octadist.calc
- class octadist.src.calc.CalcDistortion(coord)[source]
Calculate octahedral histortion parameters:
Bond distance :
calc_d_bond()
Mean bond distance :
calc_d_mean()
Bond angle around metal center atom :
calc_bond_angle()
zeta parameter :
calc_zeta()
Delta parameter :
calc_delta()
Sigma parameter :
calc_sigma()
Minimum Tehta parameter :
calc_theta_min()
Maximum Theta parameter :
calc_theta_max()
Mean Theta parametes :
calc_theta()
Volume :
calc_vol()
- Parameters:
coord (array_like) – Atomic coordinates of octahedral structure.
Examples
>>> 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]] >>> test = CalcDistortion(coord) >>> test.sigma 47.926528379270124
- calc_d_bond()[source]
Calculate metal-ligand bond distance and return value in Angstrom.
See also
calc_d_mean
Calculate mean metal-ligand bond length.
- calc_d_mean()[source]
Calculate mean distance parameter and return value in Angstrom.
See also
calc_d_bond
Calculate metal-ligand bonds length.
- calc_bond_angle()[source]
Calculate 12 cis and 3 trans unique angles in octahedral structure.
See also
calc_sigma
Calculate Sigma parameter.
- calc_zeta()[source]
Calculate zeta parameter [1] and return value in Angstrom.
See also
calc_d_bond
Calculate metal-ligand bonds length.
calc_d_mean
Calculate mean metal-ligand bond length.
References
- calc_delta()[source]
Calculate Delta parameter, also known as Tilting distortion parameter [2].
See also
calc_d_bond
Calculate metal-ligand bonds length.
calc_d_mean
Calculate mean metal-ligand bond length.
References
[2] M. W. Lufaso and P. M. Woodward. - Jahn–Teller distortions, cation ordering and octahedral tilting in perovskites. Acta Cryst. (2004). B60, 10-20. DOI: 10.1107/S0108768103026661
- calc_sigma()[source]
Calculate Sigma parameter [3] and return value in degree.
See also
calc_bond_angle
Calculate bond angles between ligand-metal-ligand.
References
[3] James K. McCusker, A. L. Rheingold, D. N. Hendrickson. Variable-Temperature Studies of Laser-Initiated 5T2 → 1A1 Intersystem Crossing in Spin-Crossover Complexes: Empirical Correlations between Activation Parameters and Ligand Structure in a Series of Polypyridyl. Ferrous Complexes. Inorg. Chem. 1996, 35, 2100.
- determine_faces()[source]
Refine the order of ligand atoms in order to find the plane for projection.
- Returns:
coord_metal (array_like) – Coordinate of metal atom.
coord_lig (array_like) – Coordinate of ligand atoms.
See also
calc_theta
Calculate mean Theta parameter
Examples
>>> bef = np.array([ [4.0674, 7.2040, 13.6117] [4.3033, 7.3750, 11.7292] [3.8326, 6.9715, 15.4926] [5.8822, 6.4461, 13.4312] [3.3002, 5.3828, 13.6316] [4.8055, 8.9318, 14.2716] [2.3184, 8.0165, 13.1152] ]) >>> metal, coord = self.determine_faces(bef) >>> metal [ 4.0674 7.204 13.6117] >>> coord_lig [[ 4.3033 7.375 11.7292] # Front face [ 4.8055 8.9318 14.2716] # Front face [ 5.8822 6.4461 13.4312] # Front face [ 2.3184 8.0165 13.1152] # Back face [ 3.8326 6.9715 15.4926] # Back face [ 3.3002 5.3828 13.6316]] # Back face
- calc_theta()[source]
Calculate Theta parameter [4] and value in degree.
See also
calc_theta_min
Calculate minimum Theta parameter.
calc_theta_max
Calculate maximum Theta parameter.
octadist.src.linear.angle_btw_vectors
Calculate cosine angle between two vectors.
octadist.src.linear.angle_sign
Calculate cosine angle between two vectors sensitive to CW/CCW direction.
octadist.src.plane.find_eq_of_plane
Find the equation of the plane.
octadist.src.projection.project_atom_onto_plane
Orthogonal projection of point onto the plane.
References
[4] M. Marchivie, P. Guionneau, J.-F. Létard, D. Chasseau. Photo‐induced spin‐transition: the role of the iron(II) environment distortion. Acta Crystal-logr. Sect. B Struct. Sci. 2005, 61, 25.
- calc_theta_min()[source]
Calculate minimum Theta parameter and return value in degree.
See also
calc_theta
Calculate mean Theta parameter
- calc_theta_max()[source]
Calculate maximum Theta parameter and return value in degree.
See also
calc_theta
Calculate mean Theta parameter