pyprocar.core.Structure

class pyprocar.core.Structure(atoms=None, cartesian_coordinates=None, fractional_coordinates=None, lattice=None, rotations=None)

Class to define a peridic crystal structure.

Parameters:

• atoms (list str) – A list of atomic symbols, with the same order as the fractional_coordinates.

• fractional_coordinates (list (n,3) float.) – A (natom,3) list of fractional coordinatesd of atoms.

• lattice (list (3,3) float.) – A (3,3) matrix representing the lattice vectors.

Returns:

None.

Methods

Structure.__init__([atoms, ...])
Structure.get_space_group_international([...])	Returns the international Space Group Number of the material
Structure.get_space_group_number([symprec])	Returns the Space Group Number of the material
Structure.get_spglib_symmetry_dataset([symprec])	Returns the spglib symmetry dataset
Structure.get_wyckoff_positions([symprec])	Returns the wyckoff positions
Structure.is_point_inside(point[, lattice])	A method to determine if a point is inside the unitcell
Structure.plot_cell_convex_hull()	A method to plot the the convex hull
Structure.supercell(matrix)	A method to transform the Structure to a supercell
Structure.transform([transformation_matrix])	Transform the crystla lattice by a transformation matrix

Attributes

Structure.a	The magnitude of the first crystal lattice vector
Structure.alpha	The angle between the of the second and third crystal lattice vectors
Structure.atomic_numbers	List of atomic numbers
Structure.b	The magnitude of the second crystal lattice vector
Structure.beta	The angle between the of the first and third crystal lattice vectors
Structure.c	The magnitude of the third crystal lattice vector
Structure.cell_convex_hull	Returns the cell convex hull
Structure.density	Density of the cell.
Structure.gamma	The angle between the of the first and second crystal lattice vectors
Structure.lattice_corners	Returns the corners of the crystal lattice
Structure.masses	list of masses of each atom.
Structure.natoms	Number of atoms
Structure.nspecies	Number of species present in the cell.
Structure.reciprocal_lattice	The reciprocal lattice matrix corresponding the the crystal lattice
Structure.species	list of different species present in the cell.
Structure.volume	Volume of the unit cell.