def from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5):
"""
Takes a `Structure` object. Uses pyspglib to perform various symmetry finding operations.
Args:
structure:
Structure object
has_timerev:
True is time-reversal symmetry is included.
symprec:
Tolerance for symmetry finding
angle_tolerance:
Angle tolerance for symmetry finding.
.. warning::
AFM symmetries are not supported.
"""
# Call spglib to get the list of symmetry operations.
finder = SymmetryFinder(structure, symprec=symprec, angle_tolerance=angle_tolerance)
data = finder.get_symmetry_dataset()
symrel = data["rotations"],
return cls(spgid=data["number"],
symrel=symrel,
tnons=data["translations"],
symafm=len(symrel) * [1],
has_timerev=has_timerev,
inord="C")
def __init__(self, struct, source='', comment=''):
"""
Args:
struct:
Structure object, See pymatgen.core.structure.Structure.
source:
User supplied identifier, i.e. for Materials Project this
would be the material ID number
comment:
comment for first header line
"""
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SymmetryFinder(struct)
data = sym.get_symmetry_dataset()
self._space_number = data["number"]
self._space_group = data["international"]
syms = [site.specie.symbol for site in struct]
for (s, data) in itertools.groupby(syms):
self._site_symbols.append(s)
self._natoms.append(len(tuple(data)))
if comment == '':
self._comment = 'None Given'
else:
self._comment = comment
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
def __init__(self, struct, source='', comment=''):
"""
Args:
struct:
Structure object, See pymatgen.core.structure.Structure.
source:
User supplied identifier, i.e. for Materials Project this
would be the material ID number
comment:
comment for first header line
"""
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SymmetryFinder(struct)
data = sym.get_symmetry_dataset()
self._space_number = data["number"]
self._space_group = data["international"]
syms = [site.specie.symbol for site in struct]
for (s, data) in itertools.groupby(syms):
self._site_symbols.append(s)
self._natoms.append(len(tuple(data)))
if comment == '':
self._comment = 'None Given'
else:
self._comment = comment
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
def from_structure(cls,
structure,
has_timerev=True,
symprec=1e-5,
angle_tolerance=5):
"""
Takes a :class:`Structure` object. Uses pyspglib to perform various symmetry finding operations.
Args:
structure: :class:`Structure` object
has_timerev: True is time-reversal symmetry is included.
symprec: Tolerance for symmetry finding
angle_tolerance: Angle tolerance for symmetry finding.
.. warning::
AFM symmetries are not supported.
"""
# Call spglib to get the list of symmetry operations.
finder = SymmetryFinder(structure,
symprec=symprec,
angle_tolerance=angle_tolerance)
data = finder.get_symmetry_dataset()
symrel = data["rotations"],
return cls(spgid=data["number"],
symrel=symrel,
tnons=data["translations"],
symafm=len(symrel) * [1],
has_timerev=has_timerev,
inord="C")
def main():
def str_examples():
examples = """
Usage example:\n
cif2spg.py silicon.cif => Open CIF file and visualize info on the spacegroup.
cif2spg.py -g silicon.cif => Same as above but use the GUI.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg:
sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('cif_file', nargs=1, help="CIF File")
parser.add_argument('-g', '--gui', action="store_true", help="Enable GUI")
# Parse command line.
try:
options = parser.parse_args()
except:
show_examples_and_exit(error_code=1)
cif_file = options.cif_file[0]
structure = abilab.Structure.from_file(cif_file)
#print(structure.to_abivars())
finder = SymmetryFinder(structure, symprec=1e-5, angle_tolerance=5)
data = finder.get_symmetry_dataset()
from pprint import pprint
if not options.gui:
pprint(data)
else:
from StringIO import StringIO
import wx
from abipy.gui.editor import SimpleTextViewer
stream = StringIO()
pprint(data, stream=stream)
stream.seek(0)
text = "".join(stream)
app = wx.App()
frame = SimpleTextViewer(None, text=text)
frame.Show()
app.MainLoop()
return 0
def get_structure(vasp_run,
outcar=None,
initial_structure=False,
additional_info=False):
"""
Process structure for static calculations from previous run.
