def generateGraphFromSlabVinkFile(slab, covalent_radii_cut_off):
all_distances = slab.get_all_distances(mic=True)
atomic_numbers = slab.get_atomic_numbers()
# so funciona se os atomos Si vierem antes dos de O (numeracao / aboria / grafo)
mapping = {}
for atom1, distances in enumerate(all_distances):
if atomic_numbers[atom1] == 14: # Si
atom1_cr = covalent_radii[atomic_numbers[atom1]]
for atom2, distance in enumerate(distances):
if atom1 == atom2:
continue
# so pega atomos de O
if atomic_numbers[atom2] != 8: # O
continue
atom2_cr = covalent_radii[atomic_numbers[atom2]]
# if the distance between two atoms is less than the sum of their covalent radii, they are considered bonded.
if (distance <
((atom1_cr + atom2_cr) * covalent_radii_cut_off)):
try:
mapping[atom1].append(atom2)
except KeyError:
mapping[atom1] = []
mapping[atom1].append(atom2)
try:
mapping[atom2].append(atom1)
except KeyError:
mapping[atom2] = []
mapping[atom2].append(atom1)
graph = bg.Graph()
for atom1 in slab:
if atom1.symbol == 'Si':
if not graph.has_node(atom1.index):
graph.add_node(atom1.index) # add nodes not bonded
try:
for n1_o in mapping[atom1.index]:
if atomic_numbers[n1_o] == 8: # O
for n2_si in mapping[n1_o]:
if atomic_numbers[n2_si] == 14: # Si
if atom1.index != n2_si:
graph.add_edge(atom1.index, n2_si)
except KeyError:
pass
# remove O atomos
del slab[[atom.index for atom in slab if atom.symbol == 'O']]
return graph
def generateGraphFromSlab(slab, covalent_radii_cut_off):
graph = bg.Graph()
atomic_numbers = slab.get_atomic_numbers()
all_distances = slab.get_all_distances(mic=True)
for atom1, distances in enumerate(all_distances):
if not graph.has_node(atom1):
graph.add_node(atom1) # add nodes not bonded
atom1_cr = covalent_radii[atomic_numbers[atom1]]
for atom2, distance in enumerate(distances):
if atom1 != atom2:
atom2_cr = covalent_radii[atomic_numbers[atom2]]
# if the distance between two atoms is less than the sum of their covalent radii, they are considered bonded.
if (distance <
((atom1_cr + atom2_cr) * covalent_radii_cut_off)):
graph.add_edge(atom1, atom2)
return graph