rdmc.mathlib.greedymin#

Modules for finding local minima on the scanned potential energy surface by a greedy algorithm. Need to parallelize this.

rdmc.mathlib.greedymin.compare_to_adjacent_point(coord: List[Tuple], energies: ndarray, unchecked_points: List[Tuple], filters: List[Tuple]) → Tuple#

Compare the energy of current point and those of other points.

Parameters:

  • coord (list of tuples) – The coordinate of the current point.

  • energies (np.ndarray) – The energies of all points.

  • unchecked_points (list of tuples) – The points that have not been checked.

  • filters (list of tuples) – The filters for searching adjacent points.

Returns:

The coordinate of the adjacent point with the lowest energy.

rdmc.mathlib.greedymin.get_energy(coord: List[Tuple], energies: ndarray) → float#

Get the energies of adjacent points considering periodic boundary condition.

Parameters:

  • coord – The coordinate of a point.

  • energies – The energies of all points.

Returns:

float – The energy of the point.

rdmc.mathlib.greedymin.get_step_to_adjacent_points(fsize: int, dim: int = 2, cutoff: float = inf) → generator#

Get a generator containing the adjacent points.

Parameters:

  • fsize – The filter size as positive integer.

  • dim – The dimension of the PES. Default is 2.

  • cutoff – The cutoff distance. only consider steps with distance smaller than the cutoff. Default is infinity, meaning no cutoff is applied.

Returns:

A generator containing the adjacent coordinates.

rdmc.mathlib.greedymin.search_for_a_minimum(coord: tuple, energies: ndarray, unchecked_points: List[Tuple], filters: List[Tuple]) → Tuple#

Search a local minimum on a given PES.

Parameters:

  • coord (tuple) – The coordinate of the current point.

  • energies (np.ndarray) – The energies of all points.

  • unchecked_points (list of tuples) – The points that have not been checked.

  • filters (list of tuples) – The filters for searching adjacent points.

  • minimum. (The coordinate of a local) –

rdmc.mathlib.greedymin.search_minimum(energies: ndarray, fsize: int, cutoff: float = inf) → List[Tuple]#

Search all the minimums on a given PES.

Parameters:

  • energies (np.ndarray) – The energies of all points.

  • fsize (int) – The filter size as positive integer.

  • cutoff (float) – The cutoff distance. only consider steps with distance smaller than the cutoff. Default is infinity, meaning no cutoff is applied.

Returns:

A list of coordinates of the minimums.