Symbols
- 1D system, The Magnetic Tunnel Junction Builder
- 2,2-dimethyl propane, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- 3D contour plot, Using the NanoLanguage Scripter
- 3D grid structure, Using the NanoLanguage Scripter
- 3D preview windows, The Nanoscope
A
- A /B/C directions, One-dimensional linear chain
- ab-initio, Introduction
- accuracy, Linear chain – the electrodes
- accuracy
parameters, Introduction
- acetaldehyde, Acetaldehyde from ethanol by changing oxygen atom properties
- aligning a molecule with a surface, Linear chain – the central region
- allotropes, Periodic systems
- amino group, Current versus geometrical changes of a molecule
- Analysis tab, Using the NanoLanguage Scripter, Optimizing the lattice parameter of a bulk system, The Magnetic Tunnel Junction Builder
- analyzing data, Optimizing the lattice parameter of a bulk system
- anti-parallel, The Magnetic Tunnel Junction Builder
- anti-parallel
spin configuration, The Magnetic Tunnel Junction Builder
- Apply, Linear chain – the central region
- ATK, Introduction
- Atomic forces, Current versus geometrical changes of a molecule
- atomic interactions in the electrode
cell, Linear chain – the electrodes
- atomic
layer, The Magnetic Tunnel Junction Builder
- Atomic Manipulator, Introduction
-
- Show button, Current versus geometrical changes of a molecule
- Atomic
Manipulator tool, Linear chain – the electrodes
- Atomic Manipulator: Surface tab, Molecule between metal surfaces
- atomic
symbol, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Atomistix ToolKit (ATK), Introduction
- Au [111]
surfaces, Molecule between metal surfaces
- Autoadjust, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments, Methane without automatic adjustments
- automatic adjustment of the hybridization, Acetaldehyde from ethanol by changing oxygen atom properties
- automatic adjustments, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Available Quantities list, Using the NanoLanguage Scripter, Optimizing the lattice parameter of a bulk system, The Magnetic Tunnel Junction Builder
B
- Band Structure tab, Carbon nanotubes
- basis atoms, Molecule between metal surfaces
- basis set, The Magnetic Tunnel Junction Builder
- bcc Li crystal, Periodic systems
- biphenyl, Using the NanoLanguage Scripter
- biphenyl molecule, Using the NanoLanguage Scripter, Current versus geometrical changes of a molecule
- bond angle, Methane without automatic adjustments
- bond length, Using the Molecular Builder
- bond order, Using the Molecular Builder, Methane without automatic adjustments, Acetaldehyde from ethanol by changing oxygen atom properties
- bond
thickness, The Nanoscope
- boundary
conditions, Molecule between metal surfaces
- Brillouin
zone integration, The Magnetic Tunnel Junction Builder
- building the biphenyl molecule, Using the NanoLanguage Scripter
- Bulk Atomic Configuration, Periodic systems
- bulk lattice constant, Optimizing the lattice parameter of a bulk system
C
- calculation engine, Introduction
- calculation parameters, The Magnetic Tunnel Junction Builder
- camera, The Nanoscope
- camera context menu, The Nanoscope
- carbon atom, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- carbon atom insertion, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- carbon nanotube, Preface, Two-probe systems, Carbon nanotubes
- carbon nanotube (4,1), Carbon nanotubes
- carbon tetrachloride, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- central
region, Two-probe systems, Linear chain – the electrodes
- checkpoint
file, The Magnetic Tunnel Junction Builder
- Checkpoint Filename, The Magnetic Tunnel Junction Builder
- Checkpoint Filename
field., Current versus geometrical changes of a molecule
- chlorine, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- cleave, Linear chain – the electrodes, Molecule between metal surfaces
- cleaving plane, Molecule between metal surfaces
- CO bond, Acetaldehyde from ethanol by changing oxygen atom properties
- complex
molecular structures, Using the Molecular Builder
- computation
time, Current versus geometrical changes of a molecule
- computations at high bias voltage, Current versus geometrical changes of a molecule
- conductance as a function of the dihedral angle, Current versus geometrical changes of a molecule
- conductance of the magnetic tunnel
junction, The Magnetic Tunnel Junction Builder
- configuration, The VNL Toolbar
- configuration
file, The Magnetic Tunnel Junction Builder
- configuration tab, The Magnetic Tunnel Junction Builder
- Contour plot, Using the NanoLanguage Scripter
