def get_symmetry_dataset(cell, 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)
"""
lattice, positions, numbers, _ = _expand_cell(cell)
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 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(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(cell, symprec=1e-5, angle_tolerance=-1.0):
"""Search symmetry dataset from an input cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
Return:
A dictionary is returned.
number:
int: International space group number
international:
str: International symbol
hall:
str: Hall symbol
choice:
str: Centring, origin, basis vector setting
transformation_matrix:
3x3 float matrix:
Transformation matrix from input lattice to standardized lattice
L^original = L^standardized * Tmat
origin shift:
float vecotr: Origin shift from standardized to input origin
rotations, translations:
3x3 int matrix, float vector:
Rotation matrices and translation vectors. Space group
operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
List of characters: Wyckoff letters
std_lattice, std_positions, std_types:
3x3 float matrix, Nx3 float vectors, list of int:
Standardized unit cell
pointgroup:
str: Pointgroup symbol
If it fails, None is returned.
"""
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
if lattice is None:
return None
keys = ('number',
'hall_number',
'international',
'hall',
'choice',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms',
'std_lattice',
'std_types',
'std_positions',
# 'pointgroup_number',
'pointgroup')
spg_ds = spg.dataset(lattice, positions, numbers, symprec, angle_tolerance)
if spg_ds is None:
_set_error_message()
return None
dataset = {}
for key, data in zip(keys, spg_ds):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['choice'] = dataset['choice'].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()
_set_error_message()
return dataset
def get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0):
"""Search symmetry dataset from an input cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
Return:
A dictionary is returned.
number:
int: International space group number
international:
str: International symbol
hall:
str: Hall symbol
choice:
str: Centring, origin, basis vector setting
transformation_matrix:
3x3 float matrix:
Transformation matrix from input lattice to standardized lattice
L^original = L^standardized * Tmat
origin shift:
float vecotr: Origin shift from standardized to input origin
rotations, translations:
3x3 int matrix, float vector:
Rotation matrices and translation vectors. Space group
operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs:
List of characters: Wyckoff letters
std_lattice, std_positions, std_types:
3x3 float matrix, Nx3 float vectors, list of int:
Standardized unit cell
pointgroup:
str: Pointgroup symbol
If it fails, None is returned.
"""
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
if lattice is None:
return None
keys = (
'number',
'hall_number',
'international',
'hall',
'choice',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'equivalent_atoms',
'std_lattice',
'std_types',
'std_positions',
# 'pointgroup_number',
'pointgroup')
spg_ds = spg.dataset(lattice, positions, numbers, symprec, angle_tolerance)
if spg_ds is None:
_set_error_message()
return None
dataset = {}
for key, data in zip(keys, spg_ds):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['choice'] = dataset['choice'].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()
_set_error_message()
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 get_symmetry_dataset(cell,
symprec=1e-5,
angle_tolerance=-1.0,
hall_number=0):
"""Search symmetry dataset from an input cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
hall_number: If a serial number of Hall symbol (>0) is given,
the database corresponding to the Hall symbol is made.
Return:
A dictionary is returned. Dictionary keys:
number (int): International space group number
international (str): International symbol
hall (str): Hall symbol
choice (str): Centring, origin, basis vector setting
transformation_matrix (3x3 float):
Transformation matrix from input lattice to standardized
lattice:
L^original = L^standardized * Tmat
origin shift (3 float):
Origin shift from standardized to input origin
rotations (3x3 int), translations (float vector):
Rotation matrices and translation vectors. Space group
operations are obtained by
[(r,t) for r, t in zip(rotations, translations)]
wyckoffs (n char): Wyckoff letters
equivalent_atoms (n int): Symmetrically equivalent atoms
mapping_to_primitive (n int):
Original cell atom index mapping to primivie cell atom index
Idealized standardized unit cell:
std_lattice (3x3 float, row vectors),
std_positions (Nx3 float), std_types (N int)
std_rotation_matrix:
Rigid rotation matrix to rotate from standardized basis
vectors to idealized standardized basis vectors
L^idealized = R * L^standardized
std_mapping_to_primitive (m int):
std_positions index mapping to those of primivie cell atoms
pointgroup (str): Pointgroup symbol
If it fails, None is returned.
"""
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
if lattice is None:
return None
spg_ds = spg.dataset(lattice, positions, numbers, hall_number, symprec,
angle_tolerance)
if spg_ds is None:
_set_error_message()
return None
keys = (
'number',
'hall_number',
'international',
'hall',
'choice',
'transformation_matrix',
'origin_shift',
'rotations',
'translations',
'wyckoffs',
'site_symmetry_symbols',
'equivalent_atoms',
'mapping_to_primitive',
'std_lattice',
'std_types',
'std_positions',
'std_rotation_matrix',
'std_mapping_to_primitive',
# 'pointgroup_number',
'pointgroup')
dataset = {}
for key, data in zip(keys, spg_ds):
dataset[key] = data
dataset['international'] = dataset['international'].strip()
dataset['hall'] = dataset['hall'].strip()
dataset['choice'] = dataset['choice'].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['site_symmetry_symbols'] = [
s.strip() for s in dataset['site_symmetry_symbols']
]
dataset['equivalent_atoms'] = np.array(dataset['equivalent_atoms'],
dtype='intc')
dataset['mapping_to_primitive'] = np.array(dataset['mapping_to_primitive'],
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['std_rotation_matrix'] = np.array(dataset['std_rotation_matrix'],
dtype='double',
order='C')
dataset['std_mapping_to_primitive'] = np.array(
dataset['std_mapping_to_primitive'], dtype='intc')
dataset['pointgroup'] = dataset['pointgroup'].strip()
_set_error_message()
return dataset