qem.atomic_column

Functions

dataclass([cls, init, repr, eq, order, ...])	Returns the same class as was passed in, with dunder methods added based on the fields defined in the class.
field(*[, default, default_factory, init, ...])	Return an object to identify dataclass fields.

Classes

AtomicColumns(lattice, lattice_ref, ...)

A class to represent atomic columns projected from a 3D atomic lattice onto a 2D plane.

class qem.atomic_column.AtomicColumns(lattice: ase.Atoms, lattice_ref: ase.Atoms, elements: ~typing.List[str] = <factory>, tol: float = 0, pixel_size: float = 0.1, reference: ~typing.Dict[str, numpy.ndarray] = <factory>)

A class to represent atomic columns projected from a 3D atomic lattice onto a 2D plane.

Variables:

• lattice (Atoms) – The 3D atomic lattice.

• lattice_ref (Atoms) – The reference 3D atomic lattice.

• elements (List[str]) – List of element symbols.

• tol (float) – Tolerance for the projection.

• pixel_size (float) – Size of each pixel.

• projection_params (Dict[str, np.ndarray]) – Dictionary containing origin, vector_a, and vector_b for projection.

lattice: ase.Atoms

lattice_ref: ase.Atoms

elements: List[str]

tol: float = 0

pixel_size: float = 0.1

reference: Dict[str, numpy.ndarray]

get_columns()

project the 3d atomic lattice onto the 2d plane in z direction and return the unique atomic columns

Parameters:

tol (float) – tolerance for the projection, within which the atoms are considered to be in the same column

Returns:

coords_2d (np.ndarray) – 2d coordinates of the atomic columns atomic_numbers (np.ndarray): atomic numbers of the atoms in the atomic columns

get_columns_ref()

project the 3d atomic lattice onto the 2d plane in z direction and return the unique atomic columns

Parameters:

tol (float) – tolerance for the projection, within which the atoms are considered to be in the same column

Returns:

coords_2d (np.ndarray) – 2d coordinates of the atomic columns atomic_numbers (np.ndarray): atomic numbers of the atoms in the atomic columns

get_local_displacement(cutoff: float, units='pixel') → numpy.ndarray

Return an array of local displacements.

get_column_displacement(units='pixel') → numpy.ndarray

Return the displacement of the column.

property positions_pixel: numpy.ndarray

Return an array of positions.

property positions_pixel_ref: numpy.ndarray

property x: numpy.ndarray

Return an array of x coordinates.

property y: numpy.ndarray

Return an array of y coordinates.

property x_ref: numpy.ndarray

Return an array of x_ref coordinates.

property y_ref: numpy.ndarray

Return an array of y_ref coordinates.

property num_columns: int

Return the total number of AtomicColumns.

property atomic_numbers: numpy.ndarray

Return an array of atom types.

property column_elements: List[str]

Return a list of column elements.

property atom_types: numpy.ndarray

Return a numpy array of atom types.

get_strain_xy(cutoff: float = 0) → numpy.ndarray

Return the strain matrix.

get_strain(cutoff: float = 3.0) → numpy.ndarray

Return the strain tensor.

__init__(lattice: ase.Atoms, lattice_ref: ase.Atoms, elements: ~typing.List[str] = <factory>, tol: float = 0, pixel_size: float = 0.1, reference: ~typing.Dict[str, numpy.ndarray] = <factory>) → None