def get_symmetry_dataset(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
number: International space group number
international: International symbol
hall: Hall symbol
transformation_matrix:
Transformation matrix from lattice of input cell to Bravais lattice
L^bravais = L^original * Tmat
origin shift: Origin shift in the setting of 'Bravais lattice'
rotations, translations:
Rotation matrices and translation vectors
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
"""
positions = np.array(bulk.get_scaled_positions(),
dtype='double',
order='C')
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
numbers = np.array(bulk.get_atomic_numbers(), dtype='intc')
keys = ('number', 'hall_number', 'international', 'hall',
'transformation_matrix', 'origin_shift', 'rotations',
'translations', 'wyckoffs', 'equivalent_atoms', 'brv_lattice',
'brv_types', 'brv_positions')
dataset = {}
for key, data in zip(
keys,
spg.dataset(lattice, positions, numbers, symprec,
angle_tolerance)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(
dataset['transformation_matrix'], dtype='double', order='C')
dataset['origin_shift'] = np.array(dataset['origin_shift'], dtype='double')
dataset['rotations'] = np.array(dataset['rotations'],
dtype='intc',
order='C')
dataset['translations'] = np.array(dataset['translations'],
dtype='double',
order='C')
letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'],
dtype='intc')
dataset['brv_lattice'] = np.array(np.transpose(dataset['brv_lattice']),
dtype='double',
order='C')
dataset['brv_types'] = np.array(dataset['brv_types'], dtype='intc')
dataset['brv_positions'] = np.array(dataset['brv_positions'],
dtype='double',
order='C')
return dataset
def get_symmetry_dataset(structure, symprec=1e-3, angle_tolerance=-1.0):
"""
Return a full set of symmetry information from a given input structure.
Mapping values:
number: International space group number
international: International symbol
hall: Hall symbol
transformation_matrix:
Transformation matrix from lattice of input cell to Bravais lattice
L^bravais = L^original * Tmat
origin shift: Origin shift in the setting of 'Bravais lattice'
rotations, translations:
Rotation matrices and translation vectors
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
Examples::
>>> from qmpy.io import read
>>> from qmpy.analysis.symmetry import get_symmetry_dataset
>>> structure = read('POSCAR')
>>> get_symmetry_dataset(structure)
"""
keys = ('number', 'international', 'hall', 'transformation_matrix',
'origin_shift', 'rotations', 'translations', 'wyckoffs',
'equivalent_atoms')
cell = structure.cell.T.copy()
coords = np.array(structure.site_coords)
comps = structure.site_compositions
numbers = [comps.index(c) for c in comps]
numbers = np.array(numbers, dtype='intc')
dataset = {}
for key, data in zip(
keys, spg.dataset(cell, coords, numbers, symprec,
angle_tolerance)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(
dataset['transformation_matrix']).T
dataset['origin_shift'] = np.array(dataset['origin_shift'])
dataset['rotations'] = np.array(dataset['rotations'])
dataset['translations'] = np.array(dataset['translations'])
letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'])
return dataset
def get_symmetry_dataset(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
number: International space group number
international: International symbol
hall: Hall symbol
transformation_matrix:
Transformation matrix from lattice of input cell to Bravais lattice
L^bravais = L^original * Tmat
origin shift: Origin shift in the setting of 'Bravais lattice'
rotations, translations:
Rotation matrices and translation vectors
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
"""
positions = np.array(bulk.get_scaled_positions(), dtype='double', order='C')
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
numbers = np.array(bulk.get_atomic_numbers(), dtype='intc')
keys = ('number',
'international',
'hall',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms')
dataset = {}
for key, data in zip(keys, spg.dataset(lattice,
positions,
numbers,
symprec,
angle_tolerance)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(
dataset['transformation_matrix'], dtype='double', order='C')
dataset['origin_shift'] = np.array(dataset['origin_shift'], dtype='double')
dataset['rotations'] = np.array(dataset['rotations'],
dtype='intc', order='C')
dataset['translations'] = np.array(dataset['translations'],
dtype='double', order='C')
letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'],
dtype='intc')
return dataset
def get_symmetry_dataset(self):
"""
Returns the symmetry dataset as a dict.
Returns:
number:
International space group number
international:
International symbol
hall:
Hall symbol
transformation_matrix:
Transformation matrix from lattice of input cell to Bravais lattice
L^bravais = L^original * Tmat
origin shift:
Origin shift in the setting of 'Bravais lattice'
rotations, translations:
Rotation matrices and translation vectors.
