The httk.atomistic package

This page documents the features of the httk.atomistic package most relevant for regular users. For a complete listing of members and subpackages, please refer to the full API documentation instead, Full httk API documentation.

Introduction

The httk.atomistic package

Classes and utilities for dealing with high-throughput calculations of atomistic systems.

Atomistic description

class httk.atomistic.Structure(assignments, rc_sites=None, rc_cell=None, other_reps=None)[source]

A Structure represents N sites of, e.g., atoms or ions, in any periodic or non-periodic 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 sequence-type 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 3-level-list of coordinates, e.g. [[[0,0,0],[0.5,0.5,0.5]],[[0.25,0.25,0.25]]] where level-1 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 2-level 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 / non-periodic

nonperiodic_vecs = integer, number of basis vectors, counted from the first, which are non-periodic

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

class httk.atomistic.Cell(basis, lattice_system, orientation=1)[source]

Represents a cell (e.g., a unitcell, but also possibly just the basis vectors of a non-periodic system)

(The ability to represent the cell for a non-periodic system is also the reason this class is not called Lattice.)

class httk.atomistic.UnitcellStructure(assignments=None, uc_sites=None, uc_cell=None)[source]

A UnitcellStructure represents N sites of, e.g., atoms or ions, in any periodic or non-periodic 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 sequence-type 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 3-level-list of coordinates, e.g. [[[0,0,0],[0.5,0.5,0.5]],[[0.25,0.25,0.25]]] where level-1 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 2-level 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 / non-periodic

nonperiodic_vecs = integer, number of basis vectors, counted from the first, which are non-periodic

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

class httk.atomistic.RepresentativeSites(reduced_coordgroups=None, cartesian_coordgroups=None, reduced_coords=None, cartesian_coords=None, counts=None, hall_symbol=None, pbc=None, wyckoff_symbols=None, multiplicities=None)[source]

Represents any collection of sites in a unitcell

class httk.atomistic.UnitcellSites(reduced_coordgroups=None, reduced_coords=None, counts=None, hall_symbol='P 1', pbc=None)[source]

Represents any collection of sites in a unitcell

class httk.atomistic.Assignments(siteassignments, extensions=[])[source]

Represents a possible vector of assignments

class httk.atomistic.Compound(element_wyckoff_sequence, formula, spacegroup_number, extended, extensions, wyckoff_sequence, anonymous_wyckoff_sequence, anonymous_formula, formula_symbols, formula_counts, pbc)[source]
class httk.atomistic.CompoundStructure(compound, structure)[source]
class httk.atomistic.StructurePhaseDiagram(structures, energies, hull_indices, competing_indices, hull_competing_indices, hull_distances, coord_system, phase_lines)[source]

Represents a phase diagram of structures