Symbols
- 3D plot window, Starting the Molecular Builder, The Bulk Builder Table View, Nanoscope, 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, Camera settings, Configuration
- α, Selecting lattice type
- β, Selecting lattice type
- γ, Selecting lattice type
A
- a, Selecting lattice type
- A, Bulk Repetitions
- A/B/C directions, Crystal Cupboard, Editing crystals and nanotubes, Atomic configuration plot
- accuracy, Introduction, About this manual, Cleaving a periodic system, The central region of a two-probe system
- adjust geometry, User adjustments
- adjustment, Adjusting molecules
- alignment, Creating molecules
- ammonia, Ammonia
- analysis, Analysis
-
- NanoLanguage Scripter tab, General Description
- angle, Bond angles
- ATK, Job Manager, How to get more help
- atom, Atomic configuration plot
-
- delete, Creating molecules
- insert, The Periodic Table tool, Creating molecules
- replace, Water, Ammonia, The Periodic Table tool
- atomic
-
- basis, Crystal Cupboard, Editing crystals and nanotubes, Nanotube Grower
- configuration, Creating molecules, Atomic configuration plot
- coordinates, Creating molecules, Translating molecules and electrodes, Nanoscope
- element, Defining the element type
- atomic configuration
-
- repetition, Atomic configuration plot
- visible, Atomic configuration plot, Controlling which plots are displayed
- Atomic Manipulator, Atomic Manipulator, Editing crystals and nanotubes, Creating two-probe systems, Cleaving a periodic system, The central region of a two-probe system
- Atomistix ToolKit (ATK), Introduction, How to get more help
- atoms
-
- changing, The Bulk Builder Table View
- inserting, The Bulk Builder Table View
- selecting, The Bulk Builder Table View
- autoadjust, Building simple molecules, Methane, Adjusting molecules, Autoadjustments, Building ions – setting atomic charges
- axes, Coordinate axes plot
B
- b, Selecting lattice type
- B, Bulk Repetitions
- background color, Creating molecules, Camera settings
- backwards compatibility, Backwards compatibility
- band structure
-
- carbon nanotube, Nanotube Grower
- barrier, Changing the barrier region
- basic introduction, Getting started — a small tutorial
- basis
(atomic), Crystal Cupboard, Editing crystals and nanotubes, Nanotube Grower
- basis set, Method parameters
- biphenyl, Join
- bond, Atomic configuration plot
-
- autoadjust, Building ions – setting atomic charges
- length, Nanotube Grower
- bond distance
-
- adjusting, Adjusting bond distances
- bond order, Setting the bond order
- boundary conditions, Editing crystals and nanotubes, Cleaving a periodic system
- buckling, Changing the structure of the interface
- building, Introduction, Going further with VNL
-
- bulk, Bulk Builder
- molecules, Molecular Builder
- two-probes, Atomic Manipulator
- bulk atomic configuration, Atomic configuration plot
- Bulk Builder, Bulk Builder
-
- starting, Starting the Bulk Builder
- bulk configuration, Crystal Cupboard, Atomic Manipulator, Cleaving a periodic system
-
- edit, Editing crystals and nanotubes
- bulk sample, Creating two-probe systems
- bulk unit cell, Crystal Cupboard, Editing crystals and nanotubes, Nanotube Grower, Atomic configuration plot
C
- c, Selecting lattice type
- C, Bulk Repetitions
- calculation
-
- parameters, Method
- camera, Creating molecules, Nanoscope, Rotating, panning, and zooming the camera
-
- pan, Rotating, panning, and zooming the camera
- properties, Camera settings
- reset, Rotating, panning, and zooming the camera
- rotate, Rotating, panning, and zooming the camera
- zoom, Rotating, panning, and zooming the camera
- carbon nanotube, Editing crystals and nanotubes, Cleaving a periodic system, Nanotube Grower
- cell
-
- electrode, Cleaving a periodic system
- surface, Cleaving a periodic system
- central region, Creating two-probe systems, The central region of a two-probe system
-
- width, The central region of a two-probe system
- central region interaction, Size and shape of the surface cell
- charge, Building ions – setting atomic charges
- checkpoint filename, Self-Consistent Calculation
- chiral vector, Nanotube Grower
- chirality, Chirality and cis/trans isomers
