def get_reciprocal_point_group_operations(
structure: Structure,
symprec: float = defaults["symprec"],
time_reversal: bool = True,
):
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
sga = SpacegroupAnalyzer(structure, symprec=symprec)
if sga.get_symmetry_dataset() is None:
# sometimes default angle tolerance doesn't work as expected
sga = SpacegroupAnalyzer(structure,
symprec=symprec,
angle_tolerance=-1)
rotations = sga.get_symmetry_dataset()["rotations"].transpose((0, 2, 1))
translations = sga.get_symmetry_dataset()["translations"]
is_tr = np.full(len(rotations), False, dtype=bool)
if time_reversal:
rotations = np.concatenate([rotations, -rotations])
translations = np.concatenate([translations, -translations])
is_tr = np.concatenate([is_tr, ~is_tr])
rotations, unique_ops = np.unique(rotations, axis=0, return_index=True)
translations = translations[unique_ops]
is_tr = is_tr[unique_ops]
# put identity first and time-reversal last
sort_idx = np.argsort(
np.abs(rotations - np.eye(3)).sum(axis=(1, 2)) + is_tr * 10)
return rotations[sort_idx], translations[sort_idx], is_tr[sort_idx]
def get_unique_site_indices(structure):
sa = SpacegroupAnalyzer(structure)
symm_data = sa.get_symmetry_dataset()
# equivalency mapping for the structure
# i'th site in the struct equivalent to eq_struct[i]'th site
eq_atoms = symm_data["equivalent_atoms"]
return np.unique(eq_atoms).tolist()
def cif2geom_sym2(cif):
parser=CifParser.from_string(cif)
struct=parser.get_structures()[0]
sg = SpacegroupAnalyzer(struct)
struct = sg.get_conventional_standard_structure()
sg = SpacegroupAnalyzer(struct)
geomlines=["CRYSTAL"]
geomlines += ["0 0 1"]
geomlines += [str(sg.get_spacegroup_number())]
cry_sys = sg.get_crystal_system()
lattice = struct.lattice
if cry_sys == 'trigonal' or cry_sys == 'hexagonal' or cry_sys == 'tetragonal':
geomlines += ["%s %s" %(lattice.a,lattice.c)]
elif cry_sys == 'cubic':
geomlines += ["%s" %(lattice.a)]
elif cry_sys == 'triclinic':
geomlines += ["%s %s %s %s %s %s" %(lattice.a,lattice.b,lattice.c,lattice.alpha,lattice.beta,lattice.gamma)]
elif cry_sys == 'monoclinic':
geomlines += ["%s %s %s %s" %(lattice.a,lattice.b,lattice.c,lattice.beta)]
elif cry_sys == 'orthorhombic':
geomlines += ["%s %s %s" %(lattice.a,lattice.b,lattice.c)]
else:
print('Error printing symmetrized structure.')
quit()
ds = sg.get_symmetry_dataset()
eq_sites = np.unique(ds['equivalent_atoms'])
geomlines += [str(len(eq_sites))]
for eq_site in eq_sites:
site = struct.sites[eq_site]
geomlines += ["%s %s %s %s" %(site.specie.Z+200,site.a,site.b,site.c)]
return geomlines,struct
def from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5):
"""
Takes a :class:`Structure` object. Uses spglib 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.
spga = SpacegroupAnalyzer(structure, symprec=symprec, angle_tolerance=angle_tolerance)
data = spga.get_symmetry_dataset()
return cls(
spgid=data["number"],
symrel=data["rotations"],
tnons=data["translations"],
symafm=len(symrel) * [1],
has_timerev=has_timerev,
inord="C",
)
def __init__(self, structure):
self.structure = structure
sa = SpacegroupAnalyzer(self.structure)
symm_data = sa.get_symmetry_dataset()
# equivalency mapping for the structure
# i'th site in the input structure equivalent to eq_atoms[i]'th site
self.eq_atoms = symm_data["equivalent_atoms"]
def from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5):
"""
Takes a |Structure| object. Uses spglib 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.
spga = SpacegroupAnalyzer(structure, symprec=symprec, angle_tolerance=angle_tolerance)
data = spga.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 from_structure(cls, structure: Structure) -> "SymmetryData":
symprec = SETTINGS.SYMPREC
sg = SpacegroupAnalyzer(structure, symprec=symprec)
symmetry: Dict[str, Any] = {"symprec": symprec}
if not sg.get_symmetry_dataset():
sg = SpacegroupAnalyzer(structure, 1e-3, 1)
symmetry["symprec"] = 1e-3
symmetry.update({
"source":
"spglib",
"symbol":
sg.get_space_group_symbol(),
"number":
sg.get_space_group_number(),
"point_group":
sg.get_point_group_symbol(),
"crystal_system":
CrystalSystem(sg.get_crystal_system().title()),
"hall":
sg.get_hall(),
"version":
spglib.__version__,
})
return SymmetryData(**symmetry)
def determine_symmetry_positions(st, element):
"""
determine non-equivalent positions for atoms of type *element*
element (str) - name of element, for example Li
return list of lists - atom numbers for each non-equivalent position
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
stp = st.convert2pymatgen()
spg = SpacegroupAnalyzer(stp)
info = spg.get_symmetry_dataset()
positions = {}
for i, (el, pos) in enumerate(zip(st.get_elements(), info['equivalent_atoms'])):
if el == element and pos not in positions:
positions[pos] = []
if el == element:
positions[pos].append(i)
printlog('I have found ', len(positions), 'non-equivalent positions for', element, ':',positions.keys(), imp = 'y', end = '\n')
printlog('Atom numbers: ', positions, imp = 'y')
sorted_keys = sorted(list(positions.keys()))
pos_lists = [positions[key] for key in sorted_keys ]
return pos_lists
def set_output_data(self, d_calc, d):
"""
set the 'output' key
"""
d["output"] = {
"structure": d_calc["output"]["structure"],
"density": d_calc.pop("density"),
"energy": d_calc["output"]["energy"],
"energy_per_atom": d_calc["output"]["energy_per_atom"]
}
d["output"].update(self.get_basic_processed_data(d))
sg = SpacegroupAnalyzer(
Structure.from_dict(d_calc["output"]["structure"]), 0.1)
if not sg.get_symmetry_dataset():
sg = SpacegroupAnalyzer(
Structure.from_dict(d_calc["output"]["structure"]), 1e-3, 1)
d["output"]["spacegroup"] = {
"source": "spglib",
"symbol": sg.get_space_group_symbol(),
"number": sg.get_space_group_number(),
"point_group": sg.get_point_group_symbol(),
"crystal_system": sg.get_crystal_system(),
"hall": sg.get_hall()
}
if d["input"]["parameters"].get("LEPSILON"):
for k in [
'epsilon_static', 'epsilon_static_wolfe', 'epsilon_ionic'
]:
d["output"][k] = d_calc["output"][k]
def from_structure(cls, structure, equivalent_wyckoff_sites=None):
"""
Parameters
----------
structure : pymatgen.Structure
equivalent_wyckoff_sites : list of lists
List of Wyckoff sites that are treated as the same sublattice, e.g. [['b', 'f']] will
give combine Wyckoff site 'b' and Wyckoff site 'f' into one sublattice. Putting the same
Wyckoff site in multiple equivalent groups will produce undefined results.