- convergence for systems under high bias voltages, Current versus geometrical changes of a molecule
- covalent radius, The Nanoscope
- Crystal Cupboard, Introduction, Periodic systems, Molecule between metal surfaces
- current as a function of the dihedral angle, Current versus geometrical changes of a molecule
- current versus geometrical changes of a molecule, Current versus geometrical changes of a molecule
D
- DABP molecular formula, Current versus geometrical changes of a molecule
- DABP molecule, Current versus geometrical changes of a molecule
- default basis set, Using the NanoLanguage Scripter
- default cell, Molecule between metal surfaces
- Delete Atom, Molecular systems
- delete molecule, Molecular systems
- Delete molecule using context
menu, Current versus geometrical changes of a molecule
- Delete new
molecule, Molecular systems
- density file, The Magnetic Tunnel Junction Builder
- density functional theory, Introduction
- density-functional theory (DFT), Introduction
- DFT method, Introduction
- Diagonal Mixing
Parameter, The Magnetic Tunnel Junction Builder
- diamino biphenyl, Current versus geometrical changes of a molecule
- dihedral angle, Methane without automatic adjustments
- Dihedral Angle field, Eclipsed ethane
- distance between chains, One-dimensional linear chain
- dithiol-benzene (DTB)
molecule, Molecule between metal surfaces
- double bond, Acetaldehyde from ethanol by changing oxygen atom properties
- DoubleZetaDoublePolarized, Optimizing the lattice parameter of a bulk system
- DoubleZetaPolarized, Optimizing the lattice parameter of a bulk system
- drag-and-drop from Molecular Builder, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- DTB, Molecule between metal surfaces
- DTB distance from the S atom to the surface, Molecule between metal surfaces
- DTB molecules separation, Molecule between metal surfaces
E
- Eigenstate
Occupation dialog, The Magnetic Tunnel Junction Builder
- electrode
constraint, The Magnetic Tunnel Junction Builder
- electrode movement, Linear chain – the central region
- electrode
surfaces, Linear chain – the central region
- electrode
temperature, The Magnetic Tunnel Junction Builder
- Electrode
Voltages, Current versus geometrical changes of a molecule
- electrodes, The Magnetic Tunnel Junction Builder
- electron ballistic current, Current versus geometrical changes of a molecule
- Electron density, Current versus geometrical changes of a molecule
- Electron-Density
dialog, The Magnetic Tunnel Junction Builder
- electronic current, Current versus geometrical changes of a molecule
- electronic structure, Introduction
- energy of biphenyl for some dihedral angles, Using the Method Editor tool with the NanoLanguage Scripter
- Energy Shift, Using the Method Editor tool with the NanoLanguage Scripter, Current versus geometrical changes of a molecule
- Energy-Contour
dialog, The Magnetic Tunnel Junction Builder
- ethane, Eclipsed ethane, Building ethanol using Join and the Molecule Cupboard
- ethane eclipsed, Eclipsed ethane
- ethane staggered, Eclipsed ethane
- ethanol, Building ethanol using Join and the Molecule Cupboard, Acetaldehyde from ethanol by changing oxygen atom properties
- examples directory, The Nanoscope
- Exchange Correlation Functional, Using the Method Editor tool with the NanoLanguage Scripter
- Exchange-Correlation-Functional dialog
, The Magnetic Tunnel Junction Builder
- executing a script, Using the NanoLanguage Scripter
- execution on a local system, The Magnetic Tunnel Junction Builder
- export
image, The Nanoscope
G
- Geometry Manager tool, Methane without automatic adjustments
-
- dihedral angle, Methane without automatic adjustments
- GGA.PBE, Using the Method Editor tool with the NanoLanguage Scripter
- global coordinate system, Linear chain – the central region
- global molecular orientation, Linear chain – the central region
- global
repetition, The Magnetic Tunnel Junction Builder
- gold bulk, Current versus geometrical changes of a molecule
- gold electrodes, Current versus geometrical changes of a molecule
- grayed out tabs, Optimizing the lattice parameter of a bulk system
- groups of atoms, Molecular systems
H
- help system, Going further with Virtual NanoLab
- heterogeneous, The Magnetic Tunnel Junction Builder
- History Steps, The Magnetic Tunnel Junction Builder
- hovering
mouse cursor over atom, Linear chain – the central region
- hybridization, Using the Molecular Builder
- hybridized carbon atom, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- hydrogen molecule, Preface, Molecular systems, Linear chain – the electrodes, Linear chain – the central region
