plotter#

Plotting functions for defect calculations

Functions

`plot_binding_energies`	Plot binding energies for complex of defects as a function of the fermi level
`plot_charge_transition_levels`	Plotter for the charge transition levels.
`plot_formation_energies`	Produce defect Formation energy vs Fermi energy plot.
`plot_pO2_vs_concentrations`	Plot defect and carrier concentrations in a range of oxygen partial pressure.
`plot_pO2_vs_conductivity`	Plot conductivity as a function of the oxygen partial pressure.
`plot_pO2_vs_fermi_level`	Plot Fermi level as a function of the oxygen partial pressure.
`plot_variable_species_vs_concentrations`	Plot defect and carrier concentrations in a range of oxygen partial pressure.
`plot_variable_species_vs_conductivity`	Plot conductivity as a function of the oxygen partial pressure.
`plot_variable_species_vs_fermi_level`	Plot Fermi level as a function of the oxygen partial pressure.
`plot_x_vs_concentrations`	Plot defect concentrations as a function of generic data on the x-axis.
`plot_x_vs_conductivity`	Plot conductivity as a function of the oxygen partial pressure.
`plot_x_vs_fermi_level`

plot_binding_energies(entries, vbm, band_gap, temperature=0, names=None, xlim=None, ylim=None, figsize=(6, 6), fontsize=None, colors=None, format_legend=True, ax=None, **eform_kwargs)[source]#

Plot binding energies for complex of defects as a function of the fermi level

Parameters:

entries (list) – List of entries to calculate.
vbm (float) – Valence band maximum in eV.
band_gap (float) – Band gap of bulk material in eV.
temperature (float) – Temperature in K. If no custom formation energy is provided, this arg has no effect.
names (list) – List of strings with names of DefectEntry. If None, all defect complexes are plotted.
xlim (tuple) – Tuple giving the range of the x (fermi energy) axis
ylim (tuple) – Tuple giving the range for the formation energy axis
figsize (tuple) – Figure size.
fontsize (float) – Font size.
colors (list) – List of colors for line plot.
format_legend (bool) – Bool for getting latex-like legend based on the name of defect entries.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
eform_kwargs (dict) – Kwargs to pass to entry.formation_energy.

Return type:

matplotlib.axes.Axes

plot_charge_transition_levels(entries, vbm, band_gap, temperature=0, ylim=None, figsize=(6, 6), fontsize=None, colors=None, fermi_level=None, format_legend=True, get_integers=True, ax=None, **eform_kwargs)[source]#

Plotter for the charge transition levels.

Parameters:

entries (list) – List of entries to calculate.
vbm (float) – Valence band maximum in eV.
band_gap (float) – Band gap of bulk material in eV.
temperature (float) – Temperature in K. If no custom formation energy is provided, this arg has no effect.
ylim (tuple) – y-axis limits.
figsize (tuple) – Figure size.
fontsize (float) – Font size.
colors (list or str) – Colors for CTL lines and charge labels. Provide a string to use the same color for all species.
fermi_level (float) – Plot Fermi energy position.
format_legend (bool) – Bool for getting latex-like legend based on the name of defect entries.
get_integers (bool) – Get charge transition levels as integers.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
eform_kwargs (dict) – Kwargs to pass to entry.formation_energy.

Return type:

matplotlib.axes.Axes

plot_formation_energies(entries, chemical_potentials, vbm, band_gap, temperature=0, xlim=None, ylim=None, title=None, fermi_level=None, grid=True, figsize=(6, 6), fontsize=12, colors=None, show_legend=True, format_legend=True, ax=None, **eform_kwargs)[source]#

Produce defect Formation energy vs Fermi energy plot.

Parameters:

entries (list) – List of entries to calculate.
chemical_potentials (dict) – Dictionary with chemical potentials of the elements {‘element’:chempot}.
vbm (float) – Valence band maximum in eV.
band_gap (float) – Band gap of bulk material in eV.
temperature (float) – Temperature in K. If no custom formation energy is provided, this arg has no effect.
xlim (tuple) – Tuple giving the range of the x (fermi energy) axis.
ylim (tuple) – Tuple giving the range for the formation energy axis.
title (str) – Title of the figure.
fermi_level (float) – Plot Fermi energy position with a vertical line.
grid (bool) – Show grid.
figsize (float or tuple) – Figure size.
fontsize (float) – Font size.
colors (list) – List of colors for line plot.
show_legend (bool) – Show legend.
format_legend (bool) – Get latex-like legend based on the name of defect entries.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
eform_kwargs (dict) – Kwargs to pass to entry.formation_energy.

Return type:

matplotlib.axes.Axes

plot_pO2_vs_concentrations(thermodata, output='total', figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None, **kwargs)[source]#

Plot defect and carrier concentrations in a range of oxygen partial pressure.

Parameters:

thermodata (ThermoData) –
ThermoData object that contains the thermodynamic data:

partial_pressures(list)
list with partial pressure values.

defect_concentrations(list or dict)
Defect concentrations in the same format as the output of DefectsAnalysis.

carrier_concentrations(list)
List of tuples with intrinsic carriers concentrations (holes,electrons).
output (str) –
Type of output for defect concentrations:
- ”all”: The output is the concentration of every defect entry.
- ”stable”: The output is the concentration of the stable charge for every defect at each fermi level point.
- ”total”: The output is the sum of the concentration in every charge for each specie.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list) – List of colors to use for plotting with matplotlib. If None the defaults are used.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
kwargs (dict) – Kwargs to pass to DefectConcentrations.filter_concentrations(**kwargs). If provided, only the filtered concentrations will be plotted. If output is set to “total”, only the filtered concentrations will be used to compute the total concentration.

