httk.atomistic.unitcellstructure module¶

class
httk.atomistic.unitcellstructure.
UnitcellStructure
(assignments=None, uc_sites=None, uc_cell=None)[source]¶ Bases:
httk.core.httkobject.HttkObject
A UnitcellStructure represents N sites of, e.g., atoms or ions, in any periodic or nonperiodic arrangement. It keeps track of all the copies of the atoms within a unitcell.
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.
Naming conventions in httk.atomistic:
 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

classmethod
create
(structure=None, uc_cell=None, uc_basis=None, uc_lengths=None, uc_angles=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, volume_per_atom=None, assignments=None, periodicity=None, nonperiodic_vecs=None, other_reps=None, refs=None, tags=None)[source]¶ A FullStructure represents N sites of, e.g., atoms or ions, in any periodic or nonperiodic arrangement, where the positions of all cites are given (as opposed to a set of unique sites + symmetry operations).
This is a swissarmytype constructor that allows several different ways to create a FullStructure object.
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: uc_prefixes are consistently enforced for any quantity that would be different in a UniqueSitesStructure. This is to allow for painless change between the various structuretype objects without worrying about accidently using the wrong type of sites object.
Note: see help(Structure) for parameter naming conventions, i.e., what type of object is expected given a parameter name.
Input parameters:
ONE OF: ‘uc_cell’; ‘uc_basis’, ‘uc_length_and_angles’; ‘uc_niggli_matrix’; ‘uc_metric’; all of: uc_a,uc_b,uc_c, uc_alpha, uc_beta, uc_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: ‘uc_assignments’, ‘uc_atomic_numbers’, ‘uc_occupations’ (uc_assignments requires an Assignments object or a sequence.), uc_occupations repeats similar site assignments as needed
ONE OF: ‘uc_sites’, ‘uc_coords’ (IF uc_occupations OR uc_counts are also given), or ‘uc_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’].
 uc_sites requires a Sites object or a python list on a very specific format, (so unless you know what you are doing, use one of the others.)
 ONE OF: uc_scale, uc_volume, or volume_per_atom:
scale = multiply the basis vectors with this scaling factor, volume = the unit cell volume (overrides ‘scale’ if both are given) volume_per_atom = cell volume / number of atoms
ONE OF periodicity or nonperiodic_vecs

formula_builder
¶

pbc
¶

supercell
¶

uc_a
¶

uc_alpha
¶

uc_b
¶

uc_basis
¶

uc_beta
¶

uc_c
¶

uc_cartesian_coordgroups
¶

uc_cartesian_coords
¶

uc_cartesian_occupationscoords
¶

uc_cell_orientation
¶

uc_counts
¶

uc_gamma
¶

uc_lengths_and_angles
¶

uc_reduced_coordgroups
¶

uc_reduced_coords
¶

uc_volume
¶

uc_volume_per_atom
¶