Returns
-------
PRLStructure
"""
struct = PRLStructure.from_dict(structure.as_dict())
# normalize the input structure to a pure element to get Wyckoff sites
structure = Structure.from_dict(structure.as_dict())
structure.replace_species({sp.name: "H" for sp in structure.species})
sga = SpacegroupAnalyzer(structure)
wyckoff_sites = sga.get_symmetry_dataset()['wyckoffs']
true_sublattices = sorted(set(wyckoff_sites))
if equivalent_wyckoff_sites is not None:
# transform the true sublattices by combining equivalent sites
combined_sublattices = [''.join(sorted(sites)) for sites in equivalent_wyckoff_sites]
def match_subl(candidate):
for subl in combined_sublattices:
# if the candidate site is in the combined sublattice, return the combined sublattice
if candidate in subl:
return subl
# no match found
return candidate
new_subl_model = sorted(set([match_subl(subl) for subl in true_sublattices]))
else:
new_subl_model = true_sublattices
#ratios = [sum([1 if site in subl else 0 for site in wyckoff_sites]) for subl in new_subl_model]
config = []
occ = []
ratios = []
for subl in new_subl_model:
species_frequency_dict = {}
for site, wyckoff_site in zip(struct.sites, wyckoff_sites):
if wyckoff_site in subl:
species = site.specie.name
species_frequency_dict[species] = species_frequency_dict.get(species, 0) + 1
total_subl_occupation = sum(species_frequency_dict.values())
subl_species = sorted(set(species_frequency_dict.keys()))
subl_occpancy = [species_frequency_dict[sp]/total_subl_occupation for sp in subl_species]
config.append(subl_species)
occ.append(subl_occpancy)
ratios.append(total_subl_occupation)
#config = [sorted(set([site.specie.name for site, wyckoff in if wyckoff in subl])) for subl in new_subl_model]
struct.sublattice_configuration = config
struct.sublattice_occupancies = occ
struct.sublattice_site_ratios = ratios
return struct
def get_equiv_sites(self, s, site):
"""Find identical sites from analyzing space group symmetry."""
sga = SpacegroupAnalyzer(s, symprec=0.01)
sg = sga.get_space_group_operations
sym_data = sga.get_symmetry_dataset()
equiv_atoms = sym_data["equivalent_atoms"]
wyckoffs = sym_data["wyckoffs"]
sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
equivs = sym_struct.find_equivalent_sites(site)
return equivs
def analyze_symmetry(args):
tolerance = args.symmetry
t = []
for filename in args.filenames:
s = Structure.from_file(filename, primitive=False)
finder = SpacegroupAnalyzer(s, tolerance)
dataset = finder.get_symmetry_dataset()
t.append([filename, dataset["international"], dataset["number"],
dataset["hall"]])
print(tabulate(t, headers=["Filename", "Int Symbol", "Int number", "Hall"]))
def as_dict(self):
"""
Returns the CTRL as a dictionary. "SITE" and "CLASS" are of
the form {'CATEGORY': {'TOKEN': value}}, the rest is of the
form 'TOKEN'/'CATEGORY': value. It gets the conventional standard
structure because primitive cells use the conventional
a-lattice parameter as the scaling factor and not the a-lattice
parameter of the primitive cell.
"""
ctrl_dict = {
"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
}
if self.header is not None:
ctrl_dict["HEADER"] = self.header
if self.version is not None:
ctrl_dict["VERS"] = self.version
sga = SpacegroupAnalyzer(self.structure)
alat = sga.get_conventional_standard_structure().lattice.a
plat = self.structure.lattice.matrix / alat
"""
The following is to find the classes (atoms that are not symmetry
equivalent, and create labels. Note that LMTO only attaches
numbers with the second atom of the same species, e.g. "Bi", "Bi1",
"Bi2", etc.
"""
eq_atoms = sga.get_symmetry_dataset()["equivalent_atoms"]
ineq_sites_index = list(set(eq_atoms))
sites = []
classes = []
num_atoms = {}
for s, site in enumerate(self.structure.sites):
atom = site.specie
label_index = ineq_sites_index.index(eq_atoms[s])
if atom.symbol in num_atoms:
if label_index + 1 > sum(num_atoms.values()):
num_atoms[atom.symbol] += 1
atom_label = atom.symbol + str(num_atoms[atom.symbol] - 1)
classes.append({"ATOM": atom_label, "Z": atom.Z})
else:
num_atoms[atom.symbol] = 1
classes.append({"ATOM": atom.symbol, "Z": atom.Z})
sites.append({"ATOM": classes[label_index]["ATOM"], "POS": site.coords / alat})
ctrl_dict.update(
{
"ALAT": alat / bohr_to_angstrom,
"PLAT": plat,
"CLASS": classes,
"SITE": sites,
}
)
return ctrl_dict
def __init__(self, struct, source='', comment=''):
if struct.is_ordered:
self.struct = struct
self.source = source
sym = SpacegroupAnalyzer(struct)
data = sym.get_symmetry_dataset()
self.space_number = data["number"]
self.space_group = data["international"]
self.comment = comment or "None given"
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
def parse_symmetry(args):
tolerance = float(args.tolerance[0])
for filename in args.filenames:
s = Structure.from_file(filename)
if args.spacegroup:
finder = SpacegroupAnalyzer(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 = Structure.from_file(filename)
if args.spacegroup:
finder = SpacegroupAnalyzer(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 determine_symmetry_positions(st, element, silent=0):
"""
determine non-equivalent positions for atoms of type *element*
element (str) - name of element, for example Li
return list of lists - atom numbers for each non-equivalent position
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
stp = st.convert2pymatgen()
spg = SpacegroupAnalyzer(stp)
info = spg.get_symmetry_dataset()
positions = {}
for i, (el,
pos) in enumerate(zip(st.get_elements(),
info['equivalent_atoms'])):
if el == element and pos not in positions:
positions[pos] = []
if el == element:
positions[pos].append(i)
if not silent:
printlog('I have found ',
len(positions),
'non-equivalent positions for',
element,
':',
positions.keys(),
imp='y',
end='\n')
positions_for_print = {}
for key in positions:
positions_for_print[key] = [p + 1 for p in positions[key]]
if not silent:
printlog('Atom numbers: ', positions_for_print, imp='y')
sorted_keys = sorted(list(positions.keys()))
pos_lists = [positions[key] for key in sorted_keys]
return pos_lists
def _get_data_from_single_dirc(dirc, src_str="str_relax.out",
src_ene='energy'):
"""
指定したdircから構造とエネルギーを読み取る
"""
src = os.path.join(dirc, src_str)
strout = StrOut.from_file(src)
src = os.path.join(dirc, src_ene)
with open(src, 'r') as rfile:
lines = rfile.readlines()
num_atoms = sum(strout.structure.composition.
to_data_dict['unit_cell_composition'].values())
energy = float(lines[0]) / num_atoms
analyzer = SpacegroupAnalyzer(strout.structure)
#std_prim = analyzer.get_primitive_standard_structure()
std_str = analyzer.get_conventional_standard_structure()
analyzer = SpacegroupAnalyzer(std_str)
wyckoffs = analyzer.get_symmetry_dataset()['wyckoffs']
formula = std_str.composition.to_data_dict['unit_cell_composition']
symbol_spg = analyzer.get_spacegroup_symbol()
num_spg = analyzer.get_spacegroup_number()
spg = [symbol_spg, num_spg]
lattice = std_str.as_dict()['lattice']
equiv_sites = analyzer.get_symmetrized_structure().equivalent_sites
equiv_indices = analyzer.get_symmetrized_structure().equivalent_indices
# Wycoffs labelと組み合わせたsites_groupのlistを作る
sites_and_wyckoffs = []
for eq_s, eq_i in zip(equiv_sites, equiv_indices):
sites_and_wyckoffs.append({'wyckoffs': wyckoffs[eq_i[0]],
'site_grp': eq_s})
# check
for i in range(len(eq_i)-1):
if wyckoffs[eq_i[i]] != wyckoffs[eq_i[i+1]] or \
len(eq_s) != len(eq_i):
print("wyckoffs label is wrong !!!!")
