pymatgen.analysis.chemenv.coordination_environments.structure_environments module

This module contains objects that are used to describe the environments in a structure. The most detailed object (StructureEnvironments) contains a very thorough analysis of the environments of a given atom but is difficult to used as such. The LightStructureEnvironments object is a lighter version that is obtained by applying a “strategy” on the StructureEnvironments object. Basically, the LightStructureEnvironments provides the coordination environment(s) and possibly some fraction corresponding to these.

class ChemicalEnvironments(coord_geoms=None)

Bases: monty.json.MSONable

Class used to store all the information about the chemical environment of a given site for a given list of coordinated neighbours (internally called “cn_map”).

Initializes the ChemicalEnvironments object containing all the information about the chemical environment of a given site.

Parameters

coord_geoms – coordination geometries to be added to the chemical environment.

add_coord_geom(mp_symbol, symmetry_measure, algo='UNKNOWN', permutation=None, override=False, local2perfect_map=None, perfect2local_map=None, detailed_voronoi_index=None, other_symmetry_measures=None, rotation_matrix=None, scaling_factor=None)

Adds a coordination geometry to the ChemicalEnvironments object.

Parameters

• mp_symbol – Symbol of the coordination geometry added.

• symmetry_measure – Symmetry measure of the coordination geometry added.

• algo – Algorithm used for the search of the coordination geometry added.

• permutation – Permutation of the neighbors that leads to the csm stored.

• override – If set to True, the coordination geometry will override the existent one if present.

• local2perfect_map – Mapping of the local indices to the perfect indices.

• perfect2local_map – Mapping of the perfect indices to the local indices.

• detailed_voronoi_index – Index in the voronoi containing the neighbors set.

• other_symmetry_measures – Other symmetry measure of the coordination geometry added (with/without the central atom, centered on the central atom or on the centroid with/without the central atom).

• rotation_matrix – Rotation matrix mapping the local geometry to the perfect geometry.

• scaling_factor – Scaling factor mapping the local geometry to the perfect geometry.

Raises

ChemenvError if the coordination geometry is already added and override is set to False –

as_dict()

Returns a dictionary representation of the ChemicalEnvironments object.

Returns

A dictionary representation of the ChemicalEnvironments object.

classmethod from_dict(d)

Reconstructs the ChemicalEnvironments object from a dict representation of the ChemicalEnvironments created using the as_dict method.

Parameters

d – dict representation of the ChemicalEnvironments object.

Returns

ChemicalEnvironments object.

is_close_to(other, rtol=0.0, atol=1e-08)

Whether this ChemicalEnvironments object is close to another one.

Parameters

• other – Another ChemicalEnvironments object.

• rtol – Relative tolerance for the comparison of Continuous Symmetry Measures.

• atol – Absolute tolerance for the comparison of Continuous Symmetry Measures.

Returns

True if the two ChemicalEnvironments objects are close to each other.

minimum_geometries(n=None, symmetry_measure_type=None, max_csm=None)

Returns a list of geometries with increasing continuous symmetry measure in this ChemicalEnvironments object.

Parameters

n – Number of geometries to be included in the list.

Returns

List of geometries with increasing continuous symmetry measure in this ChemicalEnvironments object.

Raises

ValueError if no coordination geometry is found in this ChemicalEnvironments object. –

minimum_geometry(symmetry_measure_type=None, max_csm=None)

Returns the geometry with the minimum continuous symmetry measure of this ChemicalEnvironments.

Returns

tuple (symbol, csm) with symbol being the geometry with the minimum continuous symmetry measure and csm being the continuous symmetry measure associated to it.

Raises

ValueError if no coordination geometry is found in this ChemicalEnvironments object. –

class LightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)

Bases: monty.json.MSONable

Class used to store the chemical environments of a given structure obtained from a given ChemenvStrategy. Currently, only strategies leading to the determination of a unique environment for each site is allowed This class does not store all the information contained in the StructureEnvironments object, only the coordination environment found.

Constructor for the LightStructureEnvironments object.

Parameters

• strategy – ChemEnv strategy used to get the environments.

• coordination_environments – The coordination environments identified.

