You need to specify which file and which
saved configuration you want to base the following analysis on (there may be several configurations in
a single file).
Select the saved file zero-bias.hdf5 – the configurations stored in that data file are then
automatically detected and listed. Only one configuration is in this case available; it has object ID
“gID000”. Make sure that configuration is ticked, and click OK.

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  Tip

The ID number of each object is indicated below its icon on the LabFloor. To distinguish different
configurations in the same file, you can use the General information plugin to inspect the most
important parameters of the calculation.

Next, edit the DeviceDensityOfStates settings, which should be similar to the settings used for
computing the transmission spectrum:
energy range from -4 eV to +4 eV with 201 points.
7x7 k-point sampling.
Krylov self-energy calculator.
No changes need be made to the ElectrostaticDifferencePotential analysis.

The analysis script is now ready. Save it as analysis.py and execute it using the Job Manager or from
command line – it takes only a few minutes to run. You can also download the script here:  analysis.py.

When the job is done, observe that the analysis results have appeared on the LabFloor:

DeviceDensityOfStates

ElectrostaticDifferencePotential

Device density of states

Select the DeviceDensityOfStates object and click 2D plot in the right-hand plugins bar to visualize it.

The 2D Plot window opens with the DDOS plottet on the left. The right-hand panel allows you to also

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visualize the configuration and select atoms and orbitals to project the DOS onto:

Under Configuration HDF5 File , select the output file zero-bias.hdf5 for visualizing the device
configuration (which is not saved in analysis.hdf5 ).
Under Projection selector, select atom indices 8,9,10,11 in order to preject the DOS onto the middle
part of the ZnO layer.
Then zoom in on the projected DOS like shown in the figure below.

You should notice that the shape of the DDOS resembles the shape of the transmission spectrum
analyzed above: Both plots show a broad energy region around the Fermi energy with low values,
reflecting the semi-conducting nature of ZnO; for energies below -2 eV there are many sharp peaks; finally,
both the transmission spectrum and the DDOS display a broad peak around +3 eV. The correspondence
between the transmission spectrum and DDOS is a very general feature often observed in device
calculations.

Electrostatic difference potential

The ElectrostaticDifferecePotential object contains a 3D grid that represents the difference between the
electrostatic potential of the self-consistent valence charge density (the solution to the Poisson equation
with this density) and the electrostatic potential from a superposition of atomic valence densities. You
will use this object later when calculating the voltage drop.

You can of course use the Viewer to visualize such 3D grids, just like you did for the transmission
eigenstates a few sections up. Another way to visualize a quantity represented on a 3D grid is to use the
1D Projector. With this tool you can project a potential or density along a certain direction, integrated or
averaged over the two directions perpendicular to it. For devices, it is often most interesting to plot the
potential along the transport direction (C) and to average over the A and B directions.

Select the ElectrostaticDifferencePotential object on the LabFloor, and open the 1D Projector from the
right-hand plugins bar.
Change “Projection type” to Average and click Add line.

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You should now see a plot like shown in the figure above, where the electrostatic difference potential,
ΔVE, is plotted against the fractional C-coordinate (ranging from 0 to 1).

A significant charge transfer seems to take place at both Zn–ZnO interfaces, causing the self-consistent
electrostatic potential to differ significantly from that of the atomic valence densities. In the metallic Zn
regions near the electrodes, oscillations are rather small, indicating that the self-consistent charge
distribution is not much different from the atomic valence charges in those regions.

Finite-bias calculations
All calculations performed so far have been with zero voltage on the left and right electrodes, i.e. at zero
bias. In this section you will use the zero-bias calculation as a starting point for finite-bias calculations,
where the left and right electrode voltages are different. This shifts the left and right electrode Fermi
levels relative to each other – a basic mode of operation for electronic devices.

The recommended method for obtaining fast and reliable SCF convergence for finite-bias QuantumATK
transport calculations is to start out from a zero-bias calculation and change the bias in small steps. You
will now perform a device calculation at -0.5 V bias.

Set up the calculation

In the QuantumATK Project Files list, tick the file zero-bias.hdf5 to see its contents on the LabFloor, and
drag the DeviceConfiguration (gID000) onto the Script Generator. This will setup the Slater-Koster
calculator parameters identically to those used for the zero-bias calculation.

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Add three blocks to the script: Initial State, Analysis ‣ ElectrostaticDifferencePotential, and
Analysis ‣ TransmissionSpectrum.

Then change the default output file to finite-bias.hdf5 , and open the New Calculator to apply a bias:

Set the Left electrode voltage to -0.5 V.

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Next, open the Initial State block to instruct QuantumATK to use the zero-bias state as an initial guess
for the finite-bias calculation:

Tick Use old calculation, and choose zero-bias.hdf5 as the filename of the Old Calculation.

Lastly, set up the TransmissionSpectrum parameters identically to those used for the zero-bias
calculation:

Energy window of -4 eV to +4 eV with 201 energy points.

7x7 transverse k-points.

