pymatgen.analysis.structure_analyzer module¶
This module provides classes to perform topological analyses of structures.
-
class
OxideType(structure, relative_cutoff=1.1)[source]¶ Bases:
objectSeparate class for determining oxide type.
- Parameters
structure – Input structure.
relative_cutoff – Relative_cutoff * act. cutoff stipulates the max. distance two O atoms must be from each other. Default value is 1.1. At most 1.1 is recommended, nothing larger, otherwise the script cannot distinguish between superoxides and peroxides.
-
class
RelaxationAnalyzer(initial_structure, final_structure)[source]¶ Bases:
objectThis class analyzes the relaxation in a calculation.
Please note that the input and final structures should have the same ordering of sites. This is typically the case for most computational codes.
- Parameters
-
get_percentage_bond_dist_changes(max_radius=3.0)[source]¶ Returns the percentage bond distance changes for each site up to a maximum radius for nearest neighbors.
- Parameters
max_radius (float) – Maximum radius to search for nearest neighbors. This radius is applied to the initial structure, not the final structure.
- Returns
Bond distance changes as a dict of dicts. E.g., {index1: {index2: 0.011, …}}. For economy of representation, the index1 is always less than index2, i.e., since bonding between site1 and siten is the same as bonding between siten and site1, there is no reason to duplicate the information or computation.
-
class
VoronoiAnalyzer(cutoff=5.0, qhull_options='Qbb Qc Qz')[source]¶ Bases:
objectPerforms a statistical analysis of Voronoi polyhedra around each site. Each Voronoi polyhedron is described using Schaefli notation. That is a set of indices {c_i} where c_i is the number of faces with i number of vertices. E.g. for a bcc crystal, there is only one polyhedron notation of which is [0,6,0,8,0,0,…]. In perfect crystals, these also corresponds to the Wigner-Seitz cells. For distorted-crystals, liquids or amorphous structures, rather than one-type, there is a statistical distribution of polyhedra. See ref: Microstructure and its relaxation in Fe-B amorphous system simulated by molecular dynamics,
Stepanyuk et al., J. Non-cryst. Solids (1993), 159, 80-87.
- Parameters
cutoff (float) – cutoff distance to search for neighbors of a given atom (default = 5.0)
qhull_options (str) – options to pass to qhull (optional)
-
analyze(structure, n=0)[source]¶ Performs Voronoi analysis and returns the polyhedra around atom n in Schlaefli notation.
- Parameters
structure (Structure) – structure to analyze
n (int) – index of the center atom in structure
- Returns
- <c3,c4,c6,c6,c7,c8,c9,c10>
where c_i denotes number of facets with i vertices.
- Return type
voronoi index of n
-
analyze_structures(structures, step_freq=10, most_frequent_polyhedra=15)[source]¶ Perform Voronoi analysis on a list of Structures. Note that this might take a significant amount of time depending on the size and number of structures.
- Parameters
structures (list) – list of Structures
(float (cutoff) – cutoff distance around an atom to search for neighbors
step_freq (int) – perform analysis every step_freq steps
qhull_options (str) – options to pass to qhull
most_frequent_polyhedra (int) – this many unique polyhedra with highest frequences is stored.
- Returns
A list of tuples in the form (voronoi_index,frequency)
-
class
VoronoiConnectivity(structure, cutoff=10)[source]¶ Bases:
objectComputes the solid angles swept out by the shared face of the voronoi polyhedron between two sites.
- Parameters
structure (Structure) – Input structure
cutoff (float) –
-
property
connectivity_array[source]¶ Provides connectivity array.
- Returns
An array of shape [atomi, atomj, imagej]. atomi is the index of the atom in the input structure. Since the second atom can be outside of the unit cell, it must be described by both an atom index and an image index. Array data is the solid angle of polygon between atomi and imagej of atomj
- Return type
connectivity
-
get_connections()[source]¶ Returns a list of site pairs that are Voronoi Neighbors, along with their real-space distances.
-
get_sitej(site_index, image_index)[source]¶ Assuming there is some value in the connectivity array at indices (1, 3, 12). sitei can be obtained directly from the input structure (structure[1]). sitej can be obtained by passing 3, 12 to this function
- Parameters
site_index (int) – index of the site (3 in the example)
image_index (int) – index of the image (12 in the example)
-
average_coordination_number(structures, freq=10)[source]¶ Calculates the ensemble averaged Voronoi coordination numbers of a list of Structures using VoronoiNN. Typically used for analyzing the output of a Molecular Dynamics run.
- Parameters
structures (list) – list of Structures.
freq (int) – sampling frequency of coordination number [every freq steps].
- Returns
Dictionary of elements as keys and average coordination numbers as values.
-
contains_peroxide(structure, relative_cutoff=1.1)[source]¶ Determines if a structure contains peroxide anions.
- Parameters
structure (Structure) – Input structure.
relative_cutoff – The peroxide bond distance is 1.49 Angstrom. Relative_cutoff * 1.49 stipulates the maximum distance two O atoms must be to each other to be considered a peroxide.
- Returns
Boolean indicating if structure contains a peroxide anion.
-
get_max_bond_lengths(structure, el_radius_updates=None)[source]¶ Provides max bond length estimates for a structure based on the JMol table and algorithms.
- Parameters
structure – (structure)
el_radius_updates – (dict) symbol->float to update atomic radii
- Returns: (dict) - (Element1, Element2) -> float. The two elements are
ordered by Z.
-
oxide_type(structure, relative_cutoff=1.1, return_nbonds=False)[source]¶ Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide
- Parameters
structure (Structure) – Input structure.
relative_cutoff (float) – Relative_cutoff * act. cutoff stipulates the max distance two O atoms must be from each other.
return_nbonds (bool) – Should number of bonds be requested?