Args:
vasp_run:
Vasprun object that contains the final structure from previous
run.
outcar:
Outcar object that contains the magnetization info from
previous run.
initial_structure:
Whether to return the structure from previous run. Default is
False.
additional_info:
Whether to return additional symmetry info related to the
structure. If True, return a list of the refined structure (
conventional cell), the conventional standard structure,
the symmetry dataset and symmetry operations of the structure
(see SymmetryFinder doc for details)
Returns:
Returns the magmom-decorated structure that can be passed to get
Vasp input files, e.g. get_kpoints.
"""
#TODO: fix magmom for get_*_structures
if vasp_run.is_spin:
if outcar and outcar.magnetization:
magmom = {"magmom": [i['tot'] for i in outcar.magnetization]}
else:
magmom = {
"magmom": vasp_run.to_dict['input']['parameters']['MAGMOM']
}
else:
magmom = None
structure = vasp_run.final_structure
if magmom:
structure = structure.copy(site_properties=magmom)
sym_finder = SymmetryFinder(structure, symprec=0.01)
if initial_structure:
return structure
elif additional_info:
info = [
sym_finder.get_refined_structure(),
sym_finder.get_conventional_standard_structure(),
sym_finder.get_symmetry_dataset(),
sym_finder.get_symmetry_operations()
]
return [sym_finder.get_primitive_standard_structure(), info]
else:
return sym_finder.get_primitive_standard_structure()
def get_structure(vasp_run, outcar=None, initial_structure=False,
additional_info=False):
"""
Process structure for static calculations from previous run.
Args:
vasp_run:
Vasprun object that contains the final structure from previous
run.
outcar:
Outcar object that contains the magnetization info from
previous run.
initial_structure:
Whether to return the structure from previous run. Default is
False.
additional_info:
Whether to return additional symmetry info related to the
structure. If True, return a list of the refined structure (
conventional cell), the conventional standard structure,
the symmetry dataset and symmetry operations of the structure
(see SymmetryFinder doc for details)
Returns:
Returns the magmom-decorated structure that can be passed to get
Vasp input files, e.g. get_kpoints.
"""
#TODO: fix magmom for get_*_structures
if vasp_run.is_spin:
if outcar and outcar.magnetization:
magmom = {"magmom": [i['tot'] for i in outcar.magnetization]}
else:
magmom = {
"magmom": vasp_run.to_dict['input']['parameters']
['MAGMOM']}
else:
magmom = None
structure = vasp_run.final_structure
if magmom:
structure = structure.copy(site_properties=magmom)
sym_finder = SymmetryFinder(structure, symprec=0.01)
if initial_structure:
return structure
elif additional_info:
info = [sym_finder.get_refined_structure(),
sym_finder.get_conventional_standard_structure(),
sym_finder.get_symmetry_dataset(),
sym_finder.get_symmetry_operations()]
return [sym_finder.get_primitive_standard_structure(),
info]
else:
return sym_finder.get_primitive_standard_structure()
def _make_struc_file(self, file_name):
sym = SymmetryFinder(self._bs._structure, symprec=0.01)
with open(file_name, "w") as f:
f.write(self._bs._structure.composition.formula + " " + str(sym.get_spacegroup_symbol()) + "\n")
for i in range(3):
line = ""
for j in range(3):
line += "%12.5f" % (Length(self._bs._structure.lattice.matrix[i][j], "ang").to("bohr"))
f.write(line + "\n")
ops = sym.get_symmetry_dataset()["rotations"]
f.write(str(len(ops)) + "\n")
