def __init__(self, wyckoff_sites, lattice, group):
self.wyckoff_sites = wyckoff_sites
self.group = group
#Extract coords and species
species = []
coords = []
for ws in wyckoff_sites:
species += [ws.specie] * ws.multiplicity
for c in ws.coords:
coords.append(c)
coords = np.array(coords)
Structure.__init__(self, lattice.matrix, species, coords)
def __init__(self, refined_structure, spacegroup, equivalent_positions):
Structure.__init__(
self,
refined_structure.lattice,
[site.species_and_occu for site in refined_structure],
refined_structure.frac_coords,
)
self._spacegroup = spacegroup
site_map = zip(self._sites, equivalent_positions)
site_map = sorted(site_map, key=lambda x: x[1])
self._equivalent_sites = [[x[0] for x in g] for k, g in itertools.groupby(site_map, key=lambda x: x[1])]
def __init__(self, mol_sites, lattice, group):
self.mol_sites = mol_sites
self.group = group
#Extract coords and species
species = []
coords = []
for ms in mol_sites:
coords1, species1 = ms.get_coords_and_species()
species += species1
for c in coords1:
coords.append(c)
coords = np.array(coords)
Structure.__init__(self, lattice.matrix, species, coords)
def __init__(self, structure, spacegroup, equivalent_positions):
Structure.__init__(self, structure.lattice,
[site.species_and_occu
for site in structure],
structure.frac_coords,
site_properties=structure.site_properties)
self._spacegroup = spacegroup
u, inv = np.unique(equivalent_positions, return_inverse = True)
self.equivalent_indices = [[] for i in xrange(len(u))]
self._equivalent_sites = [[] for i in xrange(len(u))]
for i, inv in enumerate(inv):
self.equivalent_indices[inv].append(i)
self._equivalent_sites[inv].append(self.sites[i])
def __init__(self, structure, spacegroup, equivalent_positions):
Structure.__init__(self,
structure.lattice,
[site.species_and_occu for site in structure],
structure.frac_coords,
site_properties=structure.site_properties)
self._spacegroup = spacegroup
u, inv = np.unique(equivalent_positions, return_inverse=True)
self.equivalent_indices = [[] for i in range(len(u))]
self._equivalent_sites = [[] for i in range(len(u))]
for i, inv in enumerate(inv):
self.equivalent_indices[inv].append(i)
self._equivalent_sites[inv].append(self.sites[i])
def __init__(self, structure, spacegroup, equivalent_positions):
"""
Args:
structure:
Original structure
spacegroup:
An input spacegroup from SymmetryFinder.
equivalent_positions:
Equivalent positions from SymmetryFinder.
"""
Structure.__init__(self,
structure.lattice,
[site.species_and_occu for site in structure],
structure.frac_coords,
site_properties=structure.site_properties)
self._spacegroup = spacegroup
site_map = zip(self._sites, equivalent_positions)
site_map = sorted(site_map, key=lambda x: x[1])
self._equivalent_sites = [[
x[0] for x in g
] for k, g in itertools.groupby(site_map, key=lambda x: x[1])]
def __init__(self, structure, spacegroup, equivalent_positions):
"""
Args:
structure:
Original structure
spacegroup:
An input spacegroup from SymmetryFinder.
equivalent_positions:
Equivalent positions from SymmetryFinder.
"""
Structure.__init__(
self,
structure.lattice,
[site.species_and_occu for site in structure],
structure.frac_coords,
site_properties=structure.site_properties,
)
self._spacegroup = spacegroup
site_map = zip(self._sites, equivalent_positions)
site_map = sorted(site_map, key=lambda x: x[1])
self._equivalent_sites = [[x[0] for x in g] for k, g in itertools.groupby(site_map, key=lambda x: x[1])]
def __init__(self, structure, spacegroup, equivalent_positions):
"""
Args:
structure:
Original structure
spacegroup:
An input spacegroup from SymmetryFinder.
equivalent_positions:
Equivalent positions from SymmetryFinder.
"""
Structure.__init__(self,
structure.lattice,
[site.species_and_occu for site in structure],
structure.frac_coords,
site_properties=structure.site_properties)
self._spacegroup = spacegroup
u, inv = np.unique(equivalent_positions, return_inverse=True)
self.equivalent_indices = [[] for i in xrange(len(u))]
self._equivalent_sites = [[] for i in xrange(len(u))]
for i, inv in enumerate(inv):
self.equivalent_indices[inv].append(i)
self._equivalent_sites[inv].append(self.sites[i])
def __init__(self, structure, spacegroup, equivalent_positions):
"""
Args:
structure:
Original structure
spacegroup:
An input spacegroup from SymmetryFinder.
equivalent_positions:
Equivalent positions from SymmetryFinder.
"""
Structure.__init__(self, structure.lattice,
[site.species_and_occu
for site in structure],
structure.frac_coords,
site_properties=structure.site_properties)
self._spacegroup = spacegroup
u, inv = np.unique(equivalent_positions, return_inverse = True)
self.equivalent_indices = [[] for i in xrange(len(u))]
self._equivalent_sites = [[] for i in xrange(len(u))]
for i, inv in enumerate(inv):
self.equivalent_indices[inv].append(i)
self._equivalent_sites[inv].append(self.sites[i])