• all_nbs_sites – All the possible neighbors for each site in the structure.

• neighbors_sets – The neighbors sets of each site in the structure.

• structure – The structure.

• valences – The valences used to get the environments (if needed).

• valences_origin – How the valences were obtained (e.g. from the Bond-valence analysis or from the original structure).

DEFAULT_STATISTICS_FIELDS = ['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present']

DELTA_MAX_OXIDATION_STATE = 0.1

class NeighborsSet(structure, isite, all_nbs_sites, all_nbs_sites_indices)

Bases: object

Class used to store a given set of neighbors of a given site (based on a list of sites, the voronoi container is not part of the LightStructureEnvironments object).

Constructor for NeighborsSet.

Parameters

• structure – Structure object.

• isite – Index of the site for which neighbors are stored in this NeighborsSet.

• all_nbs_sites – All the possible neighbors for this site.

• all_nbs_sites_indices – Indices of the sites in all_nbs_sites that make up this NeighborsSet.

as_dict()

A JSON serializable dict representation of the NeighborsSet.

classmethod from_dict(dd, structure, all_nbs_sites)

Reconstructs the NeighborsSet algorithm from its JSON serializable dict representation, together with the structure and all the possible neighbors sites.

As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the LightStructureEnvironments. The from_dict method is thus using the structure and all_nbs_sites when reconstructing itself. These two are both in the LightStructureEnvironments object.

Parameters

• dd – a JSON serializable dict representation of a NeighborsSet.

• structure – The structure.

• all_nbs_sites – The list of all the possible neighbors for a given site.

Returns: a NeighborsSet.

property neighb_coords

Coordinates of neighbors for this NeighborsSet.

property neighb_indices_and_images

List of indices and images with respect to the original unit cell sites for this NeighborsSet.

property neighb_sites

Neighbors for this NeighborsSet as pymatgen Sites.

property neighb_sites_and_indices

List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

as_dict()

Bson-serializable dict representation of the LightStructureEnvironments object. :returns: Bson-serializable dict representation of the LightStructureEnvironments object.

clear_environments(conditions=None)

Get the clear environments in the structure.

Parameters

conditions – Conditions to be checked for an environment to be “clear”.

Returns: Set of clear environments in this structure.

contains_only_one_anion(anion)

Whether this LightStructureEnvironments concerns a structure with only one given anion type.

Parameters

anion – Anion (e.g. O2-, …).

Returns: True if this LightStructureEnvironments concerns a structure with only one given anion.

contains_only_one_anion_atom(anion_atom)

Whether this LightStructureEnvironments concerns a structure with only one given anion atom type.

Parameters

anion_atom – Anion (e.g. O, …). The structure could contain O2- and O- though.

Returns: True if this LightStructureEnvironments concerns a structure with only one given anion_atom.

environments_identified()

Return the set of environments identified in this structure.

Returns: Set of environments identified in this structure.

classmethod from_dict(d)

Reconstructs the LightStructureEnvironments object from a dict representation of the LightStructureEnvironments created using the as_dict method.

Parameters

d – dict representation of the LightStructureEnvironments object.

Returns

LightStructureEnvironments object.

classmethod from_structure_environments(strategy, structure_environments, valences=None, valences_origin=None)

Construct a LightStructureEnvironments object from a strategy and a StructureEnvironments object.

Parameters

• strategy – ChemEnv strategy used.

• structure_environments – StructureEnvironments object from which to construct the LightStructureEnvironments.

• valences – The valences of each site in the structure.

• valences_origin – How the valences were obtained (e.g. from the Bond-valence analysis or from the original structure).

Returns: a LightStructureEnvironments object.

get_site_info_for_specie_allces(specie, min_fraction=0.0)

Get list of indices that have the given specie.

Parameters

specie – Specie to get.

Returns: Dictionary with the list of coordination environments for the given species, the indices of the sites

in which they appear, their fractions and continuous symmetry measures.

get_site_info_for_specie_ce(specie, ce_symbol)

Get list of indices that have the given specie with a given Coordination environment.

Parameters

• specie – Specie to get.

• ce_symbol – Symbol of the coordination environment to get.

