aim2dat.plots.surface¶

Surface energy plots.

Module Contents¶

Classes¶

class aim2dat.plots.surface.SurfacePlot(area_unit='angstrom', energy_unit='eV', plot_element=None, plot_type='chem_potential', plot_properties='surface_energy', plot_labels=None, show_x_label=True, show_y_label=True, **kwargs)[source]¶

Bases: aim2dat.plots.base_plot._BasePlot

Plot the surface energy with respect to the chemical potential.

Overview

Properties¶

area_unit	Unit of the surface area.
backend	used backend library to plot the data. Supported values are "matplotlib" and
bulk_phase	Bulk phase.
custom_alpha	Alpha value(s) controlling the opacity of plot elements.
custom_colors	Colors used in the plot.
custom_hatch	Hatch value(s) controlling the hatch of plot elements.
custom_linestyles	Line styles used in the plot (This feature is not supported by all plot
custom_linewidths	Line widths used in the plot (This feature is not supported by all plot
custom_markers	Marker types used in the plot (This feature is not supported by all plot
custom_xticklabels	List of labels for the ticks on the x-axis.
custom_xticks	List of values to set ticks on the x-axis.
custom_yticklabels	List of labels for the ticks on the y-axis.
custom_yticks	List of values to set ticks on the y-axis.
data_labels	List of labels for all data sets.
elemental_phases	Elemental phases.
energy_unit	Energy unit.
equal_aspect_ratio	Set equal aspect ratio of the plot(s).
legend_bbox_to_anchor	Shift between box and anchor. The default value is (1, 1).
legend_loc	Location of the legend. The default value is 1.
legend_ncol	Columns of the legend (only supported for the matplotlib backend).
legend_sort_entries	Sort entries of the legend.
plot_grid	Whether to draw a grid in the plot. The default value is False.
plot_properties	Properties that are plotted on the y-axis.
plot_type	Plot type. Supported options are ‘chem_potential’ or ‘excess_atoms’.
ratio	Length-to-width ratio of the plot given as a tuple of two numbers.
show_colorbar	Show colorbar (not supported by all plots).
show_grid	Whether to draw a grid in the plot. The default value is False.
show_legend	Show legend. The default value is False.
show_plot	Show plot. The default value is False.
store_path	Path of the folder to store the plot. The default value is ./.
store_plot	Store plot. The default value is False.
style_sheet	Custom matplotlib style sheet.
subplot_adjust	Keyword arguments for the matplotlib subplots_adjust function.
subplot_align_ylabels	Align y label of plot. The default value is False.
subplot_gridspec	Grid spec values.
subplot_hspace	Vertical spacing between the subplots.
subplot_ncols	Number of columns. The default value is 1.
subplot_nrows	Number of rows. The default value is 2.
subplot_share_colorbar	Use one common colorbar for all subplots.
subplot_share_legend	Merge legend items of all subplots.
subplot_sharex	Share the x-axis of subplots located in the same column.
subplot_sharey	Share the y-axis of subplots located in the same row.
subplot_sup_title	Title of the whole figure.
subplot_sup_x_label	x-label of the whole figure.
subplot_sup_y_label	y-label of the whole figure.
subplot_tight_layout	Tight layout of plot. The default value is False.
subplot_wspace	Horizontal spacing between the subplots.
x_label	Label of the x-axis. If None is given no label will be shown. The
x_range	Range of the x-axis. The default value is None.
y_label	Label of the y-axis. If None is given no label will be shown. The
y_range	Range of the y-axis. The default value is None.

Methods¶

add_surface_facet(data_label, formula, total_energy, surface_area, miller_indices, termination_label, area_unit, energy_unit, **kwargs)	Add surface.
auto_set_axis_properties(set_x_label, set_y_label)	Whether the axis labels and other axis properties are auto-generated.
create_default_gridspec(nrows, ncols, nplots, heights, widths, center_last_row)	Create default grid for multiple plots.
import_from_pandas_df(data_label, data_frame, termination_labels, ter_labeling_scheme, extract_electronic_properties)	Import surface facets from a results pandas data frame of the workflow builder.
plot(data_labels, plot_title, plot_name, subplot_assignment)	Plot the data sets.
reset_gridspec()	Reset gridspec settings.
return_data_labels()	Return the labels of all data sets.
set_bulk_phase(formula, total_energy, unit)	Set bulk phase.
set_elemental_phase(element, total_energy, nr_atoms, unit)	Set elemental phase.

property area_unit¶

Unit of the surface area.

