SlaterKosterCalculator¶

class SlaterKosterCalculator(basis_set, pair_potentials=None, charge=None, numerical_accuracy_parameters=None, iteration_control_parameters=None, poisson_solver=None, checkpoint_handler=None, spin_polarization=None, fixed_spin_moment=None, dynamical_matrix_parameters=None, algorithm_parameters=None, hamiltonian_derivatives_parameters=None, parallel_parameters=None)¶

Class for representing calculations using a Slater-Koster tightbinding model for configurations of the type MoleculeConfiguration and BulkConfiguration.

Parameters:

basis_set (SlaterKosterTable | DFTBDirectory | HotbitDirectory) – An object describing the basis set used for the SlaterKoster calculation.
pair_potentials (DFTBDirectory | HotbitDirectory | list of PairPotential) – The repulsive pair potentials used for total energy and force calculations
Default: No pair potential
charge (float) – The charge of the system; a charge of -1 corresponds to one extra electron.
Default: 0.0

numerical_accuracy_parameters (NumericalAccuracyParameters) –

The NumericalAccuracyParameters used for the self-consistent SlaterKoster calculation.
Default:

NumericalAccuracyParameters(
    density_mesh_cutoff=10.0*Hartree,
    k_point_sampling=MonkhorstPackGrid(1, 1, 1),
    radial_step_size=0.01*Angstrom,
    density_cutoff=1.0e-6,
    interaction_max_range=10.0*Angstrom,
    number_of_reciprocal_points=1024,
    reciprocal_energy_cutoff=1250.0*Hartree,
    occupation_method=FermiDirac(300.0*Kelvin))

iteration_control_parameters (IterationControlParameters) – The IterationControlParameters used for the self-consistent SlaterKoster calculation. For non-self-consistent calculations set this parameter to NonSelfconsistent.
Default: NonSelfconsistent
poisson_solver (DirectSolver | MultigridSolver | FastFourierSolver | FastFourier2DSolver) – The Poisson solver used to determine the electrostatic potential.
Default: Configuration dependent. FastFourierSolver for a BulkConfiguration without any metallic or dielectric SpatialRegion.
checkpoint_handler (CheckpointHandler) – The CheckpointHandler used for specifying the save-file and the time interval. between saving the calculation during the SCF-loop.
Default: A default CheckpointHandler object.
spin_polarization (Unpolarized | Polarized | Noncollinear | SpinOrbit) – Flag indicating if the calculation is spin-polarized or not.
Default: Unpolarized
fixed_spin_moment (float | False) – Total spin moment (per unit cell) to use, defined as \(\Delta N = N_\up - N_\down\), where \(N_up\) and \(N_down\) are the number of electrons in the Up and Down spin channels, respectively. When specified the spin moment will be fixed at the given value by introducing separate Fermi levels for the Up and Down spin channels. Can only be specified when doing a calculation with polarized spin. If set to False the spin moment will not be fixed - a single Fermi level is used.
Default: False
dynamical_matrix_parameters (not used) –
Deprecated: from v2015, see the DynamicalMatrix analysis object.

algorithm_parameters (AlgorithmParameters) –

The AlgorithmParameters used for calculating the density matrix.
Default:

AlgorithmParameters(
    density_matrix_method=DiagonalizationSolver(),
    store_grids=True,
    store_basis_on_grid=Automatic,
    store_energy_density_matrix=Automatic,
    scf_restart_step_length=0.1*Angstrom,
    use_symmetries=False)

hamiltonian_derivatives_parameters (not used) –
Deprecated: from v2015, see the HamiltonianDerivatives analysis object.

parallel_parameters (ParallelParameters) –

The parameters used to control parallelization options.
Default:

ParallelParameters(
    processes_per_neb_image=None,
    processes_per_individual=None,
    processes_per_bias_point=None,
    processes_per_saddle_search=1)

algorithmParameters()¶

Returns:: The algorithm parameters.
Return type:: AlgorithmParameters

basisSet()¶

Returns:: The basis set associated with the Hamiltonian parametrization.
Return type:: BasisSet

charge()¶

Returns:: The charge of the system.
Return type:: float

checkpointHandler()¶

Returns:: The CheckpointHandler used for specifying the save-file and the time interval. between saving the calculation during the scf-loop.
Return type:: CheckpointHandler

dynamicalMatrixParameters()¶: This method is deprecated.

fixedSpinMoment()¶

Get the fixed spin moment.

Returns:: The fixed spin moment or False if the spin moment is not held fixed.
Return type:: float | False

hamiltonianDerivativesParameters()¶: This method is deprecated.

hamiltonianParametrization()¶

Returns:: The Hamiltonian parametrization associated with a semi-empirical calculator.
Return type:: SemiEmpiricalHamiltonianParametrization

isConverged()¶

Returns:: True when the call to “update()” resulted in a converged SCF loop.
Return type:: bool

iterationControlParameters()¶

Returns:: The IterationControlParameters used for a self-consistent calculation. For non-self-consistent calculations this parameter is NonSelfconsistent.
Return type:: IterationControlParameters

metatext()¶

Returns:: The metatext of the object or None if no metatext is present.
Return type:: str | None

numberOfSpins()¶

Returns:: The number of spins.
Return type:: int

numericalAccuracyParameters()¶

Returns:: The NumericalAccuracyParameters used for the self-consistent Huckel calculation.
Return type:: NumericalAccuracyParameters

pairPotentials()¶

Returns:: The repulsive pair potentials used for total energy and force calculations.
Return type:: PairPotential

parallelParameters()¶

Returns:: The parameters used to control parallelization options.
Return type:: ParallelParameters

poissonSolver()¶

Returns:: The Poisson solver used to determine the electrostatic potential.
Return type:: DirectSolver | MultigridSolver | FastFourierSolver | FastFourier2DSolver

setBasisSet(basis_set)¶

Set the basis set.