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
"""
keys = ('number',
'international',
'hall',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms')
dataset = {}
for key, data in zip(keys, spg.dataset(self._lattice.transpose().copy(), self._positions, self._numbers, self._symprec, self._angle_tol)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(dataset['transformation_matrix'])
dataset['origin_shift'] = np.array(dataset['origin_shift'])
dataset['rotations'] = np.array(dataset['rotations'])
dataset['translations'] = np.array(dataset['translations'])
letters = "abcdefghijklmnopqrstuvwxyz"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'])
return dataset
def get_symmetry_dataset(structure, symprec=1e-3, angle_tolerance=-1.0):
"""
Return a full set of symmetry information from a given input structure.
Mapping values:
number: International space group number
international: International symbol
hall: Hall symbol
transformation_matrix:
Transformation matrix from lattice of input cell to Bravais lattice
L^bravais = L^original * Tmat
origin shift: Origin shift in the setting of 'Bravais lattice'
rotations, translations:
Rotation matrices and translation vectors
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
Examples::
>>> from qmpy.io import read
>>> from qmpy.analysis.symmetry import get_symmetry_dataset
>>> structure = read('POSCAR')
>>> get_symmetry_dataset(structure)
"""
keys = ('number',
'hall_number',
'international',
'hall',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms',
'std_lattice',
'std_types',
'std_positions',
'pointgroup_number',
'pointgroup')
cell = structure.cell.T.copy()
coords = np.array(structure.site_coords)
comps = structure.site_compositions
numbers = [ comps.index(c) for c in comps ]
numbers = np.array(numbers, dtype='intc')
dataset = {}
for key, data in zip(keys, spg.dataset(cell,
coords,
numbers,
symprec,
angle_tolerance)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(dataset['transformation_matrix'], dtype='double', order='C')
dataset['origin_shift'] = np.array(dataset['origin_shift'], dtype='double')
dataset['rotations'] = np.array(dataset['rotations'], dtype='intc', order='C')
dataset['translations'] = np.array(dataset['translations'], dtype='double', order='C')
letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'], dtype='intc')
dataset['std_lattice'] = np.array(np.transpose(dataset['std_lattice']), dtype='double', order='C')
dataset['std_types'] = np.array(dataset['std_types'], dtype='intc')
dataset['std_positions'] = np.array(dataset['std_positions'], dtype='double', order='C')
dataset['pointgroup'] = dataset['pointgroup'].strip()
return dataset
def get_symmetry_dataset(bulk, symprec=1e-5, angle_tolerance=-1.0):
"""
number: International space group number
international: International symbol
hall: Hall symbol
transformation_matrix:
Transformation matrix from input lattice to standardized lattice
L^original = L^standardized * Tmat
origin shift: Origin shift from standardized to input origin
rotations, translations:
Rotation matrices and translation vectors
Space group operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
Wyckoff letters
std_lattice, std_types, std_positions:
Standardized unit cell
pointgroup_number, pointgroup_symbol: Point group number (see get_pointgroup)
"""
positions = np.array(bulk.get_scaled_positions(), dtype='double', order='C')
lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
numbers = np.array(bulk.get_atomic_numbers(), dtype='intc')
keys = ('number',
'hall_number',
'international',
'hall',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms',
'std_lattice',
'std_types',
'std_positions',
'pointgroup_number',
'pointgroup')
dataset = {}
for key, data in zip(keys, spg.dataset(lattice,
positions,
numbers,
symprec,
angle_tolerance)):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['transformation_matrix'] = np.array(
dataset['transformation_matrix'], dtype='double', order='C')
dataset['origin_shift'] = np.array(dataset['origin_shift'], dtype='double')
dataset['rotations'] = np.array(dataset['rotations'],
dtype='intc', order='C')
dataset['translations'] = np.array(dataset['translations'],
dtype='double', order='C')
letters = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
dataset['wyckoffs'] = [letters[x] for x in dataset['wyckoffs']]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'],
dtype='intc')
dataset['std_lattice'] = np.array(np.transpose(dataset['std_lattice']),
dtype='double', order='C')
dataset['std_types'] = np.array(dataset['std_types'], dtype='intc')
dataset['std_positions'] = np.array(dataset['std_positions'],
dtype='double', order='C')
dataset['pointgroup'] = dataset['pointgroup'].strip()
return dataset
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]]