print(wyckoffs)
print(eq_i)
print(len(eq_s))
print(dirc)
exit()
return {'formula': formula, 'lattice': lattice, 'spg': spg,
'sites_and_wyckoffs': sites_and_wyckoffs, 'energy': energy,
'str_id': os.path.basename(dirc)}
def run_task(self, fw_spec):
self.user_incar_settings.update({"NPAR": 2})
# Get kpoint density per vol
vol = Poscar.from_file("POSCAR").structure.volume
kppra_vol = self.kpoints_density / vol
new_set = MPStaticSet.from_prev_calc(
os.getcwd(),
user_incar_settings=self.user_incar_settings,
reciprocal_density=kppra_vol)
new_set.write_input('.')
structure = new_set.structure
sga = SpacegroupAnalyzer(structure, 0.1)
return FWAction(stored_data={
'refined_structure': sga.get_refined_structure().as_dict(),
'conventional_standard_structure': sga.get_conventional_standard_structure().as_dict(),
'symmetry_dataset': sga.get_symmetry_dataset(),
'symmetry_operations': [x.as_dict() for x in sga.get_symmetry_operations()]})
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
sym = SpacegroupAnalyzer(struct)
data = sym.get_symmetry_dataset()
self.space_number = data["number"]
self.space_group = data["international"]
self.comment = comment or "None given"
else:
raise ValueError("Structure with partial occupancies cannot be converted into atomic coordinates!")
def _make_struc_file(self, file_name):
sym = SpacegroupAnalyzer(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 get_sym_inequiv_components(
components: List[Component],
spg_analyzer: SpacegroupAnalyzer) -> List[Component]:
"""Gets and counts the symmetrically inequivalent components.
Component data has to have been generated with ``inc_site_ids=True``.
Args:
components: A list of structure components, generated using
:obj:`pymatgen.analysis.dimensionality.get_structure_components`,
with ``inc_site_ids=True``.
spg_analyzer: A `pymatgen.symmetry.analyzer.SpacegroupAnalyzer` analyzer
object for the structure containing the components.
Returns:
A list of the symmetrically inequivalent components. Any duplicate
components will only be returned once. The component objects are in the
same format is given by
:obj:`pymatgen.analysis.dimensionality.get_structure_components` but
the additional property:
- ``"count"`` (:obj:`int`): The number of times this component appears
in the structure.
"""
components = deepcopy(components)
sym_inequiv_components = {}
equivalent_atoms = spg_analyzer.get_symmetry_dataset()['equivalent_atoms']
for component in components:
sym_indices = frozenset(equivalent_atoms[x]
for x in component['site_ids'])
# if two components are composed of atoms that are symmetrically
# equivalent they are the same.
if sym_indices in sym_inequiv_components:
sym_inequiv_components[sym_indices]['count'] += 1
continue
component['count'] = 1
sym_inequiv_components[sym_indices] = component
return list(sym_inequiv_components.values())
def sg_pg_compare(mpid='mp-989535'):
stru = m.get_structure_by_material_id(mpid)
spa = SpacegroupAnalyzer(stru)
pg_name = spa.get_symmetry_dataset()['pointgroup']
pg_ops = PointGroup(pg_name).symmetry_ops
sp_ops = []
sp_mats = []
pg_mats = []
for op in pg_ops:
rotation = op.rotation_matrix
pg_mats.append(jsanitize(rotation))
for op in spa.get_symmetry_operations():
rotation = op.rotation_matrix
sp_mats.append(jsanitize(rotation))
sp_ops.append(SymmOp.from_rotation_and_translation(
rotation, (0, 0, 0)))
sp_ops = set(sp_ops)
#pg_mats.sort();sp_mats.sort()
return pg_mats, sp_mats
def cif2geom_sym2(cif):
parser = CifParser.from_string(cif)
struct = parser.get_structures()[0]
sg = SpacegroupAnalyzer(struct)
struct = sg.get_conventional_standard_structure()
sg = SpacegroupAnalyzer(struct)
geomlines = ["CRYSTAL"]
geomlines += ["0 0 1"]
geomlines += [str(sg.get_spacegroup_number())]
cry_sys = sg.get_crystal_system()
lattice = struct.lattice
if cry_sys == 'trigonal' or cry_sys == 'hexagonal' or cry_sys == 'tetragonal':
geomlines += ["%s %s" % (lattice.a, lattice.c)]
elif cry_sys == 'cubic':
geomlines += ["%s" % (lattice.a)]
elif cry_sys == 'triclinic':
geomlines += [
"%s %s %s %s %s %s" % (lattice.a, lattice.b, lattice.c,
lattice.alpha, lattice.beta, lattice.gamma)
]
elif cry_sys == 'monoclinic':
geomlines += [
"%s %s %s %s" % (lattice.a, lattice.b, lattice.c, lattice.beta)
]
elif cry_sys == 'orthorhombic':
geomlines += ["%s %s %s" % (lattice.a, lattice.b, lattice.c)]
else:
print('Error printing symmetrized structure.')