- cleaving, Editing crystals and nanotubes, Creating two-probe systems, Cleaving a periodic system
- color, Color references
-
- atom, Atomic configuration plot
- background, Camera settings
- bond, Atomic configuration plot
- coordinate axes, Coordinate axes plot
- unit cell, Changing the appearance of plots
- color bar, Contour plot, Isosurface plot, Volume plot, Coloring of three-dimensional plots
- coloring of plots, Coloring of three-dimensional plots
- comparing with old versions, Comparing with old versions
- configuration
-
- bulk, Crystal Cupboard, Atomic Manipulator, Creating two-probe systems, Cleaving a periodic system, Atomic configuration plot
- create, Creating two-probe systems, Nanotube Grower
- molecular, Atomic Manipulator, Creating two-probe systems, The central region of a two-probe system, Atomic configuration plot
- NanoLanguage Scripter tab, General Description
- nanotube, Nanotube Grower
- stored as script, NanoLanguage scripts
- two-probe, Atomic Manipulator, Creating two-probe systems, Cleaving a periodic system, The central region of a two-probe system, Atomic configuration plot
- constraint
-
- electrode, Method parameters
- geometry optimization, Configuration
- context menu, Nanoscope
- contour plot, Contour plot
- coordinate axes, Coordinate axes plot
- coordinates, Creating molecules, Translating molecules and electrodes, Nanoscope
-
- internal, Adjusting bond distances, Creating molecules
- corrupted images, Troubleshooting
- covalent radius, Atomic configuration plot
- crashes, Troubleshooting
- create
-
- configuration, Molecular Builder, Crystal Cupboard, Bulk Builder, Atomic Manipulator, Creating molecules, Creating two-probe systems, Magnetic Tunnel Junction Builder, Nanotube Grower
- equivalent bulk, Creating two-probe systems, Creating equivalent bulk systems
- two-probe, Atomic Manipulator
- create configuration, Transfer of information between tools, Methane
- Crystal Cupboard, Crystal Cupboard
- current, Analysis parameters
- cut plane, Contour plot
D
- data
-
- NanoLanguage script, Data handling in VNL
- VNL file, Data handling in VNL
- delete
-
- atom, Creating molecules
- molecule, Creating molecules
- plot, Modifying plots
- density-functional theory (DFT), Introduction
- dihedral angle, Dihedral angles
- display plots, Controlling which plots are displayed
- distance, Adjusting bond distances
- drag-and-drop between tools, Drag-and-drop between tools
E
- edit
-
- crystal, Crystal Cupboard
- script, Script Editor
- editor
-
- method, Method Editor
- effective potential, Inserting plots
- electrode, Atomic Manipulator, Creating two-probe systems, Cleaving a periodic system, The central region of a two-probe system, Changing the electrode, Atomic configuration plot
-
- cell, Cleaving a periodic system, Atomic configuration plot
- configuration, Atomic configuration plot
- requirements, Depth of the electrode cell
- translate, The central region of a two-probe system, Translating molecules and electrodes
- voltage, Method parameters
- electrode cell, Size and shape of the surface cell
- electrode/oxygen distance, Changing the structure of the interface
- electron density, Inserting plots
- electrostatic difference potential, Inserting plots
- electrostatic
interaction, Editing crystals and nanotubes, Cleaving a periodic system
- Energy Spectrometer, Energy Spectrometer
- equivalent bulk
-
- create, Creating two-probe systems, Creating equivalent bulk systems
- errors, Troubleshooting
- ethene, Setting the bond order
- exchange correlation functional, Method parameters
- export
-
- plot, Exporting and printing 3D plots
I
- icons, Description of the Virtual NanoLab Toolbar
- ideal angles, User adjustments
- import
-
- xyz file, Open various file formats
- inner layer separation, Changing the structure of the interface
- insert, The Molecule Cupboard
-
- atom, The Periodic Table tool, Creating molecules
- molecule, Creating molecules, The central region of a two-probe system
- plot, Inserting plots
- installation, Introduction, Troubleshooting
- insulating barrier, Magnetic Tunnel Junction Builder
- interface, The central region of a two-probe system