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 Krylov self-energy calculator.

Save the script as finite-bias.py and run it. The calculation will take a little more time than the zero-bias
calculation. If needed, you can download the final script here:  finite-bias.py.

 Note

Electrode voltages and current

In a zero-bias calculation, the local chemical potential is constant throughout the device, including the
electrodes. Applying a potential difference
U = VL − VR between the electrodes is identical to shifting the electrode Fermi levels with respect to
each other,

eU = e(VL − VR) = μR − μL,

where
μL and
μR are the left and right electrode Fermi levels, respectively, and
e the (positive) elementary charge.

The bias voltage

U is therefore positive when the applied potential on the left electrode is higher than on the right
electrode. This situation is also called forward bias, and implies that the chemical potential in the left
electrode is moved down such that
μL < μR. Conversely, under reverse bias, we have
VL < VR, and therefore a negative bias voltage and opposite ordering of the chemical potentials,
μL > μR.

A positive current corresponds to charges moving from left to right, meaning that electrons move from
right to left (since electrons have a negative charge). The current is therefore positive under forward
bias and negative under reverse bias, so you should expect to get a negative current with the bias
setting specified above.

Type Bias voltage Electrode potentials Chemical potentials Current

Forward U >0 VL > VR μL < μR I>0

Reverse U <0 VL < VR μL > μR I<0

 Attention

NEGF contour integral

For finite-bias calculations, a potentially important convergence parameter is the Real axis point
density, which is specified under Contour integral parameters. This parameter determines how many
energy points are used when integrating the left and right spectral density matrices along the real
energy axis between the chemical potentials of the left and right electrodes. For the present
calculation you can proceed with the default value, but be aware that a convergence test of this
parameter should in general be performed.

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 The settings Integral lower bound and Circle points are another important set of parameters. The
NEGF contour integral needs to include all eigenvalues on the energy axis, but these are in general not
known a priori . The default lower bound for the integral is 1.5 Ha below the Fermi level, but for DFT
calculations with “hard” pseudopotentials (many valence electrons, possibly semi-core states), there
may well be eigenvalues deeper than that. In that case, the Integral lower bound should be increased,
and possibly also the number of circle points. Poor device SCF convergence is often due to such
issues.

Analyzing the results

Go to the QuantumATK main window and open finite-bias.hdf5 on the LabFloor. Use again the
Transmission Analyzer to plot the transmission spectrum. Notice that the chemical potential of the left
and right electrodes are separated by the bias of 0.5 V and distributed evenly around the average
electrode Fermi levels, which still is the energy zero reference. Also, you can see that there is a (very
small) negative current flowing in this system, consistent with the direction in which the bias was applied.

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The finite-bias transmission looks essentially the same as found for zero bias. Recall from the analysis in
section Device density of states that you found similar shapes of the ZnO DDOS and the transmission
function. The shape of the transmission function is thus in this system largely determined by the density
of states of the ZnO, and not so much by the electronic structure of the electrodes. Since the transmission
values are very small in the bias window, the current is low and hence the change in DDOS in the ZnO is
small. This is not necessarily the case in other systems, especially not if the bias is large enough to bridge
the band gap of the scattering region.

Voltage drop

Your next task is to calculate the potential profile along the device transport direction at finite bias, also
known as the voltage drop or the induced electrostatic potential. This can be computed as the difference
between the electrostatic difference potentials at finite and zero bias,

ΔVE(r) = δVEfinite−bias − δVEzero−bias.

 Hint

Each electrostatic difference potential is the difference between the electrostatic potential of the self-
consistent valence charge density and the electrostatic potential from a superposition of atomic
valence densities. Since the atomic valence charge densities are the same for the zero and finite bias
calculations, the calculated difference,
ΔVE(r), is the potential due to the differences between the two self-consistent charge densities, which
is exactly the voltage drop.

The QuantumATK Grid Operations plugin is a very convenient tool. It allows you to perform arithmetic
operations on 3D grids, such as addition and subtractions of one grid from another, and also
multiplication and division. You will now use the plugin to compute
ΔVE(r), save it in a file, and then plot it in the Viewer:

By default, the Labfloor groups all items by filename. Change the option Group by to Item Type .
Then select the two ElectrostaticDifferencePotential items, and open the Grid Operations tool.

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In the Grid Operations tool, the grids are assigned aliases. Depending on the order in which you selected
the two items, the finite and zero bias potentials will be called A1 and B1, or opposite. To compute the
voltage drop (the induced potential), subtract the zero-bias potential from the finite-bias potential by
entering A1-B1 (or opposite) in the box next to f(x)= and press Enter on your keyboard.

You can then immediately plot the result as a cut-plane or an iso-value contour in the 3D window to the
right, and/or save the difference grid in a new HDF5 file by clicking the Save button in the lower left corner.

Save the difference grid as voltage_drop.hdf5 , and observe the GridValues object appear on the LabFloor.

 Note

GridValues is a general container for quantities represented on 3D grids.

