def test_init(self):
# test init with the following space group:
# 71.538 (BNS number), I_cmmm (BNS label)
# 65.10.554 (same space group as above, OG number), C_Immm (OG label)
msg_from_bns_1 = MagneticSpaceGroup("I_cmmm")
msg_from_bns_2 = MagneticSpaceGroup([71, 538])
msg_from_og_1 = MagneticSpaceGroup.from_og("C_Immm")
msg_from_og_2 = MagneticSpaceGroup.from_og([65, 10, 554])
self.assertEqual(msg_from_bns_1, msg_from_bns_2)
self.assertEqual(msg_from_og_1, msg_from_og_2)
self.assertEqual(msg_from_bns_1, msg_from_og_1)
def test_equivalence_to_spacegroup(self):
# first 230 magnetic space groups have same symmetry operations
# as normal space groups, so should give same orbits
labels = ["Fm-3m", "Pnma", "P2/c", "P-1"]
points = [[0, 0, 0], [0.5, 0, 0], [0.11, 0.22, 0.33]]
for label in labels:
sg = SpaceGroup(label)
msg = MagneticSpaceGroup(label)
self.assertEqual(sg.crystal_system, msg.crystal_system)
for p in points:
pp_sg = np.array(sg.get_orbit(p))
pp_msg = np.array(msg.get_orbit(p, 0)[0]) # discarding magnetic moment information
pp_sg = pp_sg[np.lexsort(np.transpose(pp_sg)[::-1])] # sorting arrays so we can compare them
pp_msg = pp_msg[np.lexsort(np.transpose(pp_msg)[::-1])]
self.assertTrue(np.allclose(pp_sg, pp_msg))
def test_str(self):
msg = MagneticSpaceGroup([4, 11])
ref_string = """BNS: 4.11 P_b2_1
Operators: (1|0,0,0) (2y|0,1/2,0) (1|0,1/2,0)' (2y|0,0,0)'
Wyckoff Positions:
4e (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
(-x,y,-z;mx,-my,mz)
2d (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
2c (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
2b (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
2a (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
Alternative OG setting exists for this space group."""
ref_string_all = """BNS: 4.11 P_b2_1 OG: 3.7.14 P_2b2'
OG-BNS Transform: (a,2b,c;0,0,0)
Operators (BNS): (1|0,0,0) (2y|0,1/2,0) (1|0,1/2,0)' (2y|0,0,0)'
Wyckoff Positions (BNS):
4e (x,y,z;mx,my,mz) (-x,y+1/2,-z;-mx,my,-mz) (x,y+1/2,z;-mx,-my,-mz)
(-x,y,-z;mx,-my,mz)
2d (1/2,y,1/2;mx,0,mz) (1/2,y+1/2,1/2;-mx,0,-mz)
2c (1/2,y,0;mx,0,mz) (1/2,y+1/2,0;-mx,0,-mz)
2b (0,y,1/2;mx,0,mz) (0,y+1/2,1/2;-mx,0,-mz)
2a (0,y,0;mx,0,mz) (0,y+1/2,0;-mx,0,-mz)
Operators (OG): (1|0,0,0) (2y|0,1,0) (1|0,1,0)' (2y|0,0,0)'
Wyckoff Positions (OG): (1,0,0)+ (0,2,0)+ (0,0,1)+
4e (x,y,z;mx,my,mz) (-x,y+1,-z;-mx,my,-mz) (x,y+1,z;-mx,-my,-mz)
(-x,y,-z;mx,-my,mz)
2d (1/2,y,1/2;mx,0,mz) (-1/2,y+1,-1/2;-mx,0,-mz)
2c (1/2,y,0;mx,0,mz) (-1/2,y+1,0;-mx,0,-mz)
2b (0,y,1/2;mx,0,mz) (0,y+1,-1/2;-mx,0,-mz)
2a (0,y,0;mx,0,mz) (0,y+1,0;-mx,0,-mz)"""
self.assertStrContentEqual(str(msg), ref_string)
self.assertStrContentEqual(msg.data_str(), ref_string_all)
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
def test_is_compatible(self):
cubic = Lattice.cubic(1)
hexagonal = Lattice.hexagonal(1, 2)
rhom = Lattice.rhombohedral(3, 80)
tet = Lattice.tetragonal(1, 2)
ortho = Lattice.orthorhombic(1, 2, 3)
msg = MagneticSpaceGroup("Fm-3m")
self.assertTrue(msg.is_compatible(cubic))
self.assertFalse(msg.is_compatible(hexagonal))
msg = MagneticSpaceGroup("Pnma")
self.assertTrue(msg.is_compatible(cubic))
self.assertTrue(msg.is_compatible(tet))
self.assertTrue(msg.is_compatible(ortho))
