The VNL Toolbar


Introduction	The Nanoscope

When you launch Virtual NanoLab (VNL), the first thing which appears is the VNL Toolbar window.

Figure 1: The contents of the VNL Toolbar.

The Toolbar provides access to all the individual tools that are used in VNL. In summary, these are

Tool	Icon	Description
Crystal Cupboard		Database of bulk crystals
Magnetic Tunnel Junction Builder		Build your basic magnetic tunnel junction ready to be used in other VNL tools (for further modifications, use the Atomic Manipulator).
Nanotube Grower		Create and visualize perfect carbon nanotubes
Atomic Manipulator		Set up two-probe systems and make modifications to magnetic tunnel junctions.
Molecular Builder		Build and construct your own molecules ready to be used in other VNL tools
Bulk Builder		Build and construct bulk systems ready to be studied and analyzed with other VNL tools
NanoLanguage Scripter		Create complete calculation set-ups and store these as NanoLanguage script.
Method Editor		Predefine DFT and NEGF parameters for reuse in the NanoLanguage Scripter when generating NanoLanguage scripts.
Script Editor		Manually edit and extend NanoLanguage scripts constructed by the different set of VNL tools.
Job Manager		Execute scripts using the ATK computation engine.
Nanoscope		Visualize atomic geometries and calculated properties in 3D
Result Browser		Browse the contents of VNL files including all stored samples and results within them.

The Toolbar icons give you quick access to tools used for

creating and modifying molecule, bulk, and two-probe systems.
setting up DFT calculations and defining the physical properties that should be extracted from the calculations.
executing calculations, as well as inspecting and analyzing results.

Before you can study the electronic properties of a system, you first have to construct a model of the atomic configuration you wish to investigate. VNL provides you with several tools that assists you in defining the geometry of complex nanoscale systems. We refer to the systems that you build as configurations.

Once a configuration has been build, you store it in a NanoLanguage script on your file system. The script files can then be imported for use in other tools, where it, for example, can be modified and exported to a new script file. Configurations from different scripts can also be combined in tools in order to define composite two-probe geometries or to perform calculations.

All configurations as well as the specification of the DFT methods and calculations is stored on disk as an editable NanoLanguage script. This implies that you seamlessly can include other software application in the handling of the data flow generated by VNL:

Use your favorite text editor to produce a script for setting up a skeleton model of the system you wish to study
Copy-and-paste the configuration directly into the VNL tools for further fine-tuning and modification.
Add the final configuration to the NanoLanguage Scripter to setup a final computation method and specify the physical analysis of your system.

In VNL, results calculated for a particular sample are stored in a so-called VNLFile (stored VNLFiles carry the extension vnl). VNLFiles can be browsed, analyzed, and their data can be extracted by using the Result Browser tool , which is backwards compatible with previous versions of VNL (2.01 and earlier).

	Note
	For more information about the VNLFile and NanoLanguage Script format, please consult the section called “Data handling in VNL” in the VNL Manual.

During the tutorial, we will become acquainted which each particular tool in VNL. To jump in, we start off by using and exploring the Nanoscope tool.