symmetry_function_ani1
SymmetryFunctionsANI1
Atomic environment symmetry functions, based on the ANI-1 descriptors [1]
References
[1] J.S. Smith et al. Chem. Sci., 2017, 8, 3192-3203 https://dx.doi.org/10.1039/C6SC05720A
Source code in chmpy/descriptors/symmetry_function_ani1.py
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calc_angular_function(cm_xyz, nearest_atoms, cm_atom_xyz, cutoff, r_s_lst, theta_lst, eta, zeta, only_intermolecular=False, separate_angular=True)
Angular function (eq (4) of Smith et al. (2017)) For a given atom returns a list of angular functions of length r_s (and theta - they must be the same length)
list of xyz of all atoms in a finite cluster larger than cutoff
not in the central molecule
cm_atom_xyz : xyz of a given atom in the central molecule cutoff : float, max L1 distance where atom contributions are included r_s : list of hyperparameters controlling position of each gaussian theta: list of hyperparameters contrlling the angular position of each gaussian eta : float, hyperparameter controlling width of each gaussian zeta : float, hyperparameter controlling the width of each gaussian
Source code in chmpy/descriptors/symmetry_function_ani1.py
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calc_radial_function(cm_xyz, nearest_atoms, cm_atom_xyz, cutoff, r_s_lst, eta, only_intermolecular=False, separate_radial=True)
Radial function (eq (3) of Smith et al. (2017)) For a given atom returns a list of radial functions of length r_s
list of xyz of all atoms in a finite cluster larger than cutoff
not in the central molecule
cm_atom_xyz : xyz of a given atom in the central molecule cutoff : float, max L1 distance where atom contributions are included r_s : list of hyperparameters controlling position of each gaussian eta : float, hyperparameter controlling width of each gaussian