aim2dat.strct.ext_analysis¶

Methods acting on a Structure object to calculate structural properties and features.

Submodules¶

Package Contents¶

Functions¶

aim2dat.strct.ext_analysis.calculate_acsf_descriptor(structure: aim2dat.strct.strct.Structure, r_cut: float = 7.5, g2_params: list = None, g3_params: list = None, g4_params: list = None, g5_params: list = None, elements: list = None, periodic: bool = False, sparse: bool = False, dscribe_n_jobs: int = 1, dscribe_only_physical_cores: bool = False) → list[float][source]¶

Calculate ACSF descriptor as defined in doi:10.1063/1.3553717. This method is based on the implementations of the dscribe python package.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_cut (float) – Cutoff value.

• g2_params (np.array) – List of pairs of eta and R_s values for the G^2 functions.

• g3_params (np.array) – List of kappa values for the G^3 functions.

• g4_params (np.array) – List of triplets of eta, zeta and lambda values for G^4 functions.

• g5_params (np.array) – List of triplets of eta, zeta and lambda values for G^5 functions.

• elements (list) – List of atomic numbers or chemical symbols.

• periodic (bool) – Whether to consider periodic boundary conditions.

• sparse (bool) – Whether to return a sparse matrix or a dense array.

• dscribe_n_jobs (int) – Number of jobs used by dscribe to calculate the interaction matrix.

• dscribe_only_physical_cores (bool) – Whether to only use physicsl cores.

Returns:¶

list – ACSF descriptor.

aim2dat.strct.ext_analysis.calculate_ffingerprint_order_p(structure: aim2dat.strct.strct.Structure, r_max: float = 15.0, delta_bin: float = 0.005, sigma: float = 0.05, distinguish_kinds: bool = False) → tuple[float, list[float]][source]¶

Calculate order parameters for the total structure and for each individual site.

The calculation is based on equation (5) in doi:10.1016/j.cpc.2010.06.007.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

• delta_bin (float (optional)) – Bin size to descritize the function in angstrom.

• sigma (float (optional)) – Smearing parameter for the Gaussian function.

• distinguish_kinds (bool (optional)) – Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as different elements if True.

Returns:¶

• total_order_p (float) – Order parameter of the structure.

• atomic_fingerprints (list) – List of order parameters for each atomic site.

aim2dat.strct.ext_analysis.calculate_interaction_matrix(structure: aim2dat.strct.strct.Structure, matrix_type: str = 'coulomb', n_atoms_max: int = None, enforce_real: bool = False, permutation: str = 'eigenspectrum', sigma: float = None, seed: int = None, sparse: bool = False, ewald_accuracy: float = 1e-05, ewald_w: int = 1, ewald_r_cut: float = None, ewald_g_cut: float = None, ewald_a: float = None, dscribe_n_jobs: int = 1, dscribe_only_physical_cores: bool = False) → list[source]¶

Calculate interaction matrices as defined in doi:10.1002/qua.24917. This method is based on the implementations of the dscribe python package.

Variables:¶

structure : aim2dat.strct.Structure¶

Structure object.

matrix_type : str¶

Matrix type. Supported options are 'coulomb', 'ewald_sum' or 'sine'.

permutation : str¶

Defines the output format. Options are: 'none', 'sorted_l2', 'eigenspectrum' or 'random'.

sigma : float¶

Standar deviation of the Gaussian distributed noise when using 'random' for permutation.

seed : int¶

Seed for the random numbers in case 'random' is chosen for the permutation attibute.

sparse : bool¶

Whether to return a sparse matrix or a dense 1D array.

ewald_accuracy : float¶

Accuracy threshold for the Ewald sum.

ewald_w : int¶

Weight parameter.

ewald_r_cut : float or None¶

Real space cutoff parameter.

ewald_g_cut : float or None¶

Reciprocal space cutoff parameter.

ewald_a : float or None¶

Parameter controlling the width of the Gaussian functions.

dscribe_n_jobs : int¶

Number of jobs used by dscribe to calculate the interaction matrix.

dscribe_only_physical_cores : bool¶

Whether to only use physicsl cores.

