wulfric.Crystal

class wulfric.Crystal(lattice: Lattice = None, atoms=None, relative=True, **kwargs)

Crystal class.

It is a child of Lattice class.

Iterable over atoms. All attributes of the Lattice are accessible directly from the crystal:

>>> import wulfric as wulf
>>> cub = wulf.lattice_example("CUB")
>>> crystal = wulf.Crystal(cub)
>>> crystal.pearson_symbol
'cP'

For the full description of the lattice attributes and methods see Lattice.

Parameters:

latticeLattice, optional

Lattice of the crystal. If not provided, then orthonormal lattice is used ("CUB with \(a = 1\)).

atomslist, optional

List of Atom objects.

relativebool, default True

Whether atoms positions are in relative coordinates.

**kwargs

Keyword arguments for Lattice initialization.

Attributes:

atomslist

List of atoms of the crystal.

Methods:

add_atom([new_atom, relative])	Add atom to the crystal.
copy()	Copy of the crystal.
cure_negative()	Shifts all atoms with the same vector in a way that all relative coordinates becomes non-negative.
find_primitive_cell()	Detect primitive cell.
get_atom(name[, index, return_all])	Return atom object of the crystal.
get_atom_coordinates(atom[, R, index, relative])	Getter for the atom coordinates.
get_distance(atom1, atom2[, R, index1, ...])	Getter for distance between the atom1 and atom2.
get_vector(atom1, atom2[, R, index1, ...])	Getter for vector from atom1 to atom2.
remove_atom(atom[, index])	Remove atom from the crystal.
shift_atoms([gravity_point, relative])	Shifts all atoms with the same vector in a way that the gravity_point is located in the middle between minimum and maximum relative coordinates of the atoms, individually for each lattice vector.
standardize()	Standardize cell with respect to the Bravais lattice type as defined in [R01e341c7223d-1].
type([eps_rel, angle_tol])	Identify the lattice type.
voronoi_cell([reciprocal, normalize])	Computes Voronoi edges around (0,0,0) point.

Properties:

C_matrix	Transformation matrix that transforms primitive cell (Lattice.cell()) to the conventional standardized cell.
S_matrix	Transformation matrix that transforms the primitive cell to the standardized primitive cell.
a	Length of the first lattice vector \(\vert\boldsymbol{a_1}\vert\).
a1	First lattice vector \(\boldsymbol{a_1}\).
a2	Second lattice vector \(\boldsymbol{a_2}\).
a3	Third lattice vector \(\boldsymbol{a_3}\).
alpha	Angle between second and third lattice vector.
angle_tol	Absolute tolerance for the angle.
b	Length of the second lattice vector \(\vert\boldsymbol{a_2}\vert\).
b1	First reciprocal lattice vector.
b2	Second reciprocal lattice vector.
b3	Third reciprocal lattice vector.
beta	Angle between first and third lattice vector.
c	Length of the third lattice vector \(\vert\boldsymbol{a_3}\vert\).
cell	Unit cell of the lattice.
centring_type	Centring type.
conv_a	Length of the first vector of the conventional cell.
conv_a1	First vector of the conventional cell.
conv_a2	Second vector of the conventional cell.
conv_a3	Third vector of the conventional cell.
conv_alpha	Angle between second and third conventional lattice vector.
conv_b	Length of the second vector of the conventional cell.
conv_beta	Angle between first and third conventional lattice vector.
conv_c	Length of the third vector of the conventional cell.
conv_cell	Conventional cell.
conv_gamma	Angle between first and second conventional lattice vector.
conv_parameters	Return conventional cell parameters.
conv_unit_cell_volume	Volume of the conventional unit cell.
convention	Convention used for the standardization of the unit cell.
crystal_family	Crystal family.
eps	Absolute tolerance for the distance.
eps_rel	Relative tolerance for the distance.
gamma	Angle between first and second lattice vector.
k_a	Length of the first reciprocal lattice vector \(\vert\boldsymbol{b_1}\vert\).
k_alpha	Angle between second and third reciprocal lattice vector.
k_b	Length of the second reciprocal lattice vector \(\vert\boldsymbol{b_2}\vert\).
k_beta	Angle between first and third reciprocal lattice vector.
k_c	Length of the third reciprocal lattice vector \(\vert\boldsymbol{b_3}\vert\).
k_gamma	Angle between first and second reciprocal lattice vector.
kpoints	Instance of Kpoints with the high symmetry points and path.
lattice	Lattice of the crystal.
name	Human-readable name of the Bravais lattice type.
parameters	Return cell parameters.
pearson_symbol	Pearson symbol.
rcell	Reciprocal cell.
reciprocal_cell	Reciprocal cell.
reciprocal_cell_volume	Volume of the reciprocal cell.
reciprocal_parameters	Return reciprocal cell parameters.
unit_cell_volume	Volume of the unit cell.
variation	Variation of the lattice, if any.