Site

class ase2sprkkr.sprkkr.sites.Site(atoms, occupation, reference_system=None, mesh=None)

Definition of an atomic site. (By symmetry) equivalent sites should share the same definition. However, two same (by their atomic number) atoms in a spatially different positions (i.e. not by symmetry equal) should not share the same property.

Class hierarchy

Constructor

__init__(atoms, occupation, reference_system=None, mesh=None)

Parameters

• occupation (dict) –

  { AtomicType: fraction } The type of the atom

  Occupation of the site. If None is given, the default occupation of { T : 1.0 } is used, where T is determined by ASE atomic number corresponding to the site.

• atoms (SPRKKRAtoms) – The atoms, into which the Site belongs

• reference_system (ReferenceSystem) – Default reference system is used if None is given

• mesh (Mesh) – Default ExponentialMesh is used if None is given

copy()

Create a copy of the site.

reset()

Set the properties of the site to the default.

Currently, it resets the mesh.

property occupation

Occupation<ase2sprkkr.sprkkr.occupations.Occupation>` - that represent the occupation of the site by atoms. The occupation captures the probability of occurence of the given atoms on the site. There can be only partial occupancy (the probability, that there is an atom on the site is not 100%).

The method creates the occupation, if it not exists, according to the ASE atoms object (using occpancy and symbols)

Type

The method returns the `

Type

class

property primary_symbol

Symbol of the most important (most probable) chemical element present on the site.

index()

Return the the sites-array (of the owning atoms object) index for this site.

update_atoms()

Update atomic numbers and occupation according to the sites data.

is_vacuum()

Is the site vacuum pseudoatom?

Return type

bool

property atomic_types

This method provides the access to the atomic types of the current site.

Returns

atomic_types – Object, that can be indexed either by integer - position in the occupation (ordered) dictionary, or string - chemical symbol. It returns the atomic type, corresponding to the current position.

Return type

AtomicTypesLookup

static copy_sites(sites)