for c in ops:
f.write("\n".join([" ".join([str(int(i)) for i in row]) for row in c]))
f.write("\n")
def parse_symmetry(args):
tolerance = float(args.tolerance[0])
for filename in args.filenames:
s = read_structure(filename)
if args.spacegroup:
finder = SymmetryFinder(s, tolerance)
dataset = finder.get_symmetry_dataset()
print filename
print "Spacegroup : {}".format(dataset["international"])
print "Int number : {}".format(dataset["number"])
print "Hall symbol : {}".format(dataset["hall"])
print
def parse_symmetry(args):
tolerance = float(args.tolerance[0])
for filename in args.filenames:
s = read_structure(filename)
if args.spacegroup:
finder = SymmetryFinder(s, tolerance)
dataset = finder.get_symmetry_dataset()
print filename
print "Spacegroup : {}".format(dataset["international"])
print "Int number : {}".format(dataset["number"])
print "Hall symbol : {}".format(dataset["hall"])
print
def _make_struc_file(self, file_name):
sym = SymmetryFinder(self._bs._structure, symprec=0.01)
with open(file_name, 'w') as f:
f.write(self._bs._structure.composition.formula+" " +
str(sym.get_spacegroup_symbol())+"\n")
for i in range(3):
line = ''
for j in range(3):
line += "%12.5f" % (
Length(self._bs._structure.lattice.matrix[i][j],
"ang").to("bohr"))
f.write(line+'\n')
ops = sym.get_symmetry_dataset()['rotations']
f.write(str(len(ops))+"\n")
for c in ops:
f.write('\n'.join([' '.join([str(int(i)) for i in row])
for row in c]))
f.write('\n')
def __init__(self, struct, source='', comment=''):
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SymmetryFinder(struct)
data = sym.get_symmetry_dataset()
self._space_number = data["number"]
self._space_group = data["international"]
syms = [site.specie.symbol for site in struct]
for (s, data) in itertools.groupby(syms):
self._site_symbols.append(s)
self._natoms.append(len(tuple(data)))
if comment == '':
self._comment = 'None Given'
else:
self._comment = comment
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
def __init__(self, struct, source='', comment=''):
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SymmetryFinder(struct)
data = sym.get_symmetry_dataset()
self._space_number = data["number"]
self._space_group = data["international"]
syms = [site.specie.symbol for site in struct]
for (s, data) in itertools.groupby(syms):
self._site_symbols.append(s)
self._natoms.append(len(tuple(data)))
if comment == '':
self._comment = 'None Given'
else:
self._comment = comment
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
def main():
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('cif_file', nargs=1, help="CIF File")
parser.add_argument('-g', '--gui', action="store_true", help="Enable GUI")
# Parse command line.
try:
options = parser.parse_args()
except:
show_examples_and_exit(error_code=1)
cif_file = options.cif_file[0]
structure = abilab.Structure.from_file(cif_file)
#print(structure.to_abivars())
finder = SymmetryFinder(structure, symprec=1e-5, angle_tolerance=5)
data = finder.get_symmetry_dataset()
from pprint import pprint
if not options.gui:
pprint(data)
else:
from StringIO import StringIO
import wx
from abipy.gui.editor import SimpleTextViewer
stream = StringIO()
pprint(data, stream=stream)
stream.seek(0)
text = "".join(stream)
app = wx.App()
frame = SimpleTextViewer(None, text=text)
frame.Show()
app.MainLoop()
return 0
def __init__(self, struct, comment=None):
"""
Args:
struct:
Structure object, See pymatgen.core.structure.Structure.