- Hydrogen sulfide, p-benzene-dithiol from benzene and H2S
I
- importing a DTB molecule, Molecule between metal surfaces
- importing a molecule in Atomic Manipulator, Linear chain – the central region
- include other software application, The VNL Toolbar
- Initial
Scaled Spin radio button , The Magnetic Tunnel Junction Builder
- input
parameters, Introduction
- Insert and Join, p-benzene-dithiol from benzene and H2S
- Insert Atom, Molecular systems
- insert molecule, Molecular systems
- Insert
new molecule, Molecular systems
- inserting an atom, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- installation guide, Preface
- insulating thin layer, The Magnetic Tunnel Junction Builder
- integral lower
bound, The Magnetic Tunnel Junction Builder
- intensity-voltage curve, Current versus geometrical changes of a molecule
- interatomic distance in a hydrogen molecule, Molecular systems
- internal
coordinates, Linear chain – the central region
- iron-magnesium
oxide-iron, The Magnetic Tunnel Junction Builder
- isosurfaces, Using the NanoLanguage Scripter
- Iteration
Control, Using the Method Editor tool with the NanoLanguage Scripter
- Iteration-Control
dialog, The Magnetic Tunnel Junction Builder
- Iteration-Mixing
dialog, The Magnetic Tunnel Junction Builder
L
- last used
configuration, Molecular systems
- lattice constant, Periodic systems, Molecule between metal surfaces
- lattice parameter, Optimizing the lattice parameter of a bulk system, Periodic systems
- lattice parameter optimization, Optimizing the lattice parameter of a bulk system
- Lattice
tab, Optimizing the lattice parameter of a bulk system
- left/right surfaces, Linear chain – the electrodes
- Li (bcc) stable phase, Periodic systems
- Li (beta), Periodic systems
- Li-DTB system, Molecule between metal surfaces
- linear atomic chain, Two-probe systems
- Linear chain, Linear chain – the central region
-
- central
region, Linear chain – the central region
- linear chain electrodes, Molecule between metal surfaces
- linear chain of lithium atoms, One-dimensional linear chain
- lithium atoms, Linear chain – the electrodes
- lithium chain, Preface, Linear chain – the electrodes
- lithium
electrodes instead of gold, Molecule between metal surfaces
- local coordinate system, Linear chain – the central region
- local execution, Using the Method Editor tool with the NanoLanguage Scripter
- LogWindow, Using the NanoLanguage Scripter, Optimizing the lattice parameter of a bulk system
- low-temperature phases, Periodic systems
M
- magnesium oxide layer, The Magnetic Tunnel Junction Builder
- magnetic polarization, The Magnetic Tunnel Junction Builder
- magnetic tunnel junction, The Magnetic Tunnel Junction Builder
- Magnetic Tunnel Junction Builder, The Magnetic Tunnel Junction Builder
- main window of the
Molecular Builder, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- manual for Atomistix ToolKit, Going further with Virtual NanoLab
- Mesh cut-off, Using the NanoLanguage Scripter, Using the Method Editor tool with the NanoLanguage Scripter
- metal surfaces, Two-probe systems
- metallic nanotube, Carbon nanotubes
- methane, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Method Editor, Introduction, The NanoLanguage Scripter, Using the Method Editor tool with the NanoLanguage Scripter
- Method tab, Using the NanoLanguage Scripter, The Magnetic Tunnel Junction Builder
- methyl
group, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Miller indices, Molecule between metal surfaces
- Molecular Builder, Introduction, Using the Molecular Builder
-
- Angle field, Methane without automatic adjustments
- Bond Order, Methane without automatic adjustments
- clearing 3D view, Methane without automatic adjustments
- Distance field, Methane without automatic adjustments
- inserting a carbon atom, Methane without automatic adjustments
- inserting a hydrogen atom, Methane without automatic adjustments
- last selected atom, Methane without automatic adjustments
- Molecular Builder
icon, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Molecular Builder
tool, Using the Molecular Builder
- molecule between two metal surfaces, Linear chain – the central region, Molecule between metal surfaces
- Molecule Cupboard tool, Building ethanol using Join and the Molecule Cupboard
- molecule of experimental interest, Current versus geometrical changes of a molecule
- molecule
origin, Linear chain – the central region
- molecules, Molecular systems
- monovalent hydrogen atom, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- Mulliken population, Current versus geometrical changes of a molecule
