Virtual NanoLab

Table of Contents

• Introduction
  • About this manual
• Comparing with old versions
  • Changes since VNL 2.0
• The VNL Toolbar
  • Launching VNL
  • Description of the Virtual NanoLab Toolbar
    • The Toolbar menu
  • Data handling in VNL
    • NanoLanguage scripts
    • VNLFiles
    • Transfer of information between tools
  • Getting started — a small tutorial
  • Going further with VNL
• Molecular Builder
  • Starting the Molecular Builder
  • Building simple molecules
    • Methane
    • Water
    • Ammonia
  • Adjusting molecules
    • Autoadjustments
    • User adjustments
  • The Periodic Table tool
  • The Molecule Cupboard
    • Filtering templates
  • Joining and fusing molecules
    • Join
    • Fuse
  • Chirality and cis/trans isomers
    • Cis-trans isomers
  • The Geometry Manager tool
    • Defining the element type
    • Building ions – setting atomic charges
    • Hybridization
    • Setting the bond order
    • Adjusting bond distances
    • Bond angles
    • Dihedral angles
  • Keyboard shortcuts.
• Crystal Cupboard
• Bulk Builder
  • Starting the Bulk Builder
  • Setting coordinate types
  • Defining the Lattice
    • Selecting lattice type
    • Editing lattice parameters
    • Converting between Bravais lattices
    • Periodic Atom Configurations
  • Defining the Basis atoms
    • The Bulk Builder Table View
    • The BulkBuilder 3D-View
  • Bulk Repetitions
• Atomic Manipulator
  • Creating molecules
  • Editing crystals and nanotubes
  • Creating two-probe systems
    • Cleaving a periodic system
    • The central region of a two-probe system
  • Translating molecules and electrodes
  • Rotating molecules
  • Creating equivalent bulk systems
• Magnetic Tunnel Junction Builder
  • General Description
    • Using the Magnetic Tunnel Junction Builder
  • Magnetic Tunnel Junction Builder parameters
• Nanotube Grower
• Nanoscope
  • Inserting plots
    • Contour plot
    • Isosurface plot
    • Volume plot
    • Atomic configuration plot
    • Coordinate axes plot
  • Modifying plots
  • Coloring of three-dimensional plots
  • Changing the appearance of plots
  • Controlling which plots are displayed
  • Rotating, panning, and zooming the camera
  • Exporting and printing 3D plots
    • Exporting
    • Printing
  • Exporting and printing 2D plots
  • Camera settings
    • Rendering
    • Printing
• NanoLanguage Scripter
  • General Description
  • Configuration
  • Method
    • Method parameters
  • Self-Consistent Calculation
    • Self-consistent parameters
  • Analysis
    • Saving analysis results
    • Analysis parameters
• Method Editor
  • Method Editor
• Script Editor
  • Script Editor
  • Examples
    • Loop over mesh cut-offs
• Job Manager
• Result Browser
  • Introduction
  • Launching the Result Browser
  • Loading and unloading samples in the Result Browser
  • Visualizing contents of files using the Result Browser
  • Backwards compatibility
    • Restoring old VNL sessions
    • Open various file formats
• Energy Spectrometer
• Troubleshooting
  • Internal errors
  • Printed/Exported images are corrupted
  • Random crashes
  • Installation and license issues
  • Known minor problems
• How to get more help
• A. Color references
• Index