comment:
comment for first header line
"""
if struct.is_ordered:
self._struct = struct
self._site_symbols = []
self._natoms = []
sym = SymmetryFinder(struct)
data = sym.get_symmetry_dataset()
self._space_number = data["number"]
self._space_group = data["international"]
syms = [site.specie.symbol for site in struct]
for (s, data) in itertools.groupby(syms):
self._site_symbols.append(s)
self._natoms.append(len(tuple(data)))
self._comment = comment
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
class SymmetryFinderTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SymmetryFinder(self.structure, 0.001)
parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif'))
self.disordered_structure = parser.get_structures()[0]
self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species_and_occu, site.frac_coords)
self.sg3 = SymmetryFinder(s, 0.001)
parser = CifParser(os.path.join(test_dir, 'Graphite.cif'))
graphite = parser.get_structures()[0]
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SymmetryFinder(graphite, 0.001)
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_spacegroup_symbol(),
"P4_2/nmc")
self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma")
self.assertEqual(self.sg4.get_spacegroup_symbol(), "R-3m")
def test_get_space_number(self):
self.assertEqual(self.sg.get_spacegroup_number(), 62)
self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137)
self.assertEqual(self.sg4.get_spacegroup_number(), 166)
def test_get_hall(self):
self.assertEqual(self.sg.get_hall(), '-P 2ac 2n')
self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n')
def test_get_pointgroup(self):
self.assertEqual(self.sg.get_point_group(), 'mmm')
self.assertEqual(self.disordered_sg.get_point_group(), '4/mmm')
def test_get_symmetry_dataset(self):
ds = self.sg.get_symmetry_dataset()
self.assertEqual(ds['international'], 'Pnma')
def test_get_crystal_system(self):
crystal_system = self.sg.get_crystal_system()
self.assertEqual('orthorhombic', crystal_system)
self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system())
def test_get_symmetry_operations(self):
fracsymmops = self.sg.get_symmetry_operations()
symmops = self.sg.get_symmetry_operations(True)
self.assertEqual(len(symmops), 8)
latt = self.structure.lattice
for fop, op in zip(fracsymmops, symmops):
for site in self.structure:
newfrac = fop.operate(site.frac_coords)
newcart = op.operate(site.coords)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart),
newfrac))
found = False
newsite = PeriodicSite(site.species_and_occu, newcart, latt,
coords_are_cartesian=True)
for testsite in self.structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
def test_get_refined_structure(self):
for a in self.sg.get_refined_structure().lattice.angles:
self.assertEqual(a, 90)
refined = self.disordered_sg.get_refined_structure()
for a in refined.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(refined.lattice.a, refined.lattice.b)
parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
s = parser.get_structures()[0]
sg = SymmetryFinder(s, 0.001)
self.assertEqual(sg.get_refined_structure().num_sites, 4 * s.num_sites)
def test_get_symmetrized_structure(self):
symm_struct = self.sg.get_symmetrized_structure()
for a in symm_struct.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(len(symm_struct.equivalent_sites), 5)
symm_struct = self.disordered_sg.get_symmetrized_structure()
self.assertEqual(len(symm_struct.equivalent_sites), 8)
self.assertEqual(map(len, symm_struct.equivalent_sites), [16,4,8,4,2,8,8,8])
s1 = symm_struct.equivalent_sites[1][1]
s2 = symm_struct[symm_struct.equivalent_indices[1][1]]
self.assertEqual(s1, s2)
self.assertEqual(self.sg4.get_symmetrized_structure()[0].magmom, 0.1)
def test_find_primitive(self):
"""
F m -3 m Li2O testing of converting to primitive cell
"""
parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure)
primitive_structure = s.find_primitive()
self.assertEqual(primitive_structure.formula, "Li2 O1")
# This isn't what is expected. All the angles should be 60
self.assertAlmostEqual(primitive_structure.lattice.alpha, 60)
