def get_adsorbate_indices(self, atoms, position):
"""Returns the indices of the adsorbate at the supplied position"""
dmin = 1000.
for a in atoms:
d = np.linalg.norm(a.position - position)
if d < dmin:
dmin = d
ind = a.index
mbl = 1.5 # max_bond_length
nl = aseNeighborList([mbl / 2. for i in atoms],
skin=0.0, self_interaction=False)
nl.update(atoms)
return list(set(self._get_indices_in_adsorbate(atoms, nl, ind, [])))
def get_adsorbate_indices(self, atoms, position):
"""Returns the indices of the adsorbate at the supplied position"""
dmin = 1000.
for a in atoms:
d = np.linalg.norm(a.position - position)
if d < dmin:
dmin = d
ind = a.index
mbl = 1.5 # max_bond_length
nl = aseNeighborList([mbl / 2. for i in atoms],
skin=0.0,
self_interaction=False)
nl.update(atoms)
return list(set(self._get_indices_in_adsorbate(atoms, nl, ind, [])))
def get_all_adsorbate_indices(self, atoms):
ac = atoms.copy()
ads_ind = [a.index for a in ac
if a.symbol in self.adsorbate_set]
mbl = 1.5 # max_bond_length
nl = aseNeighborList([mbl / 2. for i in ac],
skin=0.0, self_interaction=False)
nl.update(ac)
adsorbates = []
while len(ads_ind) != 0:
i = int(ads_ind[0])
mol_ind = self._get_indices_in_adsorbate(ac, nl, i)
for ind in mol_ind:
if int(ind) in ads_ind:
ads_ind.remove(int(ind))
adsorbates.append(sorted(mol_ind))
return adsorbates