def calc_param(coord):
"""
Calculate octahedral distortion parameters.
Parameters
----------
coord : array_like
Atomic coordinates of octahedral structure.
Returns
-------
computed : dict
Computed parameters.
"""
dist = octadist.CalcDistortion(coord)
zeta = dist.zeta # Zeta
delta = dist.delta # Delta
sigma = dist.sigma # Sigma
theta = dist.theta # Theta
computed = {"zeta": zeta, "delta": delta, "sigma": sigma, "theta": theta}
return computed
# The first atom must be metal center atom of octahedral structure.
# If not, please see example_2.py for how to handle this issue.
atom = ["Fe", "O", "O", "N", "N", "N", "N"]
coord = [
[2.298354000, 5.161785000, 7.971898000], # <- Metal atom
[1.885657000, 4.804777000, 6.183726000],
[1.747515000, 6.960963000, 7.932784000],
[4.094380000, 5.807257000, 7.588689000],
[0.539005000, 4.482809000, 8.460004000],
[2.812425000, 3.266553000, 8.131637000],
[2.886404000, 5.392925000, 9.848966000],
]
dist = oc.CalcDistortion(coord)
zeta = dist.zeta # Zeta
delta = dist.delta # Delta
sigma = dist.sigma # Sigma
theta = dist.theta # Theta
print("\nAll computed parameters")
print("-----------------------")
print("Zeta =", zeta)
print("Delta =", delta)
print("Sigma =", sigma)
print("Theta =", theta)
# All computed parameters
# -----------------------
# Zeta = 0.22807256171728651
coor = [
[1.885657000, 4.804777000, 6.183726000],
[1.747515000, 6.960963000, 7.932784000],
[2.298354000, 5.161785000, 7.971898000], # <- Metal atom
[4.094380000, 5.807257000, 7.588689000],
[0.539005000, 4.482809000, 8.460004000],
[2.812425000, 3.266553000, 8.131637000],
[2.886404000, 5.392925000, 9.848966000],
]
# If the first atom is not metal atom, you can rearrange the sequence
# of atom in list using coord.extract_octa method.
atom_octa, coord_octa = oc.molecule.extract_octa(atom, coor)
dist = oc.CalcDistortion(coord_octa)
zeta = dist.zeta # Zeta
delta = dist.delta # Delta
sigma = dist.sigma # Sigma
theta = dist.theta # Theta
print("\nAll computed parameters")
print("-----------------------")
print("Zeta =", zeta)
print("Delta =", delta)
print("Sigma =", sigma)
print("Theta =", theta)
# All computed parameters
# -----------------------
# Zeta = 0.22807256171728651