ichor.core.analysis.dlpoly package

Submodules

ichor.core.analysis.dlpoly.dlpoly_analysis module

get_dlpoly_energies(optimum_energy: float, dlpoly_directory: Path, output: Path = PosixPath('dlpoly-energies.xlsx'))
read_fflux(fflux_file: Path) → Dict[str, ndarray]
read_wfn_energy(wfn_file: Path) → float

ichor.core.analysis.dlpoly.dlpoly_files module

ichor.core.analysis.dlpoly.mae_forces module

mae_forces(predicted_forces_array: ndarray, true_forces_array: ndarray, atom_names: List, output_name='output.png')

Plots a matshow in matplotlib of the MAE of the predicted forces array vs the true forces array

Parameters:

  • predicted_forces_array – Predicted forces array of shape ntimesteps x natoms x 3.

  • true_forces_array – True forces array of shape ntimesteps x natoms x 3

ichor.core.analysis.dlpoly.plot_energy module

format_energy_plots(ax, xlabel='Timestep', major_grid_linewidth=4.0, minor_grid_linewidth=4.0, xlabel_fontsize=20, label_pad=1.0, tick_params_labelsize=48, tick_params_pad=15, major_tick_params_length=6.0, major_tick_params_width=4, minor_tick_params_length=3.0, minor_tick_params_width=4.0)
plot_differences(data: DlPolyFFLUX | FFLUXDirectory, until_converged: bool = True, absolute: bool = False, title: str = '')

Plots the differences between one timestep and the next timestep (in kJ mol-1) from the FFLUX file for every pair of timesteps

If until_coverged is True, it will only plot the difference until the timestep where the difference to the next timestep is less that 1e-4 kJ mol-1.

Parameters:

  • data – A FFLUX file or directory containing a FFLUX file to read data from.

  • until_converged – Plot timesteps and ifference until energy is converted to 1e-4 kJ mol-1, defaults to True

  • absolute – Plot the absolute of the differences between each timestep

  • title – Title for plot

plot_total_energy(data: DlPolyFFLUX | FFLUXDirectory | List[DlPolyFFLUX] | List[FFLUXDirectory], until_converged: bool = True, reference: List[float] | None = None, HEIGHT=6, WIDTH=12, FIGURE_LABEL_SIZE=30, X_Y_LABELS_FONTSIZE=30, TICKLABELS_FONTSIZE=22, LABELPAD=10, AXES_PADDING=10.0, LINEWIDTH=2.0, MAJOR_TICK_LENGTH=6.0, MINOR_TICK_LENGTH=3.0, PAD_INCHES=0.05, add_letter=False, filename: str = 'total_energy.svg')

Plots the predicted total energy of the system (in kJ mol-1) from the fflux simulation for every timestep.

If until_coverged is True, it will only plot the timesteps until the timestep where the difference to the next timestep is less that 1e-4 kJ mol-1.

Parameters:

  • data – A FFLUX file or directory containing a FFLUX file to read data from.

  • until_converged – Plot timesteps until energy is converted to 1e-4 kJ mol-1, defaults to True.

  • reference – A reference value to subtract (could be the Gaussian optimized minimum). This value has to be in kJ mol-1. If a list is passed in as data, then this reference must also be a list of the same length as data.

  • FIGURE_LABEL_SIZE – The size of the figure labels (A, B, C, etc.), defaults to 30

  • X_Y_LABELS_FONTSIZE – The size of the x and y axis labels, defaults to 30

  • TICKLABELS_FONTSIZE – The size of the tick labels on the axes, defaults to 22

  • LABELPAD – The padding of the x and y labels from the plot, defaults to 10

  • AXES_PADDING – The padding of the number on the axes from the plots, defaults to 10.0

  • LINEWIDTH – The width of the lines, defaults to 2.0

  • MAJOR_TICK_LENGTH – The length of the major ticks, defaults to 6.0

  • MINOR_TICK_LENGTH – The length of the minor ticks, defaults to 3.0

  • PAD_INCHES – Padding on the sides of the plot (as tight layout is used), defaults to 0.05

  • filename – The filename to save as. Note that the extension determines how the fine is saved (png, svg), defaults to “total_energy.svg”

plot_total_energy_from_array(data: ndarray, title: str = '', reference: float | None = None)

Plots the given predicted data (in kJ mol-1) against timesteps

If until_coverged is True, it will only plot the timesteps until the timestep where the difference to the next timestep is less that 1e-4 kJ mol-1.