quit()
ds = sg.get_symmetry_dataset()
eq_sites = np.unique(ds['equivalent_atoms'])
geomlines += [str(len(eq_sites))]
for eq_site in eq_sites:
site = struct.sites[eq_site]
geomlines += [
"%s %s %s %s" % (site.specie.Z + 200, site.a, site.b, site.c)
]
return geomlines, struct
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-f',
'--file',
default='POSCAR',
type=str,
help='path to input file')
parser.add_argument('-t',
'--tol',
default=1e-3,
type=float,
help='symmetry tolerance (default 1e-3)')
parser.add_argument('-o',
'--output',
default='poscar',
help='output file format')
args = parser.parse_args()
struct = Structure.from_file(args.file)
sym = SpacegroupAnalyzer(struct, symprec=args.tol)
data = sym.get_symmetry_dataset()
print("Initial structure has {} atoms".format(struct.num_sites))
print("\tSpace group number: {}".format(data['number']))
print("\tInternational symbol: {}".format(data['international']))
print("\tLattice type: {}".format(sym.get_lattice_type()))
# seekpath conventional cell definition different from spglib
std = spglib.refine_cell(sym._cell, symprec=args.tol)
seek_data = seekpath.get_path(std)
# now remake the structure
lattice = seek_data['conv_lattice']
scaled_positions = seek_data['conv_positions']
numbers = seek_data['conv_types']
species = [sym._unique_species[i - 1] for i in numbers]
conv = Structure(lattice, species, scaled_positions)
conv.get_sorted_structure().to(filename="{}_conv".format(args.file),
fmt=args.output)
print("Final structure has {} atoms".format(conv.num_sites))
def __init__(self, struct, source='', comment=''):
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SpacegroupAnalyzer(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 symmetry_order_2d(structure, point_group_list):
'''
Find symmetry order in a two dimensional structure
Args:
structure: pymatgen structure
point_group_list
Return:
Number of symmetry operations, and
site symmetry order of the input structure
'''
s = SpacegroupAnalyzer(structure, symprec=0.1)
point_group_symbols = s.get_symmetry_dataset()['site_symmetry_symbols']
point_group_order = 0
for point_group_symbol in point_group_symbols :
point_group_order += point_group_list[point_group_symbol.replace('.', '')]
# return s.get_space_group_symbol(), s.get_space_group_number(),
return len(s.get_space_group_operations()), point_group_order/len(point_group_symbols)
def __init__(self, struct, source='', comment=''):
if struct.is_ordered:
self._struct = struct
self._source = source
self._site_symbols = []
self._natoms = []
sym = SpacegroupAnalyzer(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()
parser.add_argument('-f',
'--file',
type=str,
default='POSCAR',
help='path to input file')
parser.add_argument('-t',
'--tol',
default=1e-3,
type=float,
help='symmetry tolerance (default 1e-3)')
args = parser.parse_args()
struct = Structure.from_file(args.file)
sym = SpacegroupAnalyzer(struct, symprec=args.tol)
data = sym.get_symmetry_dataset()
print("Space group number: {}".format(data['number']))
print("International symbol: {}".format(data['international']))
print("Lattice type: {}".format(sym.get_lattice_type()))
def __init__(self,
bonded_structure: StructureGraph,
use_symmetry_equivalent_sites: bool = False,
symprec: float = 0.01,
minimum_geometry_op: float = 0.4,
use_iupac_formula: bool = True):
self.bonded_structure = bonded_structure
self.use_iupac_formula = use_iupac_formula
self.minimum_geometry_op = minimum_geometry_op
self.site_fingerprints = get_site_fingerprints(
bonded_structure.structure)
sga = SpacegroupAnalyzer(bonded_structure.structure, symprec=symprec)
equivalent_sites = sga.get_symmetry_dataset()['equivalent_atoms']
if use_symmetry_equivalent_sites:
self.equivalent_sites = list(equivalent_sites)
else:
self.equivalent_sites = self._calculate_equivalent_sites()
self.symmetry_labels = self._calculate_symmetry_labels(
equivalent_sites)
def __init__(self, structure, symprec=1e-3):
self.structure = structure
# use sym as a quick way to access the cell data
sym = SpacegroupAnalyzer(structure, symprec=symprec)
self._spg_data = sym.get_symmetry_dataset()
# make primitive and conventional cell from seekpath output
std = spglib.refine_cell(sym._cell, symprec=symprec)
self._seek_data = seekpath.get_path(std)
prim_lattice = self._seek_data["primitive_lattice"]
prim_scaled_positions = self._seek_data["primitive_positions"]
prim_numbers = self._seek_data["primitive_types"]
prim_atoms = [sym._unique_species[i - 1] for i in prim_numbers]
self.prim = Structure(prim_lattice, prim_atoms, prim_scaled_positions)
conv_lattice = self._seek_data["conv_lattice"]
conv_scaled_positions = self._seek_data["conv_positions"]
conv_numbers = self._seek_data["conv_types"]
conv_atoms = [sym._unique_species[i - 1] for i in conv_numbers]
self.conv = Structure(conv_lattice, conv_atoms, conv_scaled_positions)
def main(
hexagonal_relax_pk: int,
group_pk: int,
plot_energies: bool = False,
vmax: float = None,
):
grp = Group.get(id=group_pk)
data = []
print("load data: total {} data".format(len(grp.nodes)))
for i, node in enumerate(grp.nodes):
print("loading data: number {}".format(i + 1))
twinpy = Twinpy.initialize_from_aiida_twinboundary(
twinboundary_relax_pk=node.pk,
hexagonal_relax_pk=hexagonal_relax_pk,
)
pmgstruct = get_pymatgen_structure(
twinpy.twinboundary_analyzer.relax_analyzer.final_cell)
spg = SpacegroupAnalyzer(pmgstruct, symprec=1e-1)
sg = spg.get_symmetry_dataset()['international']
print("pk: %d" % node.pk + " " + node.label + " space group: %s" % sg)
tb_analyzer = twinpy.twinboundary_analyzer
xshift = tb_analyzer.twinboundary_structure.xshift
yshift = tb_analyzer.twinboundary_structure.yshift
energy = tb_analyzer.get_formation_energy()
data.append([xshift, yshift, energy])
data = np.array(data)
# plot plane interval
if plot_energies:
plt.figure()
im = plt.scatter(data[:, 0],
data[:, 1],
c=data[:, 2],
cmap=cm.jet,
vmax=vmax)
plt.colorbar(im)
plt.show()
def num_equivalent_clusters(structure: Structure,
inserted_atom_coords: Optional[list],
removed_atom_indices: Optional[list],
symprec: float = SYMMETRY_TOLERANCE,
angle_tolerance: float = ANGLE_TOL
) -> Tuple[int, str]:
"""Calculate number of equivalent clusters in the structure.
Args:
structure (Structure):
Supercell is assumed to big enough.
inserted_atom_coords (list):
removed_atom_indices (list):
Needs to begin from 0.
symprec (float):
angle_tolerance (float):
Angle tolerance in degree used for identifying the space group.
Returns:
Tuple of (num_equivalent_clusters (int), point_group (str))
"""
inserted_atom_coords = inserted_atom_coords or []
removed_atom_indices = removed_atom_indices or []
sga = SpacegroupAnalyzer(structure, symprec, angle_tolerance)
num_symmop = len(sga.get_symmetry_operations())
structure_with_cluster = structure.copy()
for i in inserted_atom_coords:
structure_with_cluster.append(DummySpecie(), i)
structure_with_cluster.remove_sites(removed_atom_indices)
sga_with_cluster = \
SpacegroupAnalyzer(structure_with_cluster, symprec, angle_tolerance)
sym_dataset = sga_with_cluster.get_symmetry_dataset()
point_group = sym_dataset["pointgroup"]
return int(num_symmop / num_symmetry_operation(point_group)), point_group
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--file', default='POSCAR', type=str,
help='path to input file')
parser.add_argument('-t', '--tol', default=1e-3, type=float,
help='symmetry tolerance (default 1e-3)')
parser.add_argument('-o', '--output', default='poscar',
help='output file format')
args = parser.parse_args()
struct = Structure.from_file(args.file)
sym = SpacegroupAnalyzer(struct, symprec=args.tol)
data = sym.get_symmetry_dataset()
print('Initial structure has {} atoms'.format(struct.num_sites))
print('\tSpace group number: {}'.format(data['number']))
print('\tInternational symbol: {}'.format(data['international']))
print('\tLattice type: {}'.format(sym.get_lattice_type()))
# first standardise the cell using the tolerance we want (seekpath has no
# tolerance setting)
std = spglib.refine_cell(sym._cell, symprec=args.tol)
seek_data = seekpath.get_path(std)
transform = seek_data['primitive_transformation_matrix']
# now remake the structure
lattice = seek_data['primitive_lattice']
scaled_positions = seek_data['primitive_positions']
numbers = seek_data['primitive_types']
species = [sym._unique_species[i - 1] for i in numbers]
prim = Structure(lattice, species, scaled_positions)
prim.get_sorted_structure().to(filename='{}_prim'.format(args.file),
fmt=args.output)
print('Final structure has {} atoms'.format(prim.num_sites))
print('Conv -> Prim transformation matrix:')
print('\t' + str(transform).replace('\n', '\n\t'))
def set_output_data(self, d_calc, d):
"""
set the 'output' key
"""
d["output"] = {
"structure": d_calc["output"]["structure"],
"density": d_calc.pop("density"),
"energy": d_calc["output"]["energy"],
"energy_per_atom": d_calc["output"]["energy_per_atom"]}
d["output"].update(self.get_basic_processed_data(d))
sg = SpacegroupAnalyzer(Structure.from_dict(d_calc["output"]["structure"]), 0.1)
if not sg.get_symmetry_dataset():
sg = SpacegroupAnalyzer(Structure.from_dict(d_calc["output"]["structure"]), 1e-3, 1)
d["output"]["spacegroup"] = {
"source": "spglib",
"symbol": sg.get_space_group_symbol(),
"number": sg.get_space_group_number(),
"point_group": sg.get_point_group_symbol(),
"crystal_system": sg.get_crystal_system(),
"hall": sg.get_hall()}
if d["input"]["parameters"].get("LEPSILON"):
for k in ['epsilon_static', 'epsilon_static_wolfe', 'epsilon_ionic']:
d["output"][k] = d_calc["output"][k]
def get_uniq_layercoords(struct, nlayers, top=True):
"""
returns the coordinates of unique sites in the top or bottom
nlayers of the given structure.
