Python spglib.get_spacegroup方法代碼示例

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def get_spacegroup(structure,
                   symprec=1e-3,
                   symbol_type=0):
    """
    Get the space group symbol and number of a crystal structure.

    Args:
        structure: :class:`qmpy.Structure` object with the crystal structure.
        symprec: Float with the Cartesian distance tolerance.
        symbol_type: Integer with the type: 0 - Schoenflies, 1 - ITC short

    Returns:
        String with the space group symbol and number. E.g. u"R-3m (166)"

        None if `spglib` fails to determine the space group.

    Raises:
        ImportError: If `spglib` cannot be imported.

    """
    _check_spglib_install()
    return spglib.get_spacegroup(
        _structure_to_cell(structure),
        symprec=symprec,
        symbol_type=symbol_type
    ) 

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def get_spacegroup(self, symprec=1e-5, angle_tolerance=-1.0):
        """

        Args:
            symprec:
            angle_tolerance:

        Returns:

        https://atztogo.github.io/spglib/python-spglib.html
        """
        lattice = np.array(self.get_cell(), dtype="double", order="C")
        positions = np.array(
            self.get_scaled_positions(wrap=False), dtype="double", order="C"
        )
        numbers = np.array(self.get_atomic_numbers(), dtype="intc")
        space_group = spglib.get_spacegroup(
            cell=(lattice, positions, numbers),
            symprec=symprec,
            angle_tolerance=angle_tolerance,
        ).split()
        if len(space_group) == 1:
            return {"Number": ast.literal_eval(space_group[0])}
        else:
            return {
                "InternationalTableSymbol": space_group[0],
                "Number": ast.literal_eval(space_group[1]),
            } 

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def get_primitive_cell(self, symprec=1e-5, angle_tolerance=-1.0):
        """

        Args:
            symprec:
            angle_tolerance:

        Returns:

        """
        el_dict = {}
        for el in set(self.get_chemical_elements()):
            el_dict[el.AtomicNumber] = el
        lattice = np.array(self.get_cell().T, dtype="double", order="C")
        positions = np.array(
            self.get_scaled_positions(wrap=False), dtype="double", order="C"
        )
        numbers = np.array(self.get_atomic_numbers(), dtype="intc")
        cell, coords, atomic_numbers = spglib.find_primitive(
            cell=(lattice, positions, numbers),
            symprec=symprec,
            angle_tolerance=angle_tolerance,
        )
        # print atomic_numbers, type(atomic_numbers)
        el_lst = [el_dict[i_a] for i_a in atomic_numbers]

        # convert lattice vectors to standard (experimental feature!) TODO:
        red_structure = Atoms(elements=el_lst, scaled_positions=coords, cell=cell)
        space_group = red_structure.get_spacegroup(symprec)["Number"]
        # print "space group: ", space_group
        if space_group == 225:  # fcc
            alat = np.max(cell[0])
            amat_fcc = alat * np.array([[1, 0, 1], [1, 1, 0], [0, 1, 1]])

            red_structure.cell = amat_fcc
        return red_structure 

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def get_lattice_type(cryst):
    '''Find the symmetry of the crystal using spglib symmetry finder.

    Derive name of the space group and its number extracted from the result.
    Based on the group number identify also the lattice type and the Bravais
    lattice of the crystal. The lattice type numbers are
    (the numbering starts from 1):

    Triclinic (1), Monoclinic (2), Orthorombic (3),
    Tetragonal (4), Trigonal (5), Hexagonal (6), Cubic (7)

    :param cryst: ASE Atoms object

    :returns: tuple (lattice type number (1-7), lattice name, space group
                     name, space group number)
    '''

    # Table of lattice types and correcponding group numbers dividing
    # the ranges. See get_lattice_type method for precise definition.
    lattice_types = [
            [3,   "Triclinic"],
            [16,  "Monoclinic"],
            [75,  "Orthorombic"],
            [143, "Tetragonal"],
            [168, "Trigonal"],
            [195, "Hexagonal"],
            [231, "Cubic"]
        ]

    sg = spg.get_spacegroup(cryst)
    m = re.match(r'([A-Z].*\b)\s*\(([0-9]*)\)', sg)
    sg_name = m.group(1)
    sg_nr = int(m.group(2))

    for n, l in enumerate(lattice_types):
        if sg_nr < l[0]:
            bravais = l[1]
            lattype = n+1
            break

    return lattype, bravais, sg_name, sg_nr 

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def get_spacegroup(self, symprec=1e-5):
        return spg.get_spacegroup(cell=self.spglib_cell, symprec=symprec) 

# 需要導入模塊: import spglib [as 別名]
# 或者: from spglib import get_spacegroup [as 別名]
def _make_atoms_dict(atoms):
    '''
    Convert an ase.Atoms object into a dictionary for json storage.

    Arg:
        atoms   ase.Atoms object
    Returns:
        atoms_dict  A dictionary with various atoms information stored
    '''
    # If the atoms object is relaxed, then get the magnetic moments from the
    # calculator. We do this because magnetic moments of individual atoms
    # within a structure are mutable and actually change when the atom is
    # pulled from the structure (even inside a list comprehension).
    try:
        magmoms = atoms.get_magnetic_moments()
        atoms_dict = OrderedDict(atoms=[{'symbol': atom.symbol,
                                         'position': json.loads(encode(atom.position)),
                                         'tag': atom.tag,
                                         'index': atom.index,
                                         'charge': atom.charge,
                                         'momentum': json.loads(encode(atom.momentum)),
                                         'magmom': magmoms[i]}
                                        for i, atom in enumerate(atoms)],
                                 cell=atoms.cell,
                                 pbc=atoms.pbc,
                                 info=atoms.info,
                                 constraints=[c.todict() for c in atoms.constraints])

    # If the atoms object is unrelaxed, then get the magnetic moment from the
    # individual atom
    except RuntimeError:
        atoms_dict = OrderedDict(atoms=[{'symbol': atom.symbol,
                                         'position': json.loads(encode(atom.position)),
                                         'tag': atom.tag,
                                         'index': atom.index,
                                         'charge': atom.charge,
                                         'momentum': json.loads(encode(atom.momentum)),
                                         'magmom': atom.magmom}
                                        for atom in atoms],
                                 cell=atoms.cell,
                                 pbc=atoms.pbc,
                                 info=atoms.info,
                                 constraints=[c.todict() for c in atoms.constraints])

    # Redundant information for search convenience.
    atoms_dict['natoms'] = len(atoms)
    cell = atoms.get_cell()
    atoms_dict['mass'] = sum(atoms.get_masses())
    syms = atoms.get_chemical_symbols()
    atoms_dict['spacegroup'] = spglib.get_spacegroup(make_spglib_cell_from_atoms(atoms))
    atoms_dict['chemical_symbols'] = list(set(syms))
    atoms_dict['symbol_counts'] = {sym: syms.count(sym) for sym in syms}
    if cell is not None and np.linalg.det(cell) > 0:
        atoms_dict['volume'] = atoms.get_volume()

    return json.loads(encode(atoms_dict))