SemiEmpiricalCalculator¶
- class SemiEmpiricalCalculator(hamiltonian_parametrization, 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, algorithm_parameters=None, parallel_parameters=None)¶
Class for representing calculations using semi-empirical models for configurations of the type
MoleculeConfiguration
andBulkConfiguration
.- Parameters:
hamiltonian_parametrization (
HuckelHamiltonianParametrization
|SlaterKosterHamiltonianParametrization
|NRLHamiltonianParametrization
) – An object describing the Hamiltonian parametrization for the semi-empirical calculation.pair_potentials (
PairPotential
) – The repulsive pair potentials used for total energy and force calculations. Default: No pair potentialcharge (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 semi-empirical 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
) – TheIterationControlParameters
used for the self- consistent semi-empirical calculation. For non-self-consistent calculations set this parameter toNonSelfconsistent
. Default:NonSelfconsistent
.poisson_solver (
DirectSolver
|MultigridSolver
|FastFourierSolver
|FastFourier2DSolver
) – The Poisson solver used to determine the electrostatic potential. Default: Configuration dependent.FastFourierSolver
for aBulkConfiguration
without any metallic or dielectricSpatialRegion
.checkpoint_handler (
CheckpointHandler
) – TheCheckpointHandler
used for specifying the save-file and the time interval. between saving the calculation during the scf-loop. Default: A defaultCheckpointHandler
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 toFalse
the spin moment will not be fixed - a single Fermi level is used. Default:False
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)
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:
- basisSet()¶
- Returns:
The basis set associated with the Hamiltonian parametrization.
- Return type:
- 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:
- 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
- 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 isNonSelfconsistent
.- Return type:
- 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:
- pairPotentials()¶
- Returns:
The repulsive pair potentials used for total energy and force calculations.
- Return type:
- parallelParameters()¶
- Returns:
The parameters used to control parallelization options.
- Return type:
- poissonSolver()¶
- Returns:
The Poisson solver used to determine the electrostatic potential.
- Return type:
DirectSolver
|MultigridSolver
|FastFourierSolver
|FastFourier2DSolver
- setCheckpointHandler(checkpoint_handler)¶
Set the the checkpoint handler.
- Parameters:
checkpoint_handler (
CheckpointHandler
) – TheCheckpointHandler
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
) – TheIterationControlParameters
used for a self-consistent calculation. For non-self-consistent calculations this parameter isNonSelfconsistent
.
- 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
) – TheNumericalAccuracyParameters
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
Usage Examples¶
Perform a self-consistent semi-empirical calculation for a maximum of 20 SCF steps by setting the IterationControlParameters.
iteration_control_parameters = IterationControlParameters(
max_steps=20,
)
# In this example, we use a default Huckel-type Hamiltonian parametrization.
hamiltonian_parametrization = HuckelHamiltonianParametrization()
calculator = SemiEmpiricalCalculator(
hamiltonian_parametrization=hamiltonian_parametrization,
iteration_control_parameters=iteration_control_parameters,
)
Restart a semi-empirical calculation using the self-consistent state from a previous calculation
# Read in the BulkConfiguration with the old SCF state.
old_calculation = nlread('filename.hdf5', BulkConfiguration)[0]
# Define the BulkConfiguration with the same number of atoms and the same elements.
new_calculation = BulkConfiguration(...)
# Define the 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 usage and details of the different Hamiltonian parametrizations, see HuckelHamiltonianParametrization, SlaterKosterHamiltonianParametrization and NRLHamiltonianParametrization.
Default is that the semi-empirical calculation is non-self-consistent. To make it self-consistent you must set the IterationControlParameters.