Args:
struct: input structure
nlayers: number of layers
top: top or bottom layers, default is top layer
Return:
numpy array of unique coordinates
"""
coords = np.array([site.coords for site in struct])
z = coords[:, 2]
z = np.around(z, decimals=4)
zu, zuind = np.unique(z, return_index=True)
z_nthlayer = z[zuind[-nlayers]]
zfilter = (z >= z_nthlayer)
if not top:
z_nthlayer = z[zuind[nlayers - 1]]
zfilter = (z <= z_nthlayer)
# site indices in the layers
indices_layers = np.argwhere(zfilter).ravel()
sa = SpacegroupAnalyzer(struct)
symm_data = sa.get_symmetry_dataset()
# equivalency mapping for the structure
# i'th site in the struct equivalent to eq_struct[i]'th site
eq_struct = symm_data["equivalent_atoms"]
# equivalency mapping for the layers
eq_layers = eq_struct[indices_layers]
# site indices of unique atoms in the layers
__, ueq_layers_indices = np.unique(eq_layers, return_index=True)
# print(ueq_layers_indices)
indices_uniq = indices_layers[ueq_layers_indices]
# coordinates of the unique atoms in the layers
return coords[indices_uniq]
def get_uniq_layercoords(struct, nlayers, top=True):
"""
returns the coordinates of unique sites in the top or bottom
nlayers of the given structure.
Args:
struct: input structure
nlayers: number of layers
top: top or bottom layers, default is top layer
Return:
numpy array of unique coordinates
"""
coords = np.array([site.coords for site in struct])
z = coords[:, 2]
z = np.around(z, decimals=4)
zu, zuind = np.unique(z, return_index=True)
z_nthlayer = z[zuind[-nlayers]]
zfilter = (z >= z_nthlayer)
if not top:
z_nthlayer = z[zuind[nlayers - 1]]
zfilter = (z <= z_nthlayer)
# site indices in the layers
indices_layers = np.argwhere(zfilter).ravel()
sa = SpacegroupAnalyzer(struct)
symm_data = sa.get_symmetry_dataset()
# equivalency mapping for the structure
# i'th site in the struct equivalent to eq_struct[i]'th site
eq_struct = symm_data["equivalent_atoms"]
# equivalency mapping for the layers
eq_layers = eq_struct[indices_layers]
# site indices of unique atoms in the layers
__, ueq_layers_indices = np.unique(eq_layers, return_index=True)
# print(ueq_layers_indices)
indices_uniq = indices_layers[ueq_layers_indices]
# coordinates of the unique atoms in the layers
return coords[indices_uniq]
class SpacegroupAnalyzerTest(PymatgenTest):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure('Li10GeP2S12')
self.disordered_sg = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure('Graphite')
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
self.structure4 = graphite
def test_primitive(self):
s = Structure.from_spacegroup("Fm-3m", np.eye(3) * 3, ["Cu"],
[[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertEqual(len(s), 4)
self.assertEqual(len(a.find_primitive()), 1)
def test_is_laue(self):
s = Structure.from_spacegroup("Fm-3m", np.eye(3) * 3, ["Cu"],
[[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertTrue(a.is_laue())
def test_magnetic(self):
lfp = PymatgenTest.get_structure("LiFePO4")
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
magmoms = [0] * len(lfp)
magmoms[4] = 1
magmoms[5] = -1
magmoms[6] = 1
magmoms[7] = -1
lfp.add_site_property("magmom", magmoms)
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_space_group_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_space_group_symbol(),
"P4_2/nmc")
self.assertEqual(self.sg3.get_space_group_symbol(), "Pnma")
self.assertEqual(self.sg4.get_space_group_symbol(), "P6_3/mmc")
def test_get_space_number(self):
self.assertEqual(self.sg.get_space_group_number(), 62)
self.assertEqual(self.disordered_sg.get_space_group_number(), 137)
self.assertEqual(self.sg4.get_space_group_number(), 194)
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_symbol(), 'mmm')
self.assertEqual(self.disordered_sg.get_point_group_symbol(), '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):
for sg, structure in [(self.sg, self.structure),
(self.sg4, self.structure4)]:
pgops = sg.get_point_group_operations()
fracsymmops = sg.get_symmetry_operations()
symmops = sg.get_symmetry_operations(True)
latt = structure.lattice
for fop, op, pgop in zip(fracsymmops, symmops, pgops):
# translation vector values should all be 0 or 0.5
t = fop.translation_vector * 2
self.assertArrayAlmostEqual(t - np.round(t), 0)
self.assertArrayAlmostEqual(fop.rotation_matrix,
pgop.rotation_matrix)
for site in 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 structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
