def test_to_from_dict(self):
op = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
magop = MagSymmOp.from_symmop(op, -1)
magop2 = MagSymmOp.from_dict(magop.as_dict())
self.assertEqual(magop2.time_reversal, -1)
self.assertEqual(magop2.as_xyzt_string(), '3x-2y-z+1/2, -x+12/13, z+1/2, -1')
def test_to_from_dict(self):
op = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
magop = MagSymmOp.from_symmop(op, -1)
magop2 = MagSymmOp.from_dict(magop.as_dict())
self.assertEqual(magop2.time_reversal, -1)
self.assertEqual(magop2.as_xyzt_string(), '3x-2y-z+1/2, -x+12/13, z+1/2, -1')
def symmetry_ops(self):
"""
Retrieve magnetic symmetry operations of the space group.
:return: List of :class:`pymatgen.core.operations.MagSymmOp`
"""
ops = [op_data['op'] for op_data in self._data['bns_operators']]
# add lattice centerings
centered_ops = []
lattice_vectors = [l['vector'] for l in self._data['bns_lattice']]
for vec in lattice_vectors:
if not (np.array_equal(vec, [1, 0, 0])
or np.array_equal(vec, [0, 1, 0])
or np.array_equal(vec, [0, 0, 1])):
for op in ops:
new_vec = op.translation_vector + vec
new_op = MagSymmOp.from_rotation_and_translation_and_time_reversal(op.rotation_matrix,
translation_vec=new_vec,
time_reversal=op.time_reversal)
centered_ops.append(new_op)
ops = ops+centered_ops
return ops
def _parse_operators(b):
'''Parses compact binary representation into list of MagSymmOps.'''
if len(b) == 0: # e.g. if magtype != 4, OG setting == BNS setting, and b == [] for OG symmops
return None
raw_symops = [b[i:i+6] for i in range(0, len(b), 6)]
symops = []
for r in raw_symops:
point_operator = _get_point_operator(r[0])
translation_vec = [r[1]/r[4], r[2]/r[4], r[3]/r[4]]
time_reversal = r[5]
op = MagSymmOp.from_rotation_and_translation_and_time_reversal(rotation_matrix=point_operator['matrix'],
translation_vec=translation_vec,
time_reversal=time_reversal)
# store string representation, e.g. (2x|1/2,1/2,1/2)'
seitz = '({0}|{1},{2},{3})'.format(point_operator['symbol'],
Fraction(translation_vec[0]),
Fraction(translation_vec[1]),
Fraction(translation_vec[2]))
if time_reversal == -1:
seitz += '\''
symops.append({'op': op, 'str': seitz})
return symops
def transform_symmop(
self, symmop: Union[SymmOp,
MagSymmOp]) -> Union[SymmOp, MagSymmOp]:
"""
Takes a symmetry operation and transforms it.
:param symmop: SymmOp or MagSymmOp
:return:
"""
W = symmop.rotation_matrix
w = symmop.translation_vector
Q = np.linalg.inv(self.P)
W_ = np.matmul(np.matmul(Q, W), self.P)
I = np.identity(3)
w_ = np.matmul(Q, (w + np.matmul(W - I, self.p)))
w_ = np.mod(w_, 1.0)
if isinstance(symmop, MagSymmOp):
return MagSymmOp.from_rotation_and_translation_and_time_reversal(
rotation_matrix=W_,
translation_vec=w_,
time_reversal=symmop.time_reversal,
tol=symmop.tol,
)
if isinstance(symmop, SymmOp):
return SymmOp.from_rotation_and_translation(rotation_matrix=W_,
translation_vec=w_,
tol=symmop.tol)
raise RuntimeError
def symmetry_ops(self):
"""
Retrieve magnetic symmetry operations of the space group.