- interface deformation, Changing the structure of the interface
- internal coordinates, Creating molecules
- internal error, Troubleshooting
- ions
-
- building, Building ions – setting atomic charges
- isomer
-
- cis, Chirality and cis/trans isomers, Cis-trans isomers
- trans, Chirality and cis/trans isomers, Cis-trans isomers
- isosurface, Isosurface plot
- isovalue, Isosurface plot
- iteration, Method parameters
L
- lattice
-
- constant, Crystal Cupboard, Editing crystals and nanotubes, Changing the electrode, General Description
- defining, Defining the Lattice
- edit, Editing crystals and nanotubes
- parameters, Editing crystals and nanotubes
- setting
parameters, Editing lattice parameters
- vector, Editing crystals and nanotubes
- vectors, Crystal Cupboard, Editing crystals and nanotubes, Atomic configuration plot
- viewing, The BulkBuilder 3D-View
- lattice
basis, Defining the Basis atoms
- lattice coordinates, Setting coordinate types
- launching VNL
-
- Linux, Launching VNL
- Windows, Launching VNL
- layer separation, General Description
- layers, Cleaving a periodic system, Depth of the electrode cell, Changing the electrode, General Description
- license, Troubleshooting
M
- Magnetic Tunnel Junction Builder, Magnetic Tunnel Junction Builder
- magnification factor
-
- export plot, Exporting and printing 3D plots
- print, Camera settings
- manual, About this manual, The Toolbar menu, How to get more help
- material, General Description
- memory, Troubleshooting
- mesh cut-off, Method parameters
- methane, Methane
- method, Method Editor
-
- NanoLanguage Scripter tab, General Description
- Miller indices, Cleaving a periodic system, Size and shape of the surface cell
- mirror, Chirality and cis/trans isomers
- mixing, Method parameters
- modify plot, Modifying plots
- molecular atomic configuration, Atomic configuration plot
- Molecular Builder, Getting started — a small tutorial, Molecular Builder
- molecular configuration, Atomic Manipulator, The central region of a two-probe system
- Molecular Cupboard, The Molecule Cupboard
-
- filter, Filtering templates
- molecular sample, Creating two-probe systems, Atomic configuration plot
- molecule, Creating molecules
-
- delete, Creating molecules
- insert, Creating molecules, The central region of a two-probe system
- orientation, Creating molecules
- origin, Creating molecules
- rename, Creating molecules
- rotate, Creating molecules, Rotating molecules
- translate, Creating molecules, Translating molecules and electrodes
- molecule template, The Molecule Cupboard
- mouse commands, Translating molecules and electrodes, Rotating molecules, Rotating, panning, and zooming the camera
N
- NanoLanguage script, Data handling in VNL, NanoLanguage scripts
- NanoLanguage Scripter, Getting started — a small tutorial, NanoLanguage Scripter
- Nanoscope, Getting started — a small tutorial, Nanoscope, Inserting plots, Contour plot, Isosurface plot, Volume plot
- nanotube, Editing crystals and nanotubes, Cleaving a periodic system, Cleaving a nanotube, Nanotube Grower
-
- edit, Editing crystals and nanotubes
- in central region, The central region of a two-probe system
- padding factor, Editing crystals and nanotubes
- unit cell, Nanotube Grower
- Nanotube Grower, Nanotube Grower
- naphthalene, Fuse
- New, Starting the Molecular Builder
- non-equilibrium Green's functions (NEGF), Introduction
- normal direction
-
- cut plane, Contour plot
P
- padding factor, Editing crystals and nanotubes, Cleaving a periodic system, Method parameters
-
- nanotube, Cleaving a nanotube
- pan camera, Rotating, panning, and zooming the camera
- parameters, Introduction, Method
-
- Brillouin zone integration, Method parameters
- density of states, Analysis parameters
- edit, Script Editor
- energy bands, Analysis parameters
- energy contour, Method parameters
- geometry optimization, Configuration
- local density of states, Analysis parameters
- mixing, Method parameters
- projected Hamiltonian eigenstates, Analysis parameters
- projected Hamiltonian energy spectrum, Analysis parameters
- SCF iteration, Method parameters
- setting, Method Editor
- transmission coefficients, Analysis parameters
- transmission eigenstates, Analysis parameters
