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The best way to learn how to use VNL and ATK as effectively as possible is to look as some concrete examples.
The manuals contains several detailed examples intended to show users how to operate specific parts of the software. In this section, we will collect more "topical" 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 here 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. In addition, we will here publish various other tutorials that are not part of the manual (yet).
The tutorials are separated into two groups, dealing with the two different packages offered by QuantumWise:
The main reason for this separation is the slightly different user interfaces. Do note, however, that several of the fundamental concepts, in particular those described in the two basic ATK Tutorials (under the DFT section) are common for both packages.
Tutorials for ATK 2010.01
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Title & Abstract
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VNL basic tutorial
This is a general, quick introduction to the graphical user interface VNL (version 2010.01). By performing some simple molecule calculations, using the semi-empirical edition of ATK, the user will be guided through the basic concepts of the software. The focus of this tutorial is not on the results themselves, but on how to operate the software.
Open tutorial (HTML | PDF)
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Basic tutorial: Transport in graphene nanoribbons
This basic 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.
There is a similar tutorial for ATK 2008.10 too.
Open tutorial (html | PDF)
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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.
Open tutorial (html | PDF)
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Going further with graphene
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.
Open tutorial (html | PDF)
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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.
Open tutorial
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Introduction to GPAW in VNL
A brief tutorial which presents how to do some simple calculations using GPAW from within VNL.
Open tutorial (PDF | HTML)
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Tutorials for ATK/VNL 2008.10 (DFT edition)
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Title & Abstract
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ATK Tutorial
What Everyone Should Know About ATK
The title says it all - this is a very fundamental (albeit not basic) presentation of all the important details that you should know about ATK. Part 1 is related to the geometry setup and the self-consistent calculation, while Part 2 deals with transmission analysis. The focus is naturally on two-probe systems, but important points for bulk and molecular calculations are also presented.
Download Part 1 (PDF)
Download Part 2 (PDF)
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Graphene nanoribbons
Research on both fundamental aspects and device applications of graphene is a very active field. In this tutorial we will present how the capabilities in Atomistix ToolKit and Virtual NanoLab can be utilized to study various types of systems involving graphene, ranging from a simple, infinite sheet of graphene to complex junctions that are investigated for e.g. field-effect transistor applications.
Download tutorial (PDF)
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graphene_ribbon.py
align.py
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Spin Bloch states in 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.
Download tutorial (PDF)
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graphene_ribbon.py
spinpoldensityplot.py
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Band structure & DOS calculations
This tutorial provides an add-on module for computing and plotting band structures that extends the functionality in ATK in several ways.
It also includes a script to compute the density of states (DOS) in a bulk system.
Download tutorial (PDF)
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bandstructure.py
bulk_dos.py
export_bs.py
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Convergence tricks
This tutorial describes a variety of techniques for solving convergence problems, ranging from how to properly choose the electrode configuration to relatively advanced parameter settings in ATK. All steps are explained in detail using VNL, and as the example system is used an FeMgO magnetic tunnel junction with anti-parallel spin-polarized electrodes, which is one of the hardest configurations to converge.
Download tutorial (PDF)
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femgofe_para.py
femgofe_antipara.py
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Work function of metal surfaces
ATK can be used to accurately compute the work function of metal surfaces. This tutorial describes in detail how to set up and run such a calculation.
This tutorial is courtesy of Cybernet Systems Co..
Download tutorial (PDF)
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work_function.py
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Electron transport through monovalent atomic wires
How to compute the conductance of metallic atomic wires, complete with analysis of the transmission spectrum and k-point resolved transmisson coefficients. Inspired by Y. J. Lee et al., PRB 69, 125409 (2004).
Download tutorial (PDF)
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GoldMonowires_Scripts.zip
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Transmission coefficients
This slightly more advanced tutorial focuses on a very specific topic: how to most efficiently compute and plot the k-point resolved transmission coefficients. In particular, we show how to take advantage of symmetries in the system, which sometimes can reduce the computational burder significantly.
Download tutorial (PDF)
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transmission_scripts.zip
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Tutorials