self.assertAlmostEqual(primitive_structure.lattice.beta, 60)
self.assertAlmostEqual(primitive_structure.lattice.gamma, 60)
self.assertAlmostEqual(primitive_structure.lattice.volume,
structure.lattice.volume / 4.0)
def test_get_ir_reciprocal_mesh(self):
grid=self.sg.get_ir_reciprocal_mesh()
self.assertEquals(len(grid), 216)
self.assertAlmostEquals(grid[1][0][0], 0.1)
self.assertAlmostEquals(grid[1][0][1], 0.0)
self.assertAlmostEquals(grid[1][0][2], 0.0)
self.assertEquals(grid[1][1], 2)
def test_get_conventional_standard_structure(self):
parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 9.1980270633769461)
self.assertAlmostEqual(conv.lattice.b, 9.1980270633769461)
self.assertAlmostEqual(conv.lattice.c, 9.1980270633769461)
parser = CifParser(os.path.join(test_dir, 'btet_1915.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 5.0615106678044235)
self.assertAlmostEqual(conv.lattice.b, 5.0615106678044235)
self.assertAlmostEqual(conv.lattice.c, 4.2327080177761687)
parser = CifParser(os.path.join(test_dir, 'orci_1010.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 2.9542233922299999)
self.assertAlmostEqual(conv.lattice.b, 4.6330325651443296)
self.assertAlmostEqual(conv.lattice.c, 5.373703587040775)
parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 4.1430033493799998)
self.assertAlmostEqual(conv.lattice.b, 31.437979757624728)
self.assertAlmostEqual(conv.lattice.c, 3.99648651)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 117.53832420192903)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 14.033435583000625)
self.assertAlmostEqual(conv.lattice.b, 3.96052850731)
self.assertAlmostEqual(conv.lattice.c, 6.8743926325200002)
parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 120)
self.assertAlmostEqual(conv.lattice.a, 3.699919902005897)
self.assertAlmostEqual(conv.lattice.b, 3.699919902005897)
self.assertAlmostEqual(conv.lattice.c, 6.9779585500000003)
def test_get_primitive_standard_structure(self):
parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.beta, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.gamma, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.a, 7.9657251015812145)
self.assertAlmostEqual(prim.lattice.b, 7.9657251015812145)
self.assertAlmostEqual(prim.lattice.c, 7.9657251015812145)
parser = CifParser(os.path.join(test_dir, 'btet_1915.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 105.015053349)
self.assertAlmostEqual(prim.lattice.beta, 105.015053349)
self.assertAlmostEqual(prim.lattice.gamma, 118.80658411899999)
self.assertAlmostEqual(prim.lattice.a, 4.1579321075608791)
self.assertAlmostEqual(prim.lattice.b, 4.1579321075608791)
self.assertAlmostEqual(prim.lattice.c, 4.1579321075608791)
parser = CifParser(os.path.join(test_dir, 'orci_1010.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 134.78923546600001)
self.assertAlmostEqual(prim.lattice.beta, 105.856239333)
self.assertAlmostEqual(prim.lattice.gamma, 91.276341676000001)
self.assertAlmostEqual(prim.lattice.a, 3.8428217771014852)
self.assertAlmostEqual(prim.lattice.b, 3.8428217771014852)
self.assertAlmostEqual(prim.lattice.c, 3.8428217771014852)
parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 90)
self.assertAlmostEqual(prim.lattice.beta, 90)
self.assertAlmostEqual(prim.lattice.gamma, 164.985257335)
self.assertAlmostEqual(prim.lattice.a, 15.854897098324196)
self.assertAlmostEqual(prim.lattice.b, 15.854897098324196)
self.assertAlmostEqual(prim.lattice.c, 3.99648651)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 63.579155761999999)
self.assertAlmostEqual(prim.lattice.beta, 116.42084423747779)
self.assertAlmostEqual(prim.lattice.gamma, 148.47965136208569)
self.assertAlmostEqual(prim.lattice.a, 7.2908007159612325)
self.assertAlmostEqual(prim.lattice.b, 7.2908007159612325)
self.assertAlmostEqual(prim.lattice.c, 6.8743926325200002)
parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 90)
self.assertAlmostEqual(prim.lattice.beta, 90)
self.assertAlmostEqual(prim.lattice.gamma, 120)
