本文整理汇总了Python中pymatgen.symmetry.groups.SpaceGroup.from_int_number方法的典型用法代码示例。如果您正苦于以下问题：Python SpaceGroup.from_int_number方法的具体用法？Python SpaceGroup.from_int_number怎么用？Python SpaceGroup.from_int_number使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pymatgen.symmetry.groups.SpaceGroup的用法示例。
在下文中一共展示了SpaceGroup.from_int_number方法的7个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_get_slab
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
def test_get_slab(self):
s = self.get_structure("LiFePO4")
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
s = gen.get_slab(0.25)
self.assertAlmostEqual(s.lattice.abc[2], 20.820740000000001)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab = gen.get_slab()
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10, primitive=False)
slab_non_prim = gen.get_slab()
self.assertEqual(len(slab), 6)
self.assertEqual(len(slab_non_prim), len(slab) * 4)
#Some randomized testing of cell vectors
for i in range(1, 231):
i = random.randint(1, 230)
sg = SpaceGroup.from_int_number(i)
if sg.crystal_system == "hexagonal" or (sg.crystal_system == \
"trigonal" and sg.symbol.endswith("H")):
latt = Lattice.hexagonal(5, 10)
else:
#Cubic lattice is compatible with all other space groups.
latt = Lattice.cubic(5)
s = Structure.from_spacegroup(i, latt, ["H"], [[0, 0, 0]])
miller = (0, 0, 0)
while miller == (0, 0, 0):
miller = (random.randint(0, 6), random.randint(0, 6),
random.randint(0, 6))
gen = SlabGenerator(s, miller, 10, 10)
a, b, c = gen.oriented_unit_cell.lattice.matrix
self.assertAlmostEqual(np.dot(a, gen._normal), 0)
self.assertAlmostEqual(np.dot(b, gen._normal), 0)示例2: test_is_compatible
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
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)
sg = SpaceGroup("Fm-3m")
self.assertTrue(sg.is_compatible(cubic))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("R-3m:H")
self.assertFalse(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(hexagonal))
sg = SpaceGroup("R-3m:R")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("Pnma")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("P12/c1")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup("P-1")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertTrue(sg.is_compatible(rhom))
self.assertTrue(sg.is_compatible(hexagonal))
sg = SpaceGroup("Pmmn:2")
self.assertTrue(sg.is_compatible(cubic))
self.assertTrue(sg.is_compatible(tet))
self.assertTrue(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertFalse(sg.is_compatible(hexagonal))
sg = SpaceGroup.from_int_number(165)
self.assertFalse(sg.is_compatible(cubic))
self.assertFalse(sg.is_compatible(tet))
self.assertFalse(sg.is_compatible(ortho))
self.assertFalse(sg.is_compatible(rhom))
self.assertTrue(sg.is_compatible(hexagonal))示例3: get_symops
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in ["_symmetry_equiv_pos_as_xyz",
"_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"]:
if data.data.get(symmetry_label):
try:
symops = [SymmOp.from_xyz_string(s)
for s in data.data.get(symmetry_label)]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in ["_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall",
"_space_group_name_Hall_",
"_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"]:
if data.data.get(symmetry_label):
try:
spg = space_groups.get(sub_spgrp(
data.data.get(symmetry_label)))
if spg:
symops = SpaceGroup(spg).symmetry_ops
break
except ValueError:
continue
if not symops:
# Try to parse International number
for symmetry_label in ["_space_group_IT_number",
"_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops示例4: test_subgroup_supergroup
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
def test_subgroup_supergroup(self):
with warnings.catch_warnings() as w:
warnings.simplefilter("ignore")
self.assertTrue(SpaceGroup('Pma2').is_subgroup(SpaceGroup('Pccm')))
self.assertFalse(SpaceGroup.from_int_number(229).is_subgroup(
SpaceGroup.from_int_number(230)))示例5: get_symops
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in ["_symmetry_equiv_pos_as_xyz",
"_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"]:
if data.data.get(symmetry_label):
xyz = data.data.get(symmetry_label)
if isinstance(xyz, six.string_types):
warnings.warn("A 1-line symmetry op P1 CIF is detected!")
