Home Tutorials
Tutorials

The best way to learn how to use VNL and ATK as effectively as possible is to look as some concrete examples.

In this section, we will collect tutorials that outline a more complete work flow, from the initial definition of the geometry through to the final analysis of the results. Typically, we will be focusing on a particular type of system or calculation, and we will also demonstrate how to combine scripting and the graphical user interface in VNL in a flexible and powerful way.

Note for ATK 11.8 users: Since there are some technical differences between ATK 12.x/13.x and 11.8 in where to locate certain tools, buttons etc, we maintain a separate list of links to the 11.8 version of the tutorials for the benefit of users of the older program version.

 


 

Getting started


Title & Abstract
Comments
ATK

ATK basic tutorial

This is a general, quick introduction to basic calculations in ATK, with a focus on getting to know the graphical user interface, Virtual NanoLab (VNL). By performing some simple calculations, you will be guided through many of the important basic concepts used in ATK. The tutorials consists of two parts:

  1. Calculating the band structure of SiC YouTubeYouKu
  2. Transmission spectrum of a graphene nanoribbon with a distortion YouTubeYouKu
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Builder

Builder Tutorials

Learn how to use the Builder tool in Virtual NanoLab to define advanced atomic geometries, ranging from basic nanotubes with defects to complex interfaces, molecular junctions, and transistor-like nanowire geometries. Most tutorials are available as videos, which also can be accessed on QuantumWiseTV (watch on YouTube or YouKu).

These tutorials require ATK 12.2 or higher.
ScriptGenerator

Mini-tutorials

A set of quick demonstrations of some basic features in ATK. Not as much details and hand-holding as in the other tutorials, but they offer a great way to quickly get to know some basics, and get some tips on more advanced usage.


ATK

Introduction to transport calculations with ATK

The most outstanding feature in ATK is its ability to compute the ballistic tunneling current in nanoscale device structures. This tutorial provides an introduction to transport calculations with ATK by considering a toy system (a hydrogen molecule embedded in an atomic chain of Li atoms), and presents basic concepts such as computing the transmission spectrum, I-V curve, and voltage drop, and also shows to optimize the geometry, etc.

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Longer tutorials

bilayer

Au(111)-Pentacene metal-organic interface

A very important feature in ATK is that the two electrodes in a device system do not need to be the same. This enables studies of true interfaces, and this tutorial teaches you in a detailed way how to set up and compute the properties of a metal-organic interface (pentacene on gold (111) to be precise). The tutorial presents a number of advanced techniques for obtaining an optimized geometry of a complex interface, including the use of the BSSE technique and verification of accuracy, etc. You will furthermore compute the transmission spectrum and other transport properties, which will be comparable to those published in K. Stokbro and S. Smidstrup, Phys. Rev B 88, 075317 (2013), where this system is used to show that the conventional semiconductor transport models across Schottky barriers need to be modified in order to describe metal-organic interfaces. 

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newRequires ATK 13.8

bilayer

Grimme's DFT-D2 model (van der Waals interactions) + counterpoise correction for BSSE

The alternative title is "How to correctly determine the interlayer distance in bilayer graphene". As you will learn in this tutorial, a reasonably accurate answer is obtained with simple GGA, but only because two errors cancel each other: the omission of dispersion forces due to van der Waals interactions, and basis set superposition errors (BSSE). By carefully taking both of these effects into account, using Grimme's DFT-D2 semi-empirical potential and the counterpoise correction, you will also get a good answer - but this time for the right reasons.

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newRequires ATK 13.8

cbs

Phonons calculations

Learn how to study phonons with ATK! In this tutorial you will first compute the phonon bandstructure and DOS of a graphene nanoribbon, and learn how phonon calculations work. Next you will study a device system and calculate the electronic and phonon thermal transport coefficients, as well as the electrical transport coefficients. From those coefficients you obtain the thermodynamic figure of merit ZT.

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newRequires ATK 13.8

cbs

Polarization

Ferroelectric materials have a spontaneous electric polarization that can be reversed by the application of an external electric field. They have applications in capacitors, ferroelectric random access memory (RAM), and more recently in ferroelectric tunnel junction (FTJ) displaying giant electroresistance effects. This tutorial will show you how to compute the polarization of BaTiO3, a commonly used material, using ATK. The tutorial also contains a script for computing the Born effective charges.

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newRequires ATK 13.8

cbs

Complex bandstructure

In addition to the usual bandstructure of a periodic system, ATK can also compute the complex bandstructure of semiconductors and insulators. This is relevant for, for instance, nanowires, oxide barriers in magnetic tunnel junctions, and other materials that form a tunneling barrier for electrons in a nanoscale device. The complex bandstructure provides a quick way to estimate and compare the possible tunneling current between e.g. different directions in the crystal, without actually performing a time-consuming transport calculation.

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Requires ATK 12.8 or higher

si100

Reconstruction of the Si (100) surface

Although LDA and GGA may not be able to produce a proper band gap in Si (and most other semiconductors), these "simple" DFT functionals are very capable when it comes to predicting geometrical properties. In this short tutorial you will learn how to use ATK to study the reconstruction of a Si (100) surface. By performing a geometry optimization it will be shown that the so-called asymmetric dimer is the lowest energy configuration.

new

nanowire

Silicon nanowire field effect transistor

This tutorial shows how to set up and perform calculations for a silicon nanowire. You will define the structure of a H-passivated silicon nanowire along the (100) direction, and set up a field effect transistor (FET) structure with a wrap-around gate. Then the transmission spectrum and conductance will be computed as the gate bias is varied.

