def O_O(atoms, n_Al):
'''
finds the distance between two oxygen atoms where H is bonded
Inputs:
atoms: ase atoms object
n_Al : number of Al atoms in qm region
Output: distance between two oxygen atoms where H is bonded [0 if n_Al = 1]
'''
H_index, O_index = [], [] #indexes of H and O atoms
if n_Al == 1:
distance = 0
elif n_Al == 2:
for atom in atoms:
'find H atoms in qm region'
if atom.symbol == 'H':
H_index.append(atom.index)
for H in H_index:
'find closest O to the H'
d_min = 100 #start with a large value (dummy value)
for atom in atoms:
if atom.symbol == 'O':
if atoms.get_distance(H, atom.index) < d_min:
d_min = atoms.get_distance(H, atom.index)
O_atom = atom.index
O_index.append(O_atom)
distance = atoms.get_distance(O_index[0], O_index[1])
return distance
def Al_Al(atoms):
'''
finds distance between 2 Al atoms in qm region
Input : ase atoms object
Output: Al-Al distance [unless there is one Al, distance then is 0] and number of Al atoms
'''
n_Al = 0 #number of Al atoms
Al_index = [] #index of Al atom
for atom in atoms:
if atom.symbol == 'Al':
n_Al += 1
Al_index.append(atom.index)
if n_Al == 1:
distance = 0
elif n_Al == 2:
distance = atoms.get_distance(Al_index[0], Al_index[1])
return distance, n_Al
def Pd_H(atoms, n_Al):
'''
finds the distance between Pd and H
Inputs:
atoms: ase atoms object
n_Al : number of Al atoms in qm region
Output: distance between H and Pd atom [0 if n_Al = 1]
'''
if n_Al == 1:
distance = 0
elif n_Al == 2:
for atom in atoms:
'find H atoms in qm region'
if atom.symbol == 'H':
H_index = atom.index
elif atom.symbol == 'Pd':
Pd_index = atom.index
distance = atoms.get_distance(Pd_index, H_index)
return distance