Returns: Dictionary with the list of indices in the structure that have the given specie in the given

environment, their fraction and continuous symmetry measures.

get_statistics(statistics_fields=['anion_list', 'anion_atom_list', 'cation_list', 'cation_atom_list', 'neutral_list', 'neutral_atom_list', 'atom_coordination_environments_present', 'ion_coordination_environments_present', 'fraction_atom_coordination_environments_present', 'fraction_ion_coordination_environments_present', 'coordination_environments_atom_present', 'coordination_environments_ion_present'], bson_compatible=False)

Get the statistics of environments for this structure. :param statistics_fields: Which statistics to get. :param bson_compatible: Whether to make the dictionary BSON-compatible.

Returns

A dictionary with the requested statistics.

setup_statistic_lists()

Set up the statistics of environments for this LightStructureEnvironments.

site_contains_environment(isite, ce_symbol)

Whether a given site contains a given coordination environment.

Parameters

• isite – Index of the site.

• ce_symbol – Symbol of the coordination environment.

Returns: True if the site contains the given coordination environment.

site_has_clear_environment(isite, conditions=None)

Whether a given site has a “clear” environments.

A “clear” environment is somewhat arbitrary. You can pass (multiple) conditions, e.g. the environment should have a continuous symmetry measure lower than this, a fraction higher than that, …

Parameters

• isite – Index of the site.

• conditions – Conditions to be checked for an environment to be “clear”.

Returns: True if the site has a clear environment.

structure_contains_atom_environment(atom_symbol, ce_symbol)

Checks whether the structure contains a given atom in a given environment.

Parameters

• atom_symbol – Symbol of the atom.

• ce_symbol – Symbol of the coordination environment.

Returns

True if the coordination environment is found, False otherwise

structure_has_clear_environments(conditions=None, skip_none=True, skip_empty=False)

Whether all sites in a structure have “clear” environments. :param conditions: Conditions to be checked for an environment to be “clear”. :param skip_none: Whether to skip sites for which no environments have been computed. :param skip_empty: Whether to skip sites for which no environments could be found.

Returns: True if all the sites in the structure have clear environments.

property uniquely_determines_coordination_environments

True if the coordination environments are uniquely determined.

class StructureEnvironments(voronoi, valences, sites_map, equivalent_sites, ce_list, structure, neighbors_sets=None, info=None)

Bases: monty.json.MSONable

Class used to store the chemical environments of a given structure.

Constructor for the StructureEnvironments object.

Parameters

• voronoi – VoronoiContainer object for the structure.

• valences – Valences provided.

• sites_map – Mapping of equivalent sites to the unequivalent sites that have been computed.

• equivalent_sites – List of list of equivalent sites of the structure.

• ce_list – List of chemical environments.

• structure – Structure object.

• neighbors_sets – List of neighbors sets.

• info – Additional information for this StructureEnvironments object.

AC = <pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions object>

class NeighborsSet(structure, isite, detailed_voronoi, site_voronoi_indices, sources=None)

Bases: object

Class used to store a given set of neighbors of a given site (based on the detailed_voronoi).

Constructor for NeighborsSet.

Parameters

• structure – Structure object.

• isite – Index of the site for which neighbors are stored in this NeighborsSet.

• detailed_voronoi – Corresponding DetailedVoronoiContainer object containing all the possible neighbors of the give site.

• site_voronoi_indices – Indices of the voronoi sites in the DetailedVoronoiContainer object that make up this NeighborsSet.

• sources – Sources for this NeighborsSet, i.e. how this NeighborsSet was generated.

add_source(source)

Add a source to this NeighborsSet.

Parameters

source – Information about the generation of this NeighborsSet.

angle_plateau()

Returns the angles plateau’s for this NeighborsSet.

property angles

Angles for each neighbor in this NeighborsSet.

as_dict()

A JSON serializable dict representation of the NeighborsSet.

property coords

Coordinates of the current central atom and its neighbors for this NeighborsSet.

distance_plateau()

Returns the distances plateau’s for this NeighborsSet.

property distances

Distances to each neighbor in this NeighborsSet.

classmethod from_dict(dd, structure, detailed_voronoi)

Reconstructs the NeighborsSet algorithm from its JSON serializable dict representation, together with the structure and the DetailedVoronoiContainer.

