HotbitDirectory¶

class HotbitDirectory(path)¶

Constructor for the Hotbit directory parser.

Parameters:	path (str) – The path of the directory to read files from.

fillingMethod(element)¶

Parameters:	element (PeriodicTableElement) – The element for which to query the filling method.
Returns:	The method used for setting up the initial occupation for the given element.
Return type:	SphericalSymmetric | Anisotropic

onsiteSpinOrbitSplit(element)¶

Query the onsite spin-orbit split energies for a given element.

Parameters:	element (PeriodicTableElement) – The element for which to query the spin-orbit split energies.
Returns:	The onsite spin-orbit split for this element.
Return type:	PhysicalQuantity of type energy

onsiteSpinSplit(element)¶

Query the onsite spin-split energies for a given element.

Parameters:	element (PeriodicTableElement) – The element for which to query the spin splits.
Returns:	The onsite spin-split energies for this element as a square matrix of size n where n is the number of subshells of the given element.
Return type:	PhysicalQuantity of type energy

pairPotentials(configuration)¶

Query function for getting the pair potentials.

Parameters:	configuration (MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration) – The configuration defining which elements to load.
Returns:	The pair-potentials.
Return type:	list of PairPotential

setFillingMethod(element, filling_method)¶

Set the method used for setting up the initial occupation for the given element.

Parameters:	element (PeriodicTableElement) – The element for which to set the filling method. filling_method (SphericalSymmetric | Anisotropic) – The method used for setting up the initial occupation.

setOnsiteSpinOrbitSplit(element, split)¶

Set the onsite spin-orbit split energies for a given element in the configuration.

Parameters:	element (PeriodicTableElement) – The element for which to set the spin-orbit splits. split (PhysicalQuantity of type energy) – The onsite spin-split energies for this element as a square matrix of size n where n is the number of subshells of the given element.

setOnsiteSpinSplit(element, split)¶

Set the onsite spin split energies for a given element in the configuration.

Parameters:	element (PeriodicTableElement) – The element for which to set the spin splits. split (PhysicalQuantity of type energy) – The on-site spin-split energies for each subshell pair of the element.

setVacuumLevel(element, vacuum_level)¶

Set the energy shift of the vacuum level for a given element.

Parameters:	element (PeriodicTableElement) – The element for which to set the energy shift of the vacuum level. vacuum_level (PhysicalQuantity of type energy) – The energy shift of the vacuum level.

table(configuration)¶

Query function for getting the SlaterKosterTable representation of the parameter files in the directory.

Parameters:	configuration (MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration) – The configuration defining which elements to load.
Returns:	A SlaterKosterTable instance representing the parameter files in the directory.
Return type:	SlaterKosterTable

vacuumLevel(element)¶

Parameters:	element (PeriodicTableElement) – The element for which to query the energy shift of the vacuum level.
Returns:	The energy shift of the vacuum level for the given element.
Return type:	PhysicalQuantity of type energy

# Set up a graphene crystal
bulk_configuration = BulkConfiguration(
    bravais_lattice=Hexagonal(2.4612*Angstrom, 6.709*Angstrom),
    elements=[Carbon, Carbon],
    cartesian_coordinates=[[ 0.        ,  0.        ,  0.        ],
                         [ 1.2306    ,  0.71050145,  0.        ]]*Angstrom
    )

# setup slater-koster calculator with hotbit parameters

basis_set = HotbitDirectory("hotbit/standard")

pair_potentials = HotbitDirectory("hotbit/standard")

numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(4, 4, 1) )

calculator = SlaterKosterCalculator(
    basis_set=basis_set,
    pair_potentials=pair_potentials,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )
bulk_configuration.setCalculator(calculator)

initial_velocity = MaxwellBoltzmannDistribution(
        temperature=1000.0*Kelvin
    )

method = NVEVelocityVerlet(
        time_step=1.0*femtoSecond,
        initial_velocity=initial_velocity
    )

molecular_dynamics = MolecularDynamics(
        bulk_configuration,
        constraints=[],
        trajectory_filename='trajectory.nc',
        steps=50,
        log_interval=1,
        method=method
    )