DefectDiffusionRates¶

class DefectDiffusionRates(defect_diffusion_table)¶

defect_diffusion_table, Usually

Columns:

initial defect (NamedPointDefect) final defect (NamedPointDefect) best_final defect (NamedPointDefect) [not used] initial cpdc (ChargedPointDefectConfiguration) [not used] final cpdc (ChargedPointDefectConfiguration) [not used] neb (single path from initial defect to final) diffusivity (DefectDiffusivity) (optional).

Parameters:: defect_diffusion_table (Table) – The defect diffusion table.

static calculateDiffusivity(defect_diffusivity, parameters_store=None)¶

Calculate the macroscopic diffusivity of both defects forming the endpoints of the supplied NEB.

Parameters:

defect_diffusivity (DefectDiffusivity) – The defect diffusivity.
parameters_store (Store) – The parameters store.

Returns:

The calculated diffusivities of the initial and final defect.

Return type:

tuple of (initial diffusivity, final diffusivity)

calculateRateAndTransitionMatrix(temperature=None, defect_type=None, enable_finite_size_corrections=False, include_vibrations=False, assumed_transition_prefactor=PhysicalQuantity(10000000000000.0, 1 / s))¶

Calculate the rate matrix and discrete-time transition matrix.

Parameters:

temperature (PhysicalQuantity of type temperature) – The temperature at which the diffusivity should be calculated.
Default: 300 * Kelvin.
defect_type (DeepLevelDefect | ShallowAcceptor | ShallowDonor) – The assumption of the type of defect to use for aligning the transition levels in the band gap calculated with band_gap_calculator. Note that this parameter only has an effect if band_gap_calculator is different from formation_energy_calculator.
Default: DeepLevelDefect.
enable_finite_size_corrections (bool) – Whether to include finite size corrections for the supercell in the calculation of the formation energy.
Default: False.
include_vibrations (bool) – Whether vibrational terms are included, if available. That includes the migration entropy, harmonic prefactor and vibrational contribution to the internal energy.
Default: False.
assumed_transition_prefactor (PhysicalQuantity of type frequency) – The assumed prefactor for this transition. This parameter is only used if include_vibrations is False.
Default: 10**13 * Second**(-1)

Returns:

The rate matrix and transition matrix.

Return type:

tuple of (numpy array, PhysicalQuantity of type frequency)

static connectionName(initial_defect_name, final_defect_name)¶

The name of the connection

Parameters:

initial_defect_name (str) – Name of initial defect.
final_defect_name (str) – Name of final defect.

Returns:

name of connection.

Return type:

str

createMapping()¶

Create mapping from defect name to specific image of NEB with the lowest forward barrier.

Returns:: The mapping.
Return type:: dict

graph()¶

Create the graph.

Returns:: The network graph.
Return type:: networkx.Graph

hasDiffusivity()¶

Returns:: True, then the DefectDiffusionRates object has a table with DefectDiffusivity.
Return type:: bool

hasVibrations()¶

Returns:: True, then the all DefectDiffusivity objects have vibrational corrections.
Return type:: bool

nodeOrEdgeObject(name)¶

The image of the defect with the name.

Parameters:: name (str) – Name of defect or the path between defects.
Returns:: The requested configuration or the NudgedElasticBand of the connection.
Return type:: MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration | NudgedElasticBand

tableInfo(parameters_store=None)¶

Generate the table info.

Parameters:: parameters_store (Store) – The parameters store.
Returns:: The table info.
Return type:: list of dict

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

Notes¶

The DefectDiffusionRates object calculates the final diffusion network and diffusivities resulting from a series of defect diffusion calculations. The object is created by supplying a table of defects, defect configurations, NEB and optionally the DefectDiffusivity object for each transition. These resulting object can then be visualized in the Defect Diffusion Rates Analyzer.