def __init__(self, structure, symprec=1e-5, angle_tolerance=5):
"""
Args:
structure:
Structure object
symprec:
Tolerance for symmetry finding
angle_tolerance:
Angle tolerance for symmetry finding.
"""
self._symprec = symprec
self._angle_tol = angle_tolerance
self._structure = structure
self._lattice = structure.lattice.matrix
self._positions = np.array([site.frac_coords for site in structure])
unique_species = []
zs = []
for species, g in itertools.groupby(structure, key=lambda site: site.species_and_occu):
try:
ind = unique_species.index(species)
zs.extend([ind + 1] * len(tuple(g)))
except ValueError:
unique_species.append(species)
zs.extend([len(unique_species)] * len(tuple(g)))
self._unique_species = unique_species
self._numbers = np.array(zs)
self._spacegroup_data = spg.spacegroup(self._lattice.transpose().copy(), self._positions.copy(), self._numbers, self._symprec, self._angle_tol)
def get_spacegroup(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
# Atomic positions have to be specified by scaled positions for spglib.
return spg.spacegroup(bulk.get_cell().T.copy(),
bulk.get_scaled_positions().copy(),
np.intc(bulk.get_atomic_numbers()).copy(), symprec,
angle_tolerance)
def get_spacegroup(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
# Atomic positions have to be specified by scaled positions for spglib.
return spg.spacegroup(bulk.get_cell().T.copy(),
bulk.get_scaled_positions().copy(),
np.intc(bulk.get_atomic_numbers()).copy(),
symprec,
angle_tolerance)
def get_spacegroup(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
# Atomic positions have to be specified by scaled positions for spglib.
return spg.spacegroup(
np.array(bulk.get_cell().T, dtype='double', order='C'),
np.array(bulk.get_scaled_positions(), dtype='double', order='C'),
np.array(bulk.get_atomic_numbers(), dtype='intc'),
symprec,
angle_tolerance)
def get_spacegroup(structure, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
cell = structure.cell.T.copy(),
scaled = structure.site_coords.copy()
comps = structure.site_compositions
numbers = [comps.index(c) for c in comps]
numbers = np.array(numbers, dtype='intc')
# Atomic positions have to be specified by scaled positions for spglib.
return int(
spg.spacegroup(cell, coords, numbers, symprec,
angle_tolerance).strip(' ()'))
def get_spacegroup(structure, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
cell = structure.cell.T.copy(),
scaled = structure.site_coords.copy()
comps = structure.site_compositions
numbers = [ comps.index(c) for c in comps ]
numbers = np.array(numbers, dtype='intc')
# Atomic positions have to be specified by scaled positions for spglib.
return int(spg.spacegroup(cell,
coords,
numbers,
symprec,
angle_tolerance).strip(' ()'))
def get_spacegroup(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return space group in international table symbol and number
as a string.
"""
lattice = np.array(bulk.cell * bulk.scale, dtype='double', order='C')
# print 'vladan get_spacegroup: lattice:\n', lattice
posMat = np.array([
np.dot(atom.pos, np.linalg.inv(np.transpose(bulk.cell)))
for atom in bulk
],
dtype='double',
order='C')
# print 'vladan get_spacegroup: posMat:\n', posMat
syms = np.array(
[periodic_table.symbols.index(atom.type) + 1 for atom in bulk],
dtype='intc')
# print 'vladan get_spacegroup: syms:\n', syms
# Atomic positions have to be specified by scaled positions for spglib.
return spg.spacegroup(lattice, posMat, syms, symprec, angle_tolerance)