N
- NanoLanguage script, Introduction, The VNL Toolbar, Using the NanoLanguage Scripter, Linear chain – the central region, The Magnetic Tunnel Junction Builder
- NanoLanguage Scripter, Introduction, The VNL Toolbar, The NanoLanguage Scripter, The Magnetic Tunnel Junction Builder
- NanoLanguage Scripter tutorial, Using the NanoLanguage Scripter
- NanoLanguageScript [Finished], Optimizing the lattice parameter of a bulk system
- NanoLanguageScript [Running], Optimizing the lattice parameter of a bulk system
- NanoLanguageScript [Waiting], Optimizing the lattice parameter of a bulk system
- Nanoscope, Introduction, The Nanoscope
-
- context menu, The Nanoscope
- Nanoscope tool, The Nanoscope
- nanotube cleave, Creating a nanotube two-probe system
- Nanotube Grower, Carbon nanotubes
- nanotube two-probe system, Creating a nanotube two-probe system
- nanotubes as electrodes, Creating a nanotube two-probe system
- Naphthalene, Naphthalene by fusing of two benzene molecules
- neglected atomic interactions, Linear chain – the electrodes
- neglected interaction between chains, One-dimensional linear chain
- non-equilibrium Green's functions, Introduction
- non-equilibrium Green's functions (NEGF), Introduction
- NOTE (in Atomic
Manipulator), Linear chain – the electrodes
- number of surface
layers, Linear chain – the electrodes
- numerical methods, Introduction
P
- p-benzene-dithiol, p-benzene-dithiol from benzene and H2S
- Padding Factor, Creating a nanotube two-probe system
- pan, Molecular systems
- pan camera, The Nanoscope
- parabolic fit, Optimizing the lattice parameter of a bulk system
- parallel, The Magnetic Tunnel Junction Builder
- parallel
spin configuration, The Magnetic Tunnel Junction Builder
- parameters for the DFT calculation, Optimizing the lattice parameter of a bulk system
- perfect carbon nanotube, Carbon nanotubes, Creating a nanotube two-probe system
- periodic boundary conditions, Molecule between metal surfaces
- periodic boundary
conditions in the transverse plane, Creating a nanotube two-probe system
- periodic systems, Periodic systems
- Periodic Table
tool, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- physical properties, Introduction, Optimizing the lattice parameter of a bulk system
- physical quantities, Optimizing the lattice parameter of a bulk system
- positioning a molecule between electrodes, Linear chain – the central region
- positioning mouse over an atom, Linear chain – the central region
- potential energy surface, Using the Method Editor tool with the NanoLanguage Scripter
- predefined crystals, Periodic systems
- primitive lattice vectors, Periodic systems
- primitive surface vectors SA and SB, Molecule between metal surfaces
- print image, The Nanoscope
- Properties context menu, Molecule between metal surfaces
- Properties dialog, The Nanoscope, Periodic systems
R
- real axis
infinitesimal, The Magnetic Tunnel Junction Builder
- Real Space Electron Density, Using the NanoLanguage Scripter
- RealSpaceDensity, The Magnetic Tunnel Junction Builder
- relaxed H molecule between
Li chains, Linear chain – the central region
- rename, AM context menu, Molecule between metal surfaces
- Repetition, Periodic systems
- reset the 3D-View, Methane without automatic adjustments
- Result Browser, Introduction
- Result Browser tool, The VNL Toolbar, Using the NanoLanguage Scripter
- right electrode, Linear chain – the central region
- right electrode positioning, Molecule between metal surfaces
- rotate camera angle, The Nanoscope
- rotate dialog box, Linear chain – the central region
- rotate from
the context menu, Linear chain – the central region
- rotating molecule, Linear chain – the central region
- rotating molecules in Atomic Manipulator, Linear chain – the central region
- rotation, Molecular systems
- running a script, Using the Method Editor tool with the NanoLanguage Scripter
S
- S atoms in the DTB
molecule, Molecule between metal surfaces
- Save
button, The Magnetic Tunnel Junction Builder
- scattering
region, The Magnetic Tunnel Junction Builder
- screening layers, Linear chain – the electrodes, Molecule between metal surfaces
-
- convergence, Linear chain – the electrodes
- screening length, Linear chain – the electrodes
- script
name, Optimizing the lattice parameter of a bulk system
- scripts in one single batch, Optimizing the lattice parameter of a bulk system
- second-order matrix elements, Molecule between metal surfaces
- Selected Quantities list, Using the NanoLanguage Scripter, Optimizing the lattice parameter of a bulk system, The Magnetic Tunnel Junction Builder
