Core components#

Sublattices#

class icet.core.sublattices.Sublattices(allowed_species, primitive_structure, structure, fractional_position_tolerance)[source]#

This class stores and provides information about the sublattices of a structure.

Note

As a user you will usually not interact directly with objects of this type.

Parameters:

  • allowed_species (List[List[str]]) – List of the allowed species on each site of the primitve structure. For example this can be the chemical_symbols from a cluster space.

  • primitive_structure (Atoms) – The primitive structure the allowed species reference to.

  • structure (Atoms) – The structure that the sublattices will be based on.

  • fractional_position_tolerance (float) – Tolerance applied when comparing positions in fractional coordinates.

property active_sublattices: List[Sublattice]#

List of the active sublattices.

property allowed_species: List[List[str]]#

Lists of the allowed species on each sublattice in order.

assert_occupation_is_allowed(chemical_symbols)[source]#

Asserts that the current occupation obeys the sublattices.

get_allowed_numbers_on_site(index)[source]#

Returns the allowed atomic numbers on the site.

Parameters:

index (int) – Lattice site index.

Return type:

List[int]

get_allowed_symbols_on_site(index)[source]#

Returns the allowed symbols on the site.

Parameters:

index (int) – Lattice site index.

Return type:

List[str]

get_sublattice_index_from_site_index(index)[source]#

Returns the index of the sublattice the index in the structure belongs to.

Parameters:

index (int) – Index of site in the structure.

Return type:

int

get_sublattice_sites(index)[source]#

Returns the sites that belong to the sublattice with the corresponding index.

Parameters:

index (int) – Index of the sublattice.

Return type:

List[int]

property inactive_sublattices: List[Sublattice]#

List of the active sublattices.

class icet.core.sublattices.Sublattice(chemical_symbols, indices, symbol)[source]#

This class stores and provides information about a specific sublattice. A sublattice is always supercell specific since it contains lattice indices.

Note

As a user you will usually not interact directly with objects of this type.

Parameters:

  • chemical_symbols (List[str]) – The allowed species on this sublattice.

  • indices (List[int]) – The lattice indices the sublattice consists of.

  • symbol (str) – String used to mark the sublattice.

property symbol#

Symbol representation of sublattice, i.e. A, B, C, etc.

Variable transformations#

icet.tools.variable_transformation.get_transformation_matrix(structure, full_orbit_list)[source]#

Determines the matrix that transforms the cluster functions in the form of spin variables, \(\sigma_i\in\{-1,1\}\), to their binary equivalents, \(x_i\in\{0,1\}\). The form is obtained by performing the substitution (\(\sigma_i=1-2x_i\)) in the cluster expansion expression of the predicted property (commonly the energy).

Parameters:

  • structure (Atoms) – Atomic configuration.

  • full_orbit_list (OrbitList) – Full orbit list.

Return type:

ndarray

icet.tools.variable_transformation.transform_parameters(structure, full_orbit_list, parameters)[source]#

Transforms the list of parameters, obtained using cluster functions in the form of of spin variables, \(\sigma_i\in\{-1,1\}\), to their equivalents for the case of binary variables, \(x_i\in\{0,1\}\).

Parameters:

  • structure (Atoms) – Atomic configuration.

  • full_orbit_list (OrbitList) – Full orbit list.

  • parameters (ndarray) – Parameter vector (spin variables).

Return type:

ndarray

Constituent strain#

class icet.tools.constituent_strain.KPoint(kpt, multiplicity, structure_factor, strain_energy_function, damping)[source]#

Class for handling each k point in a supercell separately.

Parameters:

  • kpt (ndarray) – k-point coordinates.

  • multiplicity (float) – Multiplicity of this k-point.

  • structure_factor (float) – Current structure associated with this k-point.

  • strain_energy_function (Callable[[float, List[float]], float]) – Function that takes a concentration and a list of parameters and returns strain energy.

  • damping (float) – Damping at this k-point in units of Ångstrom.

icet.tools.constituent_strain_helper_functions.redlich_kister(x, *coeffs)[source]#

Evaluate Redlich-Kister polynomial with coefficients coeff at point(s) x.

Parameters:

  • x (float) – Point in interval [0, 1] where polynomial should be evaluated.

  • coeffs (float) – Redlich-Kister coefficients, coeffs[0] (1 - 2x)^0 x (1 - x) + coeffs[1] * (1 - 2x)^1 x (1 - x) + ...

Return type:

float

icet.tools.constituent_strain_helper_functions.redlich_kister_vector(x, *coeffs)[source]#

Evaluate Redlich-Kister polynomial with coefficients coeff at points(s) x.

Parameters:

  • x (ndarray) – Array of points in interval [0, 1] where polynomial should be evaluated.

  • coeffs (float) – Redlich-Kister coefficients, coeffs[0] (1 - 2x)^0 x (1 - x) + coeffs[1] * (1 - 2x)^1 x (1 - x) + ...

Return type:

float

Configuration manager#

class mchammer.ConfigurationManager(structure, sublattices)[source]#

The ConfigurationManager owns and handles information pertaining to a configuration being sampled in a Monte Carlo simulation.

Note

As a user you will usually not interact directly with objects of this type.

Parameters:

  • structure (Atoms) – Configuration to be handled.

  • sublattices (Sublattices) – Sublattices used to define allowed occupations and handle related information.

get_flip_state(sublattice_index, allowed_species=None, allowed_sites=None)[source]#

Returns a site index and a new species for the site.

Parameters:

  • sublattice_index (int) – Index of sublattice from which to pick a site.

  • allowed_species (Optional[List[int]]) – List of atomic numbers for allowed species.

  • allowed_sites (Optional[List[int]]) – List of indices for allowed sites.

Return type:

Tuple[int, int]

get_occupations_on_sublattice(sublattice_index)[source]#

Returns the occupations on one sublattice.

Parameters:

sublattice_index (int) – Sublattice by index for which the occupations should be returned.

Return type:

List[int]

get_swapped_state(sublattice_index, allowed_species=None, allowed_sites=None)[source]#

Returns two random sites (first element of tuple) and their occupation after a swap (second element of tuple). The new configuration will obey the occupation constraints associated with the ConfigurationManager object.

Parameters:

  • sublattice_index (int) – Sublattice by index from which to pick sites.

  • allowed_species (Optional[List[int]]) – List of atomic numbers for allowed species.

  • allowed_sites (Optional[List[int]]) – List of indices for allowed sites.

Return type:

Tuple[List[int], List[int]]

is_swap_possible(sublattice_index, allowed_species=None)[source]#

Checks if a swap trial move is possible on a specific sublattice.

Parameters:

  • sublattice_index (int) – Index of sublattice to be checked.

  • allowed_species (Optional[List[int]]) – List of atomic numbers for allowed species.

Return type:

bool

property occupations: ndarray#

Occupation vector of the configuration (copy).

property structure: Atoms#

Atomic structure associated with configuration (copy).

property sublattices: Sublattices#

Sublattices of the configuration.

update_occupations(sites, species)[source]#

Updates the occupation vector of the configuration being sampled. This will change the state in both the configuration in the calculator and the configuration manager.

Parameters:

  • sites (List[int]) – Indices of sites of the configuration to change.

  • species (List[int]) – New occupations by atomic number.

Return type:

None