def expand_structure(structure, radius=10):
"""expand the structure to include more atoms.
For each atom in the original structure, ensure
that around it a raidus of 10 angstrom there are atoms in
the structure. Keep the index for atoms in the original structure
Return:
a expanded structure with index for the original structure fixed
"""
species = structure.species
coords = structure.cart_coords
molecule = Molecule(species, coords)
a = structure.lattice.matrix[0]
b = structure.lattice.matrix[1]
c = structure.lattice.matrix[2]
ni = max(int(10 / norm(a)), 1)
nj = max(int(10 / norm(b)), 1)
nk = max(int(10 / norm(c)), 1)
for i in range(-ni, ni + 1):
for j in range(-nj, nj + 1):
for k in range(-nk, nk + 1):
if i == 0 and j == 0 and k == 0:
continue
for site in structure.sites:
specie = site.specie
coords = site.coords + i * a + j * b + k * c
molecule.append(specie, coords)
return molecule
