def test_relative_to_crystal_axes(self):
lattice = Lattice.from_parameters(5, 10, 5, 90, 110, 90)
moment = [1, 0, 2]
magmom = Magmom.from_moment_relative_to_crystal_axes(moment, lattice)
self.assertTrue(
np.allclose(magmom.moment, [0.93969262, 0.0, 1.65797986]))
self.assertTrue(
np.allclose(magmom.get_moment_relative_to_crystal_axes(lattice),
moment))
def _unique_coords(self, coords_in, magmoms_in=None, lattice=None):
"""
Generate unique coordinates using coord and symmetry positions
and also their corresponding magnetic moments, if supplied.
"""
coords = []
coords_num = []
if magmoms_in:
magmoms = []
if len(magmoms_in) != len(coords_in):
raise ValueError
for tmp_coord, tmp_magmom in zip(coords_in, magmoms_in):
count = 0
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if isinstance(op, MagSymmOp):
# Up to this point, magmoms have been defined relative
# to crystal axis. Now convert to Cartesian and into
# a Magmom object.
magmom = Magmom.from_moment_relative_to_crystal_axes(
op.operate_magmom(tmp_magmom), lattice=lattice)
else:
magmom = Magmom(tmp_magmom)
if not in_coord_list_pbc(
coords, coord, atol=self._site_tolerance):
coords.append(coord)
magmoms.append(magmom)
count = count + 1
coords_num.append(count)
return coords, magmoms, coords_num
else:
for tmp_coord in coords_in:
count = 0
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if not in_coord_list_pbc(
coords, coord, atol=self._site_tolerance):
coords.append(coord)
count = count + 1
coords_num.append(count)
return coords, [Magmom(0)
] * len(coords), coords_num # return dummy magmoms
def parse_magmoms(self, data, lattice=None):
"""
Parse atomic magnetic moments from data dictionary
"""
if lattice is None:
raise Exception(
'Magmoms given in terms of crystal axes in magCIF spec.')
try:
magmoms = {
data["_atom_site_moment_label"][i]:
Magmom.from_moment_relative_to_crystal_axes([
str2float(data["_atom_site_moment_crystalaxis_x"][i]),
str2float(data["_atom_site_moment_crystalaxis_y"][i]),
str2float(data["_atom_site_moment_crystalaxis_z"][i])
], lattice)
for i in range(len(data["_atom_site_moment_label"]))
}
except (ValueError, KeyError):
return None
return magmoms
def test_relative_to_crystal_axes(self):
lattice = Lattice.from_parameters(5, 10, 5, 90, 110, 90)
moment = [1, 0, 2]
magmom = Magmom.from_moment_relative_to_crystal_axes(moment, lattice)
self.assertTrue(np.allclose(magmom.moment, [0.93969262, 0.0, 1.65797986]))
self.assertTrue(np.allclose(magmom.get_moment_relative_to_crystal_axes(lattice), moment))