self.assertAlmostEqual(prim.lattice.a, 3.699919902005897)
self.assertAlmostEqual(prim.lattice.b, 3.699919902005897)
self.assertAlmostEqual(prim.lattice.c, 6.9779585500000003)
class SymmetryFinderTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SymmetryFinder(self.structure, 0.001)
parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif'))
self.disordered_structure = parser.get_structures()[0]
self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species_and_occu, site.frac_coords)
self.sg3 = SymmetryFinder(s, 0.001)
parser = CifParser(os.path.join(test_dir, 'Graphite.cif'))
graphite = parser.get_structures()[0]
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SymmetryFinder(graphite, 0.001)
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_spacegroup_symbol(),
"P4_2/nmc")
self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma")
self.assertEqual(self.sg4.get_spacegroup_symbol(), "R-3m")
def test_get_space_number(self):
self.assertEqual(self.sg.get_spacegroup_number(), 62)
self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137)
self.assertEqual(self.sg4.get_spacegroup_number(), 166)
def test_get_hall(self):
self.assertEqual(self.sg.get_hall(), '-P 2ac 2n')
self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n')
def test_get_pointgroup(self):
self.assertEqual(self.sg.get_point_group(), 'mmm')
self.assertEqual(self.disordered_sg.get_point_group(), '4/mmm')
def test_get_symmetry_dataset(self):
ds = self.sg.get_symmetry_dataset()
self.assertEqual(ds['international'], 'Pnma')
def test_get_crystal_system(self):
crystal_system = self.sg.get_crystal_system()
self.assertEqual('orthorhombic', crystal_system)
self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system())
def test_get_symmetry_operations(self):
fracsymmops = self.sg.get_symmetry_operations()
symmops = self.sg.get_symmetry_operations(True)
self.assertEqual(len(symmops), 8)
latt = self.structure.lattice
for fop, op in zip(fracsymmops, symmops):
for site in self.structure:
newfrac = fop.operate(site.frac_coords)
newcart = op.operate(site.coords)
self.assertTrue(
np.allclose(latt.get_fractional_coords(newcart), newfrac))
found = False
newsite = PeriodicSite(site.species_and_occu,
newcart,
latt,
coords_are_cartesian=True)
for testsite in self.structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
def test_get_refined_structure(self):
for a in self.sg.get_refined_structure().lattice.angles:
self.assertEqual(a, 90)
refined = self.disordered_sg.get_refined_structure()
for a in refined.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(refined.lattice.a, refined.lattice.b)
parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
s = parser.get_structures()[0]
sg = SymmetryFinder(s, 0.001)
self.assertEqual(sg.get_refined_structure().num_sites, 4 * s.num_sites)
def test_get_symmetrized_structure(self):
symm_struct = self.sg.get_symmetrized_structure()
for a in symm_struct.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(len(symm_struct.equivalent_sites), 5)
symm_struct = self.disordered_sg.get_symmetrized_structure()
self.assertEqual(len(symm_struct.equivalent_sites), 8)
self.assertEqual(map(len, symm_struct.equivalent_sites),
[16, 4, 8, 4, 2, 8, 8, 8])
s1 = symm_struct.equivalent_sites[1][1]
s2 = symm_struct[symm_struct.equivalent_indices[1][1]]
self.assertEqual(s1, s2)
self.assertEqual(self.sg4.get_symmetrized_structure()[0].magmom, 0.1)
def test_find_primitive(self):
"""
F m -3 m Li2O testing of converting to primitive cell
"""
parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure)
primitive_structure = s.find_primitive()
self.assertEqual(primitive_structure.formula, "Li2 O1")
# This isn't what is expected. All the angles should be 60
self.assertAlmostEqual(primitive_structure.lattice.alpha, 60)
self.assertAlmostEqual(primitive_structure.lattice.beta, 60)
self.assertAlmostEqual(primitive_structure.lattice.gamma, 60)
self.assertAlmostEqual(primitive_structure.lattice.volume,
structure.lattice.volume / 4.0)
def test_get_ir_reciprocal_mesh(self):
