Stationary points

Functions to produce a contour plot for a two-dimensional surface with the kinetic transition network containing minima and transition states overlaid onto it

topsearch.plotting.stationary_points.compute_function_grid(potential: Potential, x_array: NDArray[Any, Any], y_array: NDArray[Any, Any], fineness: int) → NDArray[Any, Any]

Returns the function value evaluated for the grid of meshgrid input for plotting

topsearch.plotting.stationary_points.function_call(potential: Potential, x_value: NDArray[Any, Any]) → float

Returns function value

topsearch.plotting.stationary_points.make_xy_grid(bounds: list, fineness: int) → tuple[NDArray[Any, Any], NDArray[Any, Any]]

Produce the xy grid that the function will be evaluated on for the contour plot

topsearch.plotting.stationary_points.plot_contours(potential: Potential, bounds: list, fineness: int, contour_levels: int, cmap: Colormap) → NDArray[Any, Any]

Make a contour plot of the potential within the range bounds

topsearch.plotting.stationary_points.plot_stationary_points(potential: Potential, ktn: KineticTransitionNetwork, bounds: list, label: str = '', contour_levels: int = 50, fineness: int = 50, colour_scheme: str = 'cool', label_min: bool = False) → None

Plot all minima and transition states of the function. Each transition state is given in red and each minimum in green with a labelling matching min.data. Connected minima of each transition state are joined by solid black lines

topsearch.plotting.stationary_points.self_connected(ktn: KineticTransitionNetwork) → int

Count the number of edges that connect minima to themselves