# Make sure this works for any position, not just the atomic
# ones.
random_fcoord = np.random.uniform(size=(3))
random_ccoord = latt.get_cartesian_coords(random_fcoord)
newfrac = fop.operate(random_fcoord)
newcart = op.operate(random_ccoord)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart),
newfrac))
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)
s = self.get_structure('Li2O')
sg = SpacegroupAnalyzer(s, 0.01)
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([len(i) for i in 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)
self.assertEqual(symm_struct.wyckoff_symbols[0], '16h')
# self.assertEqual(symm_struct[0].wyckoff, "16h")
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 = SpacegroupAnalyzer(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.assertEqual(len(grid), 216)
self.assertAlmostEqual(grid[1][0][0], 0.1)
self.assertAlmostEqual(grid[1][0][1], 0.0)
self.assertAlmostEqual(grid[1][0][2], 0.0)
self.assertAlmostEqual(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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, 'orac_632475.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 3.1790663399999999)
self.assertAlmostEqual(conv.lattice.b, 9.9032878699999998)
self.assertAlmostEqual(conv.lattice.c, 3.5372412099999999)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 'hex_1170.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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, 'orac_632475.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 144.40557588533386)
self.assertAlmostEqual(prim.lattice.a, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.b, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.c, 3.5372412099999999)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 'hex_1170.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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)
parser = CifParser(os.path.join(test_dir, 'rhomb_3478_conv.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.beta, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.gamma, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.a, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.b, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.c, 5.9352627428399982)
class SpacegroupAnalyzerTest(PymatgenTest):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure('Li10GeP2S12')
self.disordered_sg = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure('Graphite')
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
self.structure4 = graphite
def test_primitive(self):
s = Structure.from_spacegroup("Fm-3m",
np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertEqual(len(s), 4)
self.assertEqual(len(a.find_primitive()), 1)
def test_is_laue(self):
s = Structure.from_spacegroup("Fm-3m",
np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertTrue(a.is_laue())
def test_magnetic(self):
lfp = PymatgenTest.get_structure("LiFePO4")
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
magmoms = [0] * len(lfp)
magmoms[4] = 1
magmoms[5] = -1
magmoms[6] = 1
magmoms[7] = -1
lfp.add_site_property("magmom", magmoms)
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_space_group_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_space_group_symbol(),
"P4_2/nmc")
self.assertEqual(self.sg3.get_space_group_symbol(), "Pnma")
self.assertEqual(self.sg4.get_space_group_symbol(), "P6_3/mmc")
def test_get_space_number(self):
self.assertEqual(self.sg.get_space_group_number(), 62)
self.assertEqual(self.disordered_sg.get_space_group_number(), 137)
self.assertEqual(self.sg4.get_space_group_number(), 194)
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_symbol(), 'mmm')
self.assertEqual(self.disordered_sg.get_point_group_symbol(), '4/mmm')
def test_get_symmetry_operations(self):
coordinates = np.array([[0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.5, 1.0, 0.0], [1.0, 0.5, 0.0]])
species = ['H'] * len(coordinates)
molecule = Molecule(species, coordinates)
so = PointGroupAnalyzer(molecule, 0.3).get_symmetry_operations()
self.assertEqual(len(so), 16) # D4h contains 16 symmetry elements
for o in so:
self.assertEqual(isinstance(o, SymmOp), True)
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):
for sg, structure in [(self.sg, self.structure),
(self.sg4, self.structure4)]:
pgops = sg.get_point_group_operations()
fracsymmops = sg.get_symmetry_operations()
symmops = sg.get_symmetry_operations(True)
latt = structure.lattice
for fop, op, pgop in zip(fracsymmops, symmops, pgops):
# translation vector values should all be 0 or 0.5
t = fop.translation_vector * 2
self.assertArrayAlmostEqual(t - np.round(t), 0)
self.assertArrayAlmostEqual(fop.rotation_matrix,
pgop.rotation_matrix)
for site in 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 structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
# Make sure this works for any position, not just the atomic
# ones.
random_fcoord = np.random.uniform(size=(3))
random_ccoord = latt.get_cartesian_coords(random_fcoord)
newfrac = fop.operate(random_fcoord)
newcart = op.operate(random_ccoord)
self.assertTrue(
np.allclose(latt.get_fractional_coords(newcart), newfrac))
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)
s = self.get_structure('Li2O')
sg = SpacegroupAnalyzer(s, 0.01)
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([len(i) for i in 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)
self.assertEqual(symm_struct.wyckoff_symbols[0], '16h')
# self.assertEqual(symm_struct[0].wyckoff, "16h")
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 = SpacegroupAnalyzer(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.assertEqual(len(grid), 216)
self.assertAlmostEqual(grid[1][0][0], 0.1)
self.assertAlmostEqual(grid[1][0][1], 0.0)
self.assertAlmostEqual(grid[1][0][2], 0.0)
self.assertAlmostEqual(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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, 'orac_632475.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 3.1790663399999999)
self.assertAlmostEqual(conv.lattice.b, 9.9032878699999998)
self.assertAlmostEqual(conv.lattice.c, 3.5372412099999999)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 'hex_1170.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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, 'orac_632475.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 144.40557588533386)
self.assertAlmostEqual(prim.lattice.a, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.b, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.c, 3.5372412099999999)
parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 'hex_1170.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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)
parser = CifParser(os.path.join(test_dir, 'rhomb_3478_conv.cif'))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.beta, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.gamma, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.a, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.b, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.c, 5.9352627428399982)
class SpacegroupAnalyzerTest(PymatgenTest):
def setUp(self):
p = Poscar.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure("Li10GeP2S12")
self.disordered_sg = SpacegroupAnalyzer(self.disordered_structure,
0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species, site.frac_coords)
self.sg3 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure("Graphite")
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
self.structure4 = graphite
def test_primitive(self):
s = Structure.from_spacegroup("Fm-3m",
np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertEqual(len(s), 4)
self.assertEqual(len(a.find_primitive()), 1)
def test_is_laue(self):
s = Structure.from_spacegroup("Fm-3m",
np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
a = SpacegroupAnalyzer(s)
self.assertTrue(a.is_laue())
def test_magnetic(self):
lfp = PymatgenTest.get_structure("LiFePO4")
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
magmoms = [0] * len(lfp)
magmoms[4] = 1
magmoms[5] = -1
magmoms[6] = 1
magmoms[7] = -1
lfp.add_site_property("magmom", magmoms)
sg = SpacegroupAnalyzer(lfp, 0.1)
self.assertEqual(sg.get_space_group_symbol(), "Pnma")
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_space_group_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_space_group_symbol(),
"P4_2/nmc")
self.assertEqual(self.sg3.get_space_group_symbol(), "Pnma")
self.assertEqual(self.sg4.get_space_group_symbol(), "P6_3/mmc")
def test_get_space_number(self):
self.assertEqual(self.sg.get_space_group_number(), 62)
self.assertEqual(self.disordered_sg.get_space_group_number(), 137)
self.assertEqual(self.sg4.get_space_group_number(), 194)
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_symbol(), "mmm")
self.assertEqual(self.disordered_sg.get_point_group_symbol(), "4/mmm")
def test_get_symmetry_operations(self):
for sg, structure in [(self.sg, self.structure),
(self.sg4, self.structure4)]:
pgops = sg.get_point_group_operations()
fracsymmops = sg.get_symmetry_operations()
symmops = sg.get_symmetry_operations(True)
latt = structure.lattice
for fop, op, pgop in zip(fracsymmops, symmops, pgops):
# translation vector values should all be 0 or 0.5
t = fop.translation_vector * 2
self.assertArrayAlmostEqual(t - np.round(t), 0)
self.assertArrayAlmostEqual(fop.rotation_matrix,
pgop.rotation_matrix)
for site in 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,
newcart,
latt,
coords_are_cartesian=True)
