grid.becke module

Becke Weights Module.

class BeckeWeights(radii=None, order=3)[source]

Bases: object

Becke weights functions holder class.

__init__(radii=None, order=3)[source]

Initialize class.

Parameters

  • radii (dict, optional) – Dictionary of atomic number and corresponding atomic radius. If None, Bragg-Slater empirically measured covalent radii (in atomic units) are used.

  • order (int, optional) – Order of iteration for switching function.

compute_atom_weight(points, atcoords, atnums, select, cutoff=0.45)[source]

Compute Becke weights for given atomic grid points.

Parameters

  • points (np.ndarray(N, 3)) – Coordinates of points from given atomic grid

  • atcoords (np.ndarray(M, 3)) – Coordinates of nucleis

  • atnums (np.ndarray(M,)) – Atomic number for each nuclei

  • select (int) – Index of atom A for computing the weights

  • cutoff (float, optional) – Cufoff for a_AB if the value is too big or too small

Returns

Becke weights of points for selected atom

Return type

np.ndarray(N,)

compute_weights(points, atcoords, atnums, *, select=None, pt_ind=None)[source]

Compute becke weights for given points and select atoms.

Parameters

  • points (np.ndarray(N, 3)) – Cartesian coordinates of \(N\) grid points.

  • atcoords (np.ndarray(M, 3)) – Cartesian coordinates of \(M\) atoms in molecule.

  • atnums (np.ndarray(M,)) – Atomic number of \(M\) atoms in molecule.

  • select (list or integer, optional) – Index of atom index to calculate Becke weights

  • pt_ind (list, optional) – Index of points for splitting sectors

Returns

Becke integration weights of \(N\) grid points.

Return type

np.ndarray(N, )

generate_weights(points, atcoords, atnums, *, select=None, pt_ind=None)[source]

Calculate Becke integration weights of points for select atom.

The units of the points and coordinates should match radii attribute.

Parameters

  • points (np.ndarray(N, 3)) – Cartesian coordinates of \(N\) grid points.

  • atcoords (np.ndarray(M, 3)) – Cartesian coordinates of \(M\) atoms in molecule.

  • atnums (np.ndarray(M,)) – Atomic number of \(M\) atoms in molecule.

  • select (list or integer, optional) – Index of atom index to calculate Becke weights

  • pt_ind (list, optional) – Index of points for splitting sectors

Returns

Becke integration weights of \(N\) grid points.

Return type

np.ndarray(N, )