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new

neb

Using DFTB in ATK + introductory tutorial on NEB

The DFTB model in ATK can be extended with parameters from dftb.org. This tutorial shows how to install these parameters, and then proceeds to use them for a simple nudged elastic bands (NEB) simulation to calculate the reaction barrier for the inversion of an ammonia molecule.

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optical

Optical properties using meta-GGA

Two really exciting new features in ATK 11.8 is meta-GGA and the possibility to calculate optical properties like the dielectric constant or the optical absorption spectrum. Combined with meta-GGA (also a new feature in 11.8) which provides very accurate band gaps for semiconductors, this means ATK can now be used to predict important properties of materials like novel high-k dielectrics. This tutorial shows a simple example on how to perform such calculations.

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slaterkoster

Implementing your own Slater-Koster tight binding models in ATK

Starting with ATK 11.8 it is possible for the user to implement his own Slater-Koster tight binding models in ATK. This tutorial demonstrates in detail how to set up two different types of basis sets: a single-orbital pi-model for carbon, and a nearest-neighbor tight-binding model for Si-H. In both cases, interesting usage examples are also provided. For instance, we compute the complex band structure of a Si-H nanowire (the same, in fact, as used in the nanowire tutorial just above).

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VASPScripter1

Setting up VASP calculations with VNL

ATK can also be used as a GUI for other codes, as long as you define a plugin to generate the necessary input files. We have developed such a plugin for VASP, and this tutorial demonstrates how to use it, to easily set up a NEB calculation. It also serves as a manual for using the VASP plugin.

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graphene

Transport in graphene nanoribbons

This tutorial serves as an introduction to many of the basic features in ATK and VNL, by studying electronic structure and transport properties of both perfect and distorted graphene nanoribbons. So, even if you are not ultimately interested in graphene, it's a good tutorial for learning key concepts in ATK!

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graphene

Analyze a molecular device configuration

This tutorial focuses on the calculation and analysis of a molecular device consisting of a di-thiol benzene (DTB) molecule in contact with two gold (111) surfaces. This classic molecular device, sometimes called the fruit fly of molecular electronics, provides an excellent introduction for users interested in using ATK to study molecular devices.

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graphene

Spin-dependent Bloch states in graphene nanoribbons

Depending on the edge shape, graphene nanoribbons have metallic or semiconducting characteristics, but spin also plays an important role. We will use the capabilities of ATK to study the spin-dependent band structure of a zigzag ribbon. By plotting conduction and valence band Bloch states, we will see how the two spin-components are localized on opposite sides of the ribbon. We will also consider the spin polarization of the electron density.

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LDA+u

Electronic structure of NiO with LDA+U

By tuning the empirical Hubbard parameter U, one can obtain the correct band gap for semiconductors even with LDA or GGA. This tutorial shows how to approach this type of calculations by taking NiO as an example, and at the same time it also introduces the density of states (DOS) functionality in ATK.

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Benzene SET

Benzene single electron transistor

Insipred by K. Kaasbjerg and K. Flensberg, Nano Letters, 8, 3809 (2008), this rather advanced tutorial presents in detail how ATK can be used to investigate weakly coupled single electron transistor devices, where the transport mechanism is sequential tunneling (Coulomb blockade), rather than ballistic tunneling. Specifically, the fully self-consistent charge stability diagram is computed (picture left), using the electrostatic gate capability in ATK.

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Benzene SET

Fe/MgO/Fe magnetic tunneling junction

ATK is an ideal tool for studying TMR and other properties of magnetic tunnel junctions (MTJ) such as the famous Fe/MgO/Fe system, studied intensively both experimentally and theoretically. This tutorial introduces a custom builder for MTJs, discusses basic concepts such as how to optimize the geometry of the central region, and goes on to compute both the parallel and anti-parallel zero-bias conductance and TMR.

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Graphene Moebius ribbon

Exploring graphene with ATK

This advanced tutorial goes deeper into the the Python scripting language in ATK, and shows how scripting, in combination with the functionality in the graphical user interface, can be used to set up advanced structures such as twisted graphene ribbons. The tutorial presents how users themselves can construct Custom Builders in VNL, a form of graphical plug-ins that make it easy to define and manipulate parameterized geometries.

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Graphene Junction Device

Graphene junction device - a nanoscale transistor

This extensive tutorial presents how the semi-empirical method in ATK can be used to investigate a nanoscale transistor. The structure is a graphene junction, inspired by Q. Yan et al., Nano Letters 7, 1469 (2007). We study the current as a function of the electrode bias, the gate potential, and even the (electron) temperature.

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GPAW

Introduction to GPAW in VNL

A brief tutorial which presents how to do some simple calculations using GPAW from within VNL.

NOTE: This tutorials is outdated as of ATK 11.8. Some useful additional information is available on our User Forum.

 

General guides


Title & Abstract
parallel

Parallel guide

Running ATK in parallel can provide a substantial performance benefit. In fact, you don't even need a cluster to take advantage of parallelism, since ATK also uses OpenMP to speed up the calculations on multicore machines! This guide will explain how to run ATK in parallel, which parts of the calculations that are parallelized, and many other useful details. It also discusses various strategies for balancing the number of nodes and cores, and even provides some example PBS scripts.

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