xyz = [xyz]
try:
symops = [SymmOp.from_xyz_string(s)
for s in xyz]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in ["_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall",
"_space_group_name_Hall_",
"_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"]:
sg = data.data.get(symmetry_label)
if sg:
sg = sub_spgrp(sg)
try:
spg = space_groups.get(sg)
if spg:
symops = SpaceGroup(spg).symmetry_ops
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." % symmetry_label)
break
except ValueError:
# Ignore any errors
pass
try:
for d in _get_cod_data():
if sg == re.sub("\s+", "",
d["hermann_mauguin"]) :
xyz = d["symops"]
symops = [SymmOp.from_xyz_string(s)
for s in xyz]
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." % symmetry_label)
break
except Exception as ex:
continue
if symops:
break
if not symops:
# Try to parse International number
for symmetry_label in ["_space_group_IT_number",
"_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops示例6: _generate_ordered_structures
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
#.........这里部分代码省略.........
structures_to_remove.append(check_idx)
if len(structures_to_remove):
self.logger.info(
"Removing {} duplicate ordered structures".format(
len(structures_to_remove)
)
)
ordered_structures = [
s
for idx, s in enumerate(ordered_structures)
if idx not in structures_to_remove
]
ordered_structures_origins = [
o
for idx, o in enumerate(ordered_structures_origins)
if idx not in structures_to_remove
]
# also remove low symmetry structures
if self.truncate_by_symmetry:
# by default, keep structures with 5 most symmetric space groups
if not isinstance(self.truncate_by_symmetry, int):
self.truncate_by_symmetry = 5
self.logger.info("Pruning low symmetry structures.")
# first get a list of symmetries present
symmetry_int_numbers = [
s.get_space_group_info()[1] for s in ordered_structures
]
# then count the number of symmetry operations for that space group
num_sym_ops = [
len(SpaceGroup.from_int_number(n).symmetry_ops)
for n in symmetry_int_numbers
]
# find the largest values...
max_symmetries = sorted(list(set(num_sym_ops)), reverse=True)
# ...and decide which ones to keep
if len(max_symmetries) > self.truncate_by_symmetry:
max_symmetries = max_symmetries[0:5]
structs_to_keep = [
(idx, num)
for idx, num in enumerate(num_sym_ops)
if num in max_symmetries
]
# sort so that highest symmetry structs are first
structs_to_keep = sorted(
structs_to_keep, key=lambda x: (x[1], -x[0]), reverse=True
)
self.logger.info(
"Removing {} low symmetry "
"ordered structures".format(
len(ordered_structures) - len(structs_to_keep)
)
)
ordered_structures = [ordered_structures[i] for i, _ in structs_to_keep]
ordered_structures_origins = [
ordered_structures_origins[i] for i, _ in structs_to_keep
]
# and ensure fm is always at index 0
fm_index = ordered_structures_origins.index("fm")
ordered_structures.insert(0, ordered_structures.pop(fm_index))
ordered_structures_origins.insert(
0, ordered_structures_origins.pop(fm_index)
)
# if our input structure isn't in our generated structures,
# let's add it manually and also keep a note of which structure
# is our input: this is mostly for book-keeping/benchmarking
self.input_index = None
self.input_origin = None
if self.input_analyzer.ordering != Ordering.NM:
matches = [
self.input_analyzer.matches_ordering(s) for s in ordered_structures
]
if not any(matches):
ordered_structures.append(self.input_analyzer.structure)
ordered_structures_origins.append("input")
self.logger.info(
"Input structure not present in enumerated structures, adding..."
)
else:
self.logger.info(
"Input structure was found in enumerated "
"structures at index {}".format(matches.index(True))
)
self.input_index = matches.index(True)
self.input_origin = ordered_structures_origins[self.input_index]
self.ordered_structures = ordered_structures
self.ordered_structure_origins = ordered_structures_origins示例7: test_subgroup_supergroup
# 需要导入模块: from pymatgen.symmetry.groups import SpaceGroup [as 别名]
# 或者: from pymatgen.symmetry.groups.SpaceGroup import from_int_number [as 别名]
def test_subgroup_supergroup(self):
self.assertTrue(SpaceGroup('Pma2').is_subgroup(SpaceGroup('Pccm')))
self.assertFalse(SpaceGroup.from_int_number(229).is_subgroup(
SpaceGroup.from_int_number(230)))