:return: List of :class:`pymatgen.core.operations.MagSymmOp`
"""
ops = [op_data["op"] for op_data in self._data["bns_operators"]]
# add lattice centerings
centered_ops = []
lattice_vectors = [l["vector"] for l in self._data["bns_lattice"]]
for vec in lattice_vectors:
if not (np.array_equal(vec, [1, 0, 0]) or np.array_equal(
vec, [0, 1, 0]) or np.array_equal(vec, [0, 0, 1])):
for op in ops:
new_vec = op.translation_vector + vec
new_op = MagSymmOp.from_rotation_and_translation_and_time_reversal(
op.rotation_matrix,
translation_vec=new_vec,
time_reversal=op.time_reversal,
)
centered_ops.append(new_op)
ops = ops + centered_ops
# apply jones faithful transformation
ops = [self.jf.transform_symmop(op) for op in ops]
return ops
def _parse_operators(b):
"""Parses compact binary representation into list of MagSymmOps."""
if len(
b
) == 0: # e.g. if magtype != 4, OG setting == BNS setting, and b == [] for OG symmops
return None
raw_symops = [b[i:i + 6] for i in range(0, len(b), 6)]
symops = []
for r in raw_symops:
point_operator = _get_point_operator(r[0])
translation_vec = [r[1] / r[4], r[2] / r[4], r[3] / r[4]]
time_reversal = r[5]
op = MagSymmOp.from_rotation_and_translation_and_time_reversal(
rotation_matrix=point_operator["matrix"],
translation_vec=translation_vec,
time_reversal=time_reversal,
)
# store string representation, e.g. (2x|1/2,1/2,1/2)'
seitz = "({0}|{1},{2},{3})".format(
point_operator["symbol"],
Fraction(translation_vec[0]),
Fraction(translation_vec[1]),
Fraction(translation_vec[2]),
)
if time_reversal == -1:
seitz += "'"
symops.append({"op": op, "str": seitz})
return symops
def symmetry_ops(self):
"""
Retrieve magnetic symmetry operations of the space group.
:return: List of :class:`pymatgen.core.operations.MagSymmOp`
"""
ops = [op_data['op'] for op_data in self._data['bns_operators']]
# add lattice centerings
centered_ops = []
lattice_vectors = [l['vector'] for l in self._data['bns_lattice']]
for vec in lattice_vectors:
if not (np.array_equal(vec, [1, 0, 0]) or np.array_equal(
vec, [0, 1, 0]) or np.array_equal(vec, [0, 0, 1])):
for op in ops:
new_vec = op.translation_vector + vec
new_op = MagSymmOp.from_rotation_and_translation_and_time_reversal(
op.rotation_matrix,
translation_vec=new_vec,
time_reversal=op.time_reversal)
centered_ops.append(new_op)
ops = ops + centered_ops
return ops
def test_xyzt_string(self):
xyzt_strings = [
'x, y, z, +1', 'x, y, z, -1', '-y+1/2, x+1/2, x+1/2, +1'
]
for xyzt_string in xyzt_strings:
op = MagSymmOp.from_xyzt_string(xyzt_string)
xyzt_string_out = op.as_xyzt_string()
self.assertEqual(xyzt_string, xyzt_string_out)
op = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
magop = MagSymmOp.from_symmop(op, -1)
magop_str = magop.as_xyzt_string()
self.assertEqual(magop.time_reversal, -1)
self.assertEqual(magop_str, '3x-2y-z+1/2, -x+12/13, z+1/2, -1')
def test_xyzt_string(self):
xyzt_strings = ['x, y, z, +1',
'x, y, z, -1',
'-y+1/2, x+1/2, x+1/2, +1']
for xyzt_string in xyzt_strings:
op = MagSymmOp.from_xyzt_string(xyzt_string)
xyzt_string_out = op.as_xyzt_string()
self.assertEqual(xyzt_string, xyzt_string_out)
op = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
magop = MagSymmOp.from_symmop(op, -1)
magop_str = magop.as_xyzt_string()
self.assertEqual(magop.time_reversal, -1)
self.assertEqual(magop_str, '3x-2y-z+1/2, -x+12/13, z+1/2, -1')
def test_operate_magmom(self):
# all test magmoms are the same
magmoms = [
Magmom([1, 2, 3]), # as Magmom
[1, 2, 3], # as list
Magmom([-3, 2, 1], saxis=[1, 0, 0]),
] # as Magmom with non-default saxis
xyzt_strings = ["x, y, z, +1", "x, y, z, -1", "x, -y, z, -1", "-x, -y, z, -1"]
transformed_magmoms = [[1, 2, 3], [-1, -2, -3], [1, -2, 3], [1, 2, -3]]
for xyzt_string, transformed_magmom in zip(xyzt_strings, transformed_magmoms):
for magmom in magmoms:
op = MagSymmOp.from_xyzt_string(xyzt_string)
self.assertTrue(np.allclose(transformed_magmom, op.operate_magmom(magmom).global_moment))
def transform_symmop(self, symmop):
# type: (Union[SymmOp, MagSymmOp]) -> Union[SymmOp, MagSymmOp]
"""
Takes a symmetry operation and transforms it.
