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 sitespecific 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
¶ None
 Type
Return

property
is_one_to_many
¶ 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
¶ None
 Type
Return

property
is_one_to_many
¶ 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 NPhard, 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 timeconsuming 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¶

ALGO_COMPLETE
= 1¶

ALGO_ENUMERATE
= 3¶

ALGO_FAST
= 0¶

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
¶ None
 Type
Return

property
is_one_to_many
¶ True
 Type
Return

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
¶ None
 Type
Return

property
is_one_to_many
¶ 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 intstring 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
¶ None
 Type
Return

property
is_one_to_many
¶ 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.

property
inverse
¶ Returns: TranslateSitesTranformation with the reverse translation.

property
is_one_to_many
¶ False
 Type
Return