aiida_vasp.common.transform

Collection of process functions for AiiDA, used for structure transformation

Module Contents

Functions

magnetic_structure_decorate	Create Quantum Espresso style decorated structure with given magnetic moments.
magnetic_structure_dedecorate	Remove decorations of a structure with multiple names for the same specie given that the decoration was previously created to give different species name for different initialisation of magnetic moments.
rattle	Rattle the structure by a certain amplitude
random_rattle	Rattle the structure by a certain amplitude
get_primitive	Create primitive structure use pymatgen interface
get_standard_primitive	Create the standard primitive structure via seekpath
spglib_refine_cell	Create the standard primitive structure via seekpath
get_standard_conventional	Create the standard primitive structure via seekpath
get_refined_structure	Create refined structure use pymatgen’s interface
get_conventional_standard_structure	Create conventional standard structure use pymatgen’s interface
make_supercell	Make supercell structure, keep the tags in order
niggli_reduce	Peroform niggli reduction using ase as the backend - this will rotate the structure into the standard setting
niggli_reduce_spglib	Peroform niggli reduction using spglib as backend - this does not rotate the structure
neb_interpolate	Interpolate NEB frames using the starting and the final structures
fix_atom_order	Fix atom order by finding NN distances bet ween two frames. This resolves the issue where two closely matching structures having diffferent atomic orders. Note that the two frames must be close enough for this to work
match_atomic_order_	Reorder the atoms to that of the reference.
create_additional_species	Create additional species depending on magnetic moments. For example, create Fe1 and Fe2 if there are Fe with different magnetisations.
convert_to_plain_list	Covert from a decorated species list to a plain list of symbols and magnetic moments.

API

aiida_vasp.common.transform.magnetic_structure_decorate(structure: aiida.orm.StructureData, magmom: aiida.orm.List) → dict[str, Any]

Create Quantum Espresso style decorated structure with given magnetic moments.

aiida_vasp.common.transform.magnetic_structure_dedecorate(structure: aiida.orm.StructureData, mapping: aiida.orm.Dict) → dict[str, Any]

Remove decorations of a structure with multiple names for the same specie given that the decoration was previously created to give different species name for different initialisation of magnetic moments.

aiida_vasp.common.transform.rattle(structure: aiida.orm.StructureData, amp: aiida.orm.Float) → aiida.orm.StructureData

Rattle the structure by a certain amplitude

aiida_vasp.common.transform.random_rattle(structure: aiida.orm.StructureData, amp: aiida.orm.Float) → aiida.orm.StructureData

Rattle the structure by a certain amplitude

This function is similar to rattle, but it uses a random seed so it generates different structures when called with the same structure.

aiida_vasp.common.transform.get_primitive(structure: aiida.orm.StructureData) → aiida.orm.StructureData

Create primitive structure use pymatgen interface

aiida_vasp.common.transform.get_standard_primitive(structure: aiida.orm.StructureData, **kwargs: Any) → aiida.orm.StructureData

Create the standard primitive structure via seekpath

aiida_vasp.common.transform.spglib_refine_cell(structure: aiida.orm.StructureData, symprec: Any) → aiida.orm.StructureData

Create the standard primitive structure via seekpath

aiida_vasp.common.transform.get_standard_conventional(structure: aiida.orm.StructureData) → aiida.orm.StructureData

Create the standard primitive structure via seekpath

aiida_vasp.common.transform.get_refined_structure(structure: aiida.orm.StructureData, symprec: aiida.orm.Float, angle_tolerance: Any) → aiida.orm.StructureData

Create refined structure use pymatgen’s interface

aiida_vasp.common.transform.get_conventional_standard_structure(structure: aiida.orm.StructureData, symprec: aiida.orm.Float, angle_tolerance: Any) → Any

Create conventional standard structure use pymatgen’s interface

aiida_vasp.common.transform.make_supercell(structure: Any, supercell: Any, **kwargs: Any) → dict[str, Any]

Make supercell structure, keep the tags in order

aiida_vasp.common.transform.niggli_reduce(structure: aiida.orm.StructureData) → aiida.orm.StructureData

Peroform niggli reduction using ase as the backend - this will rotate the structure into the standard setting

aiida_vasp.common.transform.niggli_reduce_spglib(structure: aiida.orm.StructureData) → aiida.orm.StructureData

Peroform niggli reduction using spglib as backend - this does not rotate the structure

aiida_vasp.common.transform.neb_interpolate(init_structure: aiida.orm.StructureData, final_strucrture: aiida.orm.StructureData, nimages: aiida.orm.Int) → dict[str, aiida.orm.StructureData]

Interpolate NEB frames using the starting and the final structures

Get around the PBC wrapping problem by calculating the MIC displacements from the initial to the final structure

The initial structure is not changed, while the final structure is modified to be consistent with the initial structure in terms of absolute displacements, i.e. the final structure is unwrapped.

aiida_vasp.common.transform.fix_atom_order(reference: aiida.orm.StructureData, to_fix: aiida.orm.StructureData) → aiida.orm.StructureData

Fix atom order by finding NN distances bet ween two frames. This resolves the issue where two closely matching structures having diffferent atomic orders. Note that the two frames must be close enough for this to work

aiida_vasp.common.transform.match_atomic_order_(atoms: ase.Atoms, atoms_ref: ase.Atoms) → Tuple[ase.Atoms, List[int]]

Reorder the atoms to that of the reference.

Only works for identical or nearly identical structures that are ordered differently. Returns a new Atoms object with order similar to that of atoms_ref as well as the sorting indices.

aiida_vasp.common.transform.create_additional_species(species: list[str], magmoms: list[float]) → tuple[list[str], dict[str, float]]

Create additional species depending on magnetic moments. For example, create Fe1 and Fe2 if there are Fe with different magnetisations.

Returns:

a tuples of (newspecies, magmom_mapping)

aiida_vasp.common.transform.convert_to_plain_list(species: list[str], magmom_mapping: dict[str, float]) → tuple[list[str], list[float]]

Covert from a decorated species list to a plain list of symbols and magnetic moments.

Returns:

A tuple of (symbols, magmoms)