Returns:¶

list – Interaction matrix descriptor.

aim2dat.strct.ext_analysis.calculate_mbtr_descriptor(structure: aim2dat.strct.strct.Structure, geometry: dict = {'function': 'inverse_distance'}, grid: dict = {'min': 0, 'max': 1, 'n': 100, 'sigma': 0.1}, weighting: dict = {'function': 'exp', 'scale': 1.0, 'threshold': 0.001}, normalize_gaussians: bool = True, normalization: str = 'l2', elements: list = None, periodic: bool = False, sparse: bool = False, dscribe_n_jobs: int = 1, dscribe_only_physical_cores: bool = False) → list[float][source]¶

Calculate MBTR descriptor as defined in doi:10.1088/2632-2153/aca005. This method is based on the implementations of the dscribe python package.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• geometry (dict) – Setup the geometry function.

• grid (dict) – Setup the discretization grid.

• weighting (dict) – Setup the weighting function and its parameters.

• normalize_gaussians (bool) – Whether to normalize the gaussians to an area of 1.

• normalization (str) – Method for normalizing. Supported options are 'none', 'l2', 'n_atoms', 'valle_oganov'.

• elements (list) – List of atomic numbers or chemical symbols.

• periodic (bool) – Whether to consider periodic boundary conditions.

• sparse (bool) – Whether to return a sparse matrix or a dense array.

• dscribe_n_jobs (int) – Number of jobs used by dscribe to calculate the interaction matrix.

• dscribe_only_physical_cores (bool) – Whether to only use physicsl cores.

Returns:¶

list – MBTR descriptor.

aim2dat.strct.ext_analysis.calculate_planes(structure: aim2dat.strct.strct.Structure, r_max: float = 15.0, fragment: list = None, threshold: float = 0.05, margin: float = 1.0, vector_lengths: list[float] = None, min_nr_atoms: int = 5, use_scaled_coordinates: bool = False) → list[source]¶

Find planar arangements of atoms in the structure.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

• fragment (list or None (optional)) – Whether to restrict the search to a fragment of the structure.

• threshold (float (optional)) – Numerical threshold to consider an atom to be part of the plane.

• margin (float (optional)) – Margin between the plane vectors and outermost atoms.

• vector_lengths (list (optional)) – Absolute lengths of the plane vectors (overwrites margin).

• use_scaled_coordinates (bool (optional)) – Whether to use scaled coordinates for the calculation.

Returns:¶

list – List of planes.

aim2dat.strct.ext_analysis.calculate_prdf(structure: aim2dat.strct.strct.Structure, r_max: float = 20.0, delta_bin: float = 0.005, distinguish_kinds: bool = False) → tuple[dict, dict][source]¶

Calculate the partial radial distribution function. The calculation is based on: doi:10.1103/PhysRevB.89.205118.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

• delta_bin (float (optional)) – Bin size to descritize the function in angstrom.

• distinguish_kinds (bool (optional)) – Whether different kinds should be distinguished e.g. Ni0 and Ni1 would be considered as different elements if True.

Returns:¶

• element_prdf (dict) – Dictionary containing all partial radial distribution functions of the structure summed over all atoms of the same element.

• atomic_prdf (dict) – Dictionary containing all individual partial radial distribution functions for each atomic site.

aim2dat.strct.ext_analysis.calculate_soap_descriptor(structure: aim2dat.strct.strct.Structure, r_cut: float = 7.5, n_max: list = 8, l_max: list = 6, sigma: float = 1.0, rbf: str = 'gto', weighting: dict = None, compression: dict = {'mode': 'off', 'species_weighting': None}, average: str = 'off', elements: list = None, periodic: bool = False, sparse: bool = False, dscribe_n_jobs: int = 1, dscribe_only_physical_cores: bool = False) → list[float][source]¶

Calculate SOAP descriptor as defined in doi:10.1103/PhysRevB.87.184115. This method

is based on the implementations of the dscribe python package.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_cut (float) – Cutoff value.

• n_max (int) – The number of radial basis functions.

• l_max (int) – The maximum degree of spherical harmonics.

• sigma (float) – The standard deviation of the gaussians.

• rbf (str) – The radial basis functions to use. Supported options are: 'gto' or 'polynomial'.

• weighting (dict) – Contains the options which control the weighting of the atomic density.

• compression (dict) – Feature compression options.

• average (str) – The averaging mode over the centers of interest. Supported options are: 'off', 'inner' or 'outer'.

• elements (list) – List of atomic numbers or chemical symbols.

• periodic (bool) – Whether to consider periodic boundary conditions.

• sparse (bool) – Whether to return a sparse matrix or a dense array.

• dscribe_n_jobs (int) – Number of jobs used by dscribe to calculate the interaction matrix.