Type:¶

str

property backend¶

used backend library to plot the data. Supported values are "matplotlib" and "plotly".

Type:¶

str

property bulk_phase¶

Bulk phase.

property custom_alpha¶

Alpha value(s) controlling the opacity of plot elements.

Type:¶

float, list or tuple

property custom_colors¶

Colors used in the plot.

Type:¶

list or tuple

property custom_hatch¶

Hatch value(s) controlling the hatch of plot elements.

Type:¶

float, list or tuple

property custom_linestyles¶

Line styles used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_linewidths¶

Line widths used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_markers¶

Marker types used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_xticklabels¶

List of labels for the ticks on the x-axis.

Type:¶

list

property custom_xticks¶

List of values to set ticks on the x-axis.

Type:¶

list

property custom_yticklabels¶

List of labels for the ticks on the y-axis.

Type:¶

list

property custom_yticks¶

List of values to set ticks on the y-axis.

Type:¶

list

property data_labels¶

List of labels for all data sets.

Type:¶

list

property elemental_phases¶

Elemental phases.

property energy_unit¶

Energy unit.

Type:¶

str

property equal_aspect_ratio¶

Set equal aspect ratio of the plot(s).

Type:¶

bool

property legend_bbox_to_anchor¶

Shift between box and anchor. The default value is (1, 1).

Type:¶

tuple or list

property legend_loc¶

Location of the legend. The default value is 1.

Type:¶

int

property legend_ncol¶

Columns of the legend (only supported for the matplotlib backend).

Type:¶

int

property legend_sort_entries¶

Sort entries of the legend.

Type:¶

bool

property plot_grid¶

Whether to draw a grid in the plot. The default value is False.

Type:¶

bool

property plot_properties¶

Properties that are plotted on the y-axis.

Type:¶

str, tuple or list

property plot_type¶

Plot type. Supported options are ‘chem_potential’ or ‘excess_atoms’.

Type:¶

str

property ratio¶

Length-to-width ratio of the plot given as a tuple of two numbers.

Type:¶

tuple or list

property show_colorbar¶

Show colorbar (not supported by all plots).

Type:¶

bool

property show_grid¶

Whether to draw a grid in the plot. The default value is False.

Type:¶

bool

property show_legend¶

Show legend. The default value is False.

Type:¶

bool

property show_plot¶

Show plot. The default value is False.

Type:¶

bool

property store_path¶

Path of the folder to store the plot. The default value is ./.

Type:¶

str

property store_plot¶

Store plot. The default value is False.

Type:¶

bool

property style_sheet¶

Custom matplotlib style sheet.

Type:¶

str

property subplot_adjust¶

Keyword arguments for the matplotlib subplots_adjust function.

Type:¶

dict

property subplot_align_ylabels¶

Align y label of plot. The default value is False.

Type:¶

bool

property subplot_gridspec¶

Grid spec values.

Type:¶

list or tuple

property subplot_hspace¶

Vertical spacing between the subplots.

Type:¶

float

property subplot_ncols¶

Number of columns. The default value is 1.

Type:¶

int

property subplot_nrows¶

Number of rows. The default value is 2.

Type:¶

int

property subplot_share_colorbar¶

Use one common colorbar for all subplots.

Type:¶

bool

property subplot_share_legend¶

Merge legend items of all subplots.

Type:¶

bool

property subplot_sharex¶

Share the x-axis of subplots located in the same column.

Type:¶

bool

property subplot_sharey¶

Share the y-axis of subplots located in the same row.

Type:¶

bool

property subplot_sup_title¶

Title of the whole figure.

Type:¶

str

property subplot_sup_x_label¶

x-label of the whole figure.

Type:¶

str

property subplot_sup_y_label¶

y-label of the whole figure.