Parameters:

  • data – A np array containing predicted total energy data

  • title – Title for plot

  • referece – reference Gaussain energy

round_base_10(x)

ichor.core.analysis.dlpoly.true_vs_predicted module

get_random_geometries_from_fflux_simulation(history: DlpolyHistory | Path | str, k: int = 1000, fflux_file: DlPolyFFLUX | Path | str | None = None)

Gets random geometries from fflux simulation, so that the true energy from Gaussian can be computed from the geometries. This function writes out several files. 1. New trajectory containing random geometries to be submitted to Gaussian. 2. A txt file containing the indices of the random geometries taken from the HISTORY 3. If a FFLUX file is given, it writes out a .npy file containing the predicted total energy associated with the random geometries. If not give, the user can use the .txt file and obtain the energies from the FFLUX file themselves.

Parameters:

  • history – A HISTORY file or path to HISTORY file containing FFLUX geometries

  • k – How many geometries to get from the HISTORY, defaults to 1000

  • fflux_file – A FFLUX file where to get the total predicted energies associated with the HISTORY file, defaults to None. If given, this will write out a .npy file containing predicted total energies array. If not given, it will not write out the np array.

plot_true_vs_predicted_from_arrays(predicted_energies_array_hartree: ndarray, true_energies_array_hartree: ndarray | List[PointsDirectory], absolute_diff: bool = True, FIGURE_LABEL_SIZE=48, WIDTH=16, HEIGHT=6, X_Y_LABELS_FONTSIZE=48, TICKLABELS_FONTSIZE=30, LABELPAD=15.0, AXES_PADDING=10.0, LINEWIDTH=2.0, MAJOR_TICK_LENGTH=6.0, MINOR_TICK_LENGTH=3.0, LEGEND_BORDERPAD=15.0, LEGEND_FRAME_WIDTH=2.0, COLORBAR_PADDING=5.0, PAD_INCHES=0.05, add_fig_letter=False, r2_bbox_anchor=(0.9, 0.23), colorbar_label_fontsize=15, filename='output.svg')

Plots true vs predicted energies, as well as calculates R^2 value

Parameters:

  • predicted_energies_array_hartree – np array containing FFLUX predicted energies In hartrees

  • true_energies_array_hartree – a np.array cotaning true energies (in hartrees) or a PointsDirectory (containing ordered wfns from which to get the array) again in Hartrees

  • title – The title of the plot, defaults to “”

  • absolute_diff – Whether to use the absolute of the differences of true and predicted or not, defaults to True

  • FIGURE_LABEL_SIZE – The label size of the figures (A, B, C, etc.), defaults to 48

  • X_Y_LABELS_FONTSIZE – The size of the x and y axis labels, defaults to 48

  • TICKLABELS_FONTSIZE – The fontsize of the ticklabels, defaults to 30

  • LABELPAD – The padding of the x y labels from plot, defaults to 15.0

  • AXES_PADDING – The padding of axes numbers from plot, defaults to 10.0

  • LINEWIDTH – The width of lines, defaults to 2.0

  • MAJOR_TICK_LENGTH – The width of major tickmarks, defaults to 6.0

  • MINOR_TICK_LENGTH – The width of minor tickmarks, defaults to 3.0

  • LEGEND_BORDERPAD – The border padding of the legend, defaults to 15.0

  • LEGEND_FRAME_WIDTH – The width of the legend frame, defaults to 2.0

  • COLORBAR_PADDING – The padding of the colorbar axes, defaults to 5.0

  • PAD_INCHES – padding on the sides (as tight layout is used), defaults to 0.05

  • filename – The filename. Note the extension affects the format of the file , defaults to “output.svg”

plot_true_vs_predicted_from_arrays_one_system(predicted_energies_array_hartree: ndarray, true_energies_array_hartree: ndarray | List[PointsDirectory], absolute_diff: bool = True, filename='output.svg')

Plots true vs predicted energies, as well as calculates R^2 value

Parameters:

  • predicted_energies_array_hartree – np array containing FFLUX predicted energies In hartrees

  • true_energies_array_hartree – a np.array cotaning true energies (in hartrees) or a PointsDirectory (containing ordered wfns from which to get the array) again in Hartrees

  • absolute_diff – Whether to use the absolute of the differences

r2_score(true, predicted)

Module contents