:param symmop: SymmOp or MagSymmOp
:return:
"""
W = symmop.rotation_matrix
w = symmop.translation_vector
Q = np.linalg.inv(self.P)
W_ = np.matmul(np.matmul(Q, W), self.P)
I = np.identity(3)
w_ = np.matmul(Q, (w + np.matmul(W - I, self.p)))
if isinstance(symmop, MagSymmOp):
return MagSymmOp.from_rotation_and_translation_and_time_reversal(rotation_matrix=W_,
translation_vec=w_,
time_reversal=symmop.time_reversal,
tol=symmop.tol)
elif isinstance(symmop, SymmOp):
return SymmOp.from_rotation_and_translation(rotation_matrix=W_, translation_vec=w_, tol=symmop.tol)
def test_operate_magmom(self):
# all test magmoms are the same
magmoms = [Magmom([1, 2, 3]), # as Magmom
[1, 2, 3], # as list
Magmom([-3, 2, 1], saxis=[1, 0, 0])] # as Magmom with non-default saxis
xyzt_strings = ['x, y, z, +1',
'x, y, z, -1',
'x, -y, z, -1',
'-x, -y, z, -1']
transformed_magmoms = [[1, 2, 3],
[-1, -2, -3],
[1, -2, 3],
[1, 2, -3]]
for xyzt_string, transformed_magmom in zip(xyzt_strings, transformed_magmoms):
for magmom in magmoms:
op = MagSymmOp.from_xyzt_string(xyzt_string)
self.assertTrue(np.allclose(transformed_magmom, op.operate_magmom(magmom).global_moment))
def get_magsymops(self, data):
"""
Equivalent to get_symops except for magnetic symmetry groups.
Separate function since additional operation for time reversal symmetry
(which changes magnetic moments on sites) needs to be returned.
"""
magsymmops = []
# check to see if magCIF file explicitly contains magnetic symmetry operations
if data.data.get("_space_group_symop_magn_operation.xyz"):
xyzt = data.data.get("_space_group_symop_magn_operation.xyz")
if isinstance(xyzt, six.string_types):
xyzt = [xyzt]
magsymmops = [MagSymmOp.from_xyzt_string(s) for s in xyzt]
if data.data.get("_space_group_symop_magn_centering.xyz"):
xyzt = data.data.get("_space_group_symop_magn_centering.xyz")
if isinstance(xyzt, six.string_types):
xyzt = [xyzt]
centering_symops = [
MagSymmOp.from_xyzt_string(s) for s in xyzt
]
all_ops = []
for op in magsymmops:
for centering_op in centering_symops:
new_translation = [
i - np.floor(i) for i in op.translation_vector +
centering_op.translation_vector
]
new_time_reversal = op.time_reversal * centering_op.time_reversal
all_ops.append(
MagSymmOp.
from_rotation_and_translation_and_time_reversal(
rotation_matrix=op.rotation_matrix,
translation_vec=new_translation,
time_reversal=new_time_reversal))
magsymmops = all_ops
# else check to see if it specifies a magnetic space group
elif data.data.get("_space_group_magn.name_BNS") or data.data.get(
"_space_group_magn.number_BNS"):
if data.data.get("_space_group_magn.name_BNS"):
# get BNS label for MagneticSpaceGroup()
id = data.data.get("_space_group_magn.name_BNS")
else:
# get BNS number for MagneticSpaceGroup()
# by converting string to list of ints
id = list(
map(int, (data.data.get(
"_space_group_magn.number_BNS").split("."))))
msg = MagneticSpaceGroup(id)
if data.data.get("_space_group_magn.transform_BNS_Pp_abc"):
if data.data.get("_space_group_magn.transform_BNS_Pp_abc"
) != "a,b,c;0,0,0":
return NotImplementedError(
"Non-standard settings not currently supported.")
elif data.data.get("_space_group_magn.transform_BNS_Pp"):
return NotImplementedError(
"Incomplete specification to implement.")
magsymmops = msg.symmetry_ops
if not magsymmops:
warnings.warn(
"No magnetic symmetry detected, using primitive symmetry.")
magsymmops = [MagSymmOp.from_xyzt_string("x, y, z, 1")]
return magsymmops
