
	Welcome to Atomistix ToolKit 2008.10

Atomistix ToolKit

Manual

Version 2008.10

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Table of Contents

Welcome to Atomistix ToolKit 2008.10
Introduction
Quick tour
Tutorials
Reference manual
- KohnSham module
- TwoProbe module
- Future module
- Consortia module
- File input/output
- Units
- PeriodicTable
- Core NanoLanguage elements
  - AtomicOrbitals — Available basis sets in ATK
  - basisSetParameters — Controls the basis set used on a global (all atoms) or per atom basis.
  - brillouinZoneIntegrationParameters — Controls the Brillouin zone sampling (i.e. number of k-points).
  - calculateAtomicForces — Calculates the atomic forces on each atom in the system.
  - calculateEffectivePotential — Calculates the real-space Kohn-Sham effective potential.
  - calculateElectronDensity — Calculates the real-space electron density.
  - calculateElectrostaticDifferencePotential — Calculates the real-space electrostatic difference potential.
  - calculateMullikenPopulation — Calculates the Mulliken population of each atom in the system.
  - calculateOptimizedAtomicGeometry — Find the optimized geometric configuration of a system.
  - calculateTotalEnergy — Calculates the total energy of a system.
  - eigenstateOccupationParameters — Controls the occupation of Kohn-Sham orbitals using a Fermi distribution.
  - electronDensityParameters — Specifies the mesh cut-off and whether or not (and to what degree) the atomic configuration should be considered as a spin-polarized system.
  - Exchange-Correlation functionals — Determines which approximation to use for the exchange-correlation functional.
  - executeSelfConsistentCalculation — Initiates a self-consistent calculation.
  - geometricOptimizationParameters — Parameters controlling the geometric optimization of an atomic configuration.
  - iterationControlParameters — Controls the end criteria for the self-consistent calculation.
  - iterationMixingParameters — Controls the mixing at the end of a cycle in the self-consistent calculation.
  - PeriodicAtomConfiguration — Used to represent a periodic arrangement of atoms which is not a crystal structure (e.g. electrodes, slabs etc.).
  - poissonEquationParameters — Parameters controlling the evaluation of the Poisson equation.
  - pseudoPotentialParameters — Specifies a custom pseudo-potential for a specific element.
  - runtimeParameters — Controls the filename used to store results from and the verbosity level of the self-consistent calculation.
  - Spin.Type — Used to distinguish between which part (Spin.Up, Spin.Down or both) that should be treated in a given calculation.
  - twoCenterIntegralParameters — Parameters for controlling evaluation of two-center integrals in ATK.
  - Bravais Lattices — The 14 Bravais lattices used to describe crystal structures.
  - addToSample — Adds an object (calculation result, atomic configuration, etc.) to a VNL input file.
  - nlPrint — Print the object in a nicely formatted way to screen or, more in general, to the standard output.
  - checkpointFilename — Tells the filename of the file into which results from the self-consistent calculation are stored.
  - readAtomicConfigurations — Returns the atomic configurations stored in a VNL input file.
  - restoreSelfConsistentCalculation — Restores results from a previously performed calculation.
  - setCheckpointFilename — Controls the name of the (NetCDF) file into which the results from a self-consistent calculation are stored. If a file name is not specified using this function, a NetCDF file is not written.
  - setVerbosityLevel — Controls the degree of output from ATK.
  - verbosityLevel — Tells the degree of output from ATK
  - VNLFile — Used to create and control I/O interaction with input files for VNL
  - BulkConfiguration — Used to construct a bulk system based on a crystal structure.
  - calculateEigenstateOccupations — Calculates the occupation of eigenstates for a molecule.
  - calculateEigenstates — Calculates eigenstates (Bloch states) for molecular and bulk systems.
  - calculateEnergyBands — Calculates the band structure of a bulk system.
  - calculateFermiEnergy — Calculates the Fermi energy for a molecular or bulk system.
  - calculateMolecularEnergySpectrum — Calculates the energy spectrum (eigenvalues) of a molecule.
  - KohnShamMethod — Represents the parameters that controls the density-functional electronic structure calculation of molecules and bulk systems.
  - MoleculeConfiguration — Used to create a single isolated molecule.
  - calculateCurrent — Calculates the ballistic electrical current through a two-probe system.
  - calculateDensityOfStates — Calculates the Density Of States (DOS) for a two-probe system.
  - calculateLocalDensityOfStates — Calculates the density of states (DOS) for atoms located in the central region of a two-probe system.
  - calculateProjectedHamiltonianEigenstates — Calculates the eigenstates of atoms in the central region.
  - calculateProjectedHamiltonianEnergySpectrum — Calculates the molecular-projected self-consistent Hamiltonian (MPSH) energy spectrum for atoms in the central region.
  - calculateTransmissionCoefficients — Calculates transmission coefficients for a two-probe system.
  - calculateTransmissionEigenstates — Calculates transmission eigenstates.
  - calculateTransmissionEigenvalues — Calculates transmission eigenvalues.
  - calculateTransmissionSpectrum — Calculates transmission spectrum for a two-probe system.
  - ElectrodeParameters — Defines calculation specific parameters for electrodes in a two-probe system.
  - energyContourIntegralParameters — Defines the complex contour integration
  - GatedTwoProbeMethod — Extends the TwoProbeMethod class to simulate a two-probe system with a gate electrode.
  - TwoProbeConfiguration — The TwoProbeConfiguration class is used to construct a two-probe system, which consist of two, not necessarily identical, semi-infinite electrodes and a central scattering region containing e.g. a molecule, an interface, or a nanotube.
  - TwoProbeMethod — The TwoProbeMethod class is used to represent parameters that control the combined density-functional electronic structure calculation and the non-equilibrium Green's function calculation of two-probe systems.
  - twoProbeAlgorithmParameters — Defines the parameters of the algorithm for the two-probe calculation.
  - calculateLinearResponseCurrent — Calculate the electrical current for a two-probe system for a given set of bias voltages using the linear-response approximation.
  - calculateSpinCurrent — Calculate the spin current for a two-probe system for a given set of bias voltages using the linear-response approximation.
  - calculateCollinearSpinTorque — Function for calculating the parallel spin torque for collinear spins.
Appendix
Index