for testsite in structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
# Make sure this works for any position, not just the atomic
# ones.
random_fcoord = np.random.uniform(size=(3))
random_ccoord = latt.get_cartesian_coords(random_fcoord)
newfrac = fop.operate(random_fcoord)
newcart = op.operate(random_ccoord)
self.assertTrue(
np.allclose(latt.get_fractional_coords(newcart), newfrac))
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())
orig_spg = self.sg._space_group_data["number"]
self.sg._space_group_data["number"] = 0
try:
crystal_system = self.sg.get_crystal_system()
except ValueError as exc:
self.assertEqual(str(exc), "Received invalid space group 0")
finally:
self.sg._space_group_data["number"] = orig_spg
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)
structure = self.get_structure("Li2O")
structure.add_site_property("magmom", [1.0] * len(structure))
sg = SpacegroupAnalyzer(structure, 0.01)
refined_struct = sg.get_refined_structure(keep_site_properties=True)
self.assertEqual(refined_struct.site_properties["magmom"],
[1.0] * len(refined_struct))
structure = self.get_structure("Li2O")
structure.add_site_property("magmom", [1.0] * len(structure))
sg = SpacegroupAnalyzer(structure, 0.01)
refined_struct = sg.get_refined_structure(keep_site_properties=False)
self.assertEqual(refined_struct.site_properties.get("magmom", None),
None)
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([len(i) for i in 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)
self.assertEqual(symm_struct.wyckoff_symbols[0], "16h")
# self.assertEqual(symm_struct[0].wyckoff, "16h")
# Check copying
self.assertEqual(symm_struct.copy(), symm_struct)
d = symm_struct.as_dict()
from pymatgen.symmetry.structure import SymmetrizedStructure
ss = SymmetrizedStructure.from_dict(d)
self.assertEqual(ss.wyckoff_symbols[0], "16h")
self.assertIn("SymmetrizedStructure", ss.__str__())
def test_find_primitive(self):
"""
F m -3 m Li2O testing of converting to primitive cell
"""
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "Li2O.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(structure)
primitive_structure = s.find_primitive()
self.assertEqual(primitive_structure.formula, "Li2 O1")
self.assertTrue(
primitive_structure.site_properties.get("magmom", None) is None)
# 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)
structure = parser.get_structures(False)[0]
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure)
primitive_structure = s.find_primitive(keep_site_properties=True)
self.assertEqual(primitive_structure.site_properties["magmom"],
[1.0] * len(primitive_structure))
structure = parser.get_structures(False)[0]
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure)
primitive_structure = s.find_primitive(keep_site_properties=False)
self.assertEqual(
primitive_structure.site_properties.get("magmom", None), None)
def test_get_ir_reciprocal_mesh(self):
grid = self.sg.get_ir_reciprocal_mesh()
self.assertEqual(len(grid), 216)
self.assertAlmostEqual(grid[1][0][0], 0.1)
self.assertAlmostEqual(grid[1][0][1], 0.0)
self.assertAlmostEqual(grid[1][0][2], 0.0)
self.assertAlmostEqual(grid[1][1], 2)
def test_get_conventional_standard_structure(self):
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "bcc_1927.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "btet_1915.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orci_1010.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orcc_1003.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orac_632475.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 3.1790663399999999)
self.assertAlmostEqual(conv.lattice.b, 9.9032878699999998)
self.assertAlmostEqual(conv.lattice.c, 3.5372412099999999)
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "monoc_1028.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "hex_1170.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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)
structure = Structure.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "tric_684654.json"))
s = SpacegroupAnalyzer(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure()
self.assertAlmostEqual(conv.lattice.alpha, 74.09581916308757)
self.assertAlmostEqual(conv.lattice.beta, 75.72817279281173)
self.assertAlmostEqual(conv.lattice.gamma, 63.63234318667333)
self.assertAlmostEqual(conv.lattice.a, 3.741372924048738)
self.assertAlmostEqual(conv.lattice.b, 3.9883228679270686)
self.assertAlmostEqual(conv.lattice.c, 7.288495840048958)
structure = Structure.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "tric_684654.json"))
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure(keep_site_properties=True)
self.assertEqual(conv.site_properties["magmom"], [1.0] * len(conv))
structure = Structure.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "tric_684654.json"))
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure, symprec=1e-2)
conv = s.get_conventional_standard_structure(
keep_site_properties=False)
self.assertEqual(conv.site_properties.get("magmom", None), None)
def test_get_primitive_standard_structure(self):
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "bcc_1927.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "btet_1915.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orci_1010.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orcc_1003.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "orac_632475.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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, 144.40557588533386)
self.assertAlmostEqual(prim.lattice.a, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.b, 5.2005185662155391)
self.assertAlmostEqual(prim.lattice.c, 3.5372412099999999)
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "monoc_1028.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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(PymatgenTest.TEST_FILES_DIR, "hex_1170.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(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)
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "rhomb_3478_conv.cif"))
structure = parser.get_structures(False)[0]
s = SpacegroupAnalyzer(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure()
self.assertAlmostEqual(prim.lattice.alpha, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.beta, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.gamma, 28.049186140546812)
self.assertAlmostEqual(prim.lattice.a, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.b, 5.9352627428399982)
self.assertAlmostEqual(prim.lattice.c, 5.9352627428399982)
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "rhomb_3478_conv.cif"))
structure = parser.get_structures(False)[0]
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure(keep_site_properties=True)
self.assertEqual(prim.site_properties["magmom"], [1.0] * len(prim))
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "rhomb_3478_conv.cif"))
structure = parser.get_structures(False)[0]
structure.add_site_property("magmom", [1.0] * len(structure))
s = SpacegroupAnalyzer(structure, symprec=1e-2)
prim = s.get_primitive_standard_structure(keep_site_properties=False)
self.assertEqual(prim.site_properties.get("magmom", None), None)
def test_tricky_structure(self):
# for some reason this structure kills spglib1.9
# 1.7 can't find symmetry either, but at least doesn't kill python
s = Structure.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"POSCAR.tricky_symmetry"))
sa = SpacegroupAnalyzer(s, 0.1)
sa.get_space_group_symbol()
sa.get_space_group_number()
sa.get_point_group_symbol()
sa.get_crystal_system()
sa.get_hall()
def convert_to_ieee(self, structure, atol = 0.1, ltol = 0.05):
"""
Given a structure associated with a tensor, attempts a
calculation of the tensor in IEEE format according to
the 1987 IEEE standards.
Args:
structure (Structure): a structure associated with the
tensor to be converted to the IEEE standard
atol (float): angle tolerance for conversion routines
ltol (float): length tolerance for conversion routines
"""
def get_uvec(vec):
""" Gets a unit vector parallel to input vector"""
return vec / np.linalg.norm(vec)
# Check conventional setting:
sga = SpacegroupAnalyzer(structure)
dataset = sga.get_symmetry_dataset()
trans_mat = dataset['transformation_matrix']
conv_latt = Lattice(np.transpose(np.dot(np.transpose(
structure.lattice.matrix), np.linalg.inv(trans_mat))))
xtal_sys = sga.get_crystal_system()
vecs = conv_latt.matrix
lengths = np.array(conv_latt.abc)
angles = np.array(conv_latt.angles)
a = b = c = None
rotation = np.zeros((3,3))
# IEEE rules: a,b,c || x1,x2,x3
if xtal_sys == "cubic":
rotation = [vecs[i]/lengths[i] for i in range(3)]
# IEEE rules: a=b in length; c,a || x3, x1
elif xtal_sys == "tetragonal":
rotation = np.array([vec/mag for (mag, vec) in
sorted(zip(lengths, vecs))])
if abs(lengths[2] - lengths[1]) < ltol:
rotation[0], rotation[2] = rotation[2], rotation[0].copy()
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: c<a<b; c,a || x3,x1
elif xtal_sys == "orthorhombic":
rotation = [vec/mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis = 0)
# IEEE rules: c,a || x3,x1, c is threefold axis
# Note this also includes rhombohedral crystal systems
elif xtal_sys in ("trigonal", "hexagonal"):
# find threefold axis:
tf_mask = abs(angles-120.0) < atol
non_tf_mask = np.logical_not(tf_mask)
rotation[2] = get_uvec(vecs[tf_mask][0])
rotation[0] = get_uvec(vecs[non_tf_mask][0])
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: b,c || x2,x3; alpha=beta=90, c<a
elif xtal_sys == "monoclinic":
# Find unique axis
umask = abs(angles - 90.0) > atol
n_umask = np.logical_not(umask)
rotation[1] = get_uvec(vecs[umask])
# Shorter of remaining lattice vectors for c axis
c = [vec/mag for (mag, vec) in
sorted(zip(lengths[n_umask], vecs[n_umask]))][0]
rotation[2] = np.array(c)
rotation[0] = np.cross(rotation[1], rotation[2])
# IEEE rules: c || x3
elif xtal_sys == "triclinic":
rotation = [vec/mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis = 0)
rotation[1] = get_uvec(np.cross(rotation[2], rotation[1]))
rotation[0] = np.cross(rotation[1], rotation[2])
return self.rotate(rotation)
def convert_to_ieee(self, structure, initial_fit=True):
"""
Given a structure associated with a tensor, attempts a
calculation of the tensor in IEEE format according to
the 1987 IEEE standards.