Parameters:: basis_set (SlaterKosterTable | DFTBDirectory | HotbitDirectory) – An object describing the basis set used for the calculation.

setCheckpointHandler(checkpoint_handler)¶

Set the the checkpoint handler.

Parameters:: checkpoint_handler (CheckpointHandler) – The CheckpointHandler used for specifying the save-file and the time interval. between saving the calculation during the scf-loop.

setHamiltonianParametrization(hamiltonian_parametrization)¶

Set and check the Hamiltonian parametrization.

Parameters:: hamiltonian_parametrization (HamiltonianParametrization) – An object describing the Hamiltonian parametrization for the semi-empirical calculation.

setIterationControlParameters(iteration_control_parameters)¶

Set the iteration control parameters.

Parameters:: iteration_control_parameters (IterationControlParameters) – The IterationControlParameters used for a self-consistent calculation. For non-self-consistent calculations this parameter is NonSelfconsistent.

setMetatext(metatext)¶

Set a given metatext string on the object.

Parameters:: metatext (str | None) – The metatext string that should be set. A value of “None” can be given to remove the current metatext.

setNumericalAccuracyParameters(numerical_accuracy_parameters)¶

Set the numerical accuracy parameters.

Parameters:: numerical_accuracy_parameters (NumericalAccuracyParameters) – The NumericalAccuracyParameters used for the self-consistent Huckel calculation.

setPairPotentials(pair_potentials)¶

Set the pair potentials.

Parameters:: pair_potentials (PairPotential) – The repulsive pair potentials used for total energy and force calculations.

setParallelParameters(parallel_parameters)¶

Set the parallel paramters.

Parameters:: parallel_parameters (ParallelParameters) – The parameters used to control parallelization options.

setPoissonSolver(poisson_solver)¶

Set the poisson solver.

Parameters:: poisson_solver (DirectSolver | MultigridSolver | FastFourierSolver | FastFourier2DSolver) – The Poisson solver used to determine the electrostatic potential.

setSpinPolarization(spin_polarization)¶

Set the spin polarization.

Parameters:: spin_polarization (Unpolarized | Polarized | Noncollinear | SpinOrbit) – Flag indicating if the calculation is spin-polarized or not.

spinPolarization()¶

Returns:: Flag indicating if the calculation is spin-polarized or not.
Return type:: Unpolarized | Polarized | Noncollinear | SpinOrbit

uniqueString()¶: Return a unique string representing the state of the object.

upgrade(configuration)¶: Private method for updating the calculator from the configuration, if it is possible. @private

versionUsed()¶

Returns:: The version of ATK used to update the calculator.
Return type:: str

Attention

The SlaterKosterCalculator is being deprecated. Use the SemiEmpiricalCalculator with the SlaterKosterHamiltonianParametrization instead.

Usage Examples¶

Define a spin polarized SlaterKosterCalculator with a Carbon pi model

# Generate a basis set for a Carbon p-p Pi model
# The p-p Pi model is described using s orbitals
# Parameters from: Hancock et. al., J. Low Temp Phys. 153, 393 (2008)
carbon_onsite = SlaterKosterOnsiteParameters(
    element=Carbon,
    angular_momenta=[0],
    occupations=[1],
    ionization_potential=[0.0]*eV,
    onsite_hartree_shift=ATK_U(Carbon, ['2p']),
    onsite_spin_split=ATK_W(Carbon, ['2p'])
    )

# Specify the distances for which the matrix elements are specified
distances = [1.422, 2.463 ,2.844, 3.1]*Ang

# Specify the p-p Pi matrix elements
pp_pi = [[-2.7], [-0.2], [-0.18], [0.0]]*eV
Carbon_Basis = SlaterKosterTable(
    carbon_carbon_sss=zip(distances,pp_pi),
    carbon=carbon_onsite)
    calculator=SlaterKosterCalculator(basis_set = Carbon_Basis,
    spin_polarization=True
    )

Restart a Slater-Koster calculation using the self-consistent state from a previous calculation

# Read in the BulkConfiguration with the old SCF state
old_calculation=nlread("filename.nc",BulkConfiguration)[0]

# Define the BulkConfiguration with similar number of atoms
new_calculation=BulkConfiguration(...)

# extract the old calculator
old_calculator = old_calculation.calculator()

# make a clone of the old calculator
new_calculator = old_calculator()

# Attach the calculator and use the old initial state
new_calculation.setCalculator(new_calculator, initial_state=old_calculation)

Notes¶

For the details of the Slater-Koster model, see the chapter on Semi Empirical.