- transmission eigenvalues, Analysis parameters
- transmission spectrum, Analysis parameters
- pattern recognition, Autoadjustments
- performance, Size and shape of the surface cell, Camera settings
- periodic boundary conditions, Size and shape of the surface cell
- periodic system, Isosurface plot
- periodic table, Ammonia, The Periodic Table tool
- periodicity requirement, Cleaving a periodic system
- Phong shading, Changing the appearance of plots
- physical property, Analysis
- plot, Nanoscope, Modifying plots
-
- appearance, Changing the appearance of plots
- atomic configuration, Atomic configuration plot, Controlling which plots are displayed
- axes, Coordinate axes plot
- coloring, Coloring of three-dimensional plots
- contour, Contour plot
- delete, Modifying plots
- display, Controlling which plots are displayed
- export, Exporting and printing 3D plots, Exporting and printing 2D plots
- geometry, Atomic configuration plot
- hide, Creating two-probe systems, Atomic configuration plot, Controlling which plots are displayed
- insert, Inserting plots
- isosurface, Isosurface plot
- modify, Modifying plots
- print, Exporting and printing 3D plots, Exporting and printing 2D plots
- properties, Creating molecules, Nanoscope, Modifying plots
- rename, Modifying plots
- repetition, Contour plot, Isosurface plot, Atomic configuration plot
- sub-plot, Nanoscope, Atomic configuration plot
- title, Inserting plots
- visible, Creating two-probe systems, Atomic configuration plot, Controlling which plots are displayed
- volume, Volume plot
- Postscript, Exporting and printing 3D plots, Exporting and printing 2D plots
- primitive unit cell, Atomic configuration plot
- printing plots, Exporting and printing 3D plots, Exporting and printing 2D plots
-
- preferences, Camera settings
- problems, Troubleshooting
- program error, Troubleshooting, How to get more help
- properties
-
- camera, Camera settings
- plot, Creating molecules, Nanoscope, Inserting plots, Modifying plots
- pseudo bond, Setting the bond order
- Python, NanoLanguage scripts
R
- radius
-
- atoms, Atomic configuration plot
- bonds, Atomic configuration plot
- covalent, Adjusting bond distances, Atomic configuration plot
- van der Waals, Atomic configuration plot
- references
-
- Crystal Cupboard, Crystal Cupboard
- region widths, The central region of a two-probe system
- rename, Editing crystals and nanotubes
-
- molecule, Creating molecules
- plot, Modifying plots
- repetition
-
- atomic configuration, Atomic configuration plot
- electrode, General Description
- electrode atoms, Cleaving a periodic system, Atomic configuration plot
- plot, Contour plot, Isosurface plot
- surface atoms, Cleaving a periodic system
- replace atom, The Periodic Table tool
- representation
-
- surface, Changing the appearance of plots
- reset camera, Rotating, panning, and zooming the camera
- resolution
-
- export, Exporting and printing 3D plots, Exporting and printing 2D plots
- print, Camera settings
- restore calculation, Self-Consistent Calculation
- Result Browser, VNLFiles, Getting started — a small tutorial, Result Browser
- results
-
- visualize, Nanoscope
- rotate, Creating molecules, Rotating molecules
-
- camera, Rotating, panning, and zooming the camera
- molecule, Creating molecules, Rotating molecules
- rotation axis, Rotating molecules
S
- S1/S2, Size and shape of the surface cell
- SA/SB/SC directions, Cleaving a periodic system
- sample
-
- visualize, Nanoscope
- save configuration, Transfer of information between tools
- scattering region, Creating two-probe systems
- screening, The central region of a two-probe system
- script, NanoLanguage scripts
-
- generating, Getting started — a small tutorial, NanoLanguage Scripter
- scripter
-
- NanoLanguage, NanoLanguage Scripter
- search
-
- in Crystal Cupboard, Crystal Cupboard
- second order matrix elements, Cleaving a periodic system
- self-consistent calculation
-
- NanoLanguage Scripter tab, General Description
- set
-
- ideal angles, User adjustments
- shading, Volume plot, Changing the appearance of plots
- shallow electrode, Cleaving a periodic system
- shortcuts, Keyboard shortcuts.
