Plotting

Plotting#

autode.plotting.calculate_reaction_profile_energies(reactions, units, free_energy=False, enthalpy=False)#

Calculate a list of energies comprising the reaction profile

Parameters:

units (autode.units.Units)

Keyword Arguments:

  • free_energy (bool) – Calculate ∆Gs

  • enthalpy (bool) – Calculate ∆Hs

Returns:

(np.ndarray(autode.plotting.Energy))

autode.plotting.error_on_stationary_points(x, energies)#

Calculate the difference between the stationary points of an interpolated function and those observed (given in the energies array). Example:

  |      .
E |.   / |        The points indicate the true stationary points
  | |_/  |.
  |_____________
        zi
Parameters:

energies (np.ndarray) – Observed stationary points

Returns:

A measure of the error

Return type:

(float)

autode.plotting.get_reaction_profile_warnings(reactions)#

Get a string of warnings for a reaction

Returns:

List of warnings to annotate the plot with

Return type:

(str)

autode.plotting.get_stationary_points(xs, dydx)#

Compute the productive of the derivative at points x(i-1) and x(i) which is negative if there is a point x(k) between x(i-1) and x(i) that has dy/dx|x(k) = 0

Parameters:

dydx (function)

autode.plotting.plot_bracket_method_energy_profile(filename: str, left_points: List[Tuple[int, Energy]], cineb_point: tuple | None, right_points: List[Tuple[int, Energy]], x_title: str) → None#

Plot the energy profile from a bracketing method run, showing the points from left and right image and final CI-NEB (if done), in different colours. Energies should be in kcal/mol.

Parameters:

  • filename (str) – Filename with extension

  • left_points (list[tuple]) – List of tuples containing position and energies from left image

  • cineb_point (tuple|None) – Tuple with position and energy for CI-NEB peak

  • right_points (list[tuple]) – List of tuples containing position and energies from right image

  • x_title (str) – Title of the x-axis

autode.plotting.plot_optimiser_profile(history: OptimiserHistory, plot_energy: bool, plot_rms_grad: bool, filename: str)#

Plot the energy and RMS gradient profile from an optimiser history. Skips plotting of points where energy/grad is not available

Parameters:

  • plot_energy (bool) – Whether to plot energy or not

  • plot_rms_grad (bool) – Whether to plot rms grad or not

  • filename (str) – Name of plotted file

autode.plotting.plot_points(zi_s, energies, ax)#

Plot a reaction profile just adding the points to the graph

Parameters:

  • energies (list(autode.plotting.Energy)) – len(energies) = len(zi_s)

  • ax (matplotlib.axes.Axes)

autode.plotting.plot_reaction_profile(reactions: Sequence[Reaction], units: Unit | str, name: str, free_energy: bool = False, enthalpy: bool = False) → None#

For a set of reactions plot the reaction profile using matplotlib

Parameters:

  • units (autode.units.Units | str)

  • name (str)

  • free_energy (bool) – Plot the free energy profile (G)

  • enthalpy (bool) – Plot the enthalpic profile (H)

autode.plotting.plot_smooth_profile(zi_s, energies, ax)#

Plot a smooth reaction profile by spline interpolation and finding the stationary points. This will not afford the correct number of stationary points for some energy arrays, so raise an exception if it fails

Parameters:

  • energies (list(autode.plotting.Energy)) – len(energies) = len(zi_s)

  • ax (matplotlib.axes.Axes)

autode.plotting.save_plot(figure: Figure, filename: str, **kwargs)#

Save a pyplot figure

Parameters:

  • figure (matplotlib.figure.Figure) – The matplotlib figure object

  • filename (str) – Name of the file to plot

  • **kwargs – Other keyword arguments for matplotlib which are passed onto figure.savefig()

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