pymatgen.alchemy.transmuters module

This module implements various transmuter classes. Transmuters are essentially classes that generate TransformedStructures from various data sources. They enable the high-throughput generation of new structures and input files.

It also includes the helper function, batch_write_vasp_input to generate an entire directory of vasp input files for running.

class CifTransmuter(cif_string, transformations=None, primitive=True, extend_collection=False)[source]

Bases: pymatgen.alchemy.transmuters.StandardTransmuter

Generates a Transmuter from a cif string, possibly containing multiple structures.

Generates a Transmuter from a cif string, possibly containing multiple structures.

Parameters
  • cif_string – A string containing a cif or a series of cifs

  • transformations – New transformations to be applied to all structures

  • primitive – Whether to generate the primitive cell from the cif.

  • extend_collection – Whether to use more than one output structure from one-to-many transformations. extend_collection can be a number, which determines the maximum branching for each transformation.

static from_filenames(filenames, transformations=None, primitive=True, extend_collection=False)[source]

Generates a TransformedStructureCollection from a cif, possibly containing multiple structures.

Parameters
  • filenames – List of strings of the cif files

  • transformations – New transformations to be applied to all structures

  • primitive – Same meaning as in __init__.

  • extend_collection – Same meaning as in __init__.

class PoscarTransmuter(poscar_string, transformations=None, extend_collection=False)[source]

Bases: pymatgen.alchemy.transmuters.StandardTransmuter

Generates a transmuter from a sequence of POSCARs.

Parameters
  • poscar_string – List of POSCAR strings

  • transformations – New transformations to be applied to all structures.

  • extend_collection – Whether to use more than one output structure from one-to-many transformations.

Initializes a transmuter from an initial list of pymatgen.alchemy.materials.TransformedStructure.

Parameters
  • transformed_structures ([TransformedStructure]) – Input transformed structures

  • transformations ([Transformations]) – New transformations to be applied to all structures.

  • extend_collection (int) – Whether to use more than one output structure from one-to-many transformations. extend_collection can be an int, which determines the maximum branching for each transformation.

  • ncores (int) – Number of cores to use for applying transformations. Uses multiprocessing.Pool. Default is None, which implies serial.

static from_filenames(poscar_filenames, transformations=None, extend_collection=False)[source]

Convenient constructor to generates a POSCAR transmuter from a list of POSCAR filenames.

Parameters
  • poscar_filenames – List of POSCAR filenames

  • transformations – New transformations to be applied to all structures.

  • extend_collection – Same meaning as in __init__.

class StandardTransmuter(transformed_structures, transformations=None, extend_collection=0, ncores=None)[source]

Bases: object

An example of a Transmuter object, which performs a sequence of transformations on many structures to generate TransformedStructures.

Initializes a transmuter from an initial list of pymatgen.alchemy.materials.TransformedStructure.

Parameters
  • transformed_structures ([TransformedStructure]) – Input transformed structures

  • transformations ([Transformations]) – New transformations to be applied to all structures.

  • extend_collection (int) – Whether to use more than one output structure from one-to-many transformations. extend_collection can be an int, which determines the maximum branching for each transformation.

  • ncores (int) – Number of cores to use for applying transformations. Uses multiprocessing.Pool. Default is None, which implies serial.

add_tags(tags)[source]

Add tags for the structures generated by the transmuter.

Parameters

tags – A sequence of tags. Note that this should be a sequence of strings, e.g., [“My awesome structures”, “Project X”].

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

Appends a transformation to all TransformedStructures.

Parameters
  • transformation – Transformation to append

  • extend_collection – Whether to use more than one output structure from one-to-many transformations. extend_collection can be a number, which determines the maximum branching for each transformation.

  • clear_redo (bool) – 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.

Returns

List of booleans corresponding to initial transformed structures each boolean describes whether the transformation altered the structure

append_transformed_structures(tstructs_or_transmuter)[source]

Method is overloaded to accept either a list of transformed structures or transmuter, it which case it appends the second transmuter”s structures.

Parameters

tstructs_or_transmuter – A list of transformed structures or a transmuter.

apply_filter(structure_filter)[source]

Applies a structure_filter to the list of TransformedStructures in the transmuter.

Parameters

structure_filter – StructureFilter to apply.

extend_transformations(transformations)[source]

Extends a sequence of transformations to the TransformedStructure.

Parameters

transformations – Sequence of Transformations

static from_structures(structures, transformations=None, extend_collection=0)[source]

Alternative constructor from structures rather than TransformedStructures.

Parameters
  • structures – Sequence of structures

  • transformations – New transformations to be applied to all structures

  • extend_collection – Whether to use more than one output structure from one-to-many transformations. extend_collection can be a number, which determines the maximum branching for each transformation.

Returns

StandardTransmuter

redo_next_change()[source]

Redo the last undone transformation in the TransformedStructure.

Raises

IndexError if already at the latest change.

set_parameter(key, value)[source]

Add parameters to the transmuter. Additional parameters are stored in the as_dict() output.

Parameters
  • key – The key for the parameter.

  • value – The value for the parameter.

undo_last_change()[source]

Undo the last transformation in the TransformedStructure.

Raises

IndexError if already at the oldest change.

write_vasp_input(**kwargs)[source]

Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{formula}_{number}.

Parameters

**kwargs – All kwargs supported by batch_write_vasp_input.

batch_write_vasp_input(transformed_structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', create_directory=True, subfolder=None, include_cif=False, **kwargs)[source]

Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

Parameters
  • transformed_structures – Sequence of TransformedStructures.

  • vasp_input_set – pymatgen.io.vaspio_set.VaspInputSet to creates vasp input files from structures.

  • output_dir – Directory to output files

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

  • subfolder – Function to create subdirectory name from transformed_structure. e.g., lambda x: x.other_parameters[“tags”][0] to use the first tag.

  • include_cif (bool) – Boolean indication whether to output a CIF as well. CIF files are generally better supported in visualization programs.