self.assertFalse(msg.is_compatible(rhom))
self.assertFalse(msg.is_compatible(hexagonal))
msg = MagneticSpaceGroup("P2/c")
self.assertTrue(msg.is_compatible(cubic))
self.assertTrue(msg.is_compatible(tet))
self.assertTrue(msg.is_compatible(ortho))
self.assertFalse(msg.is_compatible(rhom))
self.assertFalse(msg.is_compatible(hexagonal))
msg = MagneticSpaceGroup("P-1")
self.assertTrue(msg.is_compatible(cubic))
self.assertTrue(msg.is_compatible(tet))
self.assertTrue(msg.is_compatible(ortho))
self.assertTrue(msg.is_compatible(rhom))
self.assertTrue(msg.is_compatible(hexagonal))
def setUp(self):
self.msg_1 = MagneticSpaceGroup([70, 530])
self.msg_2 = MagneticSpaceGroup([62, 448])
self.msg_3 = MagneticSpaceGroup([20, 37])
self.msg_4 = MagneticSpaceGroup([2, 7], "c,1/4a+1/4b,-1/2a+1/2b;0,0,0")
def __init__(self, structure):
"""
Args:
"""
self.input_structure = structure.copy()
iso_location = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'iso/')
self.input_filename_cif = os.path.join(iso_location,
'findsym_input.mcif')
self.output_filename_cif = os.path.join(iso_location, 'findsym.cif')
# self.input_filename_findsym = os.path.join(iso_location, 'findsym_in.in')
self.input_filename_findsym = 'findsym_in.in'
self.write_cif_input()
# write initial input from mcif file
findsym_command = 'findsym_cifinput ' + self.input_filename_cif
logger.debug("""starting isotropy session in {}
using isotropy in: {}""".format(
os.getcwd(), iso_location))
self.findsym_cifinput_process = Command(os.path.join(
iso_location, findsym_command),
stdout=Capture(buffer_size=1),
env={"ISODATA": iso_location})
try:
self.findsym_cifinput_process.run(input=PIPE, async_=False)
except FileNotFoundError:
raise Exception(
"Couldn't find Isotropy (findsym) for Linux, see installation instructions"
)
with open(self.input_filename_findsym, "w") as io_file:
# move past initial output
keep_reading = True
while keep_reading:
# this_line = self.iso_process.stdout.readline().decode()
this_line = self.findsym_cifinput_process.stdout.readline(
).decode()
if this_line: # don't log until isotropy responds
logger.debug("isotropy: {}".format(this_line))
io_file.write(this_line)
else:
keep_reading = False
# run findsym
findsym_command = 'findsym ' + self.input_filename_findsym
self.findsym_process = Command(os.path.join(iso_location,
findsym_command),
stdout=Capture(buffer_size=1),
env={"ISODATA": iso_location})
try:
self.findsym_process.run(input=PIPE, async_=False)
except FileNotFoundError:
raise Exception(
"Couldn't find Isotropy (findsym) for Linux, see installation instructions"
)
# # move past initial output
# keep_reading = True
# while keep_reading:
# this_line = self.findsym_process.stdout.readline().decode()
# # this_line = self.read_iso_line()
# if this_line: # don't log until isotropy responds
# logger.debug("isotropy: {}".format(this_line))
# else:
# keep_reading = False
self.output_cif_file = CifFile.from_file(self.output_filename_cif)
msg_int_symbol = int(self.output_cif_file.data['findsym-output'].
data['_symmetry_Int_Tables_number'])
self.magnetic_space_group = MagneticSpaceGroup(msg_int_symbol)
def setUp(self):
self.msg_1 = MagneticSpaceGroup([70, 530])
self.msg_2 = MagneticSpaceGroup([62, 448])
self.msg_3 = MagneticSpaceGroup([20, 37])