grid = self.sg.get_ir_reciprocal_mesh()
self.assertEquals(len(grid), 216)
self.assertAlmostEquals(grid[1][0][0], 0.1)
self.assertAlmostEquals(grid[1][0][1], 0.0)
self.assertAlmostEquals(grid[1][0][2], 0.0)
self.assertEquals(grid[1][1], 2)
def test_get_conventional_standard_structure(self):
parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 9.1980270633769461)
self.assertAlmostEqual(conv.lattice.b, 9.1980270633769461)
self.assertAlmostEqual(conv.lattice.c, 9.1980270633769461)
parser = CifParser(os.path.join(test_dir, 'btet_1915.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 5.0615106678044235)
self.assertAlmostEqual(conv.lattice.b, 5.0615106678044235)
self.assertAlmostEqual(conv.lattice.c, 4.2327080177761687)
parser = CifParser(os.path.join(test_dir, 'orci_1010.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 2.9542233922299999)
self.assertAlmostEqual(conv.lattice.b, 4.6330325651443296)
self.assertAlmostEqual(conv.lattice.c, 5.373703587040775)
parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 4.1430033493799998)
self.assertAlmostEqual(conv.lattice.b, 31.437979757624728)
self.assertAlmostEqual(conv.lattice.c, 3.99648651)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 117.53832420192903)
self.assertAlmostEqual(conv.lattice.gamma, 90)
self.assertAlmostEqual(conv.lattice.a, 14.033435583000625)
self.assertAlmostEqual(conv.lattice.b, 3.96052850731)
self.assertAlmostEqual(conv.lattice.c, 6.8743926325200002)
parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 90)
self.assertAlmostEqual(conv.lattice.beta, 90)
self.assertAlmostEqual(conv.lattice.gamma, 120)
self.assertAlmostEqual(conv.lattice.a, 3.699919902005897)
self.assertAlmostEqual(conv.lattice.b, 3.699919902005897)
self.assertAlmostEqual(conv.lattice.c, 6.9779585500000003)
def test_get_primitive_standard_structure(self):
parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.beta, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.gamma, 109.47122063400001)
self.assertAlmostEqual(prim.lattice.a, 7.9657251015812145)
self.assertAlmostEqual(prim.lattice.b, 7.9657251015812145)
self.assertAlmostEqual(prim.lattice.c, 7.9657251015812145)
parser = CifParser(os.path.join(test_dir, 'btet_1915.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 105.015053349)
self.assertAlmostEqual(prim.lattice.beta, 105.015053349)
self.assertAlmostEqual(prim.lattice.gamma, 118.80658411899999)
self.assertAlmostEqual(prim.lattice.a, 4.1579321075608791)
self.assertAlmostEqual(prim.lattice.b, 4.1579321075608791)
self.assertAlmostEqual(prim.lattice.c, 4.1579321075608791)
parser = CifParser(os.path.join(test_dir, 'orci_1010.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 134.78923546600001)
self.assertAlmostEqual(prim.lattice.beta, 105.856239333)
self.assertAlmostEqual(prim.lattice.gamma, 91.276341676000001)
self.assertAlmostEqual(prim.lattice.a, 3.8428217771014852)
self.assertAlmostEqual(prim.lattice.b, 3.8428217771014852)
self.assertAlmostEqual(prim.lattice.c, 3.8428217771014852)
parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 90)
self.assertAlmostEqual(prim.lattice.beta, 90)
self.assertAlmostEqual(prim.lattice.gamma, 164.985257335)
self.assertAlmostEqual(prim.lattice.a, 15.854897098324196)
self.assertAlmostEqual(prim.lattice.b, 15.854897098324196)
self.assertAlmostEqual(prim.lattice.c, 3.99648651)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 63.579155761999999)
self.assertAlmostEqual(prim.lattice.beta, 116.42084423747779)
self.assertAlmostEqual(prim.lattice.gamma, 148.47965136208569)
self.assertAlmostEqual(prim.lattice.a, 7.2908007159612325)
self.assertAlmostEqual(prim.lattice.b, 7.2908007159612325)
self.assertAlmostEqual(prim.lattice.c, 6.8743926325200002)
parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 90)
self.assertAlmostEqual(prim.lattice.beta, 90)
self.assertAlmostEqual(prim.lattice.gamma, 120)
self.assertAlmostEqual(prim.lattice.a, 3.699919902005897)
self.assertAlmostEqual(prim.lattice.b, 3.699919902005897)
self.assertAlmostEqual(prim.lattice.c, 6.9779585500000003)