As an inner (nested) class, the NeighborsSet is not supposed to be used anywhere else that inside the StructureEnvironments. The from_dict method is thus using the structure and detailed_voronoi when reconstructing itself. These two are both in the StructureEnvironments object.

Parameters

• dd – a JSON serializable dict representation of a NeighborsSet.

• structure – The structure.

• detailed_voronoi – The Voronoi object containing all the neighboring atoms from which the subset of neighbors for this NeighborsSet is extracted.

Returns: a NeighborsSet.

get_neighb_voronoi_indices(permutation)

Return the indices in the detailed_voronoi corresponding to the current permutation.

Parameters

permutation – Current permutation for which the indices in the detailed_voronoi are needed.

Returns: List of indices in the detailed_voronoi.

property info

Summarized information about this NeighborsSet.

property neighb_coords

Coordinates of neighbors for this NeighborsSet.

property neighb_coordsOpt

Optimized access to the coordinates of neighbors for this NeighborsSet.

property neighb_sites

Neighbors for this NeighborsSet as pymatgen Sites.

property neighb_sites_and_indices

List of neighbors for this NeighborsSet as pymatgen Sites and their index in the original structure.

property normalized_angles

Normalized angles for each neighbor in this NeighborsSet.

property normalized_distances

Normalized distances to each neighbor in this NeighborsSet.

property source

Returns the source of this NeighborsSet (how it was generated, e.g. from which Voronoi cut-offs, or from hints).

voronoi_grid_surface_points(additional_condition=1, other_origins='DO_NOTHING')

Get the surface points in the Voronoi grid for this neighbor from the sources. The general shape of the points should look like a staircase such as in the following figure :

^

0.0|

B—-C

| |

| |

a | k D——-E n | | | g | | | l | | | e | j F—-n———G

| |

| |

A—-g——-h—-i———H

1.0+————————————————->

1.0 distance 2.0 ->+Inf

Parameters

• additional_condition – Additional condition for the neighbors.

• other_origins – What to do with sources that do not come from the Voronoi grid (e.g. “from hints”).

add_neighbors_set(isite, nb_set)

Adds a neighbor set to the list of neighbors sets for this site.

Parameters

• isite – Index of the site under consideration.

• nb_set – NeighborsSet to be added.

as_dict()

Bson-serializable dict representation of the StructureEnvironments object.

Returns

Bson-serializable dict representation of the StructureEnvironments object.

differences_wrt(other)

Return differences found in the current StructureEnvironments with respect to another StructureEnvironments.

Parameters

other – A StructureEnvironments object.

Returns

List of differences between the two StructureEnvironments objects.

classmethod from_dict(d)

Reconstructs the StructureEnvironments object from a dict representation of the StructureEnvironments created using the as_dict method.

Parameters

d – dict representation of the StructureEnvironments object.

Returns

StructureEnvironments object.

get_coordination_environments(isite, cn, nb_set)

Get the ChemicalEnvironments for a given site, coordination and neighbors set.

Parameters

• isite – Index of the site for which the ChemicalEnvironments is looked for.

• cn – Coordination for which the ChemicalEnvironments is looked for.

• nb_set – Neighbors set for which the ChemicalEnvironments is looked for.

Returns: a ChemicalEnvironments object.

get_csm(isite, mp_symbol)

Get the continuous symmetry measure for a given site in the given coordination environment.

Parameters

• isite – Index of the site.

• mp_symbol – Symbol of the coordination environment for which we want the continuous symmetry measure.

Returns: Continuous symmetry measure of the given site in the given environment.

get_csm_and_maps(isite, max_csm=8.0, figsize=None, symmetry_measure_type=None)

Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

Parameters

• isite – Index of the site for which the plot has to be done.

• max_csm – Maximum continuous symmetry measure to be shown.

• figsize – Size of the figure.

• symmetry_measure_type – Type of continuous symmetry measure to be used.