Type:¶

str

property subplot_tight_layout¶

Tight layout of plot. The default value is False.

Type:¶

bool

property subplot_wspace¶

Horizontal spacing between the subplots.

Type:¶

float

property x_label¶

Label of the x-axis. If None is given no label will be shown. The default value is None.

Type:¶

str or None

property x_range¶

Range of the x-axis. The default value is None.

Type:¶

tuple or list

property y_label¶

Label of the y-axis. If None is given no label will be shown. The default value is None.

Type:¶

str or None

property y_range¶

Range of the y-axis. The default value is None.

Type:¶

tuple or list

add_surface_facet(data_label, formula, total_energy, surface_area, miller_indices=None, termination_label=None, area_unit='angstrom', energy_unit='eV', **kwargs)[source]¶

Add surface.

Parameters:¶

• data_label (str) – Internal label used to plot and compare multiple data sets.

• formula (dict, list or str) – Chemical formula of the surface slab.

• total_energy (float) – Total energy of the surface slab.

• surface_area (float) – Surface area of the facet.

• area_unit (str (optional)) – Unit of the surface area. The default value is 'angstrom'.

• energy_unit (str (optional)) – Unit of the energy. The default value is 'eV'.

auto_set_axis_properties(set_x_label=True, set_y_label=True)¶

Whether the axis labels and other axis properties are auto-generated.

Parameters:¶

• set_x_label (bool) – Set x-axis label automatically.

• set_y_label (bool) – Set y-axis label automatically.

create_default_gridspec(nrows, ncols, nplots, heights=1, widths=1, center_last_row=True)¶

Create default grid for multiple plots.

Parameters:¶

• nrows (Int) – Number of rows.

• ncols (int) – Number columns.

• nplots (int) – Number of subplots.

• heights (int (optional)) – Height of subplots.

• widths (int (optional)) – Width of subplots.

• center_last_row (bool (optional)) – Center the plots of the last row.

import_from_pandas_df(data_label, data_frame, termination_labels=None, ter_labeling_scheme=None, extract_electronic_properties=False)[source]¶

Import surface facets from a results pandas data frame of the workflow builder.

Parameters:¶

• data_label (str) – Internal label used to plot and compare multiple data sets.

• data_frame (pandas.DataFrame) – Pandas data frame.

• termination_labels (list (optional)) – List of termination indicies. If set to None the termination index for each facet is extracted from the input SurfaceData of the workflow.

• ter_labeling_scheme (str (optional)) – Automatic labeling for surface slabs.

• extract_electronic_properties (bool (optional)) – Whether to extract the band gap and the ionization potential from the calculated band structure.

plot(data_labels, plot_title=None, plot_name='plot.png', subplot_assignment=None)¶

Plot the data sets.

Parameters:¶

• data_labels (list or str) – List of data labels of the data sets that are plotted or in case only one data set is plotted a string.

• plot_title (list or str (optional)) – Title of the plots or subplots.

• plot_name (str (optional)) – The file name of the plot.

• subplot_assignment (list or None (optional)) – Assignment of the data sets to individual subplots.

Returns:¶

fig (matplotlib.pyplot.figure or plotly.graph_objects.Figure) – Figure object of the plot.

reset_gridspec()¶

Reset gridspec settings.

return_data_labels()¶

Return the labels of all data sets.

Returns:¶

data_labels (list) – List of the labels of all data sets.

set_bulk_phase(formula, total_energy, unit='eV')[source]¶

Set bulk phase.

Parameters:¶

• formula (dict, list or str) – Chemical formula of the bulk phase.

• total_energy (float) – Total energy of the phase.

• unit (str (optional)) – Unit of the energy. The default value is 'eV'.

set_elemental_phase(element, total_energy, nr_atoms=1, unit='eV')[source]¶

Set elemental phase.

Parameters:¶

• element (str, int) – Name, symbol or atomic number of the element.

• total_energy (float) – Total energy of the phase.

• nr_atoms (int (optional)) – Number of atoms of the phase. The default value is 1.

• unit (str (optional)) – Unit of the energy. The default value is 'eV'.