pymatgen.alchemy.materials module

This module provides various representations of transformed structures. A TransformedStructure is a structure that has been modified by undergoing a series of transformations.

class TransformedStructure(structure: Structure, transformations: list[AbstractTransformation] = None, history: list[AbstractTransformation | dict[str, Any]] = None, other_parameters: dict[str, Any] = None)[source]

Bases: monty.json.MSONable

Container object for new structures that include history of transformations.

Each transformed structure is made up of a sequence of structures with associated transformation history.

Initializes a transformed structure from a structure.

Parameters

  • structure (Structure) – Input structure

  • transformations (list[Transformation]) – List of transformations to apply.

  • history (list[Transformation]) – Previous history.

  • other_parameters (dict) – Additional parameters to be added.

append_filter(structure_filter: pymatgen.alchemy.filters.AbstractStructureFilter) → None[source]

Adds a filter.

Parameters

structure_filter (StructureFilter) – A filter implementing the AbstractStructureFilter API. Tells transmuter what structures to retain.

append_transformation(transformation, return_alternatives=False, clear_redo=True)[source]

Appends a transformation to the TransformedStructure.

Parameters

  • transformation – Transformation to append

  • return_alternatives – Whether to return alternative TransformedStructures for one-to-many transformations. return_alternatives can be a number, which stipulates the total number of structures to return.

  • clear_redo – Boolean indicating whether to clear the redo list. By default, this is True, meaning any appends clears the history of undoing. However, when using append_transformation to do a redo, the redo list should not be cleared to allow multiple redos.

as_dict() → dict[str, Any][source]

Dict representation of the TransformedStructure.

extend_transformations(transformations: list[pymatgen.transformations.transformation_abc.AbstractTransformation], return_alternatives: bool = False) → None[source]

Extends a sequence of transformations to the TransformedStructure.

Parameters

  • transformations – Sequence of Transformations

  • return_alternatives – Whether to return alternative TransformedStructures for one-to-many transformations. return_alternatives can be a number, which stipulates the total number of structures to return.

static from_cif_string(cif_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None, primitive: bool = True, occupancy_tolerance: float = 1.0) → pymatgen.alchemy.materials.TransformedStructure[source]

Generates TransformedStructure from a cif string.

Parameters

  • cif_string (str) – Input cif string. Should contain only one structure. For cifs containing multiple structures, please use CifTransmuter.

  • transformations (list[Transformation]) – Sequence of transformations to be applied to the input structure.

  • primitive (bool) – Option to set if the primitive cell should be extracted. Defaults to True. However, there are certain instances where you might want to use a non-primitive cell, e.g., if you are trying to generate all possible orderings of partial removals or order a disordered structure.

  • occupancy_tolerance (float) – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1.

Returns

TransformedStructure

classmethod from_dict(d) → pymatgen.alchemy.materials.TransformedStructure[source]

Creates a TransformedStructure from a dict.

static from_poscar_string(poscar_string: str, transformations: Optional[list[pymatgen.transformations.transformation_abc.AbstractTransformation]] = None) → pymatgen.alchemy.materials.TransformedStructure[source]

Generates TransformedStructure from a poscar string.

Parameters

  • poscar_string (str) – Input POSCAR string.

  • transformations (list[Transformation]) – Sequence of transformations to be applied to the input structure.

classmethod from_snl(snl: pymatgen.util.provenance.StructureNL) → pymatgen.alchemy.materials.TransformedStructure[source]

Create TransformedStructure from SNL.

Parameters

snl (StructureNL) – Starting snl

Returns

TransformedStructure

get_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, **kwargs) → dict[str, Any][source]

Returns VASP input as a dict of vasp objects.

Parameters

vasp_input_set (pymatgen.io.vaspio_set.VaspInputSet) – input set to create vasp input files from structures

redo_next_change() → None[source]

Redo the last undone change in the TransformedStructure.

Raises

IndexError – If already at the latest change.

set_parameter(key: str, value: Any) → None[source]

Set a parameter

Parameters

  • key – The string key

  • value – The value.

property structures: list[pymatgen.core.structure.Structure][source]

Copy of all structures in the TransformedStructure. A structure is stored after every single transformation.

to_snl(authors, **kwargs) → pymatgen.util.provenance.StructureNL[source]

Generate SNL from TransformedStructure.

Parameters

  • authors – List of authors

  • **kwargs –

    All kwargs supported by StructureNL.

Returns

StructureNL

undo_last_change() → None[source]

Undo the last change in the TransformedStructure.

Raises

IndexError – If already at the oldest change.

property was_modified: bool[source]

Boolean describing whether the last transformation on the structure made any alterations to it one example of when this would return false is in the case of performing a substitution transformation on the structure when the specie to replace isn’t in the structure.

write_vasp_input(vasp_input_set: type[pymatgen.io.vasp.sets.VaspInputSet] = <class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir: str = '.', create_directory: bool = True, **kwargs) → None[source]

Writes VASP input to an output_dir.

Parameters

  • vasp_input_set – pymatgen.io.vaspio_set.VaspInputSet like object that creates vasp input files from structures

  • output_dir – Directory to output files

  • create_directory – Create the directory if not present. Defaults to True.

  • **kwargs – All keyword args supported by the VASP input set.