httk.atomistic.representativestructure module

class httk.atomistic.representativestructure.RepresentativeStructure(assignments, rc_sites=None, rc_cell=None)[source]

Bases: HttkObject

A RepresentativeStructure represents N sites of, e.g., atoms or ions, in any periodic or non-periodic arrangement. It keeps track of a set of representative atoms in a unit cell (the conventional cell) and the symmetry group / operations that are to be applied to them to get all atoms.

This is meant to be a light-weight Structure object. For a heavy-weight with more functionality, use Structure.

The RepresentativeStructure object is meant to be immutable and assumes that no internal variables are changed after its creation. All methods that ‘changes’ the object creates and returns a new, updated, structure object.

clean()[source]
classmethod create(structure=None, rc_cell=None, rc_basis=None, rc_lengths=None, rc_angles=None, rc_niggli_matrix=None, rc_metric=None, rc_a=None, rc_b=None, rc_c=None, rc_alpha=None, rc_beta=None, rc_gamma=None, rc_sites=None, rc_reduced_coordgroups=None, rc_cartesian_coordgroups=None, rc_reduced_coords=None, rc_cartesian_coords=None, rc_reduced_occupationscoords=None, rc_cartesian_occupationscoords=None, rc_occupancies=None, rc_counts=None, wyckoff_symbols=None, multiplicities=None, spacegroup=None, hall_symbol=None, spacegroupnumber=None, setting=None, rc_scale=None, rc_scaling=None, rc_volume=None, vol_per_atom=None, assignments=None, periodicity=None, nonperiodic_vecs=None, refs=None, tags=None)[source]

A Structure represents N sites of, e.g., atoms or ions, in any periodic or non-periodic arrangement.

This is a swiss-army-type constructor that allows a selection between a large number of optional arguments.

To create a new structure, three primary components are:
  • cell: defines the basis vectors in which reduced coordinates are expressed, and the

    unit of repetition (if the structure has any periodicity - see the ‘periodicity’ parameter)

  • assignments: a list of ‘things’ (atoms, ions, etc.) that goes on the sites in the structure

  • sites: a sensible representation of location / coordinates of the sites.

Note: rc_-prefixes are consistently enforced for any quantity that would be different in a UnitcellStructure. This is to allow for painless change between the various structure-type objects without worrying about accidently using the wrong type of sites object.

Input parameters:

  • ONE OF: ‘cell’; ‘basis’, ‘length_and_angles’; ‘niggli_matrix’; ‘metric’; all of: a,b,c, alpha, beta, gamma. (cell requires a Cell object or a very specific format, so unless you know what you are doing, use one of the others.)

  • ONE OF: ‘assignments’, ‘atomic_numbers’, ‘occupancies’ (assignments requires an Assignments object or a sequence.), occupations repeats similar site assignments as needed

  • ONE OF: ‘rc_sites’, ‘rc_coords’ (IF rc_occupations OR rc_counts are also given), ‘uc_coords’ (IF uc_occupations OR uc_counts are also given) ‘rc_B_C’, where B=reduced or cartesian, C=coordgroups, coords, or occupationscoords

    Notes:

    • occupationscoords may differ from coords by order, since giving occupations as, e.g., [‘H’,’O’,’H’] does not necessarily have the same order of the coordinates as the format of counts+coords as (2,1), [‘H’,’O’].

    • rc_sites and uc_sites requires a Sites object or a very specific format, so unless you know what you are doing, use one of the others.)

  • ONE OF: scale or volume:

    scale = multiply the basis vectors with this scaling factor, volume = the representative (conventional) cell volume (overrides ‘scale’ if both are given) volume_per_atom = cell volume / number of atoms

  • ONE OF periodicity or nonperiodic_vecs

See help(Structure) for more information on the data format of all these data representations.

formula_builder
property pbc
property rc_a
property rc_alpha
property rc_b
property rc_basis
property rc_beta
property rc_c
property rc_cartesian_coordgroups
property rc_cartesian_coords
property rc_cartesian_occupationscoords
property rc_cell_orientation
property rc_gamma
property rc_lengths_and_angles
property rc_volume
property uc_volume_per_atom
classmethod use(other)[source]
httk.atomistic.representativestructure.main()[source]