def cons_specific_cell(self, sites, e_num=None, symprec=1e-5):
"""
cons_specific_cell_and_c generate configurations of specific cell
and specific concentration.
parameters:
sites: list of (lists or tuples), represent element disorder of each sites
e_num: tuple, number of atoms in disorderd sites.
e_num 特指无序位点的浓度，也就是原子比，而不是整体构型的元素原子比。有可能其他位点存在相同构型。
!!限制，无序位点的组成必须是相同的，而上面几个函数的无序位点是可以不同的。!!
"""
lat_cell = self._cell.lattice
lat_pcell = self._pcell.lattice
mat = numpy.matmul(lat_cell, numpy.linalg.inv(lat_pcell))
if is_int_np_array(mat):
mat = numpy.around(mat).astype('intc')
else:
print("cell:\n", lat_cell)
print("primitive cell:\n", lat_pcell)
raise ValueError(
"cell lattice and its primitive cell lattice not convertable")
hfpg = PermutationGroup(self._pcell, mat)
perms = hfpg.get_symmetry_perms(symprec)
supercell = self._pcell.extend(mat)
for mol, d in remove_redundant(supercell.positions, sites, perms, e_num=e_num):
c = Cell(supercell.lattice, mol[0], mol[1])
yield (c, d)
def get_perms(cell,symprec=1e-3):
latt = cell.lattice
pos = cell.positions
pos = np.dot(pos,latt)
n = pos.shape[0]
pcell = cell.get_primitive_cell()
lat_pcell = pcell.lattice
mat = np.matmul(latt, np.linalg.inv(lat_pcell))
if is_int_np_array(mat):
mat = np.around(mat).astype('intc')
else:
print("cell:\n", lat_cell)
print("primitive cell:\n", lat_pcell)
raise ValueError(
"cell lattice and its primitive cell lattice not convertable")
hfpg = PG(pcell, mat)
return hfpg.get_symmetry_perms(symprec)
def _is_hnf_dup(hnf_x, hnf_y, rot_list, prec=1e-5):
"""
A hnf act in a cell,
if H_x * R.T^-1 * H_y ^-1 is an int matrix:
H_x and H_y produce the same supercell.
Algorithm: Hermite normal form (HNF) matrices remove translation symmetry duplications
However, rotation symmetry duplications also need to be removedself.
That is what this function ``_is_hnf_dup`` do.
"""
for rot in rot_list:
m = numpy.matmul(numpy.matmul(hnf_x, numpy.linalg.inv(rot.T)),
numpy.linalg.inv(hnf_y))
# TODO: stackoverflow add answer
# is_int1 = numpy.all(numpy.isclose(m, m.astype(numpy.int), atol=1e-3))
# is_int2 = numpy.allclose(numpy.mod(m, 1), numpy.zeros_like(m), atol=prec)
# is_array_int = numpy.all(numpy.isclose(m, numpy.around(m), atol=prec))
if is_int_np_array(m, prec):
return True
return False