pymatgen.transformations.site_transformations module

This module defines site transformations which transforms a structure into another structure. Site transformations differ from standard transformations in that they operate in a site-specific manner. All transformations should inherit the AbstractTransformation ABC.

class AddSitePropertyTransformation(site_properties)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

Simple transformation to add site properties to a given structure

Parameters

site_properties (dict) – site properties to be added to a structure

apply_transformation(structure)[source]

Apply the transformation.

Arg:
structure (Structure): A structurally similar structure in

regards to crystal and site positions.

Returns

Returns a copy of structure with sites properties added.

property inverse[source]

None

Type

Return

property is_one_to_many[source]

False

Type

Return

class InsertSitesTransformation(species, coords, coords_are_cartesian=False, validate_proximity=True)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

This transformation substitutes certain sites with certain species.

Parameters
  • species – A list of species. e.g., [“Li”, “Fe”]

  • coords – A list of coords corresponding to those species. e.g., [[0,0,0],[0.5,0.5,0.5]].

  • coords_are_cartesian (bool) – Set to True if coords are given in cartesian coords. Defaults to False.

  • validate_proximity (bool) – Set to False if you do not wish to ensure that added sites are not too close to other sites. Defaults to True.

apply_transformation(structure)[source]

Apply the transformation.

Arg:
structure (Structure): A structurally similar structure in

regards to crystal and site positions.

Returns

Returns a copy of structure with sites inserted.

property inverse[source]

None

Type

Return

property is_one_to_many[source]

False

Type

Return

class PartialRemoveSitesTransformation(indices, fractions, algo=1)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

Remove fraction of specie from a structure. Requires an oxidation state decorated structure for ewald sum to be computed.

Given that the solution to selecting the right removals is NP-hard, there are several algorithms provided with varying degrees of accuracy and speed. The options are as follows:

ALGO_FAST:

This is a highly optimized algorithm to quickly go through the search tree. It is guaranteed to find the optimal solution, but will return only a single lowest energy structure. Typically, you will want to use this.

ALGO_COMPLETE:

The complete algo ensures that you get all symmetrically distinct orderings, ranked by the estimated Ewald energy. But this can be an extremely time-consuming process if the number of possible orderings is very large. Use this if you really want all possible orderings. If you want just the lowest energy ordering, ALGO_FAST is accurate and faster.

ALGO_BEST_FIRST:

This algorithm is for ordering the really large cells that defeats even ALGO_FAST. For example, if you have 48 sites of which you want to remove 16 of them, the number of possible orderings is around 2 x 10^12. ALGO_BEST_FIRST shortcircuits the entire search tree by removing the highest energy site first, then followed by the next highest energy site, and so on. It is guaranteed to find a solution in a reasonable time, but it is also likely to be highly inaccurate.

ALGO_ENUMERATE:

This algorithm uses the EnumerateStructureTransformation to perform ordering. This algo returns complete orderings up to a single unit cell size. It is more robust than the ALGO_COMPLETE, but requires Gus Hart’s enumlib to be installed.

Parameters
  • indices – A list of list of indices. e.g. [[0, 1], [2, 3, 4, 5]]

  • fractions – The corresponding fractions to remove. Must be same length as indices. e.g., [0.5, 0.25]

  • algo – This parameter allows you to choose the algorithm to perform ordering. Use one of PartialRemoveSpecieTransformation.ALGO_* variables to set the algo.

ALGO_BEST_FIRST = 2[source]
ALGO_COMPLETE = 1[source]
ALGO_ENUMERATE = 3[source]
ALGO_FAST = 0[source]
apply_transformation(structure, return_ranked_list=False)[source]

Apply the transformation.

Parameters
  • structure – input structure

  • return_ranked_list (bool) – Whether or not multiple structures are returned. If return_ranked_list is a number, that number of structures is returned.

Returns

Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {“structure” = …. , “other_arguments”} the key “transformation” is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class.

property inverse[source]

None

Type

Return

property is_one_to_many[source]

True

Type

Return

class RadialSiteDistortionTransformation(site_index, displacement=0.1, nn_only=False)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

Radially perturbs atoms around a site. Can be used to create spherical distortion due to a point defect.

Parameters
  • site_index (int) – index of the site in structure to place at the center of the distortion (will not be distorted). This index must be provided before the structure is provided in apply_transformation in order to keep in line with the base class.

  • displacement (float) – distance to perturb the atoms around the objective site

  • nn_only (bool) – Whether or not to perturb beyond the nearest neighbors. If True, then only the nearest neighbors will be perturbed, leaving the other sites undisturbed. If False, then the nearest neighbors will receive the full displacement, and then subsequent sites will receive a displacement=0.1 / r, where r is the distance each site to the origin site. For small displacements, atoms beyond the NN environment will receive very small displacements, and these are almost equal. For large displacements, this difference is noticeable.

apply_transformation(structure)[source]

Apply the transformation.

Parameters

structure – Structure or Molecule to apply the transformation to

Returns

the transformed structure

property inverse[source]

Returns the inverse transformation if available. Otherwise, should return None.

property is_one_to_many[source]

Determines if a Transformation is a one-to-many transformation. If a Transformation is a one-to-many transformation, the apply_transformation method should have a keyword arg “return_ranked_list” which allows for the transformed structures to be returned as a ranked list.

property use_multiprocessing[source]

Indicates whether the transformation can be applied by a subprocessing pool. This should be overridden to return True for transformations that the transmuter can parallelize.

class RemoveSitesTransformation(indices_to_remove)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

Remove certain sites in a structure.

Parameters

indices_to_remove – List of indices to remove. E.g., [0, 1, 2]

apply_transformation(structure)[source]

Apply the transformation.

Arg:
structure (Structure): A structurally similar structure in

regards to crystal and site positions.

Returns

Returns a copy of structure with sites removed.

property inverse[source]

None

Type

Return

property is_one_to_many[source]

False

Type

Return

class ReplaceSiteSpeciesTransformation(indices_species_map)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

This transformation substitutes certain sites with certain species.

Parameters

indices_species_map – A dict containing the species mapping in int-string pairs. E.g., { 1:”Na”} or {2:”Mn2+”}. Multiple substitutions can be done. Overloaded to accept sp_and_occu dictionary. E.g. {1: {“Ge”:0.75, “C”:0.25} }, which substitutes a single species with multiple species to generate a disordered structure.

apply_transformation(structure)[source]

Apply the transformation.

Arg:
structure (Structure): A structurally similar structure in

regards to crystal and site positions.

Returns

Returns a copy of structure with sites replaced.

property inverse[source]

None

Type

Return

property is_one_to_many[source]

False

Type

Return

class TranslateSitesTransformation(indices_to_move, translation_vector, vector_in_frac_coords=True)[source]

Bases: pymatgen.transformations.transformation_abc.AbstractTransformation

This class translates a set of sites by a certain vector.

Parameters
  • indices_to_move – The indices of the sites to move

  • translation_vector – Vector to move the sites. If a list of list or numpy array of shape, (len(indices_to_move), 3), is provided then each translation vector is applied to the corresponding site in the indices_to_move.

  • vector_in_frac_coords – Set to True if the translation vector is in fractional coordinates, and False if it is in cartesian coordinations. Defaults to True.

apply_transformation(structure)[source]

Apply the transformation.

Arg:
structure (Structure): A structurally similar structure in

regards to crystal and site positions.

Returns

Returns a copy of structure with sites translated.

as_dict()[source]

Json-serializable dict representation.

property inverse[source]

Returns: TranslateSitesTranformation with the reverse translation.

property is_one_to_many[source]

False

Type

Return