httk.atomistic.structure module¶

class
httk.atomistic.structure.
Structure
(assignments, rc_sites=None, rc_cell=None, other_reps=None)[source]¶ Bases:
httk.core.httkobject.HttkObject
A Structure represents N sites of, e.g., atoms or ions, in any periodic or nonperiodic arrangement. The structure 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.
This is the general heavy weight structure object. For lightweight structure objects, use UnitcellStructure or RepresentativeStructure.
Naming conventions in httk.atomistic:
 Structure cell type abbreviations:
 rc = Representative cell: only representative atoms are given inside the conventional cell.
 they need to be replicated by the symmetry elements.
 uc = Unit cell: any (imprecisely defined) unit cell (usually the unit cell used to define the structure
 if it was not done via a representative cell.) with all atoms inside.
pc = Primitive unit cell: a smallest possible unit cell (the standard one) with all atoms inside.
cc = Conventional unit cell: the high symmetry unit cell (rc) with all atoms inside.
 For cells:
 cell = an abstract name for any reasonable representation of a ‘cell’ that defines
 the basis vectors used for representing the structure. When a ‘cell’ is returned, it is an object of type Cell
basis = a 3x3 sequencetype with (in rows) the three basis vectors (for a periodic system, defining the unit cell, and defines the unit of repetition for the periodic dimensions)
lengths_and_angles = (a,b,c,alpha,beta,gamma): the basis vector lengths and angles
niggli_matrix = ((v1*v1, v2*v2, v3*v3),(2*v2*v3, 2*v1*v3, 2*v2*v3)) where v1, v2, v3 are the vectors forming the basis
metric = ((v1*v1,v1*v2,v1*v3),(v2*v1,v2*v2,v2*v3),(v3*v1,v3*v2,v3*v3))
 For sites:
 These following prefixes are used to describe types of site specifications:
representative cell/rc = only representative atoms are given, which are then to be repeated by structure symmetry group to give all sites
unit cell/uc = all atoms in unitcell
reduced = coordinates given in cell vectors
cartesian = coordinates given as direct cartesian coordinates
 sites = used as an abstract name for any sensible representation of a list of coordinates and a cell,
 when a ‘sites’ is returned, it is an object of type Sites
counts = number of atoms of each type (one per entry in assignments)
coordgroups = coordinates represented as a 3levellist of coordinates, e.g. [[[0,0,0],[0.5,0.5,0.5]],[[0.25,0.25,0.25]]] where level1 list = groups: one group for each equivalent atom
counts and coords = one list with the number of atoms of each type (one per entry in assignments) and a 2level list of coordinates.
 For assignments of atoms, etc. to sites:
assignments = abstract name for any representation of assignment of atoms. When returned, will be object of type Assignment.
atomic_numbers = a sequence of integers for the atomic number of each species
occupations = a sequence where the assignments are repeated for each coordinate as needed (prefixed with uc or rc depending on which coordinates)
 For cell scaling:
scaling = abstract name for any representation of cell scaling
scale = multiply all basis vectors with this number
volume = rescaling the cell such that it takes this volume
 For periodicity:
periodicity = abstract name of a representation of periodicity
pbc = ‘periodic boundary conditions’ = sequence of True and False for which basis vectors are periodic / nonperiodic
nonperiodic_vecs = integer, number of basis vectors, counted from the first, which are nonperiodic
 For spacegroup:
spacegroup = abstract name for any spacegroup representation. When returned, is of type Spacegroup.
hall_symbol = specifically the hall_symbol string representation of the spacegroup

anonymous_formula
¶

anonymous_wyckoff_sequence
¶

cc
¶

cc_formula_parts
¶

classmethod
create
(structure=None, assignments=None, rc_cell=None, rc_basis=None, rc_lengths=None, rc_angles=None, rc_cosangles=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, uc_cell=None, uc_basis=None, uc_lengths=None, uc_angles=None, uc_cosangles=None, uc_niggli_matrix=None, uc_metric=None, uc_a=None, uc_b=None, uc_c=None, uc_alpha=None, uc_beta=None, uc_gamma=None, uc_sites=None, uc_reduced_coordgroups=None, uc_cartesian_coordgroups=None, uc_reduced_coords=None, uc_cartesian_coords=None, uc_reduced_occupationscoords=None, uc_cartesian_occupationscoords=None, uc_occupancies=None, uc_counts=None, uc_scale=None, uc_scaling=None, uc_volume=None, uc_is_primitive_cell=False, uc_is_conventional_cell=False, volume_per_atom=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 nonperiodic arrangement.
This is a swissarmytype constructor that allows a selection between a large number of optional arguments.
Note: if redundant and noncompatible information is given, the behavior is undefined. E.g., don’t try to call this with a structure + a volume in hopes to get a copy with rescaled volume.
 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 structuretype 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.

element_wyckoff_sequence
¶

extended
¶

extensions
¶

formula
¶

formula_counts
¶

formula_spaceseparated
¶

formula_symbols
¶

hall_symbol
¶

has_rc_repr
¶ Returns True if the structure already contains the representative coordinates + spacegroup, and thus can be queried for this data without launching an expensive symmetry finder operation.

has_uc_repr
¶ Returns True if the structure contains any unit celltype coordinate representation, and thus can be queried for this data without launching a somewhat expensive cell filling operation.

io
¶

number_of_elements
¶

pbc
¶

pc
¶

pc_a
¶

pc_alpha
¶

pc_b
¶

pc_beta
¶

pc_c
¶

pc_counts
¶

pc_formula_parts
¶

pc_gamma
¶

pc_nbr_atoms
¶

pc_volume
¶

rc
¶

rc_a
¶

rc_alpha
¶

rc_b
¶

rc_basis
¶

rc_beta
¶

rc_c
¶

rc_cartesian_coordgroups
¶

rc_cartesian_coords
¶

rc_cartesian_occupationscoords
¶

rc_cell_orientation
¶

rc_counts
¶

rc_gamma
¶

rc_lengths_and_angles
¶

rc_nbr_atoms
¶

rc_occupancies
¶

rc_occupationssymbols
¶

rc_reduced_coordgroups
¶

rc_reduced_coords
¶

rc_volume
¶

spacegroup
¶

spacegroup_number
¶

spacegroup_number_and_setting
¶

supercell
¶

symbols
¶

uc
¶

uc_a
¶

uc_alpha
¶

uc_b
¶

uc_basis
¶

uc_beta
¶

uc_c
¶

uc_cartesian_coordgroups
¶

uc_cartesian_coords
¶

uc_cartesian_occupationscoords
¶

uc_cell
¶

uc_cell_orientation
¶

uc_counts
¶

uc_formula
¶

uc_formula_counts
¶

uc_formula_parts
¶

uc_formula_symbols
¶

uc_gamma
¶

uc_lengths_and_angles
¶

uc_nbr_atoms
¶

uc_occupancies
¶

uc_occupationssymbols
¶

uc_reduced_coordgroups
¶

uc_reduced_coords
¶

uc_reduced_occupationscoords
¶

uc_sites
¶

uc_volume
¶

volume_per_atom
¶

wyckoff_sequence
¶