- spin, Method parameters
- stacking fault, Cleaving a periodic system
- standard phase, Crystal Cupboard
- stereo, Camera settings
- Strukturbericht, Crystal Cupboard, Editing crystals and nanotubes
- style guidelines, About this manual
- sub-plot, Nanoscope, Atomic configuration plot
- substituents
-
- swap, Cis-trans isomers
- support, Troubleshooting, How to get more help
- surface, Cleaving a periodic system, General Description
-
- atoms, The central region of a two-probe system, Changing the electrode
- cell, Cleaving a periodic system
- configuration, Atomic configuration plot
- representation, Changing the appearance of plots
- vectors, Cleaving a periodic system
- surface cell, Size and shape of the surface cell
- surface layers, Size and shape of the surface cell
- surface unit vector, Size and shape of the surface cell
- surface vectors, Size and shape of the surface cell
- system type, Method Editor, Script Editor
T
- template
-
- adjust molecule using, Autoadjustments
- text editor, NanoLanguage scripts
- tool
-
- Atomic Manipulator, Atomic Manipulator
- Bulk Builder, Bulk Builder
- Crystal Cupboard, Crystal Cupboard
- editor, Script Editor
- Job Manager, Job Manager
- Magnetic Tunnel Junction Builder, Magnetic Tunnel Junction Builder
- method, Method Editor
- Molecular Builder, Molecular Builder
- NanoLanguage Scripter, NanoLanguage Scripter
- Nanoscope, Nanoscope, Inserting plots, Contour plot, Isosurface plot, Volume plot
- Nanotube Grower, Nanotube Grower
- Result Browser, Result Browser
- tool tips, The Toolbar menu
- toolbar, The VNL Toolbar
- tools, Description of the Virtual NanoLab Toolbar
- translate, Creating molecules, Translating molecules and electrodes
-
- electrode, The central region of a two-probe system, Translating molecules and electrodes
- molecule, Translating molecules and electrodes
- troubleshooting, Troubleshooting
- tube indices, Nanotube Grower
- tutorial, About this manual, The Toolbar menu, How to get more help
-
- basic introduction, Getting started — a small tutorial
- two center integral, Method parameters
- two sided lighting, Camera settings
- two-probe
-
- atomic configuration, Atomic configuration plot
- create, Atomic Manipulator
- system, Introduction, Editing crystals and nanotubes, Creating two-probe systems, Cleaving a periodic system, The central region of a two-probe system
U
- unit cell
-
- bulk, Crystal Cupboard, Editing crystals and nanotubes, Atomic configuration plot
- color, Changing the appearance of plots
- electrode, Cleaving a periodic system, Atomic configuration plot
- molecular, Editing crystals and nanotubes
- nanotube, Editing crystals and nanotubes, Nanotube Grower
- surface, Cleaving a periodic system
- user adjustment, Adjusting molecules
V
- van der Waals radius, Atomic configuration plot
- verbosity level, Self-Consistent Calculation
- Virtual NanoLab Toolbar, The VNL Toolbar
-
- description, Description of the Virtual NanoLab Toolbar
- icons, Description of the Virtual NanoLab Toolbar
- menu, The Toolbar menu
- visible plots, Creating two-probe systems, Controlling which plots are displayed
- visualize, Introduction
-
- geometry, Nanoscope
- results, Nanoscope
- VNL file, Data handling in VNL, VNLFiles
- VNLFile
-
- configuration, Result Browser
- volume plot, Volume plot