- Self-Consistent Calculation tab, The Magnetic Tunnel Junction Builder
- semi-metallic, Carbon nanotubes
- setting dihedral angles, Eclipsed ethane
- setting
properties, The Magnetic Tunnel Junction Builder
- setting
up a biphenyl molecule, Using the NanoLanguage Scripter
- Si (alpha) 5.0(1).vnl, Optimizing the lattice parameter of a bulk system
- Si bulk files, Optimizing the lattice parameter of a bulk system
- silane, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- silicon bulk crystal, Using the Method Editor tool with the NanoLanguage Scripter
- silicon
bulk system, Optimizing the lattice parameter of a bulk system
- simple batch
queue, The Magnetic Tunnel Junction Builder
- simple job queue, Current versus geometrical changes of a molecule
- size of the
atom, The Nanoscope
- sp2, Acetaldehyde from ethanol by changing oxygen atom properties
- sp3, Acetaldehyde from ethanol by changing oxygen atom properties
- sp3 hybridization, Methane, silane, carbon tetrachloride, and 2,2-dimethyl propane with automatic adjustments
- specify basis set by element
type, Using the NanoLanguage Scripter, Current versus geometrical changes of a molecule
- spin, The Magnetic Tunnel Junction Builder
- spin polarization, The Magnetic Tunnel Junction Builder
- spin polarized
transport, The Magnetic Tunnel Junction Builder
- square of the cosine of the dihedral angle, Current versus geometrical changes of a molecule
- stacking fault, Molecule between metal surfaces
- stacking sequence ABC, Molecule between metal surfaces
- Store Results in VNL File, checkbox, The Magnetic Tunnel Junction Builder
- storing a two-probe configuration, Linear chain – the central region
- style guidelines, Preface
- suggested accuracy parameters, Using the Method Editor tool with the NanoLanguage Scripter
- support, Going further with Virtual NanoLab
- surface atoms, Linear chain – the electrodes
- surface cell, Molecule between metal surfaces
- surface from a bulk
crystal, Linear chain – the electrodes
- surface
layer, The Magnetic Tunnel Junction Builder
- surface layers, Linear chain – the electrodes
- surface regions too wide, Linear chain – the electrodes
- Surface tab, Linear chain – the electrodes
- surface unit cell, Molecule between metal surfaces
- surface unit vectors, Molecule between metal surfaces
- Surface Vector 1 (S1), Current versus geometrical changes of a molecule
- Surface Vector 2 (S2), Current versus geometrical changes of a molecule
- surface vectors S1 and S2, Molecule between metal surfaces
- surface vectors SA and SB, Molecule between metal surfaces
- system type, Optimizing the lattice parameter of a bulk system
T
- template for a linear
chain, One-dimensional linear chain
- templates, Periodic systems
- Terminated Normally, Optimizing the lattice parameter of a bulk system
- tetragonal lattices, One-dimensional linear chain
- tetragonal Li unit cell, Linear chain – the central region
- text editor, The VNL Toolbar
- thiol group, p-benzene-dithiol from benzene and H2S
- tight-binding band structure, Carbon nanotubes
- Tolerance, Using the Method Editor tool with the NanoLanguage Scripter
- Total energy, Optimizing the lattice parameter of a bulk system, Current versus geometrical changes of a molecule, The Magnetic Tunnel Junction Builder
- total energy calculation, Using the NanoLanguage Scripter
- Translate, Linear chain – the central region
- Translate
dialog, Linear chain – the central region
- translation
operation, Linear chain – the central region
- transmission spectrum, Current versus geometrical changes of a molecule, The Magnetic Tunnel Junction Builder
- transmission spectrum accuracy, Linear chain – the electrodes
- transport direction, Molecule between metal surfaces, The Magnetic Tunnel Junction Builder
- transport properties, Introduction
- tube indices, Carbon nanotubes
- tunneling
barrier, The Magnetic Tunnel Junction Builder
- tutorial, Preface
- two-probe systems, Two-probe systems
- Two-Probe tab, Linear chain – the electrodes
- TwoProbe-Algorithm dialog, The Magnetic Tunnel Junction Builder
V
- valence electrons, Molecule between metal surfaces
- virtual experiments, Introduction
- Virtual NanoLab, Preface
- Visible
option, Molecule between metal surfaces
- VNL
Toolbar, The VNL Toolbar
- VNL tools, The VNL Toolbar
- VNLFile, The VNL Toolbar, Using the NanoLanguage Scripter, Optimizing the lattice parameter of a bulk system
- VNLFile Name, Current versus geometrical changes of a molecule, The Magnetic Tunnel Junction Builder
- volume plots, Using the NanoLanguage Scripter
