pyiron_atomistics.atomistics.structure.has_structure.TransformStructure

class pyiron_atomistics.atomistics.structure.has_structure.TransformStructure(source: HasStructure, modify: Callable[[Atoms], Atoms])

Bases: HasStructure

Modifies any HasStructure by applying a function to each structure lazily.

__init__(source: HasStructure, modify: Callable[[Atoms], Atoms])

Methods

__init__(source, modify)
animate_structures([spacefill, show_cell, ...])	Animate a series of atomic structures.
collect_structures([filter_function])	Collects a copy of all structures in a compact StructureStorage.
get_structure([frame, wrap_atoms, ...])	Retrieve structure from object.
iter_structures([wrap_atoms])	Iterate over all structures in this object.
transform_structures(modify)	Return a modified object by applying a function to each object lazily.

Attributes

number_of_structures

maximum iteration_step + 1 that can be passed to get_structure().

animate_structures(spacefill: bool = True, show_cell: bool = True, center_of_mass: bool = False, particle_size: float = 0.5, camera: str = 'orthographic')

Animate a series of atomic structures.

Parameters:

• spacefill (bool) – If True, then atoms are visualized in spacefill stype

• show_cell (bool) – True if the cell boundaries of the structure is to be shown

• particle_size (float) – Scaling factor for the spheres representing the atoms. (The radius is determined by the atomic number)

• center_of_mass (bool) – False (default) if the specified positions are w.r.t. the origin

• camera (str) – camera perspective, choose from “orthographic” or “perspective”

Returns:

nglview IPython widget

Return type:

animation

collect_structures(filter_function=None) → StructureStorage

Collects a copy of all structures in a compact StructureStorage.

This can be used to force lazily applied modifications with transform_structures() or simply to obtain a known object type from a generic HasStructure object.

Parameters:

filter_function (function) – include structure only if this function returns True for it

Returns:

a copy of all (filtered) structures

Return type:

StructureStorage

get_structure(frame=-1, wrap_atoms=True, iteration_step=None)

Retrieve structure from object. The number of available structures depends on the job and what kind of calculation has been run on it, see number_of_structures.

Parameters:

frame (int, object) – index of the structure requested, if negative count from the back; if

:param _translate_frame() is overridden: :param frame will pass through it: :param iteration_step: deprecated alias for frame :type iteration_step: int :param wrap_atoms: True if the atoms are to be wrapped back into the unit cell :type wrap_atoms: bool

Returns:

the requested structure

Return type:

pyiron_atomistics.atomistics.structure.atoms.Atoms

Raises:

IndexError – if not -number_of_structures <= iteration_step < number_of_structures

iter_structures(wrap_atoms=True)

Iterate over all structures in this object.

Parameters:

wrap_atoms (bool) – True if the atoms are to be wrapped back into the unit cell; passed to get_structure()

Yields:

pyiron_atomistics.atomistitcs.structure.atoms.Atoms – every structure attached to the object

property number_of_structures

maximum iteration_step + 1 that can be passed to get_structure().

Type:

int

transform_structures(modify) → TransformStructure

Return a modified object by applying a function to each object lazily.

Parameters:

modify (function) – applied to each structure, has to return the modified structure

Returns:

a container with the modified structures

Return type:

TransformStructure