crystals.Crystal

class crystals.Crystal(unitcell: Iterable[Atom | AtomicStructure], lattice_vectors: _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes], source: str | None = None, **kwargs)

The Crystal class is a set-like container that represent crystalline structures. In addition to constructing the Crystal object yourself, other constructors are also available (and preferred):

• Crystal.from_cif(): create an instance from a CIF file;

• Crystal.from_pdb(): create an instance from a Protein Data Bank entry;

• Crystal.from_database(): create an instance from the internal database of CIF files;

• Crystal.from_cod(): create an instance from a Crystallography Open Database entry;

• Crystal.from_mp(): create an instance from the Materials Project database;

• Crystal.from_pwscf(): create an instance from the output of the PWSCF program;

• Crystal.from_ase(): create an instance from an ase.Atoms instance;

• Crystal.from_poscar(): create an instance from VASP POSCAR files.

Parameters:

• unitcell (iterable of Atom or AtomicStructure) – Unit cell atoms or substructures. It is assumed that the atoms are in fractional coordinates.

• lattice_vectors (iterable of array_like) – Lattice vectors. If lattice_vectors is provided as a 3x3 array, it is assumed that each lattice vector is a row.

• source (str or None, optional) – Provenance, e.g. filename. Only used for bookkeeping.

__init__(unitcell: Iterable[Atom | AtomicStructure], lattice_vectors: _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes], source: str | None = None, **kwargs)

Methods

__add__(other)	Create a new structure made from the combination of two structures.
__array__(*args, **kwargs)	Returns an array in which each row represents an Atom instance.
__bool__()	An AtomicStructure is False if empty, and True otherwise
__contains__(item)	Check containership of Atom instances or AtomicStructure substructures recursively.
__delattr__(name, /)	Implement delattr(self, name).
__dir__()	Default dir() implementation.
__eq__(other)	Return self==value.
__format__(format_spec, /)	Default object formatter.
__ge__(value, /)	Return self>=value.
__getattribute__(name, /)	Return getattr(self, name).
__gt__(value, /)	Return self>value.
__hash__()	Return hash(self).
__init__(unitcell, lattice_vectors[, source])
__init_subclass__	This method is called when a class is subclassed.
__iter__()	Yields Atom instances from the structure and substructures recursively.
__le__(value, /)	Return self<=value.
__len__()	Number of Atom instances present in the structure and substructures
__lt__(value, /)	Return self<value.
__ne__(value, /)	Return self!=value.
__new__(**kwargs)
__reduce__()	Helper for pickle.
__reduce_ex__(protocol, /)	Helper for pickle.
__repr__()	Verbose string representation of this instance.
__setattr__(name, value, /)	Implement setattr(self, name, value).
__sizeof__()	Size of object in memory, in bytes.
__str__()	String representation of this instance.
__subclasshook__	Abstract classes can override this to customize issubclass().
_from_spglib_cell(lattice_vectors, ...)	Build a Crystal object from the return value of many SPGLIB routines.
_spglib_cell()	Returns an array in spglib's cell format.
_to_string(natoms)	Generate a string representation of this Crystal.
asymmetric_cell()	Calculates the asymmetric cell that generates the crystal unit cell.
bounded_reflections(bound[, min_bound])	Generates reflections (hkl) with norm(G) <= bound
frac_mesh(*xi[, indexing])	Coordinate arrays for fractional coordinates.
from_ase(atoms, **kwargs)	Returns a Crystal object created from an ASE Atoms object.
from_cif(path, **kwargs)	Returns a Crystal object created from a CIF 1.0, 1.1 or 2.0 file.
from_cod(num[, revision, download_dir, ...])	Returns a Crystal object built from the Crystallography Open Database.
from_database(name, **kwargs)	Returns a Crystal object create from the internal CIF database.
from_mp(query[, api_key, download_dir, ...])	Returns a Crystal object built from the Materials Project.
from_parameters(a, b, c, alpha, beta, gamma)	Create a Lattice instance from three lengths and angles.
from_pdb(ID[, download_dir, overwrite])	Returns a Crystal object created from a Protein DataBank entry.
from_poscar(path, **kwargs)	Returns a Crystal object created from a VASP's POSCAR file.
from_pwscf(path, **kwargs)	Returns a Crystal object created from an output file of PWSCF.
groupby(by[, symprec, angle_tolerance])	Group unit cell atoms by some measure of site symmetry, for example Wyckoff letters or crystallographic orbits.
ideal([symprec])	Returns a Crystal object with an idealized unit cell.
indexed_by(lattice)	Return a crystal structure, indexed by another lattice/crystal structure.
itersorted(*[, key, reverse])	Yields Atom in sorted order.
mesh(*xi[, indexing])	Cartesian coordinate arrays from fractional coordinate vectors.
miller_indices(scattering_vector)	Miller indices from scattering vector components.
primitive([symprec])	Returns a Crystal object in the primitive unit cell.
reciprocal_symmetry_operations([symprec])	Get the symmetry operations that the reciprocal unit cell respects.
satisfying(predicate)	Builds a new AtomicStructure from atoms satisfying a predicate.
scattering_vector(reflection)	Scattering vector from Miller indices.
supercell(n1, n2, n3)	Create a supercell from this crystal, i.e. an atomic structure where the crystal unit cell is duplicated along lattice vectors.
symmetry([symprec, angle_tolerance])	Returns a dictionary containing space-group information.
symmetry_operations([symprec])	Get the symmetry operations that the crystal unit cell respects.
to_ase(**kwargs)	Convert a into an ase.Atoms object.
to_cif(filename)	Convert this Crystal instance to a CIF file.
to_poscar(filename, **kwargs)	Convert this Crystal instance to a POSCAR file.
to_xyz(filename)	Convert this Crystal instance to a XYZ file.
transform(*operators)	Return a transformed AtomicStructure based on symmetry operators.

Attributes

__annotations__
builtins
centering	Centering type of this crystals.
chemical_composition	Chemical composition of this structure as an ordered dictionary.
chemical_formula	Empirical chemical formula for this structure based on the chemical symbols.
hall_number	Hall number (between 1 and 531).
hall_symbol	Hall symbol.
hm_symbol	Hermann-Mauguin symbol.
international_full	International Tables of Crystallography space-group full symbol.
international_number	International Tables of Crystallography space-group number (between 1 and 230).
international_symbol	International Tables of Crystallography space-group short symbol.
lattice_parameters	Lattice parameters as three lengths [Å] and three angles [degrees].
lattice_system	One of the seven lattice system, returned in the form of the LatticeSystem enumeration.
lattice_vectors	Iterable of lattice vectors
periodicity	Crystal periodicity in x, y and z direction from the lattice constants.
pointgroup	International Tables of Crystallography point-group.
reciprocal	Reciprocal lattice
reciprocal_vectors	Reciprocal lattice vectors, defined as:
unitcell	Generator of atoms forming the crystal unit cell.
volume	Lattice cell volume Angtroms cubed