• dscribe_only_physical_cores (bool) – Whether to only use physicsl cores.

Returns:¶

list – SOAP descriptor.

aim2dat.strct.ext_analysis.calculate_warren_cowley_order_p(structure: aim2dat.strct.strct.Structure, r_max: float = 20.0, max_shells: int = 3)[source]¶

Calculate Warren-Cowley like order parameters as defined in doi:10.1103/PhysRevB.96.024104.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

• max_shells (int) – Number of neighbour shells that are evaluated.

Returns:¶

dict – Dictionary containing the order parameters.

aim2dat.strct.ext_analysis.create_graph(structure: aim2dat.strct.strct.Structure, graphviz_engine: str = 'circo', graphviz_edge_rank_colors: list[str] = ['blue', 'red', 'green', 'orange', 'darkblue'], r_max: float = 20.0, cn_method: str = 'minimum_distance', min_dist_delta: float = 0.1, n_nearest_neighbours: int = 5, econ_tolerance: float = 0.5, econ_conv_threshold: float = 0.001, voronoi_weight_type: float = 'rel_solid_angle', voronoi_weight_threshold: float = 0.5)[source]¶

Create graph based on the coordination.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• graphviz_engine (str) – Graphviz engine used to create the graph. The default value is 'circo'.

• graphviz_edge_rank_colors (list) – List of colors of the different edge ranks.

• r_max (float) – Cut-off value for the maximum distance between two atoms in angstrom. The default value is set to 20.0.

• cn_method (str) – Method used to calculate the coordination environment. The default value is 'minimum_distance'.

• min_dist_delta (float) – Tolerance parameter that defines the relative distance from the nearest neighbour atom for the 'minimum_distance' method. The default value is 0.1.

• n_nearest_neighbours (int) – Number of neighbours that are considered coordinated for the 'n_neighbours' method. The default value is 5.

• econ_tolerance (float) – Tolerance parameter for the econ method. The default value is 0.5.

• econ_conv_threshold (float) – Convergence threshold for the econ method. The default value is 0.001.

• voronoi_weight_type (str (optional)) – Weight type of the Voronoi facets. Supported options are 'covalent_atomic_radius', 'area' and 'solid_angle'. The prefix 'rel_' specifies that the relative weights with respect to the maximum value of the polyhedron are calculated.

• voronoi_weight_threshold (float (optional)) – Weight threshold to consider a neighbouring atom coordinated.

Returns:¶

• nx_graph (nx.MultiDiGraph) – networkx graph of the structure.

• graphviz_graph (graphviz.Digraph) – graphviz graph of the structure.

aim2dat.strct.ext_analysis.determine_molecular_fragments(structure: aim2dat.strct.strct.Structure, exclude_elements: list[str] = [], end_point_elements: list[str] = [], r_max: float = 20.0, cn_method: str = 'minimum_distance', min_dist_delta: float = 0.1, n_nearest_neighbours: int = 5, econ_tolerance: float = 0.5, econ_conv_threshold: float = 0.001, voronoi_weight_type: float = 'rel_solid_angle', voronoi_weight_threshold: float = 0.5, okeeffe_weight_threshold: float = 0.5)[source]¶

Find molecular fragments in a larger molecule/cluster of periodic crystal.

Parameters:¶

• structure (aim2dat.strct.Structure) – Structure object.

• exclude_elements (list) – List of elements that are excluded from the search.

• end_point_elements (list) – List of elements that serve as an end point for a fragment.

• r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

• cn_method (str (optional)) – Method used to calculate the coordination environment.

• min_dist_delta (float (optional)) – Tolerance parameter that defines the relative distance from the nearest neighbour atom for the 'minimum_distance' method.

• n_nearest_neighbours (int (optional)) – Number of neighbours that are considered coordinated for the 'n_neighbours' method.

• econ_tolerance (float (optional)) – Tolerance parameter for the econ method.

• econ_conv_threshold (float (optional)) – Convergence threshold for the econ method.

• voronoi_weight_type (str (optional)) – Weight type of the Voronoi facets. Supported options are 'covalent_atomic_radius', 'area' and 'solid_angle'. The prefix 'rel_' specifies that the relative weights with respect to the maximum value of the polyhedron are calculated.

• voronoi_weight_threshold (float (optional)) – Weight threshold to consider a neighbouring atom coordinated.

Returns:¶

list – List of fragments.