Introduction

The builder_icon Builder is an essential part of the Virtual NanoLab (VNL) graphical user interface to the Atomistix ToolKit (ATK) calculator engines. The Builder provides a range of powerful tools for building advanced atomic-scale structures, e.g. bulk crystals, 1D nanowires, 2D nanosheets, clusters, and device configurations with either one or two probes. After a structure is built, it can be used either in ATK calculations or be exported to external file formats for use in other atomic-scale simulation packages.

This manual provides an overview of the Builder functionalities. For specific advice and tips for building atomistic structures, please refer to the QuantumWise Tutorials website and visit the public QuantumWise Forum, where specific questions may be answered by experienced users.

Layout and basic operations

When the Builder starts up for the first time in a VNL session, it is empty. You will soon learn how to add structures to it, but let us first get an overview of the Builder main window.

As illustrated below, the main parts of the Builder are:

Stash:Storage for all created structures
Stash menu:Tools for adding items to the Stash, and for copying and deleting Stash items.
3D viewer:Visualization of active Stash items.
Toolbar:Simple plugins for modifying Stash items, e.g. moving a particular atom.
Panelbar:Advanced plugins for editing Stash items, e.g. creating a device configuration.
Drag-and-Drop:Use the mouse to drop the active Stash item onto another VNL tool.
Send-to button:Use a menu list to send the active Stash item to another VNL tool.
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Stash

All structures you are working on in the Builder are stored in the Stash. Each Stash item is represented by an icon, and corresponds to a single configuration.

Stash items can be selected and/or active – there is a difference: You can select more than one structure, but only one can be active. Some Builder plugins operate on more than one Stash item at a time (e.g. to combine two configurations into one), and you can therefore select other items than the currently active one.

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Fig. 5 The Stash item named “Silicon (alpha)” is active, as indicated by the red line around the icon. The active item is always the one shown in the 3D viewer, and operations like “delete atom” or “change lattice constant” will be carried out on this structure. The Stash item named “Methane” is merely selected, which is indicated by the orange background.

Stash operations

There are several ways to add new structures to the Stash:

  • You can simply drop configurations from the VNL main window onto the builder_icon Builder. The structure is automatically added to the Stash. See the tutorial Getting familiar with Virtual NanoLab for an introduction to the VNL main window.
  • Use the Stash menu to add completely new structures to the Stash. The Add menu contains a range of tools for creating configurations from scratch.
  • The Add menu also allows you to import structures from saved files.

The Stash menu also allows you to Copy and Delete active items. When you copy an item, a new and identical item is added to the Stash.

Right-click a Stash item to open its context menu. This allows you to rename, copy, delete, and in various ways save/export the structure to files, or send the structure to another VNL tool.

Tip

The keyboard shortcut F2 may be used for renaming Stash items, while pressing the Delete key is a shortcut to the Delete operation.

Plugin tools

As indicated in Fig. 5, the horizontal Toolbar above the 3D viewer and the vertical Panelbar to the right of the 3D viewer both contain plugin tools for interacting with Stash items, and for applying more or less complex operations on the active Stash item, e.g. change the lattice constant of a bulk configuration. Note that a plugin tool usually operates on the active Stash item only.

The horizontal Toolbar plugins are applied by clicking the icon. Hover the mouse over each icon to see a tooltip describing it.

The vertical Panelbar plugins are grouped in panels, e.g. Bulk Tools and Device Tools. Click a panel to expand it – a list of relevant plugins is revealed.