def refine_cell(structure, symprec=1e-5, angle_tolerance=-1.0):
"""
Return refined cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(structure.sites)
cell = structure.cell.T.copy()
coords = np.zeros((num_atom * 4, 3), dtype='double')
coords[:num_atom] = structure.site_coords.copy()
comps = structure.site_compositions
numbers = [comps.index(c) for c in comps]
numbers = np.array(numbers * 4, dtype='intc')
num_atom_bravais = spg.refine_cell(cell, coords, numbers, num_atom,
symprec, angle_tolerance)
coords = wrap(coords)
comps = [comps[i] for i in numbers]
if num_atom_bravais > 0:
structure.cell = cell.T
structure.set_nsites(num_atom_bravais)
structure.site_coords = coords[:num_atom_bravais]
structure.site_compositions = comps[:num_atom_bravais]
return structure
else:
return structure
def refine_cell(structure, symprec=1e-5, angle_tolerance=-1.0):
"""
Return refined cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = len(structure.sites)
cell = structure.cell.T.copy()
coords = np.zeros((num_atom * 4, 3), dtype='double')
coords[:num_atom] = structure.site_coords.copy()
comps = structure.site_compositions
numbers = [ comps.index(c) for c in comps ]
numbers = np.array(numbers*4, dtype='intc')
num_atom_bravais = spg.refine_cell(cell,
coords,
numbers,
num_atom,
symprec,
angle_tolerance)
coords = wrap(coords)
comps = [ comps[i] for i in numbers ]
if num_atom_bravais > 0:
structure.cell = cell.T
structure.set_nsites(num_atom_bravais)
structure.site_coords = coords[:num_atom_bravais]
structure.site_compositions = comps[:num_atom_bravais]
return structure
else:
return structure
def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return refined cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = bulk.get_number_of_atoms()
lattice = bulk.get_cell().T.copy()
pos = np.zeros((num_atom * 4, 3), dtype='double')
pos[:num_atom] = bulk.get_scaled_positions()
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = np.intc(bulk.get_atomic_numbers())
num_atom_bravais = spg.refine_cell(lattice, pos, numbers, num_atom,
symprec, angle_tolerance)
return (lattice.T.copy(), pos[:num_atom_bravais].copy(),
numbers[:num_atom_bravais].copy())
def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return refined cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = bulk.get_number_of_atoms()
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
pos = np.zeros((num_atom * 4, 3), dtype='double')
pos[:num_atom] = bulk.get_scaled_positions()
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
num_atom_std = spg.refine_cell(lattice, pos, numbers, num_atom, symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(pos[:num_atom_std], dtype='double',
order='C'), np.array(numbers[:num_atom_std],
dtype='intc'))
def get_refined_structure(self):
"""
Return refined Structure
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = self._structure.num_sites
lattice = self._lattice.T.copy()
pos = np.zeros((num_atom * 4, 3), dtype=float)
pos[:num_atom] = self._positions.copy()
numbers = np.zeros(num_atom * 4, dtype=int)
numbers[:num_atom] = self._numbers.copy()
num_atom_bravais = spg.refine_cell(lattice,
pos,
numbers,
num_atom,
self._symprec,
self._angle_tol)
zs = numbers[:num_atom_bravais]
species = [self._unique_species[i - 1] for i in zs]
return Structure(lattice.T.copy(), species, pos[:num_atom_bravais])
def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
Return refined cell
"""
# Atomic positions have to be specified by scaled positions for spglib.
num_atom = bulk.get_number_of_atoms()
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
pos = np.zeros((num_atom * 4, 3), dtype='double')
pos[:num_atom] = bulk.get_scaled_positions()
numbers = np.zeros(num_atom * 4, dtype='intc')
numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
num_atom_bravais = spg.refine_cell(lattice,
pos,
numbers,
num_atom,
symprec,
angle_tolerance)
return (np.array(lattice.T, dtype='double', order='C'),
np.array(pos[:num_atom_bravais], dtype='double', order='C'),
np.array(numbers[:num_atom_bravais], dtype='intc'))
def refine_cell(self):
"""
get refined data from symmetry finding
"""
if self.sym:
# Temporary storage of structure info
_lattice = self._lattice.T.copy()
_scaled_coords = self._scaled_coords.copy()
_symprec = self._symprec
_angle_tol = self._angle_tol
_numbers = self._numbers.copy()
keys = ('number',
'international',
'hall',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms')
dataset = {}
dataset['number'] = 0
while dataset['number'] == 0:
# refine cell
num_atom = len(_scaled_coords)
ref_lattice = _lattice.copy()
ref_pos = np.zeros((num_atom * 4, 3), dtype=float)
ref_pos[:num_atom] = _scaled_coords.copy()
ref_numbers = np.zeros(num_atom * 4, dtype=int)
ref_numbers[:num_atom] = _numbers.copy()
num_atom_bravais = spg.refine_cell(ref_lattice,
ref_pos,
ref_numbers,
num_atom,
_symprec,
_angle_tol)
for key, data in zip(keys, spg.dataset(ref_lattice.copy(),
ref_pos[:num_atom_bravais].copy(),
ref_numbers[:num_atom_bravais].copy(),
_symprec,
_angle_tol)):
dataset[key] = data
_symprec = _symprec * 0.5
# an error occured with met9, org1, org9 whereby no
# symmetry info was being printed for some reason.
# thus a check is done after refining the structure.
if dataset['number'] == 0:
warning("WARNING - Bad Symmetry found!")
self.sym = False
else:
self.dataset['number'] = dataset['number']
self.dataset['international'] = dataset['international'].strip()
self.dataset['hall'] = dataset['hall'].strip()
self.dataset['transformation_matrix'] = np.array(dataset['transformation_matrix'])
self.dataset['origin_shift'] = np.array(dataset['origin_shift'])
self.dataset['rotations'] = np.array(dataset['rotations'])
self.dataset['translations'] = np.array(dataset['translations'])
letters = "abcdefghijklmnopqrstuvwxyz"
self.dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
self.dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'])
self._lattice = ref_lattice.T.copy()
self._scaled_coords = ref_pos[:num_atom_bravais].copy()
self._numbers = ref_numbers[:num_atom_bravais].copy()
self._element_symbols = [ATOMIC_NUMBER[i] for
i in ref_numbers[:num_atom_bravais]]