chemcoord.ric_functions.RIC_interpolate

chemcoord.ric_functions.RIC_interpolate(start, end, N, *, opt_alg='LM', coord_idx=None, max_iter=500, seeds=None, bond_dict=None, linearity_thrshld=5, schedule='automatic', rtol=0.0001, atol=1e-08, weights=None, default_weights=None)[source]

Generates an N-image interpolation between start and end.

Parameters:

  • start (Cartesian) – starting structure

  • end (Cartesian) – ending structure

  • N (int) – number of images, including start and end (so minimum 2)

  • opt_alg (Literal['gauss', 'LM']) – default ‘LM’, either Levenberg-Marquardt or Gauss-Newton, the optimization algorithm used to generate Cartesian representations of RedundantInternalCoordinates via get_cartesian()

  • coord_idx (None | SortedSet) – default None, optional specification of internal coordinate set to use

  • max_iter (int) – default 500, maximum number of steps for the get_cartesian() optimization cycle

  • seeds (Cartesian | Sequence[Cartesian] | None) – default None, specifies the seed value for the get_cartesian() optimization cycle. Can be set to one Cartesian, which is used for each image, or to a sequence of Cartesian of length N. If it is None, it uses appropiate method-dependent seeds, e.g. for "from_start" it uses the previous, converged solution.

  • bond_dict (Mapping[AtomIdx, Set[AtomIdx]] | None) – default None, optional specification of connectivity. If not specified, generated automatically. NOTE: this connects disconnected fragments in both start and end with a bond between the closest two atoms in each fragment

  • linearity_thrshld (float) – default 5, tolerance for linearity, in degrees

  • schedule (Literal['automatic', 'independent', 'from_both', 'from_start', 'from_end']) – default “automatic”, the scheduling to be used when generating the path. Can be “from_both” which builds it from the endpoints in, “from_start”, or “from_end”. “automatic” attempts each in that order, returning the first one to succeed

  • rtol (float) – default 1e-4, relative tolerance for convergence

  • atol (float) – default 1e-8, absolute tolerance for convergence

  • weights (ndarray[tuple[int], dtype[floating]] | Sequence[float] | None) – default None, weights used for each internal coordinate in the weighted least-squares step. A higher value means that that coordinate will be more likely to change linearly. Using values far above 1 can cause instability

  • default_weights (DefaultWeights | Mapping[str, float] | None) – default {“length” : 1.0, “angle” : 0.1, “dihedral” : 0.05, “bending” : 0.01}, the weights which each type of coordinate default to

Returns:

The generated path as list of Cartesian.

Return type:

list[Cartesian]

References

The algorithm is described in [4]. If you use this function, please cite it.