Args:
structure (Structure): a structure associated with the
tensor to be converted to the IEEE standard
initial_fit (bool): flag to indicate whether initial
tensor is fit to the symmetry of the structure.
Defaults to true. Note that if false, inconsistent
results may be obtained due to symmetrically
equivalent, but distinct transformations
being used in different versions of spglib.
"""
def get_uvec(v):
""" Gets a unit vector parallel to input vector"""
l = np.linalg.norm(v)
if l < 1e-8:
return v
return v / l
# Check conventional setting:
sga = SpacegroupAnalyzer(structure)
dataset = sga.get_symmetry_dataset()
trans_mat = dataset['transformation_matrix']
conv_latt = Lattice(np.transpose(np.dot(np.transpose(
structure.lattice.matrix), np.linalg.inv(trans_mat))))
xtal_sys = sga.get_crystal_system()
vecs = conv_latt.matrix
lengths = np.array(conv_latt.abc)
angles = np.array(conv_latt.angles)
rotation = np.zeros((3, 3))
# IEEE rules: a,b,c || x1,x2,x3
if xtal_sys == "cubic":
rotation = [vecs[i] / lengths[i] for i in range(3)]
# IEEE rules: a=b in length; c,a || x3, x1
elif xtal_sys == "tetragonal":
rotation = np.array([vec / mag for (mag, vec) in
sorted(zip(lengths, vecs),
key=lambda x: x[0])])
if abs(lengths[2] - lengths[1]) < abs(lengths[1] - lengths[0]):
rotation[0], rotation[2] = rotation[2], rotation[0].copy()
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: c<a<b; c,a || x3,x1
elif xtal_sys == "orthorhombic":
rotation = [vec / mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis=0)
# IEEE rules: c,a || x3,x1, c is threefold axis
# Note this also includes rhombohedral crystal systems
elif xtal_sys in ("trigonal", "hexagonal"):
# find threefold axis:
tf_index = np.argmin(abs(angles - 120.))
non_tf_mask = np.logical_not(angles == angles[tf_index])
rotation[2] = get_uvec(vecs[tf_index])
rotation[0] = get_uvec(vecs[non_tf_mask][0])
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: b,c || x2,x3; alpha=beta=90, c<a
elif xtal_sys == "monoclinic":
# Find unique axis
u_index = np.argmax(abs(angles - 90.))
n_umask = np.logical_not(angles == angles[u_index])
rotation[1] = get_uvec(vecs[u_index])
# Shorter of remaining lattice vectors for c axis
c = [vec / mag for (mag, vec) in
sorted(zip(lengths[n_umask], vecs[n_umask]))][0]
rotation[2] = np.array(c)
rotation[0] = np.cross(rotation[1], rotation[2])
# IEEE rules: c || x3
elif xtal_sys == "triclinic":
rotation = [vec / mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis=0)
rotation[1] = get_uvec(np.cross(rotation[2], rotation[1]))
rotation[0] = np.cross(rotation[1], rotation[2])
result = self.copy()
if initial_fit:
result = result.fit_to_structure(structure)
return result.rotate(rotation, tol=1e-2)
def get_ieee_rotation(structure, refine_rotation=True):
"""
Given a structure associated with a tensor, determines
the rotation matrix for IEEE conversion according to
the 1987 IEEE standards.
Args:
structure (Structure): a structure associated with the
tensor to be converted to the IEEE standard
refine_rotation (bool): whether to refine the rotation
using SquareTensor.refine_rotation
"""
# Check conventional setting:
sga = SpacegroupAnalyzer(structure)
dataset = sga.get_symmetry_dataset()
trans_mat = dataset['transformation_matrix']
conv_latt = Lattice(np.transpose(np.dot(np.transpose(
structure.lattice.matrix), np.linalg.inv(trans_mat))))
xtal_sys = sga.get_crystal_system()
vecs = conv_latt.matrix
lengths = np.array(conv_latt.abc)
angles = np.array(conv_latt.angles)
rotation = np.zeros((3, 3))
# IEEE rules: a,b,c || x1,x2,x3
if xtal_sys == "cubic":
rotation = [vecs[i] / lengths[i] for i in range(3)]
# IEEE rules: a=b in length; c,a || x3, x1
elif xtal_sys == "tetragonal":
rotation = np.array([vec / mag for (mag, vec) in
sorted(zip(lengths, vecs),
key=lambda x: x[0])])
if abs(lengths[2] - lengths[1]) < abs(lengths[1] - lengths[0]):
rotation[0], rotation[2] = rotation[2], rotation[0].copy()
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: c<a<b; c,a || x3,x1
elif xtal_sys == "orthorhombic":
rotation = [vec / mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis=0)
# IEEE rules: c,a || x3,x1, c is threefold axis
# Note this also includes rhombohedral crystal systems
elif xtal_sys in ("trigonal", "hexagonal"):
# find threefold axis:
tf_index = np.argmin(abs(angles - 120.))
non_tf_mask = np.logical_not(angles == angles[tf_index])
rotation[2] = get_uvec(vecs[tf_index])
rotation[0] = get_uvec(vecs[non_tf_mask][0])
rotation[1] = get_uvec(np.cross(rotation[2], rotation[0]))
# IEEE rules: b,c || x2,x3; alpha=beta=90, c<a
elif xtal_sys == "monoclinic":
# Find unique axis
u_index = np.argmax(abs(angles - 90.))
n_umask = np.logical_not(angles == angles[u_index])
rotation[1] = get_uvec(vecs[u_index])
# Shorter of remaining lattice vectors for c axis
c = [vec / mag for (mag, vec) in
sorted(zip(lengths[n_umask], vecs[n_umask]))][0]
rotation[2] = np.array(c)
rotation[0] = np.cross(rotation[1], rotation[2])
# IEEE rules: c || x3
elif xtal_sys == "triclinic":
rotation = [vec / mag for (mag, vec) in sorted(zip(lengths, vecs))]
rotation = np.roll(rotation, 2, axis=0)
rotation[1] = get_uvec(np.cross(rotation[2], rotation[1]))
rotation[0] = np.cross(rotation[1], rotation[2])
rotation = SquareTensor(rotation)
if refine_rotation:
rotation = rotation.refine_rotation()
return rotation
class SpacegroupAnalyzerTest(PymatgenTest):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure('Li10GeP2S12')
self.disordered_sg = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure('Graphite')
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(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)
s = self.get_structure('Li2O')
sg = SpacegroupAnalyzer(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([len(i) for i in 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 = SpacegroupAnalyzer(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.assertEqual(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.assertEqual(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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 = SpacegroupAnalyzer(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)