Select one of the DeviceConfigurations and open it with the Viewer. Then drag and drop the GridValues
object onto the Viewer canvas in order to visualize it on top of the device configuration. Choose the Cut-
plane visualization type, and set the color map to RGB.

The visualization should look like shown below. The potential drop occurs in the center of the device
region, around the ZnO layers, showing that this is where scattering of the electrons takes place.

For a more quantitative analysis, open the saved difference grid with the 1D Projector, choose Average as

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projection type, and click Add line. You should now see a plot like the one shown below. The potential
values are given in Volt. The right-to-left potential drop is -0.5 V, which is exactly the applied bias voltage.

Also note that the induced potential is flat towards the electrodes, indicating that the Zn layers in the left
and right ends of the central region provide sufficient screening.

I–V curve
The last finite-bias device analysis in this tutorial is the I–V curve. You will first compute it using the IV
Characteristics analysis in the Study Objects, and then visualize it using the IV-Characteristics Analyzer
plugin.

 Attention

The Study Objects ‣ IV Characteristics analysis has been implemented since the O-2018.06
version. If you use an older version, you can use the Analysis ‣ IVCurve object instead.

Calculations

Drag and drop the zero-bias.hdf5 or zero-bias.hdf5 file onto the Scripter. It automatically keeps the
settings of the zero-bias calculation. Now do the following:

Add the Initial State block.

Add the Study Objects ‣ IVCharacteristics block.
Change the default output filename to iv-curve.hdf5 .

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Next, open the Initial State block to instruct QuantumATK to use the zero-bias state as an initial guess
for the finite-bias calculation:

Tick Use old calculation, and choose zero-bias.hdf5 or zero-bias.hdf5 as the filename of the Old
Calculation.

Edit the IVCharacteristics block:

Decrease the number of voltage points to 5 (for speed).

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The QuantumATK Python script is now done. Save it as iv-curve.py and execute it using the Job
Manager or from the command line. This calculation will take some time, because a self-consistent
calculation and a transmission spectrum analysis must be done at each bias point, so probably around 10
minutes in 16 cpus.

If needed, you can download the script here:  iv-curve.py. If you do not want to perform the calculation
yourself, you can also just download the results:  iv-curve.hdf5.

Visualization

The calculation should now be done, and the IVCharacteristics data item should now be included

in the iv-curve.hdf5 output file. Five new output files were also created, prefixed ivcharacteristics ; they
contain the log file at each bias point.

 Note

The IVCharacteristics item contains the calculated I–V curve, including the transmission

spectra computed at each bias voltage.

Select the IVCharacteristics item on the LabFloor and click the IV-Characteristics Analyzer tool in

the right-hand plugins bar. The I–V curve is plotted in the window that pops up.

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Select the Drain-Source Plot tab and choose the scale of current by right-clicking and choosing
Customize. Change the maximum for the y-axis to 1.8e-07 to get the plot shown below.

The table in the IV-Characteristics Analyzer shows the current and status of convergence at each finite
voltage. Once you click the right-hand side plot icon ( ) in the table for the first time, the Analyzer will
load in the Transmission spectra from the file. You can the visualize the transmission spectrum
corresponding to a specific bias voltage point by clicking the icon and choosing Transmission spectrum .

A somewhat finer bias-point sampling would yield a more accurate current. To this end, you should
increase the number of bias points to 21, for example, and re-run the script with IVCharacteristics
study object. It will automatically re-calculate the new points. You can also download the result here:
 iv-curve_fine.hdf5.

 Note

The IVCharacteristics study object enables addition of more bias points. Simply add more voltage
points in the IVCharacteristics object with the same calculator settings, then run it in the existing
output file directory. The IVCharacteristics recognizes the existing bias points smartly, and just
runs the additional voltage points. It will be faster and not waste the computational cost. See also the
dedicated tutorial: Electrical characteristics of devices using the IVCharacteristics study object for
more information.

The finely sampled I–V curve is illustrated below. Compare it to the coarsely sampled one shown above
even though the IV-curves look very similar.

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Summary
You have now been introduced electronic transport calculations with QuantumATK.

You have gained an understanding of the general structure of a device geometry, and can continue
with setting up other device geometries: Getting started with QuantumATK.
You have learned about important convergence parameters, such as transverse k-points, density mesh
cut-off energy, and NEGF contour integral settings.
You are now able to calculate the transmission spectrum at zero and finite bias voltage, and analyze
the results using the Transmission Analyzer.
You have also been introduced to other analysis tools like projected device density of states,
electrostatic difference potential, transmission eigenvalues and eigenstates, and I–V curve using the
IV characteristics study object.
You are also able to visualize 3-dimensional objects with the 3D Viewer or by using 1D projections.

 Tip

What’s next?
Now that you know the basics of electron transport calculations, it would be wise to continue to the
tutorial Phonons, Bandstructure and Thermoelectrics to learn about simulating phonon transport with
QuantumATK.

 Previous Next 

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