AtomsRegion

class ase2sprkkr.sprkkr.atoms_region.AtomsRegion(name, slice, cell, pbc=[True, True, True], inherit_cell=False, atoms=None)

AtomsRegion define a region of Atoms object, that can have its own cell and pbc.

E.g. this system:

|^^T^^^^^^^^^^^^^^^^^^^T^^|
|  |                   |  |
|__|___________________|__|

has two semiinfinite 3D periodic regions and a central 2D-symmetric region.

Class hierarchy

Constructor

Parameters

• name (str) –

• slice (slice) –

• cell (Union[Cell, ndarray]) –

• pbc (List[Optional[bool]]) –

• inherit_cell (Union[bool, List[bool]]) –

• atoms (Atoms) –

__init__(name, slice, cell, pbc=[True, True, True], inherit_cell=False, atoms=None)

Atoms region defines a spatial part of an Atoms object. The cell can has zero vectors - such vectors are taken from the parent atoms object.

Parameters

• slice (slice) – Which sites (atoms) belong to the region

• cell (Union[Cell, ndarray]) – The primitive cell

• pbc (List[Optional[bool]]) – The peridodicity vector (see ase.Atoms)

• inherit_cell (Union[bool, List[bool]]) – Inherit the cell and the pcb from the parent atoms for given axes. Use of this argument is the same, as setting pcb to None and cell to [0,0,0] for the given axes.

• atoms (Optional[Atoms]) – The master object, of which the region is defined

• name (str) –

static from_atoms(from_atoms, name, slice, inherit_cell=False, atoms=None)

Creates a region from the property of the given atoms object. The pbc and cell are taken from it.

Parameters

• from_atoms (Atoms) –

• name (str) –

• slice (slice) –

• atoms (Optional[Atoms]) –

property cell

Return the cell.

If the cell has some zero vectors, these are replaced with parent atoms cell vectors

property pbc

Return the pbc

If the pbc has None items, these are replace with parent atoms pbc values

property slice

_clear_cache()

set_atoms(atoms, add=True)

Set the master atoms - of which the region is described

create_atoms()

Create an atoms object, that contains only the region

property symbols

Return the symbols in the region

shared_ids_with(region)

Return ids of the sites, that belongs to the both regions

property ids

Returns ids of sites that belongs to the region

property set_of_ids

Returns set of ids of sites that belongs to the region

property positions

only_vacuum_atoms()