Return type:

matplotlib.axes.Axes

plot_pO2_vs_conductivity(partial_pressures, conductivities, label=None, figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, ax=None)[source]#

Plot conductivity as a function of the oxygen partial pressure.

Parameters:

partial_pressures (list) – list with partial pressure values.
conductivities (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and conductivity list as values. If is a list only one line is plotted with label taken from the “label” argument.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plot_pO2_vs_fermi_level(partial_pressures, fermi_levels, band_gap, label=None, figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None)[source]#

Plot Fermi level as a function of the oxygen partial pressure.

Parameters:

partial_pressures (list) – list with partial pressure values.
fermi_levels (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and fermi level list as values. If is a list only one line is plotted with label taken from the “label” argument.
band_gap (float) – Band gap of the bulk material.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list) – List with colors for Fermi level data.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plot_variable_species_vs_concentrations(thermodata, output='total', figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None, **kwargs)[source]#

Plot defect and carrier concentrations in a range of oxygen partial pressure.

Parameters:

thermodata (ThermoData) –
ThermoData object that contains the thermodynamic data:

partial_pressures(list)
list with partial pressure values.

defect_concentrations(list or dict)
Defect concentrations in the same format as the output of DefectsAnalysis.

carrier_concentrations(list)
List of tuples with intrinsic carriers concentrations (holes,electrons).
output (str) –
Type of output for defect concentrations:
- ”all”: The output is the concentration of every defect entry.
- ”stable”: The output is the concentration of the stable charge for every defect at each fermi level point.
- ”total”: The output is the sum of the concentration in every charge for each specie.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list) – List of colors to use for plotting with matplotlib. If None the defaults are used.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
kwargs (dict) – Kwargs to pass to DefectConcentrations.filter_concentrations(**kwargs). If provided, only the filtered concentrations will be plotted. If output is set to “total”, only the filtered concentrations will be used to compute the total concentration.

Return type:

matplotlib.axes.Axes

plot_variable_species_vs_conductivity(xlabel, variable_concentrations, conductivities, label=None, figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, ax=None)[source]#

Plot conductivity as a function of the oxygen partial pressure.

Parameters:

xlabel (str) – Label for concentration axis (cm^-3 is added).
variable_concentrations (list) – List of concentrations of variable species.
conductivities (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and conductivity list as values. If is a list only one line is plotted with label taken from the “label” argument.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plot_variable_species_vs_fermi_level(xlabel, variable_concentrations, fermi_levels, band_gap, label=None, figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None)[source]#

Plot Fermi level as a function of the oxygen partial pressure.

Parameters:

xlabel (str) – Label for concentration axis (cm^-3 is added).
variable_concentrations (list) – List of concentrations of variable species.
fermi_levels (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and fermi level list as values. If is a list only one line is plotted with label taken from the “label” argument.
band_gap (float) – Band gap of the bulk material.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list) – List with colors for Fermi level data.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plot_x_vs_concentrations(x, xlabel, defect_concentrations, carrier_concentrations, output='total', figsize=(8, 8), fontsize=14, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None, **kwargs)[source]#

Plot defect concentrations as a function of generic data on the x-axis.

Parameters:

x (list) – List with data on x-axis.
xlabel (str) – Label for x-axis.
defect_concentrations (list) – List of DefectConcentrations objects.
carrier_concentrations (list) – List of tuples with carrier concentrations (holes,electrons).
output (str) –
Type of output for defect concentrations:
- ”all”: The output is the concentration of every defect entry.
- ”stable”: The output is the concentration of the stable charge for every defect at each fermi level point.
- ”total”: The output is the sum of the concentration in every charge for each specie.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list) – List of colors to use for plotting with matplotlib. If None the defaults are used.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.
kwargs (dict) – Kwargs to pass to DefectConcentrations.filter_concentrations(**kwargs). If provided, only the filtered concentrations will be plotted. If output is set to “total”, only the filtered concentrations will be used to compute the total concentration.

Return type:

matplotlib.axes.Axes

plot_x_vs_conductivity(x, xlabel, conductivities, label=None, figsize=(8, 8), fontsize=22, xlim=(1e-20, 10000000000.0), ylim=None, ax=None)[source]#

Plot conductivity as a function of the oxygen partial pressure.

Parameters:

x (list) – List with data on x-axis.
xlabel (str) – Label for x-axis.
conductivities (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and conductivity list as values. If is a list only one line is plotted with label taken from the “label” argument.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plot_x_vs_fermi_level(x, xlabel, fermi_levels, band_gap, label=None, figsize=(8, 8), fontsize=20, xlim=(1e-20, 10000000000.0), ylim=None, colors=None, ax=None)[source]#

Parameters:

x (list) – List with data on x-axis.
xlabel (str) – Label for x-axis.
fermi_levels (dict or list) – If is a dict multiples lines will be plotted, with labels as keys and fermi level list as values. If is a list only one line is plotted with label taken from the “label” argument.
band_gap (float) – Band gap of the bulk material.
label (str) – Label for the data.
figsize (tuple) – Size of the matplotlib figure.
fontsize (float) – Size of font for matplotlib rcParams.
xlim (tuple) – Range of x-axis.
ylim (tuple) – Range of y-axis.
colors (list,) – List with colors for Fermi level data.
ax (matplotlib.axes.Axes) – Axis to plot into. If None, a new figure and axis are created.

Return type:

matplotlib.axes.Axes

plotter

Contents

plotter#