Returns

Matplotlib figure and axes representing the csm and maps.

get_csms(isite, mp_symbol)

Returns the continuous symmetry measure(s) of site with index isite with respect to the

perfect coordination environment with mp_symbol. For some environments, a given mp_symbol might not be available (if there is no voronoi parameters leading to a number of neighbours corresponding to the coordination number of environment mp_symbol). For some environments, a given mp_symbol might lead to more than one csm (when two or more different voronoi parameters lead to different neighbours but with same number of neighbours).

Parameters

• isite – Index of the site.

• mp_symbol – MP symbol of the perfect environment for which the csm has to be given.

Returns

List of csms for site isite with respect to geometry mp_symbol

get_environments_figure(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, colormap=None, figsize=None, strategy=None)

Plotting of the coordination environments of a given site for all the distfactor/angfactor regions. The chemical environments with the lowest continuous symmetry measure is shown for each distfactor/angfactor region as the value for the color of that distfactor/angfactor region (using a colormap).

Parameters

• isite – Index of the site for which the plot has to be done.

• plot_type – How to plot the coordinations.

• title – Title for the figure.

• max_dist – Maximum distance to be plotted when the plotting of the distance is set to ‘initial_normalized’ or ‘initial_real’ (Warning: this is not the same meaning in both cases! In the first case, the closest atom lies at a “normalized” distance of 1.0 so that 2.0 means refers to this normalized distance while in the second case, the real distance is used).

• colormap – Color map to be used for the continuous symmetry measure.

• figsize – Size of the figure.

• strategy – Whether to plot information about one of the Chemenv Strategies.

Returns

Matplotlib figure and axes representing the environments.

init_neighbors_sets(isite, additional_conditions=None, valences=None)

Initialize the list of neighbors sets for the current site.

Parameters

• isite – Index of the site under consideration.

• additional_conditions – Additional conditions to be used for the initialization of the list of neighbors sets, e.g. “Only anion-cation bonds”, …

• valences – List of valences for each site in the structure (needed if an additional condition based on the valence is used, e.g. only anion-cation bonds).

plot_csm_and_maps(isite, max_csm=8.0)

Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

Parameters

• isite – Index of the site for which the plot has to be done

• max_csm – Maximum continuous symmetry measure to be shown.

plot_environments(isite, plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None, strategy=None)

Plotting of the coordination numbers of a given site for all the distfactor/angfactor parameters. If the chemical environments are given, a color map is added to the plot, with the lowest continuous symmetry measure as the value for the color of that distfactor/angfactor set.

Parameters

• isite – Index of the site for which the plot has to be done.

• plot_type – How to plot the coordinations.

• title – Title for the figure.

• max_dist – Maximum distance to be plotted when the plotting of the distance is set to ‘initial_normalized’ or ‘initial_real’ (Warning: this is not the same meaning in both cases! In the first case, the closest atom lies at a “normalized” distance of 1.0 so that 2.0 means refers to this normalized distance while in the second case, the real distance is used).

• figsize – Size of the figure.

• strategy – Whether to plot information about one of the Chemenv Strategies.

save_environments_figure(isite, imagename='image.png', plot_type=None, title='Coordination numbers', max_dist=2.0, figsize=None)

Saves the environments figure to a given file.

Parameters

• isite – Index of the site for which the plot has to be done.

• imagename – Name of the file to which the figure has to be saved.

• plot_type – How to plot the coordinations.

• title – Title for the figure.

• max_dist – Maximum distance to be plotted when the plotting of the distance is set to ‘initial_normalized’ or ‘initial_real’ (Warning: this is not the same meaning in both cases! In the first case, the closest atom lies at a “normalized” distance of 1.0 so that 2.0 means refers to this normalized distance while in the second case, the real distance is used).

• figsize – Size of the figure.

update_coordination_environments(isite, cn, nb_set, ce)

Updates the coordination environment for this site, coordination and neighbor set.

Parameters

• isite – Index of the site to be updated.

• cn – Coordination to be updated.

• nb_set – Neighbors set to be updated.

• ce – ChemicalEnvironments object for this neighbors set.

update_site_info(isite, info_dict)

Update information about this site.

Parameters

• isite – Index of the site for which info has to be updated.

• info_dict – Dictionary of information to be added for this site.